BIOS101 Notes for Exam 3
BIOS101 Notes for Exam 3 BIOS 101
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Date Created: 04/25/16
11. 1 Deviations from Hardy Weinberg. Natural selection causes heritable variation - what is evolutionarily feasible. Ecologically acceptable, trying to survive. -> Results in combining what is evolutionarily feasible and ecologically acceptable. EX) Friend got a Chihuahua (domestic dog) All breeds of domestic dogs, we see the inner wolf. Now you go to the national park, Serengeti -- has lions, wild dogs, hyenas. Dump dogs there, the domestic dogs would not survive well. Examine dogs a year later, all of them would be gone. Experiment was done in Australia, Smokey mountains (pets dogs went there) = Same result: wind up with the dingo dog, a species in Australia (feral desert dog) Natural selection occurs on an adaptive landscape. It is a graph (x-axis is what is evolutionarily feasible (all phenotypes); y-axis is the fitness (per capita growth rate)). The max fitness is what we expect natural selection to lead to. Genetic drift: sampling error in a finite population. Via sampling error, alleles get lost, or the allele frequency can drift from its original frequency. Genetic drift is a stronger influence on smaller populations than larger populations. Always (over time, no mutations or selection) results in the elimination of an allele. Population becomes more homozygous. Mutations and Genetic Drift. GRAPH: Natural selection puts us at the blue dot, mutation puts the drift from the blue dot (the arrows). Forces variation away from where it would be adaptive. If we have a small population, genetic drift is shown by the small other circles, alleles may get fixed on accident…fix the population's phenotype. G. D. works against natural selection. If it is a function of population size, genetic drift doesn’t have much influence when population is large. Strength of selection: if it is weak, then genetic drift has a bigger effect. EX) Wolves of Minnesota: Sampling of wolves. They are uniform in size and morphology. Suggests strong selection. Coat color has a big range. Color may be caused by genetic drift and mutation because selection is not strong. Length of tails also varies, too short or too long will be weeded out by selection. Founder Effect: New population gets established, it is comprised of only a handful of individuals. Can be used to trace the ancestry. EX) Starlings released to central park in NY from Europe. EX) California cypress, genes present in this small introductory population is exaggerated. Traits gets perpetuated. EX) Minority of Amish people. EX) Domestic and feral animals on animals. Introduced rats, goats, pigeons, and bunnies on to islands and other places. Lighthouse keeper off of Scotland: White rabbits were released, they grow, eat, etc --> then he can hunt them. BUT after a few years, natural selection occurred, they turned brown in color, harder to hunt. They became leaner, skittish, dug deeper burrows, hard to shoot, and camo color. Completely white tail. Island off of S. Africa: Take one leave one, fresh meat was a problem. They dumped domestic goats on the island. When you need meat, just get a goat from the island. They kept getting the easy goats to catch. After 50 years, you could not catch the goats, they adapted to be hard to catch. They became faster, fearful, and camo color. Originally were domestic goats, then they are feral. Bottle Neck: Start with large population, and then some big disaster happens. EX) Bringing slaves to US. EX) The crows. Crows used to be abundant, west Nile virus killed 99% of crows. Now they are coming back from the bottle neck. EX) Species that we over hunted. Cheetah, their genes come from 20 cheetahs, there was an extreme bottle neck. EX) Northern Elephant Seal: Several hundred/thousands. In 1930, there was less than 20 because they were hunted. EX) Holocaust Wright's shifting balance theory of evolution: serve and compliment N.S. Two red dots on graph are phenotypes that were preferred. Evolution by N.S. By itself can never cross a valley on adaptive landscape. It has to have higher fitness. How do we get to the blue dot, BY genetic drift (allows species to explore the adaptive landscape, they compliment each other and can lead to speciation or diversification. 11.2 Wright's shifting balance theory: Y-axis: fitness, always a set of evolutionarily feasible phenotypes Peaks: Where natural selection (NS) is best Evolution by NS will never by itself cross a valley in an adaptive landscape. NS is a passive process going up the peaks. How do you get across the valley? Genetic Drift, if it was a small population and strong enough **Genetic drift has largest effect when NS is weak Small deviation in red dot (phenotype) cause huge shifts in fitness. TRENDS: Where peak is "flatter", NS is weaker. (This is when genetic drift has higher chance of moving across the peak.) Steeper peak is stabilizing selection. Natural selection promotes adaptations. The Neutral Theory of Molecular Evolution: **Absence of natural selection. Neutral substitution: silent substitutions in codons; Mutations that occur in noncoding regions Motoo Kimura: Developed neutral theory Mutations rates are constant and random. Number of neutral substitutions act like a clock. More mutations that people have that are unique, to find common ancestor. Age of divergence, how many amino acids are different. Cytoclome C is billions of years old. Nearly Neutral Theory Flat (peak) landscape: mutations that are nearly neutral. Deleterious mutations: moves you down the peak. When you are on the peak, there is no advantageous mutations. 1 Some mutations are neutral, some are strong in affecting phenotypes 2 Depending on trait and where you are, tells us how strong NS is When NS is weak or when population is small, genetic drift becomes important Population Structure: Patchiness is woods , leads species in certain patches don’t interact (subpopulations - groups of individuals that occupy the same area (interact strongly), and don't interact as much with other subpopulations). EX) How many wards are in Chicago, there are 52. We probably won't visit them. EX) Cubs fans won't go to White Sox field, vice versa. How do they interact: allele flow. Subpopulations allow for ecotype (subpopulations that have specialized adaptations for their environments). Homogenize the populations. Allele flow: 1 Break down ecotype variance. 2 Effectively increases population size, genetic drift is less likely. 3 Select ecotype of source population. Allele flow vs. Genetic Drift M is proportion of migrants (rate of migration) N is size of subpopulations. M > (1/(2N)) Allele flow is > more important than genetic drift. Allele flow vs. NS (IMPORTANT SLIDE) Allele flow opposes natural selection. BUT NO, allele flow works with NS. NS promotes adaptations given the circumstances. Allele flow becomes part of the ecology of the organism. Important: integration, influences whether the adaption is a single generalist (high allele flow/homogeneity) or a specialized (low allele flow/heterogeneity). If there is no migration, there will be two (sorta extreme) ecotypes favored. High migration equals one favored ecotype, that is like a mid of the 2 ecotypes. EX) Cancer. Blue tumor cells, good competitors. We know: 1) not a lot of movement between areas or 2) Heterogeneity EX) Fox and grey. Fox in deep woods, grey in boundaries. Is it because of allele flow (NO), then it may be selection. Margins of woods are very different than interior. 11.3 12.1 NS Does not operate on genes, operates on phenotypes. Heritable variation: Mutations create new alleles, affect fitness (if they are not neutral), then there is selection for that allele. Components of fitness: refer to the aptitudes of the animal, it may have high death rate: death, selected against. Births and deaths occur because of ability to detect, respond, and survive predators. (Fearless mouse - given a world of predators) 1 Absolute fitness (per capita growth rate) 1 Relative fitness (how fit a population is compared to other populations with different phenotypes) a Grey squirrels that don’t know where the nuts are, will not survive as well. b Grey squirrels have big bushy tails, one squirrel (a stub) lost its tail (maybe in a fight)--it was not genetically coded for, we can mark them compared to normal grey squirrels and not their survivorship. Stubs have half the life expectancy. c Bald morph, genetic abnormality. Hairless. It would do horrible in the winter. Relative fitness: Alleles produce genotype, take most fit genotype and score it one. Ex) w(AA) = 1 w(Aa)=1 w(aa)=1-s Ex) Beetles, hetero is most fit. Take highest fitness and scale them to one, then divide the survivorship of the other two of the by the hetero number (.93). Selection coefficient is 1 - s, so yellow has second to best fitness. Directional selection: one sort of trait, natural selection favors the extreme phenotype. Ex) larger individuals favored, then the whole curve shifts to the right. On adaptive landscape, the dot moves towards the peak. The location of the dot, find the slope, that gives us the direction and the magnitude gives us how strong the selection is. Ex) Industrial rev. they burned a lot of coal, peppered moth feeds off the beech and birch trees that are light in color. Hence the moths try to have white wings to avoid predation by birds. Then trees got covered by soot, so then moths began the dark morph to better camouflage. EX) Hazel moth in England Ex) in USA, 1960s, Pittsburgh, they had to wipe soot off the cars everyday. EX) Industrial rev. insects. Pleiotropy (one trait affects changes in other traits) EX) Forest fires, blackened landscape, grasshoppers adapted. EX) Pocket mouse in rocky areas. Light colored, or black colored where there is lava stone. 12.2 Stabilizing selection: graph of frequency distribution, selection is favoring the center, not the extremes. On adaptive landscape: Green dot is where it was, then the stabilizing selection goes towards the peak, and then the curve pushes to keep us at the peak. All traits are being held by stabilizing selection, ex) squirrel coat color, keeps phenotypes at their adaptations. How do we know this: Lab experiments, you select for more extremes, it shifts toward that evolution. So when there isn't change, stabilizing selection is occurring. EX) Mersa disease, is now resistant to our antibiotics. Strong selection for the bacteria to have resistant. Requires a cost, they sacrifice wither their metabolism or growth rate. So they evolve back to be being susceptible to antibiotics. EX) Himalayan Tar, needs to look attractive to get a mate. Form of selection: Disruptive selection: Opposite of stabilizing selection (Population is on the valley--meaning any other phenotype is better, this is an opportunity for the population to split and lead to speciation) Natural selection could not drive you down to a valley, BUT YES it can happen: if a species is in a valley, it is at maximum disruptive; the valley moves faster than the species Only way out of the valley is to have polymorphism or for the species to split into two. EX) Apple maggot flies, laying eggs in apples. Species had no evolutionary history prior to apples. Speciated from the real Hawthorne flies. Happened in 50 years. --> This happens from frequency-dependent selection. Your best phenotype depends on the phenotypes of others. Your fitness depends on the fitness of other organisms. EX) Squirrel. We feed them, to tear up a piece of sod, put the peanut under to hide them. 1 Under selection to bury and hide nuts to have them for winter. 2 Other squirrels are looking for them. Since other squirrels look for the nuts, this is frequency dependent. 3 Pretend to bury the peanut, but its in their mouth. 4 Once a peanut is found, they stop burying them. EX) Elderflower, two colors, yellow and purple. Bees pollinate them. Flowers provide pollin and nectar, elderflowers cheat, they provide no reward. No nectar. Then bees wise up. They know the purple one doesn’t have nectar, but they still go to the white ones which are scarce. Behavioral Ecology: Behaviors themselves are interesting adaptations. Behaviors are harder to pinpoint to genes. Behaviors are the genes. Ability to assess and respond to behaviors. (Assess accurately and respond appropriately) Afferent/efferent. Universal Properties of Life: Births and Deaths Need for energy and resources (for growth and reproduction) Feeding behaviors (adaptive) 1 Feed quickly (The better the food is the faster they eat it, because at one point in time they didn’t have a lot of food) (If you finish your food first, you can eat others) 2 Efficiently (Forging) 3 Safely Foraging Ecology Studies: Study the feeding behaviors for populations, etc. Diet choice: to eat or not to eat R = Resource density E = energy reward (how valuable it is) A = encounter probability H = handling time (how quickly can you eat the food) 12.3 Foraging ecology - Find it quickly, safely, and efficiently. 1 Diet choice: What to eat 2 Patch Use: Acorns run out, then they start moving to another area to find acorns 3 Habitat selection: where to locate drey, establish home range. Drey= the leaf nest of a squirrel a What is a drey? (question 41 on exam 3) · Consequences of feeding · Develop math models - how organism should feed (with 1/2/3) o Develop theories and test them in eviro · Worth eating/not? 1. R=resource density 1. E=energy reward 1. A=encounter probability 1. H=handling time Abundance of material How valuable? Rewarding? How much we like it? How easy is it to find it? How easy is it to handle it/how quickly eat it? Walnut-brazilian-cocnut (---hardest to open) Harvest Rate Model. Foraging theory H=energy per item/ (search time + handling time) · Search time=inverse of items/time = 1/aR H= ***know parameters (determines to eat or not to eat) 1. Energy /handling time 1. When should you be picky? Food 1 is preferred to food 2 if: A1e1R1/(1+a1h1r1) > Classic Diet Choice 1. All or nothing "bang bang diet choice" 1. Go for only proffered thing - selective 2. Eat everything - opportunistic 2. Eat last preferred food or not - independent 1. Decision to eat red acorns (more preferred) is independent of abundance of white (less 2. IN NATURE: partially selective diets in reality - not like the model preferred) i. Handling and search independent of each other in the model ii. Some foods are filling and some aren't (bulky food can make squirrel slow) Expand diet as food declines Do squirrels like peanuts better than sunflower seeds? · Make patches · Mix together? o Peanuts preferred if next to a tree o Sunflower preferred if further away from a tree · Peanuts (smell) are easier to find when patch depletes Depletable food patches · Giving up density o Giraffes feeding on fornacatia - gives up and moves on · Some leafs are better than others (not yummy) · Thorns o Peanut butter jar · Harvest rate going down and decide when to leave it · Leave: o Go to other one is easier o No alternatives - stay o Use rich patches>poor Optimal Patch Use · Econ decision · Benefits of foraging=harvest rate=H · Costs to foraging o Metabolic=C o Cost of predation=P o Missed opportinity cost=MOC (don’t do something else) GUD · Increase with · 1 · 2 · 3 Food easier to find= GUD lowers Handling time up=GUD up High nutritional value=GUD down 13.1 Game theory H = C + P + MOC Giving up density: EX) squirrel tries to find food in food patches, gives up. Foraging perimeters: If food is easier to find, they will higher encounter probability. Handling time Nutritional EX) The elephant shrew eats about anything, use nose to forage. Vs. the namakua mouse has a similar diet, they forage with their feet. Experiment: food patches (3 different ones), which substrate does the mouse that forages with its nose prefers. Elephant shrew's favorite substrate was the pebbles, tells us that they prefer habitat with rocks to probe around. Also can tell which food they prefer, they most prefer the mealworm. Same experiment conducted with namakua mouse. They preferred sand and sunflower seed. --> Pachus, works and able to learn how the two mice coexist. Density dependent habitat selection: Have two habitats (a and b), there is adjacent habitat, if you are a squirrel, you will not only assess the quality but also how crowded the habitats are. The habitats have different fitness. They should make the population sizes equal. (LOOK AT EQUATION) EX) Choosing shortest grocery line. EX) Amani Sunbird (most endangered sunbird), found in a forest in Kenya. Arabuko Sokoke Forest, all Amani Sunbirds live in the Brachystegia woodland (7600 hectors). Huge trees with spread out branches, lot of light hits floor. Two other sunbirds live there. Studied foraging behavior. Forage 60-100 feet off of the ground. Collard sunbird is the interference dominant (bullies the amani sunbirds). Predation risk is higher in the higher canopy so the collard sunbird doesn’t go that high. Why do the amani sunbirds not relocate? There are plain backed sunbirds abundunt near by, the amani are outcompeted outside the forest. To up number of amani, create bigger habitat or kill plain back sunbird. Evolutionary game. The amani's behavior depends on the other sunbirds. Your strategy depends on the strategies of others. Game theory: strategic decision making, your best strategy depend on their best strategy. Solution to game, no one wants to unilartey change thair stragey. Games have player rules, straategies. Collectively, the best stag Producer Scrounger Games *+(ad you 13.2 Prisoners dilemma. Second chart (disclose): Games of enlightened self interest. As you pursure your own pie, you leave a bigger pie for everyone else. Battle of sexes: asymmetric gain. Playing it well requires coordination. If it is not coordinated, ex) Joe always gets his way then there is dominance and it is abusive to the relationship. Big-pig Little Pig Game: Getting food, the pig needs to go to the end of the cave, pull the lever. Then go to the trough. Subordinate pig (little) does better without pulling the lever. If individuals that are so disadvantaged that they have nothing to be gained by acting, then they leverage the other individual to do something. They should coordinate. Big pig needs to slow down if the little pig pulls the lever. Evolutionary Game: Individuals are the players. Heritable phenotypes are strategies, if there is phenotypic plasticity, they choose their strategies. Per capita growth rates is the payoff. Environment sets the rules. Players come and go, but the strategies persist. EX) Digger wasp: Produce (Dig a hole), Scrounge (Enter a hole that is already there and take it over). Frequency dependent, if everyone makes them, it is easier to scrounge one. If everyone is scrounging, there are no holes to use. Brockmann: They noticed it is not genetic. Behaviorally flexible, can be a producer and scrounger. If worlds can invade each other, they form a equilibrium, which is called a mixed strategy solution. ESS- Key concept: A strategy that when everyone is using it, there is no incentive to change what you are doing. Adaptive landscape: If you are the red dot, then any heritable trait that has a fitness higher than the value, can invade. The blue dot does not have any strategy that does better than it, cannot be invaded. **ON EXAM**Solving Evolutionary Games: Row is your strategy, column is strategy of everyone else. Payoff is little letters. A vs A is the best. If a>c, then there is no incentive to change my strategy from A to B. a then is an ESS. If d>b, then A cannot invade. If neither are ESS, then A and B can coexist. EX) Digger Wasp, Snowdrift Game. Snow blocking the road If both people dig, both get the benefit and you split the cost. If everyone is digging, there is no ESS. "If everyone has it under control, I guess im not needed." It is invadible. EX) Caching and Plifering, Squirrels. Do both, steal and find own food. Leads to wasted effort, fake caching, secondary caching, and caching in risky places (where there are predators). Causes squirrels to spend more time in the risky habitat, predation is easier. Game of chicken: If everyone plays dove, divide the benefit, and then you want to play Hawk. If both play Hawk, split benefit but the cost is too big, you lose the benefit. 14.1 Macroevolution: Micro is work within populations. EX) Neanderthals. Alleles enter population and selected for (micro) Then they get diversify enough to the point where they cannot hybridize (reproduce) Darwin came up with natural selection but since he thought evolution was very slow process, but geology occurs in shorter time periods. Species Concepts: Ecological Biological: mate and produce babies but can't with other species. Phylogenetic: branch on tree of life. Species as lineage. In there is objective, common ancestors are dead, so infer existence. Morphological: hard to tell species apart EX) Tollymonster fossils only found in IL. Speciation: NS plays a role in speciation. Usually it is geography that is what pushes speciation. Reproductively isolation, is when species become different. Cryptic species. Sympatric species live in the same place. Barriers: Habitat isolation (toads in desert create burrow, reproduce in water. Soil type. One morph turns into a canabal Ex) Different lice, different species, habitaTs are your head. Temporal isolation: mate at different times. Behavioral Isolation: organisms who mto makte with 14.2 Game theory Ex) date is mean to waiter, if someone is rude to the wait staff, they systematically are abusive/rude to those who are lesser than them Act ethically when people will notice you being ethical Squirrels cache their nuts in dangerous places but that gets them eaten Evolution of new species results from barriers to allele flow among populations of an existing species: Reproductive isolation: causes speciation. Species have subpopulations but they are still successful reproductively with other subpopulation (result of enough allele flow). Ex. Geese Squirrels being on two continents, they are probably going to evolve to reproductive isolation => speciation. A reason to do someone favor is so that person is also likely to do you a favor. Prezygotic isolation mechanism results from genetics, they cause barriers to reproductive isolation and geographic isolation. Postzygotic: when you hybridize species they are less fit, as in they don’t hatch/come to life, or they are healthy but are sterile. Causes natural selection on females to be less selected. Allo= differ Sim = same Pat=dad Ex) Salamanders: salamanders dispersed to the west and east, isolating them as they colonized. Where the salamanders meet they are reproductively isolated. Speciation complete in the south but not in other places. Geographic barrier, the species may meld together by allele flow Incipient species Ground squirrels are on opposite sides of grand canyon EX) case of allopatric speciation - the Drongo, has crest on feathers EX) Ismis of panama: the shrimp are isolated and evolve allopatric speciation. The time frame for speciation is hard to predict, could be 1 million years, usually (from fish evidence), A long time, millimilion years (?) EX) Poeciliopsis sonorensis: Fish, the female suffer the consequences. IF they mate with the wrong species, all of their male offspring will die. Sympatric Speciation Polyploidy 14.3 Genetically modified crops: don’t necessarily give you cancer. How long does Allopatric speciation take? GMO’s ~not all of them are bad Host Shift ~non random mating due to host shift ~ex: parasites like apple maggots Parapatry ~incomplete allopatric speciation ~ex: garter snakes b/c they can interbreed but only with populations close to it since they don’t like to cross large areas to mate Phylogeny ~family tree explaining how species are related using cladogenesis Systematics—study of phylogeny, can’t tell time lines Taxonomy—naming of organisms based on their phylogeny Cladogenesis—the origin of lineages ~starts with speciation events Inferring Phylogeny ~morphology ~DNA sequencing ~fossil records (double checking molecular clocks, test hypothesis) ~a lot of evidence about timelines but not helpful for phylogenetic trees Homology—trait that exist because 2 species have inherited it from a common ancestor ~5 fingers is a homology we inherited from an undiscovered early tetrapod ancestor Cladistics—widely accepted school of systematics ~Apomorphy—an evolutionary novelty for one group ~shared with respect to a particular group ~Plesiomorphy—an evolutionarily primitive state ~Synapomorphy—a novel (derived) trait that a group has inherited because the common ancestor of that group had a novel characteristic and passed it on ~Synplesiomorphy—an evolutionarily primitive trait that a group has inherited because the common ancestor of that group had inherited the primitive condition, unchanged, from an earlier group 15.1 Homology Synapomorphy is shared characteristic shared for a group of individuals (mammals having 5 fingers) Details of evolutionary history Driven by adaptive selection Build family trees (not by social behavior) EX. Bee wing vein: each change affects a lot of the function of the wing. Homoplasy: characteristic that evolved by convergent evolution. -Ex. Sucking for survival (insects) Mosquitos are flies with sucking mouth parts. Original fly ate animal tissue and drank blood. Evolution into a channel, like a syringe. Different insects have different mouths. Evolved independently. -Ex. Red and giant pandas, dna analysis showed they are distant relatives. Convergent evolved because they eat bamboo. Extinction: Fundamental to evolution. -Ex. Pandas are doomed, anthropogenic changes are causing them to go extinct. Mass extinction caused by humans. -Almost all species that have ever lived are extinct. -Ex. Dinosaurs were good at adapting in new environments. -Important to speciation. Ecological species go extinct as well, which gives opportunities for new species to form and take that niche. -High biodiversity, rate determines the extinction rate. -Volcanic islands, species go extinct. Non-catastrophic climates also cause extinction. (Ex. A virus could have caused humans to go extinct.) --Background extinction rate. -BER: look at species before extinction. Birds and mammals have high BER. Oceanic proriferoba have great fossil record to count extinction rate. -Mass extinctions are from catastrophes. Don't weed out weak or unfit individuals, species. -5 Natural, 1 unnatural causes Late Devonian Mid Ordovician Permian Triassic (antrhopogenic change) Late Triassic Cretaceous-Paleogene Global glaciation has happened in the past. Cause mass extinction Holy mammoth: walked with humans. Basin looked not so deep because of tar coating on it. Lost many a mammoths. Human hunting: drop in diversity of carnivores, as be evolved. They evolved better survival characteristics. THIS IS WHERE HE JUMPS BY SLIDES> … Holocene Mass Extinction: Singapore, predict extinct. Distaser Taxa: do well after a catastrophe. Modified biosphere for our benefit. Fragmented habitats Edges of habitats are less favored by some species EX) Bird Losing orhids, salmon Introduce Exotics: Zebra mussels, snake that ate guam. Garlic mustard Overexpolition Makes species more vulnerable - - --- ----- -------
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