Evolution

Transitional Forms

* Creatoceous Amber fossils represent a transition between ants and wasps * 100 mya

Transcription factors and Binding Sites

* DNA Sequence resulting in light wings and dark abdomen * A new binding site produces dark wings * A lost binding site leads to loss of black coloration in abdomen

Ecological Niche Modeling

* Data from current distributions(Georeferenced locations) * Climatic Data * Geological Data (Elevation) * Predicts Fundamental Niche

Developmental regulatory genes that are expressed in distantly related taxa in similar areas of embryo, but which result in different structures are an example of:

* Deep Homology

Cladogram or Phylogram

* Depicts same information about relationships, but phylogram also gives information about rate of evolution. * Long branches indicate more change, short branches less change * When lots of taxa in a clade have short branches, diversification occurred relatively fast compared to other groups

Haeckel

* Development stages recapitulate evolutionary stage * Expanded on Meckel * "Ontogeny is a precise and compressed recapitulation of phylogeny" (here recapitulate means replay) * New species got new stuff at end of development

Meckel

* Developmental stages mirror the scala naturae; * All developmental stages step through scala naturae before adulthood * Built on Greek philosopher ideas: simple to complex * Ontogeny stepped through simple traits until reached complex traits

Index Fossils

* Diagnostic fossils that can be found anywhere in the world - The assemblage of fossils in any given strata is a good indicator of the age of rocks

Possible biogeographic history

* Dispersal via migratory birds (tarweeds have sticky seeds) (=phoresy) * Molecular dating place the first immigration at about 5 million years on Kauai.

Populations are not the only things that evolve

* Diversification of languages

What is a paralog?

* Duplicate of an existing gene

HOX genes and Evolution

* Evolutionary Diversification of arthropods controlled by changes in HOX gene expression * HOX genes are conserved across Metazoa - Colinearity - Expression in embryo

Vicariance results in sympatric speciation.

* False

What is a fossil?

* Fossil: Any evidence of ancient life * Over 10,000 years old

Hoxgenes -Body plan

* Gene products from combinations of Hoxgenes -Act as signals that create a map of where structures will develop -Signals occur locally and indirectly specify what structures other genes should form in localized regions * Conserved 180-bp sequence found in Hoxgenes -homeobox

Homolog

* Genes sharing a common ancestor and generally retain same function

Chromosomal Changes and Hominin evolution

* Genes that are substantially different are associated : Smell, Hearing, bone growth and protien metabolism

Master Switch Genes

* Genes that control where, when, and how other genes are expressed -Make proteins that signal, activate, mark, or otherwise communicate with other genes and their products -Often sequentially expressed in a set pattern -Also called "homeotic" (HOX) or developmental regulatory genes * Changes in their pattern of expression or regulation dramatically changes morphology

Wind Dispersal

* Have you ever blown on a dandelion head and watched the seeds float away? This is wind dispersal. Seeds from plants like dandelions, swan plants and cottonwood trees are light and have feathery bristles and can be carried long distances by the wind. Some plants, like kauri and maple trees, have 'winged' seeds. They don't float away but flutter to the ground. With wind dispersal, the seeds are simply blown about and land in all kinds of places. To help their chances that at least some of the seeds land in a place suitable for growth, these plants have to produce lots of seeds.

Physical characteristics: Geology

* Hawaiian soils are formed from lava flows—no soil prior to island creation (naturally!) * Rich in mineral content * Soil age predicts fertility

Heterochrony

* Heterochrony: changes in the timing of developmental traits •Changes that affect the timing of the appearance of nonreproductivetraits= somatic traits •Changes that affect the timing of the onset of reproductive traits Vocabulary: •Paedomorphosis, peramorphosis•Acceleration, progenesis, neoteny, hypermorphosis

Development ...

* Homeotic Genes (i.e HOX) - Transcription Factors -- Function as master switch genes -- Encode proteins that activate or repress gene expression * Regulatory Enhancer Sequences - DNA region that can bind control elements -- Upstream from coding region of gene

MADS-BOX Genes

* Homeotic genes that affect flower development * MADS-BOX genes are transcription factors

Paralogs

* Homologs in same species related via duplication * Paralogs are genes evolving in parallel within species after duplication

Oceanic islands that have never been connected to a land mass can only have acquired their biotas by "jump"dispersal.

* If dispersal is the paradigm of island biogeography, then we would expect random models of speciation (e.g. founder effect, etc.)

Case study: Evolution of Feathers

* Integument as an example of nested-ness of homology * Feathers are modified scales * Keratin covering divided in increasingly precise way * Downy, divided proto-feathers provide insulation -Subsequent modification leads to feathers capable of flight? * Phylogenetic trees are invaluable in understanding this transformation from scale to feather

Evolutionary Implications of changes in development

* Major morphological changes can be inherited "in bulk" through activation or alteration of pathway * Similarity b/w juveniles and adults of closely related species can be explained simply * Modularity and differentiation relatively easy to manipulate and evolve

Mass Extinction

* Mass Extinction - the sudden disappearance of a large number of species (75%) in a short period of time. * Raup (1991) calculated the percentage of taxa that went extinct in each of the 1-myr intervals since the cambrian explosion. * Average length of a species in the geological record is ~4 my.

For phylogenetic analyses, the most informative groups for determining close relationships are:

* Monophyletic

Homo genus still under debate How?

* Selection and Adaption - Postcranial Skull- Bipedalism - Size of body and cranium * Genes - 1500 genes under positive selection in H. Sapiens compared P. troglodytes * Sperm proteins, ion and nervous impulse transport, Sound perception, speech * Behavior - Toolmaking - Languange

Is H. floresiensis simply a small H. sapiens or a separate species?

* Seperate species

Sympleisiomorphy

* Shared, ancestral characters that are homologous

Fossils are used for Relative Dating

* Superposition : Older rocks are below and younger rocks are above * Isotopes are used for absolute dating - The ratio between the parent isotope and the daughter product

Big Five

* Terminal-Ordovician (~444 Mya) - global cooling/planetary instability - 2nd largest extinction; 1/3 of mainly aquatic living species * Late Devonian (~360 Mya) - global cooling - loss of mainly aquatic life (70%) due to ↑ atmospheric CO2 * Permian (251 Mya) - volcanic eruptions and global warming - 83% of genera went extinct * Triassic (200 Mya) - planetary instability - 48% of genera went extinct * Cretaceous-Paleogene (K-T) (65 Mya) - 50% of genera went extinct

How are humans different?

* Tool use? * Bipedal * Brain Size - language and culture * Body Proportions

3 modes of Horizantal Gene Transfer

--Mechanism for incorporating DNA from other organisms A. Transduction via phage infection B. Transformation - incorporating environmental DNA C. Conjugation - Contact with another cell (May confer advantages)

Tree of Life

• Archaea - Chemosynthesis - Extremophiles -- Anoxic conditions • Bacteria - Photosynthesis - Development of oxygenated atmosphere

History of Development and Evolution

* "Law of Parallelism" -Life was viewed as a continuous chain of increasing complexity (scala naturae or "Great Chain of Being"). -Ontogeny paralleled this chain •Ontogeny = development of an individual over its lifetime -Simple traits during early development -More complex traits develop later •J. F. Meckel(1781-1833) & Etienne Serres(1786-1868) * Karl von Baer 1828

Cosmopolitan

* (not necessarily entirely cosmopolitan): e.g., Drosophila melanogaster, Caenorhabditis elegans, common rock pigeon

A symplesiomorphyfor the minimal monophyletic clade including B, C & E would be:

* 1 or 2

Permian Extinction

* 250 Mya * Massive loss of Biodiversity (Primary Producers, ancestral verts and arthropods, amphibians, echinoderms and land plants) * Atmospheric Ash (vulcanization) killed photosynthesis, O2 levels decreased, acid rains and ocean acidification (loose reefs) * >10 my before repopulation of planet - cartiliganous fishes to bony fishes

Australopithecines Africanus

* 3.3 - 2.5 mya * Braincase rounded, relatively larger * Palate more parabolic than u-shaped * Toe and Hand morphology arboreality *

Kenyanthropus

* 3.5 - 3.3 mya * Flat face and small teeth

Australopithecines afarensis

* 4-3 mya - relatively good fossil record, like lucy * Prognathous face, U shaped palate * Brain - 430 cc, definitively bipedal

Extinction is an ongoing process...

* 50% of the wildlife on the planet has disappeared since 1970 * 875 extinctions have been documented since 1500 AD - but hard to study (most species are undescribed, so most extinctions likely to be undocumented) * We suspect, for example, that many large mammals were hunted to extinction by humans in recent past - examples include mammoths, mastodons

H. Neanderthalensis

* 500-24 kya -N. Africa, middle east and europe * Broader, shorter, more robust body * Larger nasal cavity, more brow ridges * Capable of speech * DNA .3% different than ours

Dispersal Barriers

* A dispersal barrier may mean that the dispersal range of a species is much smaller than the species distribution. An artificial example is habitat fragmentation due to human land use. Natural barriers to dispersal that limit species distribution include mountain ranges and rivers. An example is the separation of the ranges of the two species of chimpanzee by the Congo River. * On the other hand, human activities may also expand the dispersal range of a species by providing new dispersal methods (e.g., ships). Many of them become invasive, like rats and stinkbugs, but some species also have a slightly positive effect to human settlers like honeybees and earthworms.[20]

Synpamorphy

* A synapomorphy is a common property shown by two or more groups of organisms, that can be traced back to the most recent ancestor that both the groups evolved from. However, this character may not be shown by other closely-related groups, because some of them may have evolved further, or lost the character altogether. * Synapomorphic traits are those which have appeared only in the last common ancestor for the first time, and not in more primitive organisms. This helps researchers find out which ancestral organism first evolved a particular character, that is now seen in different species or populations. It helps them establish evolutionary relationships between different groups of organisms, like birds, reptiles, and mammals, that show similar properties. * Synapomorphies play an important role in the system of 'cladistics', which groups organisms into different categories, or 'clades', depending on their common ancestors. Only synapomorphic traits can be used to link various groups together, because if a property shared by different organisms is not ancient, it means that they share a recent, common ancestor who developed it.

The Hawaiian silversword alliance is an intriguing example of adaptive radiation.

* Adaptive radiation is the development of many species derived from a single ancestral population. The Hawaiian silversword `ohana (family) is probably the foremost example of adaptive radiation among plants in the world. Over the course of millions of years, the descendants of the pioneer plant evolved into 28 distinct species in three genera, occupying many different habitats. *Scientists believe that the entire silversword family probably descended from a member of the sunflower family, similar to Muir's Tarweed, from California. The barbed fruit of this tarweed may have been carried to Hawai`i on the feathers of a bird. Since this tarweed came from an alpine shrubland, it most likely became established in Hawai`i in a similar kind of habitat. * Since so few organisms successfully colonized Hawai`i, many diverse habitats were available. Over time, descendants of the tarweed slowly adapted to many of these habitats. Beneficial mutations enabled the plant forms to change and become quite different from the ancestor. The end result was extensive and spectacular adaptive radiation. * Today, plants of the silversword family occupy every terrestrial habitat in Hawai`i--from wet forests to dry forests and from near sea level to alpine shrublands. Although these plants are still closely related (all species are able to hybridize, they often look extremely different from one another. * The silversword family tree is divided into three genera: Argyroxiphium (5 species), Wilkesia (2 species), and Dubautia (21 species). Dubautia species are the most diverse. All members of the silversword family are endemic to Hawai`i; 82% are to a single island. Approximately one half of these single island endemic species are further limited in distribution, often growing only in one area or microclimate. It is a very special `ohana! * The size and the form of a plant are adaptations to the habitat in which it grows. For example, large trees, shrubs and vines occur in wet areas; small shrubs, mats rosettes tend to occur in drier areas. Rainfall, sunlight, temperature, and elevation all affect the size and form of a plant. Plants growing in bogs are unable to use the stagnant, acidic water, so their roots are shallow. These plants display similar adaptations to plants growing in very dry areas

Consequences of Mass Extinctions

* Adaptive radiations: -Bony fishes (post permian) - Mammals (post KT)

Peramorphisis (More Development)

* Adults of the species achieve new morphologies thru extension of development (recapitulation) * Acceleration = Faster rate over same interval * Hypermorphosis = Same rate over longer interval

Developmental Regulatory Genes

* Affect specific regions in developing embryo by specifying where morphological structures will grow * Encode proteins that control the switching on and off of a cascade of other genes -In a set pattern -- Affects cell size, shape, division, positioning within body plan

Molecular Differences between Homo & Pan

* Alternative splicing of existing genes(6-8%) * Recombination hotspots in different places -TAP2 (associated w/ diabetes, schiophironeza, celiac) * Humans have n=23 chromosomes; apes: n=24 * Chromosome 2 in in humans resulted from fusion of 2 chromosomes

Adaptive Radiation

* An adaptive radiation generally means an event in which a lineage rapidly diversifies, with the newly formed lineages evolving different adaptations. Different factors may trigger adaptive radiations, but each is a response to an opportunity. * The evolution of a key adaptation - A key adaptation usually means an adaptation that allows the organism to evolve to exploit a new niche or resource. A key adaptation may open up many new niches to an organism and provide the opportunity for an adaptive radiation. For example, beetle radiations may have been triggered by adaptations for feeding on flowering plants. * Release from competition/vacated niches - Lineages that invade islands may give rise to adaptive radiations because the invaders are free from competition with other species. On the mainland, other species may fill all the possible ecological niches, making it impossible for a lineage to split into new forms and diversify. On an island, however, these niches may be empty. Extinctions can also empty ecological niches and make an adaptive radiation possible. For example, open niches vacated by dinosaur extinctions may have allowed mammals to radiate into these positions in the terrestrial food web. * Specialization - Specialization may subdivide a single niche into many new niches. For example, cichlid fishes have diversified in East African lakes into more than 600 species. This diversification may have been possible because different fish li

Convergent characters are also?

* Analogous

Hominini: Homo and Pan and their relatives

* Anatomy : shape of pelvis and fusion of tarsals

The idea that life evolves from simple to complex began with

* Ancient Greeks

Marsupial Species

* Australia has many more marsupial species than South America. In Australia, marsupials inhabit all known niches. Is this an adaptive radiation or evidence of an old lineage that has sent sparse colonists across Gondwana?

Background Extinction

* Background Extinction - the sum total of the local extinction of lineages over time. * Van Valen (1973) provides evidence that the likelihood of species extinction is independent of the age of the taxon. * Jablonski (1986) the likelihood of species extinction is inversely proportional to the size of the species range.

KT Boundary

* Bad luck - rather than bad genes? • KT boundary is unique because the correlations between small geographic ranges and extinction rate breaks down - species with large ranges go extinct as often as the ones with small ranges. • What are some possible causes for mass extinctions? climate changes, particularly cooling, drying sea level changes predation, epidemic disease competition with other species exotic, external causes • Are species and ecosystems fragile?

The likelihood of finding a fossil (in terms of fossil formation)?

* Barnacle > Tree Trunk

How to avoid Mass Extinction ?

* Be Broadly geographically distributed * Be an omnivore * Unknown traits

Biogeography In Depth

* Biogeography — the study of how species are scattered across the planet, and how they got that way. * Wallace had already accepted evolution when he began his travels in 1848 through the Amazon and Southeast Asia. On his journeys, he sought to demonstrate that evolution did indeed take place, by showing how geography affected the ranges of species. He studied hundreds of thousands of animals and plants, carefully noting exactly where he had found them. The patterns he found were compelling evidence for evolution. He was struck, for example, by how rivers and mountain ranges marked the boundaries of many species' ranges. The conventional explanation that species had been created with adaptations to their particular climate made no sense since he could find similar climatic regions with very different animals in them. * Wallace came to much the same conclusion that Darwin published in the Origin of Species: biogeography was simply a record of inheritance. As species colonized new habitats and their old ranges were divided by mountain ranges or other barriers, they took on the distributions they have today * Wallace pushed the study of biogeography to grander scales than Darwin. As he traveled through Indonesia, for example, he was struck by the sharp distinction between the northwestern part of the archipelago and the southeastern, despite their similar climate and terrain. Sumatra and Java were ecologically more like the Asian mainland, while New Guinea was more like Australia. He traced a remarkably clear boundary that snaked among the islands, which later became known as "Wallace's Line." He later recognized six great biogeographical regions on Earth, and Wallace's Line divided the Oriental and the Australian regions.

Types of Fossils

* Body Fossils - Direct or Altered remains of an organism - includes biomarkers ("chemical fossils") * Trace Fossils - Evidence of the activity of organisms - Tracks, trails, burrows, borings and bite marks. * Perimineralized Fossils * Compression Fossils * Casts and Molds

Heterochrony

* Changes in the relative timing of developmental (reproductive and non-reproductive) events leads to new adult morphologies -Changes in timing of events, or in their rate * Ex. = Jaws of Hyracotherium and Equus

Specific ways in which development can be implicated in evolution

* Changes in the timing of developmental events - heterochrony * Changes in the pattern of expression of regulatory genes in development - "Evo-Devo"

Cladogram + Phylogram + Chronogram

* Cladogram : Shows Branching order of nodes * Phylogram : Shows the branching order of nodes AND distances * Chronogram : Shows evolutionary time through branch lengths

HOX Genes

* Clustered along chromosomes * Pattern of expression along the anterior-posterior axis is colinear with their location on the chromosome * Play an important role in setting up body plans * Colinearity -Relative position on chromosome is correlated with position of body part regulated by gene --Genes regulating structures for mouthparts on one end of chromosome --Genes regulating thorax, in middle --Genes regulating abdominal structures on other end of chromosome

What's all that extra DNA doing?

* Coding vs Non-Coding DNA region

MODERN EVO-DEVO

* Control of gene expression is regulated by numerous gene families (homeotic genes[= transcription factors] and regulatory enhancer sequences): -Animal body-plans HOXgenes -Eyes -PAX -Animal limbs -WNT, HOX, Dll -Flower Evolution -MADS-box genes -Galapagos beak size -BMP4 -Treehopper helmets -several * This MECHANISM explains the evolution of complex yet common features

Sahelanthropus

* Cranium, teeth, lower jaw - 6-7 mya, Chad * No postcranial skeleton * Cranial Capacity 350 cc - human = 1350 cc - chimpanzee = 350 cc * Small canines, brow ridges hominin-like

G-Value Paradox

* Despite large differences in organismal complexity, multicellular eukaryotes tend to have similar #'s of protein-coding genes G-value paradox - why? • # protein-coding genes a poor indicator of complexity • Organisms differ greatly in gene regulatory networks, despite having similarities in protein-coding genes • Transcription factors (TFs) - Back to Evo-Devo! - Nematode (500), Drosophila (700), humans (2000) • Interactions among TFs increase regulatory complexity • Noncoding regions may also affect gene expression regulation • Protein-coding genes may have more than one function - Alternative splicing of multi-exon gene

Galapagos Finches - BM4

* Different patterns for expression of BM4 (Bone Morphgentic protein 4) * Up-regulated = large, deep beak (more and earlier) * Forced Expression in developing embryo of chicken = similar shape to G. magnirostris (Large, deep beak)

Jump Dispersal

* Dispersal: Movement beyond distribution limits * Jump Dispersal: long distances over inhospitable habitat - example: oceanic islands - mostly by volant organisms (flight) ex.: Galapagos Islands - rare, large (distance), and "surprising" events - explains large discontinuous distributions of some organisms - explains taxonomic similarity of distant biotas and populations

Gene Duplication

* Duplicate genes may influence gene expression levels - increase production * Paralogs may diverge by dividing work of original gene - subfunctionalization * Duplicated genes may diverge, evolve new (related) functions -neofunctionalization

Von Baer's interpretation of similarity

* Early embryos of all vertebrates look alike * Differentiation during development leads to different morphologies -Stage 1 embryos most similar - Stage 4 embryos least similar * Similarity of certain forms for longer periods of developmental time is expected, because they have a longer shared phylogenetic history

The Hawaiian biota has been shaped by long-distance dispersal (migration) and adaptive radiation

* Ecological niches are formed from microclimate, soils, and elevation * 1,100 native plant species are descended from 300 founder species. •7,000 native insect species are descended from only 350-400 founder species.Ecological niches are formed from microclimate, soils, and elevationHoneycreeper

History of Paleonto

* Edward Cope, O.C. Marsh, and the "bone wars" 1877- 1892 "Great Dinosaur Rush" * Mantell * Roy Chapman Andrews * Samotherium - giant relative of a modern giraffe

Species have definite geographic distributions

* Endemic = taxa are restricted to a particular area - Nearly all species have restricted geographic distributions * Cosmopolitan = taxa that are found on all the continents on the globe except antarctica

Eukaryote genomes

* Endosymbiotic origin of organelles * Eukaryotes have either two or three genomes * Non-photosynthetic eukaryotes: mtDNA + nDNA * Photosynthetic eukaryotes: cpDNA + mtDNA + nD * Multiple endosymbiotic events complicates the evolutionary patterns for plastid genomes • Non-photosynthetic eukaryotes: - Nuclear genome + mitochondrial genome • Photosynthetic eukaryotes: - Nuclear genome + mitochondrial genome + plastid genome

History of Development & Evolution

* Ernst Haekel (1866) * Ontogeny recapitulates phylogeny (=Biogenetics law) * Ontogeny = development of an individual over its lifetime - simple traits during early development - More complex traits develop later

A phylogenetic analysis is useful for the following type of study:

* Ethological Isolation and Sexual Selection

Development

* Every multicellular organism develops from a single cell * Except for sperm and eggs, every cell in the body of a multicellular organism contains the same genes (i.e. totipotency) * But, different tissues look and function differently

Ecological Niche

* Every species has a role that it plays in nature. That role is defined by a combination of the organism's behaviors, habitat, and interaction with other species. For example, a garden creature is a predator that hunts for prey among plants, while an oak tree grows to dominate a forest canopy, turning sunlight into food. The role that a species plays is called its ecological niche. * A niche includes more than what an organism eats or where it lives. Environmental factors, such as climate, soil chemistry, and elevation, also play a role in defining a niche

Homologous

* Evolutionary theory predicts that related organisms will share similarities that are derived from common ancestors. Similar characteristics due to relatedness are known as homologies. Homologies can be revealed by comparing the anatomies of different living things, looking at cellular similarities and differences, studying embryological development, and studying vestigial structures within individual organisms.

If a character trait is polyphyletic, it has likely:

* Evolved more than once

Because lungfish have a C-value 100 X that of humans, they must have more genes than do humans.

* False

Case Studies: Evolution of Traits

* Flowers * Galapagos Finches Beaks

Mass Extinction

* Fossil record shows that rates of extinction vary over time; when they spike it's referred to as a mass extinction. * 40 to 50% of all species in many major taxa, over a broad geographic range * Mass Extinctions associated w/ major upheavals in Biosphere (glaciation, vuclanism, asteriod impacts, gamma ray bursts)

Fundamental vs Realized Niche

* Fundamental niche is the entire set of conditions under which an animal (population, species) can survive and reproduce itself. * Realized niche is the set of conditions actually used by given animal (pop, species), after interactions with other species (predation and especially competition) have been taken into account.

Realized Niche

* Generally, however, there are competitors for the same lifestyle. Rabbits compete with groundhogs for food. Grasses compete with shrubs for soil, and bacteria compete with mold for nutrients among the leaf litter. The niche that a species actually inhabits, taking into account interspecific competition, is its realized niche

Orthrolog

* Genes (Homologs) in different species derived from a single ancestral gene in the LCA (arise from speciation) * Orthrologs are genes diverging due to species lineages seperating.

Genetic Toolkit

* Genes and proteins and developmental pathways that encode morphological development * Tinkering with the toolkit results in new morphologies

What happened to the Neanderthals?

* Genetic Interchange? - mtDNA= does not support this - However, many nuclear loci found in humans of European and Asian Origin

Southern land mass after the Permian was:

* Gondwana

Ontogeny recapitulates phylogeny

* Haekel argued that developmental stages reflected evolutionary history of lineage

How to increase your likelihood of going extinct?

* Have a narrow geographical range or small population size, so random ecological factors become more powerful - Small populations are more vulnerable to go extinct: 1. Demographic Stochastity 2. Genetic Detrioation, Reduced Heterozygosity 3. social, behavioral deterioration 4. Extrinsic Forces - Fossilization Potential is low * Have high trophic position or rely on specialized diet * Low genetic Diversity - Drift has high impact - Resilience to environmental change, disease may be low

The K-T Crater

* Hildebrand et. al 1991 * Sinkhole crater centered around the Yutacan pennisula (Chicxulub) * Crater was identified by detection of gravitional anomalies and presence of shocked quartz and minerals common in space

Oceans pose a formidable barrier to dispersal!

* How do organisms overcome this barrier? 1) Phoresy: stick to another organism and hitchhike. 2) Wind dispersal: grow wings or become tiny. 3) Protective coverings: surround propagules in a jacket to protect it from the elements

Transposons can disrupt gene order & chromosome structure via recombinational hotspots

* Human chromosome and gene location on mice chromosomes * Some chromosomes are more conserved than others (e.g., X chromosome)

Ex. of Synapomorphy

* Humans and cats, despite being from different groups (primates and carnivores respectively), show similarity in their forearm bone structure. Though they evolved by different paths, these common traits were passed down to both groups by the last common ancestor that they shared. Similarly, the bones in bat wings have a similar arrangement to human arm bones, with the bones at the top being very similar to those of our hands. * The category of 'land plants' includes different groups, like the Coleochaete (a type of algae), liverworts (flowerless plants), conifers, and angiosperms (flowering plants). Despite this, only liverworts, conifers, and angiosperms show a multicellular sporophyte (spore-producing stage), while the Coleochaete does not. This is a synapomorphy passed down to them by the last ancestor that they shared. * The genus Homo includes all great apes, such as Homo erectus (upright man), Homo neanderthalensis (neanderthals), and Homo sapiens (modern man). Despite the differences between them, they all shared the similar property of having large brain-cases, indicating their higher intelligence. This is because, their most recent and common ancestor―Australopithecus―evolved this trait for the first time, and passed it down to them. Of these species, we are the only ones still surviving today. * The superclass Tetrapoda includes all four-footed animals, such as reptiles (like lizards and crocodiles), amphibians (like salamanders and frogs), birds, and mammals. Despite their enormous diversity, all these animals show four limbs and an amniotic egg (embryo development inside an egg), which indicates that they evolved from a common ancestor. Interestingly, some synapomorphies are seen only in mammals, such as hair and mammary glands, and are absent in other tetrapods.

Changes in rate--How quickly does development occur within the specified time period?

* If the rate is slower, the descendant adults resemble ancestral juveniles (paedomorphosis) * If the rate is faster, then the descendants can attain larger size or new structures (peramorphosis)

Number of HOX gene clusters and chordate phylogeny

* Increase in # from gene duplication * Paralogs = duplicated genes; can evolve new functions & new developmental pathways

DNA sequence alignment

* Infer a change in base (A to G or G to A) * Infer an insertion (or deletion) Alignments do matter - Assessment of homology

KT Boundary Impact

* Initial Impact of a 10 km asteriod or comet Object strikes surface at full speed, no slowing by atmosphere Explosion = 100 million megatons of TNT 100km3 of Earth rock and meteor thrown 100km into the atmosphere Fireball and blast ignites everything for 1000s km across Molten debris causes massive wildfires, 90% of all plant life burns earthquakes cause massive Tsunamis ... devastate coastlines

K-T Boundary

* Iridium - Worldwide - Higher in North America - Impact or Vulcanism (Deccan Plateau) * Shocked Quartz * Soot- lots of it * Alvarez theory given huge boost by discovery of the Chicxulub impact crater, which dates to 65 mya * 300 km diameter, caused by asteroid 10 km in diameter, which was 2 million times more powerful than largest nuclear bomb

Which of the following is NOT a tenet of island biogeography?

* Islands with mountains have fewer species than those that are mostly flat

Which mass extinction led to the disappearance of the dinosaurs?

* KT Boundary

Homo Advances

* Major Homo Advances: - Brain Size - Better Bipedalism - Hunting - Fire (H. Erectus) - Tools - Built Shelters - Clothing - Language

Mass Extinction

* Mass Extinction - the sudden disappearance of a large number of species (75%) in a short period of time. • Sepkoski & Raup (1984) claim that there is a periodicity to large extinctions ~26 my • Most famous is the Cretaceous-Tertiary (KT) • All marine reptiles, dinosaurs went extinct. • Many mammals, birds, terrestrial reptiles • Dramatic shift in vegetation (angiosperms pollen decreased; fern spores went up, plankton levels collapse). • Duration is a vital bit of information • How long did the extinction events last? Years or millions of years? • Do mass extinctions differ from background rates? Perhaps not - extinctions appear clumped at roughly 26 my intervals. • Kill curve - shows average length of time between extinction events of some magnitude. * Mass Extinctions are rare * Largest extinction on record is the End Permian Event(245 mya) * Most recent mass extinction was end-Pleistocene but it was mostly mammals (75%) - Maybe due to early hunting

MacArthur and Wilson's (1963) Equilibrium model of island biogeography

* Model predicts relationship of species richness dependent on island size and distance to nearest land mass: ŜLN> ŜLF~ ŜSN> ŜSF where L= large, S= small, N= near, F= far * Model also predicts this relationship among turnover rates: ŤSN> ŤSF~ ŤLN> ŤLF

Extinction

* Most species are extinct (>99.9%) * Species are a group of individual organisms that share a common pool of genetic material. * Thousands of species extinctions, no good evidence as to why the vast majority of these extinctions happened. * Circular to say that species are unfit because they went extinct - so why did they?

Neotony and Progenesis

* Neoteny (/niːˈɒtɪni/ /niːˈɒtni/[1][2][3] or /niːˈɒtəni/,[4] (also called juvenilization)[5] is the delaying or slowing of the physiological (or somatic) development of an organism, typically an animal. Neoteny is found in modern humans.[6] In progenesis (also called paedogenesis), sexual development is accelerated.[7] * Both neoteny and progenesis result in paedomorphism (or paedomorphosis), a type of heterochrony.[8] Some authors define paedomorphism as the retention of larval traits, as seen in salamanders.[9][10][11] * Both neoteny and progenesis cause the retention in adults of traits previously seen only in the young. Such retention is important in evolutionary biology, domestication, and evolutionary developmental biology. * Progenesis is the speeding up of the germ line. The result is paedomorphosis - reproduction happens in what was ancestrally a juvenile morphologic stage * Neoteny is the slowing down of somatic development. The result is that reproduction happens in what was ancestrally a juvenile morphologic stage. * Humans have also been argued to be neotenous. As adults, we are morphologically similar to the juvenile forms of great apes. This paedomorphosis, if it is real (and there is a serious argument that it is not), would be neotenous rather than progenetic because our age of breeding has not shifted earlier relative to other apes; our age of first breeding is actually later than other apes. Our somatic development therefore has not simply slowed down while reproductive development has stayed the same: what happened was that our somatic development slowed down even more than our reproductive development.

The situation in which an organism undergoes a slower developmental rate over the same duration relative to an ancestor's lifetime is called:

* Neotony - Neotony = slower rate, same duration - Progenesis = shorter interval, same rate

Paedomorphosis-less development (rate)

* Neotony-The onset of somatic traits is late in development -Humans stop developing at this stage - Chimps continue to this stage

Von Baer

* No Recapitulation: Embryos development increasingly diverse * Traits in early developmental extremely resistant to evolutionary change * Only later in development do traits emerge that distinguish species

Which of the following areas was not part of Gondwanaland?

* Norway

HOX genes in Cnidirians ?

* One of the most ancient animal groups * No segments, limbs or organs * Phylogenetic analyses of whole genome reveal the presence of HOX genes - Involved in body plan

Climate influences geographic distributions

* Organisms will often migrate in response to climate change * Pleistocene refugia - European mammals retreated to southern extremes of the continent - isolating populations and accelerating genetic differentiation

Orthology

* Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Normally, orthologs retain the same function in the course of evolution. Identification of orthologs is critical for reliable prediction of gene function in newly sequenced genomes. * Orthologs are homologous genes that are the result of a speciation event. * Orthologous genes are homologous genes that diverged after evolution gives rise to different species, an event known as speciation. The genes generally maintain a similar function to that of the ancestral gene that they evolved from. In this type of homologous gene, the ancestral gene and its function is maintained through a speciation event, though variations may arise within the gene after the point in which the species diverged.

The development sequence on left is for the chimpanzee, the one on the right is for humans. For humans, this is a case of:A.Peramorphosis& hypermorphosisB.Paedomorphosis& neotenyC.Peramorphosis& accelerationD.Paedomorphosis& progenesis

* Paedomorphis & Neotony

Parology

* Paralogs are genes related by duplication within a genome. Orthologs retain the same function in the course of evolution, whereas paralogs evolve new functions, even if these are related to the original one * Paralogs are homologous genes that are the result of a duplication event. * Paralogous genes are homologous genes that have diverged within one species. Unlike orthologous genes, a paralogous gene is a new gene that holds a new function. These genes arise during gene duplication where one copy of the gene receives a mutation that gives rise to a new gene with a new function, though the function is often related to the role of the ancestral gene.

When reconstructing phylogeny from multilocus genes, one has to be particularly aware of:

* Paralogy

Punctuated Equilibrium

* Pattern of change in the fossil record - Long periods of little or no change (stasis) followed by rapid change Stasis is punctuated by rapid change * A hypothesis about the evolutionary process - Evolutionary change accompanied speciation which occurred "off stage" in small (allopatric) populations (i.e., subpopulations of a species).

Phoresy

* Phoresy is the act of 'hitching a lift' on another organism. As invertebrates are small and not all have wings many travel comparatively long distances by using other, more mobile, organisms. * For example, flower mites are wingless and so use foraging bees to travel to new flowers. When bees enter a flower to collect nectar or pollen the mites climb on to the bee. The bee then flies to the next flower and the mites climb off the bee. * Another good example is that of pseudoscorpions are small arachnids that resemble scorpions without the long tail and sting. When a flying insect lands nearby the pseudoscorpions grab hold of the larger insect using their pincers. When the insect flies to a new location they carry the pseudoscorpion with them.

The evolutionary history of a group is usually dictated by multiple episodes of vicariance and dispersal

* Phylogenetic suseful to help decipher patterns of evolution related to biogeography

Polyphyly

* Polyphyly: characterized by a convergent feature (e.g., homeothermy) * Pachyderms are polyphyletic. * Share a convergent character(hide lacks fur)

Paedomorphosis -less development (timing)

* Progenesis -Reproductive traits appear early in development

Charts of Neotony(Rate) and Progenesis(Timing)

* Progenesis = shorter interval, same rate as normal morphology * Neotony = slower rate than normal morphology, same duration

Vicariance vs Dispersal

* Scientists have long been fascinated by the existence of disjunct (geographically discontinuous) distribution patterns such as the one shown in Fig. 1a, in which the members of a group of organisms are distributed across the southern continents, now separated by thousands of miles of ocean. How did this type of widely scattered distribution originate? Traditionally, two alternative explanations have been proposed: dispersal across a preexisting geographical barrier (for example, a mountain chain); or vicariance, the fragmentation of a widespread ancestral distribution by the appearance of a new barrier. Both biogeographical processes result in the isolation of a population by a geographic barrier, followed by differentiation of a new taxon by allopatric (geographically separated) speciation. However, the barrier in the dispersal explanation is older than the geographic disjunction, whereas the appearance of the geographic barrier is responsible for the geographic disjunction in the vicariance explanation, so it cannot be older than the resulting speciation event. Although vicariance and dispersal are not mutually exclusive processes—the opening of the Gibraltar Strait between North Africa and Iberia in the Pliocene was simultaneously a vicariance event for terrestrial organisms and a dispersal event for marine organisms—the history of biogeography as an evolutionary science could be considered until recently as the history of a debate between dispersal and vicariance explanations.

Wind Dispersal (Seed Dispersal)

* Seed dispersal is the movement or transport of seeds away from the parent plant. Plants have very limited mobility and consequently rely upon a variety of dispersal vectors to transport their propagules, including both abiotic and biotic vectors. Seeds can be dispersed away from the parent plant individually or collectively, as well as dispersed in both space and time. The patterns of seed dispersal are determined in large part by the dispersal mechanism and this has important implications for the demographic and genetic structure of plant populations, as well as migration patterns and species interactions. There are five main modes of seed dispersal: gravity, wind, ballistic, water, and by animals. Some plants are serotinous and only disperse their seeds in response to an environmental stimulus.

Synamorphy

* Shared, derived characters that are homologous

Chloroplast DNA phylogeny of the silversword alliance

* Silversword ancestor diverges from other asters * California Tarweeds

Is limblessness convergent within squamates?

* Similar physical and mechanical constraints in amphisbaenians, snakes, dibamids, and anguiidsled to a similar evolutionary solution (limb loss) * Expect SIMILAR environmental/physical factors to be implicated * Limblessness is common in squamates (incluing snakes, amphisbaenians, dibamids, and members of each major lizard group), and is thought to have evolved as many as five times independently. * Limb lost independently several times (not homologous)

Galapagos

* Single species of finch from South America * Adaptive radiation for finches and many other species

Fundamental Niche

* Sometimes other species will compete for the same niche. Lions on the African savanna compete with hyenas for food. Daisies and dandelions in a field compete for sunlight and soil. Competition from other species for the same niche is called interspecific competition. * In order to better understand an organism, ecologists try to determine what sort of niche it would have in the absence of such competition. They might ask, 'How would a lion behave if there were no other predators competing for a zebra's flesh?' or 'What would a stand of water lilies look like if there was no duckweed living in the same area of the pond?' A fundamental niche is the term for what an organism's niche would be in the absence of competition from other species. * The male red-winged blackbird's mating call can be heard in the marshes in early spring. At that time, they hold the prime real estate in the marsh. However, as the season progresses, the more aggressive tri-color blackbirds move in. The tri-colors take over the best territory and force the red-wings to choose the leftovers. The entire marsh represents the red-winged blackbirds' fundamental niche. * Spartina alterniflora is a grass species that is very tolerant of salt. It lives in salt marshes along the eastern North American coast. These marshes go underwater at high tide. While it is found all along the coast, it does not live in nearby freshwater environments.

Can meteors cause extinctions?

* Sulfur dioxide and water vapor would have dramatically increased in the atmosphere, forming sulfuric acid - leading to acid rain - sulfur dioxide would lead to global cooling because it reflects sunlight - Also particulate matter would have been released - Earthquake and vulcanism could have been initiated by the impact - Tsunami as high as 4km - evidence in Brassos TX and Haiti - less productivity by phytoplankton - widespread ecological disruption * Next 10-1000 years ... - Atmospheric debris and smoke block sunlight - Temp. plummets - Photosyntehsis stops, so plants die - Food chain collapses - Eventually, debris settles and the sun shines again * Global warming happens... - CO2 from fires causes greenhouse effect * Few species survive this ordeal

Which of the following characters are phylogenetically informative ?

* Synapamorphy

Hawaiian Islands

* The Hawaiian islands are as far away from anywhere as you can get - The nearest continental landmass is about 2000 miles away * The Hawaiian islands were formed as the Pacific Plate moved over a volcanic "hotspot" * Islands are older with increasing distance from hotspot

Plate Tectonics

* The biogeographic regions of the world that Wallace recognized roughly coincide with the continents themselves. But in the twentieth century, scientists have recognized that biogeography has been far more dynamic over the course of life's history. In 1915 the German geologist Alfred Wegener (left) was struck by the fact that identical fossil plants and animals had been discovered on opposite sides of the Atlantic. Since the ocean was too far for them to have traversed on their own, Wegener proposed that the continents had once been connected. Only in the 1960s, as scientists carefully mapped the ocean floor, were they able to demonstrate the mechanism that made continental drift possible — plate tectonics. * Biogeographers now recognize that as continents collide, their species can mingle, and when the continents separate, they take their new species with them. Africa, South America, Australia, and New Zealand, for example, were all once joined into a supercontinent called Gondwanaland. The continents split off one by one, first Africa, then New Zealand, and then finally Australia and South America. The evolutionary tree of some groups of species — such as tiny insects known as midges — show the same pattern. South American and Australian midges, for example, are more closely related to one another than they are to New Zealand species, and the midges of all three land masses are more closely related to one another than they are to African species. In other words, an insect that may live only a few weeks can tell biogeographers about the wanderings of continents tens of millions of years ago.

Kauai Precipitation

* The center of the island receives more rain than outer regions of the island

Examples of Paralogous and Orthlogous Genes

* The genes that produce the hemoglobin and myoglobin proteins are homologous genes that have both orthologous and paralogous relationships. Both humans and dogs hold the genes for both hemoglobin and myoglobin proteins, indicating that the hemoglobin and myoglobin genes evolved before human's and dog's last common ancestor. Myoglobin arose in this ancestral species as a paralogous gene to hemoglobin; a mutation in the hemoglobin gene during a duplication event resulted in a separate myoglobin gene that carries out a new, yet similar, function. Since divergence in human and dog hemoglobin did not occur until after speciation, these genes are orthologous. Human myoglobin and dog hemoglobin, however, are homologous genes that are neither paralogous or orthologous.

Parsimony in depth

* The parsimony principle is basic to all science and tells us to choose the simplest scientific explanation that fits the evidence. In terms of tree-building, that means that, all other things being equal, the best hypothesis is the one that requires the fewest evolutionary changes. * Hypothesis 1 requires six evolutionary changes and Hypothesis 2 requires seven evolutionary changes, with a bony skeleton evolving independently, twice. Although both fit the available data, the parsimony principle says that Hypothesis 1 is better — since it does not hypothesize unnecessarily complicated changes. * This principle was implicit in the tree-building process we went through earlier with the vertebrate phylogeny. However, in most cases, the data are more complex than those used in our example and may point to several different phylogenetic hypotheses. In those cases, the parsimony principle can help us choose between them. * One reliable method of building and evaluating trees, called parsimony, involves grouping taxa together in ways that minimize the number of evolutionary changes that had to have occurred in the characters. The idea here is that, all other things being equal, a simple hypothesis (e.g., just four evolutionary changes) is more likely to be true than a more complex hypothesis (e.g., 15 evolutionary changes). So, for example, based on the morphological data, the tree at left below requires only seven evolutionary changes and, based on the available evidence, is a better hypothesis than the tree at right, which requires nine evolutionary changes.

Silversword alliance family

* The silversword alliance is made up of Argyroxiphium, Wilkesia,and Dubautia 1) Argyroxiphium-5 species 2)Wilkesia-2 species 3) Dubautia-23 species •They inhabit a wide variety of ecological niches, and have acquired a diversity of growth forms.

Mesosaurus

* There are many examples of fossils found on separate continents and nowhere else, suggesting the continents were once joined. If Continental Drift had not occurred, the alternative explanations would be: 1) The species evolved independently on separate continents - contradicting Darwin's theory of evolution. 2) They swam to the other continent/s in breeding pairs to establish a second population * Remains of Mesosaurus, a freshwater crocodile-like reptile that lived during the early Permian (between 286 and 258 million years ago), are found solely in Southern Africa and Eastern South America. It would have been physiologically impossible for Mesosaurus to swim between the continents. This suggests that South America and Africa were joined during the Early Permian.

But remember!

* These are just mechanisms-alternatives to the protein encoding "Mendelian" genes * Variants in regulatory genes still arise through random mutation * Selection (any kind) still acts to shape the effects of the mutation in terms of fitness and frequency of population

H. Floresiensis

* Tools from 94-13 kya * 3'3 feet tall, 55 lbs * Separate species or microcephaliacs?

Physical Characteristics: Climate

* Trade winds in the tropics generally run fromE to W (easterly) * Northern and eastern faces of the islands receive more rain than the southern and western faces * Higher altitude regions are drier than low altitude regions.

Which of the following is NOT a type of horizontal gene transfer?

* Transcription

HOX gens encode

* Trnascription Factors

Presence of a great southern continent predicted before discovery of plate tectonics

* True

The fossil record can be used to understand climate change

* True

Evo Devo (Evolutionary Developmental Biology

* Understanding the molecular mechanisms underlying morphological diversity

Autapomorphy

* Unique Characters

Convergent evolution occurs when

* When 2 or more populations or species become more similar to each other because they are exposed to similar selective conditions

Australopithecines

* Widespread in Africa -Multiole species, - 4.5 to 2.5 mya * Bipedal, relatively large brain - proportions are apelike

Polyphyly

* characterized by a convergent feature (e.g., homeothermy) * Pachyderms are polyphyletic. * Share a convergent character(hide lacks fur)

Paraphyly:

* characterized by a shared primitive feature. Doesn't include all of the transformations of the feature in question (e.g., scales but not feathers).-has common ancestor, but not all descendants (taxonomic)

Autamorphy

* derived trait that is unique to one group * A derived trait that is unique to a particular taxa. These are not useful in determining how groups are related since only one group will have the particular trait. However, these are extremely useful in identifying taxa. For example, feathers only occur in birds. This makes the character "feathers" and autapomorphy for class Aves. The character "feathers" is also a synapomorphy for taxa within class Aves. Raptors and songbirds both have feathers and they inherited them from a common ancestor.

Ardipithicus

* lower jaw, isolated postcranial bones -4-5 mya * Forest rather than savannah * small canines, small molar hominin-like * Phylogenetic position of Ardipithecus was uncertain. Skeletal features are intermediate between homo and pan lineage, but computer constructions place it with the hominins.

Sympleisioamorhy

* shared primitive trait * A shared, ancestral character state. This is any trait that was inherited from the ancestor of a group and has been passed on into more than one descendant lineage. To carry on with the example for a plesiomorphy, the fact that crocodiles and turtles are both exothermic, but

Genetics of Hominini: Homo and Pan

- 4% difference in whole genome • Insertions, duplications, & deletions of genes - 29% of variable genes still code for same proteins - Average difference between homologous sequences ~1.24%

Paedomorphosis

- Neotony(Deceleration) = Slower Rate - Progenesis = Samerate, earlier stopping time

Phylogenetic Trees

-Diversification is not always bifurcating, may be reticulate -May be in conflict across different data sets-Biological signal for: hybridization, incomplete lineage sorting, horizontal gene transfer -Phylogeny = hypothesis

Robert MacArthur and E. O. Wilson (1963, 1967) --equilibrium theory of island biogeography; dynamic equilibrium

-The major contribution to biogeography was the theoretical aspect of modeling -Searched for general patterns in the distributions of diverse kinds of species

Origin of Homo Sapiens

1) Multiregional Hypothesis - H. Erectus leaves africa nearly 2 million years ago and settles multiple regions of the globe - Modest Gene flow prevents branching speciation - Gradually these populations evolve into H. Sapiens 2) Out-of-Africa Hypothesis - An initial wave of H. Erectus leaves africa nearly 2 million years ago - Modern H. Sapiens evolves in africa. Approximately 100,000 years ago its spreads across the globe in a second wave of migration * MtDNA supports Out-of-Africa

Dispersal

1. A priori assumptions can be tested for the hypothesis that many species can disperse great distances through environments that could not support survival or reproduction 2. Results of recent dispersals can be observed (e.g., 1883 Krakatoa eruption killed all life, but within 50 years, the island was covered with forest inhabitants that clearly came from Java and Sumatra) 3. Several types of dispersal mechanisms (e.g., corridors, filter bridges, sweepstakes; according to Simpson) 4. Ability to disperse varies greatly from group to group (e.g., bats are the only mammals native to New Zealand and Hawaii)

Endemic (Restricted to a particular region)

1. Alfred Russell Wallace (and other early biogeographers) realized that many endemic taxa had approximately congruent distributions (e.g., in particular regions of Indonesia), forming "Biogeographic Realms" 2. Although a particular type of habitat might occur in several widely scattered places throughout the world, species in one habitat are more closely related to nearby species in other habitats than to species in the same habitat elsewhere (in other realms) 3. Despite this, species in corresponding habitats often have convergently similar adaptations

Landmark Genome Sequencing Projects

1. Fragment and clone DNA before sequencing 2. PCR amplify regions; DNA-walking 3. Massively parallel sequencing (NextGeneration Sequencing)

Vicariance

1. Hypothesize disjunct patterns result from changes imposed on an originally continuous distribution (e.g., by changes in the distribution of land, by continental or tectonic shifts, mountain-building, etc.) For example, the breakup of Gondwanaland in the Mesozoic can explain the distribution of some ancient groups like ratites and marsupials 2. Vicariant hypotheses also include explaining disjunct distributions by extinctions of intervening populations 3. Both dispersal and subsequent vicariance may be required to explain a particular pattern, but the pattern is vicariant if the dispersal resulted in a continuous distribution (e.g., present distribution of Camelidae is explained by vicariance because it was originally a continuously-ranging group that was fragmented by extinctions)

Disjunct (Seperated)

1. The major problem that Darwin raised in explaining the origin of species by evolution (because descent requires that different species have evolved from common ancestors; how can common ancestors be inferred at a common point of origin if descendants are completely separated geographically?) 2. Disjunct distributions usually fall into one of a fairly small number of patterns...

Processes that favor transposition

1. Transposon copies itself to a new site on the chromosome 2. Transposon copies itself to a plasmid, which can then move to the genome of the host cell or to another cell 3. Transposon copies itself to homologue, propagates via meiosis

Phylogenetic trees are used to:

A. construct hypotheses about common ancestors B. construct hypotheses about how various species are related to each other C. test hypotheses about the relationships between various species

It is correct to say that humans evolved from chimps.

False, Humans and Chimpanzees are one another's closest relatives among extant primates • It is never correct to say that one pair of a sister species "evolved from" the other. - Did you evolve from your sibling? No. • However, sister taxa do share a common ancestor. - Humans and chimpanzees shared a common ancestor 3.5 mya - Both evolved from an African great ape

MADS BOX Genes - ABC Model

Gene A = Whorl 1 (Sepal) Gene A+B = Petal (W2) Gene B+C = Stamen (W3) Gene C = Carpel (W4) * Evolution of floral types associated with evolution of MADS-BOX genes

Convergent Evolution

In evolutionary biology, convergent evolution is the process whereby organisms not closely related (not monophyletic), independently evolve similar traits as a result of having to adapt to similar environments or ecological niches. It is the opposite of divergent evolution, where related species evolve different traits. On a molecular level, this can happen due to random mutation unrelated to adaptive changes; see long branch attraction. In cultural evolution, convergent evolution is the development of similar cultural adaptations to similar environmental conditions by different peoples with different ancestral cultures. An example of convergent evolution is the similar nature of the flight/wings of insects, birds, pterosaurs, and bats. All four serve the same function and are similar in structure, but each evolved independently. Some aspects of the lens of eyes also evolved independently in various animals. Convergent evolution is similar to, but distinguishable from, the phenomena of evolutionary relay and parallel evolution. Evolutionary relay refers to independent species acquiring similar characteristics through their evolution in similar ecosystems, but not at the same time (e.g. dorsal fins of extinct ichthyosaurs and sharks). Parallel evolution occurs when two independent species evolve together at the same time in the same ecospace and acquire similar characteristics (extinct browsing-horses and extinct paleotheres). Structures that are the result of convergent evolution are called analogous structures or homoplasies; they should be contrasted with homologous structures, which have a common origin.

Phylogenies are testable hypothese

Morphology = A Theria hypothesis Mitochondrial DNA = B Marsupionta hypothesis * Nuclear DNA phylogeny supports Theria hypothesis

Amniote phylogeny

Paraphyly: characterized by a shared primitive feature. Doesn't include all of the transformations of the feature in question (e.g., scales but not feathers).-has common ancestor, but not all descendants (taxonomic)

Groupong

Since current evolutionary theory says that traits arise (are derived) in lineages through evolution, only synapomorphies can be used to establish relationships. Autapomorphies contain no information about relationships (because they don't group organisms together); symplesiomorphies should not be used to unite taxa. For example, if you are comparing a clubmoss, a fern and a flowering plant, the trait "free-sporing" (as opposed to "non-free-sporing") can not be used to group the clubmoss and the fern into one group, since this feature is ancestral to both, that is, inherited from the ancestor of all land plants. On the other hand, the trait "megaphyll" (as opposed to "microphyll") unites the fern and the flowering plant into a group, excluding the clubmoss. Organisms that are united by one or more synapomorphies share a common ancestor which possessed these derived traits. They belong to a monophyletic group (Figure 2.4; A) in which all descendants of the common ancestor have to be included. This is also referred to as a "natural" or "evolutionary" group or as a lineage. In modern evolutionary biology, we work hard to recognize only monophyletic groups. If a group does not include all the descendants of a common ancestry, the group is termed paraphyletic (Figure 2.4; B), or a grade. An example of this is the Bryophyta, which includes liverworts, mosses and hornworts, but not the vascular plants. Another example may be "gymnosperms" when used to refer to non-angiosperm seed plants. If the group includes some or all of the descendants, but not the common ancestor, it is called polyphyletic (Figure 2.4; C). For example, a group of all epiphytic plants regardless of their ancestry would be extremely polyphyletic. A sister group (or sister taxon) is defined as the closest relative to a monophyletic group as determined by one or more synamorphies uniting the groups. (Figure 2.5 on next page).

Calories

Whey Protein Shake = 210(3) Greek Yogurt = 120(3) Airhead= 120 lemonade = 80 Mcflurry = 130 Salmon = 230 total = 1550 26+120+45

Which of the following tends to contribute to an overall increase in genome size over evolutionary time?

a. small genetic elements capable of self-catalyzing their movement

The C-value paradox is

a. the lack of correlation between genome size and organismal complexity.

Fossil Record - complete enough

• 99.99% of all the species that have ever lived are now extinct - - The fossil record is only source—some info about SOME of these species • Was every species that ever lived fossilized? i.e., is it complete? - No, only a very small percentage of organisms fossilize. • The key question is - is the fossil record complete enough to study the history of life

Precambrian Life - major steps

• Autotrophy (3.5 bya) - Chemosynthesis - Photosynthesis • Heterotrophy (3.5 bya) - Predation, scavenging • Symbiosis (Eukaryota) - ~ 3 to 2 bya • Sexual reproduction (2 - 3 bya) • Multicellular organisms (2 bya) • Resistant skeletons (600 mya) - Hard parts (exoskeletons)

Macroevolution

• Big transitions - Origin of mammals - Rise of flowering plants • Difficult to document, infer patterns - Geology - Fossils - Living organisms

Prokaryote Genome

• Circular in structure; one copy per cell - Some exceptions (more than one per cell, or linear in structure) • 85-95% protein-coding sequence • Introns - Mostly in rRNA or tRNA - Lacking spliceosomal introns of eukaryotes • Incorporates DNA from prophages, other prokaryotes, and from the environment • May include plasmids - Non-essential, but contain additional functions (e.g., antibiotic resistance; virulence factors)

Virus particle genomes

• DNA or RNA • Single-stranded or double-stranded • Genome size small & compressed - Overlapping reading frames - Different reading frames in same gene * Selection for fast & efficient replication and small virus particle size

Some features of prokaryote genomes

• Gene order not conserved across many groups - Translocations, inversions, deletions, insertions, etc. • Codon usage bias - Mutation rates, natural selection, or availability of tRNAs... • Variation in GC content - Mutation rates G to A and C to T more common than A to G and T to C; results in decreased GC content - Increase may result from asymmetrical gene conversion

Differences in Genome size

• Genome amplification via whole genome duplication - Hybridization (allopolyploidy) - Non-reduction of gametes (autopolyploidy) • Aneuploidy - Chromosome replication errors during mitosis - Meiotic error (uneven division of chromosmes) - Genome reduction after polyploidization * Cell size increases with Genome Size

Molecular evolution of genomes

• Genomes respond to natural selection - Genomes are analogous to fossil record • Record of past evolutionary events • Comparisons of genetic variation among extant taxa enable a reconstruction of evolutionary process - Null hypothesis = neutral model of evolution

Advantage of small genome size?

• Less time for replication & cell division • Higher metabolic efficiency * Large populations: larger effect of natural selection for reducing genome size (Prokaryotes) -smaller genome size = faster replication

Legacy of endosymbiosis

• Loss of most of the prokaryote genome in organelles • Transfer of genes to nucleus - Partitioning of function and gene expression • rbcS & rbcL as an example • For plant mtDNA - Accumulation of DNA from other genomes - mtDNA sequences highly conserved, but structure of genome quite variable

Background Extinction

• Mass extinctions account for 4% of all extinctions • Likelihood of extinction not correlated with past survival • Causes: - Predation & Competition - Disease - Climate Change • Anthropogenic causes: - Migration & hunting • Large land birds, large herbivores - Habitat modification • Agriculture • Commerce - Invasive species - Climate change

Extinction

• Most fossil genera are short-lived. • Most fossil genera have a small number of species. • Most species have few individuals. • Most species are geographically restricted. • Skewed variation is common in biological systems - and alone suggests that some genera are far more likely to go extinct than others.

Exceptional Preservation of Fossils

• Most fossils are of mineralized or other resistant skeletal parts. • Rarely, nonmineralized parts (skin, chitinous cuticle, guts, hair, feathers) are preserved. • Conditions conducive to fossilization of nonmineralized parts: - Elimination of biodegraders through anoxia, salinity changes, desiccation, etc.

Nuclear genome

• Multiple linear chromosomes • DNA sequences for: - Protein-coding genes - Control elements - rRNA, tRNA, microRNAs - Noncoding regions --Transposons -- Introns -- Structural: centromeres & telomeres -- Repetitive elements --- SINE, LINE, Mini- & Microsatellites, etc.

Highlights of Earth's Biotic History

• Precambrian - 4.5 to 0.5 billion years ago - Earth forms & first continents appear - Oldest rocks in Western Australia - 4.4 billion years (Valley et al. 2014; Nature Geoscience) - Oceans and atmosphere form - First glacial cycles - Life appears ~ 3.5 billion years ago

Prokaryote and organelle genome size comparison

• Prokaryote: ca 1-10 Mb • mtDNA for animals: ca 15-18 kb • mtDNA for plants: ca 195 kb - 2.4 Mb - Why so big???? • cpDNA for photosynthetic plants: ca 150 kb - cpDNA for nonphotosynthetic plants: • Smallest genome ca 50 kb - "use it or lose it" syndrome....

Small genome size example: Prokaryotes

• Small size has a selective advantage? - Faster replication = better competition • Small size an artifact of deletion bias? - No association of maximum replication rate and genome size - Rate of deletion is higher than rate of insertion • Selection pressure for smaller genomes balanced by selection against the loss of functional genes

C-value

• The amount of DNA per cell is the Cvalue • C-value paradox - Differences in genome sizes not correlated with number of protein-coding genes - Not correlated with phenotypic complexity * Lungfish C-value = 40-133 * Human C-value = 3.5 * Salamander C-value = 16-81

Conservation Biology

• The characterization of biodiversity and study of how to maintain it. - Natural resource management - "discipline with a deadline" • Cost-benefit analyses of extinctions

Non-Coding DNA

• Transposable elements - Self replicating • Repeated elements (mini- & microsatellites) • Introns • Centromeric and telomeric regions

Large Genome Size (Ex: Vertebrates)

• Trend for large organisms with relatively small populations - Getting rid of "junk DNA" a bit more challenging via natural selection • Not as big of an effect as in prokaryotes • Extra DNA available for co-opting into other functions - Gene duplications

Phylogeny and Earth History

•"Gondwana" hinted at by distribution of fossil forms •Similarity of Southern fauna across continents •Role of continental drift in vicariance * The distinct distributions of some living taxa suggest that their ancestral forms radiated acrosss gondwana land in the permian period

Globin Gene - An ex of gene family

•7 α-globin genes on chromosome 16 •6 β-globin genes on chromosome 11•Similar in structure-All have 3 exons separated by 2 introns, repeated sequence motifs that allow us to recognize them as similar •Duplications WITHIN α and β globin lineages lead to more copies of each •Family includes "pseudogenes"that are non-functional as globin genes -Usually not transcribed -Pseudogenes may eventually evolve new function or role through changes in sequence or in transcription pattern

Von Baer explains this thru developmental mechanisms

•An embryo exhibits the general characters of the group to which it belongs first; more specific features develop later. •Less general structural elements form after more general ones, and so on, until the most specific appear.

Gene Phylogeny

•Ancestral duplication led to 2 kinds of globins-α and β -Ancestral function seems to be enzymatic rather than respiratory •Each subfamily has own trajectory -β-globin genes monophyletic -α-globin genes monophyletic •All α-globins share a more recent common ancestor with one another than they do with β-globins

Biogeography is a synthetic discipline

•Biology -evolution, ecology, systematics-physiology of organisms + anatomy, development •Earth Sciences -geology, paleontology, climatology, limnology-geography and historical geography-plate tectonics, glaciation •Geography

Gene Families

•Clusters of genes similar in structure and sequence-HOX genes, Actins, Tubulins, Histones, Keratins, Heat-Shock Proteins, Globins, Immunoglobulins •Different from high-copy genes (like rRNAgenes) that have many essentially identical copies scattered throughout genome

Types of islands

•Continental -Have been part of a continent at some point in their geological history -- Not always adjacent to a continent today •Oceanic -No contact with a continent --Mid-oceanic ridges --Places where tectonic plates interact --Hot-spots in the mantel

Globin Genes

•Different genes expressed at different times in development •Each gene product slightly different -Fetal product has higher affinity for oxygen, etc •Selection acts independently on each gene

Dispersal influences Geographic Distributions

•Dispersal -Organisms move passively or actively to another region. -Range expansion -move across continuous habitat ("geodispersal")-Jump dispersal -movement across a barrier.

Orthology and Paraology

•Does it matter? -Yes, definitely •Orthology: genes are related by common descent -Can be used to reconstruct an accurate phylogeny for that particular gene •Parology: After duplication, each gene has a unique evolutionary history -Phylogenetic trees for each locus may be different

Three fundamental processes in biogeography

•Evolution, Extinction, Dispersal -The relative importance of these processes varies from one group to another -Biogeography investigates the relationships between pattern and process •Historical science; models of predictive value (e.g., island biogeography)

Evo-Devo

•Evolutionary Developmental Biology -Evolutionary changes in developmental pathways between species, genera, etc., --Developmental regulatory genes -a function of where and when these "genetic switches" are flipped on or off

Genetic Evidence

•Homologous genes encode the same information •Many genes are multi-copy! •Genetic information less detailed but more numerous -Each nucleotide is an independent character! •Additions and deletions of bases in non-coding regions make comparing sequences complicated -Need to align your sequences —not always easy!

Optimality criteria

•How do you know you have the right tree? -The tree that best (most accurately) summarizes the data is always the "right"tree for those data •Measures of relative nodal support can give some confidence -Values >70 for bootstrap or jackknife •How do you know that this is the "true"tree?-You never do -Agreement with other data?-Comparison to outside evidence from earth history, fossils, other genes, etc.

Ecology limits geographic distribution

•Hutchinson and MacArthur 1)Fundamental niche=the regions in which they could theoretically live given the range of physical factors 2)Realized niche=the regions in which they actually live -smaller than fundamental niche •Competition with other species. •Or historical (never made it to the other area).

How can we test whether Heterochrony has occurred?

•Identify sibling lineages characterized by morphologies that can be tied to developmental differences •Characterize the interval of development and the rate at which features of interest develop

The use of phylogenetic trees

•Infer relationships and evolutionary history of taxa •Examine evolution of traits in organisms •Molecular and genome evolution discovery •Prospecting for bioactive compounds •Understanding disease and developing treatments •Understanding the geological history of earth

General tenets of island biogeography

•Large islands are more species-rich than small islands •Islands closer to a large land mass are more species-rich than remote islands. •Mountainous (high-altitude) islands are more species-rich than low-altitude islands. •In island archipelagos, islands become more species rich as they get older.

Climatic and Biogeographic Consequences of Plate Tectonics

•Mountain orogeny -Plate collisions and subductionzone activity •Biotic exchange •Climatic shifts correlated with continental movements-Drying trends and glaciation •Mass extinctions associated with tectonic events

HOX gene mutants: Homeotic

•Mutation in gene can cause "misplacement" of body parts •Homeotic transformation -Changing segment identity during development

How are trees made?

•Parsimony -The phylogeny with the fewest evolutionary changes is the best estimate -All things being equal, the simplest explanation is usually the best! (Occam's razor) •Maximum Likelihood -Probability of the tree can be computed given the data and a model of evolution -Very tedious because you need to do complex calculations for all possible trees

Bayesian Methods

•Similar to Maximum Likelihood, except: -Finds tree that is a posteriori most probable given that we observe these data. •Same models of evolution used as in ML •Major difference: in Bayesian, a true probability, rather than a likelihood score, is assigned to each possible tree.

Changes in timing--When does development stop?

•Stops early-Descendant adults resemble ancestral juveniles (paedomorphosis)•Stops late (continues past previous endpoint)-Descendant adults attain larger size or have new structures (peramorphosis) •Haeckel's "ontogeny recapitulates phylogeny" presumes terminal addition--new structures develop at the end of existing sequence

Vicariance influences Geographic Distributions

•The splitting of continents could cause speciation by vicariance. •Predictions:-Multiple species occupying the same regions could undergo simultaneous speciation.-These speciation events coincided with continental movements

What other systems function as islands?

•Vernal pools, ponds, forest remnants, nature reserves, hosts for parasites, individual plants, etc. -Caves, oases, urban green spaces

Common descent as a null hypothesis for similarity?

•When we see similar attributes, we usually assume they are the same -Shared descent is testable, and can be rejected if a trait is shown to be convergent in a particular set of taxa -Fundamental assumption related to scientific process •Our observations are reliable and meaningful •Homology is the null hypothesis that needs to be tested through detailed studies of anatomy, development, and genetics

"Pull of the recent"

Patterns are harder to detect clearly the farther in the past you go - Organisms harder to interpret - Record more fragmentary

Parallelism in development

B. Was the idea that developmental stages progress from the simple to the complex, reflecting the scala naturae.

Biogeography as Evidence for Evolution

Biogeography as Evidence for Evolution * ....connects together and renders intelligible a vast number of independent and hitherto unexplained facts. The natural system of arrangement of organic beings, their geographic distribution, their geological sequence.... * Granted the law, and many of the most important facts in Nature could not have been otherwise, but are almost as necessary deductions from it, as are the elliptical orbits of the planets from the law of gravitation.Wallace, 1855 * A species: 1.has a definite site or region of origin 2.achieves a broader distribution by dispersal 3.Becomes modified and gives rise to descendant species in the various regions to which it migrates * Species of large geographic areas tend to be more closely related to other local species than to ecologically similar species elsewhere in the globe

Whole Genome Sequencing

• 1976 - bacteriophage MS2 (RNA virus) - DNA structure: 1953 - Genetic code deciphered: 1966 - First whole genome sequence: 1976 • Number of WGS projects in GenBank: - 8,294 in 2014; today greater than 35,000 - Many of these are organelle genome sequences • Number of TSA (transcriptome shotgun assemblies) in GenBank: too many to list

Theory of Continental Drift(Plate Tectonics)

•has had the largest impact on biogeography •evidence is conclusive