BIO 152 EVOLUTION UNIT

describe sarcopterygii

Sarcopterygii: the lobe-finned fishes PLUS the tetrapods Coelocanths (Actinistia): lobe-finned fishes (KNOW THIS) -long period of not being in fossil record/slow genomic changes Lung fishes (Dipnoi): lungs (aerial respiration) sister group to tetrapods

how does heritability predict the response to directional selection

Response to selection = (heritability)(strength of selection) Heritability = 0 -No response to selection (selection depends on heritability → traits are influenced by genetic factors) Heritability = 1 -Mean of the selected individuals equals the mean of the population in the next generation

whats the founder effect

Small population (highly prone to genetic drift) isolated from a larger population By chance, an atypical set of alleles is represented in the new population with respect to the source population The new population is also prone to high rates of fixation/loss events until its population increases ex: Galapagos finches -commonly observed in populations of colonists on small islands

why is selection is less effective in small populations

Small populations: Trade-off between selection and genetic drift Detrimental alleles (i.e., under negative selection) can become fixed in small populations Beneficial alleles (i.e., under positive selection) can become lost in small populations *genetic drift overwhelming power of natural selection*

what is the evidence for natural selection what did peter and rosemary grant do

Finches: -although finches are part of the same group, they all have different beaks for different objectives -number of finches has decreased over the years -most finches that survived had large beaks --because large seeds were only available, so you had an advantage if you had a large beak peter and rosemary grant: -there was a drought, wipes out small seeds, only large seeds, the big beak benefits -height of beaks increased over time (inherited change in shape of species in one generation)

describe frequency dependent selection

Fitness of a phenotype declines as it becomes more common Selection favors whichever phenotype is rare in the population at a particular generation rarer of the 2 is the one that has the advantage

describe gene duplication

Gene duplication (an important kind of mutation) •A light-receptor gene on the X chromosome duplicated - the two copies became specialized for red vs. green light --end up with same region duplicating --new gene gets new functionality

what caused deviation from HW

Genotypes classes differed in fitness (=capacity for survival and reproduction) This is natural selection: **Fitness differences between genotype classes due to interaction with the environment**

how can chemosymbionts escape dead hosts to enrich free-living bacterial population

Hydrothermal vent communities rely on chemosymbiosis to persist --bc no light present to make living --chemoautotrophy: using chemical energy to make your own food --tells of evidence of what they looked at before If the host dies, the chemosymbionts will leave the animal tissues and resume free-living lifestyle --once energy in ecosystem disappears when vent closed, they die --eat worm on way out, then can be free living

types of sexual selection describe: -intrasexual -intersexual

Intrasexual (within a sex) -Male-male combat (for access to territory or mate) -Sperm competition (improve quality of sperm in order to complete with other males. ex: produce more pollen in male plants ) -Female competition for oviposition (egg-laying) sites Intersexual (differential preference female may have for mating partners) -Female choice based on male performance/quality (mating dances, courtship rituals, ornamentation - bright colors, large anthers) -"Good genes" hypothesis—secondary sexual characteristics as proxies (signal that weeds out) for male genetic quality

what are proifera considered to be what are choanocytes, what do they do do they have tissues how is sponge structure maintained it sponge reproduction asexual or sexual

Porifera (sponges) are considered simple animals Feeding cells called choanocytes with beating flagella that move water through the sponge body No true tissues and no through gut; digestion occurs in the mesohyl (layer between cells) via amoebocytes Sponge structure is maintained by spicules, which are formed by sclerocytesand/or sponginfibers (collagen derivatives) Sponge reproduction can be asexual (budding) or sexual (production of gametes by hermaphroditic individuals)

what are postzygotic barriers and what are the three types

Postzygotic barriers maintain boundaries between species Postzygotic barriers: Mechanisms that prevent survival or reproduction of hybrid progeny after egg and sperm meet 1. Hybrid inviability --Hybrid organisms are incapable of development or survival 2. Hybrid infertility --Hybrid viable, but incapable of mating with parent species or other hybrids --mule 3. Hybrid breakdown --Hybrids viable and fertile in F1 generation, but inviable/infertile in F2 or upon backcrossing with outcome: inability to exchange genes from one species to another

describe the impact of Jean-Baptiste Pierre Antoine de Monet, Chevalier de Lamarck

Pre-Darwinian scientist who developed a hypothesis of "evolution" (transmutation) --> thought species could change -Coined the term "invertebrate" and one of the first to use the term "biology" in its modern sense -Major contributions to invertebrate zoology (and particularly the study of mollusks) -Pre-Darwinian scientist who developed a hypothesis of "evolution" (transmutation) -Inheritance of acquired characteristics: If an organism changes during life in order to adapt to its environment, those changes are transmitted to its offspring --giraffes stretching their necks led to having a longer neck -species arose separately, then progressed up a similar ladder of advancement -life progresses series of transformation from one species to next -thought did not believe in common ancestry, thought species arose separately.

what are nematodes

Nematoda: possibly the most abundant phylum Thousands of parasitic species Reduced head, longitudinal muscles only (no circumferential musculature) Caenorhabditis elegans: a key model organism

describe alternative mating strategies: -often reaching an equilibrium frequency, what this results in, and what this is an example of -what type of selection is this an example of

Often reach an equilibrium frequency --If too many alpha males, rare beta males (cheaters) have an advantage (higher payoff for beta males) --If too many beta males, rare alpha males (territorials) have an advantage (higher payoff for alpha males) -trade off This condition results in evolutionary stable strategies (different polymorphism resulting from different solution to problems imposed to pressures) -persists for a long period of time This is an example of frequency-dependent selection: relative fitness of a phenotype depends on how common it is in the population --Result of natural or sexual selection favoring the less common phenotype --rarer you are, the greater selection you have

what is the earliest evidence of life

Oldest fossils: "at least 3,770 million and possibly 4,280 million years old in ferruginous [iron-oxide containing] sedimentary rocks"

what do phylogenetic trees represent what are tips and taxa

Phylogenetic trees are representations of evolutionary ancestry •In a phylogenetic tree of extant (living) organisms, the tips represent living organisms •A taxon (plural taxa) is a taxonomic group of any rank (e.g., species, genus, phylum) •All extant taxa that share a given common ancestor are equally evolved (equal amount of time to evolve)

how do you make a phylogentic tree

Phylogenies are inferred using characters Character 1: Protruding "nose" (absent = 0; present = 1) Character 2: Eyes (fused eye = 0; a separated pair of eyes = 1) Character 3: Toe pads (absent = 0; present = 1) Character 4: "Sleeping bag" anterior margin (set back = 0; behind the neck = 1) parisomy analysis: -Start with a dataset of characters (traits) scored for each terminal -Find the tree topology that minimizes the number of changes in the tree...the tree topology that is the most parsimonious 1. make all possible combinations of trees 2. take a column of character 1, put a dash on each letter that has the characteristic 3. look at the next column, if the only change is that species C has a characteristic that it didn't have before, add a dash to where A, B, and C would all have this characteristic (note: this dash is between nodes) 4. look at next column, if A and C have characteristic that B doesn't have, then put dash below A and C 5. look at next column, if A and B have characteristic that C doesn't have, then put dash below A and B 6. add all the dashes up, the one with the least number of dashes/changes is the most PARSIMONIOUS SOLUTION

what are the different types of deuterostome phylogeny

Phylum Echinodermata ("spiny skin") -Also deuterostomes! -Pentaradial (5-ray) symmetry Hemichordates ("acorn worms") - Marine worms with a tripartite body (proboscis, collar, and trunk), and pharyngeal gill slits

what are characteristics inferred about LUCA. what is evidence

Prokaryotic Hyperthermophilic Chemoautotroph evidence: most parsimonious tree using ancestral rate reconstruction

what is the great oxygenation of earth 2. what does oxygenic photosynthesis require

Propagation of cyanobacterial photosynthesis resulted in rapid proliferation of O2 levels Ca. 2.4 Gya: O2 levels rise from 1% of current atmospheric concentration to 10% of current atmospheric concentration Anaerobic life forms severely selected against (O2 interferes with anaerobic metabolic processes) 2. requires two photosystems

describe the great oxygenation of earth

Propagation of cyanobacterial photosynthesis resulted in rapid proliferation of O2levels Ca. 2.4 Gya: O2levels rise from 1% of current atmospheric concentration to 10% of current atmospheric concentration Anaerobic life forms severely selected against (O2interferes with anaerobic metabolic processes)

what characterstics does Urochordata share with cephalochordata and chordata

The larva of Urochordatahas all the characteristics of Cephalochordata and Chordata! The adult has shed the tail and become sessile Early developmental stages often provide better predictions of phylogenetic relationships than comparison of adult life stages.

what are the assumptions of Hardy-Weinberg equilibrium

The population is *not undergoing mutation* Reason: Mutations can introduce new alleles and change the balance of the equation The population is *not undergoing migration* Reason: Migration can introduce new alleles and/or change allele frequencies The population is *not undergoing selection* Reason: Selection of one allele combination over another will change allele frequencies The population is *mating randomly* (no disadvantage when segregating alleles) Reason: Non-random mating among individuals of a given phenotype will change allele frequencies The population is *large* (if probability will be constant, you need a large number of alleles) Reason: Genetic drift

what do population bottlenecks result in what does graph look like

bottleneck population: The phenomenon in which a population lineage shrinks to a small size for a period, causing that population to lose genetic variation when the population is small, there is more fluctuation intense genetic drift even if population grows again, lots of variation has been lost --the alleles in the small population are not a reflection of the allele frequencies we started out with

what is the endosymbiotic theory with where mitochondrion descended from

lots of phylogenetic evidence that Mitochondrion descended from an aerobic alpha-proteobacterium

BB Bb bb generation 1: 250 500 250 generation 2: 400 200 400 generation 3: 400 200 400 is it in HWE

no, despite allele frequencies staying the same -bc selection is favoring the homozygotes

where is polyploid speciation seen

polyploidy is commonly encountered in plants and can be induced for agricultural purposes polyploid: failures during meiosis

what fitness do we care about for modeling evolution

relative fitness One genotype's fitness is assigned to 1.0 E.g. - A1 individuals produce an average of 20% more offspring than A2 individuals then, ⍵1= 1.2 and ⍵2= 1.0 OR ⍵1= 1.0 and ⍵2= 0.8333

alternative mating strategies result is what

result of a tradeoff between... ...investing in secondary sexual characteristics (→improved chance of mating) costs: amazing nutrition, good genes ... when you don't have good secondary characteristics: investing in sperm production (→improved change of producing offspring)

what is speciation and biological species concept

speciation: lineage speciation biological species concept: a species is a set of populations capable of interbreeding and producing viable, fertile offspring

A population of daddy-long-legs has two alternative male strategies: alpha males guard territories, while sneaker males mimic females to sneak copulations. Which of the four graphs to the right displays the payoffs for the alpha vs. the sneaker strategy?

the graph where the two intersect -needs to be equilibrium between alpha and beta -payoff: what you stand in as function as abundance there has to be equilibrium otherwise phenomenon will not evolve

describe motile urochordates

•Also pelagic forms •Includes solitary and colonial forms •Incurrent and excurrent siphons at opposite ends of the body Urochordata is the sister group of vertebrates!

some more terms for character states -what is apomorphy and plesiomorphy -what is synapomorphy

•An apomorphy is a DERIVED character state --In the tree to the right, the filled square is apomorphic •A plesiomorphy is an ANCESTRAL character state --In the tree to the right, the open square is plesiomorphic •A synapomorphy is a shared derived character state --In the tree to the right, the filled square is a synapomorphy of the clade (A + B + C)

What synapomorphy unites Echinodermata + Hemichordata?

•DEVELOPMENT! •The larva of both these phyla... ...has a three-part (tripartite) coelom ...is bilaterally symmetrical and ciliated Hemichordate and echinoderm development is very similar!

A population contains 360 BB beetles/ladybugs, 200 Bb, and 440 bb(= 1000 total) What is the frequency of the B allele?

360 + 100 = 460 460/1000 = 46% you can always do this when given frequencies/# of individuals of genotypes → you can determine frequencies of alleles

describe actinopterygii

Actinopterygii: the ray-finned fishes Fins possess lepidotrichia, or rays, for support Skeleton made of bone Most dominant class of vertebrates (30,000 species)

the geological time scale describe beginning of earth

Age of the Earth is estimated at 4.54 Gya (billion years ago) 4.54-4.0 Gya: A time of intense heat, meteor strikes (causes craters), volcanism, and little oxygen (an anaerobic Earth) --evidence: surface of earth and moon. craters before atmohpere forms Oceans form after Earth cools down

describe agnatha

Agnatha: the jawless fishes -Hagfish -Lampreys

describe natural selection

-A deceptively simple idea --Genetic variants that are better adapted will tend to increase in frequency in a population -Over enough time, selection (of various kinds) can dramatically change the morphology, physiology, and behavior of organisms

what are traditional views of natural history : William Paley

-A watch implies a watchmaker (complex entity must have come from somewhere (god)) -Naturally occurring complex structures (e.g., an eye) are comparable to human inventions (e.g., a telescope) -no one believed in extinction -look at earth to try to explain god -encouraged people to look at biological structures

describe the components of Hardy-Weinberg equilibrium equation

-Allele A1 occurs at frequency p -Allele A2 occurs at frequency q gene pool: set of all copies of all alleles at all loci in a population (collection of all gene copies) diploid: homozygous A1A1 or A2A2 heterozygous: A1A2 -if the population is large and alleles are randomly paired in generation 2 genotype frequencies: probability (A1A1) = pp=p² probability (A1A2) = pq + qp= 2pq probability (A2A2) = qq=q² p + q = 1 p²+2pq+q² = 1 assumptions: -reproducing randomly -not at detriment for having certain gene -large population Hardy-Weinberg equilibrium says: -If a population meets these two conditions of Hardy-Weinberg equilibrium, then it is consistent with a population that is not evolving (null hypothesis) -Hardy-Weinberg equilibrium is a null model of population dynamics

what are traditional views of natural history : artistole

-Aristotle viewed species as fixed and arranged them on a scala naturae - start with simple forms (worm), go to more complex organisms (vertebrae) --ladder like series of evolution --Forms of life were considered permanent and unchanging -"the same parts of the whole earth are not always either sea or land, but that all this changes in the course of time" today we see higher organisms/higher vertebraes vs lower said unlike organisms, geological is NOT static, the earth changes over course of time -geological features change over time

what did darwin try to explain heredity with? who actually discovered heredity?

-Darwin proposed the idea of PANGENESIS!!!!! --Small particles of inheritance (gemmules) are shed by all cells of the body and migrate into the reproductive organs of parent organisms→wrong --Idea partly relied on inheritance of acquired characteristics --Darwin never encountered the work of Gregor Mendel, whose laws of heredity were rediscovered after 1900 genetics is one of the mechanisms of heredity (inheritance)

describe Charles Lyell: one of Darwin's influences

-Foremost geologist of his time and a contemporary of Darwin (lived at the same time as Darwin) -Popularized James Hutton's idea of uniformitarianism (Earth could be shaped by the same processes that occur today and that the earth was old) -Argued that the Earth must be older than 300 million years and divided geological "deep time" into discrete periods -Wrote Principles of Geology—which Darwin carried with him on the HMS Beagle

what are the elements of modern evolutionary theory

-Natural selection --A mechanism of change that can explain the fit of organisms to their way of life -Common ancestry --Diverse living species descend from common ancestors --species connected to each other but also change over time

precursors and prerequisites of evolutionary thinking: What did Thomas Malthus

-Populations (grow exponentially) grow faster than resources (grow linearly); must intersect -At a certain threshold, available resources will limit population growth -Populations grow faster than resources -At a certain threshold, available resources will limit population growth

describe Charles Darwin

-Trained to be a doctor - then a minister -Loved natural history (plants, beetles, barnacles, geology) -Travelled around the world on H.M.S. Beagle Voyage of the HMS Beagle --"When on board H.M.S. Beagle, as naturalist, I was much struck with certain facts in the distribution of the inhabitants of South America, and in the geological relations of the present to the past inhabitants of that continent" (first sentence, Origin of Species) great influence on his thought and evidence of geological changes

what is darwins great analogy with artifical selection in The Origin of Species

-all dogs are single species -we change traits of species of dogs by choosing what we like the most -different breeds, we interbreed them -artificial selection acts quickly -you can change shape of skull in single human lifespan bc selectively breed traits **if humans could change shape of species it could happen in nature** -we can put selective pressure to prefer traits, we can change shape and sizes over time -must happen in nature, different environment imposing different pressures

describe the cambrian time scale what is the cambrian explosion what complex features appeared by the cambrian

-beg of phanerozoic Defined in the geological time scale by the earliest appearance of the fossil Treptichnuspedum This is an example of a *trace fossil* - a three-dimensional burrow left behind by this species A complex burrow means evidence of *musculature, or locomotory components of the body* - the physical division of labor in an organism begins here - very early animal left behind The Cambrian Explosion: -see unambiguous evidence of animal diversification -cambiran is not exact age of animals •The seemingly sudden appearance of fossils of nearly all major animal groups with skeletons from 520 - 530 Mya complex features: •Compound eyes evolved in the Cambrian -complex appendages and complex eating structures evolved by middle cambrian

what is evolution

-change of particular unit Descent with modification (process of change that gave rise to animal life today) --Pattern of change (record of natural change - what came before, how organisms are today) recorded in anatomy, fossils, embryos, genomes, and distributions (where animals are found today) --Process of change consisting of observable and testable mechanisms - not historical, happening in real time (we observe it) A change in the genetic composition of a population over time -Genetic composition of a population is measured by frequencies of alleles -The population is the unit of evolution -individuals do not evolve alleles: copies of genes in organism (we are diploid) -determined phenotype, change in genotype leads to change in phenotype

what are the different types of selection

-directional (ex: large beak in finches) --mean of population is moving in 1 direction -disruptive -stabilizing --selective advantage for heterozygotes --if A1 = 0.1, and there is stabilizing selection (favoring the heterozygote), A1 comes up to 0.5→maintains presence of both alleles since you need both to be heterozygous bc that's whats favored deleterious exist in heterozygous population→causes genetic disorder to exist in humans→heterozygous protect deleterious allele

what is nephrozoa

A clade composed of protostomes plus deuterostomes, but excluding worms like acoels United by nephridia (kidneys in us), organs dedicated to excretion (siltering of ions to detoxify circulating sugar → urine)

what is the evidence that proteobacteria and mitochondrion are closely related

-mitochondira sits with bacteria -shows it did not come from nucleus (autogenous model is FALSE) -shows endo is true -a cell engulfed α-proteobacteria, made eukaryotes and mitochondria -supports symbiosis and that 2 separate genomes come in together

1. what is tree of life based on 2. how can we tell is evolution is occuring in populaiton of organisms

1. its a family tree based on reproduction of organisms 2. through law of segregation (2 alleles segregating into egg and sperm) and law of independent assortment (genes are not connected and occur in various combinations) -allele: gene variant --particular variant of sequence at one locus

descrive Alfred Russel Wallace what is the Sarawak Law? - KNOW

-not as rich as darwin -British naturalist, explorer, and geographer -Extensive fieldwork in Amazon and Southeast Asia -Father of biogeography (where animals are distributed in the world)→loses all his work on Helen -The Sarawak Law: "Every species has come into existence coincident both in space and time with a closely allied species" -new species evolve from existing ones, rather than simply appearing where they are. --distribution of organisms are not random, bc ancestors came from there -Evolution, as conceived before the theory of natural selection

what are traditional views of natural history : Carolus Linnaeus

-established the binomial classification system we use today (examined diversity of life in earth) -Three kingdoms: Mineral, vegetable, and animal -"Nature does not proceed by leaps and bounds" --similar entities can be places in similar groups -build on a system -still use today (genus) -The 1st edition of the Systema Naturae (1735) was 11 pages; the 10th edition included over 12,000 species --> divided animals into diff rankings -Swedish botanist, zoologist, and physician -Laid the foundations of the modern binomial system of nomenclature -Held a chair in Uppsala University where he studied and spent most of his career -Ennobled in 1761; a major scientific celebrity in his day he had lots of influence; this is what ppl said ab him: -Swiss philosopher Jean-Jacques Rousseau: "...I know no greater man on Earth" -German writer Johann W. von Goethe: "With the exception of Shakespeare and Spinoza, I know no one among the no longer living who has influenced me more strongly" -"Deus creavit, Linnaeus disposuit" (God created, Linnaeus organized) -Linnaeus saw species as part of the divine plan; Earth and species were immutable --believes species were constant, did NOT BELIEVE IN EVOLUTION -von Linné's system has lasted 286 years through various codes of nomenclature today --Imperium (Empire) - everything --Regnum (Kingdom) - animal, plant, mineral --Classis (Class) - in the animal kingdom, there were six: mammals, birds, amphibians, fishes, insects, and worms --Ordo (Order) - subdivisions of class --Genus - subdivisions of order --Species - subdivisions of genus --Varietas (Variety) - species varieties or "sub-species"

what are founder effects in human populations

-founder effect is used in human and medical contexts because there's a larger population and we look at isolated subsets of population where genetic diseases are overrepresented founder effect: inbred, like in european interbreeding pingelap atoll in micronesia Population reduced to 20 survivors after a 1775 typhoonToday: Complete achromatopsia (color blindness) in 10% of the population --inc frequency of this population -condition was present in king of pingelap; descendants had it too (bc they were carriers of disease) culturally isolated genetic populations: Ellis-van Creveld syndrome in Amish populations Tay-Sachs disease in Ashkenazi Jewish populations Hemophilia in Queen Victoria's descendants

what are the 2 interconnected problems Darwin faces

1. no direct observations of populations were changing in the wild 2. no known mechanism of heredity

describe common ancestry what is biological species concept, what doesn't this concept work for

-means there is a "tree of life" -classifications are nested hierarchies -predicted under a tree-like ancestry -reproduction leads to GENEALOGIES (generations) -genealogies lead to relationships among POPULATIONS -relationships between populations lead to species (PHYLOGENETIC) relationships --at some points, gene flow is no longer possible -in phylogenetic tree, the point where two species divide is called lineage splitting or SPECIATION (stop of gene flow) --biological species concept: a species is a set of populations capable of interbreeding (exchanging genetic info) and producing viable (you can produce offspring), fertile(offspring can also reproduce and transmit genetic info from one generation to the next) offspring this def is problem in fossils and asexual reproduction --example: mule (horse and donkey hybrid) is NOT a species, its a hybrid of 2 species (its viable, but sterile - cannot reproduce) shared certain traits, common ancestry provided a mechanism for nested hierarchy/tree like structure; mechanism by common ancestry

how do you test a cyanobacterial origin of chloroplast

-something derived from cyanobacteria resulted from chloroplast from being formed -explain success of eukaryotes dominating

precursors and prerequisites of evolutionary thinking: Jean Léopold Nicolas Frédéric Cuvier

-the father of paleontology (fossils) --Developed the study of fossils by expanding the SystemaNaturae to include extinct forms -Observed the pattern that fossil and living organisms become increasingly dissimilar as the age of the stratum increases -Suggested that the fauna of the past was once dominated by reptiles, not mammals, based on dinosaur bones -Key to the development of the idea that extinction is a widespread process --controversy since people thought it was static -did NOT BELIEVE IN EVOLUTION--> thought species remained what they were

why os phylogenetics hard to do

-there are three possible unrooted trees with 4 taxa -number of unrooted trees increases significantly with # of taxa •Finding an exact solution in any analysis of phylogeny is NP-hard for trees with many taxa •This is a problem that cannot be solved exactlyeven with the fastest computers •Empirical phylogenetic methods are heuristic (they employ a search strategy that is never guaranteed to find the optimal solution)

at this point, expect to know: 1. Hardy-Weinberg equilibrium: When a population is not evolving 2. what is genetic drift 3. population bottleneck: When a population changes in size Effect of bottleneck population size Effect of bottleneck duration 4. stabilizing selection 5. disruptive selection 6. directional selection

1. The population is not undergoing mutation The population is not undergoing migration The population is not undergoing selection The population is mating randomly The population is large 2. when a (whole) population is SMALL 3. effect on pop. size: effect on bottleneck duration: -the longer the bottleneck, the worse it is for population -more likely to be fixed or lost when bottleneck is longer because there is more time for genetic drift to act -on pop size: smaller the bottleneck pop, more severe effect of bottleneck and more severe effect of genetic drift 4. : When the heterozygote's relative fitness is highest -graph looks like 2 alleles coming together at 0.5 5. When both homozygotes' relative fitness values are higher than the heterozygote - graph looks like S shaped going to fixation and lost 6. When one homozygote's relative fitness value is greater than or equal to the heterozygote's - graph looks like parabola, longer to get fixed or lsot *know what graphs look like for 4-6)

1. how did Darwin and Wallace independently conceive idea of evolution;

1. -Darwin quietly worked on his theory for two decades in the 1830s to the 1850s -1858: Wallace sent Darwin material for his studies, and sought his help in publishing his own theory of evolution—nearly identical to Darwin's own -Darwin, aided by Charles Lyell and Joseph Hooker, rushed to publish On the Origin of Species in 1859

1. what is a clade/monophyletic group 2. what is polyphyletic group 3. what is grade/paraphyletic group

1. A clade or monophyletic group includes a common ancestor and all of its descendants 2. A polyphyletic group includes some descendants of multiple common ancestors 3. A grade or paraphyletic group includes a common ancestor and some of its descendants

1. A population under Hardy-Weinberg equilibrium has two alleles. Both of them (A1 and A2) occur with frequency 0.5. What is the expected frequency of the genotypes? 2. A population of orchids has 9% long-stemmed individuals (LL). You know that this locus (the gene) is under Hardy-Weinberg equilibrium. The Ll and ll genotypes encode intermediate- and short-stemmed plants, respectively. What is the expected frequency of the intermediate-stemmed (Ll) individuals? 3. The dominant lactose tolerance allele (A) has a frequency of 10% in the Andaman Islands. Assuming HWE, what is the expected frequency of lactose tolerant individuals in this population?

1. A1A1 = 25%; A1A2 = 50%; A2A2 = 25%. 2. 42% 3. 0.19

bird population RR: 360 Rr: 600 rr: 240 1. what is frequency of R? 2. if population goes through 100 generations of random mating, what should frequency of white feathered birds be

1. R: 0.55 2. r = .45 (1-.55) .45² = .2025

describe traits of eukaryotes

1. Cells typically 10x larger than prokaryotes 2. Many internal membrane-bound compartments •Nucleus •Mitochondria •Plastids (e.g., chloroplasts and leucoplasts) - in some eukaryotes •Endomembrane system 3. Top predators of the microbial world

1. how are archaea similar to prokaryotes 2. what are two diff groups in archaea 3. what do TACK have in common with Eukarya than the Euryarchaeota

1. paraphyletic 2. euryarchaea + eocytes •The TACK Archaea have more in common with Eukarya than the Euryarchaeota ex: actin •TACK: Four different lineages of Archaea that includes eocytes --innovations we associate with eukaryotes occur in common ancestor of TACK + eukaryotes

what do the graphs of before and after selection look like for: 1. if heritability = 0 2. if heritability = 1 3. if heritability = 0.5 what does selection remove

1. the graphs look the same 2. the graph after selection is to the right are more narrow 3. the graph is slightly to the right and slightly more narrow HIGHER HERITABILITY, MORE SELECTION THERE IS --SELECTION REMOVES GENETIC VARIATION

1. describe subphylum cephalochordata 2. describe subphylum urochordata

1. •Commonly known as lancelets or amphioxus •Ca. 35 species •Important food source in parts of Asia 2. •"Tunicates" •Often very colorful! •Sessile, U-shaped gut with two siphons

what are take home messages

1. Major clades of animals (e.g., Bilateria, Nephrozoa, Deuterostomia, Protostomia, Spiralia and Ecdysozoa) are each defined by a set of synapomorphies 2. Developmental characters are a reliable source of synapomorphiesfor the evolutionary history of animals

what is evidence of endosymbiotic theory

1. Mitochondria and plastids (in chromosomes) have their own cell membranes, inside of the eukaryotic cell 2. Mitochondria and plastids (in chloroplasts) are usually inherited uniparentally (in animals, usually inherited maternally) - have their own genome -get mitochondria from mom 3. Mitochondria and plastids have their own cell cycles 4. Mitochondria and plastids have their own highly reduced genomes -look like bacteria genome 5. The ribosomes, genetic codes, and enzymes of mitochondria and plastids are different from those of the eukaryotic nuclei --bacteria has some ribosomes as mitochondria and chloroplast

1. what life is possible in extreme environments 2. what analogous extreme environments exist today in deep sea -what do hydrothermal vent communities rely on to persist

1. Some modern prokaryotes are hyperthermophiles -modern bacteria gives evidence to life without O2 Most eukaryotes cannot sustain metabolic activity above 35 ̊ C 2. Hydrothermal vents in the deep sea -Communities stratified (subdivide territory) by distance to vent opening --Thermophilic bacteria --Vent worms (Annelida) --Mussels and clams (Bivalvia) -Hydrothermal vent communities rely on chemosymbiosis to persist -chemoautotropy: using chemical energy to make your own food

1. shape of dog skull changing from one breed to the next is an example of what 2. what is "species arise in time and space with closely related species" 3. if relative fitnesses are A1A1: 1; A1A2: 0.5, A2A2: 0.5, what allele is dominant 4. if relative fitnesses are A1A1: 1; A1A2: 1, A2A2: 0.5, what allele is dominant

1. selection 2. The Sarawak Law 3. A2, BUT this allele gets quickly lost since lower fitness (since this lets the heterozygote be prevalent) A1 gets fixed, A2 gets lost quickly; heterozygote and A2A2 gets lost quickly - REVIEW 4. A1, disease is able to be carried. A1 gets fixed, A2 gets lost, A1A2 gets lost eventually

simulating genetic drift 1. what is effect of population size on allele frequency flucuations 2. What is the effect of allele frequency on the probability of fixation/loss? 3. What is the effect of population size on the number of generations it takes to reach fixation/loss?

1. as population increases, allele frequencies becomes less prone to genetic drift when N = 10: much more fluctuation between alleles (which all start at 0.5) -more likely to get fixed or lost when N = 100: the alleles are more likely to stay around 0.5, fluctuate less, don't get fixed or lost 2. *As an allele's frequency increases, the probability of fixation increases.* *As an allele's frequency decreases, the probability of loss increases.* --when population is small, it doesn't matter what allele frequency is because you're more prone to genetic drift (more likely to get lost by chance) Genetic drift is mathematically easy to model (model breaks as population size decreases) ****The probability of an allele reaching fixation is equal to its frequency in the population.**** 3. *As population size increases, the time to fixation for a common allele increases.* *As population size decreases, the time to loss for a rare allele decreases.*

given the previous equations in flashcard before, what problems can we now solve

1. You can calculate the number of alleles present in a population, given the distribution of genotypes (the ladybug example). 2. You can calculate the expected distribution of genotypes under Hardy-Weinberg equilibrium, given the frequency of the alleles (the lactose intolerance example). --only use if it explicitly stated/says population is evolving ideally

1. what are the 3 domains of life 2. what are Archea? is it mono, poly, or paraphyletic?

1. archaea, eukarya, bacteria 2. ARCHEA IS PARAPHYLETIC (eukaryotes are rested inside archeans; more closely related to Eocytes) --Archaea have cell membranes with ether-linked lipids (ester-linked in bacteria and eukaryotes). --part of prokaryotes (paraphyletic assembly) --archaea: euryarchaea + eocytes; --prokaryotes: bacteria + archaea Transcription and translation mechanisms are shared by Archaea and Eukarya, to the exclusion of Bacteria

Why is the variance smaller after a response to selection? A. Selection removes genetic variation B. Selection favors average individuals C. Selection is a random process

A

A. A fungus is more closely related to a mouse than to a fern B. A fungus is more closely related to a fern than a mouse C. A fungus is equally closely related to a mouse and a fern D. A fungus is related to a fern, but not to a mouse

A fungus and mouse share common ancestor that is more closely related to both of those than they are to the plant *you are your sister are equally related to first cousin*

A population of spiders has the distribution of dorsal spines seen in the upper graph. The next generation is obtained only from eggs from the spiders with the most spines. What can we conclude? *the graphs are the same between the populations) A. Heritability is 0.0 B. Heritability is 1.0 C. This result is impossible - spine number must change in in this experiment

A if choosing from a certain population did not effect the way the spines are, then that means there is no selection happening, because there is no genetics affecting it. this means that is all environment, meaning that heritability is 0

maintenance of species boundaries what is a hybrid zone what are the 3 possible possible fates of hybrid

A hybrid zone is a region of overlapping distribution of two species where hybrids are created The fate of the hybrids in this zone determines the fate of the two parent species Reinforcement: The hybrids are selected against -boundary between 2 species is reinforced -# of hybrids decline over time Fusion: The hybrids are selected for; the two species collapse back into 1 -hybrids overtake the other 2 species Stability: The hybrids are selectively neutral; they occur only in the hybrid zone

describe Choiaridleyi(phylum Porifera) what is Synapomorphy of these

A fossil sponge (in the class Demospongiae) Synapomorphy:Skeletons made of spicules (characteristic of sponges)

what is heritability what values mean what for selection

A measure of how much of the variation in a trait in a certain population is explained by genetics All environment: Heritability (h2) = 0.0 All genetics: Heritability (h2) = 1.0 - mendialian traits Predicts response to selection 0 = do not respond to selection

what is a pseudogene

A pseudogene is a gene that has suffered so much mutation that it no longer encodes a functional protein The GULOP gene is detectable in the human genome as a pseudogene

describe how allele frequency will drift through time (describe graph of genetic drift)

A random walk, like the flips of a coin Genetic drift is constantly occurring, therefore, *evolution is always occurring in finite populations* --it is random and change of sampling graph of genetic drift: slide 27 of 10/17 alleles start at .5, and then constantly fluctuate, they can either get fixed or lost, but don't need to do this

-what are vertebra a subphylum of -what do they have -what are the major groups are intervertebrates monophyletic, paraphyletic, or polyphyletic

A subphylum of Chordata Vertebral column Major groups: Agnatha Chondrichthyes Actinopterygii Sarcopterygii Tetrapoda - 2 pairs of locomotor apperatus intervertebrates are paraphyletic: one entire linage minus descendants

describe the Fore Tribe and Kuru

A tribe from New Guinea Between 1957 and 1968, over 1100 of the South Fore died from kuru, a prion disease Kuru was primarily transmitted by cannibalism

what is sexual selection what are the components of it

A type of natural selection within species Preferences of one gender for qualities in the other gender lead to unequal abilities to find reproductive partners components: -sexual dimorphism (2 diff anatomies - male and female morph - can be v diff) -secondary sexual characteristics --anatomical augmentation present in one sex but not the other --purpose: to attract mates

what balancing selection

A type of selection that acts to maintain genetic variation in a population Example: Heterozygote advantage Example: Frequency-dependent selection

example of speciation driven by habitat isolation: describe allopatric speciation

Allopatric speciation: Speciation occurs when populations become geographically separated leads to cessation of gene flow→2 different speciation

polyploid speciation what is allopolyploidy

Allopolyploidy: Two parent species with different chromosome numbers hybridize to form a third species that contains the sum of the two parent species' chromosomes e: wheat *genome comes from 2 diff sources*

What is the smallest number of characters we need to fully resolve a 5-taxon unrooted tree? what is the rule for # of branches and number of characters

Answer: Two...I need one character for each internal branch. For N taxa, I have (N - 3) internal branches.

describe arthopoda

Arthropoda: The largest animal phylum, united by an exoskeleton, segmentation, and jointed appendages Powered flight; present in almost every part of the biosphere >80% of all described animal species are arthropods

what is secondary and teritary endosymbiosis

Atypical plastids with more than two surrounding membranes -secondary: primary eukaryotes get eaten by something --digest everything expect chloroplasts, not chloroplasts with 3 membranes Red algae have been key contributors to secondary endosymbiosis events (resulting organelles are called rhodoplasts) These events are tested using phylogenetic methods for each organelle type -cell has 3 membranes --2ndary endosymbiosis; same in plants; if it does happen again, 4 membranes?? (CONFRIM) - from getting eaten by something having a plastids with more than 2 membranes says that endosymbiosis has occurred many times

sympatric speciation: polyploid speciation what is autopolyploidy

Autopolyploidy: Parent species with 2n chromosomes undergoes whole genome duplication to form a tetraploid (4n) species -1 parent species, duplicate genome 2n=6 →mitosis→4n=12 failure of cell division after chromosome duplication gives rise to tetraploid tissue after meisosis, 2n forms. gametes produced are diploid after fertilization, offsrping with tetraploid karyotypes may be viable and fertile (new species) plants get away with this because they can self-fertilize

EXAM QUESTION True or false:In a large, randomly mating population of diploid animals, there are three alleles: A1, A2, and A3. These alleles occur at the frequencies p, q, and r, respectively.The frequencies of the genotypes in the next generation is thus given by the formula (p + q + r)3= 1 A. True B. False

B. False -might work in triploid, but NOT diploid If:p + q + r = 1 Then:p2 + q2+ r2 + 2(pq + pr + qr) = 1 (punnet square)

describe bacteria and 1. transformation 2. transduction 3. bacterial conjugation

Bacteria can acquire DNA from outside of their cell Diverse modes of reproduction and genome evolution --Binary fission --Transformation: Acquisition of DNA from the environment (plasmid) --Transduction: Acquisition of DNA from viruses --Bacterial conjugation: Exchange of genomic material from two bacteria (usually of the same "species") ---bacteria can acquire DNA from dead or living cells

what are quantitative genetics what happens as number of alleles increases

Beyond two alleles With only two alleles, we only have three phenotype classes (A1A1, A1A2, A2A2) How do we explain traits with continuous distributions? In a monohybrid cross, the genotype frequency ratio is 1:2:1 In a dihybrid cross, the genotype frequency ratio is 1:1:2:2:4:2:2:1:1 In a trihybrid cross, the genotype frequency ratio is 1:1:1:1:2:2:2:2:2:2:4:4:4:8:4:4:4:2:2:2:2:2:2:1:1:1:1 **As the number of alleles increases, the genotype frequency distribution comes to resemble a continuous distribution**

for bilatera: -what type of symmetry does it have -how many tissues and what are they -what axis -what is cephalization

Bilateral symmetry Triploblasty, or three tissue layers (endoderm, ectoderm, mesoderm) Antero-posterior axis Cephalization: concentration of neural structures toward the anterior pole of the body

describe protostomia where is blastopore what are the two major groups

Blastopore forms the mouth (usually) Two major groups --Spiralia (Lophotrochozoa): the group of animals with the most body plan disparity --Spiral cleavage: a shifting plane of cellular division --Trochozoa: a free-swimming larva with ciliary belts and an apical ciliary tuft --Ecdysozoa: the group of animals with the greatest diversity (number of species) •Molting of cuticle (ecdysis) at least once in the life cycle •Trilayered cuticle with trilaminateepicuticle, proteinaceous exocuticle, and chitinousendocuticle

identifying population bottlenecks is key to conservation genetics -what cna they increase frequency of -what is inbreeding freqeuncy

Bottlenecks can increase the frequency of deleterious/harmful alleles Inbreeding depression refers to reduced biological fitness—the ability to survive and reproduce successfully—in populations afflicted by low genetic variation (bc deleterious alleles can come up) --**genetic drift causes deleterious alleles to be fixed due to chance alone (bc of smaller population size) --this is bc reproduction is happening between 2 individuals that are closely related due to population reduction, the species can either be -range fragmentation (severse population reduction) - forced to inbreeding depression -extinct in the wild (cataclysmic - disastrous - population reduction) -or reintroduced in the wild (recovery from population bottleneck) --danger: exposes then to all pathogens, reduces resilience because there aren't many genotypes

Which is the best argument for believing that LUCA had a prokaryotic rather than a eukaryotic cell structure? A. Prokaryotic cells are more abundant, so they are probably older B. Prokaryotic cells are simpler, and simpler forms never arise from more complex forms C. One transition from prokaryotic to eukaryotic is more likely than 3 transitions from eukaryotic to prokaryotic

C

what are the requirements for speciation

Cessation of gene flow, or reproductive isolation Simplest mechanism: geographic processes form barriers (habitat isolation) --Formation of a mountain range or valley --Submersion of land bridges --Formation of new rivers Other possible mechanisms --Loss of a pollinator common to all populations --If bee goes extinct, plants can become isolated from each other since bees is a mechanism for reproduction

what caused this change in frequency from one gene pool to the next?

Chance sampling from one generation to the next If the population is small, the alleles represented in the next generation may be different in frequency from the expected value—this is genetic drift, since its easier to change frequencies of alleles Important mechanism of evolution, especially when populations are small --very common for empirical population *note: Since evolution is a change in allele frequencies in a population over generations, a population in Hardy-Weinberg equilibrium is, by definition, not evolving.* in large population: the frequency of picking A1 is always fixed

what are chanoflaggellates, what are characteristics for them

Chanoflagellates are the sister group of animals •A group of eukaryotes that have a microvillar collar and a single flagellum encompasses by a microvillar collar -about 150 species •Unicellular, heterotrophic •Can form colonial aggregations (group together, survive to grouping) •Sister group to the Metazoa

what was found in chanoflaggellates genome

Chanoflagellates are the sister group of animals •Monosiga brevicollis genome: the first genome of a choanoflagellate •Approximately 9,200 genes •Included in the genome are cell adhesion and cell signaling genes previously thought to be restricted to Metazoa

who were the advent (arrival) of natural selection (common ancestry and evolution) what is concept of natural selection

Charles Darwin and Alfred Russel Wallace natural selection: thought species might change over time

describe chondrichthyes

Chondrichthyes: the cartilaginous fishes -Sharks, skates, rays, and chimaeras -Skeleton made of cartilage, not bone -True jaws

for cnidaria: -what are the tissue layers -what is synapomorphy (characters shared by a group of taxa due to inheritance from a common ancestor) -what is alternation of generations

Cnidaria: animals with two tissue layers Two true tissue layers: epidermis (outer) and gastrodermis (inner) Synapomorphy: specialized stinging cells called cnidocytes Alternation of generations: typically, an asexual polyp stage and a sexual medusa (jellyfish) stage

what are cryptic species

Deep genetic divergences can occur without morphological divergence Distinguishing population variation from species boundaries requires molecular tools and parametric methods -real species, have a hard time telling them apart from each other -just because lineage splitting speciation occurs, that does not mean trait evolution

what is found about dickinsonia

Dickinsonia (some sort of animal) now established as an early animal based on biomarker analysis! -left behind molecular fossils -animals have older origin than cambrian/phanerozoic •Biomarkers extracted from Dickinsonia fossils are cholesteroids (lipid derivatives) •Only animals produce cholesteroids

describe the three factors found on the voyage of the HSM Beagle

Diversity - the number of different species Endemism - the quality of being found only in one location and nowhere else Adaptation - the incidence of traits that make an organism suited to its environment

what is origins of Eukarya

Lynn Margulies' endosymbiotic theory: The eukaryotic cell arose from an anaerobic heterotrophic unicellular host cell engulfing an aerobic cell (proteobacterium) ca. 1.5 Gya -lots of evidence Multiple rounds of engulfing cyanobacteria resulted in different types of eukaryotic organelles: mitochondria and plastids (e.g., chloroplasts) A symbiosis was formed between the host cell and the endosymbiont

how many orgins of multicellularity in eukaryotes

Many (~25) individual origins of multicellularity (animals) not rare event shows us why eukaryotes are successful

what is an animal

Metazoa (animals) is divided in ca. 35 phyla A phylum is a taxonomic rank that corresponds to different body plans --Planes of symmetry --Tissue layers --Organs and organ types

what is formal name for animals what are characteristics for it

Metazoa: formal name for "animals" A monophyletic group with about 1.4 million species Characteristics of animals 1. Multicellular 2. Ingestive heterotrophs (eat other things to survive) 3. Presence of special glycoproteins (e.g., collagens - connect tissues in animals) 4. Presence of protein kinase C for cell-cell signaling 5. Neurotransmitters: RFamide peptide family, acetylcholine 6. Eggs and motile spermatozoa

Describe traits of mammals and the 3 major groups

Milk; fur; three middle ear bones (malleus, incus, stapes) Three major groups: 1. Monotremata: lay eggs, supply hatchling with milk 2. Marsupialia: live birth, but no placenta; young carried in pouch 3. Placentalia: live birth, embryo provisioned by placenta

describe traits of mitochrondia -what type of membrane do they have, how do they arise

Mitochondria have a double membrane through phagocytosis Mitochondria always arise from other mitochondria (not from the rest of the cell) Phylogenetic test: If mitochondrial genomes are separate from nuclear genomes, where do mitochondria go in the phylogenetic tree of life?

We need millions of characters to resolve the tree of life! Where do these characters come from?

Molecular sequence data provide an enormous source of phylogenetic characters Both nucleotide and peptide sequences provide phylogenetic data

if selection acts to remove variation, where does variation come from

Mutation: A change in the structure of a gene or chromosome A process that can introduce new alleles Error in DNA replication rate --1 error per 100,000 (105) base pairs (bp) means ca. 30,000 errors per our 3 billion base pairs of DNA --Proofreading mechanisms reduce error rates to one error per 100,000,000 bp(10-8) --Mismatch repair mechanisms reduce error rate to one error per 10,000,000,000 bp (10-10)

what is one thing to never say regarding the null hypothesis

NEVER SAY THE NULL HYPOTHESIS IS TRUE (we only fail to reject the null)

imagine a naturally occurring population of 1000 flamingos. You take some blood samples and discover that 50% of the birds are FF genotypes (red), 50% are ff genotypes (white), and 0% are Ff (orange). The frequencies of the population do not change from year to year. Is this population under Hardy-Weinberg equilibrium?

NO not changing year to year is not sufficient 2pq = 0 means either p = 0 or q = 0→FALSE equations don't hold

what does natural selection require can both natural selection and genetic drift lead to adaptations

Natural selection requires genetic and phenotypic variation to operate Only natural selection can lead to accumulation of adaptations in a single lineage over time (whereas genetic drift cannot) --this is because natural selection is not RANDOM --genetic drift can be positive, neutral, or detrimental; natural selection is only positive

what is origin of oxygenic photosynthesis

Origin of chained photosystems could be the result of lateral gene transfer (passed from 2 simultaneously occurring organisms → DNA getting passed from one living organism to the other) from two parent bacteria that each had a single photosystem --Evidence: The tree of photosystem encoding genes (in the chloroplast genome) is different from the rest of genome (plant nuclear genes) --genes that make photosystem come from 2 diff parts of tree of life --Analogous to the case of mitochondrial vs. nuclear genes in animals --making photosystem that can effectively drive photosynthesis Probably the most important event in the evolution of life!

describe what kind of photosystems bacteria has

Other kinds of photosynthesis occur in bacteria that consist of a single photosystem --Green sulfur bacteria and heliobacteria: similar to photosystem I --Purple and green non-sulfur bacteria: similar tophotosystem II ---have 1/2 of each system --Instead of water the electron donor is usually H2S (hydrogen sulfide)

why are secondary sexual characteristics often concentrated in males what are the 6 male solutions

Reason: Higher parental investment for females; males have to compete with each other to be chosen by the female --females have heavier cost, males are pressed to indicate quality Male solutions: -Increased sperm production/quality -Direct sperm competition (males try to remove sperm in females reproductive cavities so they have a better chance of fertilizing egg) -Ornamentation (indicators of genetic quality - colors) -Courtship rituals, mating dances, and nuptial gifts (edible, symbolic) -Mate guarding (prevent females from mating with other males) -Territoriality

evolutionary fitness -describe relative and absolute fitness

Relative fitness refers to the contribution of a genotype/phenotype to the succeeding generation's gene pool, relative to the contributions of all other genotypes/phenotypes in the population -AA and aa: 2 alleles at a locus: diploid individual ---A reference genotype/phenotype is set to ⍵= 1 ---All other genotypes/phenotypes are measured relative to the reference --how much is genotype contributing to the next generation compared to others ω = 2, means contributing twice as many offspring in next genetic pool Absolute fitness refers to ratio of the number of a genotype/phenotype after an episode of selection to the number of that genotype/phenotype before the episode of selection ⍵ absolute= (ngenerationx+y) / (ngenerationx)

what are the effects of genetic drift

Removes variation from the population (fewer possible genotypes/possibilities of alleles - unlike mutation) -this is because allele can be fixed or lost - doesn't need to Once an allele is lost - it can never reappear (except through mutation) -If an allele reaches a frequency of 1.0, it is said to be fixed in the population -If an allele reaches a frequency of 0, it is said to be lost from the population **Drift is more powerful in small populations**

what is early physical evidence of life on Earth what is a testible hypothesis with stromatolites, was it proven to be true

Stromatolites are fossilized accretions of cyanobacterial films Each layer represents a film of bacteria and sediment Properties: Found in shallow aquatic environments; growth lines irregular; calcareous Age: Some as old as 3.5-3.7 Gya A testable hypothesis: Do modern mat-forming cyanobacteria form accretions in response to light? answer: YES

what is sympatric speciation

Sympatric speciation: Speciation occurring without geographic isolation

what are the synapormorphies of trilobites

Synapomorphies: Jointed legs Segmented body Faceted eyes Approximately 20,000 species of trilobites Complex taxonomy: 10 orders, ca. 150 families, and ca. 5,000 genera Diverse in both morphology and in body size Differentiation of appendage types: sensory and locomotory to serve diff functions. occured in middle cambrian Fossil record spanning Cambrian to the end-Permian

what are synamorphies of pikaia gracilens

Synapomorphies: Notochord Dorsal nerve cord Myotomes (repeated blocks of muscles)

describe the synaporphies of phylum chordata

Synapomorphies: 1. Notochord 2. Dorsal hollow nerve cord 3. Pharyngeal gill slits 4. Post-anal tail

describe the 2 groups of tetrapods and what traits they have are reptiles and fishes mono, para, or polyphyetic

Tetrapods (humans, 2 pairs of moving around) Two major groups: Amphibia and Amniota Amphibia: frogs, toads, salamanders, caecilians --Require aquatic environments to reproduce --can be on water and land Amniota: reptiles (wraps around egg) (including birds), mammals --Possess an embryonic membrane called the amnion, which enables reproduction on land ---left aquatic behind reptiles and fishes are PARAPHYLETIC - KNOW FOR EXAM

focusing on HWE for: The population is not undergoing selection Reason: Selection of one allele combination over another will change allele frequencies describe fitness

The average reproductive output of individuals with a certain genotype --Denoted ⍵ with a subscript to indicate genotype Reproduction requires: -Surviving -Finding a mate (except in asexual species) -Producing offspring (which must also have the capacity to survive and reproduce)

describe jaw evolution in fossils

The evolution the jaw resulted from a stepwise recruitment of pharyngeal gill arches to form the mandible (lower jaw) Consistent with fossil, developmental, and genetic data

what is co-speciation

The speciation of one lineage (becoming geographically isolated) drives the speciation of another lineage (also becomes geographical separated) ex: plants and pollination -parasite and host Expectation: phylogenetic trees of both lineages match; timing of diversification must be contemporaneous how to test: -make phylogenetic of both species -check for same timing of splits -make species is very dependent on other ex: Fig wasps: Extreme case of co-speciation -Result of symbiotic relationship between plant and pollinator -when fig trees undergoes pollination, fig wasks do too

describe early tetrapods

Two pairs of appendages (anterior and posterior) Tiktaalik roseae (375-380 Mya), a fossil amphibian discovered in 2006 blend of amphibian and fish

describe the ediacaran fauna (ca. 600 mya)] why are they mysterious

Unambiguous multicellular organisms (animals) appear in the Ediacaran Phylogenetic position unclear, but these are believed to be metazoans --associated with corals -soft tissue -has some sort of directionality small shelly fossils: calcified skeletons in Ediacaran •The life forms of the Ediacaran remain mysterious because they disappear from the fossil record near the base of the Cambrian

precursors and prerequisites of evolutionary thinking: what is unifromitarisnism and who proposed it

Uniformitarianism- Changes in the Earth's crust have resulted from the action of continuous and gradually acting processes, such as erosion and sedimentation--> thought that rock was underwater at one point -Proposed by James Hutton, the father of modern geology -Natural laws that apply today must also have applied in the past -Geological "deep time" (earth could be old; did this by looking at rocks)--> takes a long time -"The past is key to the present" - catastrophic and/or supernatural events are not required to explain the history of the Earth --thought earth came from catalytic events, and that if these events take place at the same rate they do today, then the earth is very old -before him, people thought earth was only a couple years old

what is runaway sexual selection

a mechanism whereby a secondary sexual trait expressed in one sex becomes genetically correlated with a preference for the trait in the other sex. Female preference is also a heritable trait Example: Female finches (e.g., the two Australian species on the right) have a latent preference for males with a high white crest on their heads—a trait that does not occur in nature males spend time with females with no crest females spend time with males with white crest If female trait preference is linked to the male trait, the result over time is extreme sexual dimorphism and highly exaggerated male traits (which are costly) -traits get inherited together -independent assortment doesn't apply, they are linked This is called runaway selection and can generate maladaptive traits (trait should have clear negative effects on individuals' health and well-being) in one or both genders -sits close to gene that females want to spend close time with males →tradeoff between natural selection and sexual selection

what else can population bottlenecks result in (with deleterious alleles)

accumulation of deleterious alleles (alleles that are disfavored) -in bottleneck, a catastrophic event or new predator/virus causes popualtion to crash when there is a bottleneck event, there are 2 possibilities: -population can crash/become extinct -population can recover after bottleneck event, there is reduces alleles/less genetic diversity, this is more prone to genetic drift in the middle of the bottleneck, and causes alleles to be more likely to be fixed or lost due to dec population size as a result of RANDOM SAMPLING -the longer the bottleneck, the worse it is for population (more severe effect of genetic drift) -more likely to be fixed or lost when bottleneck is longer because there is more time for genetic drift to act -allele frequencies go up and down due to bottleneck -the traits that are not fixed or lost stay constant to what they are before bottleneck smaller population of bottleneck: more severe effect of bottleneck and more severe effect of genetic drift when bottleneck occurs: more genetic drift, fluctuations in population size due to RANDOM SAMPLING --when they come out of bottleneck, allele frequencies they were at gets stuck there As a result of genetic drift acting on a small bottleneck population, we get a more genetically homogenous population

what are adaptive radiations what is the expectation for the species

after species form: Diversification of lineages to fill different ecological roles or niches radiation - rapid speciation due to ecological difference Expectation: Species must be closely related and have different ecologies lots of short diff over time, diff roles filled evolve independently, have phylogenetic difference

What is the smallest number of characters we need to fully resolve a 4-taxon unrooted tree?

answer: 1

Example: In the tree on the right, the outgroup is Species N. This species has state 1 for this character, and we know that state 1 occurs in the common ancestor of all the taxa. What is the cost of this character on this tree? *look at slide 21 for 10/28*

answqer: 2 goes from 1→0 and then 0→1, there are 2 changes, thus cost is 2

how do we testing whether real data are "close enough" to Hardy-Weinberg equilibrium? what is equation to do this example: observed: A1A1: 30 A1A2: 60 A2A2: 10 expected under HW: A1A1: 25 A1A2: 50 A2A2: 25

apply statistical tests (𝛘2) Testing for Hardy-Weinberg equilibrium Compare expected frequencies under Hardy-Weinberg equilibrium with the actual frequencies Compute a 𝛘2 ("Chi-square") value 𝛘2 = Σ{[(value observed- value expected)² ] / value expected} Obtain a pvalue to interpret result

what is the alternative hypothesis to endosymbiotic theory

autogenous model: mitochondrial genome that came from breaking off the nuclear genome - 1 genome→2 genome (nuclear to mito) -no symbiosis required FALSE If the autogenous model were true, where should a mitochondrial version of a gene attach to this tree? -below the mitochondrion and nucleus

Under the endosymbiotic model where will a mitochondrial version of a gene attach to this tree?

below proteobacteria and mitochondrion -endosymbiosis required symbiosis

describe Darwin's insight into common ancestry what does common ancestry entail, and what does it require

between 2 species there is a common ancestor that links them -1st concept of phylogenetic tree -broader genealogy exists in the biota -divergence of traits over time -common ancestry entails divergence over time→requires evolutionary change -common ancestry REQUIRES evolution --the common ancestor has mixed traits of traits of 2 species. the common ancestor has traits that in groups outside of the 2 being analyzed

what is the difference between founder effect and population bottlenecks (the two are not synonymous)

bottleneck: population is sharply reduced in size from natural disaster ***FOR ONE POPULATION*** founder: small group splits off from the main population to found a colony ***CREATES 2 POPULATIONS*** the new population undergoes founder effect

what are ring species

can exchange genes with their neighbors, can't all freely exchange genes Species boundaries are not always obvious Ring species can exchange genes across most adjacent populations, but non-adjacent populations (e.g., green and purple) will not exchange genes One species or several? -species is continuum, shows how speciation occur over time

describe cyanobacteria

cyanobacteria evolved the ability to do photosynthesis -makes O2 -occurred during O2 revolution -drives hypothermal vents to bottom of ocean -changes atmosphere Ecologically important --Primary producers --Nitrogen fixers Oxygenic photosynthesis

what is alternative mating strategies with bluegill sunfish

example: Bluegill sunfish males start off the same, then there is a switch in developmental trajectory -Parental males (large, colorful, defend nests, low testis-to-body size ratio) -Satellite males (mid-size, colored to mimic females, do not defend nests) -Sneaker males (small, high testis-to-body size ratio, do not defend nests) problem: no winning strategies because there is a tradeoff --Tradeoff between weapons and testis size is common in alternative male morphs --cost to invest in secondary structures, more attractive --cost to have large testes, less attractive

how does speciation occur? what happens first and then later

first: geographic isolation (ex: seed dispersal) later: genetic differentiation -this is a process called allopatric speciation (speciation is happening in 2 diff parts of the world) -might evolve independently -populations drift apart

what does chloroplast have separate origin from

from the mitochondrion -has 2 membranes -comes from cyanobacteria -only see in subset of eukaryotes -mitochondria: originates once in common ancestor of living eukaryotes cyanobacterium: result of cyanobacterium making its way into eukaryote that has mitochondira, tested by phylogeny chloroplast thought to be part of cyanobacteria

using critical values of 𝛘2 distribution table, how do you test for HWE when do you reject \ and when you do fail to reject null

go to 0.005, then down to the specific df find critical value in table: ex: At this value of 𝛘2 , the area under the curve is 0.005. My 𝛘2 value is 12. Therefore, my p value is less than 0.005 (since 12 > 10.597, so its more to the right of the graph, so the p value will be smaller) p < 0.005 *IF 𝛘2 IS MORE THAN CRITICAL VALUE, P VALUE IS LESS THAN ALPHA, REJECT NULL* if p < alpha, REJECT NULL if p > alpha, FAIL TO REJECT NULL for our example: 𝛘2 = 12 k = 2 p value = 0.00247875 Interpretation: The probability that my sample was drawn from a population under the null model of Hardy-Weinberg equilibrium is equal to p = 0.248% A significance value of ⍺= 0.05 means that we will incorrectly reject a true null hypothesis less than 5% of the time

why is sample size crucial to p value

if p = 0.5 and q = 0.5, and sample size is 10: then p is 0.5488, and expected are 3, 6, and 1 100: then p is 0.00248, and expected are 30, 60, and 10 1000: then p is ~0, and expected is 300, 600, and 100 there is less certainty to reject null when you have small sample size, and this is why you can't do alpha of less than 0.05 because if you did it wouldn't be super accurate because the population size wouldn't be big enough to make it accurate

how is sexual selection countered

in species with exclusive paternal care of offspring, sexual dimorphism is minimized or even reversed when males take care of offspring, females fight each other additional criterion for reproductive success In species with biparental care, sexual dimorphism is often minimized—sexes are hard to distinguish Iporangaia pustulosa, a tropical daddy-long-legs with exclusive paternal care -Males and female look very similar; males guard egg clutches on leaf surfaces (reduction in sexual selection pressures) - "Cheaters" are males that drive away other males and start taking care of other males' offspring -why?? ---Females mate preferentially with males that are tending large egg clutches (a possible proxy for quality of genes or paternal care ability) ---"Cheaters" are trying to look like good fathers!

focusing on assumption of HWE: the population is large reason: genetic drift what happens if population is large vs small

is population is large: between gene pool 1 and 2, the frequency of A1 and the expected frequency of A1 is fixed (as p) if population is small: frequency of A1 fluctuates more between gene pool 1 and 2

what does linage splitting (which requires stopping of gene flow) NOT entail what does it involve, what does this allow

it does not entail trait evolution (don't have to look different) -lineage splitting involves cessation of gene flow -this ALLOWS descendant lineages to evolve independently - to acquire different traits

draw primates trait tree in notecard

ok

what are the assumptions for p and q in an ideal population of diploid individuals

p+q=1 p²+2pq+q² = 1 allele A1 occurs at frequency p allele A2 occurs at frequency q proportion (A1A1) = pp = p² proportion (A1A2) = pq + qp = 2pq proportion (A2A2) = qq = q²

accumulation of prezygotic barriers to speciation -what are prezygotic barriers -what are the 5 types of prezygotic barriers

prezygotic barriers: Mechanisms that prevent fertilization from occurring, prevent gene flow -prior to sperm and egg meeting KNOW THE BARRIERS 1. Habitat isolation: the populations never co-occur in the same habitat --Cave vs. surface dwelling --Aquatic vs. terrestrial --High altitude vs. lowland 2. Temporal isolation : the populations' reproductive cycles are out of phase (laying egg at diff times, reproducing only in spring/while mate only does fall) --Seasonality --Flowering time --Frequency of emergence/spawning 3. Behavioral isolation: the populations' reproductive habitats are not compatible --Courtship ritual --Mating call --Nesting material/design -bird song - if you have correct song, you will not attract female 4. Mechanical isolation: Anatomical differences prevent successful mating --Copulatory structure (organ size of inseminating organ) --Body size (one is too small, other is large) 5. Gametic isolation: Biomechanical mechanisms prevent successful fertilization -for not direct fertilization - ex: plants that release seeds in wind, coral --Incompatible recognition sites on egg surface --Key to genetic isolation in broadcast spawners --ex: coral

what are protostomes vs. deuterostomes

protostomes: Blastopore forms the mouth*** Deuterostomes: Blastopore forms the anus; mouth forms secondarily*** the opening of the central cavity of an embryo in the early stage of development.

what is the relationship between p value and significance (𝛘2 and p, 𝛘2 and accepting/rejecting null)

pvalue: area under the curve, to the right of your 𝛘2 value As your 𝛘2 value increases, your p value decreases --𝛘2 is a magnitude of how much doubt/skepticism you have that you sample came from a null model population The higher your 𝛘2 value (or, the lower your p value), the more confidence you have in rejecting your null hypothesis H0: Sample drawn from a population under HW equilibrium HA: Sample drawn from a population that is not under HW equilibrium

An ideal population under HWE can only achieve specific values of genotype frequencies what are these values for q², 2pq, and p²

q²: 0-1 p²: 0-1 2pq: can't go above 0.5 (50%)

Genotype frequencies at the prion protein PrPc Most human populations are polymorphic for having a methionine (M) or a valine (V) at position 129 in the protein MM MV VV Before the epidemic 0.22 0.52 0.26 After the epidemic 0.13 0.77 0.10 why the change? Before the epidemic the M allele had a frequency of 0.48. By how much did it change during the kuru outbreak? A. 0.25 B. 0.16 C. 0.09 D. 0.03

stabilizing (inc heterozygous population) D In this case: strong selection, but minimal evolution frequency of M allele: 0.48→0.51 frequency of M allele barely changes but heterozygotes still favored (this is the nature of STABILIZING SELECTION)

describe the four things needed for natural selection: a mechanism of evolution

what Darwin's ideas consisted of in origin of species 1. variation: (phenotypic variation) there is variation of traits in natural populations (species are not fixed identities) - differ in size, color, and DIFF PHENOTYPES 2. differential survival and reproduction: species produce more offspring than their environment can support --# offspring is variable --lays hundreds of eggs, only 1 egg goes to adulthood; they differ in ability to survive and reproduce 3. heredity: if some individuals inherit traits that make them more likely to survive AND reproduce (bc of variable traits), then they will leave more offspring than other individuals --certain traits cause the next generation to survive more often than the one before 4. natural selection: over time, unequal ability to survive and reproduce will lead to accumulation of favorable traits --outcome: mechanism for adaptation

what are the tissue layers, how are tissues formed

zygote→blastula→gastrula ectoderm: outer layer mesoderm: middle layer endoderm: internal later germ cells: sperm and egg

what is evidence for early earth environments

§Relative ratio of ferrous (Fe2+) (low oxygen - looks gray) and ferric (Fe3+) (high oxygen - red) oxides in Hadean and Archean deposits (rocks) enables quantitation of atmospheric O2 --evidence in change in atmospheric concentration there was 1) an oxygen revoluntion (atompshere O2 went from 0.0001 to 10) and then a second spike (O2 went from 10 to 100) evidence of organisms surviving in low levels of O2: rocks

describe stabilizing selection

ω11 < ω12 > ω22 Alleles at low frequency have an advantage, in spite of genetic drift Stabilizing selection tends to maintain* variation in the population *(for two alleles at a single locus) - not losing or gaining alleles --*when there are MANY alleles at a locus, then stabilizing selection causes genetic variation to decrease *Overdominance or heterozygote advantage* A1A1 = 0.5 A1A2 = 1 A2A2 = 0.5

describe directional selection

ω11 = ω12 < ω22 like autosomonal recessive disease --heterozygotes/carriers not a disadvantage (ex: hemophilia) --disadvantage when recessive alleles get picked together over time, one allele will be lost, but slowly (when A1A1 and A1A2 are both 1) --when A1A2 and A2A2 = 0.7, A1A1 gets fixed quicker directional selection tends to reduce variation in the population --the allele that is not favored is not getting fully lost because in order to make heterozygote you need recessive allele **deleterious allele sticks around in population for a long time** when A1A1 = 0.5 A1A2 = 0.5 A2A2 = 1 (for a autosomal dominant disease) A1 gets quickly lost bc heterozygotes, can't mask/protect it from selection

describe disruptive selection

ω11 > ω12 < ω22 select against heterozygots at A1 = 0.5, one of the alleles go up to fixation, other one gets lost (due to chance) Over time, one allele will be lost Disruptive selection tends to reduce variation in the population --in the end, end up with one allele and only one genotype -if A1 > 0.5, will get fixed -if A1 < 0.5, will get lost A1A1 = 1.0 A1A2 = 0.7 A2A2 = 1.0

what are Complex morphological phenomena that have appeared by the Mid-Cambrian:

•Embryonic cleavage •Segmentation •Muscles •Central nervous systems •Appendages (sensory, walking, swimming) •Eyes •Feeding organs (e.g., grasping appendages of Anomalocaris) •Ecological specialization: (carnivory vs.graxing/rasping) suggests there is rapid diversification in a small period of time

some characteristic are difficult to gain what characteristic is rarely observed to be gained

•Gain of powered flight is rarely observed --In the vertebrates, only three gains: birds, bats, pterosaurs (winged dinosaurs) --In the invertebrates, only one gain: insects •...but losses of powered flight are frequently observed --Over 60 species of birds have lost flight (e.g., penguins, dodo (extinct), kakapo) --Numerous lineages of flightless insects (e.g., fleas, beetles, "tree lobsters")

Balancing selection: Heterozygote advantage

•If the relative fitness of the heterozygote is higher than those of either of the homozygotes, then selection will act to maintain both alleles in the population •Example: The sickle cell anemia allele in malaria-prone regions •Individuals heterozygous for the the sickle cell anemia allele (carriers) have an advantage in resisting Plasmodium falciparum (the malaria-causing parasite) •In regions where malaria is endemic, the frequency of the sickle cell allele ("HbS") is significantly higher than the rest of the world

what is ancestral state reconstructions what is homology and homoplasy

•If we have a given tree topology and a distribution of character states......we can reconstruct the states present in the nodes (ancestors) using parsimony analysis. •Shown here is a tree with eight taxa and one character. •There are only two character states for this character. •What is the cost of this character on this tree? Answer: Two. A minimum of two changes is required to minimize the cost of this character state distribution. •The changes in character states that we assign to branches imply certain states in the ancestors (nodes) •This is called ancestral state reconstruction •Character states that are shared by some taxa AND their common ancestors are examples of homology (adjective: homologous) •Character states that are shared by some taxa, but NOT their common ancestors, are examples of homoplasy (adjective:

what are characteristics of Ediacaran vendobionts

•Late Neoproterozoic •Occurred worldwide •Shallow to deep environments •Soft bodied (imprints) or small skeletons (small shelly fossils) •Lack of complex internal structures •Trace or imprint fossils: Only two dimensional (no vertical burrows) •Colonial? Sessile? Segmented? Sexually reproducing? the life forms of Ediacaran remain mysterious because they disappear from fossil record near base of cambrian

the geological time scale what is phanerozoic era what deos Mya and Gya stand for

•Phanerozoic: The geological eon we are in now, which spans the beginning of the Cambrian (~540 Mya) to the present -multicellularity fairly present -when we see animals •Mya or Ma: An abbreviation for "million years ago" •Gya or Ga: An abbreviation for "billion years ago"

The larva of a tunicate looks almost the same as the larva of a vertebrate! what are the characteristics

•Pharyngeal gill slits •Dorsal nerve cord •Notochord—a mesoderm-derived rod-shaped structure for support

what are the units of selection and evolution

•Selection acts on an individual -decides how many individual will stick around from one population to the next --Did the individual/s survive to reproductive maturity? --Did the individual attract mates and reproduce successfully? --How many offspring (alleles) did that individual leave behind? •...BUT the unit of evolution is the population --Population: A group of organisms connected by gene flow (typically, mating and reproduction) --Evolution means changes in the population's composition (i.e., distribution of alleles) over generations

describe genetic code -how many genetic codes are there

•This table shows the standard genetic code (for the vertebrate nuclear genome) --this code is not used by mitochondira, they use a code that is similar to bacteria •By 2009, about 15 genetic codes were known •Today, NCBI has recorded 33 different genetic codes! Most of the diversity is in bacterial codes

describe the components for the graph for 𝛘2 what is the null hypothesis

𝛘2 distribution with 2 degrees of freedom (to the left) x-axis: values of the 𝛘2 statistic p value: the area under the curve to the right of my 𝛘2 value *graph is actually opposite of the one here* -as 𝛘2 increases, the p value decreases, so we reject null null: what is the probability of getting distribution as extreme or more extreme given that the population is under hardy weinberg equilibrium

what is 𝛘2, and how do we find degrees of freedom k what is k for our problems

𝛘2 is a statistic whose distribution is determined by the number of degrees of freedom k For our purposes, k is equal to the number of categories n minus 1 -k is # of free parameters in analysis --3 categories: p2, 2pq, q2 --k= (3 - 1) = 2 --one of the categories is baseline, only need to know for 2 categories