bil 304 evolution final

explain how feathers could have evolved from simpler structures in animals unable to fly, thru a series of intermediate states each of which had an advantage of some sort

*Feathers evolved from epidermal structures of dinosaurs* -evolved frm keratin structures in epidermis of amniotes >provided protection/insulation that enhanced terrestrial life >reptiles have scales, mammals have hair, birds have feathers, all made of keratin >feathers are most complex, but the simplest feather is a hollowed out cylinder of keratin, growing from a follicle produced by invagination of epidermis into the underlying dermis >several similar cylinders rise from same base, make fluffy structure, i.e. down *feathers evolved from projecting epidermal fibres in dinos* -feathers preserved only in very unusual circumstances, rapid burial in anoxic sediments that give rise to fine-grained laminated rocks -recently discovered fossils have helped fill in gaps between well known Archaeopteryx and birds > animals w filamentous feathers, couldnt have contributed to flight, most likely for thermal insulation, like mammal hair >vaned feathers but animals themselves too large to fly. short forelimbs, feathers only on tail where thy couldnt form a wing, only a few had potential for flight >microraptor had vaned feathers on forelimbs, hind wings and tail, certainly could have glided, might have flown if it flapped wings fast enough, but lacked enlarged sternum that wing muscles are attached to in modern birds >Archaeopteryx is last org, lacks only a horny toothless beak and reduction of a tail to a stump to form modern birds -nothing inevitable about transition: dinos had predisposition to express feathers in their skin, did so for a long time before feathers were co opted for gliding and flying -t-rex may have been feathered as kiddies -only when mutated versions of warm/waterproof down were expressed in much smaller animals is when flight became possible -exaptation: recruitment of structure evolved for mundane reasons that by chance creates unanticipated potential for evolving completely new way of life *represents cumulative change driven by NS* w range of intermediate stages and a range of outcomes

What is the role of variation in Lamarckian and Darwinian theories of evolution, and how are the 2 distinguished by experiment?

*Lamarckian evo* - appropriately directed modification and inheritance of acquired characteristics -individuals perceive the state of the environment in their lives, respond appropriately -an inherently progressive principle, leads to increased level of organization -selection plays a minor role -adaptation to novel environments happens primarily through spontaneous evolution of appropriately directed variation -the environment elicits a favourable mutation (which is wrong, there is no mechanism that acts as a specific directing principle that can produce appropriate genetic variation) -experiments: in bacterial genetics, challenged bacteria w new hostile environments then traced the origin of adaptation. Found that mutations allowed adaptation and increased frequency thru selection in the new environment before the environment changed even, shows that adaptation occurs through selection of pre-existing variation, not thru the elicitation of appropriate variation *darwinian evo* - selection of indirected variation -doesnt require that mutations occur at random, bc its known that some genes mutate more frequently than others, and some sites within certain genes have different rates of mutation -doesnt assert that mutations are caused by physical agents like ionizing radiation -mutations are not appropriately induced by environmental factors -experiment: expose bacteria to UV light or EMS, toxins that inhibit growth, are mutagens, an appropriate dose causes mutations. will not find that mutations induced by these stimuli are specifically resistant to UV light/EMS, shows that adaptation to an agent occurs thru undirected mutation -lack of direction taken by evolution is determined by the action of selection in each generation, not by any inherent directional property of variation itself

Discuss the interpretation of genetic elements as beneficial or parasitic, w special reference to bacterial plasmids and eukaryote transposons and retrotransposons.

*beneficial* - selfish genes can become domesticated so its behaviour is no longer a disadvantage, it will decay, and o longer have a function i.e. bacterial plasmids carrying resistance genes, beneficial because it allows bacteria to survive in a new condition (presence of antibiotic) i.e. euk telomeres based on transposons, help preserve ends of genes so they are not lost in end during replication repeatedly *parasitic* - selfish elements can kill cells that lack them ex)R1 plasmid in bacteria, w/o sok gene, hok will kill the cell by preventing respiration, -retrotransposons can be negative if they mess up coding regions for genes -retrotransposons can also be positive if they duplicate genes, which can be modified cuz since there are 2 copies it retains the OG gene function, and the new copy can b modified for new functions

Compare and contrast evolutionary patterns and processes in bacteria and eukaryotes.

*euks* -genomes have evolved novel features, linear and variable genome that is modifiable -sculpted by size and sex (recombination) -introns must be rearranged during transcription, and errors in complex replication process can lead to new genes -affected by retrotransposons *bacteria* -simple, small, circular genomes -consist of core (irreplacable, strong purifying selection), shell (common but replaceable, modifiable, purifying selection), and cloud (specialized functions, exchanged freely, for rapid evolution of novel characters -vary greatly in size -sculpted by horizontal gene transfer, distantly related lineages can exchnge -readily acquire new genes thru HGT, bacteriophages that inject DNA and incorporate it into genome -reticulate rather than branching due to exchagne

define mutation supply rate and genomic mutation rate. How do they affect evolution process?

*genomic mutation rate* - scaled by genome size -governs rate that fitness degrades at -estimated by sequencing genomes and genomic mutation rate U=Gu per genome per generation, G is genome size in bp and U is attribute of species -in MCOs, divisions occur in germline, offspring bear a new mutation/gen, if most are deleterious, offspring are less fit -mean fitness of pop in constant environment depends only on genomic mutation rate, W=exp(-U), restored to 1 w every generation -reason that it evolved is bc of its function, mutation can be beneficial but is not why it evolved -continual degradation of adaptedness is continually countered by NS by acting against individuals w more deleterious mutations > lower divergence rates of protein coding genes -mutations give new source of adaptive variation, no avg value cuz it depends on current state of adaptation in population -genomic mutation rate governs state of degradation of fitness made good by selection during lifetime of cohort of offspring -effect of mutation doesnt matter: more severe mutations cause a greater depression of mean fitness, but are *proportionately more effectively removed by selection* *mutation supply rate*: -limits rate of evolution M=Nu -N is pop size, M is attribute of populatio -larger mutation supply rate provides greater number of possible beneficial mutations, and thus increases rate of adaptation, governed by abundance, N -sheldon size spectrum: in ocean water, mass of particles in eq lg size classes is independent of size, log-log plot of density of orgs follows same rule. distributions show that 90% of individuals are in smallest size category, 90% of remainder in next, etc

Compare and contrast the evolution of genes regulating (a) meiosis, and (b) gamete fusion.

*meiosis* -highly conserved, while there is variation in details among sexual species, the main features have been retained in all modern lineages -genes for meiosis are found across all domains, even found in bacteria to repair DNA -genes have diff sequence, sizes, and orientations, and have not evolved from a recent common ancestor, unlike meiosis genes -genes governing *gamete fusion* evolve direcly from meiosis genes or vegetative fusion -reason they have evolved differently is bc constituent genomes of zygote must work together to complete meiosis, but gametes compete against one another to fuse -sexual competition mongst gametes drives variation in gamete genes, while necessary genetic collaboration to compete meiosis favours uniformity -gamete fusion genes are converely idiosyncratic, and idiomorphic, vary significantly even though sexual fusion is older than meiosis itself

how do we know mito and platids are derived from bacterial endosymbionts?

*mito* -metabolism and rep of euks still bear stamp: 1) mito replicate independently of nucleus w/o centromeres and microtubules 2) proteins that need to cross membrane must normally be tagged w transit peptide, which is then removed once their journey is complete -euks are compound orgs, rely on cooperation of their partners -mito descend from a single bacterial ancestor > all euks have mito, except a few UC parasites that lost them -MRCA of euks had mito that evolved from captured bacterium, probs planktonic marine alpha-protobacterium *plastids* -complicated ancestry -chloroplasts of green algae descended directly from cyanobacterial endosymbiont bc they have 2 membranes -all land plants have inherited this chloroplast -plastids of red seaweeds have similar structure, prob descend from same ancestral cell -PS euks all descend from sngle ancetral partnership between euk cell with mito and cyanobacterium -other algae can be more complicated, other PS euks have plastids w 3/4 membranes, and other remnants of genomes too

describe the main kinds of structural change that can lead to innovation and give an example of each

*modification* -accumulation of change thru selection of successive beneficial mutations -can result in complex structures over long periods of time -ex: feathers, nothing inevitable about transition, dinos had predisposition to feather-like structures before they evolved *duplication* -1 version of an essential gene cannot be modified bc it would impair the function -duplication can allow the copy to diverge and acquire new functions while the ancestral version can retain its normal function -occurs rapidly bc constraint is normally on modification -ex: Visual pigments *fusion* -partial/complete fusion of genomes belonging to separate lineages to create a new org -can happen almost instantaneously if the rare fusion results in a viable individual -ex: euks incorporate 2 radical innovations originating by fusion, mitochondrion fusion, shown by separate bacterial genome, and double membrane

Compare and contrast the evolution of structural and regulatory genes.

*regulatory* -mutations here can have huge effects that are hard to predict -phenotype is only expressed in genes that control it are transcribed -most genes inactive, only active if they are activated -changes in regulatory genes can greatly effect transcription of many genes which can be hard to predict -cis & trans elements affect transcription -made of combos of motifs that work together, interact through feedback loops, feedforward loops, single input modules, and dense overlapping regulons -evolution of reg. g. are facilitated by a few motifs that can be combined in numerous ways -evolution in reg. g. can evolve new attributes > evolution of cis-reg elements can be facilitaed by direct association between any mod of element and its effect on a target gene... new phenotype is immediately expressed in heterozygotes ex) bacteria have v simple reg networks w only a few genes associated in every path ex) euks are rlly complicated, each process has dozens of genes w many interactions, and any mutation in a regulatory gene can greatly affect the others in the same pathway, sensitive to change because more genes depend on eachother *both* -both can be modified and can be intertwined w eachother ex) Lac operon is made of structural genes that govern lactose use and the regulatory genes that activate their transcription -mutations in regulatory genes affect how structural genes are transcribed, and can affect the lactose pathway together *structural* -evolution of structural g. are facilitated by modular structure of proteins and genes nd the regulatory networks that make them

"Natural selection is commonplace and often strong". Evaluate the evidence for this statement and discuss how it might be affected by artefacts.

-100s of examples of NS have been documented, to where they can be used to make statistical generalizations about the frequency and intensity of NS ex) mimicry is form of NS -fond in all kinds of insects -wasps, hornets, bees all show same colour, conspicuous to predators so they are avoided due to their dangerous sting -some hover flies have same colour even tho they dont sting to seem as dangerous, and protected against predation cuz they look like wasps >Batesian mimicry is also found in snakes and butterflies >shows how species interactions and selection affect populations -NS is as strong as well aas commonplce shown by polymorphism -selection is rarely weak, only abut 3/4 of documente cases involving a selection coefficient is greater than 0.1 -studies in continuous variation have provided evidence that NS is strong as well, with selection gradients avg around 0.22 -museum artefacts provide supprot for examples of NS, ex, sea snail pops prior to and ofllowing shore crab that decimated snail pops w tall high spire shells -artefacts used to review hypothesis about NS can be useful, trends can be deteced w/o bias of OG sampling knowing what it was looking for, and in hindsight that a pattern suggesting NS emerges

what have we learned abut Lenski's long-term E.Coli experiment?

-1988, Lenski started w a single cell of e.coli, that divided into a colony -used to innoculate dozen pops that are kept separate -each maintained in batch culture, glucose medium, 1% of pop is transferred to new medium daily -unnatural environment for e.coli, normally live in animal guts, so they must evolve rapidly under strong selection, and also quantifiably and qualifiably bc genome is known -gen time: 1 year = 2000 gens, every 500 gens, lines are stored thru freezing, and have passed over 50,000 gens today -each line adapts to novel conditions it faces thru successive beneficial mutations -competitive assay used to evalue degree of adaptation, by taking 2 v of ancestral strain, identical save for one gene for metabolism of Arabinose, and one is non functional, detected by their different colours. evaluated by mixing ancestral line w one of markers with a new line. if line has evolved, freq of markers is recorded at each transfer, and if it has evolved, the fitness will be greater than ancestral in new conditions >rate of increase in freq is used to calclate how much fitness has evovled in relation to its ancestor -after 20,000 gen, selection and adaptation slow greatly bc greatest effects on fitness have already become fixed, still increases but very slowly now. -shows selection is active in preventing change, not always catalyzing change -displays that directional selection is followed by purifying selection once a certain level of adaptedness is developed, to maintain it and eliminate deleterious mutations -shows 3 metabolic features of bacteria: 1) many beneficial mutations involve loss of function in one system that cause a gain in other (i.e. cant metabolize ribose, do better in glucose) 2) general targets (genes modified) of beneficial mutations are often modified in most/all replication selection lines, whereas the specific targets are diff in all clsses, themes are repeatable, but variations are idiosyncratic 3) biochem mechanism underlying advantage of beneficial mutations is difficult to understnd

Describe how the eukaryote life cycle is divided into vegetative and sexual phases, and show how this leads to distinct processes of natural and sexual selection.

-1st euk life cycle stage is vegetative -cell grows and reproduces by division into 2+ offspring cells, which then repeat this cycle thru growth -initiated by a cell specialized for growth, called spore -manages growth and reproduction -sexual cycle: 2cells fuse to form a single cell, then divides into 2+ cells w OG genomic complement -manages fusion -life cycles explain the life of UC euk in full, but in plants and anmals, growth and repro of spore in vegetative phase gives rise to MCO, inside of it the gametes are formed in a germ line -alternating sexual cycle leads to NS cuz spore in UCO or MCO that spore develops into competes w other resources to be able to grow and eventually reproduce -competition drives NS -sexual selection is an outcome of alternating cycle bc gametes dont grow or reproduce, and thus dont compete for resources -bc their job is to fuse, they compete for partners, which is the basis for sexual selection (competiton among zygotes for fertilizing partners) -NS is driven by vegetative phase, SS is driven by sexual phase

describe the evolution of limnetic (open water) and bottom feeding (benthic) types in freshwater fish

-2 ecologically distinct types of fish have evolved in BC lakes that are not sexually isolated, but are separated in space -limnetic forms live in pelagic zone, deeper offshore, gill rakers to sieve sand, attacked by fish -benthi form: stout body, long jaw, feed on benthos large prey like amphipods/worms, attacked by dragonfly larvae -divergent selection for benthic and limnetic ways of life involve a cost of adaptation, hybrids are inferior -benthic and limnetic represent the intermediate stages in speciation, other factors are sexual selection (females prefer males of same type regarding colour/size, which can cause a threat as detection by predators) -few recently evolved types are sexually isolated from ancestor, sticklebacks, and show that speciation is a continuous process of modifications -divergent selection for benthic and limnetic types of whitefish exist, ecological speciation evovlees in whitefish and sticklebcks even thugh they have different ways of life

Adaptation in experimental populations often involved only a few mutations of large effect. Why is this? In what circumstances would adaptation be more likely to be based on many mutations, each of small effect?

-2 extreme accounts for adaptation: 1) based on mutation freq (most mutations have small effect, so adaptation is consequence of fixation of mutations at many loci 2) effect of mutatitons: beneficial mutations likely to have small effect likely to bbe lost before they can spread, so only mutations of large effect are likely to be spread -in experimental pops of bacteria, cultured bacteria that use serine as carbon and E source -most cant grow at all, those that can have large advantage and spread rapidly -greatly superior types override the crowd of beneficial mutations w more modest effects -relies on population size> low pops may benefit more from many small effect mutations cuz different sized vessel microbe experimet, large pops adapt faster

With the aid of a diagram, describe substitution of a beneficial mutation in terms of waiting time, establishment time, and passage time.

-3 phases in fixation of beneficial allele: 1 - waiting time b4 the appearance of beneficial mutation 2-establishment time before successful mutation spreads 3-passage time required for eventual fixation -waiting time depends on mutation supply rate -mutation supply rate depends on: fundamental rate of mutation per nt, pop size, probability that mutation will be beneficial -when beneficial mutations are rare, adaptation stops -ex:> lack of adaptation to growing CO2 levels in atmosphere in phytoplankton bc physiological systems involved in PS are optimally figured, so few mutations can improve it -experimental evolution will make no progress when beneficial mutations are rare so that none are likely to occur within 100-1000 gens -successful beneficial mutations only establish if they survive stochastic loss -passage time depends on intensity of selection -waiting time until appearance of beneficial mutation is 1/2 x as long as interval between successive beneficial mutations, most of which become extinct -overall rate of adaptation may be limited by establishment time or passage time, depending on the rate of supply of beneficial mutations and their effect on fitness

give brief account of C4 photosynthesis, identify conditions in which it is superior to C3 photosynthesis. How does C4 evolve from an ancestral C3 state?

-C3 plants use enzyme Rubisco for photosynthesis: catalyzes CO2 addition and helps create sugar, the crucial reason *why plants and algae convert CO2 into carbon compounds* >but, is inefficient, 100X more slow that other enzymes, must be in huge amounts(30% of soluble protein in plants) because it competes w photorespiration >when exposed to O2, its substrates will be oxidized and thus metabolically useless -thus, CO2 is fixed into 3-C acids in plants >difficult because in todays atmosphere, there is much larger amount of O2 (used to be less due to cyanobacteria ~2800Mya, when atmosphere was high [CO2]) *C4 plants evolved* -formation of "bundle sheath", where sheath of cells surround veins where rubisco is kept -have reaction sequence to pump CO into sheath cells, PEP carboxylase fixes CO2 into 4-C acids in mesophyll cells, transprted into bundle sheath cells, release CO2 within chloroplasts in proximity to rubisco >>> rubisco can be saturated in CO2 even when stomata are shut, in warmer climates, hot/dry, -C4 plants have ability to pump CO2 around rubisco, distinguishes them from C3 plants -still have the C3 biochem pathway in C3 plants, but are isolated from the atmosphere in a specialized compartment -arranged thru a characteristic arrangement of leaf tissues -C4 plants evolved thru modifying pre-existing C3 mechanisms > PEP carboxylase drives the C4 shuttle, but are still present in C3 plants -not enzymes that are changed, but their expression in tissues is different and what sets C4 plants apart -enzymes are modified in the normal way, by sub of beneficial mutations, and thus optimize their activity in C4 >i.e. substitution of serine at position 780 (of maize sequence) in Pep carboxylase is essential for C4 function -Rubisco evolves within the C4 environment >has complex tertiary structure, activity can be modified far from the active site >switch from C3 to C4 photosynthesis alters optimal config of the molecule, has led to succession of subs that improve CO2 specificity >many of these changes occur independently in different C4 lineages C4 photosynthesis evolves thru a series of intermediate states -in C3, PS happens in mesophyll cells in leaf, in C4,PS is divided between mesophyll and bundle sheath cells -intermediate stages have only partial C4 cycle, or incomplete partition of enzymes between 2 tissues, which also are demonstrated by related species within same genus i.e. Flaveria "goldentops" have c3, c4, and intermediate stages as well intermediate stages: 1) usual C3 system, which is ancestral state, no bundle sheath, no biochemical mechanism to decarboxylate C4 compounds 2) first evolution towards C4, i.e. F. ramossissima, some differentiation between mesophyll and bundle sheath, only have a rudimentary C4 pathway 3)further differentiation of meso and bundle, partial C4 cycle, i.e. F anomala 4) Full C4 cycle, but havent segregated PS enzymes between meso and bundle cells 5) fully functional C4 system, i.e. F bidentis

Explain why reproduction early in life has a much greater effect on the fitness than the corresponding amount of reproduction later in life.

-Early vigor is a crucial component of fitness -early repro makes much larger contribution to fitness than equivalent amount later in life: 1) cant guarantee that individual will reproduce later in life because its possible that they will die and just not reproduce at all 2) later investments = less profitable in the future than if it was made earlier. due to exponential growth rate of organisms, longer generation times means that population takes longer to grow and will be smaller compared to if gen times were much shorted -age of first repro is generally most important aspect of overall fitness >tendency to reproduce is favoured by selection >imporance of early repro will favour increase in fecundity early in life even if it entails a catastrophic loss of vigor later in life

explain evolution of multicellularity in Volvocales. Is this group a good model for the evolution of multicellularity in other groups such as animals and plants?

-MCOs evolve from uniC ancestors thru a series of intermediate forms >volvocales are green algae that transitioned from UCOs, thru colonial orgs w definte form but no cellular differentiation to MCOs w different kinds of cells -series from UCOs to MCO forms in volvocales : UCOS> Gonium many undifferentiated: Eudorina many cells, soma-germ distinction: Pleodoina large colony w pronounced soma-germ division of labour: Volvox -some Volvocales are unicells, reproduce by making unicellular offspring -some colonies w distint individuality in which all cells make MC offspring -colonies w soma-germ distinction show first indications of division of labour, which maximizes productivity of individual as a whole -a few major genes direct development: caused by asymmetric division early on in colony growth, gls, regA, lag -multicellular body evolves thru a series of intermediate forms >growing clone must be held together, thru incomplete cell division between daughter cells, transforms cell wall into ECM -cell differentiation> reproductive ability in soma are lost, loss of motility in germ cells -regular developmental program w fixed endpoint -unlikely to happen all at once -chloroplast gene sequence eused to map divergence of these traits -more likely to happen in Volvocales that only use binary fission, so cell all divide within the same cell wall to produce identical group of daughter cells in a small space 1) transform cell wall into ECM, most likely in volvocales 2) retention of cytoplasmic connections between cells thr incomplete cell division, permits morphogenetic movements during development,and communication between cells 3) inversion of the growing individual during development, thru prior formation of cytoplasmic connections between cells, ECM was expanded and allowed greater flexibility 4) restriction of reproduction to a group of cells, create sterile somatic caste 5) increased germ specialization, germs become immotile and move to interior of cell thru asymmetric divisions *multicellularity has evovled independently in many lineages* >not evolved thru uniform trend, leads towards increased complexity of organization, 2 major complications: 1)NS doesnt enforce uniform tendency to move towards higher levels of organization 2)MC has evolved independently in several lineages -ways that MC will evolve in different groups greatly varies but each involves mutations that change the genome so cells can cooperate and all contribute to improving reproductive fitness of the organism

Describe the social dynamics of stirred and unstirred cultures of Pseudomonas fluorescens maintained by serial transfer.

-P. fluorenscens lives on plant roots -unstirred medium: culture becomes clear, forms different layers to reflect different cell types that form -middle have smooth glossy ancestral ancestor types -tough white layer at surface, form flat wrinkly colonies >made by mutation in wss operon that causes production of fibrils that bind cells into a mat, due to oxygen gradient formed -surface cells have advantage and want to keep t, so wss operon mutation invades the cell cuz mutation can maintain their position -stirred medium = more equitable distribution of nutrients so all cells grow more or less equally -wont form the 2 distinct niches, pop remains uniform -complex social interactions develop, generate divergent selection resulting in range of specialized types -when niches of heterogeneous environment provide refuge for specialized types, freq-dependent selection will act to preserve diversity

What is the evidence that adaptation is often caused by a few mutations of large effect, and in what circumstances would you expect this generalization to break down?

-adaptation is oligogenetic -early stages = common for it to involve 1/2 loci where alleles of major effect are segregating -genes w large effect are less likely to be lost by changes in early adaptation and thus contribute disproportionately to genetic make up of derived population ex) changes responsible for the production of modern crop plans by AS on continuous characters being attributed to a few major genes > oligogemetic model, cuz AS is controlled and can be closely studied -can also be observed in natural populations i.e. genes that control armour production in stickelbacks, Pitx1 and Eda, melanism in mice (attributed to mutation at single locus, Mc1r gene and overexpression of a single regulatory gene (agouti) -generalization might break down as adaptation proceeds, as supply of beneficial mutations will dwindle and further progress can only be made thru substitutionof broader range of mutations of gradually diminishing effect -selection and adaptation are cumulative, so while potential mutations could be beneficial, not always expressed

Draw up a catalogue of the agents of selection responsible for instances of rapid evolution in contemporary or near contemporary populations, and describe how they have produced change. Do they have any features in common?

-agents of selection: -environmental fluctiations -plate teconics -novel stresses -predation -climate >>> all trigger NS that works for some, works against others -pop that cannot adapt to agents of selection doesnt succeed in its environment >invasion of shore crab Carcins maenas in america: as crabs eat sea snails, favour snails w tall high spiraled shells (thicker, easier to manipulate nd eat) -after accidental introduction, consequent declin in high spired shells imuseum specimen over the course of a century >>> predation provoking change in a natural population -previous agents can have same effect -share propensity for favuring one subset of a pop over another -shapes pop distributions and phenotypic dominance, fragment populations, or drive towards extinction -these agents cause NS to establish a new set of features that are beneficial or detrimental

why do life cycles of multicellular organisms pass thru a single-cell phase?

-all MCOs develop from single cells, which have conflicts between selfish (higher replication rates of specific alleles) and altruistic tendencies (refrain from over-replication alleles) -fundmmental tension exists between 2 types of alleles when an individual is replicating -development thru a single cell transfers selection from competition between different cell lineages to competition between individuals >gets rid of selfish alleles -selfish alleles often fail and are harmful to an individual, cuz single cells often fail alone >reduces selfish alleles because they fail to form successful individuals and are eliminated by selection over time >ensures that individual has altruistic cell lineages

Describe the adaptive radiation of dogs through artificial selection and compare it with the adaptive radiation of a group through natural selection.

-all dogs descended from wolf, large variable canid that became friends w humans 10,000 ya -unconsciously selected for long time for useful characteristics, most recently deliberately inbred to create vast range of breeds -body size varied now, exceeds wolves, canidae fam -behavioural mod is extraordinary -domestic dogs selected to suppress some behaviours and display others ex) spaniels will flush game from low undergrowth, bloodhounds smell, gazehounds see greatly, poitners detect prey + freeze w/o pursuing, foxhounds hunt in packs, shepdogs herd flocks of sheep w/o attacking, bulldogs grip prey and hang on, mastiffs are fighting and killing dogs -components or capturing prey in canids represented by a specialist breed, which is even further represented by specialist dog breeds -radiation of mammals has greatly defined diversity in last 65My -small animals diversified during mesozoic, each gave rise to one of cenozoid placentals, DNA analysis says happened in last ~100my -placental mammal radiation in cenozoic, modern orders descended from diff lineage already in existence 65mya -b4 radiation -> lack almost all shared/derived characters -after dino extinction, mammals able to radiate more, fill previously unavailable niches -thru many years of NS, mammals evolved a dominant foothold in modern ecosystems -adaptations like larger body size, mods to jaw, differentiated teeth, increase species overall fitness so they are fixed in pop -dogs guided by human choices to what character states and behavioural traits they possessed, where mammals were guided by survival an reproduction as NS determined their course of evolution

why do species become extinct

-all species eventually become extinct -become rare eventually > low resources, stochastic nature of survival and repro -extinction is balanced by speciation long term -origin of species must balance loss of old in long term 1 - combos of conditions, environmental, require particlar specialization, easy to understand extreme environments, flourish only if adapted, no species can b successful over whole range of conditions cuz adaptations reinforce success, if species is well adaped for particular way of life, extinction opens possibility for other species to exploit 2 - subtle, species adapted to partners and enemies, extiction of one may cause loss of ecological opportunitie and open others i.e. atlantic cod gadus morhua, if extinct, obligate parasite would as well, seals suffer less severely, competitors like roundfish n squid benefit i.e. short term community composition benefits at second hard org

to what extent does ancestral character state affect the subsequent evolution of that character in a clade?

-ancestral character gives genes/characters that can be modified to be made better, which gives evolution a starting point, but may be limiting sometimes because the building blocks cant be changed entirely but can be arranged in different ways or slowly modified -animals haven't evolved cellulose based skeletons > basal split between bikonts and unikonts left bikonts using cellulose and unikonts using chitin -cellulose is used in bacteria, bacteria dont use chitin

how have antifreeze proteins evolved in polar fish?

-antifreeze gene allows fish to live in antarctic waters -antifreeze gene evolved from a digestive enzyme trypsinogen, due to replication slippae, deletion, frameshift created stop codon -antifreeze gene evolved by process involving recruitment, amp, and deletion of intron and exon sequence from parts of digestive enzyme gene -independent evolution of antifreeze in arctic fish, happened in different ways from different genes, > *convergent evolution*

what are the main genetic mechanisms that lead to appearance of new genes?

-arise by mod and recomb of old genes, thru mutation and selection, by duplication an divergence, -origin of new genes is fundamental source of variation for evolution -made easier thru genes modular organization, recomb of modules

compare and contrast diversification of specialized lineages in sexual and asexual organisms

-asexual lineages diversify indefinitely, but usually become specialized to a limited number of discrete ways of life > depends n opportunity and cost, -opportunity = how "lumpy" environment is, many potential ways of life = many types may evolve, differing only slightly from one another, limited ways of life = limited types evolve -cost of adaptation is degree to which a particular way of life reduces success -inevitable tendency for diversification to be channeled into diversity of distinctively diff kinds observed in nature, factored by time -asexual dandelions have undergone mini adaptive radiation, loss of sexuality allowed them to diverge into many forms of slightly differentiated clones -Bdelloid rotifers have evolved into strongly differentiated types, no recomb, are completely asexual, clades have become adapted in long term to restricted number of ecological niches, males/sperm, in all temporary forms -baceria have high levels of diversity lumped into ecotypes: bacteria have restricted range of morphology, classical methods can only identify a few kinds, not all are named, but are *phenotypically similar uz they use similar C substrates* -infect same host, tend to be genetically similar -sex hinders divergence: sex nd gender are complementary attributes of sexual euks, can mate and produce offspring if they are the same species but diff genders -sex is governed by rules of fusion, dictates who can mate with whom, depending on the remoteness of their common ancestors -fish/other euks can be considered "sxually isolated", but this is seldomly absolute -species are only a strongly marked stage in divergence of differently specialized lineages -sexual isolation permits ecoloigcal divergence, and recomb prevents divergence -sexually isolated lineages evolve independently, tend to diverge, like asexual bdelloid rotifers/bacteria -lineages not sexually isolated diverge, but w GREAT DIFFICULTY, or not at all, bc random mating/recomb rapidly break up combinations of genes, prevent well-adapted combos from spreading in a population -sex is powerful break on diversification, pops become divergently specialized only to extent that they are sexually isolated sexual isolation can create species, when it is big enough to permit divergence sexual selecction or NS cn create new species

Give an account of the dynamics of genetic diversity in a chemostat population of bacteria.

-bacteria reproduce by binary fission, offspring will be identical to parent except for random mutations -mutations enerally deleterious, tend to accumulate bc each genome propogates the mutations it inherits while remaining vulnerable to new ones -in a chemostat, growing bacteria pop is not a single clone, but a complex and shifting mix of genotypes -beneficial mutations drive directional selection, effect of mutation depends on environment -within chemostat, conditions may be changed so that beneficial mutations become required for species' success -changes to ancient features can be lethal to cells, but carb metabolism, stress response, secretion are malleable cuz there are so many alleles with some more superior than others -mutations in here conditionally deleterious, reduce fitness when population is well adapted to a certain set of conditions, but can increase when the species changes conditions -constant conditions = allele that is the most fit to the provided conditions will dominate, and NS will enforce it thrughout the whole pop in the chemostat -adaptedness in ability to persist in given conditions, can be measred as rate of increase -fitness is ability to persist in given conditions when competing with others -amount of change in diversity in a population is proportional to the intensity of selection and quantity of genetic variation -sorting is the process of selection whereby a type eisting in the initial population increases in frequency an ultimately becomes fixed -beneficial mutations become established only if they survive stochastic loss

Explain the concept of periodic selection and describe how it can be used to study adaptation in asexual populations. Would you expect similar dynamics in a sexual population?

-beneficial mutations sweep thru asexual pops, where in sexual lineages the mutation becomes dispersed thru many lineages thru mating and recomb -asex allows mutation to remain linked w rest of genome from which it arose -single genome will replace others and consequently pass beneficial mutations is a sweep out of genetic variation by replacing the genotype divesity w a single clone -once clone is fixed, mutation will continue to operate, and genetic variation will be resoted -jagged dynamic as phage resistance and beneficial mutations compete -periodic selection will occur in pops w/o phage resistance -using gene markers in asexual pops helps detect the passage of a beneficial mutation -mix 2 strains which are genetically identical save for 1 marker, i.e. antibiotic resistance -start w equal amounts of both in a stressul medium -either one will spread to reach 100% of pops that grow best in ancestral medium to see that they do grow better than ancestor in medium -lab experiments demonstrates periodic selection, demonstrates the culmination of beneficial mutations during process of adaptation

what are the main ways new genes can arise from modification of old genes?

-by modification and recombination -modular structure of genes, exon/introns are spliced during transcription, errors can cause new exon arrangements to be transcribed, thru the rearrangement of their modules -adding/deleting/rearranging Upstream regulatory sequences can alter expression patterns of genes -recomb of modules creates new functional gene: new genes can arise thru failure of replication (deletion, translocation, recomb), or illegitimate replication (transposition, retrotrans), unlimited ways -new genes come from the modification/recomb of old genes -origin of new genes is fundamental source of variation for evolutionary innovation thru 2 processes: 1) mod of a gene by mutation, and successive substitution, can have successive improvement , unlikely to generate a new gene 2) recomb of 1+ genes to form a chimeric gene 3) duplicaton/divergence of a gene, one copy can evolve but one turns into a pseudogene

A new drug has been developed that selectively kills cancer cells. Describe how it might affect the population dynamics of a growing tumor

-cancer happens when genetic damage is present, and somatic cells uncontrollably divide >unregulated cell division, cells divide despite normal conditions or instructions -tumor population evolves and becomes better adapted to environment in process that causes progressive increase of fitness in the tumor but doesn't provide any long term benefit, and eventually dies with the host ex)CTVS is a canine cancer that can be transmitted thru dogs by sexual contact, UC parasitic mammal that originates on an insertion of a LINE retrotransposable element upstream of an oncogene that has spread worldwide

What is the evidence that the direction and intensity of selection often changes on short timescales? Be careful to take into account artefacts that might lead you erroneously to this conclusion.

-case studies on sticklebacks, finches, cepaea snails, all allow rate of change in contemporary populations derived from 2000+ studies to be calculated to abut 1kDar (doubling of character value over 1000 yrs) -more rapid change can be noticed than slow, but this figre and number of studies document rapid evolution, and establish that rapid evolution isnt unusual at all -where rapid flux in life conditions occurs, necessary for evolution to act quickly to maintain life in these areas -amount of change is almost independent of the length of time over which observations are made -selection changes magnitude and direction from generation to generation

describe and explain what is likely to happen when a culture is propagated by transfer of a single randomly chosen cell at the end of each growth cycle. How could events differ if two random cells were chosen? Or a thousand random cells?

-choosing parens of lineage randomly ensures that NS cant operate, pop evolves thru mutation alone -mean fitness declines over time in isolated cutures -as culture grows, each lineage descends from founding ancestor accumulates more mutations -cells chosen at random from one of these lineages will be a greater/lesser number of mutations, which will be necessarily fixed in the population because the cell will be the sole founder in the next generation -if 2 random cells start the line, similar processes of mutation accumulation would occur -at 1st transfer, diff lineage will be chosen to perpetuate each independent line, culminates over time, which increases on avg at each transer -variance of avg fitness increases over time -level of adaptedness declines over time when mutation is the only governing quantity of genetic variation in a population -replicates lines maintained in identical conditions will diverge steadily over time -starting w 1 cells = mutative accumulation, but not as severely, as if only 1 cell is propogating the line -with a culture of 1000 cells, there would be purifying selection to oppose the deleterious mutations -lineages bearing deleterious mutatins have opportunity to rise -more cells = sample becomes closer to representing each lineages feq in the population -tendency for fitness to decrease thru mutation will be opposed by the tendency of fitness to recover thru purifying selection

how might hybridization contribute to species breakdown an species formation?

-closely related species often hybridize. gradual emergence of new species implies hybridization may be common when it is possible -nothing inevitable or irreversible about the divergence of lineages -2 isolated or divergent lineages may continue and become sexually incompatible, it will cross less frequently when named as races, subspecies, species -outcome depends how frequently they mate -connected thru cross mating more strongly than they are separated by divergent seletion, will merge into a single lineage and stop right there -if mating is restricted nd infrequent, then more or less distinct species can be recognized despite production of many hybrids in each generation -physical separation can affect how much 2 species mate together, if they are separated and thus mate less together, they will eventually become more nd more dissimilar and speciate -nascent species of sticklebacks can collapse into a single lineage -benthic and limnetic species formedd over 20 years, differences disappered nd just represented the highly variable population that can collapse w introduction of exotic crayfish that altered ecology of benthic zone, driving them to mate more w limnetic form -hybrids can be inviable or sexually sterile, 2 barriers to hybridization in long-separated lineages: 1) failure to develop successfully thru mitosis: 2 haploid genomes may not be capable of directing development, > *hybridization opposed by natural selection* 2) failure to complete sexual cycle thru meiosis: hybrid diploid genome may not be capable of segregating successfully into functional haploid gametes > *hybridization opposed by sexual selection* -hybrids may not develop normally, i.e. in swordtail aquarium fish, pigmented by melanophore cells, when hybridized, offspring have black spots, some can have melanoma (skin cancer), crossing them results in separating the 2 species bc gene exchange between them cant be perpetuated -hybrids may not reproduce normally: develop normally but cant produce functional gametes, due to maladaptive gene interactions i.e. genes that govern meiosis or chr structure that doesnt allow pairing/separation of homologues -centric fusion: 2 chr that both have centromeres can form a single chr, then centromere is at the middle -when centric fusion occurs its hard to separate chr equally i.e. mus musculus, domestic mouse has fewer chr due to centric fusions, causes improper segregation during meiosis, hybrid males are sterile due to diff in chr structure and specific interactions between divergent genes -backX can sometimes yield fertile males, but incompatibility is likely due to interaction between few interacting loci -hybrid inferiority is caused by genetic incompatibility -lowers fitness, part of genome is part of environment, expression is dependent on regultion, that effect on fitness depends on how products interact w other genetic products -when 2 lineages separae, genomes diverge, each lineage will adapt w the genome that it has evolved -alleles that predominate this locus wil spread bc they interact favourably w alleles at other loci that predominate in the genome of the lineage -not necessarily interact favourably w diff set o alleles that have spread in other lineages

argue for and against the proposition that the species is the sole distinctive unit of natural variation, and come to a reasoned conclusion

-clssification is logical rather than real, some lineages will often divide into several incompletely separated descendant lineages that diverge to diff extents -whether lineages continue to exchange alleles thru mating affects how much they diverge -no clear line has been made between species/subspecies -species = natural unit, nominalism brings it into being -variety: most general term for distinct kind that isnt a species morph: type distinguished by a single genetic difference/few simple differences, include cryptic characters i.e. alleles at enzyme-coding loci -cultivar: variety deliberately produced by Artificial S -ecotype: variety w restricte geo distribution -race: variety w restricted geo distribution subspecies: race so strongly and consistenly differentited from others that it gets a formal taxonomic name -species: permanently distinct, sexually isolateed, distinctive eco attributes -clemidomonous: colonial algae in culture, confusing lines between colony morphology and species -specie are recognized when ecologically distintive forms become sexually isolated, species can hybridize, but often mark irreversible separation beween lienages n emergence of permanent -can say whether 2 orgs belong to diff clades, cuz a "clade" is natural category that is the outcome of . natural process -cant unambiguously assert 2 orgs are diff kind bc "kind" is an artificial category based on human judgement, often corresponds w higher rank of linnaean taxonomy -even when these are strictly monophyletic, subdivision of clade is limited to set of named sister taxa, always based on human judgement -despire subjectiveness, it focuses attention on phenotypic discontinuities between certain clades on innovations in particular groups

There are more species of insects and flowering plants than of any other multicellular terrestrial organisms. Why have they failed to occupy marine environments?

-convergence often fails due to AC, many structures fail to evolve bc the ancestral state of a group prevents and hinders evolution in a prticular direction -presence of an ecological opportunity isnt a guarntee that adaptation will occur, even in abundant groups over long periods of time -insects havent become marine: breathe thru their skin thru tracheae, pores in cuticle -stepwise gradual adaptations an insect would need to take to adapt to marine life would need to increase fitness at each step for selection to select for that process of modification -other orgs like krill, small crustaceans that already occupy those niches -angiosperm havent become marine: -dependent on PS, CO2, H2O for water and food -ancestral states have made PS pathways well adapted to current habitats -any step-wise transition to sea would be difficult to make improvements to fitness -corals, seaweed, marine plants already occupy marine environment, would be hard to outcompete them

Describe how kin selection can lead to the evolution of altruistic behaviour. Distinguish between direct and indirect effects, and how how indirect effects discounted by relatedness lead to a definition of inclusive fitness.

-cooperative behaviour can evolve thru reciprocity and retribution, but does so bc reciprocity confers an indirect benefit on behaviour -altruism confers no benefit at all to donor -profitable divison of labour amongst all MCOs ex) soma-germ distinction dpeends on relatedness of cells making up the body of an individual, from which a soma caste evolves that prioritizes the success and needs of germ line, among individuals in eusocial orgs ex) hymenopterans - ant colonies w different castes for foraging, defense, and other duties to support the few reproductive individuals -inclusive fitness = sum of direct and discounted indirect effects of behaviour on the production of offspring by focal individual (direct) and other individual (indirect) is the currency of kin selection -altruism evolves when a benefit conferred on relatives, discounted by their relatedness, exceeds the cost to the giver -summarized using hamiltons rule: rB>C -B is benefit recieved by recipient of an altruistic act -r is relatedness of actor and recipient -C is the cost of the act to the actor -altruism only spreads if the inequality is true -evolution of altruism depends on only the probability that 2 interacting individuals bear copies of the same "helpful" allele -Kin selection favours helpfulness bc relatives are more likely to have copies of the allele that governs helpful behaviour, NOT bc relatives share genes -incusive fitness = repro achieved by individual + repro achieved by relatives thru assistance given by individual -behaviour that increases inclusive ftnesss will be favoured by selection

Explain why populations adapting to a novel environment may exhibit reduced fitness in their ancestral environment.

-cost of adaptation is that org loses ability to succeed well in environments other than the one it is well adapted to -advance of fitness in new conditions is achieved in expense of a regress in other conditions > *adaptation is always conditional* -regression can arise from functional interference, structures cant be highest functionality at every task or from mutational regression -loss of function mutations in structures used for previous lifestyle are neutral, so will accumulate (i.e. cave animals losing sight) -degree of functiontional interference will be greater in lines that diverged more, leadin ot negative correlation with performance in ancestral environment -degree of mutational degradation will be a function of time alone, so all lines are expected to be equally impaired

define macroevolution and microevolution. are there any differences between them?

-difference exists between origin and fate of variation -origin of variation: governed by mutation/recomb -fate of variation: governed by NS/genetic drift *microevolution* - alterations w a small effect on phenotype that occur frequently, can be taken for granted, so selection governs outcome of this evolution *macroevolution* - alterations w large effects on phenotype, occur rarely, have a profound effect on outcome of evolution, mutation governs the outcome of this evolution -both are the same process occurring at different scales -doesnt imply that different processes are involved -potentially beneficial mutations will continually arise, their frequency is related to how large their effect is -selection can't cause beneficial genetic alterations, it can only select on them after they have appeared: -variation is produced by mutation and recomb, together determine how far a lineage will respond to selection -rate of resposne might be selected -ex: lineage w genetic predisposition to higher rates of mutation might be less fit or more fit

what is convergent evolution? explain why it occurs, and use examples from a wide a range of organisms as ossible

-different groups may independently evolve similar adaptations to a given way of life > variations on a theme can evolve from homologous characters > homology but, when variations on a theme evolve from non-homologous characters > convergent evolution conv evo. is different than parallel, bc its the convergence of *non-homologous characters in distantly related orgs* -structures are encoded by different ex) features -billed snouts in ducks, platypus, and hadrosaurs -silk production in spiders, silk moths, caddis flies ex) ways of life -insectivory among plants living in acidic, N-poor bogs -echolocation in bats, oilbirds, cave swiftlets -hovering nectar-feeding in hummingbirds, honeycreepers, sunbirds, sphinx moths

Why is the germ line of multicellular organisms segregated from somatic cell lineages early in the development of many groups?

-distinction between soma and germ cells is most important aspect of MCOs -somatic cells: help germs reproduce and increase reproductive capacity of the individual, dispensable, have the role of terminating the individual -germ cells: reproductive function -potentially immortal by descendants continuing the lineage -vulnerable to invasions by selfish cell lineages in somatic cells >mutant alleles that direct somatic cells to redifferentiate as germ cells, threaten large individuals greatly -setting aside germs during early development prevents selfish lineages from arising thru somatic mutants that disrupt development by re-entering germ line ex) Bilateria set aside early on ex) Humans set aside early on > why kidney/brain cells cannot redifferentiate as gametes ex) regA mutants of volvox give rise to colonies that are not longer motile cuz selfish mutants arise. this is really uncommon in related organisms bc normally germ cells are set aside ex) cellular slime molds are UC amoebas that can aggregate into MC "slugs" during scarcity -selfish amoebas that differentiate into spores are the ones that propagate their genome, others are altruistic and form stalks that hold up spores -without distinction between selfish/altruistic amoebas, the spores wouldnt be able to be held up and everyone would die w/o this distinction -slime molds are vulnerable to selfish cell lineage invasions bc body is formed by unrelated aggregation of amoebas

discuss that evolution inevitably leads to the appearance of more complex body plans

-distinction between soma and germ is key feature of MCOs during evolution -developmental systems that control cell proliferation evolved in conditions that favour multicellularity >cooperative division of labor to increase productivity of -after developmental systems evolved multicellularity and cooperation, these systems were modified gradually so that each major clade has a unique way of developing ex) volvocales divide labour between soma and germ, which has led to evolution of 5 other major groups: brown seaweeds, red seaweeds, green plants, fungi, metazoa -distinction between soma and germ allow organisms to endure more adverse conditions: i.e. cellular slime molds are aggregates of UC amoebas that form MCOs when food is scarce to pass on spores of amoebas to further away places, which allow further evolution -secondary somatic division: evolution of somatic cells inevitably leads to their further development >larger range of somatic cells produced to further cooperatively divide labour and create more specialized cells, which evolved thru mutation because specialization increases reproductive and productive abilities of cell ex) in animals, gastrulation is an innovation that allows complex body plans, creates distinction between inside and outside of body -gastrulation creates inside/outside distinction, which is reflected by coeloem -coeloem allows circular and longitudinal muscles to provide thrust by pulling on it, gives thrust and locomotion to animals w inside/outside distinction -coeloem is further segmented, which allows modular changes to develop without disrupting development of other modules, creates more opportunity for diverse developments -modification of modules is key to evolution of complex bodies in arthropods and chordates i.e. change in segment number in myriapods, repeated segments for different functions in arthropod limbs, and homologous parts modified differently in arthropods, i.e. crustaceans, myriapds, chelicerates

describe the failure of a major group to evolve specialization to a particular environment

-divergence often fails due to AC -goal, divergence of specialization of homo. strucures as an adaptation made by natural selection, isnt always successful cuz selection cant make incremental improvements from ancestral state -shown when not all clades radiate the same extent compared to sister clades > monotremes and therians, birds and crocodiles ex- marsupials havent evolved into fully aquatic forms, cuz their ancestor had a marsupial pouch that would be inefficient in swimming so no improvements can be generally made >one aquatic marsupial overcame AC and evolved musucular closure to is pouch and males enclose scrotum in a muscular clsoure too -lack of aquatic marsupials are explained by their prior adaptations from placental mammals tht occupied these niches and were too good of competitors for marsupials to occupy those lifestyles ex- insects havent evolved into large terrestrial forms, too small, restricted by tracheae, pores in body that allows diffusion, that would be too slow to provide O2, materials, etc to whole body if they were any larger

contrast adaptive radiation and convergent evolution

-divergence/adaptive radiation: homologous structures are modified for different ways of life within species in the same monophyletic group. may be superficially similar but are really just mods of the same ancestral structure -used to occupy different niches and exploit different opportunities than neighbour exploits that are available i.e. birds beaks convergent evolution: non homologous structures are independently modified for similar ways of life in different groups of species -species that arent related modify their own unique ancestral characters to exploit the same opportunites that another species does and they end up looking really similar i.e. wings in tetrapods and insects

what ecological processes might explain distribution of thin-shelled and thick-shelled forms of the same species of snail on a rocky shore?

-divergent adaptation generates distinct imperfectly isolated groups within species -sexual isolation creates genetically based ecotypes to evolve -Littorina are tidal snails subjected to crab predators and wave crashing can hurt them, shells cant be designed to protect against both -variety of species depends on site and distribution depends on local circumstances -2 varieties not species bc they readily interbreed, but distinct appearance is maintained thru 2 varieties being physically separated (even if its just a few m, its relative) -only found w direct development, young develop in egg mass glued to a rock, crawl away as mini adults, restricts dispersal and sexual contact between varieties, allows to maintain differences

describe the ecological and genetic factors that have led to rapid diversification in present-day animals and plants

-diversification is the natural tendency of lineages, due to cumulative nature of genetic change -any 2 lineages that dont xchange genes wil almsost certainly diverge due to 3 reasons 1- neutral subs occur randomly, extent of divergence at neutral sites can be used to date the coalescence of 2 lineages 2- beneficial mutations arise in random order, will usually be different order in every lineage, effect of the mutant allele depends on state of other loci, will alter relative fitness of other mutations. fixation on a particular mutation will make it mroe liekly that some will be fixed and less likely that others will be which applies to every successive beneficial mutation, independently evolving lineages may acquire diff combos of alleles, even in similar ways of life 3- lineages may become adapted to diff ways of life, i.e. diff food, tolerating diff physical conditions -always involves mutations in diff genes, likely to cause phenotypic divergence, process leads to emergence of lineages w distinctively diff morpholoigcal, physio, behavior charactristics that we recognize as species -varieties are readily produced by artificial selection, i.e. plant breeders, tall biennial plant brassica is bred to exagerate one srtucture, but another plant has given rise to familiar veggies -rapid speciation gives rise to swarms of sister species -hawaiian crickets have evolved rapidly thru sex. selection on male song, not ecologically distinct, but males have diff courtship songs and females prefer song of own lineage -> sexual isolation, emergence of species that arent ecologically specialized pacific tree snails in Partulidae fam in tropical Pacific, snails cross w difficulty, diverged on island but occupy different/overlapping sites -hermaphroditic snail -shell coil is a barrier to mating -can hybridize, but not always cuz abnormal genitalia due to genetic incompatibilities -most species gone extinct cuz of intro of African snail as food, but threatened crops, so another predatory snail was introduced that accidentally fed on Partula -relaxing cytogenetic constraints promotes speciation -centromeric property enables some orgs to pair along whole length, when chr break, both fragments can be stably transmitted so chr are segregated equally and offspring are viable i.e. sedges carex have diversified into 100s of species -all species eventually become extinct -become rare eventually > low resources, stochastic nature of survival and repro

explain why extremely narrow specialists and extremely broad generalists are unlikely to evolve, using economic analogies.

-division of labour: in ecosystems, cant have same task occupied by many groups, = inefficient -too specialized can be detrimental if that task is no longer needed ex printer maker dies if world doesnt need paper anymore -want to be right amount of broad, staples, so that if one part isnt useful anymore, it can survive off other revenue =production examples related to food sources/habits, species can live off many food sources so if one supply is unavailable, it is not catastrophic -cant be too broad, as demand for each resource/habit will be greater than the supply, other species will be better adapted to fill resources niche and more efficient at obtaining them -must make a compromisse -too narrow = too dependent on one ting -too generic = too many deterministic factors -economic analogies > country only importing one thing and its not available -generalist may be outcopeted by specialists -generalist my be outcompeted by specialists -buy stocks based broadly or by just one

how have main features of eukaryote cell evolved?

-euk genomes sculpted by size and sex -descended from proks, but ~10,000x larger -comound cells, have genomes outside nucleus -linear chr -replicated by mitosis driven by mt cytoskeleton -endosymbiosis helped form larger euk cells -mito evolved from endosym. bacteria, large remnants of OG bacteria genome, encode many proteins in respiratory ETC -mito contribute lots of E, when compared to proks of the same size due to SA, euks create much more E which can help them grow in size, gives capacity to enlarge nuclear genome while maintaining same E supply/gene which allows them to evolve and become more complex >euks evolved frm 5000 gnes in bacteria to 20,000 in MC euks -telomeres and centromeres evolved to help replicate the large genome enabled thru endosymbiosis -telomere: maintains ends of DNA that could be lost when RNA replicates, due to linear nature of DNA. uses RT and templates so DNA can be saved -centromeres: structure w short central region that mediates chr segregation during meiosis, ensure all chr are equally segregated during division to avoid deficiencies -low gene density due to mobile genetic elements, i.e. retrotransposons/transposons that dont contribute to performance of cell

why have feathers only evolved once, whereas MC and C4 photosynthesis have evolved independently in many lineages?

-evolution occured relatively early in amniote radiation (excludes amphibians from tetrapods), nd thus most land animals were privy to the innovation due to sharing a recent common ancestor w amniote -aquatic animals and UniC orgs dont need bc they would make them inefficient, reduce streamlining, weigh them down, too big -MC and C4 PS evolved independently in many lineages bc they were not shared by a common ancestor, but both helped to improve the fitness when they did evolve -didnt necessarily evovle in the same way as there are variations in methods and adaptations, but both produce the same innovative result

Explain the concept of evolutionary rescue and predict how the frequency of rescue will be affected by population size and the rate of environmental deterioration. Are there any other conditions that might affect the frequency of rescue?

-evolutionary rescue is recovery of a population due to adaptation -if stress isnt extremely severe, or is applied gradually, spread of resistant types may rescue it from extinction -pop first declines, as susceptible types are eliminated, but then recover as resistant types spread to higher freq -U shaped diagram emerges as time curse of evolutionary rescue is demonstrated in the lab, i.e. exposing yeast to salt concentrations -population must be large as well to have present phenotypes that are resistant -evolutionary rescue can lead to tolerance of conditions that would be lethal to ancestral pop -not limited to range of variation originally present -more likely in large pops declining slowly in abundance

major features of extensive clades (i.e. body cavities or roots) can be interpreted as a) accurate indicators of ancestry, or b) adaptations to particular ways of life. reconcile these two points of view.

-evolved design is created by functional utility and ancestry *ancestry* -homologous characters are characters amongst diff species that are similar due to their inheritance from the same ancestor, which is essentially attributes from inherited genes that are the same, show that ancestral constraint can affect how utility evolves *utility* -function of a structure can sometimes induce evolution, regardless of ancestral state, shwon thru connection between design and lifestyle, nd how utility of structures is expressed at all phylogenetic legels -body cavities: -in worms, coelom or body cavity acts as a hydrostatic skeleton that allows longitudinal and circular muscular contraction for movement -later, coordinated muscles and skeleton is used in other metazoans, like arthropods, tetrapods, which adapt on the ancestral inheritance of a body cavity but also use it for locomotion as it was used before -worms just need coeloem, -roots: -shared derived characters for terrestrial plants have roots + fluid conducting vessels, i.e. in moss, vascular plants, seaweed, all have sort of root system -seaweed doesnt need structure cuz its kept afloat by water, moss stays low to ground, but trees have lingin in bundles of tubes and is strong enough to allow trees to grow up to 30m -roots and body cavities are examples of adaptive body plans that are inherited from ancestors and shared derived characters among large groups, but are adapted finely to each species way of life

Explain the process of lineage sorting that occurs when 2 populations become permanently separated, from the time of their most recent common ancestor to the time when each has become monophyletic.

-evolving genomes diverge -happens in a more complex way than looks in phylogenetic tree, bc irl its made of many lineages proliferating over time that all must accumulate the same differences ex) S. Cerevisiae nd sister species S. Paradoxous diverged 5-10Mya, but still mate occasionally -genotype lineages eventually correspond to species lineages 1) both populations have lineages from ancestral population. neither are monophyletic 2)share a last common ancestor, the most immediate descendants from MRCA, when splitting thru acquiring different mutations, each population will have descendants from ancestors 3)number of lineages that both pops share decrease due to random loss or different environmental conditions that better genes fare in, making them more selected, differences become fixed (alleles present in one diverging pop and not in the other pop) 4)both populations continue on and dont cross back, each population will descend uniquely from its own LCA and then they become truly monophyletic 5) if the diverging pops reunite and mate again, they will converge and most do

Bright and conspicuous sexual ornaments threaten the survival of the males that bear them. How do such exaggerated male characters evolve?

-exaggerated male traits typically evolve in promiscuous species -trais rely on balance between NS and SS -f prefer males that display higher fitness characters, thru physical traits that are expensive to produce and advertise the males fitness -allels that express these characters are supporte dby NS as only fit individuals cn display them as well as being fvoured by SS -dual suport of NS and SS creates higher discrimination among females and exaggeration of sexual advertisement among male -NS may supress these traits that have been ridiculoously expressed, i.e. african widow birds tail hinders flight although f still select for it will find an eventual balance

describe the evolution of the eyes that evaluates the contributions of adaptive radiation and convergent evolution.

-eyes evolve independently but are all controlled by the same regulatory genes -at deeper phylogenetic levels, ancestral states become more different and have greater constraints, and convergent evolution becomes less apparent, but similar adaptations over wide lineages show the persistence of fundamental homologies -eye spots occur in many euks, found in 5 metazoan clades: Cnidaria, Panarthropoda, Annelida, Mollusca, Chordata, ancestral feature that shows inheritance for similar functions but have diversely radiated in all clades -pax6 gene that regulates expression of eye in mice, drosophhila, many other organisms show that *eyes are independent modifications of the same ancestral state* -eyes evolved in marine animals, all eyes filter out wavelengths in sunlight, show mark of ancestry even though it can limit eyesight of terrestrial animals and isnt a perfect design -eyes are tailored to way of life, i.e. eagles can resolve image 10,000x better than flatworms, but flatworms are 100,000x more sensitive to light. one isn't "better" than the other because they are both uniquely adapted to their way of life > adaptive radiation to better exploit their environments -vertebrate eyes are different than cephalopod eyes, show convergent evolution because they have the same function but develop individually -vertebrae: develop from neural place, inducing overlying epithelium to form lens, ciliary eyes, optical pigment packed into modified cilia -cephalopod: develop by infolding of sheet of epidermal cells > no cornea, have rhabdomeric eyes, contain opsin in microvillar extensions of cell membrane Mollusk evolution of eyes show eye at different levels, show how radiation from same ancestral character has allowed many types of mollusks to occupy different niches -no eyes: monoplacophorans, aplacophorans, scaphopods -simple eyes: nudibranch has pigment granules that detect light presence -simple eyes, more developed: pteropod , pigmented vesicle protected by epidermal layer w a single nerve cell -more complex: limpets, open cups w epidermal cells whose distal ends are pigmented, supplied w optic nerve, bivalves, archaeogastropods -even more compelx: prosobranch has multicellular vesicle embedded in skin, diff regions become specialized, interior is fluid filled, crude lens, -most complex: pelagic mollusks, cephalopods, similar to vertebrates, cornea, iris diaphragm, lens adjusted by ciliary muscles retina w light sensitive cells, pigmented ends directed outwards, nerve fibers collected into optic nerve leading to brain

describe the social dynamics of a mixure of fermenting and respiring genotypes of bacteria in a chemostat.

-fermentation uses organic compound as e acceptor, high ATP production but low yield -respiration uses external e acceptor like oxygen, which has low ATP production but high yield -fermantation is fast, but wasteful, respiration is slow but efficient -fermentation favoured by NS in animals that compete freely for available resource (i.e. sugars in solution), cuz they need to be fast to beat competitors to resources regardless of wastefulness -respiration favoured: food is eaten prior to use -inefficient fermenters release intermediate products (acetate, ethanol) that are built up in cell and reduce their metabolism if kept -respirators use these products as substrates -respirators that arise from mutations spread bc they can use the waste products > *cross feeding* -depends on both types living in the same community together >metabolically diverse community, makes it a social process -fermenters like small colonies, respirators like large -large colonies can grow on medium where small colonies previously existed -both types have inversely related population dynamic, increasing freq of respirers will give fermenters greater fitness, vice versa -when niches of heterogeneous environment provide refuges for specialized types, freq-dependent selection acts to preserve diversity

How does sex modulate the process of adaptation? How is this affected by mating behaviour (inbreeding vs. outbreeding) and meiotic recombination?

-fundamental outocme of sex is diversification -sex facilitated adaptation by providing continual soure of new genetic variation on which selection can act -accelerates evolution cuz it doesnt follow same stepwise accumulation of mutations that asexual lineages do -beneficial mutations can be combined in the same lineage via mixis, gametic fusion and recomb -selection takes over, then spreads to genome which beneficial mutations hare arisen, n can be perpetuated in combination -since they evolve more rapidly, they can adapt quicker to novel stersses compared to asexual ex) yeast experiment, 2 genes responsible for sexual repro were deleted, made into asexual lineage, then placed w a sexual lineage in stress. = no appreciable diference in lineage conditions was found in benign conditions, but under stress, the recombining lines adapt more rapidly due to genetic variance generated by recomb -recomb further separates beneficial mutations from linked alleles, means that deleterious alleles associated w beneficial mutations dont always get passed on to the offspring -sexual lineages only evolve rapidly if population is large so mutation rate is high and potential variation can be released by selection -inbreeding is not beneficial in sexual pops, and outbreeding is requirement for continual success of sexually reproducing lineages -fixed permanent genders promote outbreeding

describe early stages in evolution of an intracellular symbiont, using examples from contemporary organisms

-fusion of dissimilar cells has led to new kinds of euks, loss of cell wall gave euks ability to engulf an digest bacterial prey -heterotrophic bacterium descendants are mito -endosymbiosis sometimes evolves thru survival of prey i.e. Pelomyxa is amoeba that lives in mud, can evolve endosymbiosis w partners i.e. algae, relatinships are basd on C they fix -euks incorporate 2 radical innovations originating by fusion -most recent CA of euks had single organelle, mito, for respiration, fused w mito due to mito's bacterial genome and double membrane (including bacterial membrane and host vacuolar membrane) *euks are compound orgs that rely on cooperation of partners* *mito* -respiration w electric potential ax membrane, required for ATP synthesis -almost always reduced to core genes that encode subunits of respiratory chain enzymes *partners may not always have same interests* -nuclear and mito genomes have a common interest to propogate the cell/individual, aka, genes in nucleus or mito that enhance propogation of cell/individual tend to spread as a lineage replaces others w less effective genes >flawed argument cuz it considers them a UCO -interest of independent replicators may differ even when in the same organism -partly resolved when any process (like recomb) shifts genes from one compartment to another, movement is almost entiremy from mt genome to nuclear genome -mt genome becomes much smaller -most euks encode only a little more than set of proteins responsible for gen of high-E phosphate bonds in respiration -all mito descend from a single bacterial ancestor -all euks have mt except for a few UC parasites that have secondarily lost them *origin of plastids* -evolved along many routes -more complicated than mt -chloroplast of green algae descended directly from cyanobacterial endosymbiont bc they have 2 membranes -all land plans have inherited this chloroplast *PS euks all descend from a single ancestral partnership between euk cell w mito and cyanobacterium*

Give an account of the Hawk-Dove game and explain how it helps to understand the evolution of sharing.

-game used to analyze strategy employed when a good is discovere by 2 indviduals that can share or keep it -hawks are individuals who fight -doves share -2 doves share equally -2 hawks fight and winner gets whole -hawk and dove meet, dove runs away, hawk gets whole -outcome pairing can be expressed in a pay-off matrix, where total V value is input for each individual, and cost of losing a fight to another hawk: Hawk v hawk: V/2 - C/2, V/2 - C/2 Dove v dove: V/2, V/2 Hawk v dove: V, 0 -pure dove isnt a stable state, pure hawk can be provided cost of fighting but fighting is v costly (C>V) -ESS mix of hawk and dove, explain how sharing goods can evovle despire presence of unconditionally aggressive types

account for evolution of male and female gender

-gender evolved to restrict gamete function, and is a property of the gamete -result of combo of natural and sexual selection -purpose in UCOs is to prevent mating between members of same clone, enforces outcrossing -some species have more than 2 genders -sexual binary is defined by the small motile male sperm and large non motile female gamete -tradeoff that caused binary to arise: -size-number tradeoff for gametes, (larger gametes = fewer made) -quantity-quality tradeoff (larger zygotes will develop more successfully, but fewer can be made( -size diffeence btween potentially fusing gametes is beneficial, a few microgamete producers invading a population of macrogamete producers will produce many moderately successful zygotes (favours numbers), few macrogamete producers invading pop of microgamete producers gives rise to larger nd more successful zygotes (favors size/quality) -evolution of gametes arises from balance between NS (fewer larger gametes) and SS (more smaller gametes)

Explain how the coevolution of host and parasite can lead to an arms race.

-gene for gene system , steady state will evolve at H2/P2 cuz H2 has advantaeg over H1 if there are P1 parasites present, nd P2 has advantage of P2 -leads to perpetual strong selection among H2 for any resistance against P2 > arms race -oats in 40s susceptible to oat stem rust, disappeared after is introduction -replced by hybrid cultivars resistant to stem rust race 1,2, 5, but susceptible to 8 and 10 -as it spread, crown rust epidemic began -hybrid oat was forced out, replaced by 3rd kind, reistant to 8 and 10 but susceptible to 7 -virulent crown rust and stem race 7 began to spread -continual coevolution arms race is common outcome of monocultures

what are consequences of lateral gene transfer in bacteria?

-genes often transferred from distant relatives in bacteria, HGT represents macromutation that gives a lineage a new gene quickly w/o gradual process of mutation and selection -causes bacteria to have mosaic genes, from taking up large pieces of DNA -plasmids can cause genetic material to be transferred between different lineages thru conjugation, infects an uninfected lineage quickly and integrated into host genome and passed to progeny -bacteria acquire new genes directly from environment, pieces of DNA released by dying bacteria, has possibility to provide genetic variation that contributes to adaptation

why are hybrids often inferior in vigor to either parent?

-genetic incompatibility of parents may lead to hybrid inferiority -lower fitness levels bc expression of genes that are regulated are affected by their interactions with other products made at other loci -when lineages separate, alleles will not necessarily interact favourably when they meet again in the hybrid, majority will ot matter, but small number of loci interactins are so incompatible that they pose a big enough barrier to hybridization -hybrids may not develop normally: -swordfish aquarium fish -platyfish, related species w black spots caused by melanophore cells, can be both crossed, but crossing them effectively separates the 2 species cuz gene xchange between them cannot be perpetuated -hybrids may not reproduce normally: -cant develop functional gametes -due to maladaptive gene interactions, i.e. genes that govern meiosis or gross changes in chr structure, i.e. centric fusion, messes up centromeres so chr cannot separate properly prevents gamete formation i.e. Mus musculus domesticus mice chr have centromeres near tip, centric fusions, hybrid males are often sterile due to chr structure and specific interactions between divergent genes, backcrosses can sometimes yield fertile males

Compare and contrast group selection and kin selection in the context of helpful behaviour.

-group selection can favour and select: > helpfulness > sharing (accomodating vs attacking/exploiting partners) > subsidizing (contributing to public goods that others use) > cooperating (trading honestly despite risk of loss to cheats) > sacrificing (sacrificing personal fitness for gain of others) -traits only selected for as they confer benefit to the donor -being part of group is beneficial bc it makes individual more fit, productive, safe -kin selection favours helpfulness bc relatives are more likely to bear copies of an allele that governs helpful behaviour ex) honey bee colony, high degree of relatedness betweek queen and workers provides basis for kin selection -when fam live together and act as a group, successful families will transmit attributes to next gen disproportionately, even if fam members only assist rather than reproducing themselves -kin selection accoutns for evoltion of altruistic behaviour, which exceeds the helpfulness that group selection accounts for

Explain how selection can act among groups as well as among individuals. Compare the efficacy of individual selection and group selection.

-groups that cooperate may be likely to collapse and are more productive than selfish individuals ex) food resources exploited more effctively by larger group ex) more likely to withstand attacks -cooperative groups expand at the expense of selfish groups> expand freq of cooperation as a whole -process of selection among groups rather than individuals -selection can act on individual of there is a trait that affects individuals fecundity or viability that varies ax a population -social trait affects a groups productivity, varies among groups, and is likely to be controlled by group selection -group selection: only affects traits that influence group dynamic ex) territorality, cooperation, other social traits -diff types of selecion interact to generate fit groups made of fit individuals -group selection may have strong effect on species -if species is well adapted and group dynamic is well established, group selection may not act that strongly, and same goes for individual selection

how can duplication lead to the evolution of novelty?

-having 2 copies of a gene allows one to be modified so the OG copy can still perform its normal function -the copied gene can diverge and acquire new functions -can occur rapidly bc usual constraint on modification that the ancestral function be maintained, is relaxed *duplication provides opportunity for functional divergence* -applies to every level of structure > genes thru cells to organs to bodies -colonies: portugene man of war is blown by wind aX se, tentacles have cnidocytes, stinging cells -body is formed by interconnected zooids, which each has own complement of organs, zooids become specialized tasks -modular construction made possible for compound organisms to evolve by dividing labor among component parts -individuals: Volvox duplication of cells creates potential for some to differentiate soma-germ cells -large MCOs may become further differentiated -genomes: whole genome duplicated by dividing chr w/o usual division of cell/hybridization between related species -genes: 2 copies of gene readily created by errors during replication like unequal crossing over *gene duplication can lead to novel capabilities* -new genes evolve from simpler predecessors thru gene duplication -crossing over at meiosis in unaligned chr, causes several ancestral genes to be produced -duplicate is redundant, often deteriorates thru mutation until inactive and lost -or, duplicate can evolve new functions -whole genome duplication can lead to adaptive radiation >yeast radiation involved gain and loss, includes whole genome dup >when bakers yeast was duplicated, ~90% of duplicated genes lost -individually duplicated genes can be generated by transposition -experimental lines often show high levels of aneuploidy -yeast genome in constant state of flux

discuss the statement that "the limb of a horse is homologous to the limb of a frog but not homologous to the limb of a grasshopper."

-homologous charaters - similar characters amongst species due to inheritance from the same ancestor >shared primitive and shared derived character states are *homologous in members of a clade* -dependent on similar ancestry *true aspect of homology is that genes are homologous, not characters* *analogous characters* have similar functions but are not modified versions of the same ancestral character -horse and frog are both tetrapods, share a similar ancestor, but grasshopper is an insect and doesnt have a similar ancestor -similarity of function/utility of a leg evolved in different groups due to convergent evolution -not considered homologous bc they have arisen due to mutation, not because they are inherited from the same ancestor

What sets limits to the virulence and host range that will evolve in a pathogen population?

-host pop can adapt to pathogens ex) composite cross pops set up in Cali 40ya by crossing barley varieties -attacked by pathogenic fungi -host and parasite are variable, diff genotypes of barley are resistant to diff fungi races -after 45 gens, freq of resistance to most races of pathogenic fungi has increased -plants bore genes at diff loci confer resistance to several rave of scald, fungi diseases -OG susceptible pops exposed to more pathogens evolve higher levels of resistance thru selecitonw initial variation and recomb -cost of adaptation sets limits to parasite virulence, and host resistance -hosts drive pathogen virulence, parasites drive resistance evolution in hosts -parasite types that are successful in attacking a specific host are unlikely to attack another type

Why are males usually more highly modified than females through sexual selection?

-imbalance of forces selection acting on sperm opposed to ova is related to quantities of each gamete -ovum responsible for cytoplasm of zygote, NS acts on it the most, favours quality over quantity -NS acts thru success of offspring into which zygote develops -sperm contributes relatively little to zygote, but to be successful, the sperm must compete w million of others -gametic competition extends to organismal level, motile males compete amongst one another -sexual selection acts dif on males, while ovum can be fertilized only one, male can fertilize ova of many females -sexual competiton among males leads to more extensive sexual modification in males -diff morphologies arise to exploit weakness of other male morphologies, to increase likelihood that male will outcompete others and fertilize ovum -lineages where gamete fusion involves courtship and copulation, differnce in mod is further remarkable *males are highly modified bc they have greater variance in fitness* 1) fecundity is more strongly related to # of matings males than for females (# of offspring produces increases linearity w # of matings for males, and single mating for female can provide enough sperm to fertilize all eggs -greater variance in number of matings for males than females, and variance in fecundity in m is higher than f bc it depends on # o successful mtings they have >>>> Batemans principle

Explain how artificial selection can shift the range of character states expressed by individuals in a population completely beyond the range of variation in the ancestral population.

-in bristle exp, 35 gens of divergent selection on bristle # > ancestral population is upward and downward selected, lines come far out from the range of variation present in ancestral pop -avg value is 40 initially w most at 50, after selection, avg is 90 > impossible in ancestral gen -2 possible ways selection can reach beyond normal ancestral variation: 1) new mutations cause extreme phenotypes to occur -could have equally arisen in ancestral pop, but NS would eliminate them -spread cuz # of individuas who bear them are chosen, even if they are feeble in other qualities 2) alleles that cause increase in bristle # can be brought together by genetic recomb -bristle genes could be affected by many genes, ex) 12 genes, 2 alleles: 1 allele cause increase in #, other causes decrease in # -pop initially comprises a range of genotypes, fittest have largest # of alleles -in asexual pop, t would be fixed despite having deleterious alleles in other locations -in sexual pop, they can transcend this limit, produce recombinant progeny w range of phenotypes -recombination has effect of making all allelic diversity present in initial population, available to selection > drives pop beyond original limits of variation ex) systematic selection in Illinois corn-oil experiment from 1897-present: -outcome is similar to bristle exp - AS can modify the features of a lineage far beyond initial range of variation > upward lines rapidly evolve lower protein and oil content, hence retain considerable amount of genetic variation -lines begin to express deleterious side effects after many gens of selection > downwards lines for both protein + oil had low germination success afer ~70 gens

In the simplest life cycle a newborn would simply grow in size to become an adult. Why do complex cycles involving different kinds of individual evolve?

-indirect life cycle exist cuz mini versions of adults may not be viable ex) starfish larva cannot look exactly like adult because it would be too small to support water and vascular systems, larva is free swimming and propelled by cilia -different scales of life cycles develop indirectly from kids to adults -vegetative repro: -repro separates 2 body forms, individual exploits diff foods and uses active motile individual to find another person to have sex >cnidaria, jellyfish, polyp and medusa -sex: fundamental splitting between fusing and splitting, live as haploid and diploid, hard to tell in orgs that have haploid state thru gametes/immediate precursor cells, where haploidd produes gametes that fse and form diploid -ferns live as large sporophytes, release spores that are diplid that undergo meiosis to remake haploids -ex) trematode has many successions of complex forms that are linked by growth and development, no genetic/physiological need but just happened that way and works because each stage is well suited to exploit its environment

Describe and explain the outcome of serial-passage experiments in which bacteria are incubated in a series of host individuals.

-infecting animals w bacteria, harvesting bacteria after growth, then reinoculating new hosts taken form same ancestral, non-evolving stock -serial passage used in medical research to develop vaccines -serial transfer in a novel host is almost invariably accompanied by increase in virulence, which often increases rapidly to high levels -host body is huge stock of resources to pathogen that its poorly adapted to exploit, types that exploit well will be selected, and increased virulence is consequence of their spread -high virulence levels evole due to parasites transmission by experimenter, nd thus indifferent to health of their host ex) salmonella introduced to mice via serial transfer, increases mortality from 10 to 90%

what are the conditions that will promote adaptive radiation?

-isolated site that lacks other competitors -large site that has many niches to be filled

how did loss of most body hair and subsequent invention of clothing affect the evolution of ectoparasites of humans?

-lice have evolved w clothes -chimps infected w lice, in hair, suck their blood -humans infected w louse that shared our fate since human-chimp divergence 6Mya -human louse has 2 varieties, body louse, and head louse -invention of clothes gave lice back OG habitat, could shelter in artificial fur, making forays from time to time to eat their blood mean -different species entirely are pubic lice -divergence has 2 consequences: 1) use molecular divegence of lice to date origin of clothing, ~100,000 ya, same time humans moved from africa, clothes seldom preserved in ancient settlement sites, but evidence of lice is that full body covering was invented by some human groups around this time 2) degree of divergence between head and body lice. mrphologically v similar, molecular data shows no fixed differences, neither form distinct clade, even tho they can be traced to diff eurasian and american clades, but neither form distinct clade -clothing can be dated by mtDNA divergence -separate species can be recognized by morpholoy and habitats -subspecies, morphological diff are slight, clear evidence for interbreeding -race: too similar to warrant formal diff names -not a taxonomic entity, dont make monophyletic clades -can all be defended cuz evolution doesnt respect boundaries -formal names used when we cant to refer to type of organism, but doesnt reflect a real discontinuity in nature -lineages continually separate thru divegent specialization, and tend to cohere thru mating an recomb -when divergence dominates over coherence, nomination of species represents process -all intermediate stages can be expected between differentiated species

Discuss how local adaptation depends on the balance between local selection and immigration. How might this balance contribute to limiting the range of a species?

-local adaptation is degraded by immigration -selection causes adaptation in local conditions which is opposed by immigration and mutation -immigration degraded local adaptations cuz immigrants arriving at a site r likely to have been born in a different environment to which they are better adapted to > reduces mean fitness -immigration awy fom site where org is born in tends to spread out any genetic differences in pops, other things being equal makes whole species genetically homogenous -thus, local adaptation extent eends on balance of selection and immigration -high immigration prevents local selection from being effective unless its correspondingly strong -if local selection is weak, the range of a species will be reduced -once a species immigrates, selection needs to favour mutations that will allow the species progeny to succeed, or the species will be unable to adapt

identify the main steps that must be verified experimentally to provide a plausible route for the origin of life. which have been demonstrated so far? what are the main gaps in our current understanding?

-main kinds of orgs are readily formed by physical processes >can easily form organic molecules from inorganic ones, i.e. electric discharge in reducing atmosphere of CO2, ammonia, water vapor, can create sugars, aa, nts, etc >all basic molecules for life produced by chemical processes active in early earth system >RNA pathway not conclusively traced bc unexpectedly difficult to find how pyrimidine nucleobase cytosine and uracil can be bonded w ribose >no well established route to chemical synthesis of nts in early environment >origins discovered by 2 proceses: fossil records, range of variation among living tings *Origin of life* -3 main characteristics: able to replicate, viable populations, lineages evolve -can never be known for sure -appeared soon after liquid oceans formed cuz cellular orgs left physical and chemical traces from v early -construct series of intermediate stages between organ. molecules and simple self-replicating cells, havent achieved fully, but some crucial intermediate steps have been found *protocells* arise spontaneously and are readily selected -compartments are necessary for NS to act on phenotypes -cells key proterty os to retain physical link between chemical product and genetic system that encoded it -link of genotype and phenotype exist = NS drives evolution of more powerful and effective metabolic systems -require a cell to hold the replicator and any products it encodes -producers must have fruits of their labor accessible to them to gain any advantage by them -can be restrained more powerfully, if compartments able to replicate ever arise, they would rapidly replace all diffusive non-compartmental systems cuz they transmit improvements to progeny -compartmental systems arise rapidly uz they are strongly selected where diffusive systems rarely evolve -cell-sized hollow spheres are protocells, form spontaneously by fatty acids in water -cells/modern orgs bound by complex membranes, phospholipid bilayer, incorporates channels, pumps, pores -first cell was very simple, formed spontaneously thru chemical process, inherent ability to grow and divide -protocells could house 1st self-replicating system, cuz fatty acid bilayers are permeable to small charged molecules -first replicators were probably small RNA -short RNA molecules can form spontaneously -evidence for chemical formation of 1st self-replicators is still incomplete, dont know how how many self replicating RNA are but they had to have been really long, unlikely when mononucleotides are too dilute to add one unit to chain before its shortened, may have occured easily on charged surfaces like clay particles -main kinds of organic molecules are readily formed by physical processes -special creation: accepted theory, creationism -panspermia: -undirected panspermia: theory that life came from outside, dispersal of microbes from planet to planet, taken seriously ue to short interval between appearance of permanent oceans and 1st life signs -bacteria could easily be transported -directed panspermia: deliberate seeding of planets by aliens, incorporates an effective dispersal method -took 4By for intelligent life to evolve on earth, and we still cant travel to other stars -> taking 4By on other planets = gettin close to death of stars, -misdirected panspermia: galactic pollution

In what circumstances is competition more intense between (a) individuals of the same gender, and (b) individuals of different gender?

-males compete among themselves for access to f -f compete w one another for access to resoures -individuals unline gender who mate have common interest n producing/raising offspring -may be interest of eiteher partner to damage other if likely outcome is good for overall reproductive success >happens in promiscuous species, where there is no benefit to maintaining other partners wellbeing -competition is more intense between individuals of same gender in resoure and mating partner deficient environments -competiton between individuals of diff gender likely to be intense in situatiosn where male wishes to limit females potential to remate, otherwise increase his own fertilization success, and where ther are sufficient nutrients and mating partnrs, and when large fixed costs favour separation of male and f function

In what circumstances does sexual selection favor small size in males? Conversely, in what circumstances does sexual selection favour large size, weaponry and aggression in males?

-males generally smll to increase rate of mating -males make cheap and numerous sperm, turned over rapidly if they can find a female to mate with -beneficial for m to be small and active, where f are typically larger and sedentary as production of an egg is energetically costly -m modified largely depending on SS, males guard offspring, or fight for access to f , they evolve a larger size -sexual weapons used to discourage competitors, n are effective when resources that can b monopolized by stronger/better armed males ex) protect sexual resources - fiddlers crabs claws defend breeding burrows, guard females - sequestering f in herding animals, keep competitors away w horns/tusks -weapons used not jut to kill competitors but to evaluate strength of rival ex) red deer have beefit to standoff cuz winner gains control of up to dozen females

On what grounds might females evolve to prefer one type of male rather than another?

-males tend to maximize quantity of mates, f tend to evolve to maximize the quality of their mates -preference due to: >direct courtship benefit, like offerings to be used for individual or offspring, ex) insect "nupital gifts", or biggest minnows can make the best nests >due to sensry bias, where aspect of male morphology is naturally attractive to females ex) bright spots on guppies are preferred >basis of good genes, f may be able to identify for benefits for offspring -genetic superiority can b inferred by f, typically by vigor, epressed as expensive and lively displays in male >vigor can be result of upbringing and heritable trait, should be fixed thru pop thru NS >f chose males w lower mutational loads chosen by vigor ex) tree frogs, vigor measured as function of ability of m frogs to display mating call more vigorous males grew/survived better than less vigorous males -f may choose healthy males, courtship = meedical checkup conducted by f, variance is restored thru deleterious mutations or parasite host-co-evolution -traits that display health, i.e. wattles on male turke, cn convey strong parastie resistance or immune system to f -f may choose on genetic compatibilty ex) MHC alleles confer parasite resistance in sticklebacks, optimal MCH is 6 > f w fewer than 6 inclined to mate w m w more than 6 and vice versa -f may choose unusual males intentionally as they gie an indirect benefit thru their sons success, ex) african widow bird, long tail enhnces sexual succes but it also enhances offsprings sexual success (favoured by SS but not by NS)

describe the intermediate series of forms leading to the evolution of aquatic mammals from terrestrial ancestors

-mammals must pass thru intermediate stages to swim by modifying structures that are well adapted to terrestrial life > semi aquatic animals like mink, otter, beaver, who live in water but return to land to eat, sleep, mate, give birth -characteristic suite of features, live in freshwater, have dense non-wettable fur, light covering for living on land w sufficient insulation, mods for aquatic locomotion like webbed feet, long, propulsive tail -adaptations are inefficient cuz swimming at the surface is hampered by wave drag, KE is dissipated into PE of waves, thick fur is bad for deep diving, paddling is inefficient for moving cuz water resistance is encountered in recovery stroke >obstacles are overcome by aquatic animals by swimming fully submerged, blubber, use of hydrofoils to swim, physiological adaptations (i.e. salt secreting glands), bigger lung capacity for animals that breathe air, gills to take oxygen from water

how have mass extinctions changed the composition of the worlds biota?

-mass extinctions caused by large rare huge events >long run speciation balances extinction >long run may be v long time >extinction can occur quickly, speciaiton always takes longer >imbalance made dramatically clear during mass extinctions -mass extinctions have punctuated history of life >small magnitude events more freq than large ones >3 mass extinctions since cambrian: end of cretaceous (bye bye dino), paleozoic, end permian, destroyed entire marine biota, cleared stage for diff species that dominate seas today -most species extinct during end-Permian, unknown what happened, likely 2 events a few My apart -most likely a volvano erruption, oceans became anoxic, 90% of all species became extinct >some major paleozoic biota lost, trilobites were already declining but lost, coral reefs disppeared for 10My, grapolites, eurypterids vanished, acanthodians and placoderm fish died, crinoids and brachiopods severely pruned >1/2 of all tetrapod family lost, cynodont (mammal ancestors) and archosaurs among few survivors, eight orders of insects disappeared -evolution restored biodiversity in a diff form >end-Perm depopulates world 10-30My, until diversity began o recover in triassic -end of jurrasic, marine biodiversity restored to same levels before paleozoic -range f diversity recovered, but nature is permanently and irreversibly altered -typical paleozoic marine fauna of sessile filter feders replaced by actively foraging groups -continuous operation of evol. diversification at length filled up all ways of life that had beeen vacated, although didnt fill them w same groups or even ecologically similar representatives of unrelated groups -graptolites and trilobites gone, crnoids and brachiopods remain marginal, sea urhins and clams proliferated -evolution is a historical process, course depens on initial conditions, irreversible, mass extinctions permanently reset composition and balance of natural communities until next mass extiction

how does mutation rate evolve in asexual and sexual populations?

-microbes: more evolvable than animals/plants, are enormously more abundant than animals/plants, thus a greater N(pop size) increases mutation supply rate, thus are more variable and evolve faster -mutator genes can spread in asexual pops under stress, usually in LOF mutations in RNAP genes, which are selected against normally, but under stressful conditions may be selected for(when mean pop fitness is low) cuz they may cause a few beneficial mutations -mutator genes may spread cuz in bacteria genes, they are linked to beneficial mutations they cause, can be see in antibiotic screens -sexual populations: mutation rate is a compromise -mutator alleles occur in sexual orgs, arise freq cuz they are loss of function, dont spread cuz they become unlinked from any beneficial mutation, mutation rate is chronically low, and is driven down to value where costs of errors in rep just balance the advantage of avoiding deleterious mutations

Discuss the merits and drawbacks of using batch culture (serial transfer) or continuous culture (chemostats) to study evolution in microbes.

-microcosms allow unique opportunity to study pops capable of unlimited growth in small and simplistic ways -batch method: simplest way to transfer inoculum into fresh vial or medium -advantage of serial transfer, is that its easy and inexpensive -drawback: conditions of growth continually change, i.e. resources, to early growth, to severe depletion before transfer -continuous culture: avoid issue by constantly feeding nutrient medium into culture, while culture is drained at same rate using a chemostat -v brief adjustment period, inhabitants grow at rate determined by rate at which resource are supplied > constant growth rates -possible to study adaptation to precisely defined environents -difficult and expensive to maintain

Give examples of selfish genetic elements and explain how they evolve despite contributing nothing to the vigor of the individual.

-mito genome is not equally segregated during replication -when deleterious mutations arise, some cells can end up with all of the bad mutations, called "petite" -petite mito can be selected bc defective mito genes replicate well if the mutation increases the rate of replication i.e. deletions that reduce the size of the molecule -2 opposed functions that act on mito gene: selection among cells w good functional genes, or *selection among mito that favour defective genes if the defect increases the replication rate -selfish deleterious genes can be selected if they increase the rate of replication -selfish genes can exploit self-replicating systems that are non-specific -all replicating machinery are non-specific bc there is no mechanism that can detect what a gene will encode until it encodes it >genes and pseudogenes are treated equally >genomic parasites can exploit machinery by using it -selfish elements can compete for access to germ line, and can spread despite contributing nothing or even harming the individual as long as they are preferrentialy transmitted to offspring -selfish elements cn spread by destroying an allelic competitor in germ cells ex) gamete killers, elements that destroy gametes w/o a copy of the element, ensuring that offspring carry the selfish element ex) segregation disorder in dros. acts in hets to kill sperm w normal allele -some selfish elements spread by destroying entire genomes ex) PSR in wasps, transmit b-chr in sperm, causes ll parentally derived chr to degenerate, fertilized eggs end up as diploid females, and unfertilized eggs develop into haploid males, thus, all offspring that develop as males transmit PSR

how do deleterious, neutral, and beneficial mutations contribute to genetic variation of a population?

-mutation is the source of genetic variation, inevitable byproduct of a copying system (can never be 0 errors unless infinite resources are contributed to detection/correction) -neutral alleles: drift in freq by sampling error, no effect on protein synthesis, invisible to selection, genetic drift creates alot of fluctuating variability at intermediate frequencies in populations, occur more 5/10X more than non-synonymous mutations (cuz loss-of-function is caused by changing gene sequence, inferior are eliminated), genetic drift can change conditions and reveal beneficial mutations (show pool of potentially fuctional alleles able to contribute to future adaptation) -deleterious mutations: ones that reduce fitnes, can be expected to be lost from poplation, but may persist thru genetic drift for some time, and can be continually reintroduced by mutation, but remain at low freq, where mutation is balanced by selection. deleterious dont contribute to adaptive evolution unless that they are beneficial in some other conditions i.e. antibiotic resistance can be done by some alleles that slow down growth n reduce toxicity of antibiotics that target growth cells, which is normally deleterious, where shortcomings become benefits and spread rapidly thru population *neutral theory of genetic polymorphism* = reconciled classical and balance theory: although there is alot of genetic variance, the entire population is effectively uniform in level of fitness (cuz almost all mutations are deleterious). -heterozygote advantage (sickle cell anemia) is one example of conditional fitness, fitness of allele in individual depends on allele it is associated with -fitness of allele depends on: male/female, hap/dip, sex/veg, all can lead to polymorphism by selection, or on conditions the individual experiences thru its life -beneficial mutations: accumulate in pop if they arent stochastically lost before fixation, results in greater initial genetic diversity, or until it becomes so beneficial for fitness that all individuals possess it

how do you estimate the mutation rate in a population of fruit flies?

-mutation: provides selectable variation. its rate limits extent that adaptation can be improved by selection. required for selection -high mutation rate can cause selection to be ineffective if changes in gene frequency are caused by selection and are overwhelmed by countervailing changes caused by mutation 1- first, sequence 2 whole genomes of lineages of fruit flies isolated for a long period of time 2- count mutations directly by allowing them to reproduce for multiple gens, then count mutations, track where/when they occur 3- divide mutations by time passed 4-use 2 lineages to cross reference/check to see if they occur approx same rate *fundamental rate of mutation* = basis for genetic variation/evolutionary change, = 2.3e-10/nt / replication

A unique adaptation is one that occurs only in a single clade. List as many as you can think of. Do the clades that you have mentioned have anything in common?

-nematocysts are unique to cnidarians, specialized cells that release a poisonous harpoon, triggered by prey to catch and immobilize them -similar structure in myxozoans, which turn out to be highly reduced parasitic jellyfish, which confirms the unique origin of cnidarian nematocyst -stereom is unique to echinoderms -manner in which calcium carbonate is mobilized has distinctive phylogenetic signature -skeleton of echinoderms is made of spines made of crystals of calcite -each calcite block of the skeleton is penetrated by series of narrow canals, forming the "stereom", inherited from Cambrian ancestors

explain optimality, give situations in which 2 functions cant be maximized simultaneously

-organisms cant be perfect because they must perform many tasks that may interfere with one another i.e. interference of strong motion and rapid motion when using a lever arm, fulcrum, and applied load functional interference - when one body capable of performing one task will not be capable of performing another task perfectly optimality - best structures are compromises that limit functional interference and try to find the best structure for all jobs within the means of its resource >in nature, fitness will be optimized ex) bones resisting stress -bones designed to overcome functional interferene associated w resisting stress while not being too dense and heavy >use a hollow tube structure, which is stiffer than a solid rod, but also uses less material so its more lightweight ex) Membrane design to balance loss and gain of gases -tree species need to find optimal leaf size to allow CO2 exchagne and minimize water loss, optimal leaf size evovles depending on the conditions of the environment, specs are leaf size, pattern of small leaves on top and large on bottom -eggshells are also designed for optimal permeability and optimal strength/protection

how does long-continued geo isolation help lead to species formation

-pops that are permaneltly separated can diverge thru drift or selection -species may vary over their geo distribution to fit the needs of their environment, no distinct boundaries between areas, just a gradient of characters, i.e. tendency of body size to increase from equator to pole -races, variety of a species within a restricted geographical distribution, are divided into sharply differentiated types living within different regions, bad at dispersng but likely to evolve differently due to their range thru divergent specialization to diff conditions bc historical differences become magnified over time -divergent selection leads to more or less strongly marked varieties, combos broken down by recombination can occur less when they cant meet, cause divergence -lineages that do not meet cannot mate, once 2 sister lineages are unable to mate, they are free to diverge, evolve into different races, subspecies, and species as time goes by > simplest and most general reason -pops separated by a physical barrier will tend to diverge over time i.e. dessert pupfish in cali-nevada, completely isolated, cant get thru hot dry rock/sand, and diverged into many distinct forms, but can mate successfully in lab settings when in contact -pops separated by a physical barrier may become unable to mate w eachother, i.e. Alpheus shrimps cannot mate with similar species in carribean that used to be on other side of Isthmus of panama, shows that geo isolation has led to almost complete divergence within a few My -long-isolated lineages may not mate successfully when they meet -may become specialized for different ways of life -genes affecting sexual behaviour and development may be altered to prevent hybridization, so lineages are permanently isolated and will continue diverging

Describe with examples the circumstances in which 2 species are likely to evolve a mutually beneficial relationship.

-principle of how species interact is same principle of how same species behave together -physically close relationship = tends to promote wellbeing, evolve as mutualists -evolving separate = one exploits another, i.e. parasite and host -depends on the extent of which interests of a couple are entrained -cooperation between same species is surprising cuz they have similar attribtues nd competing interests -diff species cooperate more bc they have different interests that dont conflict -more fruitful collabs when partners differ, most extreme examples are quite diff orgs -reciprocl exchage of services benefits both partners, but vulnerable to cheating -cooperation only evolves when cheating is easily detected and punished ex) cleaner fish enter mouths of larger fish to remove dead tissue nd ectoparasites -groupers normally eat them, but learned to tolerate and solicit them > rely on reciprocity, so they can break down easily -fish could eat the bird, but bird could bite the fish too, which causes the fish to stop bc it will chase bird away, and lose beneficial mutation -partners that cant physiclly separate -> mycorrhizal fungi, fitness increment gained by one is transmitted to other, in best interest to support eachother -some partnerships are indissoluble, i.e. green hydra that hosts PS algae, flatworms w endoxymbiotic algae -if partners can readily dissociate and later aquire new partners, they will be selected to exploit one another bc their fitnesses are uncoupled -if new partnrs are related to old partners, their fitness wil be coupled bc the genes overning the interaction will continue to be associated

Give an account of the Producer-Scrounger game and explain how it helps to understand how the production of public goods can evolve.

-producer-scrounger game, free-riders wait for producer to provide food in a group setting, then rush to it -when scroungers get to food, producers have consumed the "finders share" >rest is shared amongst scroungers, but less intense gains and losses than hawk/dove -scrounger pay-off depends on freq of scroungers -producers/scroungers are not mutually exclusive, can bounce from group to group -balance between scrounging and producing altered b making food easier or difficulter to find, which alters finders share -when scrounging is less profitable, freq of this strategy falls -model of how production of goods can evolve, as it ban benefit finders (when food is scarcer/harder to get) and often the scrounger (food is easy to access and energy can be saved for other things)

explain how evolution of genes and proteins are affected by their modular structure.

-proteins are modular, combo of domains, that can fold autonomously, linkage of domains -easier to rearrange and substitutte modules (rather than changing nt by nt) to get indefinite amounts of functional proteins -genes are partly modular, elements that regulate can be upstream, exons dont need to correspond to coding sequences for modules, shufflin of exons can create new proteins by rearranging modules, changing regulatory sequences can easily change structure of gene and thus protein -recombining modules creates new functional genes and proteins, modular units linked together, each has amount of autonomy that contributes to eady-made functional unit to protein/gene -new combos can arise from: failure of replication (slippage, deletion, translocation, recomb) or illegitimate replication trans/retrotrans, mRNA cn be RT into another area, element associates w neighbors)

describe w examples how ecologically specialized varieties can evolve and be maintained within a single species

-races are geo restricted varieties -other species are divided into more or less sharply differentiated types living in diff regions -when bad at dispersing, species is likely to evolve distinct kinds in diff parts of their range thru dvergent specialization to diff conditions or somple bc historical differences become magnified over time -some speecies are divided into sharply differentiated varieties living in diff regions -spatially separate, diverge, maintain divergence -appearance is extremely variable, each colour type occupies distinct region sharply separated from neighbor -cuz each type imitates locally abundant toxic species, i.e. taricha torosa, maintains strong NS despite frequent inbreeding at margin range of each type -interbreeding replaces one another in sequence -large gulls have similar pattern on large geographical scales, range from sexually isolated pops of diff appearanes that can be given different species names -species may vary continuously over geographical distribution -clines (gradual shift in character state) are extreme cases of geo distribution of genetic variation -most broadly distributed species are intermediate between these distances -smooth increase in genetic variation over large distances can be interrupted by boundaries, created by history, migration, selection, phenotypic diffs, -species may vary continuously over their geographical distribution i.e. body size increase from tropics to poles -gradual shift over a large range - cline -divergent adaptation generates distinct imperfectly isolated groups within species i.e. Littorina, common intertidal snail on both sides of atlantic -harms to it: waves tear snail from rock, hurl it against the shore, and crab tear apart with pincers -no single design will protect the snail from both harms at the same time -2 successful variants of shel evolved, the varieties of species depend on site/circumstances -not both species cuz they readily interbreed, but distinctive appearance is maintained thru 2 varieties separated by only a few metres -only found w direct development, young develop w egg mass glued to a rock, crawl away as mini adults, restricts dispersal and sexual contact between varieties, then NS maintains differences between them *genetically based ecotypes evolve with some degree of sexual isolation, phenotypes can be modified developmentally when there is a complete mixing* -same area speciation is obstructed by recombination -NS favours divergent specialization to diff ways of life, but will be ineffective in pops when there are no barriers to mating > speciation normally requires prior spatial or temporal separation of subpops whos mating systems diverge in isolation, so that they seldomly interbreed again when they come into contact *allopatric theory of speciation* > require temporal separation, on larger or smaller scales, requires diff breeding seasons i.e. insects that feed on several host plants

Would you expect the evolutionary dynamics of predators and prey to be similar to those of parasites and hosts? In what respects might they be different?

-red queen hypothesis applies to mutually antagonistic orgs -adaptation is merely provisional, evolution is continuous process of adaptation and counter-adaptation that continues even if enviroment is stable -competitors, partners, rivals, enemies, always shape eachothers destinies -predator-prey dynamics might be diff in sense that intraspecific competition is not present among hosts so there is not really regulation of host pop in same way that would reduce abundance of predators -also predator necessarily kills its prety to use it, and many parasite just use host as a source

How has understanding the genetic basis of development helped us to understand better the evolution of body plans?

-regulatory genes control development of MCOs -in tetrapods, understanding genes have shown that all of tetrapod evolution of body plan is based on groups of multiply duplicated genes >each cell type is governed by specific set of genes that requires regulation -gene expression is regulated by proteins that bind to DNA Hox Genes: -homeodomain is a DNA binding motif that regulates development of many organisms, and seeing homeotic mutants shows the major genes that are invovled in governing major body plans >homeobox genes control development of all bilateria, show genetic collinearity and temporal collinearity -evolved from cnidaria, give rise to body axes -risen from duplication and divergence, from ProtoHox in metazoan ancestor -parahox are related but not linked to Hox -number of hox genes affects how body develops and loks -metazoan body plans are influenced by modification of genes that regulate development

Why might females evolve to produce fewer offspring than the physiological maximum?

-reproduction has a cost associated with it, parents are faced w loss of quality -NS doesnt always increase rate of reproduction bc individuals must survive in able to reproduce, and alleles will only spread if the offspring they create survive to create offspring as well >>> *important aspect of surviving that must not be left out** -reproduction can be harmful to females that must invest time and resources to rearing and developing offspring -i.e. female guppies at risk for predation cuz pregnant bellies reduce streamlined body -alleles that increase rate of repro will only spread if: >producing more offspring doesnt disproportionately reduce parents chances of surviving >greater quantity of offspring are correlated w decline in quality quality - chance of surviving to reproduce -reproductive allocation is optimized to balance offspring created with quality of parent, finds the optimal number of offspring that maximizes total number of grand offspring -sheep in Soay are exposed to harsh conditions and when females have too many offspring there is not enough resources for all of them which puts them at risk and make them more likely to die, which doesnt allow them to pass on DNA to offspring and continue evolution

What are the benefits of living together with other individuals as a member of a group?

-safety in numbers > less likely to be attacked by a predator if in a group -predators may group to attack prey easier ex) wolf can kill a moose only in a group -different stressors are alleviated when in a group depending on environment i.e. penguins in Antarctica huddle -generally, contributing to group benefits the group as a whole as well as individual

Give as many examples of the modular organization of body plans as you can think of. Why should modular organization facilitate the radiation of groups with different body plans?

-segmentation/modular organization enables diff regions of body to evolve independently from one another -alteration of 1 segment is confined, lessens effects of alteration to other segments and reduces functional interference -arthropod and chortate segmentation: >change in number of segments: -myriapods, centi/milli have many segments -icthyosaurs have flippers/more phalanges in limbs -snakes have more vertebrates -more leaves in stems of plants >repeated structures: modified after development -arthroods have repeated limbs that are modified into diff sensory structures, i.e. mouthparts, antennae, locomotory structurese, food handling, reproduction, mammal teeth >homologous parts modified diff in diff lineages: -crustacean differentiation -myriapods have succession of walking legs, chelicerates have 4 walking legs, insects have 3 pairs of walking legs

Why have vestigial structures such as the hind limbs of whales not disappeared completely?

-selection favours reduced hind limbs on whales to increase hydrodynamic body -eventually hind limbs and pelvic girdle will be lost thru selecion against mutations that cause failure of pelvic girdle to develop, will accumulate and cause it to degenerate -whales stil express the pelvic girdle due to their distant terrestrial ancestors -cuz the process isn't fully done taking them out yet -troglobytes live in caves in perpetual darkness, still have vestigial eye functions, but aren't completely gone cuz loss of function mutations accumulate bc they arent eliminated by purifying selection

Why do replicate selection lines tend to diverge in character state?

-several replicate selection lines are established from same base pop and each from same protocol in each level of selection -on avg, they respond as expected, but not all replicate liens subjected to same intensity of selection respond in exact same way > some more and some less -some respond more rapidly and some less in order to keep their rank relative to others -cause: sampling errors as lines set up as smal random samples from base pop differ in initial composition, which will be enough to increase as lines are propagated and there will be biased samples in each gen -able to scrutinize fly genotypes directly, and chose individuals w appropriate genes, errors would not exist > not possible cuz experimenter selects based off phenotype, which could be influenced by other factors i.e. food, size of egg, or other reason attributable to development -thus, look phenotypically similar, but genetic differences are what count, and thus selection lines diverge -1 selection line represent a unique historical process that cannot be precisely replicated

Why do selfish genetic elements spread more readily in outcrossed sexual populations than in asexual or inbred populations?

-sex creates opportunity for selfish genes to infect new lineages >in asexual pops, they are limited to the lineage in which they arise >in sexual pops, harmful elements can spread as a result of gamete fusion >can become fixed despite the damage that they incur to individuals that bear them -conjugation of plasmids in bacteria causes genetic elements to spread, and due to nature of selfish genes, they will spread to lineages that lack them ex) 2-micron plasmid of yeast spreads in outcrossing populations of euks, can spread more rapidly in outcrossed populations cuz if it spreads before gamete fusion, the plasmid will spread thru pop cuz gametes fuse w one another and allows plasmid to spread thru lineages -in asexual pops, frequency of plasmid bearing the strain declines cuz replciating it is burdensome to the cell -inbred pops: gamete fusion occurs and plasmid doesnt increase in frequency cuz it remains resticted t the single self-fertilizing lineage in which it arose in -Homing endonuclease genes are parasites of sexual populations, spread rapidly in outcrossed pops cuz genes het. for HEG are transcribed, cuts a homologous region in the sister chr at a specific site for HEG, which is repaired using the HEG template to insert it, and can be transcribed normally even thugh it disrupts the gene cuz HEG has an intein, aka a protein that splices the gap that HEG creates -in yeast, in self-fertilized pops, it cant infect them cu they dont have the intein element but in outcrossed pops it can infect naive lineages and become fixed within 12 gens

In what sense is sex a costly process and why does this raise difficulties for evolutionary theory?

-sex is costly based on 2 things: cost of meiosis, and cost of males -sexual repro, each partner contributes only 1/2 of their diploid set of genes to gamete -cost of males = only F in sexual pop are productive, thus males contribute nothing beyond their genes -sex = 'costly' compared t asexual repro, where 100% of individuals reproduce, and full genome is passed on -in theory, asexuals can repro twice as fast -difficult evolutionarily bc due to darwinian theory, sexual lineages should be replaced by equivalent asexual lineages rapidly as they have more reproductive power >relies on assumptions that male gametes are smaller than female, so male doesnt contribute much cytoplasm to the zygote, and offspring are reared b mother, so father only makes small contribution to offspring deveopment. >sex must offer something that makes up for this lack of productivity

how might one species split into two while occupying the same geographical area

-sexual isolation can evolve if individuals do not meet despite living in same area -can be large scale (islands/lakes) or small scale (spawning beds in same lakes) -temporal separation requires diff breeding seasons -long isolated species may not mate successfully when they meet -may become specialized to a new way of life -follow diff developmental pathways, accumulate diff complements of chromosomes =may obstruct hybridization and fusion of lineages if they are inviable or sterile, then parental lineages are completely isolated no matter how freely they mate

Explain how the short-term response to artificial selection depends on the heritability of a character and the manner in which individuals are selected. Why might this explanation fail in the long term?

-short term response to AS depends on heritability of a character and the manner that individuals are selected bc results of choosing exceptional individuals are based on quantitative characters tht vary on continuous scale -only exceptional are allowed to breed -based on eq: D = S - A ( S= selected average character state) (A = average of the population) (D = difference between average of selected individuals and the average of the population before selection) -variation sufficient for selection, but only effective when offspring of selected individuals resemble parents, > must be a heritable selected trait, and must be genetic (not environmental conditions) h^2 is heritability of a character (0-1), where h^2 = (genetic variation) / (genetic + environmental variation) -low h2 value means that its mostly due to environmental growth conditions, next gen will have similar character states regardless of parent -high h2 value means that all variation is heritable and offspring resemble their parents -use breeders equation to determine response to selection: R = (h^2)*D -used to show fraction of difference that is transmitted to offspring to selected individuals ex) Edinburgh bristle experiment -population of outbred flies used, variation in bristle number begins w h2 = 0.5, implies slection is applied likely to cause rapid change in character state in population -each line propagated by 20 m and 20 f -next gens for bristles are screened, most extremes chosen, to establish upward and downward selection lines -in short term line, fraction of individuals chosen, range of variation available, and heritability affecte how rapidly a line responded to selection -more intense selection caused proportionally greater response, actual number of bristles gained or lost was v close to predicted breeders equation -long term: selection becomes inefficient once genetic variation becomes exhausted, pop will display 1+ extremes, possibly formed by mutation/recomb -any residual variation among individuals is then purely environmental -seen in experiment where after 35-40, plateau reached, or in mce size o rats experiment plateaus as well -data shows thru a few experiments that selecting upwards eventualy doubles pop mean, and downwards 1/2 it -extensive experiments are cpable of shifting pop mean by 20 phenotypic SD, -not restricted to any system: drosophila bristles and mouse weight follow same rule -genetic variance of fitness decreases should decline as consequence of selection, eventually reaches 0, pop becomes genetically uniform, no further progress -in bristle exp, variance doesnt consistently decrease, sometimes increased -lines respond to back selection -in bristle, limit is not caused by exhaustion of genetic variance, bc mutations cause large inc in bristle number arose by mutation -applying downward selection to stalled upward lines, they readily responded and decreased bristle # -hets had more bristles, likely to be selected -homos w 2 mutant alleles died (recessive lethal allele), but thru hets, freq of allele was increased in every gen, but AS reduced by NS cuz homozygotes died -advances thru AS imposed how far bristles could be increased -special case f common phenomenon in AS -extreme phenotypes become abnormal and enfeebled in various ways, and further selection is ineffective

"The course of development reflects the course of phylogeny." Discuss this statement.

-similar stages during early development to other groups show that they share similar ancestors that affect how they look and function -distinctive body plan as adults reflect the eventual divergence of different groups thru evolution -development of orgs is controlled by regulatory genes, orgs that share the same regulatory genes are similar due to their genes. but unique end results reflect that the genes are expressed in different ways that diverge adn get more and more different from one another that reflect their diverse final forms -phylotypic stage is the point during development when embryos of monophyletic group resemble each other after gastrulation i.e. in vertebrates, Pharyngula stage is phylotypic stage when basic features are condensed and not fully differentiated, all have notochord, dorsal neural tube, segmented musculature, post-anal tail >zootype: charactersitic body plan of a given phylum thats determned by A-P expression of Hox genes that govern relative expression of body structures -sharing zootype shows similar ancestry -modifying development of an ancestor can result in different descendant species

Write an essay on the causes of variation in shell colour and pattern in the polymorphic land snail Cepaea.

-snail shells vary pink to brown, plain or patterned -polymorphisms dont vary continuously, bc design is determined by linked genes whose alleles determine the phenotype, so gene freq can be estimated by surveying phenotypes -polymorphism is maintained by selective predation by thrushes and blackbirds, who smash snails against a stone > agents of selection that influence composition of the snail pop within their territory -comparing shells found around predator birds anvil stone to local pop can be used to evaluate the selective effect of bird, who are most likely to prey on snails that have poor camoflage -grazed turf- yellow fit in, brown stand out, and opposite for leafy background, and in spotty sunny areas the patterning helps to disguis the snail -discrepancy of general pop of snails in an area and the sample of snails used to calculate intensity of local selection -proportionate difference between % of snails of a given phenotype in total area - % of phenotype's shells around anvil stone provide selection coefficient acing aainst the more easily sotted and preyed on phenotype -in snails, strong selection against unanded individuals, 20% more likely to be killed in some areas -differences in colour and pattern between different habitats are largely created by visual predators that tend to choose the types that are more conspicuous at each site, and leave the least conspicuous behind -climate also influences shell phenotype variance (paler in the south) bc darker shells heat up more esily, which can cause stress in warm areas, but beneficial in cooler areas -can be seen in slopes of croatia, where bottom of snails are dark, but lighter on top due to cold air flow thru bottom of valley at night, 15 degree differene -chance and history also effect phenotype, natural pops are exposed to many agents of change

why has the division of labour between germ cells and somatic cells be advantageous. then, why are there so many UCOs?

-some colonies only have 2 types of cells, soma and germ > only germ reproduce, MCO offspring w same division of labour are produced -in Eudorina and Pleodorina, 32-128 cells, first indication of division of labour, in soma and germ -ex: Volvox have ~1000 cells, spherical shape, flagellated, small somatic cells for photosythesis and locomotion -larger, immotile germ cells inside parental spheroid into mini Volvox (themselves have germ cells) before being released -selection favours some sterile cells, (even tho it would normally favour greatest possible rate of replication) because: >dividing labour maximizes productivity of individual as a whole >output of germline is enough to compensate for sterility of soma >alleles that govern division of labor are replicated faster than alleles that direct development of equivalent number of cells -so many UCOs bc they have other methods of genetic transfer (HGT), have shorter generation times so there is no ned to divide labour between cells, can perform labour efficiently with one cell, and have found ecological niches where unicellularity is advantageous

provide a reasonable estimate of the average longevity of a species and its variation among species. why do some species persist unchanged for very long periods of time?

-species persist ~1-10My on avg -longevity can be estimated from fossils or phylogenies >fossils based on first and last appearances, *minimal estimate* > phylogenies: estimates of time from most recent common ancestor for exant taxa, omit sister taxa for *maximal estimate* -estimates reasonably consistent -horses are well studied, abundant fossils, only a single species native to Asia, but has been domesticated nd spread aroudn world by humans -some species persist for long periods of time, aka "living fossils", Cycads, no change 25-35My, gingko tree 100My, clam shrimps 200My > once lineageis well adapted to way of life, improve adaptedness are exceedingly rare, so lineages persist w little or no change for as longa s that way of life will support pops

Describe the three basic body plans of Metazoa: sponge, cnidarian, and bilaterian. How does a simpler type of animal (i.e. a sponge) persist when a more complex type (i.e. a worm) has evolved?

-sponge: cylinder w chambers lined w flagellated cells, choanocytes, filter feeding flagella draw water into chamber to get food then water expelled out, bacteria are trapped by a mucous collar and digested -choanocytes resemble choanoflagellates -cnidarian: have *enteron*, blind gut created from gastrulation when ectoderm and mesoderm are made, food is collected w tentacles/cnidocytes -bilateria: simple cnidarians that lie on their backs, have gut, move by cilia, coeloem that allows motion, directional locomotion implies a preferred A-P body axis, sensory structures show the beginnin of head formation, crawling > implies dorsal-ventral axis w locomotory structures -although other groups have evolved, older ones still persist because they successfuly live and reproduce, fit for their way of life, complex organisms evolve more specialized to occupy diverse niches so all live together harmoniously

life is characterized by metabolism and replication. which came first?

-spontaneous generation: 2 chemical processes required for life to be possible. growth, and repro -for life to evolve, we need inheritance as well 2 possible routes for origin of life: 1) Genetics first, RNA world, RNA can self replicate w/o cells when they have raw materials and a replicase, RNA can act as enzymes due to their 2ndary structure -early archaean ocean populated by self-replicating RNA strands, which all orgs descended -compartments: self replicating RNA can persist but not improve, due to product/reactant cn slowly diffuse from eachother, thus rxn is slow, and that more efficient version of relicase ill probs encounter molecules made by less efficient versions, thus, is no heritability -micelles into cells" cell sized hollow spheres formed spontaneously by fatty acids in water, grow and divide spontaneously when provided w a supply of raw material, i.e. protocell -Genetics first: DNA and protein -2 final steps establish moderm biochem, replacement of RNA by DNA for info storage, RNA used to transfer info for metabolism, then RNA is replaced by proteins -metabolism first: metabolism appeared first, supplied the energy necessary fro later appearance of self-replicating systems -simple metabolic systems, acetogens can grow from rxn when H2 nd CO2 react -these rxns conserve chemical energy that can be used to push life process forward, first orgs would then be anaerobic chemoautotrophs that used H2-CO2 redox rxn -hydrothermal vent mounts: mounds formed when vent fluids rise to seabed, foamy structure, microcompartments w inorganic walls w transition metal sulphides, 2 important features of metabolism: concentrations within small compartments, and catalysis by FeS, NiS, MoS, still used in redox-active enzymes by anaerobid autotrophic bacteria

Describe an example of directional selection in a natural population. Can you identify cases of directional selection among organisms living near you?

-sticklebacks: -naturally heavily armoured to protect from predator fish -live in coastal waters in N oceans, during interglacial periods, ice retreat opens streams to ocean, allows sticklebacks to go into streams cuz they can like in freshwater -freshwater stick. encounter diff conditions than marine -fewer freshwater predators that have different attack methods -dragonfly larvae attack juvenile sticklebacks but armour is not effective cuz they can use spines to hold on to stickleback > armour is unnecessary and detrimental -freshwater armour is reduced and loss > directional selection, mutation of reduced armour (loss of function mutation in Eda and Pitx1 genes) -ex = squirrels and racoons unafraid of humans in urban environments have greater chance of getting fed

How do studies of contemporary populations contribute to our understanding of long-term evolutionary processes?

-studying contemporary pops allowed rate of evolutionary change to be calculated over short periods of time, same as fossils can be used -contemp. pop studies show that NS is commonplce, and is an ongoing process that acts ong term -comparing rate of changes from contemp. and fossils allows us to see that amount of change is independent from length of time over which observations are made -amount of recorded change over 100, 10,000, or 1,000,000 is the same in any given population -100 yrs = rapid evolution 1,000,000 yrs = v slow -selection changes in both magntitude and in direction from generation to gen, which can be extrapolated to long-term evolutionary processes -a given species can dominat ein its environment for 1000 yrs, until a new predator is introduced, and species must rapidly adapt or face extinction -continous adaptation must occur as life conditions change > applies to contemporary nd long term evolution

Give an account of the Trader's Dilemma game and explain how it helps to understand the evolution of honesty.

-traders dilemma ascribes outcomes to diff levels on honesty in a trade situation when goods are being exchanged. -4 outcomes: You play fair and your opponent plays fair: you get an award for honesty (A) You play fair and your opponent cheats: You get a booby prize for cooperating (B) You cheat while your opponent plays fair: you get something for nothing (C) You cheat and so does your opponent: You're in a deadlock, no one gets anything (D) In descending order of value to the individual: C > A > B > D. -cheatin yields the greatest gain at the smallest cost in 1 event -cooperation relies on repeated interactions between individuals > no benefit to helping someone u will never meet again -mutualistic relationship can be formed if repeated fairness is used -a tit for tat strategy is determined to be most successful strategy, applied to natural populations -cooperte in first move, and every next move, you do what opponent did on previous move -success is due to niceness (never cheats first) but is easily provoked (immediate retribution for cheating), and forgives quickly (one opponent becomes honest, it will too) -reciprocity reinforced with punishment -shows that evolution of honesty as one of basic principles of social behaviour, requires no consciousness or mental ability, and can apply to all organisms

Differentiate between conditions favouring the evolution of mutualism and those favouring the evolution of antagonism between 2 species.

-vertical transmission leads to partnership, horizontal transmission leads to enemies -offspring can inherit parents parents or offspring next, never really dispersing far -enemies stimulate perpetual coevolution -some parasites kill/castrate their host -when lineage separate, they become enemies bc repro is unlinked ex) fish lice in salmon attach and lice salmon body fluids, which can hurt them -salmon is part of lice's environment -individuals differ in ability to exploit environment, but when pop is close over long periods of time, its likely to evolve adaptations that help them deal with them efficiently

explain how the form of minute aquatic organisms is governed by hydrodynamic principles

-when body is small must overcome the viscous forces present that prevent motion thru fluid, must overcome friction drag > evolve towards a common body plan -require continuously acting low-power propellor so distance gained is due to present activity rather than activity in the past (no stroking motion) -body size governs ratio of inertial forces to viscous forces the body will experience -large orgs governed by inertial resistance -orgs smaller than 1mm in size use modified flagella > flexible oar that doesnt produce motion in the recovery stroke by working in 2 ways: > rotary corkscrew motion, swimming bacteria >sinusoidal motion, most swimming algae -thrust developed by flagellum is proportional to its length, but cant be too long bc it would be distorted by water currents n wouldnt be able to produce directional motion

Describe the fate of a gene when all members of a population bear loss of function mutations. Compare it w fate of character state that is no longer function, such as eyes in cave fish.

-when genes are no longer selected they decay -character state becomes progressively diminished or disappears, can turn into pseudogene, or can take on other functions by recombining/duplicating -pseudogenes: flawed genes that cant make useful proteins due to loss-of-function mutations -arise when a gene is duplicated, one can decay w/o lessening the genes initial function level -arise from retrotransposition -diverge rapidly in sister lineages -avg divergence in mammals is 5*10^-5 subs /year in non coding, 2*10^-9 in protein coding genes/year -pseudogenes soon become genetic junk, littered w mutations -add metabolic burden to replicating, when they are removed, the lineage benefits, and are gradually removed from populations altogether -eyes in cave fish used to have purpose when used in light, gene used to be functional in ancestors but in descendants where its no longer used, it can develop a new function or just degrade slowly

How is genetic diversity maintained by environmental heterogeneity?

-when het environment provides refuge for specialized types, freq-dependent selection acts to preserve diversity -P fluorenscens- both types have advantage when rare which is developed by environmental heterogeneity cuz 2 niches are refuge for special types -each region necessarily constitutes a certain fraction of the habitable space within environment and guarantees the persistence of the best type fitted to live there

How would you expect a population to evolve when reproduction becomes less risky?

-when repro is really risky, suicidal reproduction occurs, when consequence of survival cost makes any attempt to reproduce at all nearly certain to be fatal salmon show how reproduction alters when environments become less dangerous. -Pacific salmon migrate 2000km+ from where they were born, hazardous journey back means they will only be able to make it once and after they reproduce -thus contribute all of their energy and resources and create alot of offspring in one go because they will not face *prospective reproductive cost* that will deteriorate their future health because they technically have no future -atlantic salmon contribute less to reproduction as it gets less risky, can make more than one journey so they save some of their resources for the next journey -sea trout move to coastal waters and back, survive for 2+ spawning seasons and thus conserve their resources for surviving longer -freshwater salmonids make small journeys to spawning grounds and spawn for many years. post-reproductive survival here is governed by *prospective cost of reproduction*, cuz there is a risk entailed by spawning migration that they will face later on because their lifestyle isnt very risky and will probably live to old age -optimal patterns of reproduction are based on lifestyle and environment the org lives in

Why do selection lines tend to return to the ancestral character state if selection is relaxed?

-when selection is relaxed, upward and downward selection lines revert to ancestral character state -ACS is maintained by purifying selection around an optimal value -AS forces pop away from this value, and when its relaxed, purifying selection towards ACS is the only source of selection, and lines converge on ancestral state -in bristle experiment, optimal bristle number exists, reached thru purifying selection against individuals w more/fewer bristles -shows that any domesticated stock is simultaneously affected by 2 kinds of selection: 1) NS of favouring any kind that reproduces well in captivity (despite humanized environment) 2) AS applied directly by experimenter which runs contrary to NS cuz its used deliberately used to produce results we desire that NS hasnt delivered

"The course of evolutionary change may be unpredictable, even in principle." Discuss.

2 meanings to predict the course of evolutionL 1) calclating consequences of modifying diff components of a system ex) lactose diffuses from the medium to the cell membrane thru pores in the cel wall, active transport, then cleaved into glucose and galactose by enzyme. fitness of cell in lactose-limited chemostat is proportional to flux thru this pathway, any mods to pathway have calculatable effect on yield and rate of reaction 2)to predict which gene mods will be selected n response to a given stress. ex) T3 gene can be predicted ina virus substituted that G > C -however, stochastic and historical nature of evolution implies that there are some things we jsut cant predict -we can predict themees of adaptation to particular conditions, but variations that evolve in a given line are essentially unpredictable due to the many factors that influence adaptation

Describe the main stages involved in the domestication of a species of plant.

4 phases 1) *choice of orgs to domesticate* -planting edible grasses in an enclosure eases task of gathering edible seeds -planting oak for acords doesnt give same benefit cuz it takes too long to reach maturity -thus, wheat + barley were domesticated, oaks are not 2) *proliferation of particular lineages in early stages of domestication w/o conscious human intervention* ex) Wheat cultivation, plants enclosed, harvested, part of grain is re-sown -creates a novel environment that plant quickly adapts to -successful genotypes have characters like retaining seed on the stalk for efficient harvesting, rapid germination (cuz dormant seeds dont contribute to crop) -i.e. natural selection within a humanized environment 3) *deliberate selection by farmers of individuals w attributes as parents of next gen* -basic understanding of genetics (offspring resemble parents) and evolution (next gen resembles current gen) -applied to characteristis like palatability, docility, ease of handling -AS bc its applied by a conscious agent for a purpose -responsile for qualitative mod of crop plants, and domesticated animals in 1st 10,000 years of agriculture 4) *systematic selection by scientists of attributes* i.e. grain yield -individual plants grown in well-spaced rows are easy to distinguish phenotypes/select/perpetuate the crop -in wheat, overall production of pop is the target of selection -choosing largest plants =counterproductive, cuz they may suppress growth of neighbours and reduce overall yield -stage requires long-term investment in breeding trials -conducted systematially in last 100yrs

compare and contrast the innovations that might evolve in response to a) change in environment, and, b) change in genome

environment: -photorespiration: initial high [CO2] relative to [O2] in atmosphere made Rubisco enzyme efficient, increasing [O2] in todays atmosphere makes plants evolve > mesophyll vs bundle sheath cells, Pep carboxylaze, is 100x sllower than other enzymes so requires large quantities. readily reversible, O2 exposure catalyzes oxidation of ribulose phosphate to phosphyglycolate >rubisco binds more strongly to CO2, but has to compete w oxygen, so respiration competes w photosynthesis >imperfect evolution, due to presence of cyanobacteria ~2800 Mya >inefficient in hot/dry places >plants evolve by packing lots of CO2 int rubisco sites into compartments to elevate photosynthesis, recycles CO2 that would otherwise be lost in respiration -C4 plants: *pump CO2 around rubisco, distinguishes them frm C3* >have "bundle sheath", prominent sheath of cells around each leaf vein >PEP carboxylase to fix CO2 into 4-C acids in mesophyll cells, transported to bundle sheaths, release CO2 within chloroplasts when close to Rubisco >*evolved thru modifications in C3 mechanisms*, same enzymes that are expressed differently, and modified w substitution of beneficial mutations that optimize activity >rubisco evolves within the c4 environment, complex structure, modifies by changes far from active site that occur independently in C4 lineages -genome: -multicellularity in genome (not really influenced by environment), major genes directing development allow for differentiation of soma-germ cells (gls, regA, lag) -gene duplication allows for intro of new genes > *visual pigments originated thru duplication* >initial event in vision is absorption of photon by pigment molecule, cascade of events result in internal representation of external world >opsins: animal visual pigment thats bound to a vitamin A molecule retinal, changes shape in absorption of light, causes signal cascade > rhodopsin: rod cells of retina have it, detect movemet and light >Vertebrates: 4 opsin cones, basis of colour vision, genes have arisen by duplication, which introduces potential variation that can be molded by selection >opsin family ~1000 diff proteins that originate thru divergent NS or duplicated ancestral genes >evolved form old genes, similar proteins in bacteria where photon capture is used to generate energy

describe how novel genes affecting male mating behaviour have evolved in drosophila

genes affecting male sexual behaviour in drosophila have evolved recently by duplication, exon shuffling, retrotransposition -sphinx gene affects courtship in drosophila, involved in sexual function, sphinx knockouts show increased courtship intensity time, due to increased male-male courtship, due to insertion of retrotransposed sequence in ATP synthase F-chain gene -Jingwei is a testis-specific gene in drosophila, originated by duplication, retrotransposition, exon shuffling, evolved w/o destroying ancestral function -Sdic affects sperm motility encodes dynein protein active in sperm tail, includes 2 copies of other genes, illustrates the formation of a new gene process that involves duplication, exon shuffling, and retrotransposition

Compare and contrast the results of selecting for (a) individual characteristics of vegetables such as cabbage, and (b) yield per acre of grain crops such as wheat.

individual characters selected: -easy for farmer to distinguish phenotypes to select and perpetuate ex) wild mustard -> kale, cabbage, broccoli, brussel sprouts, kohlrabi, cauliflower, all created by AS selected for extremes -produces big hearty individual veggies, main goa is largest possible yield of individual cabbages yield per acre of grain crop selected: -counterproductive to choose largest plants, cuz they could be selfish and harm other plants which would decrease the total crop yield -must compare whole fields/plots that are each sown w different variety -many practical difficulties, but overall makes great advances in last 60yrs -3/4X increase in yield compared to lat 5000 yrs in agriculure

why have complex multicellular bodies evolved in euks and not in proks?

mainly due to *constraints of body plans* -peptidoglycan cell wall in bacteria obstructs cell-cell communication + prevents cytoskeleton evolution -multicellularity requires cells to organize themselves, interact with eachother -prokaryotes didn't need to form multicellularity, can benefit from multicellular eukaryotes -all multicellular bodies develop from a single cell that proliferates, diversifies to many cell lineages -single cell has inner conflict, of wanting to belong to larger individual to ensure it will be replicated (altruistic) and wanting to replicate as much as possible so its overrepresented in larger individual to ensure it will have descendants (selfish) -prokaryotes were not able to overcome selfishness

why are there many more endemic species in Lake Baikal than in lake superior?

many endemic species in Baikal because: -huge size, can hold all of great lakes combined -deep nd oxygenated at all levels -isolation of it caues impoverished fauna, which means *lack of competitors* -only a few crustacean species, no crayfish/shrimps that other lakes have -huge radiation of gammaridae, freshwater shrimps that have radiated and exploit many opportunities that are left open by lack of competitors § One group is small, smooth-bodied form that burrows in sand, eats detritus Another group is stout bodied, armored, many spines, processes that forage in littoral zone, eats invertebrates § Another group is large scavengers, 6", eat dead fish § Other group is predators that eats other invertebrates § Other group lives in abyssal depths of the lake, eyeless, no pigment § Parasitic species that live on sponges or other amphipods less species in superior bc: -much smaller -many well-adapted species that can already outcompete new forms that would try to radiate here

what is meant by a "different kind of organism"? how different is different

populations permanently separated may diverge thr drift or selection -range of variation is a continuum between organisms w.o any marked geo variation or clear division into diff kinds -some species have 2+ distinct kinds that are not species themelves: variety - most general term, disinct, but not a species morph - type distinguished by single geneetic diff ,may involve cryptic characters cultivar - variety produced by AS ecotype - variety w restricted eco distribution race- variety w restricted geo distribution subspecies - race so strongly and consistently differentiated from others, that its given a formal taxonomic name i.e. bacterial ecotypes, very diverse, but all lumped into similar groups because they use similar substrates or infect same hosts and have similar phenotypes

Distinguish between purifying selection and directional selection. What are the main causes of these processes?

purifying: removes deleterious mutations to maintain adaptedness -normally dominates regardless of environment, especially in well adapted species -conditions that favour purifying have remained the same for long time, all mutations that increase fitness are likely to already be fixed and any new mutation is deleterious -removes mutations cuz individuals bearing them likely have lower avg fitness than rest of pop directional: extends adaptedness by favouring beneficial mutations -trigged by recently changed environment that species is poorly adapted to -insufficient time for most potentially beneficial mutations to occur and become fixed -most mutations are deleterious, but some are beneficial and spread

Define senescence. Is senescence inevitable in multicellular organisms?

senescence - increase in probability of dying after a certain age -natural limit to lifespan -tendency to become frail with age -favoured by NS, senescence is favoured due to senesence's tendency to maximize reproduction over lifespan due to effects of early reproduction lifespan is limited by rate of living: -caused by wearing out of tissues depending on amount of use, physiological processes are governed by metabolism, and tissue has a limit on how much metabolic work it can endure > once work load is met by an organism, their life ends ex) C.elegans support rate of living hypothesis, can extend lives by processing food more slowly and doing less metabolic work -inevitable naturally in organisms because all tissue has same metabolic capacity in the same amount of tissue -senescence may develop directly thru functional interference or indirectly thru mutation accumulation: functional interference >early vigor may lead to exhaustion, the prospective costs of repro are biased by the general weakening of selection with age, cuz cost of reproduction has great impacts on the amount of metabolism used that is limited by ROL hypothesis mutation accumulation >deleterious mutations accumlate and increase w age, selection against deleterious mutations is more effective when younger -thru artificial selection, lifespan can be permanently extended thru selecting females that reproduce later -but not inevitable because somatic tissue, feature of all MCOs, eventually becomes worn out after use

What are the strengths and weaknesses of using laboratory experiments to understand the predicted outcome of artificial selection of livestock crops?

strengths -systematic control allows you to select the trait and perform trial experiments before implementing on large livestock crops -important to differentiate exp to level of selection that is most productive -livestock crops have long gen times, lab experimens can be performed more efficiently -beneficial to see if AS in one direction negatively impacts org weaknesses -AS could occur within variations when implemented on actual livestock crops -environmental variations can influence variation among crops -if selection in one direction negatively impacts org, then fitness will be weakened and selection will be ineffective -shows how correlated characters that respond indirectly to selection as some lines hve high freq of abnormal structures

are human activities likely to lead to mass extinction?

yes, deforestation, urban sprawl, agriculture, fossil fuels, polluting rivers/lakes/oceans, war