EEMB 3 Final!!

Three Lineages of Arthropods

1. *Chelicerata* (spiders): this group diverged really early in the evolution of arthropods 2. *Myriapoda* (centipedes) 3. *Pancrustaceans* --> *Crustaceans* (lobsters & crabs) & *Hexapoda* (insects)

"bryophytes" or non-vascular plants

1. *Hepatophyta* (liverworts): hepato = liver 2. *Bryophyta* (mosses): bryo = moss; --> have stomata 3. *Anthocerophyta* (hornworts): antho = flower, cero = horn; --> have stomata - are *monophyletic*: all share a common ancestor

2 main groups of seed plants

Gymnosperms & Angiosperms

3 key characteristics of Arthropods:

1. *A rigid exoskeleton/cuticle* : hard water-retaining structure 2. *Segmentation* 3. *Jointed appendages*

Key defining features of *Deuterostomes*

(final clade of bilaterians) Developmental Mode --> embryos have radial cleavage --> blastopore on the embryo forms from the anus (instead of the mouth) --> Gastrulation *Molecular Data/DNA sequences = most unifying characteristic* (instead of development)

Sexual Reproduction & Recombination in prokaryotes?

a close form CAN occur due to - transfer of genetic material (sex pili) - endocytosis and integration of plasmid DNA - recombination does NOT initiate reproduction - recombination is NOT is correlation w/ reproductive events

Seta

elevate sporangia off the ground

Clade Sedentaria (Annelida)

"couch potatoes" - *less mobile* than errant forms - ecologically diverse: freshwater, marine, & terrestrial - very diverse feeding ecology: *filter feeding & parasitic forms* - also have some tube dwellers - *Tentacles*: feeding gills that capture prey and are respiratory organ; have convergent evolution w/ gills in bivalve mussels - can have calcium carbonate tubes - contains *leeches* - contains *earthworms*

Derived traits of most plants (aka traits lacking in charophytes but present in embryophytes)

"derived traits" = traits unique to embryophyte lineage & wouldn't be found in any of the other ancestral lineages 1. *Alternation of Generations*: most common in all of the embyrophytes & is more or less lacking in the ancestors 2. *Multicellular, dependent embryos*: the diploid stage after fertilization 3. *Walled spores produced in sporangia* 4. *Multicellular gametangia* 5. *Apical Meristems*: allow a particular direction of growth 6. *Arbuscular Mycorrhizal association* 7. *Cuticles*: waxy surface of epidermal cells 8. *Stomata*: but NOT in liverworts ^^ these are also trait that *helped plants invade land*

Excavata

(diplomonads, euglenids, kinetoplastids) - defined initially by an *oral groove found on one side of most species* - have tough armor around them --> oral groove is only place w/o tough armor to allow it to bring food in - some have highly *reduced or absent mitochondria* - many have *dual nuclei* - pair flagella are uniform in size and are symmetrical - mostly *heterotrophs* - *euglenids* are often mixotrophic: alternate between heterotroph and photosynthetic - *kinetoplastids*: include Trypanosoma - the African Sleeping sickness - *Dipolamonads*: include Giardia

Derived Traits of Vascular Plants

(lacking in green algae, liverworts, mosses, hornworts, BUT found in ferns, lycopods, clubmoss, angiosperms, and gymnosperms) 1. *Growth w/ dichotomous branching*: when the apical meristem grows up towards the light & then splits into 2 2. *Independent sporophyte stage* 3. *Vascular Tissues (xylem & phloem)* 4. *Lignin* 5. *Well-developed roots & leaves* 6. *Sporophylls, modified leaves that bear spores* ^^^ these are also traits that *helped plants get taller & bigger*

prokaryotes changing to eukaryotes

(not all archaea evolved this way --> probably only a few groups experienced these types of changes) 1. *loss of cell wall*: led to increased flexibility and infolding (to create internal membranes) which created increased surface area --> infolding = first step to organized membrane-bound nucleus 2. *ribosome studded internal membrane* 3. *appearance of cytoskeleton*: gave physical structure to big cells 4. *formation of digestive vesicles* 5. *endosymbiosis of organelles*

Well-developed roots & leaves (Derived Traits of Vascular Plants)

(some plants lost roots or roots evolved multiple times) - *microphyll leaves*: unbranched vascular tissues & pretty small leaves (ex: Krauss's spikemoss; Lycophyte) - *megaphyll leaves*: branched vascular tissue; this adaptation allows the leaves to increase in surface area so its gets more sunlight exposure and can transport sugar, oxygen, and water more efficiently (ex: Tunbridge filmy fern; Monilophyte)

Hagfishes & Lampreys

*"the jaw-less fishes"* --> living vertebrates who's membrane lack jaws - *Hagfishes*: have *slime glands* = when they're disturbed by a potential predators, their glands secrete this mucusy polysaccharide material that fills the mouth of the predator who then swims away and leaves the hagfish alone --> slime gland could also be a possible wound healing material - *Lampreys*: are parasitic; a few freshwater species; have been considered as a pest species that are harming ecosystem services and food security in the U.S.

Gastrovascular Cavity

- for *digestions* - for *gas exchange* (no gills) - for *circulation* - a diffusion-based system: all gas & nutrient exchange is done by diffusion

One of the evolutionary advantages of heterospory in plants is to A. have sporophytes specialized in nourishing a fertilized egg. B. have gametophytes specialized in nourishing a fertilized egg. C. have sporophytes specialized in photosynthesis. D. produce fruits. E. A & D

*B. have gametophytes specialized in nourishing a fertilized egg.*

Carpels and stamens are most evolutionarily homologous and functionally similar to A. sporophyte stalks of mosses. B. sporophylls of ferns. C. gametophytes of mosses. D. gametophytes of ferns.

*B. sporophylls of ferns.*

The embryos of bryophytes grow A. outside of the parent sporophyte. B. inside or on the parent sporophyte. C. outside of the parent gametophyte. D. inside of or on the parent gametophyte.

*D. inside of or on the parent gametophyte.*

3 major groups of living mammals (categorized based on how they take care of their babies)

*Eutheria* --> placental mammals (ex: wolf) *Marsupials* --> pouched animals --> kangaroos, opossums, tasmanian devils *Monotremes* --> egg-laying mammals --> platypus --> have hair, produce milk, warm-blooded all united by A LOT of parental care for the young

Gram Stain used to separate bacteria into 2 groups

*GRAM (+)* - nothing stops stain from reaching cell wall --> cell doesn't have LPS layer - *stain purple* - simpler cell wall - less physiologically diverse - can produce *exotoxins* - ex: botulism, tetanus, plague - *NO fever* associated w/ infection w/ Gram positive cells *GRAM (-)* - theres an outer membrane made of LPS that covers the peptidoglycan wall, inhibiting the stain from reaching the wall - *stain pink* - more complex - lipopolysaccharides (LPS) attached - can produce *endotoxins* - *fever* consistently associated w/ gram negative cells - more resistant to antibiotics - Bacteria: peptidoglycan cell wall (muramic acid) - Archaea: no peptidoglycan, but can be gram(+) by other meNS

Monilophytes (Phylum Monilophyta)

*The game "monilo" means "necklace-like", and refers to the appearance of the xylem when observed is cross sections of the stem 1. *Ferns* (Filicales) 2. *Horsetails* (Equisetales) 3. *Whisk Ferns and Relatives* (Psilotales) - monilophyta is a *monophyletic group* - have *megaphylls*: larger leaves w/ branched vessels - are mostly *homosporous* (exception = water ferns like Azolla are heterosporous)

Which evolve (acquire new mutations and fix them in populations) faster? a. Organisms with haplontic lifecycles. b. Organisms with diplontic lifecyles.

*a. Organisms with haplontic lifecycles.*

Mycotrophic plants gain fixed carbon from a. associations with symbiotic fungi. b. photosynthesis in the roots. c. photosynthesis by their symbiotic fungi. d. photosynthesis in their stems.

*a. associations with symbiotic fungi.*

Which of the following groups is defined by the following traits: most have reduced or absent mitochondria, most have an asymmetric body because of an oral groove on once side of the body, most have two-eight flagella that are equal in size and length, some are heterotrophs, some are mixotrophs and some are phototrophs, some are parasitic a. excavata b. haptophyta c. stromenopila d. prokarya e. diatoms

*a. excavata*

Which of the following are characteristics of the *chytridomycota*? a. flagellated gametes b. haustorial hyphae c. a dikaryotic phase d. anisogamous gametes e. multicellular haploids and diploids

*a. flagellated gametes* *e. multicellular haploids and diploids*

The rhizoids of a Hepatophyta are a. haploid b. diploid c. triploid

*a. haploid*

The evolution of vascular plants during the Carboniferous coincides with a. increased coal deposits. b. diversification of bryophytes. c. decreased atmospheric carbon dioxide.

*a. increased coal deposits* *c. decreased atmospheric carbon dioxide.*

In the sound experiment, scientists found the pea roots grow more towards... (pick all correct answers, there can be more than one). a. the side with real water when the other side has no water. b. the side with water running in a tube when the other side has nothing. c. the side with sound of water when the other side has real water. d. the side with sound of water when the other side has nothing. e. the side with sound of water when the other side has 0 Hz playing.

*a. the side with real water when the other side has no water.* *b. the side with water running in a tube when the other side has nothing.* *e. the side with sound of water when the other side has 0 Hz playing.*

Peat bogs contain 30% of the world's carbon even though they make up only 3% of land cover because a. there is limited oxygen and slowed decay. b. decomposition rates are accelerated in peat bogs. c. there are no microbes that eat peat moss. d. peat mosses have deep true roots to store carbon underground. e. peat mosses have one of the fastest growth rates of all plants.

*a. there is limited oxygen and slowed decay.*

Eggs and sperm are all a. unicellular b. multicellular

*a. unicellular*

reproduction processes for microbial eukaryotes

*asexual reproduction*: can occur in both haploid and diploid state --> binary fission: ex: paramecium, yeast --> multiple fission: ex: tetrahimena --> budding --> spore formation: replication of ones self that is maintained internally and only breaks out if parent cell dies *Conjugation*: genetic recombination in paramecia --> *ciliates*: have 2 types of nuclei --> sexual but NOT reproductive process *sexual reproduction*: featuring gametes (haploid) and zygotes (diploid) and meiosis --> first arose w/ protists - some haploid forms are the dominant life stages - some haploids have multicellular life stages - usually haploid groups give rise to gametes that then fuse to become diploid zygotes that then goes through mitosis to become single-cellular diploid OR goes through mitosis & develops into a multicellular diploid - has *alternation of generations*

Which one of the following arthropod groups would include the dragonflies? Select one: a. Myriapods b. Hexapods c. Trilobites d. Chelicerates e. Crustaceans

*b. Hexapods* --> insects

Which of the features below is a common trait of the animals? Select one: a. Bilateral symmetry b. Similarities in their Hox genes c. Cells that contain chitin d. Spiral cleavage e. Vascular system

*b. Similarities in their Hox genes*

Which of the following characteristics is NOT associated with Phylum Porifera? Select one: a. They are decision-based animals. b. They have kidneys. c. They are sponges. d. They are often considered the simplest animals. e. They are comprised of multiple cell types.

*b. They have kidneys.* --> phylum poriferia (sponges) lack true tissues and organs & therefore don't have kidneys

The "Three bachelor" Encephalartos woodii cycads at LotusLand are ... a. monoecious b. dioecious c. homosporous d. heterosporous

*b. dioecious* *d. heterosporous*

The petals of a flower are a. haploid. b. diploid. c. triploid.

*b. diploid.*

Pollen grains contain... a. sporophyte & sperm b. gametophyte & sperm c. sporophyte & egg d. gametophyte & egg

*b. gametophyte & sperm*

Redwoods are (pick all correct answers).. a. homosporous b. heterosporous c. dioecious d. evergreen e. monoecious f. deciduous

*b. heterosporous* --> a haploid gametophyte that produces *two types of spores* *d. evergreen* --> dont lose leaves *e. monoecious* --> female & males are on the same sporophyte

Fern spores are a. heterosporous b. homosporous

*b. homosporous*

Heterospory allows plants to produce a. diploid and haploid spores at once. b. one large spore specialized for becoming the megagametophyte and one small spore to become the microgametophyte. c. one large spore specialized for becoming the megasporophyte and one small spore to become the microsporophyte. d. one type of gamete that is morphologically identical.

*b. one large spore specialized for becoming the megagametophyte and one small spore to become the microgametophyte.*

According to the metabolism flowchart in lecture 4A, *chemoheterotrophs* utilize which as their *main* method of ATP production? a. photophosphorylation b. oxidative phosphorylation c. fermentation d. substrate level phosphorylation e. chemolithography

*b. oxidative phosphorylation*

Land plants without seeds are a. polyphyletic b. paraphyletic c. monophyletic

*b. paraphyletic*

The scolex is a feature that is found in ________________________ and is used to hang onto the ____________________________ of the host? Select one: a. flukes / liver b. tapeworms / digestive tract c. tapeworms / external surface d. monogenea ectoparasites / fish gills e. larval stages / gills

*b. tapeworms / digestive tract*

In insects, which of the below are adaptation(s) to life on land, or organ systems that support life on land? Select one: a. Flight b. The exoskeleton c. All of these adaptations are related to life on land d. The tracheal system e. Malpighian tubules

*c. All of these adaptations are related to life on land*

Which of the following statements is most accurate about the alternation of generations? a. Sporophytes emerge from the clonal reproduction (mitosis) of gametophytes, and gametophytes emerge from the clonal reproduction (mitosis) of sporophytes. b. Sporophytes develop gametes that fertilize to make gametophytes. Gametophytes develop spores that undergo meiosis to make sporophytes. c. Gametophytes develop gametes that fertilize to make sporophytes. Sporophytes develop spores that undergo meiosis to make gametophytes. d. Gametophytes undergo mitosis to develop sporophytes. Sporophytes undergo meiosis to develop gametophytes.

*c. Gametophytes develop gametes that fertilize to make sporophytes. Sporophytes develop spores that undergo meiosis to make gametophytes.*

The capsules of moss sporophytes are... a. triploid b. haploid c. diploid

*c. diploid*

Are eukaryotic green algae (Chlorophyta and Charophyta) monophyletic, paraphyletic, or polyphyletic? a. monophyletic b. polyphyletic c. paraphyletic

*c. paraphyletic*

land plants without seeds (non-vascular + seedless vascular) are: a. monophyletic b. polyphyletic c. paraphyletic

*c. paraphyletic*

Stomata are... a. cells that let water in but not carbon dioxide out. b. air pores that let carbon dioxide in but not water out. c. two cells that come together or apart to let carbon dioxide in. d. two cells necessary for photosynthesis

*c. two cells that come together or apart to let carbon dioxide in.*

The carpel of angiosperms is evolutionarily homologous to the _______ of the gymnosperm

*cone scale*

Sea anemones are members of which Class? Select one: a. Cnidaria b. Ctenophora c. Scyphozoa d. Anthozoa e. Bivalvia

*d. Anthozoa* --> in the family of Phylum Cnidaria, under the specific class of Anthozoans which include corals & sea anemones

Which of these factors could potentially lead to the unprecedented coal deposits of the Carboniferous period? a. Climate change and plate tectonics b. Formation of lignin and the absence of lignin-degrading microbes. c. The accelerated diversification of flowering plants. d. a & b e. a & c f. all of the above

*d. a & b* --> Climate change and plate tectonics --> Formation of lignin and the absence of lignin-degrading microbes.

what part of an avocado do you eat?

*diploid ovary*

Sponges have a greater degree of cephalization when compared to Select one: a. All of these choices b. Gastropods c. Insects d. Flat Worms e. None of these choices

*e. None of these choices* --> sponges are the most basal lineage, & have the least degree of cephalization compared to late evolved animals

A distinguishing feature of echinoderms is the Select one: a. None of these choices b. Exoskeleton c. Broadcast spawning d. Eyespots e. Water vascular system

*e. Water vascular system* the distinguishing characteristics of echinoderms are: --> 5 pointed radial symmentry --> calcified internal skeleton (NOT exoskeleton) --> water vascular system

Which of the following is NOT a key feature that differentiates Archaea from Bacteria? a. the isoprenoid chains can be linked together b. Ether phospholipid linkages c. Isopropanol phospholipids d. glycerol chirality e. presence of a Gram stain

*e. presence of a Gram stain* --> both archaea and bacteria can gram stain

_____ where the 1st to invade land

*embyrophytes* --> 1st to adapt to soil surfaces

Eocyte Hypothesis

*eocyte hypothesis*: says that we are derived from one branch of archaea instead of us deriving and THEN all the archaea separating out --> puts eukaryota as a branch that happens much much later in the archaea tree --> explains many of the differences between archaea groups such as: - similarities in crenarchaeota and eukarya - differences between eukarya and other archaeal groups - similarities between archaeal groups yet, the three domain system persists as the dominant phylogeny for the tree of life

T or F? : Archaea are only found in extreme environments and Bacteria are only found in mesophilic environments.

*false*

True or False. Although not all plants are photoautotrophic, all photoautotrophic organisms are plants?

*false* --> Cyanobacteria are Bacteria than can photosynthesize.

T or F?: Only glomeromycota have arbuscular hyphae

*false* --> Basidiomycetes also can have arbuscular hyphae

T or F?: The oldest fossils are found in the top layer of substrate.

*false* --> the YOUNGEST fossils are found in the top layer of substrate

T or F? : The Unikont Amoebozoans have threadlike pseudopoda called sarcodines.

*false* --> the rhizarians have sarcodines

If you get a beneficial mutation, would you rather be haplontic or diplontic?

*haplontic* --> a beneficial mutation is likely to be lost by chance in diploids

an old term, now subset of autotroph

*lithotroph*

what trait to Gnetophytes, Conifers, and Angiosperms share? a. Fleshy seed coats b. Non-flagellated sperms c. Heterospory d. Dominant sporophyte stage e. Spores leave the parents

*non-flagellated sperm*

an old term, now subset of heterotroph

*organotroph*

plants are generally considered:

*photoautotrophs* or *primary producers* that fix CO2 to make sugar

Odontata (Hexapod & Arthropod)

- *cannot fold wings* against body - *dragonflies & damselflies* - aquatic larvae that metamorphose out of the water - *predators*

T or F? : Many protists are the result of endosymbiotic events between eukarya.

*true*

T/F Chordates have 3 true tissues?

*true*

T/F Multiple interacting factors such as exposure to pesticides and parasitic infection are causes for the deaths of honey bees and wild bees as well.

*true*

T/F The hagfish, an extant jawless fish, is probably appears like the ancestor to early jawed fishes.

*true*

primary producers

- *'fix'* carbon dioxide to make sugar - are a type of *autotroph*: able to make their own food - many plants are primary producers but, *plants are NOT all primary producers* --> there's exceptions such as mycotrophic plants & parasitic plants

Gymnosperms

- *'naked'* - *no fruits*, seeds are protected in fleshy or woody modified leaves - *no flowers* - ~12,000 species - very morphologically & physiologically diverse, but NOT very species rich - all gymnosperms are in ONE CLADE = *monophyletic* that is the sister group of the angiosperms

Angiosperms

- *'vessel'* - *fruits*, fleshy ovaries that enclose and nourish the seed - *flowers* - more than 250,000 species

Eudicots

- *2* cotyledons - veins usually *netlike* - vascular bundles usually *arranged in ring* - *taproot* usually present - floral parts usually in multiples of *4 or 5s* - include a very wide range of floral morphologies

50 Reefs

- *50 Reefs*: a one year initiative that aims to bolster existing coral reef conservation efforts globally by identifying coral reefs that are less vulnerable to climate change & have the greatest capacity to reseed other reefs over time - humans out trying to document where reefs are doing well - an act of *natural rescue*

Oxidative or Electron Transport Level Phosphorylation (ETLP)

- *Anaerobic*: use NO3-, FE3+, SO4-2, and CO3-2 as electron acceptor - *Aerobic*: uses O2 as electron acceptor (humans) - uses *electron transport system* and *proton motive force* - external electron acceptor - substrate is COMPLETELY oxidized to CO2 - much HIGHER yield of ATP

Anisogamous

- *Anisogamous*: not the same gametes - male and female - male = reduced gamete - female = complete gamete --> all organelle material is provided by the female gamete --> this is how we know mitochondrial DNA is coming from the female side of things

Glomeromycota: Arbuscular Mycorrhizae

- *Arbuscular Mycorrhizae* = tree-like shaped hyphae that push themselves into cells - aka arbuscular hyphae - most common form of mycorrhizae - very important step for colonization of land! - *obligate symbioses* (fungi CANNOT grow independently) --> can push itself in between the cal walls of plants and increase surface area of these plants as well as absorptive abilities --> also digests things that these plants cannot, helping to promote plant growth --> hyphae helps the plant w/ uptake of nutrients - *mycorrhizal infection/ mutualistic infection*: mycorrhizae help the plant and occasionally kills off a few cells - vascular plants helps to: prevent desiccation of the hyphae, protect the hyphae against attack - the fungi: also helps the prevent desiccation of plant, and receive organic substances from the plant the plant is supplying the structure and the fungi are supply the nutrients as well as acquiring nutrients from that photosynthetic element (reverse of lichen interaction)

Class Aves: Birds

- *Arcosaurs* - anatomy is *specialized for flight* - feathers (evolved from scales) - light hollow bones - one-way breathing system - powerful flight muscles attached to breastbone - radiation into numerous habitats: diving, aquatic forms, birds that have lost flight (penguins) - incredible diversity here

Human hookworm (parasitic nematode)

- *Ascaris lumricoides*: "soil transmitted helminthes" - environmental infection from walking on sewage or feces contaminated grounds/soil - found worldwide - injectives stages inter environment - eggs can survive is formalin --> they're super tough - heavy infections can *lead to malnutrition & bowl obstruction* (sometimes anemia) - can be easily treated

Single cell Algae

- *Avleolates*: Dinoflagellates --> red tides - *Stramenophila*: Diatoms --> important primary producers, form harmful algal blooms - *Haptophyta*: Coccolithophorids --> oceanic blooms ^^^ all apart of Chromalveolates Group

The largest seed

- *Coco de Mer* - about 10 kg = 10,000g -a coconut -- a monocut in the angiosperm group - very big to have a lot of resources & calories for fast growth in a nutrient-sparse environment

Evolutionary Step: Tissue Layers

- *Diploblastic Acoelomate*: 2 tissue layers; in cnidarian; endoderm & ectoderm - *Triploblastic Aceolomate*: 3 tissue layers; NO body cavity; ex: platyhelminth; endoderm, mesoderm, ectoderm - *Triploblastic Coelomate*: 3 tissue layers; HAVE a body cavity, ex: echinoderm, mollusc, chordate; endoderm, coelom, mesoderm (split by coelom), & ectoderm - *muscles* are found in the mesoderm layer: embryonic tissue that leads to the formation of muscles

Gaia Hypothesis

- *Gaia Hypothesis* = earth is a living entity and its biosphere regulates the climate and atmosphere at an optimum --> the regulation and cycle are run by microbial life

symbiotic mutualistic relationships in fungi --> Lichens

- *Lichens*: symbiotic complex of fungi and algae or cyanobacteria - pioneer organisms - fungi get C sometimes N from algae or cyanobacteria - algae get nutrients, water, and protection from: (1) excess light (2) desiccation (3) grazing - when lichen want to propagate, they send out spores that are BOTH the algae and the fungi - the *shape* of the lichen: due to the type of *fungi* - the *color* of the lichen: due to the *type of algae* it take in

oxygen tolerance

- *Obligate aerobe* (require O2): CO2 + H2O --> organic C; aerobic respiration - *microaerophiles*: group that 1st survived after the initial production of oxygen; use oxygen for respiration but CANT handle full atmospheric oxygen; aerobic respiration - *facultative anaerobe* (humans): can switch physiologies; w/ oxygen --> respiration... or w/o oxygen --> fermenation - *Obligate Anaerobe* (O2 is toxic): will die if oxygen is in their system; dominant in earliest forms of life on earth; SO4 --> H2S; anaerobic respiration

3 representative samples for the Ascomycota

- *Perithicium*: forms on trees, has tough outside layer, has characteristic ascus in the middle - *Saccharromyces ssp.*: (teachers fav fungus) - *Penicillium ssp.*: important in terms of medicine; have naked spores encased in ascus

3 types of Basidiomycota

- *Phallus ssp*: Maiden's Veil - *Pucciniales*: Rusts - *Bovista ssp.*: Puffballs --> emit 50,000 spores per small amount of space

The Devonian, the Age of Fishes

- *Placoderms*: early jawed fishes, gigantic armored fish, now extinct - other fishes evolved during this era: cartilaginous fishes (sharks), ray-finned fishes (tuna), lobe-ray fishes (lung fish)

human-assisted evolution (how we can help coral bleaching)

- *Ruth Gates & Madeleine van Oppen* launches a program to see if humans could get involved to try & raise corals that were thermally tolerant/can withstand climate change - included doing microevolution w/ the symbionts to see if one can raise a more thermally tolerant strain of symbiodinium - an act of *human intervention*

Ascomycota (crown fungi)

- *Sac Fungi* (sex spores made in ascus) - *septate hyphae* - yeast is a member of this group - presence of dikaryotic phase --> *long period* between plasmogamy and karyogamy -- definitive element of a dikaryotic stage - spores formed in *ascus*: sac-like structure where spores form; thin sac or lining surrounding the gametes (analogous to the thin tissue that separates slices of orange) - large fruiting bodies: *Ascocarps* - include many plant pathogens: *penicillium mold* (source of penicillin) - *ergot of rye*: hallucinogenic (derivative of LSD) --> cause of the salem witch trials

Marine Mammals

- *Secondary invaders of the sea* - acquired temperature regulation & breathing underwater - 120 species - *endotherms* - 4 groups of marine vertebrates: 1. *Sea otters* 2. *Cetaceans*: whales, dolphins, porpoises 3. *Pinnipeds*: true seal, eared seal, walruses 4. *Sirenians*: manatees, dugongs

Pycnopodia (example of an Asteroidea)

- *The sunflower star* - pycnopodia helianthoides - *24 arms* - may have *15,000 tube feet* - *speedster* @ 1 meter per minute - have NO brain, all movement & sense are done by nerves alone - can regenerate lost arms - preys on california purple sea urchins

abominable mystery

- *abominable mystery* = diversification by the angiosperm - other animals/ insects help angiosperms diversify by helping them facilitate reproduction

Trematoda: the blood flukes

- *all parasites* - have a mouth and a blind gut - inject hosts blood & tissue - complex life-cycle -cause significant human diseases

Apical Meristems (derived traits of embryophytes)

- *apical meristem*: tissues somewhat like *stem cells in humans* - cell that haven't yet been programmed to differentiate into any particular tissue type - usually found on the tips of *roots* (grow downwards to compete for water) or *shoots* (grow upwards to compete for sunlight)

Cubazoans (Cnidaria)

- *box jellies* - very small but *toxic* - sea wasp - ALL marine - Chrionex fleckeri

Class Ophiuroidea (Phylum Echinodermata)

- *brittle stars & basket stars* - ophiuroids have adapted to a wide variety of life styles : benthic species & epizoic (live on other organisms) species - often *occur in aggregates* - many marine ecosystems but *often deep (>200m)* - discovery rate of ophiuroid pieces has been going up since 1758

Clade Chondrichthyes (Vertebrates)

- *cartilaginous fishes*: skates, rays, sharks, chimaeras - *increased mobility*: NO armor as in placoderms; have fins (2 pair - pectoral and pelvic) - skeleton composed of *cartilage* - LACK true bone, except teeth & base of scales may be calcified - all predatory - economically important to us: some are eaten as food - ex: blacktop reef shark, southern stingray, spotted ratfish

types of fungi

- *chytridiomycota*: branching hyphae, only fungus with flagella - *zygomycota*: coenocytic hyphae, no motile cells and no fruiting body - *glomerycota*: aseptate haustoria hyphae, arbuscular mycorrhizae - *ascomycota - sac fungi*: septet hyphae, sexually produced spores in sacs - *basidiomycota - club fungi*: septet hyphae, most advanced fungi, large fruiting bodies

Phylum Chordata

- *clade Cephalochordata (Lancelets)* - *clade Urochordata (tunicates)* - *clade Vertebrata (vertebrates)* - this phylum has extreme diversity - range from sea squirts to mammals - body form is very diverse - complex body organization - diversity of metabolic strategies - *evolution of a larger body size* - diversity in body forms is matched in new ways of feeding

Bivalves (mollusca)

- *class bivalvia* - *clams, mussels, scallops, oysters* - 10,000 species described - freshwater & marine --> NO terrestrial bivalves - *sedentary lifestyle* - hinged shell w/ adductor muscles - lateral compression of body and foot - LACK of cephalization: virtual absence of head and associated sensory organs - ABSENCE of radula (gills for feeding) - some bivalves excrete *byssal threads* = threads that have sucker attachments @ the end of them; created from proteins that are integrated & synthesized inside the byssal gland which then secretes the threads & attaches them to the substrate; are adaptations that allow them to hold on to rocks in high/intense wave environments

Cephalopoda (Mollusca)

- *class cephalopoda* - *squids & octopus* - fast-moving, active carnivores - complex behaviors - *extreme cephalization* (esp. in octopus) - ONLY Nautilus has an external shell, in octopus & squid its greatly reduced - octopus locomotion: bipedal locomotion w/ a hydrostatic skeleton - when octopus are in environments w/ low oxygen, they start to become impart d& vision starts to drop off dramatically: these results are the first demonstration that vision in marine invertebrates is highly sensitive to oxygen availability and that the threshold for visual impairment from reduced oxygen are species-specific - traits unique among molluscans: have a *closed circulatory system*; have a large, differentiated brain that allows for incredible: behavior, memory, and learning

Gastropods

- *class gastropoda*: largest molluscan class - *visceral mass sitting atop a muscle foot* - *most diverse groups* of animals in form, habit, and habitat - 90-180 degree torsion of visceral mass and nervous system during embryonic development - *operculum*: a little trap door that can close the animals body inside of its shell - land snails & slugs = ONLY molluscan group to invade land: pulmonate snails, land and freshwater, escargot - extinction crisis for land snails & freshwater bivalves: major conservation issue

Chitons (Mollusca)

- *class polyplacophora* - 900 species - ALL marine - common in the intertidal zone - restricted to living on hard substrata, especially rocks (use muscular foot to hang on to rocks) - distinctive shell: 8 overlapping articulated plated - girdle acts as a suction cup - *grazers* - adaptations for life in areas w/ heavy wave action --> the rocky intertidal zone - have an incredibly large, very strong foot

Intermediate multicellularity

- *clonal multicellularity*: a bunch of cells together that just need to specialize to get to that multicellular state - multinucleate cells: lots of cells coming together, plasma membrane breaks down and become one larger cell - compartmentalization (forms, diatoms, radiolarians, dinoflagellates) - specialization is all that is needed to form true multicellularity from this point

Basidiomycetes (crown fungi)

- *club fungi* - defined by *basidium*: club-like element inside their fruiting body that holds the spores - some have *septate hyphae* - many have *arbuscular mycorrhizae* but ALSO basidium - have variations in their morphology: multicellular mushroom, rusts, & smuts - basidia spores are the reproductive parts --> the haploid elements - HAS dikarytoic stage! --> (haploids are not fused here) the formation of diarkyotic mycelium, basidiocap fruiting structure, mushroom stock, cap, and gills takes place here - after the dikarya stage, THEN we get fusion/karyogamy/fertilization

3 main shapes of prokaryotes

- *cocci* (sphere) - *bacilli* (rod) - *spirochetes* (spiral)

prochlorococcus spp.

- *cyanobacteria* - most likely what was enveloped by cells to become the 1st chloroplast - obligate photoautotrophs: it must produce oxygen and must take its energy from the sun and acquire CO2 as its carbon source - *uses ONLY photosystem II* - light for energy source - oxygenic process - produces majority of O2 on earth - considered very basal group - stromatolites : mats of cyanobacteria

Origin of water on Earth

- *degassing* is most widely accepted bc isotropic ratios on earth do NOT match those of asteroid or comets - *Rosetta's instrument* found that Comet 67P C-G's water vapor significantly differed compared to the earth's ocean (asteroids have a slightly bigger ratio than earth, while comets have an extremely larger D/H ratio than earth) - this does not mean some water did not come from asteroid or comets, just that *the majority of the water of earth is due to condensation by cooling*

anatomy of a generalized flatworm

- *diffusion* moves respiratory gases & nutrients - digestion completed by cells lining the gastrovascular cavity - *pharynx*: releases digestive juices onto a prey item which digests the animal ... then the pharynx sucks up the digesting nutrients off the prey which moves into the *gastrovascular cavity* - *eyespots*: capable of sensing the env - *ganglia*: integrating center for information that comes from the 2 ventral nerve cords & the env - *flame bulbs/cells*: line their body --> release nitrogenous waste --> equivalent to our kidney - flattening increases SA to volume ratio

earths chemical disequilibrium

- *earths chemical disequilibrium*: humans consume parts of the earth and the earth replenishes it --> returns to equilibrium - something (microbes) is computing this cycle - it is driven by life and its diversity and function

Energy Generation

- *energy generation*: all organisms on this planet generate their ATP using one of 3 processes 1. *Fermentation* 2. *Oxidative or Electron Transport Level Phosphorylation (ETLP)* 3. *Photophosphorylation*

Ecdysozoans (+ defining traits)

- *exoskeleton/cuticle* evolved here = key feature - contains 8 phyla, but we will only over *Nematodes & Arthropods* - *multi-layed structure* - *three-layered cuticle* = most notable characteristic shared by all ecdysozoans - *tough cuticle but flexible* and helps w/ water loss: overtime has become an important adaptation for life on land & conserving water - exoskeleton sheds as the animal grows = *ecdysis* - has the most species of any lineage of animals

cephalization & sensory capability

- *eyespots* are present - other sensors such as: chemoreceptors, mechanoreceptors, and statocysts (sense gravity & position) - primitive nervous system --> NO BRAIN - but distinct brain (central ganglion) w/ longitudinal nerve cord that integrate all the info that they get from the environment

comparison of endosymbiotic events

- *first endosymbiotic event*: gave rise to the three domains --> archaea, bacteria, eukarya - *Secondary endosymbiotic event*: only w/in eukarya which then gave rise to heterotrophs and autotrophs - *third and fourth endosymbiotic events*: between heterotrophs and autotrophs --> many different events that gave rise to many different groups

mobility (taxis) of prokaryotes

- *flagella*: long and whip-like, works by a rotations mechanism --> normally theres one long extension - *cilia*: uses a stroke mechanism, normally many small and short projections, similar to fimbriae but those are for attachment NOT movement

Phylum Platyhelminthes: flatworms

- *flat*= most distinguishing characteristic - *simplest animals* w/ bilateral symmetry - 25,000 species - increasing in physiological & ecological complexity: see real locomotion in swimming - many free-living & *parasitic forms* too - most parasites are *blood flukes & tapeworms* - *tripoblastic*: first group to evolve a true mesoderm - *Aceolomates*: no body cavity - *Cephalization* - have a *primitive gut*: some small free-living forms lack a gut - lack an anus --> one pharyngeal opening that they do everything through

winged insects

- *flight* first evolves here - important *pollinators & predators* - complex systematics (28 orders) - complex development: larval forms DONT look like miniature adults; numerous instars (stages) - three groups: 1. *cannot fold wings* against body 2. *CAN fold wings* but under *incomplete metamorphosis 3. *CAN fold wings* and undergo *COMPLETE metamorphosis*

Phylum Cnidaria Unique Characteristics

- *gastrovascular cavity* - *nematocysts* - *symbiosis in cnidarians*

Bacillus Anthracis

- *gram (+)* endospore forming Bacillus - causative agent for *Anthrax* - lives in soil --> pretty common, but only dangerous when in HIGH quantities - can be grown in aerobic or anaerobic conditions

Borrelia burgdorferi

- *gram (-)*, motile spirochete - has 10 flagella on either end of cell --> *amphi-lophotricous* - causative agent for *lyme disease* - found in some species of ticks - disease can be cleared by *sceloprus occidentalis*

Isogamous

- *isogamous*: gametes are the same - mating types such as (+) or (-) or A and alpha - NO female or male - most fungi DONT have male and female and are isogamous gametes (still participate in sexual reproduction, its just not between male and female)

Fransico Redi

- *life and spontaneous generation* - asked "do some forms of life arise repeatedly and directly from inanimate matter?" - Redi determined *NO* - placed meat in jar and covered with paper to see if flies produced from the meat itself

Photophosphorylation

- *light energy* generates proton gradient across membrane - then *proton motive force* is used to generate ATP - rather than using different molecules/chemicals to breakdown to move through hydrogens across the membrane, light energy is used

Lycophytes (seedless vascular plants)

- *lycopodiaceae* (club moss, but not a moss) --> homospory - *Selaginellaceae* (spike moss, but not a moss)--> heterospory - *Isoetaceae* (Quillwort -- an aquatic plant) --> heterospory - all have *strobili*: clusters of sporophylls - all have *microphylls*: simple leaves w/ no branched vascular tissues inside the leaves - lyco = wolf, phyla = plant

Multicellular protists (algae)

- *macrocystis*: giant kelp is *brown algae* - *red algae* - *green algae*: close ancestor to plants ^^ all apart of Plantae Group

Cell Theory: basic unit of life

- *membranes*: cells always have a membrane of some kind - *controlled aqueous system* w/in cell - *monomers to macromolecules* - information carries (*RNA & DNA*) and translation apparatus - *energy storage & flow*: metabolism which is usually run by enzymes or catalysts ^^^ these aspects make up a living cell - *catalysts*

4 main flagellar styles

- *monotrichous*: one hair - *lophotrichous*: hella hairs bunched - *peritrichous*: singular hairs all the way around - *amphitrichous*: hairs on opposite poled of the cell

amphibians (tetrapods)

- *most basal group* of the tetrapods - breath through skin and lungs in some species - *Always* connected to water - "dual life" - have not fully evolved to life on land - reproduction still tied to water - lifecycle: tadpole --> metamorphosis --> adults return to water to mate

Mycorrhizae (derived traits of embryophytes)

- *mycorrhizae*= symbiosis of roots of plants w/ fungi - mycorrhizal associations also coincides w/ the origin of embryophytes - the first land plants DIDNT have very sophisticated roots .. so fungi teamed up with the first land plants to help them anchor into the soil and get nutrients from the soil - *arbuscular mycorrhiza*: special group of fungi that are symbiotic with the roots of most plants on this planet; form structures inside the cortex of roots called *arbuscules*; spores transport nutrients thought the hyphae into the root cortex and then they exchange carbon & nutrients at the surface

Wild Bees

- *neonicotinoid* pesticides HINDER wild queen bumblebee's reproductive success - exposure to *thiamethoxam* (one of the most commonly used neonicotinoid pesticides) leads to *fewer fully developed eggs in queens* from 4 wild bumblebee species that forage in farmland - using pesticides to protect plant crops is actually killing and harming the pollinators that we depend on to get that crop

Anthocerophyta (Hornworts)

- 100 species - *'horn-like' sporophyte (2n)* that disperses haploid spores - symbiotic N2-fixing cyanobacteria

anatomical features of prokaryotes

- *nucleoid*: region where the cells' DNA is located (not enclosed by a membrane) - *ribosomes*: complexes that synthesize proteins - *plasma membrane*: membrane enclosing the cytoplasm - *cell well*: rigid structure outside the plasma membrane - *glycocalyx*: outer coating of many prokaryotes, consisting of a capsules or a slime layer; mucus/slime layer on outside that prevents infection by chemicals/toxins - some have *fimbriae*: attachment structures on the surface of some prokaryotes (not visible of TEM) - some have *flagella*: locomotion organelles of some prokaryotes

Unikonta

- *one flagellum* - includes *amoebozoa* (slime molds) and *opisthokonta* (subgroup to ameobazoa)

Defining Fungi

- *opisthokonts* (close relatives of animals) - all are chemoheterotrophic: dissolve a lot of food externally and then absorb that food - sturdy cell walls are that *chitin* and *polysaccharide reinforced*: use of chitin in cell was is a defining feature for fungi - Unicellular & multicellular species: sporulation is typical of diploid in all taxa; sexual reproduction usually under stress - have diverse lifestyles: some are detritivores (world's great recyclers), and symbiosis is common is some (mutualist: lichens & mycorrhizae; parasitic: pathogens of plants or animals)

Extraterrestrial Origin Hypothesis (for origin of life on earth)

- *panspermia*: the idea that life exists and is distributed throughout the universe in the form of germs or spores - not much support for this - life may not be unique to earth

sponges are an important source of new drugs

- *pharmaceuticals from marine invertebrates* - important argument for conservation of the worlds oceans - "marine bioprospecting"

4 types of zooids

- *pneumatophore*: the sail = the floating part - *dactylozooid*: tentacles that hang down into the water; for defense; "fishing"; 10 meters longs & covered in *nematocysts* - *gastrozooid*: for feeding - *gonozooid*: reproduction

Pollination does NOT equal Fertilization

- *pollination*: pollen grains are deposited on a stigma --> pollen grain grows a tube --> pollen tube forms --> sperm and egg join - a tiny plant forms - *fertilization*: one sperm unites with an egg - angiosperms have a long style to become more selective in what kind of genetic material gets passed on to fertilize the egg

Copepods (crustacean)

- *predatory* & *planktonic* - may be the *most abundant animal on the planet* - very small - production of fecal pellets produces "*marine snow*" - zooplankton -- food web --> transfer nutrients up into larger consumers in the ocean - right whale (baleen whale) skims the surface of the water for copepods

nutritional diversity for microbial eukaryotes

- *protozoa* (animal like) --> *phagotroph*: eats others things/heterotroph) - *algae* (plant like) --> *mixotrophy*: can eat and create their own sugars ; mostly phototrophic - *fungus like* --> *osmotroph*: digests things on outside & then absorbs nutrients and things

temperature tolerance

- *psychrophiles* --> low temps < 0-20 - *mesophiles* --> midrange temp 20-48 C - *thermophiles* --> high temp 42-68 C - *hyperthermophile* --> very high temp 65- > 110 C - prokaryotic range < 0 to 110 C -human bodies: 36-40 C

Boney fishes: Osteichthys

- *ray-finned fishes*: yellowfin tuna (thunnus albacares), red lion fish (pterois volitans), common sea horse (hippocampus ramulosus) - *lobe-finned fishes*: (very ancient) Coelacanth, Lungfishes

Archaeaplastida (plants)

- *red and green algae* - plants - some species are unicellular, multicellular, or *colonial species*: in-between uni and multicellular --> "opportunistically multicellular" - algal groups are polyphyletic

Class Holothuroidea (Phylum Echinodermata)

- *sea cucumbers* - *endoskeleton greatly reduced* --> calcareous ossicles are greatly reduced and embedded in body wall - common in shallow costal regions - very *worm-shaped* - *tentacles*: tube feet are modified --> have respiratory tentacles - *evisceration*: if disturbed by a predator, they will eviscerate some of their internal body parts and tru and get away in hopes that the predator will eat the stuff they just released --> they can then regenerate that part of the body - filled with actin & myosin (lots of protein) - a valuable wild fishery, but one that's being threatened by over collection - commercial fishing bans in 2016 in hawaii to protect the population of these sea cucumbers

Class Crinoidea (Echinoderms)

- *sea lilies and feather stars* - only 80 extant species (were more abundant as shown by the diversity found in the fossil record) - *sessile* animals - *filter feeding lifestyle*: their arms have feather-like structure coming off of them & they filter feed as the water goes by - *pinnules and tube feet* act as adhesive fiber filter - food particle moved into groove in arm; conveyor-belted via ciliary action to mouth - *mucous secreted* in some species

Class Asteroidea (Echinoderms)

- *sea stars* - *tube feet*: structure in their water vascular system that assist them in being predators & locomotion - *predators*

Class Echinoidea (Phylum Echinodermata)

- *sea urchins and sand dollars* - LACK arms but have 5-part radial symmetry - *grazers* (NOT predators) - sand dollars are "irregular urchins": they have the same body plan as sea urchins but the difference is that the spines on sand dollars are super short - sea urchins, like sea cucumbers, are really important parts of food systems around the world

locomotion & the need to find food has resulted in unique systems

- *sensory systems* are unique as compared to plants --> in animals there are a variety of sensory structures --> animals have nervous systems to process & coordinate the sensory information & "organize" a response - *behavior*: in this regard, animals are MUCH more complex than plants

4 main components of Angiosperms

- *sepals, petals, stamens, & carrels* are all modified leaves --> these organs are all derived from leaves

The Cnidarian Lifestyle

- *simple carnivore* - some swim, comes don't - *Predators*: 1st active predators on the planet - very low metabolic rates - can survive in cold & nutrient poor waters (polar oceans or the deep sea)

Reduce by "Source Reefs"

- *source reefs*: there could be a part of the reef where corals are naturally more tolerant of heat stress --> these "tougher" parts of the reed can then be a source of rescue for degrading parts of the reef - an act of *natural resilience*

Walled Spores produced in sporangia (derived traits of embryophytes)

- *sporangium*: vessels that produce the spore - *spores*: have very thick cell walls, very tolerant of dry environments & can disperse widely - *sporocyte*: cell undergo meiosis (become haploid from diploid) to make spores - *sporopollenin* in cell walls: structure in spore cell that gives protection & prevents from desiccation - "my cell walls are super hard!" - embyrophyte

Sporophylls (Derived Traits of Vascular Plants)

- *sporophylls*: modified LEAVES that bear spores --> leaves/encasings that protect the tissues that make the spores - *sporophyte*: PLANTS that make spores - *sporangia*: VESSLES that make spores

Stomata

- *stomata* = holes on the surface of leaves that are specialized in gas exchange - pores consist of 2 specialized *guard cells* around a "stoma" (singular) - having guard cells is an adaptation to preserve water - regulates gas exchange - w/o these holes, plants won't be able to get CO2 into the interior of the leaves for photosynthesis to occur

Fermentation

- *substrate level phosphorylation* - NO external electron acceptor - seen in yeast/bacteria - anaerobic: doesn't utilize any oxygen - substrate is NOT completely oxidized - only small amount of potential energy is released - when glycolysis is moving at one rate, everything else is moving slower and we get fermentation in the form of lactic acid - reduce down pyruvate into alcohol (ETOH) or lactic acid

symbiotic relationship with other eukaryotes for microbial eukaryotes

- *symbiodinium*: dinoflagellate endosymbiont w/ coral; photosynthetic; feed coral the additional sugar in exchange for protection against predators - *radiolarians*: cilia-based heterotrophs that host photosynthetic endosymbionts; protect in exchange for sugar

Parasite

- *symbionts*: live inside hosts - intimate & durable relationship - parasite benefits at the hosts expense - a parasite feeds on a host *w/o killing it*

The Cephalochordates (Phylum Chordata)

- *the Lancelets* - invertebrates - common in shallow sandy bays (to 30 meters) - small animals, 2-5cm - very simple - display all chordate characteristics *in the adult form* - *persistent notochord in adult* - usually partially buried in sand & have mouth right above the surface to collect food - move food into large sac-like pharynx with gill slits for food collection & respiration - musculature of the body is divided up into V-shapes block or *myomeres* - swimming occurs via *alternate contraction* of the myomeres on each side of the body - notochord is NOT compressible do the body does not shorten by *"bends"*

microbes (in general terms)

- *the beneficial invisible presence* - derive most of our hydrogen cycle, erosion, and decomposition - *the life force of our planet* --> play a role in climate and wind movement

Phylum Nematoda (Ecdysozoans)

- *the nematodes* -*round worms* or pin worms - nematodes are a dominant component of the soil community & are by far *the most abundant animals on earth* - account of 4/5ths of all animals on land - have all major trophic levels of the soil food web - tapered ends @ anterior & posterior parts of body - about 25,000 species - many free-living pieces in soils, compost: bacteria-vores & nutrient cycling - LACK a circulatory system: do most gas exchange by diffusion - *parasites* of plants & animals - vary in size from microscopic to 3ft long - are a global species found all over the world

Bilateria

- *three tissue layers* evolved here - *bilateral symmetry* evolved here - *cephalization* & sensory structures - locomotion - divide into 3 clades: *Lophotochozoa, Ecdysozoa, & Deuterostomia* - most animals are in the Bilateria Clade (except sponges/porifera & corals/sea anemones/Cnidaria)

Xylem (vascular tissues)

- *transport water* (up from the soil, to the roots, into the stem, out through the stomata in the leaves) *and minerals* (that are dissolved in that water) - vessel elements, *tracheids* - have *lignified secondary cell walls*: very thick cell walls - are *non-living @ maturity*: bc they don't have a functional nucleus - vessel elements evolved later in angiosperms

Parabasalids: Trichomonas ssp.

- *type of Euglenoid/ excavata* - clear in coloration but do have some photosynthetic component in them - have a semi-function mitochondria called a *hydrogenosome* --> they're parasitic so they don't need a mitochondria and can work off the nutrients and ATP of their infected host - *trichomonas vaginalis*: is the causative agent for trichomoniasis - a *STD* in humans - males can be asymptomatic, but it makes females more susceptible to STDs like HIV and can also make carrying to term difficult

Brown Algae (Phaeophyta)

- *type of stramenopile* - carotenoids give brown/gold coloration - *fucoxanthin*: pigment specific to this group, a distinguishing factor - photosynthetic - photoautotrophs - most are multicellular (seaweeds) - DO experience alternation of generation

Diatoms (aka Bacillariophyta)

- *type of stramenopile* - photosynthetic - carotenoids give them yellow/brown color - have *silica shells*: surround and protect bodies, have screen-like quality that's important for filtration which functions as *biological pumps for the ocean* - important marine phytoplankton - asexual and sexual reproduction - NO alteration of generation - harmful algal blooms (Psuedonitzchia sp.) : can kill off marine life by changing the chemistry in the ocean and making the environment unlivable

Ecological role of sea urchins are grazers

- *urchin barrens* created by the purple sea urchin form when they become over populated --> they over graze the bottom of the ocean and end up with no kelp present - otters are sea urchin predators, but with reduced population of otters on the california cost, sea urchins are over populating and destroying kelp forests - urchins take hold & graze down kelp - reducing red abalone populations - outbreak likely driven by lost of sunflower star in disease outbreak

Class Mammalia (tetrapods)

- *warm-blooded* = *homeothermy*: ability to control & maintain a high body temp --> allowed them to expand into cooler habitats - are *endotherms*: there's internal heat (reptiles & snakes are ectotherms: body temp set by the environment they're in) - mammary glands, milk for offspring - sweat glands - hair - four-chambered heart - kidney - lungs - females convert energy into support for the young

first division of insects

- *wingless* = Zygentoma (silverfish; 450 species) - *winged insects* = many orders; broken into 2 groups based on their life cycle: *complete metamorphosis* vs *incomplete metamorphosis*

Bryophyta (mosses)

- 15,000 species - mosses: Phyla Bryophyta - mosses are the dominant, *ground-covering species of bogs*: a wet & cool habitat --> require a lot of water bc they DON'T have specialized vascular tissue & need cool env. bc they have the capacity to dry out & re-wet themselves - many moss have *symbiotic association w/ cyanobacteria* : the additional N benefit lets mosses be early colonizers

The Urochordates (Phylum Chordata)

- 3 groups: Tunicates (mostly sea squirts/ascidians), Thaliaceans, & Larvaceans - *Tunicates*: adults are highly modified & become *sessile* animals & attach to a substrate - *larvae have ALL the characteristics of a chordate* - when larvae settles, the nerve cord and notochord disappear in the adult - *sea squirts*

The Crustaceans (Pancrustaceans & Arthropod)

- 40,000 species world-wide - Dominant marine arthropods --> *dominate in aquatic environment*: most found arthropod in the sea, but they're also found in freshwater & terrestrial environments - most abundant in aquatic environments due to krill & copepods - key parts of oceanic food webs - important sources of food & economic importance _ *Decapods*: lobsters, crabs, shrimp, crayfish - *Isopods*: sow bugs, terrestrial - *Amphipods*: sand fleas - *Copepods* - *Krill* - *Barnacles*

Phyla Coniferophyta

- 7 families; about 700 species - *Pines* (firs, cedars, hemlocks, larches, spruce) - *Cypress* (redwoods, junipers) - *Yew*

Ascidian Genome Project

- 80% of ciona genes are also found in humans - simpler genome: seeing our ancestral genes? - provides a good system for exploring the evolutionary origin of the chordate lineage from which all vertebrates sprouted - we can study disease processes in development in Ciona bc there would be ethical problems doing it in warm-blooded animals like kittens Smith Lab in MCDB @ UCSB

Hepatophyta (Liverworts)

- 9,000 species - liverwort haploid gametophytes appear in 2 forms, depending on the species: 1. *thallose*: grow very close to the ground/around rocks; *thallus* of the liverwort, Pellia, comprised of flat, roundish sheets of photosynthetic tissue 2. *leafy*: elevate themselves off the ground; each *phyllid (leaf-like structure* is only one cell layer thick --> leafy liverworts are often *epiphytes* = plants that live on the surface of other things, such as rock, cliffs, or other plants in moist habitats -liverworts have *primitive air pores for gas exchange* --> DON'T have stomata --> they just have pores that have no control over their opening/closing -- a lot of water vapor escapes from these leaves

Aquatic Ecosystems

- 97.5% is salt water & 2.5% is fresh - *71%* of Earths surface is occupied by ocean - mean depth of ocean = 3.8 km & goes as deep as 11 km - total volume is 1.4 X 10^7 km^3 - *300x more space for life* than on land or fresh water

Amoebozoa

- A superkingdom of eukaryotes with amoeba-like cells that move and gather food by means of pseudopodia. - *slime molds* - likely that the marine ancestral form was ancestor of fungi and animals - *Colonial Protists*: sometime unicellular, sometimes multicellular --> opportunistic multicellularity (in some cases they're permanently multicellular)

Prokaryotes are not simple!

- Basal Taxa: taxa that separated/evolved from other taxonomic groups early on --> prokaryotes are considered basal taxa - basal taxa are just as evolved as derived taxa - because prokarya have little compartmentalization w/in the cell (NO membrane bound organelles), prokarya may be EVEN MORE complex than eukarya in some metabolic processes

ocean acidification (the other CO2 problem)

- CO2 is absorbed into surface oceans and (1) lowers the pH of the ocean making it more acidic & (2) decreases carbonate levels in the ocean - this becomes challenging to organisms making calcium carbonate bc carbonate levels are low and mollusc's can't synthesize CaCO3 - the *Keeling Curve*: a global data set of atmospheric CO2 measures at the Mauna Loa Observatory in Hawaii - keeling curve shows that CO2 has been increasing dramatically since the late 50's - the ocean absorbs ~28% of CO2 emitted by industry & deforest able - larvae & juvenile mollusc are MUCH more negatively impacted by ocean acidification - adult mollusc's are challenged to do growth & calcification, but ocean acidification DOESNT kill them --> their survival is NOT impacted - seagrass & kelp (macrophytes) could be a solution: could preform enough photosynthesis that they remove CO2 from the water & keep the water more alkaline than it would be otherwise - NOAA ocean acidification program: trying to calculate the vulnerability of U.S. resources based upon stressor for future ocean acidification

Haptophyta (Coccolithophorids)

- CaCO3 shell-covered protists - have some photosynthetic capabilities - coccoliths - photoautotrophic - affected by ocean acidification bc of their CaCO3 plate - cause huge turquoise *algal blooms* that are visible from satellites - originally classified as part of the stramenopila super group (within the golden algae group) but its classification is heavily debated : while they share pigments with the brown/golden algae group, they don't have any of the other elements as far as stramenopila

Arachnids: Spiders

- Chelicerae modified into *fangs* w/ associated *poison glands* - all spiders are *predators* --> predators of insects & help with the natural control of herbivorous insects - have 4 pairs of walking legs - most spiders have special *silk glands* which produce silk - have *simple eyes* (better at detecting motion) - use *Book Lungs* for gas exchange: a stack of different membranous areas - *pedipalp*: feeding gland - have *active heart* examples of biodiversity here: - a jumping spider: Habronattus americanus: preys on a lot of pests - Goliath bird eating tarantula: Theraphosa blondi: giant spider - brown recluse spiderwebbed: Loxosceles reclusa: has a bite that's fairly toxic

Cnidarians Evolutionary Relationships

- Cnidarians: *the next "split"* from the animal lineage after sponges: they're the 1st group of animals to split away from the sponge lineage - are apart of the tree of life called "true animals" --> they're the *Eumetazoa* - most cnidarians are *marine* - the most distinct change: --> *2 embryonic cell layers (diplobastic)* --> *distinct organ systems*

Phylum Ginkgophyta

- all ginkgo's are *dioecious*: either male or female plant - fan-shaped leaves - *deciduous*: drop leaves in the winter w/ the seasons - ex: *Ginkgo biloba* - have *female ovules*: each ovule catches wind-borne pollen on a liquid drop; females known for fleshy structure they form; have megasporangia that attract the sperms/pollen - Ginkgo ovules develop into seeds that are covered by a fleshy putrid seed coat (NOT FRUIT) - *sarcotesta* = fleshy seed coat (not the ovule) - have *male microstrobili* - female ginkgo are very SMELLY --> smelly part is the *diploid seed coat*

Phylum Cycadophyta

- DONT have long trunks --> more stout & grow from the base of the ground - *palm-like leaves* - seeds and pollen are *produced in cones* - *megastrobilus* = female cycad with a seed-producing cone ; made up of many modified leaves that'll make sporangia and the spores - *microstrobilus*= male cycad with a pollen-producing cone; structures that have microsporangia; microstrobilus forms microspores, which forms a microgametophyte, which forms sperms, which forms pollen - for plants in the Cycad Phylum, the microstrobilus & megastrobilus are on *seperate individual plants* = *dioecious* - cycad spores are *heterosporous* - cycad gametophytes are *unisexual*: only have archegonia or antheridia to make either an egg or a sperm

Equisetales (horsetails)

- Equi = "horse"; seta = "branched" - equisetales is a plant order (horsetails) w/ *whorled leaves* resembling a horse's tail - *sporophyte dominant* - whorled stem arrangment - *reduced scale-like non-photosynthetic leaves*, photosynthetic stems - *strobilus* (cone-like structure) that produces sporangia - have *elaters* on spores that allow them to move (they don't need flagella)

Parasitic Plants

- Extract water and nutrients from other plants and give nothing in return - ex: *Cuscuta* (Dodder): wrap around other photosynthetic plants and suck out carbon from the green plants - take carbon *directly* from another plant w/o fungi

spicules

- Found in sponges - these consist of inorganic materials and support the animal - made of various material such as *calcium carbonate & silica* - others are made of an organic substances called *spongin* (proteinaceous)

Anthozoans (Cnidaria)

- G: flower animals - *corals & sea anemones* - corals: reef building organisms - sea anemones: have classic polyp form; usually attached to the substrate in some way; found in intertidal to deep oceans - *sea anemones & corals form associations w/ algae in a symbiotic relationship* = a highlight characteristic of Phylum Cnidarian

General Characteristics of Fungi

- Heterotrophic eukaryotes (molds, yeast, mushrooms) --> most are chemoheterotrophic - chemoorganotrophs w/ absorptive metabolism - almost all produce spores - all have alternating generations - have different roles: active predators, mycorrhizae, and parasitic fungi

Molecular Phylogeny

- Looks at *rRNA* as a tool for heritage and figuring out the Domain system - rRNA is used bc: 1. its the structural gene and evolutionary ancient 2. its *highly conserved*: can use it as a comparative toll to figure out differences between organisms 3. all living organisms have it, plays same role in translation in all organisms 4. yet, it has sufficient variability to denote differences between organisms

Seedless Vascular Plants

- Lycophyta (club mosses & relatives) - Monilophyta (ferns & relatives) --> seedless vascular plants are *paraphyletic*: the trait of being seedless & having vascular tissues is NOT monophyletic

Stanley Miller & Harold Urey

- Miller Urey Experiment: could key organic molecules have formed in the conditions of early earth? - put all of the elemental inorganic compounds into a test tube and heated it up - then supplied an electrode (a proxy for lightening) - the water vapor holding elements together was zapped by lightning - saw that cooled water contained larger organic compounds such as amino acids and nucleic acid - found ocean/atmosphere containing: methane, carbon dioxide, ammonia, hydrogen, nitrogen, but *NO OXYGEN* produced nucleotides and amino acids, precursor for DNA and proteins/enzymes

economic and ecological consequences of dealing w/ insect success and diversity

- Monsanto's YeildGard corn is designed to resist an insect pest - a gene from *Bacillus thuringiensis (Bt)*, a soil bacterium, is inserted - Bt gene enables corn to produce a protein that interferes with the digestive system of insect pests (caterpillars), which quit eating and die after they feed on the corn plant

Can you have a dioecious (separate male & female parts) plants that's also homosporous (only forming 1 type of spore)?

- NO - a moss with male and female gametophytes are sometimes called dioecious (bc the gametophyte is the dominant stage), but are *homosporous* bc there is NO microspore & megaspore

Chytrid Life Cycle

- NO dikaryotic stage --> only diploid and halpoid - haploids have flagella - haploid stage = more dominant - diploid stage = infectious stage that can really hurt kinds of animals if infected - capable (along w/ many other fungi) of switching their sex types/mating types - have *alternation of generation*: have 2 completely multicellular organisms that arise from both the haploid and the diploid state - *meiosis* takes place on the diploid sporophyte - then spore generates *haploid zoospores* which all have flagella --> these haploid spores individually germinate into haploid multicellular forms of themselves and become *gametophytes* - gametophytes have haploid fruiting body w/ 2 different mating types - gametes then fuse to form a *diploid zygote* - which then becomes a multicellular diploid *sporophyte* ... and meiosis occurs again

Glomeromycota (simple fungi)

- NO observable sexual cycle! --> seem to reproduce asexually --> have extension & binary fission of these groups - no production of spore that we know - non-septate hyphae --> haustorial - separate phylum --> *sister phylum to Dikarya*

Zygo Lifecycle

- NO true dikaryotic stage --> just a *slow process of plasmogamy then karyogamy* - formation of a zygosporangium

Hydrostatic Skeletal System of a Cnidarian

- NOT a true skeletal system - in addition is nerve nets, cnidarians also have some really simple muscles that allow them to change shape & react to stimuli in the environment - muscles are squeezing on the fluid-containing areas in the animals body & hydrostatically compressing & squishing the animals to become taller or to relax - *uses hydrostatic pressure cerated by the contraction of the muscles to change shape of the overall body* - longitudinal muscles relax, circular muscles contract: grows taller - longitudinal muscles contract, circular muscles relax: shrinks

Chytridomycota (simple fungi)

- ONLY group that's *obligately aquatic* - bc of this, they've kept their *Flagella* bc that flagellated gamete state allows them to move through the water - defined by *branched hyphae* - well known for parasitoid groups - large number of decomposers

Psilotales (whisk ferns)

- Psilo = "bald" - Psilotales is a plant order w/ *no leaves* - *Psilotum* sporophytes have photosynthetic stems (NO megaphyll leaves) and underground rhizomes (rhizomes are laterally-growing, underground stems) - the *gametophyte is tiny and non-photosynthetic* (fungi provides it with nutrients) - the gametophyte remains below the soil surface (produces antheridia & archegonia: sperm SWIM to eggs --> zygote --> sporophyte) - form Antheridia & Archegonia on the SAME gametophyte = are *homosporous* - *sporophyte dominant* - *sporangia*: produce *haploid* spores when the *diploid* spore mother dells inside the *sporangia* undergo meiosis - the spores disperse from the sporophyte, land on the soil, and develop into tiny *bisexual gametophytes*

RNA mutated to become DNA

- RNA probably mutated to DNA bc DNA is more stable than RNA and therefore better storage molecule for biological information and then retained RNA for its enzymatic properties

1. Rigid Exoskeleton

- THE #1 characteristic of arthropods - defining characteristic = epidermis produces a segmented, jointed, and hardened *chitinous exoskeleton - *multilayered structure*: contains protein, calcium, and chitin complexed together - *chitin*: a polymer --> polysaccharide - provides protection & surface for muscle attachment - PROBLEM: limits growth in animals

bumble bee conservation

- Xerces Society; conservation of inverts - Pacific NW Bumblebee Atlas

defining characteristics of molluscs

- a *muscular foot* used for locomotion or clinging - dorsal epithelium forms a *mantle* which secretes a *calcareous shell*: calcium carbonate shell - *visceral mass*: a location where all the organs are centralized in the animal

All cnidarians have...

- a basic *radial symmetry* - only 2 layers of living tissue: *epidermis & gastrodermis* - a middle gelatinous layer - the *mesoglea* - in between the 2 living layers of tissue - *tentacles* surrounding the mouth/anus - only a single opening to the digestive system: *gastrovascular cavity* = "blind gut" - *Stinging Cells* (contains structures such as *nematocysts*) that account for the "stinging" activity that is associated w/ these animals

Giardia ssp. (type of Diplomonads/ Excavata)

- a diplomonads - presence of a nonfunctional mitochondrial-remnant organelle called a *mitosome* - *8 symmetrical flagella* (paired) - parasitic - first family member of protist to be identified as an excavata - 2 phases: active phase = active flagella; insistive phase = persist in river beds and waters for long period of time - symptoms: gastrointerlogical --> prolific diarrhea/ vomiting - protist that settles in your intestine and it difficult to get rid of

Schistosomiasis

- a disease of poverty that leads to chronic ill-health - from blood flukes - connected to poor water quality & poverty -- the contamination of water - also classified as a *neglected tropical disease (NTDs)* - among human parasitic diseases, schistosomiasis ranks second behind malaria in terms of socio-economic & public health importance in tropical & subtropical areas - affects almost 240 million people worldwide and more than 700 million people live in endemic areas. the infection is prevalent in tropical & subtropical areas, in poor communities w/o potable water & adequate sanitation

Heterosporous species

- a haploid gametophyte that produces *two types of spores* - the types are *visibly distinguishable* from one another (larger megaspore and a smaller microspore) - they have usually *2 types of sporophylls* that make 2 types of spores - makes *unisexual gametophytes*: either a male or a female - the spikemoss (selaginella) and quillworts (isoetes) are heterosporous - Heterospory = *a polyphyletic trait*

Coral Farming

- a human facilitated process - people work underwater to raise coral & then plant them out to try & restore a degraded part of the reef - an act of *restoration*

coral-algal symbiosis

- a key species relationship in coral reef ecosystems - most reef building corals contain photosynthetic algae, in the genus *zooxanthellae*, that live in their tissues (*endosymbionts*) - corals & algae have a *mutualistic relationship*: the coral receives nutrition from the algae & the coral provides the algae w/ a protected environment & compounds they need for photosynthesis - corals get 90% of their nutrition from their endosymbionts photosynthetic activity

reproduction/ sporulation stages that help differentiate between fungi

- a long haploid stage or not - a long diploid stage or not - any Dikaryon (n+n) not diploid

Colony Collapse Disorder

- a multistress phenomena - bees are facing : flowerless landscapes, mites, class of insecticides called *neonicotinoids* (sprayed on crops then bioaccumulates in the bee and makes them sick), & hard winters

Cyanobacteria

- a phototroph - obligate photoautotrophs: cant produce any ATP w/o producing O2 in the process - *photosystem II* - light for energy sourve - oxygenic process (source of O2 on earth)

Rafflesia Lagascae (Corpse Flower)

- a plant that has completely *lost its chloroplast* (the organelle that does photosynthesis) - the *largest flower in the world* - *parasitic underground*: the roots of this plant grab hold of roots of other photosynthesizing autotrophic plants and sucks the carbon from them --> NOT all plant have chloroplasts!!!

The SAR group

- a poly polyphyletic group of *heterokontic protists*: have two differently shaped and differently sized flagella - *S*tramenopiles - *A*lveolates - *R*hizaria

monecious sporophyte

- a single sporophyte has both female and male sporangia - ex: *confiers*

Tilaalik

- a transition animal - has fish characters: scales, fins, gills & lungs - has tetrapod characters: neck, ribs, fin skeleton, flat skull, eyes on top of skull

*Gnetum species* of Phylum Gnetophyta

- about 35 spp. - very similar to flowering plants w// broad leaves - *dioecious* - *deciduous*

*Ephedra species* of Phylum Gnetophyta

- about 40 spp. - inhabit *arid regions* world wide --> desert/dry area - some Ephedra species contain *ephedrine*, some people make tea known as "Mormon tea"

Radiolaria (type of Rhizaria)

- all known species are *marine* - size range: 20-300 micrometers --> big size range - have internal *SiO4 skeleton* - many species are photosynthetic - very symmetrical

Myriapods (Arthropods)

- all terrestrial - body plan: *2 regions* instead of 3: *head & trunk* - *Centipedes*: 1 pair of legs per body segment, carnivorous (have toxin they inject into their prey) - *millipedes*: 2 pairs of legs per body segment, scavengers & consume some plants, very much about nutrient cycling in terrestrial ecosystems

Corals

- almost all corals are *colonial organisms*: they are composed of hundreds to hundreds of thousands of individual animals, in this case, polyps - corals take CaCO3 out of the water & turn it into their skeleton - have variable morphologies

4 major classes of tetrapods

- amphibians - reptiles - birds - mammals

what is the Vertebrate ancestor?

- an *estuarine species* --> possibly a fish-like organism - a lineage of chordates led to vertebrates - evoked during the Cambrian, 500 mya - evolved a robust and highly calcified skeleton and a more complex nervous system that led them to be better at capturing food and avoiding predators - earliest vertebrates: *conodonts* = has dental elements within head - had the evolution of the jaw

The smallest seed

- an *orchid* - a monocot of the vanilla orchid - about 0.0000008 g - many orchid seeds that are this small are initially microheterotrophic : obligately rely on fungi in new environment bc they dont have enough energy reserve inside the seed to be able to germinate on their own - advantage: very small and better for dispersal

a legume pod

- an example of a *one-carpel fruit* w/ 5 matured ovules

how did vertebrates colonize the land?

- ancestor had jointed appendages: coelocanths, lungfish - swim bladder-like structure was a primitive lung - "lungfishes" - "living fossil"

evolution of the jaw

- ancestral form has modified gill arches that became the jaw - teeth, jaws and chewing = *increased feeding efficiency* - teeth & jaw & dentition match the feeding ecology of the particular type of vertebrate

where are animals descended from?

- animals are descended from a *single ancestral line* - animal lineage is *monophyletic* - *sponges* are the sister group to all animals

filter feeding in bivalves

- animals pump water through body & extract nutrients from the water - move over feeding structure (gills) that serve as a respiratory & feeding structure - freshwater & marine versions in this group - theres 2 ports that the animals uses to move the water: *the in-current & out-current* - water passes over the gill tissue & food particles & such get stuck on the gills and are then moved towards the gut - this actions of filter feeding has resulted in these animals being able to influence water quality - while the mussel is filtering, *bioaccumulation* can occur --> if there's anything toxic in the water, the animal will accumulate and hold it in its body

unique features of Phylum Porifera

- animals that *lack tissues* - composed of *different cell types*

Krill (crustacean)

- another *planktonic crustacean* - eat phytoplankton in water & convert that into protein & lipids --> then they are eaten by fish & whales - important part of oceanic food webs

the Cambrian "explosion"

- another wave of animal diversification, including larger body sizes possibly linked to increases in atmospheric oxygen - 535-525 years ago - explosion of diversification in the ocean bc atmospheric oxygen went up in the planet & therefore so did dissolved O2 in the water, causing an appearance of new species on the planet

3. Jointed Appendages

- appendages are *modified for different functions* - *regionalized body*: defense, feeding; locomotion - walking or swimming - *specialization of body regions is a major theme in arthropod evolution* - these animals have very complex body plans that support active locomotion & diff feeding styles

Archaea and Eukarya

- archaea and eukarya are more closely related bc the first eukaryotic cell originated from an early archaea cell

microbial eukaryotes

- are ancestors to plants, fungi, and animals -characteristics of protists: a polyphyletic group! 1. *most are aquatic* 2. *nutritional diversity* 3. *locomotion* 4. *organelles and vesicles* 5. *cell surfaces*: diverse, slimey or armor surface 6. *form symbiotic relationship with other eukaryotes* 7. *reproduction processes*: varied

Zooxanthellae (type of dinoflagellates)

- are mostly dinoflagellates - photosynthetic - mixotrophic: capable of NOT photosynthesizing as well --> when they're outside of the coral poly they can consume food - *symbionts* w/ coral and other marine invertebrates - imbed themselves inside the coral poly --> provide sugars through photosynthesis and in turn, the coral polyps protects the zooxanthellae from predation - the *coloration* you see in coral is a factor of what type of dinoflagellates or *zooxanthellae* is in the coral - the *shape* of the coral is a factor of the *type of coral polyp*

angiosperm vs. gymnosperm

- as the angiosperm *ovules* develop into seeds, the *ovaries* surrounding them develop into fruits -gymnosperms DO NOT have ovaries, but they have *ovules* attached to the sporophyll

oxidative stress theory of coral bleaching

- at the onset of thermal stress, there is a *reduction in the activity of photosystem II* in the zooxanthellae chloroplasts due to direct damage of PSII itself or impairment of the dark reactions of photosynthesis by damaging proteins & enzymes in these pathways - damaged photosynthetic pathway canNOT properly transform the incoming energy & toxic oxygen free radical accumulate - oxygen free radicals cause damage to cell components & membranes and symbiosis breaks down - the algae become toxic to the animal part

Bacteria & Archaea and photosystems I and II

- bacteria and archaea only use one OR the other of photosystem I or II - do not use both

Diversity of Life

- based on fossil record - *general increase in species diversity* - punctuated by periods of mass extinction

Archaeplastida Family

- began from ancestral alga - first derived: *red algae* = still does photosynthesizes but is NOT green VIRIDIPLANTAE: anything that's green and has primarily chlorophylls a & b in its chloroplast - 2nd derived: *chlorophytes* STREPTOPHYTA - 3rd derived: *other charophytes* - 4th derived: *closet charophyte relative* PLANTAE - 5th derived: *embryophytes*

Diploids vs Haploids

- being diploid might be considered more complex & advanced than haploids, but *haploid organisms are just as evolved as diploid organisms* - haplontic life cycles can benefit organisms depending on environmental content & life history

Cadherin Proteins

- bind cells in multicellular animals - adhesion proteins shared across many organisms - a unique domain thats only found in animals (*CCD*) - used to group and create the phylogeny of animals

consequences of bleaching

- bleached coral are NOT "dead", but *if temperature anomaly persists for extended period, coral will die* - bleached corals *CAN recover* zooxanthellae if exposure to high temperature is brief*, but even recovered corals show reduced growth, calcification, reproduction & greater incidences of coral disease

Adults tunicate anatomy (Urochordate)

- bodies are covered by a leathery tunic - sack-like body w/ *two siphons*: incurrent siphon to the mouth & an excurrent siphon where wastes are released - enlarged pharynx = *pharyngeal basket* - attach to a substrate and become *suspension-feeders* (this characteristic is shared w/ protostomes)

Distinguishing characteristics of Crustaceans

- body divided into *3* regions: *head, thorax, and abdomen* - *Carapace*: head and thorax - *Nauplius larvae*: distinctive form of larvae that have median compound eye (like a cyclops)

Body plan of an Arthropod

- body is divided into *segments* - jointed appendages on different segments - moved by *attached muscles* - appendages support complex locomotion: walking, swimming, flight - helps facilitate prey capture - support sensory perception - have an *open circulatory system* - in some of these organisms there are *bristles* coming out of the exoskeleton that connect to a neuron inside the body --> animals can feel touch of their exoskeleton - their appendices work like ours, but are designed *inside out*: extensor & flexor muscles are inside the exoskeleton & they attach to the internal surface of the body

Red & Green Algae

- both groups are single and multicellular - distinguished by their photosynthetic pigments - most of these algal groups have coralline aspects to them --> they have CaCO3 deposits which are important for reef building

candidates for endosymbiotic theory

- candidate host: *archaea* based on cellular rRNA & DNA analysis - candidate bacteria: a member of the *Rickettsia* group based on mitochondrial rRNA & DNA - candidate photosynthetic bacteria: *cyanobacteria* based on plastid rRNA & DNA

carpel

- carpel is the *megasporophyll* bc its is "modified leaf" that bears megasporangia (contained in the ovule)

all angiosperms share:

- carpels - seeds w/in fruits - reduced gametophytes (NO antheridia or archegonia) - flowers - endosperm - double fertilization

carpel's evolution

- carpels evolved from leaf-like structures that bear megasporangia A. sporangia on edges of the leaf; sporangia are megasporangia B. as the carpels evolved, the margins of the megasporophyll evolved to protect the mesgaporangium; leaf enclosed on itself & brought sporangia from the edges to the interior parts to protect it C. when the margins of a megasporophyll fused to enclose the megagametophytes, the fully closed carpel has evolved D. multiple carpels can fuse: each carpel has several ovules & makes several seeds

Trichinosis (caused by a parasitic nematode)

- caused when humans eat *under-cooked meat* (usually pork, could be bear or walrus - the encysted juveniles in the meat are consumed & reproduce and get into the muscle tissue of humans

Simplification of Cell Metabolsim

- cell brings minerals in - they react those minerals to place them into dis-equilibrium - then thermodynamics of the system work to put those things back into equilibrium and potentially generate something like ATP - *cells jobs is place things out of equilibrium* so that nature can put them back into equilibrium and create something - nutrients for biosynthesis enters cell - *anabolism/biosynthesis* occurs: makes large molecules out of smaller molecules - macromolecules produced - chemical, light (energy source) enters cell - *catabolism* occurs: breakdown of complex molecules to form simpler ones, together with the release of energy --> "destructive metabolism" - energy for motility released inside of cell - waste products excreted from cell

biochemical characteristics of prokaryotes

- cell wall cell membrane structure - metabolic strategy - relationship to oxygen - relationship to temperature

organelles & vesicles for microbial eukaryotes

- cells can be *large*--> surface area to volume ratio can be a problem, as cell size increases, surface area decreases - mode of ingestion in protozoa = *endocytosis*: process of taking in food w/in vacuoles formed by invagination (oral groove) of the plasma membrane --> if food dissolved and is liquid form, its called *pinocytosis*: cellular drinking --> if the food is a particle its called *phagocytosis*: cellular eating - have *contractile vacuole*: pull in water & push out waste contents; acts like a suction on the exterior of the plasma membrane --> can attach to the plasma membrane and open in up and then expel contents out of the cell --> can also suck in contents from the outside of the cell

cellular slime molds

- cellular slime molds may engage in 2 forms of life cycles: as *solitary amoebas* (single cellular) when nutrients are abundant OR as *aggregated amoebas* when nutrients are scarce - in aggregate form, some individuals contribute to the formation of a *stalk*, on top of which sits a *fruiting body* full of spores that disseminate and germinate in the proper moist environment - form aggregate to share food and to have the critical mass to make a fruiting body and a stock - height of stalk matters for how far away spores can be released - pseudopodia extension of cytoplasm in amoeboid form - *heterotrophic* --> phagocytosis - single celled amoeba that *aggregates when food resources are low*

amniote egg

- characterized by having a lot nutrients in its yolk-sac for embryo to feed off of as it develops inside the egg - extra embryonic membranes: these act as a protective covering for the embryo that prevents desiccation but still allows gas exchange of O2 and CO2 across the shell

how do cilia differ from flagella?

- cilia are shorter, far more numerous, and move in a breast-stroke-like motion - flagella move by rotation

Symbiodinium Clade D

- clade D = the super heat-tolerant specialist - during the mass bleaching in 1998, this clade was unusually resistant to bleaching 2 lines of evidence --> clade D present in corals resistant to bleaching --> photosystem II more heat tolerant in clade D: evidence that clade D is a thermal specialist - suggested that there could be more clades yet discovered - made people think differently about endosymbionts: could we engineer more thermally tolerant algae to offer to corals?

Other factors that could potentially lead to the unprecedented coal deposits of the Carboniferous period?

- climate changed from volcanic activity & tectonic circumstances facilitated anoxia environments --> warm, humid climate increased plant productivity --> large basins formed and the crust subsided to prevent erosion

By-the-wind Sailor

- cnidarian - velella velella - predator -occur in big groups - mass stranding on beaches in california

Cribrostatin 6

- comes from a tube *sponge* - anti-neoplasic & anti-cancer therapeutic agnet - antibacterial & anti fungal properties

Turbellaria (flatworm)

- comprise only 16% of the phylum - *simplest flatworms* - mostly *free-living* - marine & freshwater

Geological and Biogeochemical changes that affected extinction and evolution

- continental drift --> sea level fall - climate change - volcanic activity - *increase in oxygen* - external events such as the asteroid event that killed off dinosaurs

the nematode cuticle

- cuticle is shed *3 times* through out the animals life - barrier between animal and environment - an extracellular matrix - composed of small proteins but predominantly of *small collagen-like proteins that are extensively cross linked* - cuticle allows the animal to live in very dry, terrestrial/soil environments

4 gymnosperm phyla

- cycadophyta - ginkgophyta - gnetophyta - coniferophyta

Decapoda (crustacean)

- decapoda = "10 footed" - *crayfish, crabs, lobsters, prawns, shrimp* - about 15,00 species & half of those are crabs - tend to be *scavengers*

Ciliates (type of Aveolate)

- defined by *presence of cilia* around all of some of the body or cell, *two types of nuclei*: macro and micro, & *used in conjugation events* - some are photosynthetic pigments but most are heterotrophic predators (many might be mixotrophic as well) - most ciliates posses an *oral groove* for feeding (bc they're heterotrophic) - ciliates are well-known for their *conjugation process* involving the micro and macronuclei (overtime the micronucleus will become a macronucleus)

Apicomplexans (type of Aveolate)

- defined by its *obligate hosts to complete its life cycle*: must be w/in a host at one point to complete their life cycle - for the most part are *parasitic aveolates* --> are mostly human and animal parasites - Gametic (male) phase exhibits heterokont flagella - generally have a single mitochondrion and an *apicoplast*: an additional mitochondrion; is an indiction that this is an additional endosymbiotic event --> evidence of maybe 4,5, or 6 endosymbiotic events; maintains a 35 kilo base circular genome - famous example of a apicomplexan: *plasmodium vivax*: protist that causes malaria --> infect RBC

Zygomycetes (simple fungi)

- defined y their *zygosporangium*: (no big fruiting body - look at slide) the closest thing int he simple fungi group to Dikarya - black bread mold : *Rhizopus stolonifer* -coenocentric hyphae - rapid spreading growth (think mold)

Louis Pasteur

- demonstrated the idea of non-spontaneous reproduction of life with evidence of *airborne microbes* as examples of microbial life and then plenitudes of "invisible life" - demonstrated that these microbial could be killed with *Pasteurization* - had a sealed container of nutrient broth with no life, then opened container to air and saw a propagation of life -- Demonstrated that microbes were biocatalyst and that different microbes produced different bioproducts

Dr. Kelley Brewer Dentist

- dental health is heavily influenced by your normal flora --> genetic predisposition for certain types of bacteria --> you get your mouth bacteria from your parents (when they feed you) - *biofilms* (a form of multicellularity in bacteria) are widespread in the mouth --> precursors to plaque --> increase the ability of microbes to live anaerobically - *Anaerobic bacteria are pathogenic in the mouth* --> they persist below the gumline - medicines, other drugs and other medical diagnoses can change the bacteria composition in your mouth --> diabetics eat more frequently, changing the pH in their mouth more often - Smoking and vaping reduce the ability to recognize periodontal disease --> *periodontal disease* causes bleeding of the gums - vaping and smoking reduces bleeding and crates dry mouth

Angiosperm Seed

- diploid seed coat on outside that's derived from the maternal plant (same genotype) = *diploid integument* - *"double integument"* = *2* layers thick - *triploid endosperm* = derived from 3 chromosome copies; multicellular; product of fusion of 1 sperm + 2 polar nuclei from the megagametophyte - sperm that makes up the triploid endosperm is different from the sperm that fertilizes the egg - have 2 sperms coming in from the pollen, 1 fertilizes the egg & the other fertilizes the 2 polar nuclei derived from the gametophyte = *double fertilization*

Gymnosperm seed

- diploid seed coat on outside that's derived from the maternal plant, megasporophyll (same genotype) = *diploid integument* - *"single integument"* = *1* layer thick - *haploid gametophyte* = food source for embryo; multicellular tissue left over from female gametophyte (megagametophyte) --> the genotype of this nourishing tissue is the same as the egg - *diploid embryo* = sporophyte of the next generation

Phylum Mollusca

- distinctive features: body plant, feeding, calcification - under Lophotrochozoa family - phylum mollusca is one of the relatively large animal phyla w/ 100,00 living species - dissimilar body shapes but united by a body plan - NO "typical" mollusc - the mollusc's are the phylum that are showing the greatest # of extinctions (w/in one phylum) in the animal kingdom - 4 main groups: CLASS POLYPLACOPHORA - chitons - mostly marine herbivores - many plates CLASS GASTROPODA - snails & slugs - aquatic & terrestrial - largest gastropod class (70,000 species) CLASS BIVALVIA - clams, scallops, oysters, mussels CLASS CEPHALOPODA - squid and octopus - exclusively marine

most traded commodities in the world

- first: *coal* (a dead plant) --> petrol oil is coming from coal which is mostly made up of fossilized plants - second: *coffee* (a plant)

feeding in molluscs

- diversity here too - *filter feeding* in bivalves - *grazing* in snails and chitons: gastropoda have a band of teeth called *radula* that are used for feeding (missing in the bivalves) - *hunting* in octopus: in place of a mouth, they have a razor sharp beak in the center of their tentacles --> are very good predators

mechanisms of heat tolerance in corals?

- does the type of symbiont one had, link to a coral being more thermally tolerant? - signs of hope: *genotype of the zooxanthellae endosymbiont has functional significance in a heat stress context* - not all zooxanthellae are the same in all corals - most belong to the genus *Symbiodinium*, but within this genus there are several genetically different clades - simple genetic tests called *restriction fragment length polymorphism* can be used to determine the genotype of Symbiodinium in corals

Arthropods (Ecdysozoans)

- dominate the eumetazoans (the animal kingdom) --> highest in numbers - the most successful animals - occult land, sea, and air - species discovered over 1.2 mya - *enormous diversity* - common ancestor of arthropods had the evolution of the *exoskeleton*: supported the huge diversity and success in this group of animals, also supported their radiation into all sorts of habitats on the planet

when did flowering plants evolve?

- during the Cretaceous Period, about 145 mya

radial symmetry

- early primitive flowers, like magnolia, water lillies, and star anise are *radially symmetric*: cut ints 6ths, theres no top or bottom - ex: Asters: made up of 100s of smaller, radio-symmetric flowers

swim bladder

- ecologically significant for fish - (sharks don't have it) - * a buoyancy organ*: neutral buoyancy - aids in *hearing underwater & sound generation* - fish regulates gas levels by exchange with the blood

proton motive force

- electron carriers are oriented in membrane that separate protons from electrons - H+ gradient created from hydrogens moving from one side of the membrane to the other - outside: (+) and Acidic from lots of H+ - inside: (-) and alkaline - gradient = generation of ATP - H+ wants to move down gradient (high to low conc) and into the cell --> this drives production of ATP

Oparin & Haldane's Reducing Atmosphere Hypothesis

- energy and reduced compounds in atmosphere led to formation of organic monomers --> true! - energy coming from something like lightening out in the air - support: *Miller Urey Experiment*

Sergei Winogradsky

- environmental microbiologist who developed first ideas of chemolithotrophy - *chemolithotrophy*: organisms obtain their energy from the oxidation of inorganic compounds and use CO2 as carbon source... they are autotrophs

origin of seed plants

- evolution & origin of the seed plants was between the Permian (290 mya) and Triassic (251 mya) periods

Bilateral flowers

- evolved later in monocots & Eudicots - divide into 2 halves

Red Algae

- ex: *porphyra sp.* = algae used to make dried seaweed in sushi rolls - has pigments *phycoerythrin* (reflects red light) which make the pigment of chlorophyll - the reason red algae isn't green or brown is bc of its habitat --> which is primarily marine and lives in deep parts of the ocean - (green algae lives in shallower environments) - *rhodophytes*: tend to be greener in shallower waters and darker in deeper waters

Phototrophs

- ex: purple & green bacteria - anaerobic - photosystem I: an oxygenic --> NOT producing oxygen - *photoautotrophs*: (some) use CO2 for C source and light energy is used to split H2S and H2 instead of water --> purple sulfur - *photoheterotrophs*: (many) use light energy and organic C for C source --> purple non sulfur

Planarians

- example of a free-living turbellarian - freshwater - most are small (<1cm) - *carnivores or scavengers* - organs like flame bulbs (excrete waste) are present - *cephalization* is apparent - *Thompson & McConnell*: biochemical memory experiments --> saw that planarians are capable of integrating smells associated w/ finding food

Yersinia pestis

- example of a gram (-) bacteria -theres a deletion in some humans that makes them immune to this bacteria - *gram (-)*, non-motile *coccobacillus* (no flagella nor cilia) - can be transferred through water/fluids - causative agent for the *bubonic plague* - facultative anaerobe: capable of living in oxygen rich and oxygen poor environments - antiphagocytic slime layer: prevents viruses from entering cell - found in certain species of fleas and prairie dogs

Hydrothermal Vent Hypothesis

- extreme gradients in temperature and vent plume chemistry led to organic monomer formation --> true! - energy coming from extreme gradients near hydrothermal vents from magma in the ocean

Malpighian Tubules

- feature in hexapoda - tubules around the gut of the animal - they recover water from the body of the animal and put it into the gut, causing all the feces to be super concentration - these structures are *water-recyclers*: reabsorb water/ions rather than pooping it out - *help conserve water while animal is excreting waste* - an adaptation for living on land

Coniferophyta (largest gymnosperm phyla)

- female & males are on the same sporophyte = *monoecious* - they produce a *microspore* (in the pollen) & a *megaspore* (eventually becomes a seed) = *Heterosporous* - each gametophyte produces one gamete = *unisexual* - most produce ovules in highly recognizable female cones = *megastrobili* - female coons are *woody when they release their seeds*

Spider Silk

- fibrous protein spun into a web by spiders to capture prey - makes the web strong - use silk gland to form webs and to cover up their eggs while their reproducing - some spiders will wrap up food and present it to the female as an offering - also use silk glands to somewhat fly in a process called *ballooning*: helps spiders disperse all over the globe

feeding strategies of animals

- filter feeders (such as mussels) - herbivores - predators - parasites (such as tape worms) - detritivores: take dead material & turn it into compounds

Mycoplasma laboratorium

- first *"truly synthetic"* organism - deletion experiments were performed to find the minimalist set of genes - minimalist set of genes were inserted into the "body" of another microbe and allowed to replicate - Dr. Craig Venter is attempting to patent this organism

an example of the Impact of being small

- for biomass: phytoplankton make up only 0.2% of all living plant matter on earth - for photosynthetic activity: phytoplankton account for 45% of the earths photosynthetic activity bc they have a high surface area to volume ratio and can be more metabolically active

how do we determine evidence and the age of that evidence?

- fossils - half-lives - molecular clocks

how are fungal groups defined?

- fungal groups are *defined primarily by their reproductive forms and lifestyles* - fungal groups are *defined also by their hyphae forms if any*

Multicellular Gametangia (derived traits of embryophytes)

- gametangia: vessel that makes the gametes - the haploid stage is multicellular - *archegonia*: the female gametophyte that produces the egg - *antheridia*: the male gametophyte that contains the sperm

Reduced Gametophyte (Shared Reproductive Traits of Seed Plants)

- gametophyte is small but *still multicellular* (at least 2 cells) - found in pollen grains - are *haploid*

Octopus Genome

- genomic changes play a critical role in the evolution of cephalopod morphological innovations, including their large & complex nervous system 1. found expansions of gene groups *protocadherins* which regulate neuronal development 2. identifies hundred of *cephalopod-specific genes*, many of which showed elevated expression levels in such specialized structures as the skin, the suckers, and the nervous system 3. uncovered large-scale genomic rearrangements that are closely associated w/ *transposable element expansions*

Echinoderms (Deuterostomes)

- greek for *"spiny skin"* - spines poke out from calcified skeleton - all are *sessile or slow-moving marine animals* - defining characteristic = unique *Water Vascular System* used for locomotion & feeding

plasmodial slime mold life cycle

- haploid spores develop into amoeboid or flagellated form, which are then fertilized to form a diploid, multinucleated mass called a *plasmodium* - this plasmodium is net-like and, upon maturation, forms a sporangium on top of the stalk - the sporangium forms haploid spores through meiosis, after which the spores disseminate, germinate, and begin the life cycle anew - the brightly colored plasmodium in the inset photo is a single-celled multinucleated mass - difference from cellular slime molds: get the formation of haploid amoeboid that come together and form a diploid zygote

life cycle of multicellular Uvla (a chlorophyte/green algae)

- has *alternation of generations* (a RARE case) - have dominant multicellular haploid stages as well as a multiceullar diploid

a tomato

- has *three fused carpels* - each carpel has many seeds/ovules

Barnacles (crustacean)

- has a sedentary life style - *semibalanus balanoides* is an obligate cross-fertilizing hermaphrodite: adults take turns being male or female from season to season - during reproductive season, penis searches an area around the adult to find a receptive 'functional female' --> this is a mechanism that keep genetic diversity moving in this population of animals

Amborella trichopoda

- has the most primitive looking flowers - people say angiosperms evolved in the southern hemisphere/pacific island region - only found in Caledonia: thought to be the origin of angiosperms

Dinoflagellates (type of Aveolate)

- have *2 flagella* of different sizes *within grooves of body armor* which is made of cellulose - bioluminescent - responsible for *red tides*: a proliferation of dinoflagellates which are eaten by shellfish --> if humans eat shellfish at these times, they can be poisonous - endosymbionts of many marine organisms that are vital to the marine environment - autotrophs, mixotrophs, and hetertrophs

Filicales (ferns)

- have *annulus*: rim of tissue that expands explosively to release spores; serves to fling the spores out of the sporangia --> the humidity in the air is working to extend and contract the cells in the annulus - sporophyte comprised of *large megaphylls* w/ a network of vascular tissues - *sporophyte dominant* - sporangia often appear in clusters on the underside of fronds

Begonia Flower

- have *unisexual* flowers - is *monoecious* --> can find female & male flowers on the same plant

body plan of a Cnidarian

- have 2 forms: *polyp or medusa* - *polyp*: in colonial things such as corals - *medusa*: in jellyfish; is a swimming type/mobile form - *mouth/anus*: has a "blind gut": one way in & one way out --> mouth & anus are the same things - have *gastrovascular cavity* in center: a region of gas exchange & digestion - *mesoglea*: jelly layer in between epidermis & gastrodermis; is what gives the medusa-type organism their buoyancy - *lack a circulatory system*: gastrovascular cavity can be highly branched in large cnidarians - *extracellular digestion*: cells in gastroderm contain digestive enzymes - *epithelial cells w/ muscle fibers that allow movement*

Mycotrophic plants

- have NO chlorophyll - are connected to fungi underground which are connected to other plants that are doing photosynthesis --> the carbon from those plants are traveling down into the roots, into the fungi, and then into the roots of the mycotrophic plants which *are NOT producing any carbon themselves* -ex: *sarcodes sanguinea* (snow plants) --- NOT green - ex: *monotropa uniflora* (Indian pipe) -- NOT green, meaning it doesn't have chlorophyll which is the source for photosynthesis

Red Algae: Rhodophyta (Plantae)

- have NO flagellated stages - key pigment: *phycoerythrin* (also phycocyanin, carotenoids, Chla) - ALL are *multicellular* (no free-living unicellular) - some secrete CaCO3

Body plan of Hexapoda

- have a *3* region body: *head, thorax, & post-genital region* - very well developed nervous system: cerebral ganglia & nerve cords - have a heart & dorsal artery - *malpighian tubules*: an excretory organ - *tracheal tubes*: part of respiratory system - compound eye - antennae

Tetrapod ancestor

- in the lobe-finned fishes lineage - 3 living lineages: *Coelocanths, Lungfishes, Ancestor of the tetrapod* - adapted to life on land, gave rise to vertebrates, had limbs & feet

Multiple Origins of life on Earth?

- many biogenesis events? - multiple time period/locations over the earths atmosphere where multiple biogenesis events could've occurred - its possible that there were multiple and likely that only one lineage survived on earth

Distinguishing Characteristics of Echinoderms

- have a *5-pointed radial symmetry in adults*, but NOT larvae: larvae are bilaterally symmetrical, after 5 weeks they metamorphose into adults - *calcified internal skeleton* that covered by a thin layer of tissue --> process of this starts in larvae; shells are called *tests* - *water vascular system*: series of fluid-filled canals connected to numerous feeding and locomotory appendages (the *tube feet*); whole system runs on hydraulics; animal brings in sea water from the environment into the canals and then had muscles that squeeze and make the tube feet work - *tube feet*: long projections that come through pores in the skeleton; used for locomotion; sucker of the tub feet have the ability to clasp onto surfaces/shells and pop bivalves open to eat

Reproduction & Sporulation in fungi

- have alternation of generation - some fungi reproduce both sexually and asexually - asexual: favorable conditions --> yeast = fission or budding - sexual: UNfavorable conditions --> *ascospore*= end of sexual reproduction; *sporangia*= structure that produces spores (n); *condidispores*= produce at tip of hyphae - Diakaryote lide stage (can be larger or smaller depending on the type of crown fungi) in higher *"crown fungi"* - fruiting bodies = *sporangia* - in the air there's 10,000 fungal spore per cubic meter (each breath= 5 spores)

prokaryotes

- have cell walls - NO organelles --> NO nucleus ; but do have cell differentiation - NO microtubules - *nucleoid* and free ribosomes - digests food *externally* - single metabolic system: JUST substrate level phosphorylation or JUST oxidative phosphorylation or JUST PS I or JUST PS II NUCLEAR MATERIAL - circular DNA - *1 chromosome* - NO membrane separating transcription and translation - 1/100 as much DNA as eukaryoes - ribosomes are *slightly smaller*

"Macrobes" (eukarya)

- have only *2* distinct physiologies 1. *phototroph* --> chloroplasts 2. *heterotroph* --> mitochondria

Eukaryotes

- have organelles - have cytoskeleton - CAN digest material *internally* - structurally larger and more complex (some eukaryotes, fungus and plants, have cell walls) - posses similar aspects to prokaryotes such as flagella, plasma membrane, ribosomes, and DNA, BUT these *elements are compartmentalized* - chained metabolic systems--> stack metabolic systems instead of having just one: glycolysis (& substrate) & Krebs and Oxidative Phosphorylation, Photosystems I & II NUCLEAR MATERIAL - more genes ... more DNA - *several linear pieces of DNA* - Nucleus contains DNA --> separation of transcription and translation - DNA contains large amounts of repeating sequences and introns --> pit fall of being eukaryotic is that there are secondary events that make it easier for them to hang on to viral DNA/broken DNA --> they are not selective immediately like prokaryotes

Vertebrates (Phylum Chordata)

- have specialized structure for: *support, locomotion, and feeding* - evolution of a *large body size*: organ systems are able to support more body - *chordates w/ a spinal column* - a bacon with vertebrate - attaching muscles to internal frame - vertebrate enclose the spinal cord, take over role of the notochord - have large set of *Hox genes* - 2 or more sets - *neural crest*: type of embryonic cell

Stramenopiles

- heterokonts w/ *one hairy* and *one smooth flagella* - carotenoids - *photosynthetic* - include: *diatoms* and *brown algae*

Aveolates (S*A*R group)

- heterokonts w/ characters air sacs below the plasma membrane called *alveoli* - 3 subgroups: *dinoflagellates, apicomplexans, & ciliates*

Hexapods (Pancrustaceans & Arthropods)

- hexapoda = "6 legs" - *the insects* - over 1 million species - *FIRST animals to evolve flight* - extremely successful in transition to land: relates to exoskeleton & its waterproof features - most are *terrestrial* - some aquatic for part or all of lifecycle (ex: mosquito reproduces in water) - few marine insects

Attributes of Fungi

- high tolerance to hypertonic environments --> due to cell wall that allows them to not deflate/burst in hyper/hypotonic environments - tolerant to low -6C and high 50C temps (freeze tolerant and heat tolerant) - good at degrading complex polymers such as cellulose, lignin, and humic - produce secondary chemical byproducts such as: *antibiotics* (penicillin, cephalosporin), *alkaloids* (ergot, lysergic acid/LSD), and *toxins* (aflatoxins psilocybin)

Euryarchaeota

- highly diverse --> has the most described species thus far - separated from the other archaeans based mainly on *rRNA sequences* and their *unique DNA polymerase* - include *methanogen*: produce methane and are often found in cow intestines - include *halobacteria*: which survive in extremely salty environment - extremely *thermophilic aerobes and anaerobes*: which generally live at temperature between 41 and 122 degrees celsius

Honey Bees

- honey bee pollination alone adds more than $15 billion in value to agricultural crops each year in the U.S. - wild bees contribute even more - in 2014, Obama related a presidential memorandum - creating a federal strategy to promote the health of honey bees & other pollinators

paraphyletic

- if the last common ancestor has the trait but not everyone derived from the ancestor has the trait

Antarctic Krill

- important species of krill - occurs in massive clouds in the southern ocean around the arctic - arctic krill are full of omega-3 - Eco-krill: capture krill & turn them into health food pills that we take to get omega-3 into our diet --> this may hurt marine ecosystems by removing too much krill - antarctic krill are being targeted by fishing vessels in a way that may damage one of our last marine wilderness in the southern ocean around the arctic - "Direct-Action Ocean Conservation": attempt to interfere w/ these kinda of fishing activities : *operation krill*

sponges vary by habitat

- in places where there's not a lot of current & its kinda gentle, like the deep sea or stiller deeper tropical waters there are: --> *deep sea glass sponge*: very fragile, can break easily --> *red barrel sponge*: huge sponges that would get knocked down if they were in wave-intense environment - body shape correlates to pattern of water movements: intertidal sponges are flat to withstand wave forces

animals require some sort of *motion* to get food

- in some cases the animal moves *in* the environment, in other cases the animals *moves* the environment - *motion is relative*: either locomote to get food, move the environment, or "sit & wait" - *energy is expended* no matter what - ex: muscles bring in water & move plankton & bacteria over the feeding organs --> they move the environment

Exoskeleton has a significant impact on arthropod evolution

- in water = protection and attachment of muscles - physical stability from the exoskeleton *supports walking on dry land* - Chitinous nature adds *waterproofing* --> reduces evaporative water loss on land - predisposed aquatic arthropods to *invade the terrestrial environment*

monocots

- include *palms, grains* (grasses and cereals which have NO petals), *lilies, orchids* - *one* cotyledon - veins usually *parallel* - vascular bundles usually *complexly arranged* - *fibrous root system* - floral parts are in multiples of *3's*

Single cell Fungi (unicellular, aka yeast)

- include *zygomycota, ascomycota, and basidiomycota* - reproduce by asexual budding, fission, or sexually - there are unicellular members of all fungal groups - collectively called *yeasts* in higher fungi (the standard "yeast" Saccharomyces is an Ascomycete) - many fungi can alternate between unicellular and multicellular - have 2 different mating types: *alpha and a* which can persist as haploid individuals indefinitely --> yet haploid individuals will find counter mating type and fuse together to form a diploid when reproduction is necessary

paraphyletic group

- includes the common ancestry and some, but NOT all, of the ancestors descendants; includes all the ancestors of a group, but not all the branches.

CAN fold wings but under incomplete metamorphosis

- incomplete metamorphosis = w/ every larval stage they look more and more like an adult - *Orthoptera*: grasshoppers, crickets, roaches, walking sticks - *Isoptera*: termites - *Homoptera*: aphids - *Dermaptera*: earwigs

consequence of being small for a microbe

- increased efficiency of nutrient uptake and waste removal --> bc theres more plasma membrane per volume unit - higher proportion of cell is metabolically active - higher grow rates --> replication is easier when the cell is small - when you decrease cell size, you increase surface area --> microbes have LARGE surface area - going from 1 cell to multiple cells maintains the surface area to volume ratio, BUT reduces each cells interaction with its environment (as we become more and more multicellular; only one side of each cell in the multicellular block is exposed to the environment, this can be good and bad

diversity & ecology of sponges

- incredibly diverse in color & shape - *predominantly marine* --> except some freshwater (spongillidae) - found at *all latitudes* and in *all marine environments* from the deep sea to the intertidal zone - body shape tends to correlate to habitat

Fern life cycle

- independent sporophyte - still has *alternation of generations* - for ferns, a single gametophyte can produce BOTH eggs and sperm: *homosporous* - *bisexual fern gametophyte* -usually the maturation stages of the sperms and eggs from a single gametophyte is *asynchronous* so that the sperms from the same gametophyte don't fertilize the eggs from the same gametophyte --> bc this wouldn't lead to cross fertilization

5-kingdom system

- initially there was a 5-kindgom system: used to believe archaea and bacteria were just unicellular things and all prokarya were clumped into 1 group: monera

major trends in vertebrates

- invasion of sea, land, and air - aquatic and terrestrial forms: air-breathers, water-breathers, medium-specific locomotion - *eat large prey items due to evolution of jaw and teeth* - different reproductive strategies: evolution of internal fertilization, viviparous animals - evoked true *powered flight*

Neural Crest Cells

- key characteristic of vertebrates - the neural crest consists of bilateral band of cells that form the neural tube - neural crest cells migrate to distant sites in embryo - they then give rise to anatomical structure unique to vertebrates & become important parts of the vertebrate head --> cranium and part of jaw

Simple Fungi

- lack Dikaryotic stage - non-crown fungi - include: *chytridomycota, zygomycota, glomeromycota*

Chemical Origin Hypothesis (for origin of life on earth)

- life evolved sequentially bc of *ideal conditions for each step over deep time* - presents lots of obstacles but also lots of time to overcome those obstacles - life still may not be unique to earth

Did lignin prevent cellulose from decomposing in the Carboniferous period?

- lignin is NOT easily decomposed - spikes of coal may be because there was no microbes at the time that could break down the lignin to get to the cellulose, so its never decomposed & turned into coal - before the evolution of lignin, there were NO fungi that could break down lignin - the evolution of lignin led to the massive deposition of plant matter - the evolution of lignin-degrading fungi led to the end of coal deposition

Lignin (Derived Traits of Vascular Plants)

- lignin is a *phenolic polymer* - makes cell walls *hydrophobi*c so water doesn't stick to the xylem - lignin makes a matrix in which cellulose is encased - cellulose can be used for energy --> biofuel - *cellulose* is the most abundant organic polymer on earth - *lignin* is likely the second most abundant

Korarchaeota

- likely the most *basal lineage*: one that diverges earliest from a phylogenic tree and has the least # of branching points on it - 16S rRNA gene sequences - does NOT belong to the main archaea groups - analysis of the genome of one korarchaeote that was enriched from a mixed culture revealed a number of both Crenarchaeota- and Euryarchaeota-like features and support the hypothesis of a deep branching history

Metabolic Diversity

- living groups defined by their *use of different energy and matter (carbon) sources to live* - indicative of diversity level in prokarya relative to eukarya - multiple metabolic pathways per metabolism; each can vary - living groups also defined by their *tolerances to energy and matter*

Lycopodium Spores

- lycopodium spores are highly combustible - historically used in photography (flash powder) - currently used in pyrotechnic displays

Major Biogeochemical Agents

- macronutrients : *C,H,O,N,P,S*: carbon, hydrogen, oxygen, nitrogen, phosphate, sulfate --> these are found in every organism and can determine living vs non-living organisms based on the chemical differences in those entities - cells are non-equilibrium systems

Isopods (crustacean)

- many marine species - *most successful crustacean that invaded land* - sow bugs & pill bugs (rolly poley)

Alternation of Generations

- means there's distinct diploid stages (2n) and distinct haploid stages (n) - for humans, haploid stage = gametes/eggs + sperm which are unicellular - for plants, haploid cells can undergo mitosis, can become multicellular, and can be completely independent of diploid stages --> when 2 haploids merge they become a diploid, then diploid can undergo meiosis and become a haploid

aquatic microbes

- microbes began in the aquatic world --> there's the biggest diversity here - include... 1. bacteria 2. archaea 3. protists 4. fungi 5. viruses which are all considered microbes and can all be found in marine environments

microbes in terrestrial ecosystems

- microbes breakdown dead/decaying matter - they play a big role in plant life by providing nutrients in the form of endosymbiotic events

Heterospory (Shared Reproductive Traits of Seed Plants)

- microspore found in pollen & megaspore found in ovule - the microspore undergoes mitosis to make multicellular pollen & the male gametophyte

changes in archaea

- modern archaea are very different ancient archaea - characteristics from modern archaea (membrane characteristics) may have evolved later in order to adapt to extreme environments - its likely that early archaea did have a cell wall and was a size similar to bacteria

Multicellular fungi (filamentous)

- molds and mushrooms - *mycelium* (body): densest part of the non-fruiting body - *Hyphae* (tubular filaments): very hair-like extensions - *Rhiziods* (modified hyphae): interacts symbiotically w/ many plant roots - *Spores*: found w/in reproductive structure, usually at the base or underneath --> can have *sporangia* (producing spores) or *conidia* (naked spores)

Green Algae: Chlorophyta (plantae)

- molecular & morphological similarities to plants but very diverse -exhibit alternation of generation - single celled: *Chlorella*: can be duck weed, floats on surface of water and makes it green - colonial: *Volvox or Spirogyra* - multicellular: *Ulva or Limu*: sea lettuce

Exoskeleton is a barrier to growth

- molting, *ecdysis* - shedding of exoskeleton is under *hormonal* & *neuronal control*: in lobsters, the Y-organ produces ecdysteriod hormone that starts facilitating this process - old cuticle is partially digested by enzymes - exoskeleton is split by water, air, or elevated blood pressure --> body swells & eventually the pressure in the body just pops the shell open

Degree Heating Weeks

- monitors the likelihood of bleaching - calculates how much heat stress has accumulated in a region over the past 12 weeks (3 months) by adding up any temperature exceeding the bleaching threshold during that 12 weeks 1. measure the number of consecutive weeks coral spends at temperatures above summer maxima = reflects *cumulative* heat stress 2. calculated over 12 weeks with an index resulting as the indicator for bleaching likelihood - 4C weeks = significant bleaching likely - 8C weeks = widespread bleach & mortality

Pros of Diploidy

- more mutations per cell; if you're badly-adapted to your environment, *mutations are good* - *increased genetic diversity* - deleterious somatic mutations (ex: cancer) are *better masked in diploids* than haploids

Cons of Diploidy

- more mutations per cell; if you're well-adapted to your environment, *mutations are bad* - *beneficial mutations are likely to be lost by chance* - deleterious somatic mutations (ex: cancer) are 'purged' in haploids but *they 'linger' in diploids*

Mosses cooling down the atmosphere

- mosses can colonize & weather rocks which leads to *decline in CO2* in the atmosphere and a *cool down* of global temperature about 450 mya - the evolution of bryophytes is thought to have lead to greater Carbon sequestration: the idea of taking carbon from the atmosphere & turning it into material that is no longer available to the atmosphere pool - the atmospheric CO2 reacts with minerals & makes bicarbonate which flows away and settles in the ocean

Emiliania huxleyi

- most famous coccolithophore / haptophyta - widespread and *responsible for aquamarine superblooms globally*

Clade Errantia (Annelida)

- most marine - are *mobile* (swim, crawl) - display diverse feeding ecology --> *predators & grazers* - also have some tube dwellers/burrowing animals - have highly *developed cephalization* - have *well developed jaws & sensory systems* - *parapodia*: use for locomotion & moving through/around the burrow; are highly vascularized, have a good blood supply; they are respiratory organs & acts as gill to do gas exchange w/ the environment - *cirri*: long sensory organs that the predators can extend from their burrows to sense prey - ex: *Nereimyra Punctata*: lives in a burrow and feeds by poking its head out and grabbing prey

CAN fold wings and undergo COMPLETE metamorphosis

- most of the winged insects (85%) - *larval and adult forms differ significantly* - larvae: feed and grow - adults: reproduction & dispersal - *Coleoptera*: beetles - *Lepidoptera*: butterflies & moths - *Diptera*: flies - *Hymenoptera*: bees, wasps, ants

Lifestyle of a Flatworm

- move around *via cilia bands* on ventral surface - about 25,000 species - freshwater & marine - complex life styles - often *hermaphroditic* - free-living members are *carnivores* or *scavengers* on dead things - many are *parasitic* - some cause important human & veterinary diseases

Foraminifera (type of Rhizaria)

- multi-chambered cell made of *CaCO3* - can see clear compartmentalization of their cell - have amorphous bulbs, not very symmetical -distribution: thought to be mainly warm water forms, mostly oceanic

Chelicerates (Arthropods)

- named for feeding appendages *chelicerae*: used to stab & inject poison into their prey - *spiders, scorpions, mites, horseshoe crabs, and sea spiders* - distinct body regions: an *abdomen & a cephalothorax* - anterior where appendages are modified to form mouth parts = *the chelicerae*: clawed for grabbing and shredding food - rest of body has 4 pairs of walking legs - LACK mandibles near the mouth

Trypanosoma ssp (type of kinetoplastid/ excavata)

- named for presence of the *kinetoplast*: a DNA mass carried w/in a single *oversized mitochondrion* in each cells --> the ONLY excavata group w/ a clear/oversized mitochondria - causative agent for *African Sleeping Sickness*: symptoms include fatigue, fever, malaise, and eventually reversal of circadian rhythms - transmitted by tsetse fly and affects the central nervous system - have 2 flagella of the same size and length, one is FREE & the other is ATTACHED

Heartworm in dogs & cats (parasitic nematode)

- nematode that affects pets - *Dirofilaria immitis* - caused by mosquito bite which transfers larvae to host (dog) - after development, juvenile worms *migrate to the heart* - microfilaria are released into the bloodstream - final maturation occurs in pulmonary arteries, and the adult worms live in the right heart & pulmonary arteries for *up to 7 years*

Encephalartos Woodii (Wood's Cycads)

- nicknamed the "three bachelors" @ LotusLand bc there are *no more females in the world* - cycad = *dioecious* --> bc theres no females left in the world, there's no plants for the male cycads to reproduce

Alternation of Generations for bryophytes

- nonvascular land plants: *sporophyte embedded in the gametophyte* - sporophyte completely dependent on the gametophyte - gametophyte anchored into the land - spores become gametophytes

chromatophore

- octopus & squid have these specialized cells on the surface of their skin - are little bags of pigment that are controlled by the nervous system - when they become excited, the coloration on their skin will be much brighter - use this phenomena in mating and camouflage

Portugese man-of-war: Siphonophore (Hydrozoan under Phylum Cnidarian)

- often called "blue bottle" in australia bc they float on surface of water - an effective predator in costal & open oceans - have awful stings

*Welsitschia mirabilis species* of Phylum Gnetophyta

- once 1 species in the world - can live for thousands of years -- one of the longest living plants on this planet - *has the largest leaves in the world* --> made up of *2* gigantic leaves - *dioecious* - pollen drops attract pollen & bring them inside to the egg

Squid

- one of the LARGEST fisheries in California - jet propulsion locomotion - *vulnerable to predation* due to loss of shell - use *photophores* (bioluminescence) & *chromatophores* to try and hide against substrates to avoid being predated on - have *squid mating orgies* where the odor in egg mops stimulates other squids to start spawning & males pass sperm to females - reproduction is a *terminal event* for this species: they die after they mate - vampire squid: only member of the order 'vampyromorphida' - architeuthis dux: giant squid

Sulfolobus solfataricus

- one of the best characterized members of the *crenarchaetoa* - grows flagella as a stress response - originally isolated from sulfuric springs in Italy - grows at high temp and acidic pH (at 80C and pH= 2-4) - round but can be irregular - unlike the vast majority of cultured thermophiles, *Sulfolobus grows aerobically and chemoorganotrophically* (easier to culture in a lab) - model organism for the study of hyperthermophiles and a large group of diverse viruses that replicate within them - one of the least extreme extremophyls

Growth w/ dichotomous branching (Derived Traits of Vascular Plants)

- one of the first innovations in vascular plants was *dichotomous branching* - a single sporophyte could have multiple sporangia due to dichotomous branch - was *a way for a single plant to reproduce more!* - still have primitive Rhizoids

Aglaophyton major

- one the first vascular plants - an extinct link between byrophytes & tracheophytes - they already had *stomata* in fossils of Aglaophyton major, an ancient vascular plant

oyster reef

- oyster reef *reduces wave action* and *filters* & cleans up the water - this leads to improved water quality which causes enhanced growth of seagrass bed because more light is able to penetrate through the water

Hirudinea (leeches)

- part of clade sedentaria - mostly freshwater (or terrestrial) - *predators* - some *parasitic forms* that feed on the blood of the host - defining characteristic = * a posterior sucker*: structure used to attach to host to get blood - *Ectoparasitic*: on outside of the body, most commonly on the blood of vertebrates - 25% nonparasitic - can be used for medicine: leeches slash the skin & create an incision on the host & then secrete an anticoagulant compound called *Hirudin* which keeps the wound open... the leech then sits and feeds on the blood as it flows from the wound they created; used to extract blood from a hematoma - the DNA of the blood found inside leeches can give indication of the biodiversity in that area: used as conservation tech

Earthworms

- part of clade sedentaria - primarily freshwater or terrestrial - eat their way through soil & *improve soil quality* - Not a lot of body plan diversity - complex organ systems - highly segmented worms - as they eat, they grind up soil and dead matter & release *worm castings* (worm poop) that improves soil nutrient quality & aerates the soil --> recycling of essential nutrients - move air and water deeper into the ground

brown algae

- part of the SAR group - photosynthesizes but *is NOT a plant*

Peat moss (Bryophyta)

- peat moss refers to mosses in the genus Sphagnum - there are ~200 species of peat moss - the gametophyte is *green & photosynthetic* - peat moss is used to supplement soil bc its really good at retaining moisture - Sphagnum moss used as wound dressing during WWI bc they *absorb 20x more water* than cotton wools --> they absorbed blood & had secondary compounds/chemicals inside the leaves that served as an antibiotic - peat moss grows very densely & creates *anaerobic soils*, in which the lack of oxygen *promotes the preservation of organic tissues* bc there's no bacteria to break down dead matter (human mummies!) - layers and layers of peat moss build up over centuries; *this peat moss is very rich in nutrients & can hold water easily*, so its harvested and sold as a soil amendment of gardeners and farmers

Bacteria cell membrane

- phospholipid bilayer - glycerol heads + *fatty acid tails* - ester linkage - D-glycerol - humans phospholipid bilayer looks more similar to bacteria.. this is because archaea probably started out with similar bilayer to bacteria and then modern day archaea evolved to use isoprene instead of fatty acids

Archaea cell membrane

- phospholipid bilayer (NO fatty acids) - some have monolayer vs bilayer - glycerol head + *isoprene tails* - ether linkage - L- glycerol

Opisthokonts

- pole flagellum --> short and rigid - includes: single-celled protist, fungi, animals

Air-Borne Pollen (Shared Reproductive Traits of Seed Plants)

- pollen are air-dispersed, hearty with *sporopollenin* covering it to keep from desiccating (also found in moss spores)

Chemical Evolution, Stage 3: polymers enclosed w/in membrane

- problem: How did early complex molecules and polymers get from independent to collected and encapsulated. How did the first reactive units evolve? - solution: *Coacervates*: aggregates of abiotically produces organic molecules that can have metabolism - coacervates CANT reproduce but have internal chemistry different from surrounding environment - are 'probiants': nearly living, but not necessarily living - *1920's Oparin demonstrated that mixing protein and polysaccharides led to formation of coacervates*: proteins and polysaccharides have diff polarities --> leads to coacervates

Chemical Evolution, Stage 1: Nucleotides and AA before cells

- problem: how ddi the 1st complex organic molecules form on earth? - solution: *reductive atmosphere* (one that is non-oxidative/ oxygen is removed from the atmosphere) or hydrothermal characteristics lead to formation of organic monomers - option 1: *Oparin & Haldane's Reducing Atmosphere Hypothesis* - option 2: *Hydrothermal Vent Hypothesis*

Chemical Evolution, Stage 2: Polymerization of macromolecules

- problem: how did macromolecules form from monomers w/o the aid of enzymes? - solution 1: *anhydrous surfaces* (surfaces that want water that's been released; polymerizes molecule to get that water) reduce energy of polymerization making polymerization more feasible - clays, pyrite, and basaltic glass = anhydrous surfaces - solution 2: *high concentrations* (and *heat*) and *reactive metals* (and *heat*) made the process more favorable - concentration of monomers at edges of hot pools --> polymerization - metal (nickel and iron) --> polymerization of amino acids w/o oxygen

Chemical Evolution, Stage 4: Evolution of cellular properties

- problem: living cells need to be able to replicate4 and store information, coacervates do NOT have the ability to do this - problem: how do you get from non-living chemical blob like a coacervate to a living cell? - DNA cannot self replicate (w/o enzymes) - DNA is not enzymatically active alone (has to be converted into RNA and then proteins) - proteins cannot store information - solution: *catalytic RNA*: RNA that's capable of catalyzing a rxn when it folds - RNA folding --> H bonds stabilize in 3D form - RNA may have mutated and specialized into DNA, and then we developed our full scheme of protein production - RNA: acted as both information carrier and catalyst - Ribozymes - Thomas Cech (1980)

primary endosymbiosis

- process but which a cell engulfs another cell (bacteria) & that bacteria becomes an organelle - single celled red & green alga are thought to be the product of primary endosymbiosis of a cyanobacteria

calcification: an important physiological process of mollusks

- production of "hard parts"/calcium carbonate - biogenic calcification: the formation of calcium carbonate by living organisms - this process can be disrupted by ocean acidification

microbes

- prokarya and eukarya - single cell or cell cluster - stand alone organisms (expect for some, for 1 life cycle stage of their life they rely on another individual as seen with parasitism and viruses) - capable of living independent of tissue - microbes do things such as: growth, energy generation, & reproduction

Plasmodium (example of Apicomplexans)

- protist that causes malaria - lives w.in mosquito as its primary host - mosquito: fertilization and formation of diploid zygote - human: haploid sporozoites form haploid gametes which are released & affect RBCs --> w/in RBCs they make gametocytes which are then cycled back through and picked up by more mosquitos and transmitted

Plasmodial Slime Molds

- pseudopodal extension of cytoplasm - *heterotrophic* --> phagocytosis - multinucleated super cell --> enclosed in a single membrane w/o walls - large masses are NOT aggregations of individual amoeboids, but rather replication of one diploid amoeboid that has no longer separated its cells - plasmodia DONT aggregate, but *multiply* --> what looks like aggregation is really just mitosis post karyogamy

sexual reproduction

- recombination that initiated meiosis or mitosis and production of one individual into two - recombination AND reproduction must be paired

phototrophs absorb light using pigments

- red & purple wavelengths do NOT reach the very deep parts of the ocean - only blue/green light reach the far bottom - Chl a & Chl b = the main pigments that green plants have - 500-600nm wavelength is the green area, however Chl a & Chl b DONT absorb in this spectrum, causing it to appear green to us and it reflects green light

why is red algae red?

- red algae is at the bottom of the ocean where red light does not penetrate causing it to look red bc it's absorbing all of the blue/green light --> it reflects red light - has a lot of *phycoerythrin* pigment and NOT a lot of Chl a or Chl b - if it had a lot of Chl a or Chl b it would reflect off all the light it has access to at the deep depths

Rhizarians (SA*R* group)

- rhizarians are typically *amoebas*: protists that move and feed by means of pseudopodia - *very different* from the other 2 groups in the SAR - grouped w/ the rest bc DNA similarities imply that they share a common ancestor and are more closely related than other protists - primarily marine, some freshwater - have many photosynthetic endosymbionts, but most are heterotrophic - *sarcodines*: pseudopodia or protoplasmic flow (threadlike)

how did flight evolve?

- scales modified to feathers - fantastic example of *convergent evolution*: bats, birds, dinosaurs all fly --> excellent examples of transitional forms in the fossil record - it's the flight stroke that matters - *ground up hypothesis*: ancestor of flying birds was on the ground and came from the ground up into tress and eventually picked up flying/gliding in that way - *trees down hypothesis*: went from trees down to try and escape predators or maybe for food - feathers are insulation? - why flight?: to escape predators, catch new prey, free hind legs as weapons, & for dispersal - *Pterosaurs*: first vertebrates to evolve flight

feeding in sea stars

- sea stars wrap themselves around a prey item & use the tube feet to pry the shells apart - then evert their stomach and put it inside the prey item & secrete digestive enzymes and digest the tissues inside the shell - then digested material is resorbed by the stomach into the body - here the tube feet become an active part of the searching predator and also are helping pry apart the shells

Alternation of Generations for Angiosperm & Gymnosperm

- seed plants: gametophyte is embedded in sporophyte; the gametophyte is the "parasitic" - reduced gametophyte dependent on sporophyte - sporophyte anchored in the ground - *gametophyte completely embedded in the sporophyte*

general molluscan body plan

- shell (can be reduced in some animals like octopus) - greatly reduced coelom (body cavity) - complete digestive system - open circulatory system: supports a more athletic lifestyle, able to take in more food & get more energy and support locomotion (except in cephalopods which have a closed system)

wingless insects

- silverfish & springtails - *simple development*: juveniles look like adults once hatched from egg

land plants (embryophytes) are descended from green algae

- similar to land plants, green algae have *sporopollenin* in the cell walls of their haploid propagules (spores) --> this is very resistant and doesn't readily degrade + protects against desiccation (chlorophytes & red algae DONT have sporopollenin) - both land plants & green algae also can *reproduce by spores*

Unikont Choanoflagellida

- single-celled protist - closest relative to animals - *colonial* - similar to sponges - individual choanoflagellates form colonies that are attached to a single stalk

Ceanorhabditis (example of a nematode)

- small free-living round worm - adopted as a model study system: developmental biology, cell biology, neurobiology - genome sequences (2002) - *1st complete, sequenced genome of a multicellular eukaryote*

Junipers & Yews

- some Conifers, such as Junipers & Yews, produce fleshy, simplified female "cones" that contain only one ovule, but these ARE NOT fruits

Ofu, American Samoa

- some coral in American Samoa have plasticity --> are a little tougher - may be locally adapted - "our results show both short-term acclamatory & longer-term adaptive acquisition of climate resistance" - shows that *plasticity exists* in coral

Multicellularity as a strategy for plants?

- some individuals in the plants groups are: unicellular, multicellular, or opportunistically multicellular - closely related, but very different stages --> strategy dictated by environmental stability , such as resource of food - similar to the unikonta group --> members in this group also show these 3 phenotypes

Apicomplexans (Plasmodium)

- some protists have developed complex reproductive life cycles that use 2 hosts to complete life cycle = *Apicomplexans* - these are the *protist that causes malaria*: has to exist inside RBC to carry out life cycle - mosquito: fertilization and formation of diploid zygote - human: haploid sporozoites form haploid gametes

feeding in sponges

- sponges feed by the collar cells waving their flagellum in the center which creates an inward-motion current - *choanocytes/collar cells*: form inner layer of cells in sponges; are feeding cells that, as they wave in the center of the sponge collect food up through the collar and into the choanocyte body itself; the central feeding cell in a sponge - *amoebocyte*: partner cell that takes nutrition from the choanocyte & moves up and down the cell to deliver food

chemical evolution (for origin of life on earth): origin of life can be viewed as 4 overlapping stages

- stage 1: *nucleotides and amino acids before cells*: bc cells are made up of these building block - stage 2: *nucleotides and amino acids polymerize* not DNA, RNA, and Proteins - stage 3: *polymers enclosed in membranes* - stage 4: *evolution of cellular properties*: like metabolism, stimulus response, adaptation, and evolution

gram stain

- stain absorbs into peptidoglycan walls of bacterial cells - archaea capable of gram staining positive or negative

Stamen

- stamen is the *microsporophyll* bc it is a "modified leaf" that bear microsporangia that makes pollen grains

stamen's evolution

- stamens also evolved from sporophylls - microsporophylls is thought to have evolved to push the sporangia to the outside, rather than protecting it in the inside - stamen evolved to become an *anther*: just the exposed sporangia & a *filament*: elevates the Anther from the base of the flower

theory of endosymbiosis: primary and secondary endosymbiosis

- start w/ *LUCA*: universal ancestor (prokaryotic) - differentiates into bacteria and archaea (specifically crenarchaetoa) - crenarchaetoa increases in cell size -then goes through endosymbiosis & engulfs bacteria: *acquisition of proteobacteria* --> acquires primitive mitochondria - from here it either engulfs a cyanobacteria: *acquisition of cyanobacteria* and becomes algae/plants - or goes on to become a protozoa/animal

cnidocytes

- stinging cells on *cnidarians* - cells are at the END of tentacles - eject a *nematocyst* - literally "thread bags" - can inject toxin into prey

Cotyledons

- the *first* photosynthetic baby-leaves that is part of the embryo inside a seed - *monocots* = has 1 cotyledon; a *monophyletic group* - *dicots* = have 2 cotyledons; a *paraphyletic group*

Scyphozoans (Cnidarians)

- the *jellyfish* or G: "cup animals" - THICK & LARGE mesoglea - large, effective swimmers - ALL marine: found in all oceans

can plants can smell?

- the *parasitic Dodder* can smell and sniff out other plants/victims

Phylum Porifera (sponges)

- the basal group of organisms in the animal lineage - Porifera = "pore bearer": the body has many holes/pores in it - 5,500 described species - *lack tissues*: body is comprised several cell types - have *spicules*: a network of skeletal fibers that provide rigidity to the cell wall of the sponge - sponge body has *2 layers of cell* separated by a gelatinous layer called *mesohyl* - reproduce w/ eggs & sperms & are *hermaphroditic*: start off as 1 sex and switch to the other sex later - *osculum*: main opening at the top of sponge where water moves out of - *spongocoel*: hollow center of sponge 3 TYPES: 1. *desmosponges* 2. *glass sponges* 3. *calcareous sponges*

Quantum solar cells could explain why plants are green

- the big problem in solar power & photosynthesizing plants is that sunlight is NOT constant bc of seasonal changes and clouds - the amount of sunlight that reaches panels (leaves) is constantly shifting - *green light is very noisy* (fluctuates and is unreliable) and is harder to create a steady flow of energy - unregulated power fluctuations lead to inefficient energy storage and fatal oxidative damage in photosynthesis - *suppression of fluctuations (not absorbing green light) acts as a regulation mechanism* that enables the efficient conversion of varying incident solar power into a steady output for absorption over a broad range of solar spectrum

Multicellular dependent embryo (derived traits of embryophytes)

- the embryo (zygote) is retained in the mother (gametophyte) - "im growing inside my haploid mom!" - embryophyte

the human body is a microbial system

- the human microbial system is 50% non-human by cell count, examples of microbial cells in: skin barrier defense & alimentary normal flora - these microbes: help to digest food, help to fight pathogens, and help to provide vitamins

Why are most land plants green?

- the maximum intensity of solar energy occurs at about 555nm, a point where most of the light that comes to the surface of our planet is mostly green - however, plants are doing everything they can to reflect the green light instead of use it for energy - *plants reflect green light and absorb red and blue lights* 1. green light was not always the most abundant wavelength reaching earth 2. chlorophyll a and b evolved first by chance in cyanobacteria & therefore became the most common chlorophyll pigments 3. *green light is the most variable thought the day, so plants dont use it* 4. chlorophyll a and b are cheaper to make than other pigments

animals first common ancestor

- the metazoan lineage is *monophyletic* - the ancestor of the animal lineage is probably a *colonial protist*, specifically a *choanoflagellida* which are colonial & thought to be related to sponges

Biostratigraphy

- the order in which we find things in the substrate - things on the lower level = older - things on higher levels = younger - can determine relative ages based on this ordering - *fossils* all in the same state indicates they all lived at the same time *stratigraphic relationship* -can determine *relative* ages of fossils - similar types of fossils found w/in *strata* (layer) in widely separated parts of the earth tells us about dispersal of different types of organisms - major changes in fossil types in the rick strata used to define time periods

the proton gradient across bacterial membranes

- the outer and inner membranes of these bacteria function similar to the inner and outer membranes in mitochondria - they form proton gradients, and these gradients drive many functions - *creation of the H+ gradient is what drives the rotations of the flagellum motor*

Resistant Seeds (Shared Reproductive Traits of Seed Plants)

- the seed is protected by its *diploid sporophyte-derived seed coat* - also contains some fat & carbon-derived food reserve for the growing embryo

Independent sporophyte stage (Derived Traits of Vascular Plants)

- the sporophyte can be independent of the gametophyte - sporophytes *have rhizoids* or *true roots* - the whole sporophyte structure that is above ground is diploid & has primitive roots/Rhizoids allowing it to be able to get nutrients and water from the soil w/o relying on the gametophyte

metabolic gradients

- there are 3 main types of phosphorylation processes in living things: (1) *substrate-level phosphorylation*/ fermentation (2) *Oxidative phosphorylation* (3) *photophosphorylation* - these processes all rely on thermodynamically favorable reactions ... either .. --> (1) phosphorylation coupled w/ large molecule catabolism: build aTP at same time we break something down --> or (2) formation of a gradient and ATP synthesis from the proton motive force associated with that movement

Crown-of-thorn seastars (CoTS)

- these animals eat all the tissue in the polyps of the coral they are over - they can kill a lot of coral through their feeding activity - outbreaks hurt coral reefs -extremely fecund mass spawners --> have population explosions - *climate change & global warming promote CoTS outbreaks* bc larvae are able to survive hot temperature more than some other species can

Animal Characteristics that distinguish them from other organisms

- they are *multicellular* organisms -- but incredibly diverse - they have a *heterotrophic metabolism* - animals MUST consume *organic compounds* bc they lack the ability to make them from inorganic molecules - they *digest internally* somehow (this is also highly variable in the animal kingdom)

Tracheal System

- tracheal system = unique respiratory gas exchange system in insects by which the animal can do gas exchange & control how much water it loses - internal system - *helps conserve water during respiration* - system of highly branches air-filled tubes called *tracheae* - branch throughout the insects body to reduce diffusion distance - a major adaption to life on land - *spiracles*: opening on the exterior surface of the animal for gas exchange

Phloem (vascular tissues)

- transport products of photosynthesis --> *mainly sucrose/sugar* - sieve cells, sieve tubes

Batrachochytrium dendrobatidis (BD)

- type of Chytrid Fungi - global amphibian decline due to this Chytrid group - Chytrid zoospores attached to frog skin and cause infection and destruction of tissue (like cancer) - chytrid-associated decline of frogs in central america - chytrid-associated decline of Rana muscosa in the Sierra Nevada

Methanosarcina barkeri

- type of euryachaeota - methane-producing extremophile - round *cocci*, can be irregular - found in fresh water environments (will be found at bottom of water here where theres less oxygen), high salt environments, and the rumen of cows (*anaerobic environments) - forms aggregate clusters - may use methane production for movement (excretion of gas --> big fart --> moves them)

Methanococcus jannaschii

- type of euryachaeota - methanogenic thermophile - *coccus* with multiple flagella (*lophotrichous*: hella flagella in a bunch) - found in *hydrothermal vents* - obligate methanogen: must produce methane to go through metabolic function - first archaea to be sequenced and focal archaea in determining similarities to eukarya

haloquadratum walsbyi

- type of euryachaeota - phototrophic halophilic (photosynthesizing & salt loving) - square, thin green cells, giagantic - found in salt lake and brackish waters - forms sheet aggregates - float to surface using gas bubbles in vacuoles --> float like mat on top of water

Euglenozoa (type of excavata)

- typically *green* - *rod structures* in flagella --> 2 subgroups w/ different versions, spiral or crystalline structure, of this rod - heterotrophic, phototrophic, mixotrophic, and parasitic species

Phylum Annedlida

- under Lophotrochozoa family - *segmented worms* - used to be broken into 4 classes: polychaete worms, leeches, Archiannelida (simple marine worms), and oligochaetes (earthworms) - in 2011 new molecular data re-organized the phylum into 2 clades: --> *Sedentaria*: sedentary --> *Errantia*: mobile - most investigated annelids belonging to Errant or Sedentary bear an identical order of protein-coding and ribosomal RNA genes

Cnidarians & Nerves

- unlike sponges, cnidarians *have nerves & muscles* - *First* animals (Eumetazoa) to have a nervous system - NOT a true "nervous system": rather, a mesh of overlapping, decentralized nerves in a network: *nerve nets* - can detect touch & respond to it

Carl Woese

- used *autoradiograph* of rRNA gene sequence - used 2 dimensions (right to left & up and down) to get double separation and see the difference in nucleotides - *saw that archaea and eukaryote close related & bacteria was far related to the 2* - did molecular biology using gene sequences to reconstruct the tree of life

Dr. Craig Venter

- used a *random shotgun sequencing approach*: made lots of copies of 1 genome and then uses endonuclease to randomly cut up fragments of DNA and then run them through a computer to match up the pieces - most famous for the Human Genome Project - was able to sequence 500 microbial genomes - Sargasso Sea metagenome - Global Ocean survey

1st evidence of vascular plants

- vascular plants began to flourish during the Devonian Period (~400 mya) -by the Carboniferous Period (~360 mya), vascular plants dominated the landscape: mild warm climate w/ many swampy lowlands w/ woody, tree-like lycopods, horsetails, and ferns

Alternation of Generations for Monilophytes & Lycophytes

- vascular seedless plants: young sporophyte starts off embedded in gametophyte, but *becomes independent* - large sporophyte & small, independent gametophyte (ex: fern) - both sporophytes & gametophytes can be independent - larger sporophyte and a more reduced, underground gametophyte

can plants feel & move?

- venus fly trap: when trigger hairs are touched, the plant closes - in reality, all plants do respond to touch & can all move, they just do so SLOWLY & during a LONGER period so we humans don't recognize them as feeling or moving

Cuticles (derived traits of embryophytes)

- waxy polymer on the outside of cell walls that keeps cells from drying out - repels water

Absolute Dating using radioactive decay

- when an organism is alive it is transpiring and should have the same ratios of certain elements in it that the environment does --> when it dies, decay takes place bc its not replacing the molecules by respiration - radioactive isotopes decay over regular equal periods of time - if you know how much isotope existed at the beginning and you know how much remains, you can calculate the age of the sample - use isotope w/ half-life similar to what your measuring

coral bleaching

- when coral is healthy, coral & algae dependent on each other to survive - when coral becomes stressed, the algae leaves the coral, causing the coral to lose its pigmentations and appear bleaches & vulnerable - is due to *stress at high temperatures* - thermal stress and/or pollution can cause the loss of *symbiotic zooxanthellae* and/or a reduction in photosynthetic pigment in zooxanthellae residing within coral - the death of coral shifts the community from a coral-dominated ecosystem to one that's dominated by algae --> shifts the type of biodiversity found there

hunger signals of cellular slime molds

- when food becomes scarce, amoeboid forms and begins to release chemical signals - *Cyclic AMP* attracts other amoeboid cells to follow trail and aggregate - they share food and form a fruiting body - in an aggregate, *only the top individuals get to reproduce*

Double Fertilization

- within the pollen grain or in the pollen tube: the *generative cell* divides by mitosis to produce 2 sperm - pollen tube enters the micropyle and delivers sperm - *2* polar nuclei are ready to unite with *1* sperm = *triploid cell* - *1* egg cell is ready to unite with *1* sperm = *zygote* - after these sperm unite with these cells,,, - triploid cell --> mitosis --> triploid tissue = *endosperm* - *diploid zygote* --> mitosis & differentiation --> embryo embedded w/in endosperm

can plants hear?

- yes, they can detect vibrations/sounds of water - put seeds into a PVC pipe that's split down the middle for the roots & wait for the roots to grow into one of the 2 compartments - then put sound/wires around 1 of the compartments and see which way the roots grow - sound = presence of 100ml of water, live sound of water running through clear PVC flexible tubing, recorded sound of water, white noise, or 0Hz sound file - found that when 1 side of the root had real water & the other side didn't, most of the roots grew towards the side that had real water - concluded that plants can detect water from just the sound & are likely detecting the vibrations of water coming through the soil

Diatomaceous earth

- you can purchase diatomaceous earth to *get rid of fleas* in your carpet/house - small silica shells scrape and puncture flea exoskeleton and draw out oils, causing fleas to desiccate - tiny shells are too small to hurt humans or pets - diatomaceous earth is also used to filter pools

root knot nematode

-*parasitic nematode* - nematodes in the soil infest the roots of some trees/shrubs - causes dysfunction of the roots & cause them to form *gauls* where the nematode lives inside - nematode steal nutrients & energy from the infested plant & reduces the health of that plant

crenarchaetoa

-also known as *crenarchaea* or *eocytes* - separated from the other archaea based on: rRNA sequences, most lack histones, stain Gram negative, morphologically diverse, rod cocci filamentous and oddly shaped cells - some sulfur-dependent extremophiles -environmental rRNA indicates these organisms may be the most abundant archaea in the marine environment - the parent cell of the eukaryotic groups - likely that eukaryote arose from an archaea cell that was w/in this group - have reverse-gyrase enzyme that prevents their DNA from denaturing at really high temps - "until recently all cultured Crenarchaea had been thermophilic or hyperthermophilic organisms, some of which have the ability to grow at up to 113 degrees celsius"

chlamydomonas reinhardtii (green algae)

-an example of a green algae thats NOT solitary - have 2 flagella that allow is mobility in aquatic environments - single-celled; contains Chl a & b - most of the life stage of chlamydomonas reinhardtii is haploid (n) = has a *haplontic life cycle* NOT alternation of generations - diploid stage is very short-lived bc it immediately undergoes meiosis to *produce 4 single haploid cells* - diploid stage is NOT independent NOT significant

Aristotle's Lantern

-specialized mouth part of Echinoidea - on the underside of their body - specialized feeding structure around the esophagus - composed of hard parts (ossicles) and muscle - used to scrape and capture prey

5 living Clade of Echinoderms

1. *Ophiroidea*: brittle stars 2. *Echinoidea*: sea urchins 3. *Holothuroidea*: sea cucumbers 4. *Asteroidea*: sea stars 5. *Crinoidea*

3 cell types in sponges

1. *choanocyte*: feeding, creates current 2. *ameobocyte*: feeding, contains enzymes for breaking down nurtients 3. *porocyte*: lines pores

the 3 different theories on where water came from?

1. *degassing & condensation* 2. comment hypothesis: comet impact --> bring ice to earth 3. asteroid hypothesis: asteroid impact --> water inside asteroid brought to earth the ratio of heavy to normal water provides clues as to how water came to earth

formation of earth in geological time

1. *earth was formed 4.5 bya*: earth forms by collisions that cause cold rock to melt together and form semi-solid magma 2. *oceans created 4.2 bya*: were very hot at about 70-100 degrees celsius 3. *oldest rock was formed 3.8-4 bya*: occurs AFTER ocean formation; microfossils might've started to form around this time --> life might've been already starting to form at the time when rock wasn't even officially rock yet 4. microfossils formed 3.5-3.8 bya*

Nutritional requirements for anabolism

1. *energy source*: chemicals (chemotroph) or light (phototroph) 2. *carbon source*: CO2 or Organic C

Endosymbiotic Theory

1. *engulfing of prokaryote by another*: our 1st ancestral eukaryotic cell (prob an archaea) engulfs a smaller bacterial cell which then proliferates 2. PROLIFERATION: bacterial cell lives symbiotically inside archaeal cell 3. *assimilation as mitochondrion*: larger cell gets all the regulatory material from the bacterial cell & makes it officially into a mitochondrion 4. further PROLIFERATION: of cell w/ mitochondria in it 5. *secondary engulfing of photosynthetic prokaryote*: prob cyanobacteria 6. PROLIFERATION: of many cells, hella probably died off and only one/a few survive and evolve 7. *Assimilation as chloroplast* 8. *3rd and 4th engulfing events*

2 interactive processes that result in changes in living organisms

1. *genetic exchange* affects their characteristics (engulfing & injection each other w/ diff genetic elements) + allows them to survive in a given environment 2. *environmental change*: influences type of organisms that have existed during different periods

4 main differences between archaea, bacteria, and eukarya

1. *glycerol chirality* 2. *ether phospholipid linkages* 3. *isopropanol phospholipids* 4. *the isoprenoid chains can be linked together*

non-vascular plants have these in common:

1. *haploid stage is dominant*: although non-vascular seedless plants have *alternation of generation*, the gametophyte stage is considered 'dominant' 2.*still require water for sperm motility*: sperms have flagella & need water to travel to archegonia 3. *small because there is NO vascular tissues, NO true roots, only rhizoids*: don't grow more than a couple inches from the ground bc they don't have the power or the structure to transport water all the way from the ground to the top --> *rhizoids*: anchor gametophyte to the ground and are HAPLOID 4. *the sporangium is elevated* .. and they also *don't have vascular tissues or seeds*

3 parasitic nematodes in animals

1. *human hookworm* 2. *heartworm in dogs* 3. *trichinosis, a human disease*

2 distinct groups of Chelicerates

1. *marine chelicerates*: very early group, not very many of them; *sea spikes & horseshoe crabs* 2. *Arachnids*: spiders

2 major clades of Cnidarians

1. *medusozoans*: have dominant medusa body plan (ex: jellies & sea wasp) 2. *anthozoans*: have dominant polyp body plant (ex: sea anemones & star corals)

Traits that set microorganisms apart from non-living chemical systems

1. *metabolism*: uptake of chemicals from their environment, their transformation w/in the cell, and elimination of wastes into the environment; the cell is thus an open system 2. *reproduction (growth)*: chemicals from the environment are turned into new cells under the direction of preexisting cells (can be multicellular tissue growth, or unicellular replication of a cell) 3. *differentiation*: formation of a new cell structure such as a spore usually as part of a cellular life cycle (multicellular: tissue differentiation; unicellular: organization w/in the cell) 4. *communication*: cells communicate/interact primarily by means of chemicals that are released or taken up --> cells aware of their external env 5. *movement*: living organisms are often capable of self-propulsion --> planktonic or directional 6. *evolution*: distinctive traits of living organisms; cells evolve to display new biological properties

Key characteristics of chordates

1. *notochord*: cartilaginous rod that runs underneath & support the nerve cord 2. *a dorsal hollow nerve cord*: lies dorsally to the notochord and connects the brain to lateral tissues --> instrumental in moving the body 2. *pharyngeal slits*: allow water to enter mouth and pass out of body (either in embryo or adult form) - *post-anal tail*

Shared Reproductive Traits of Seed Plants

1. *reduced gametophyte* 2. *heterospory* (male and female gametophytes) (an exception seen in some lycophytes) 3. *air-borne pollen* (male gametophyte) 4. *resistant seeds* (female gametophyte encasing the new sporophyte) (traits NOT shared among the seedless/vascular plants) - Gametophytes are *dependent on the sporophyte* - Gametophytes are *microscopic*: in the egg stage, the gametophyte is inside the sporophyte still, or existing very shortly as pollen grains

Hyphae

1. *septate*: incomplete cross walls 2. *coenocytic*: no septa --> multinucleated w/ no separations of cells --> just 1 large cell 3. *haustoria*: aseptate; push into cells

3 mechanisms for prokaryotic genetic recombination

1. *transformation*: when a bacterial cell engulfs a plasmid. this plasmid may or may not be incorporated into the genome 2. *transduction*: when a virus (phage) injects its DNA/RNA into a bacterium. This is often incorporated bc its part of the adaptive element of the virus 3. *conjugation*: "bacterial sex" but NOT sexual reproduction. When a donor bacterium injects its DNA into a recipient bacterium using a sex pilus ^^^ all are forms of *Lateral Gene DNA Transfer*: the gene of one species is incorporated into another

4 Classes of Flatworms (Phylum Platyhelminthes)

1. Turbellaria 2. *Trematoda* (parasitic) 3. *Monogenea* (parasitic) 4. *Cestoda* (parasitic)

Choanocyte: the key feeding

1. creates the inner-lining of the sponge (*structural*) 2. the flagella beating creates the current that facilitates moving the food (*creates current*) 3. the collar takes the food & moves it to be phagocytized inside the cell body & transferred to the amoebocyte (*does the feeding*)

why do we care about animal biodiversity?

1. diverse ecosystems are *healthier* 2. diverse ecosystems *recover from disturbance faster* 3. healthy ecosystems *provide us w/ resources, possibly even our own health*

development of a female gametophyte (embryo sac)

1. each ovule contains 1 diploid megasporocyte 2. the megasporocyte makes 4 megaspores but only 1 survives 3. the surviving megaspore undergoes 3 round of nuclear mitotic events (makes 8 nuclei) 4. 3 of the nuclei at each pole undergo *cellularization:* the formation of cell membranes around the nuclei 5. 7 cells, 8 nuclei; sometimes polar nuclei fuse to make a diploid 6. in some mature embryos, the antipodal cells degenerate before fertilization

Ecology of Fungi

1. found in lakes and ocean at a limited level 2. found in streams -- more important - decay of leaf litter more surfaces 3. Terrestrial: primer remineralizer: filamentous growth, spread through soil, translate resources - *all are heterotrophs* even though some are pigmented they do not photosynthesize - fungi are *saprobes*: very important role in decay - contain *chitin in cell walls*: makes cell walls more biochemically similar to the exoskeletons of some arthropods (insects)

Resulting biogeochemical responses from oxygenic photosynthesis

1. global O2 concentrations rise 2. O2 attacks bonds of organic matter 3. organisms developed antioxidant mechanisms - production of ozone shield: UV interacts with O2 to form O3

Alternation of Generations life cycle (ex: moss)

1. haploid spore (n) are dispered from the peristome 2. spores undergo mitosis and develop into a male or female gametophyte (n) anchored by a Rhizoid 3. inside the gametophytes, either an Antheridia or Archegonia makes the sperm or the egg respectively 4. the water is needed to transport the sperm from the Antheridia to the Archegonia & into the egg for fertilization (2n) 5. within the archegonium, a haploid structure, a diploid zygote is made (2n) which goes through mitosis to become an embryo (2n) 6. the embryo then becomes a young sporophyte (2n) which will mature and become multicellular capsule (2n) that sits onto of haploid gametophyte structure

Complex life cycle of a trematoda

1. in water and find host in a snail as its *1st intermediate host* 2. larvae undergo asexual reproduction in the freshwater snail 3. get into humans (*definitive host*) that go into water 5. adults undergo sexual reproduction in host/human

development of a male gametophyte within a pollen grain (angiosperm)

1. one anther may contain 100s or 1000s of diploid microsporocytes 2.diploid *microsporocytes* undergo meiosis to make *microspores*. Two rounds of meiosis results in 4 microspores 3. each of the 4 microspores undergo mitosis to become *multicellular gametophytes* 4. Angiosperm pollen grains will contain 2 sperms

How to be a good parasite:

1. reproduce within the host 2. get fertilized eggs or embryos *out of the host* 3. contact & recognize a new, correct host 4. get entrance into the host 5. *locate the appropriate environment* w/in the host 6. hold on to the host (maintain environment) 7. withstand what is often an oxygen-poor environment 8. avoid digestions or attack by the host's immune system 9. avoid killing the host, at least until developed to the appropriate life stage 10. very efficient at converting food to energy

theory of endosymbiosis: 3rd and 4th endosymbiotic event

1. secondary endosymbiosis: cyanobacterium is engulfed 2. this differentiates into the red algal group and then green algal group 3. proliferation 4. third endosymbiosis: red and green alga groups are engulfed by other eukaryotes (likely to be heterotrophic) 4. green alga group differentiates into the green alga group and the brown alga group 5. then the 4th endosymbiotic event results in eukaryotes

all animals share: (traits that are unique to animals)

1. sequence similarities in *5S and 18S* ribosomal RNAs 2. sharing similarities in *Hox genes* 3. a series of *special cell-cell interactions* 4. a common set of *extracellular matrix molecules* such as collagen

Life Cycle of a Conifer/Pine (a gymnosperm)

1. starts with a *mature sporophyte (2n)* --> the tree 2. *ovulate cone* on the tree contains the *ovule*, while the *pollen cone* contains the microsporangia 3. the *microsporangium (2n)* inside the microsporangia (2n) produce *haploid multicellular pollen grains (n)* 4. these pollen grains are wind dispersed into the *megasporangium (2n)*: the vessels that make megaspores 5. *megaspores stay on their sporophyte plant (in seed plants)* 6. the male gametophyte *fertilizes the ovule through the pollen tube*: theres one egg nucleus that's then fertilized by the sperm nucleus --> the ovule becomes fertilized 7. the *egg nucleus (n) and the discharged sperm nucleus (n)* undergoes mitosis and now becomes a diploid sporophyte 8. The *embryo/new sporophyte (2n)* is then made and is growing inside the female gametophyte, which is inside the mother sporophyte. A *gametophyte food supply (n)* surrounds the embryo. A *sporophyte seed coat (2n)* encases the whole things 9. seeds then fly away and start to grow on own to become a *seedling* w/ the same DNA as the new sporophyte/embryo (eventually the seed coat and gametophyte stage disappears

3 generations that make up a mature seed

1. the diploid *sporophyte* which is the seed coat derived from the parent material (branches & leaves) 2. a *gametophyte* which is the food supply (n) 3. and the diploid sporophyte *embryo* - DNA in seed coat (2n) is NOT the same as the DNA in the embryo/new sporophyte --> the embryo can contain new genetic material that wasn't found in the seed coat - Gametophyte as a result of meiosis of "mother" genome

3 things that dictate the out come of a coral stress event

1. who the coral partner w/: are they with the right type of microalgae? 2. who their parents were: genetics 3. what their environmental history has been: if they've previously survived a bleaching event they're more likely to survive another

Heterosporous Alternation of Generations

2 types of spores are produced 1. *megaspore*: haploid cells that undergo mitosis, developing into multicellular gametophytes that produce eggs (*in archegonia*) (female) 2. *microspore*: haploid cells that undergo mitosis, developing into multicellular gametophytes that produce sperm (*in antheridia*) (male) --> gametophytes are *unisexual*

Chlorophytes

= *green algae* - a *paraphyletic group* bc land plants are NOT green algae - ex: multicellular Uvla (*sea lettuce*); unicellular interval chlorophyte *Caulerpa*; & colonial *volvox* - so.. *not all 'plant' are multicellular & not all 'green algae' are unicellular* - ex: *chlamydomonas reinhardtii* ("Chlamy")

Cestoda (Platyhelminthes/flatworm)

= *the tapeworms* - all *internal parasites* - vertebrate definitive host - highly specialized for the parasitic lifestyle - NO mouth or digestive tract - greatly INCREASED external surface area - *scolex*: attachment structures that allow them to hang on the digestive tract of the vertebrate host - reproduction specalists - *Proglottid*: posterior part of their body becomes gravid in terms of having little capsules that are filled w/ eggs; when proglottid is matured, it bursts and releases tons of eggs in the gut of host; eggs are shed in feces

the most abundantly consumed food by plant

= a plant! = rice

Tracheophytes

= all vascular plants, with & without seeds

advantages vs disadvantages of breathing air instead of water (trait of the hexapoda)

ADVANTAGES - *air much less viscous* as compared to water: allows animal locomotion to be very fast (ex:flying) - *much more oxygen in air*: water has 5ml/l and air can have 210 ml O2/l total air - *oxygen delivery to tissues is better* in air environments DISADVANTAGES - Density: *air is less dense* (water is 100x more dense) --> *must designed robust skeletons* - temperature --> *thermal capacity of air is MUCH higher*: means very rapid changes in temperature in air (water environments are more thermally stable)

10 Phyla

BRYOPHYTES/NON-VASCULAR 1. Hepatophyta (liverworts) 2. Bryophyta (mosses) 3. Anthocerophyta (hornworts) SEEDLESS VASCULAR PLANTS 4. Lycophyta (club mosses & relatives) 5. Monilophyta (ferns and relatives) GYMNOSPERMS/NAKES SEEDS 6. Cycadophyta (cycads) 7. Gnetophyta 8. Coniferophyta (conifers) 9. Ginkgophyta (ginkgos) ANGIOSPERMS 10. Anthophyta or Magnoliophyta (flowering plants) -- these are all embryophytes

challenges & adaptation for success on land

CHALLENGE -*water loss*: desiccation of body, must reproduce in a xeric environment ADAPTATIONS - the *amniote egg*: adaptation in reptiles that allow these animals to radiate into the terrestrial world - *water-tight skin* - *kidneys* that can concentrate urine (so they can retain water in their bodies)

challenges & adaptations for marine endotherms

CHALLENGES - heat loss is an issue - constant & rapid loss of body heat bc water has very high heat conductance ADAPTATIONS 1. *countercurrent heat exchangers* in feet & flippers 2. *Insulation - blubber* 3. *body sizes tend to be large* (SA to volume ratio allows low heat flux )

plasmogamy, karyogamy

Karyogamy: fusing of cell nuclei Plasmogamy: fusion of two or more cells without fusing of cell nuclei

Spores VS Seeds

SPORES - for bryophyta, monilophyta, & lycophyta, the spore was the main mode of dispersal for the species - are the products of meiosis of the diploid sporophyte tissues - usually are *single-celled* - *Shorter lifespan* than seed - *1 generation*= the unicellular stage before the gametophyte stage SEEDS - seeds helps plants reproduce & colonize new land -seeds are *multicellular* - can *live for years* outside of parent - seeds have *food supply*: the gametophyte tissue can acts as a food reserve for the baby embryo - *3 generations*: 2 diploid sporophyte tissues & 1 gametophyte stage - evolution of seeds allowed plants to *disperse farther away*

Homosporous

a haploid gametophyte produces *one type of spore* - all spores appear *identical* to one another - gametophyte is *bisexual* - the *clubmoss (Lycopodiaceae) is homosporous*

Diplontic Life Cycle

a life cycle that's primarily diploid --> in which only the diploid phase is multicellular & the gametes are the only haploid stage - humans are diplontic organisms bc we go thought our lives mainly as diploid organisms & our haploid stages are rather short-lived or dependent not he Diploid organisms OR never go through a multicellular phase - found in animals, brown algae, and some fungi

Haplontic Life Cycle

a life cycle thats primarily haploid --> in which only the haploid phase is multicellular & the zygote is the only diploid stage - found most in protists, fungi, and some green algae

a monoecious flowering plant

a monoecious (megasporophyll & microsporophyll on the same plant) flowering plant can have: - *bisexual flowers*: both stamen and carpel in the same flower - or *unisexual flowers*: a single flower will only have stamens or only have carpels - you can be bisexual & monoecious, but NOT bisexual & dioecious

the heaviest known organism

a plant! -*Populus tremulodies* - 6,600 tons - have massive underground root system - thought to be the oldest known organism if you include the date of the roots which date back to 80,000 yrs ago - age estimated by belief that new populous plants can't come from seeds bc its a colonal plant

the tallest known organism

a plant! - *sequoia sempervirens* - aka the Costal Redwoods - taller than the statue of liberty

Foraminifera have which of the following characteristics? a. Chambered cells b. Calcium Carbonate Shells c. Silica shells d. Radial Symmetry e. Multicellularity

a. *Chambered cells* b. *Calcium Carbonate Shells*

Which of the following were necessary mutations in archaea for the primary endosymbiotic event (that gave rise to eukarya) to successfully occur? a. formation of rudimentary cytoskeleton b. behavior that caused infolding of the plasma membrane (engulfing behavior) c. change from isoprene-tailed membrane back to fatty acid-tailed membrane d. loss of cell wall e. increase in cell size

a. *formation of rudimentary cytoskeleton* b. *behavior that caused infolding of the plasma membrane (engulfing behavior)* d. *loss of cell wall* e. *increase in cell size*

Match the taxonomic group with monophyly, paraphyly, or polyphyly a. Seed plants b. Vascular plants c. Heterospory d. Gymnosperm e. Homospory

a. Seed plants = monophyletic b. Vascular plants = monophyletic c. Heterospory = polyphyletic d. Gymnosperm =monophyletic e. Homospory = paraphyletic

Please select cellular or plasmodial or both to assign the following concepts to cellular slime molds or plasmodial slime molds or both type of slime molds a. one multinucleated super-organism b. an aggregate of many individuals c. altruism, cheating, & kin selection d. cycle AMP signaling e. amoeboid form f. haploid and diploid stages are amoeboid g. haploids have flagellated stage

a. one multinucleated super-organism : *plasmodial* b. an aggregate of many individuals: *cellular* c. altruism, cheating, & kin selection: *cellular* d. cycle AMP signaling: *cellular* e. amoeboid form: *both* f. haploid and diploid stages are amoeboid: *both* g. haploids have flagellated stage: *plasmodial*

Chlorophyll b

absorbs red-blue light & reflects green light

are bryophytes heterosporous?

although some bryophytes produce spores that develop into genetically determined male or female gametophytes and are sometimes described as heterosporous, *they are not heterosporous* in the sense of many vascular plants because the male and female spores are *produced by the same sporangium rather than in different micro- and megasporangia*

2 main types of Rhizaria

amoeboid w/ complex shell skeletons - *radiolaria*: have silica skeletons --> most of this group has radial-symmetry to them - *foraminifera*: have CaCO3 skeletons --> are highly susceptible to ocean acidification

archaella

archaea flagella

some of the oldest living organisms

are plants! - *pinus longaeva*: bristlecone pine (4600 yrs) - the oldest *quaking aspen* (80,000 yrs)

2. Segmentation

arthropod skeleton --> segmented --> hardened, rigid - chitin --> evolution of new locomotion & gas exchange that also goes along w/ this new segmentation

Which of the following are characteristics of *Ascomycota*? a. arbuscular hyphae b. a dikaryotic stage c. spores contained within a sac-like structure d. coenocytic hyphae e. septate hyphae

b. *a dikaryotic stage* c. *spores contained within a sac-like structure* e. *septate hyphae*

Which of the following are true about Gram positive bacteria? a. They are often resistant to antibiotics b. They have a thick peptidoglycan cell wall c. They usually do not cause a fever d. They can be pathogenic e. They have a lipopolysaccharide layer

b. They have a thick peptidoglycan cell wall c. They usually do not cause a fever d. They can be pathogenic

homosporous plants typically have:

bisexual gametophytes & only produce one type of spore

Prokaryotic and Eukaryotic microbes

both are *capable of living independently of other tissues* - parasites are facilitated by host tissues

A gymnosperm seed consists of (pick all true answers)... a. the gametophyte parent that makes up the seed coat. b. the sporophyte food supply. c. the sporophyte offspring that makes up the embryo. d. the sporophyte parent that makes up the seed coat. e. the gametophyte food supply. f. the gametophyte offspring that makes up the embryo.

c. the sporophyte offspring that makes up the embryo. d. the sporophyte parent that makes up the seed coat. e. the gametophyte food supply.

phylogeny

classifying organisms based on evolutionary history

Phylum Cnidaria

contains over 10,000 species - *Anthozoans*: corals & sea anemones - *Scyphozoans*: jellyfishes - *Hydrozoans* (e.g. Hydra) - *Cubazoans*: box jellies

locomotion for microbial eukaryotes

different movement for different eukaryotes - *pseudopoda* - *cilia* - or *flagella* or a combo of these elements

polyphyletic group

does NOT include the common ancestor of the group

flagella is all a radiation of the same protein

evidence that these flagellar elements all derived from the same original protein (*TFF precursor protein*) in the Last Universal Common Ancestor

dinosaurs

extinct members of the amniote lineage

"microbes" (prokaryotes)

have *hundreds* of physiologies - ammonia oxidizers - iron oxidizers - sulfate reducers - sulfur oxidizers etc...

Dr. Penny Chisholm

her work focuses on - *prochlorococcus* and its important role in oxygen production - she (and colleagues) showed that oxygenic photosynthesis by these microbes *account for the largest production of oxygen on earth* (greater than 2o gigaton of carbon uptake)

monophyletic group

includes the common ancestor and all descendants of that ancestor - can be removed from the tree with a single 'cut'

Reproduction for prokaryotes

mostly asexual by: - *binary fission*: duplication of every thing you need in a cell; symmetrical, common - *budding*: mommy cell stays larger than the daughter cell, which eventually pinches off and gains size on its own; asymmetrical, rare

extraterrestrial input hypothesis (for origin of life on earth)

organic matter and water brought to earth via asteroid and comet collisions with earth

Mycotrophs

organisms that access food (usually in the form or organic carbon) via fungi

Chemoautotrophs

organisms that make their own food through the process of oxidation and energy from electron donors

how do we organize biodiversity?

phylogenies

Epidermal Tissues

protects plants from desiccation

how do you estimate the # of half lives that have passed?

ratio of radio isotope to stable isotope provides info about how many half lives have passed

Monogenea (flatworm)

small group of animals that are *ectoparasites*: attached to fish gills & parts of fish

land plants are autotrophs by:

taking in CO2 through their stomata or air pore cells and taking in water from the soil

endosymbiosis

the process of one cell englufing another and then those 2 cells living symbiotically together

systematics

the science of studying diversity and *reconstructing phylogeny* - about creating connections between diff phylogenic branches

taxonomy

theory and practice of the study of classifying organisms

characteristics of microbes

they all - *live in water* - *they're food for higher trophic levels* - *all are small*

Autotroph

utilizes CO2 as carbon source

Heterotroph

utilizes Organic C as carbon source

First Evolution of a Parasitic Life Style

was seen in *Platyhelminthes*