BIOL 351 Final Exam Study Guide

What is Cope's Rule, and do the basic observations that spawned it support a widespread driven trend across animal taxa?

"Cope's Rule" - observation that body size appears to increase in lineages over time No, maybe, i don't know lol

How do we calculate fitness values from survival tables?

1. Find overall survival rate --> (total survivors/total starting) 2. Find Expected survivors for each genotype --> (genotype starting * overall survival rate) 3. Fitness (omega) --> (Observed survivors / expected survivors)

How can discontinuity between populations be maintained in the absence of absolute barriers to reproduction?

Hybrids have no or low fitness

What does it mean to have a low value for h?

If h = 0, the heterozygote is exactly like the selectively favored homozygote

What is genetic drift and what is is the mechanism behind it? Why is drift bound to happen in finite populations?

Random changes in allele frequencies in population due to sampling errors in zygote formation If not everybody gets a chance to contribute to the next generation that is going to impose allele frequency changes even if every genotype has the same fitness Selection is deterministic - Drift is stochastic

What is relative fitness? How do we calculate it? Why is it not a problem to treat our parameters that way?

Relative fitness is our fitness values compared to the highest (or lowest) fitness (Each fitness value / largest fitness) = relative fitness Because they're proportions

Why are some of these creatures so hard to classify?

Weird body plans

If phenotypic variation can be driven solely by the environment, how can phenotypically plasticity evolve? What is this process called?

genetic assimilation - the evolution of a fixed trait from a phenotypically plastic variation?????

What is the difference between "extrinsic" and "intrinsic" barriers?

intrinsic - independent of the environment extrinsic - dependent on the environment

How do you calculate selection coefficient for each genotype from relative fitness values? KEEP IN MIND THAT THE EQUATION YOU GET FOR THIS IS SPECIFIC TO SCALED RELATIVE FITNESS VALUES & THE IMPORTANT CHANGE FOR UNDERDOMINANT SYSTEMS

s = 1 - relative fitness Therefore: relative fitness = 1 - s

What do we mean by fitness?

the extent to which an individual contributes to future generations an individual's lifetime contribution to the genepool of the next generation - multifaceted combination of survival and reproductive success

What is a phenotype?

the measurable properties of an organism, manifested throughout its life Morphological, physiological, biochemical, behavioral, etc... "Phenotype" includes the total setof these properties or traits, butwe're usually concerned with justa subset of these traits for a given question

What is a reaction norm? What can reaction norms tell us about GxE interactions?

the relationship between the environment and values of a phenotypically plastic traits different genotypes have different reaction norms Comparing how different different genotypes are expressed phenotypically under varying degrees of an environmental condition can show how the environment explicitly affects the expression of an allele A selection experiment on GxE variation not only changes the phenotype, but it does so by altering the reaction norm

How do we calculate allele frequencies from genotype data (there a couple of different ways of approaching this)?

two AOI per homozygote with AOI one AOI per heterozygote with AOI every individual has two alleles --> total alleles #AOI/total alleles also Freq A : freq AA + .5*freq Aa

Why do we need to consider fitness as a whole?

what are the consequences to contributing to the gene pool of the next generation? Everything that plays a role in contributing alleles, affects allele frequency over time

What is average excess? Why does it matter?

( 𝑝𝜔AA + 𝑞𝜔Aa − 𝜔avg ) average fitness effect of a gamete carrying allele A - that can combine at random with either A or a gametes in the population at their given frequencies It tell us how much these fitness values are going to represent the probabilities of these gametes coming together

How are different species interactions classified? Can you think of some examples of each or categorize some described interactions?

+/+ - mutualism - pollenation by insects +/0 - commensalism - fungi eating poop +/- - victim/exploiter - predation/parasitoidism (kill the host) or parasitism 0/- - ammensalism - someone getting pricked by a cactus -/- - competition - foxes and coyotes both eating bunnies

What is the geographic mosaic theory of coevolution? What predictions does it make? How does it provide a framework for empirical studies of coevolution?

- Interspecific interactions vary among populations - Coevolution of species interactions will also vary among populations - Populations differ in their degree of specialization - Differences in the outcome of species interactions and specialization scale up to a form a geographic mosaic of evolving interactions There are so many variables that there is going to be differences between interactions and their implications in different places. And in different places, species interactions will be at different stages of coevolution that can be analyzed together --> considering differences together gives us a bigger picture that can be applied to each interaction individually (zooming in on a mosaic doesn't mean much until you zoom out to see the big picture first) Geographic mosaic can show us potential outcomes of arms races (one species "winning") and how the species "respond" after that can give a glimpse toward a possible future for the same species in different places that haven't gotten to that point yet

What are some commons misunderstandings about natural selection? Why are they wrong?

-Selection acts on individuals, but individuals don't evolve- populations do --> allele frequency will not change in an individual, but selection will affect an individual's fitness and ability to contribute to the gene pool -Natural Selection can't see into the future --> Purely mathematical process based on the conditions within the parental generation - The results thus lags a generation behind the selective pressures (organisms might not be well adapted for their environment, but more so the environment in which they were conceived) -Selection acts on the variation existing in a givenpopulation; it doesn't addnew genetic variation --> only mutation, new genetic combination, and migration can do create new phenotype, and then selection can act on those phenotypes (only mutation can create new alleles) (as phenotypes are selected, the alleles responsible will become more frequent, and the combination of selected alleles will become more likely) (corn alleles were additive) Selection does not result in perfection • Evolution is constrained • It can't optimize all traits simultaneously Selection does not favor complexity --> Fitness can just as easily favor a loss of complexity - Increasing complexity can arise from a passive, undirected process• The Drunkard's walk - Gould's "left wall of biocomplexity" Being evolutionarily"advanced" is subjective.

What are two different ways you can go about performing selection experiments in the lab? (what are different ways of imposing selection on experimental populations?)

-Threespine sticklebacks occur in marine and freshwater populations -Freshwater populations have much better cold tolerance -Take different populations from nature and careful test thermal tolerance in lab reared generations -Then transfer to experimental ponds with cold conditions -No active control of breeding -Bring them back into the lab and rear offspring under controlled conditions -Cold tolerance improved by 2.5 C in just 3 generations Garland et al. experiment on running behavior in lab mice (artificial selection)

What is incomplete lineage sorting? How does it complicate phylogenetic trees?

-Variation present within ancestral population (predating speciation) segregates differently among ancestors and different loci This happens due to genetic variance in the ancestoral population getting sorted into diverging population and then alleles in those diverging groups going to fixation. Since alleles were lost due to drift, it may appear that they were not inherited due to phylogenetic reasons, but that's not the case. If drift events cause loss of alleles that cause progeny to differ in fixed alleles in an order different than the genetic history of those alleles in the ancestoral population, we will get a different tree than actuality depending on the gene used to sequence. This confusion can occur when there is insufficient time for alleles to evolve uniquely from other lineages to distinguish them in extant species.

What is Muller's ratchet, and what is mutation load? What does this have to do with sex?

.The process leads to the inevitable accumulation of deleterious mutations in asexual species. When mutation and drift work together and eliminate the last individual with a geneotype free of deleterious alleles, the ratchet has moved forward and cannot go back, it is gone for good. This accumulation of deleterious mutations weighs down the fitness of the population This fitness burden is called "genetic load." In sexual populations, recombination breaks the ratchet. Recombination can bring back a perfect genotype even if no one has it, but the alleles are still present, just not together. Recombination can bring them together.

Rephrase our previous natural selection postulates in light of the Modern Synthesis

1) Variation among individuals results from mutations creating new alleles arising and segregating in populations 2) Inheritance is the results of of allelic variation passing from parents to offspring 3) Through differential survival or reproductive success, not all individuals contribute to the gamete pool 4) The probability of contributing to the next generation varies as a function of individuals' genotypes

What are the two basic models for how the taxonomic composition of diversity can shift? What are some examples of each that we discussed (one came up in a later lecture)?

1. Competitive displacement - A dwindling of a certain taxon accompanied by the radiation of another to become the dominant group on Earth. (didn't really happen with mammals vs dinos) (did occur during the great american biotic interchange with the rise of the ithmus of Panama) 2. A massive event ends the dominant taxon allowing a new one to radiate with diversity

What the 4 largest divisions of geological time (eons)? In which order did they occur? What are the basic characteristics of each? Which was the longest?

1. Hadeon eon (4.5 bya to 4 bya) (about 500 million years long) - super hot and unstable - the moon happens here (about 4.4 bya) 2. Archaen eon (4 bya to 2.5 bya) (about 1.5 billion years long) - crust is cooled, we have continents and oceans, much more volcanic activity and meteroite collision than today - life occurs here probably early on (even though our earliest undisputed evidence of life is about 3.2 bya, with supplemental isotope evidence at about 3.7 bya, possibile stromatolites might put bacterial fossils at 3.5 bya) 3. Proterozoic eon (2.5 bya to 540 mya) (about 2 billion years long) (longest) - lots of microbes here, the great oxygenation event evidenced by iron branded formations, dawn of multicellularity, endosymbiosis and the dawn of eukaryotes, multicellular animals coming up at the tail end 4. Phanerozoic (540 mya to now) - the age of visible multicellular life and metazoin (multicellular animal) diversity

What are the key phases in the generalized population life cycle that forms the basis of our models? Where do Mendel's "laws" come into play along this life cycle? Where and how do our other basic probability functions fit into this?

1. Parental Generation - genotype 2. Gamete Pool derived from parental generation - allele frequencies 3. Combination of Gametes from pool into zygotes - probability based on allele frequencies 4. Offspring generation - new genotype frequencies If we make the assumption that all individuals in the parent population contribute evenly to the next population -applying Mendel's law of segregation to the population as a whole- **Frequency of gametes equals allele frequency of the parental population** Probability of two independent events occurring together is the product of their individual probabilities Probability of either of two mutually exclusive events occurring is the sum of their individual probabilities p^2 + 2pq + q^2 = 1

How do we go about constructing simply cladograms from morphological or molecular data?

1. Who has most differences from out group? They're most distantly related. 2. Rank by who has most differences to out group? 3. See what differences are shared between organisms. They're most closely related. 4. Use parsimony to reduce the amount of homoplasies.

What is a population? What is the critical part of this definition from the perspective of population genetic models?

A group of interbreeding individuals and their offspring (sexually reproducing organisms) Interbreeding is important a group of conspecific organisms occupying a more or less well defined geographic area that exhibit reproductive continuity from generation to generation reproductive continuity

What is an adaptive radiation?

A rapid diversification of new species from a single species due to new ecological opportunity When a bunch of new species start to pop up at once from a single common ancestor

How often to mutations occur (generally)?

About 10^-11 to 10^-2 substitutions per base pair per generation most around 10^-8 Humans at about 10^-7.8 have about 3 * 10^9 bp see about 47 subs per generation or about 0.000000000016% of our genome

What is the difference between an additive effect and an interaction effect? Can you draw a plot that would represent either of those in a generalized way?

Additive - each factor affects the trait independently - if a condition (like temperature) affects a trait, it should affect the trait the same way no matter what other conditions (such as fertilizer nitrogen content) are present for an organism Genetic POV - when the presence of various alleles are expressed independently of each other, and if they have similar effects, their effects are added for a more extreme phenotype (multiple height alleles at various loci all independently contributing to the height of an individual, additively) Interaction - when one condition affects a trait in an organism differently depending on other conditions for an organism Genetic POV (epistasis)- when the presence of an allele is expressed differently (or not at all) if a certain allele is present at a different locus (an allele expressing alternative growth not allowing normal growth alleles from contributing to height)

What are the different geographic "modes" of speciation? Which ones are more permissive for speciation?

Allopatry - complete geographic separation of populations during divergence Vicariance - separation of a large population into two parts Peripatric divergence - Allopatry caused by the colonization of a distant habitat from a larger population (drift might be huge here due to founder/bottleneck effects) Parapatry - Geographic separation, but not complete isolation (not allopatry) - often occurring in adjoining habitats Sympatry - No geographic separation among diverging populations - Divergence begins as polymorphism in population

What is epistasis?

An effect of the interaction among multiple loci on a phenotype (or fitness) such that the joint effect differs from the sum of the loci taken separately.

What are the lessons from the apple maggot fly story for how ecological divergence can lead to speciation, how multiple isolating mechanisms can work together, and how prezygotic and postzygotic isolation can go hand in hand?

Apple maggot flies showed how sympatric speciation can occur and it has to do with reproductive isolation that is not dependent on geological separation First they were isolated in a temporal sense that their mating seasons were thrown off by the growing season of their preferred fruit (which was determined by epistatic gene interaction) Migration was a poor force to homogenize because the hybrids were very low fitness (they were deterred by any viable fruit because of epistatic interactions in chemoreceptor genes) - this is a type of postzygotic isolation in that the hybrids were behaviorally sterile (they wouldn't reproduce because they hated all the fruit) Since they were reproductively isolated, epistatic interactions were able to build (Dobzhansky-Muller) in reproductive mechanisms, which leads to prezygotic isolation being responsible for postzygotic isolation

How old is the Earth?

Basedonradiometric dating - 4.58 billion years old

What is a bauplan? What is a major macroevolutionary question about the diversity of bodyplans that came out of the Cambrian?

Body plan - controlled by the genetic pathways that lead to specific developmental processes why do animals have the set of Bauplaሷne that they do? Is there something optimal about them that natural selection was going to inevitably reach? Or is this due to historical accident?

What are stromatolites?

Built up by biofilm communities with cyanobacteria in shallow, protected water. Biofilms of cyanobacteria keep building on top of each other in order to reach the sunlight and photosynthesize if fossils in Australia are confirmed to be stromatolites, this would date life to about 3.5 bya

What are some of the major events in our own lineage in the periods immediately following the Cambrian?

Cambrian - 540 mya to 485 mya Ordivician - 485 mya to 443 mya - mostly invertabrates such as arthropods - the only vertebrates were jawless fish Silurian - 443 mya to 419 mya - fish diversify and gain armor - jaws develop from gill arches (Placoderms) Devonian - 419 mya to 359 mya - the age of fishes - vertebrates rule - placoderms become gnathostomes (jawed vertebrates) which now dominate the oceans Early gnathostomes developed bony fish (opposed to cartilaginous fish) into actinopterygians (rayfins) and sarcoptrygians (lobe fins)

How can we quantify the change in genetic variation due to drift?

Change in heterozygosity 𝐻 = 2𝑝𝑞

What is an inversion? Why might they be important?

Change in the order of genes due to double-stranded breaks and misaligned repairs This occurs when the DNA forms a loop, breaks, and then gets reattached, but now the template strand (the one that is used) and the sense strand are reversed and do not make sense with the unaffected portion of the DNA

What are some broader corollaries of evolutionary thinking in biology (e.g. change is the norm, importance of history in biology patterns, etc)?

Change, not stasis, is the natural order of the living world. Already becoming accepted in Geology. Historical contingency imposes constraints on natural phenomenon (vagus nerve in fish vs. land animals) Biological phenomenon explained by mechanistic causes (Break from long western tradition of duality of Aristotelian Final vs. Efficient causation) Variation is a ubiquitous component of biological systems (Major break with Platonic Essentialism (world of forms))

Who are our closets living relatives and how do we know that?

Chimps and bonobos - genetic data and fossil evidence

How do mutation rates act as an evolutionary force in isolation?

Clearly, mutation is necessary for long-term evolutionary change, but it is nowhere near sufficient to explain genetic and phenotypic change in nature SLOWLY converts p to q

Why should we expect that it's important in nature?

Coevolution puts biotic interactions at the forefront of understanding adaptation. The field represents a crucial link between ecology and evolutionary biology Species interactions are ubiquitous in nature All host-pathogen interactions are inherently coevolutionary

What are some important constraints on coevolution (what did the snake/newt story tell us about this)?

Coevolutionary adaptations that increase fitness in a particular environment usually have detrimental fitness affects on other physiological processes (this is antagonistic pleiotropy) (snakes were resistant to newt poison, but their nervous systems were shit) There are also places were newts or snakes are spending resources on this coevolutionary arms race more than they need to be, lowering their fitness more than necessary (mismatch)

What are some of the big-picture patterns that form the basis of macroevolutionary questions?

Consider both that diversity as a whole and the composition of that diversity by different major clades Complexity ala Gould's left wall of complexity - the appearance that species are moving to become more and more complex Body size

What's the "law" of succession?

Correspondence among fossil and extant faunas (and floras) in space Existing things need to come from past things

What is neutral genetic variation? What types of mutations are particularly likely to be neutral?

Different neutral base substitutions among and within species Synonymous mutations

Which major component of Darwin's big idea was immediately accepted by scientists? Why did the other part take longer to catch on?

Differential Survival because populations weren't growing exponentially unchecked Natural Selection remained controversial because both Biology and Math had to catch up • Mechanisms of inheritance (genetics) • Analyzing variation in populations - Statistics

What is directional selection? What is overdominance? What is underdominance?

Directional - the highest or lowest value of a trait (and underlying allele frequency) has the highest mean population fitness - In the absence of other forces this simply leads to fixation of the favored allele OVERDOMINANCE - Heterozygote advantage UNDERDOMINANCE - Heterozygote inferiority

What is the relationship between speciation and biodiversity?

Discontinuity among organisms indicates that "species" is a biologically meaningful level of organization

What's the difference between continuous and discrete variation?

Discrete --> a genotype produces one of a small set of possible phenotypes (few intermediates between discrete states) Continuous --> a genotype produces one of a large range of possibilities somewhere on a wide spectrum

How does geographic mode influence how reproductive incompatibilities evolve?

Dobzhansky-Muller happens most readily in complete allopatry (doesn't explain sympatric very well) More migration/less geographic isolation slows the process

How do drift and migration interact in subdivided populations? What does this have to do with FST?

Drift drives the populations toward fixation while migration drives the population toward a mean (non-fixed). They counteract each other Fst - the measure of genetic differentiation between subdivided populations (drift acts to raise it, migration acts to lower it) F^st is the equilibrium Fst between acts of drift and migration occuring between two subpopulations F^st = 1/(4Nem + 1) Nem = (1 - F^st)/(4F^st) --> effective migrants per generation)

What affects the strength of genetic drift?

Drift is a stronger evolutionary force in small populations

What are the expected effects of drift within populations?

Drift is stochastic in that we can't predict the outcome If we know the starting point the system- we can't know where it will end up In terms of alleles, this means that drift tends towards fixation in the long run.

Where do humans fit into mammalian diversity? How far back does the primate lineage go? What are some of the major events in primate evolution during the Cenozoic?

Earliest fossil primates appear in Eocene ~55 mya, likely originated in North America and spread to Europe Molecular clock suggests most recent common ancestor of all primates existed 66-69 mya - pre K-Pg extinction in dinosaur times - we (real primates) split from flying lemurs during this time About 66 mya Right before K-Pg we split from actual lemurs About 55 mya apes and monkeys would split from tarsiers (here we have fossil evidence) About 40 mya new world monkeys (prehensile tails, claws, sideways facing nostrils) split from old world monkeys 30 to 25 mya apes diverge from old world monkeys about 17 mya gibbons split from great apes about 15 mya orangutans split then gorillas split at some point about 6 to 5 mya humans split from chimps and bonobos

What role might epistasis play in speciation?

Epistasis is huge in speciation epistsis can lead to increased phenotypic variance that can lead to behaviors that separate some individuals in a population from other Epistasis can also be a reason why hybrids between two groups have incredibly low fitness Epistasis can be the reason why members of different species can not form a viable zygote Epistasis can be the driving force separating individuals as well as the ultimate reason to consider them separate species

How does epistasis relate to all of this? Can you interpret a simple three dimensional adaptive topography in way that shows you understand what it means?

Epistasis is when alleles at different loci interact with each other in a way that is different if they were expressed individually and this has complex fitness effects. Different frequencies of alleles at one locus will have a different effect of mean population fitness that depends on the frequency of an allele at a different locus with which it has an epistatic effect. This is why we need to consider the dimension of mean population fitness in terms of frequency of alleles 1 and 2, for 3 total dimensions. Hell yeah I can!

What does "evolution" mean in biology?

Evolution is change in the heritable properties of populations of organisms across generations Even more simply- changes in allele frequency through time (he change in allele frequencies in populations through time)

What is the field of Evo-Devo? What does this field have to do with macroevolution?

Evolutionary Developmental Biology - the study of how developmental processes (ultimately controlled by gene expression) evolve - resulting in new morphological features. As biologists began to examine the genetic underpinnings of development, they found a deeply homologous "toolkit" across animal body plans Looking at how we develop has revealed the stagaring similarities in development for all animals. This shows that there was kind of a developmental control that natural selection changed over time from a common starting point

What do we mean by "evolutionary independence" and which concepts get close to this fundamental facet of species?

Evolutionary independence means that the evolutionary forces acting on a population don't have any bearing on the evolutionary outcome of another population. BSC and genotypic clustering get very close

What are some important outcomes of Fisher's Fundamental Theorem (in the simple, non- mathematical way we talked about it in class)?

Fisher's Fundamental Theorem of Natural Selection- change in population fitness is proportional to the variance in fitness always increase fitness: directional --> fixation underdominance --> fixation overdominance --> balanced at equivalence point

How do recessive/dominant situations affect the rate of directional selection? Do they affect the eventual outcome? Why do they differ?

For beneficial dominant alleles, at low frequencies selection acts quickly but slows down at the allele approaches fixation For beneficial recessive alleles, at low frequencies selection acts slowly but speeds up at the allele approaches fixation The difference is in the average excess -at low frequencies recessive alleles are most likely to combine with dominant gametes, therefore the fitness effect of the allele is invisible to selection. It's masked by the dominant allele

How can we quantify the degree of genetic differentiation among subdivided populations?

For this we use Fst: 1. Find Hs --> average heterozygosity between both subpopulations --> (H1 + H2)/2 2. Find pt --> average one of the allele frequencies (p) between the two subpopulations --> (p1 + p2)/2 = pt 3. Find qt --> qt = 1 - pt 4. Find Ht --> heterozygosity of a population p = pt --> Ht = 2(pt)(qt) 5. Find Fst --> (Ht - Hs)/(Ht) Fst = 1 --> subpopulations are both at fixation for different alleles (couldn't be more different) Fst = 0 --> subpopulations are identical at that locus

What are the particular types of historical events that can lead to lasting effects of drifts in otherwise large populations?

Founder effect- A new population is derived from a small number of individuals drawn from a large ancestral population Bottleneck effect - a population's history is marked by one or more generation of very small population size before regrowth

What do we mean by gene, allele, genotype, and gamete?

Gene - the discrete functional unit of heredity (not necessarily a protein coding region) In this class, gene really refers to any variable genetic locus - a specified location in the genome (total hereditary information in an organism) (the same sequence at two loci are two different genes) Alleles - variant forms of a genetic locus Genotype - The specific allelic composition of an individual - at one or more loci Gamete - In sexual reproducing taxa - specialized haploid cells resulting from meiosis

What are the sources of phenotypic variation?

Genetic variation Environmental Variation Gene x Environment INTERACTIONS - Here, we mean interaction in the same sense as when we talked about epistasis. Genes have different effects in different environments

How does the relationship between drift and selection affect the outcome of new mutations that affect fitness?

Haldane's sieve for recessive alleles: Selection acts very weakly on mutations when they are low in frequency, because they're not having a large effect on mean population fitness at that time. So if selection isn't doing much, drift can work in absence of selection to increase of decrease the frequency of that mutant allele. However, since we're talking about small numbers at that point, it is much more likely that drift will act to fix that allele to zero rather quickly because it is closer to that end of the spectrum. Dominant alleles might be a different story

Be able to discuss natural selection as a dynamic process across space and across time.

High year to year and site to site variability Constantly dynamic process - not just drought years in the Galapagos Different traits will be selected for at different times in different places

Who were the first members of the genus to leave Africa?

Homo erectus appears around 1.9 mya Immediately show up around the globe Modern humans don't leave Africa until ~80,000 - 60,000 years ago

What are orthologs and paralogs?

Homologous genes between species are called orthologs paralogs- homologous genes that diverged within a lineage (caused by a duplication event)

What are some of the basic questions asked about macroevolutionary patterns of diversity?

How has biodiversity changed over the history of life? Are there patterns of diversity that are indicative of macroevolutionary phenomena? Had diversity been steadily increasing? Did it saturate early? As the taxonomic composition of diversity changed, did diversity stay constant ?

What are some limitations of making strong inferences about calculated heritability in complex populations like humans? When I said that quantitative genetic parameters are only meaningful for a given population in a given environment, what did I mean? Why are differences in heritable traits among populations not necessarily driven by genetic differences among those populations?

Humans are very not homogenous genetically and environmentally Disentangling genetic variation from shared environment is not trivial Maternal effects and transgenerational epigenetic (methylation and whatnot) effects on human phenotypes may be more common than previously thought You cannot compare populations in different environments because there are factors affecting variation that have nothing to do with heritability

How do microevolutionary forces interact with other phenomena to drive evolution on a grand scale?

I don't know I'd say that similar selection pressures in different parts of the world drive evolution toward a particular phenotype sometimes Mass extinction events causes drift to play a large role that affects the lineages and the restructuring of the entire planet

What was the 19th century version of the "multiregional hypotheses?" Why did it persist in some circles long after evidence mounted to the contrary?

If Homo erectus occured around the world so early, did modern human evolve gradually from these populations in each different region? Racism - white people don't want to be told that they are descendants of Africans

Why is this even an issue? What is the inherent cost of sex we discussed in class?

If every female can have 4 offspring, then the most efficient way to spread genes is to have 4 females. In sexually reproducing offspring, half of the offspring will be males. You're using resources to create offspring that can't directly reproduce. So now your four children can only have 8 offspring instead of 16.

What does it mean to have a high value for h?

If h = 1, the heterozygote is exactly like the deleterious homozygote

If given a value for h, can you make a prediction about the phenotype of heterozygotes?

If it is high (higher selectivity), it is closer to the worse phenotype If it is low (lower selectivity), it is closer to the better phenotype

Be able to draw and/or interpret basic plots demonstrating patterns of the relationship between survivorship and trait values - fitness functions - (not mathematically in this context - yet, just qualitative)

If the trait is selected for, when that phenotype is expressed, proportion survivorship will increase

How can homologous traits be used to reconstruct evolutionary relationships?

If traits are homologous, they suggest relatedness. The more homologous traits two organisms have in common, the more closely related they are

Who were the Australopithecines? What about Paranthropus?

Important early human species that gave us context for human origins - Building a much more complete picture of the diversity and evolution of early Hominins "Taung Child" skull - mix of human and ape features- ~2.5 mya - Australopithecus africanus One of the most famous examples is "Lucy" a female Australopithecus afarensis skeleton ~3.2 mya. "Lucy" showed that bipedalism outdated brain size by a wide margain In the genus Australopithecus, we see clear evidence of transition from aple-like to human-like features Dating from ~4 mya - 1.9 mya East and south Africa These were upright and small brained Australopithecus gave rise to another lineage starting ~2.7 mya - the "robust" austrolopithecines - Genus Paranthropus - robustness likely related to vegetarianism - subsequent australocithecus after this split was more gracile (probably more meat eating) -Paranthropus existed with australopithecus for a long time, filling a separate niche eating plants (both were bipedal) until 1 mya - Autralopithecus, paranthropus, and homo all existed at the same time in Africa 2 mya

What are some ways that passive and driven trends are distinguished?

In driven trends both ends of the distribution change in the same direction through time - passive trends - the minimum remains unaltered while the maximum increases - driven trends - the minimum and the maximum both change in the same direction In passive trends, apparent driven pattern on the whole clade is built from even distributions of change within only certain subclades - passive trends - a few subclades happen to be moving toward the phenotype in question and this drives up the mean of the entire clade - driven trends - every subclade has the same shift toward the phenotype causing the overal distribution to be similar to each subclade We can also plot out evolutionary changes to and away from the phenotype in question - passive trends - it is mostly random and even moving toward and away from the phenotype, but few groups moves toward it, affecting the mean - driven trends - most changes are moving toward the phenotype Passive trends are the null hypothesis

How does drift operate in large populations?

In large populations, it still may be very important over long time scales • Driving a constant change at neutral loci The number of new neutral alleles occurring in a given generation in a diploid population is then equal to 2Nv The expected rate of neutral substitution by drift is just equal to the mutation rate --> v (mutation rate for neutral alleles) The effect of population size balances out perfectly (each allele have a smaller chance of fixation as more alleles are introduced) Since population size isn't a factor for neutral mutations, it is constant through time no matter how big populations get, and this is our molecular clock model

How does drift work in subdivided populations?

In subdivided populations, random changes are inevitably going to accumulate between them If drift acts alone, subdivided populations will eventually go to fixation, but every single allele of any type has an equal chance of going to fixation. So it is usually unlikely that every subdivided population will have the same alleles fixed. According to probability, the allele frequency among the entire population will not change since each type of allele's probability of going to fixation is its allele frequency, that proportion of subdivided population's will go to fixation for it, while the others go to the other allele.

How do mutation and selection interact in the case of beneficial alleles?

In the case of favorable alleles - mutation occasionally produces the fodder for adaptations shaped by selection

What is the basic question of the long-term role of directional natural selection in evolutionary trends?

Is directional natural selection actually moving toward something or just appearing to? Is it actually passive?

How does migration act as an evolutionary force?

It acts to stabilize allele frequencies toward the equilibrium point that is the average allele frequency between two subpopulations, pt Migration acts to decrease genetic differentiation between populations

How does this relate to Gould's left wall of biocomplexity?

It is a passive process that gives the appearance of a bias in directional natural selection

How can sex ratio affect this?

It is less about ratio of males to females in the total population (which will typically be 1:1), it is more about the ratio of males to females that are actually having sex and contributing to the next generation. The elk were 1:1 total, but for every 25 females that were reproducing, only one male was. In other words, the average male was reproducing with 25 females. That is how we calculate effective population size. 500 total individuals --> 250 are female. If there's only one male reproducer per 25 females, that's 10 males into the equation: Ne = 4(males)(females)/(males + females) --> Ne = 4(10)(250)/(260)

What does this have to do with the rate of debilitating genetic conditions in humans?

It is not always correct? Example with cystic fibrosis

How is evolutionary biology important to the rest of biology as whole (including applications)?

It spans all levels of biological organization - linking molecules to populations and ecosystems. Our overall understanding of any pathogen - like HIV - is fully rooted in evolutionary biology We need to know how model organisms are related to us in order to learn from them

What does variation in aging within and among species tell us?

It tells us there are differences in the surivival/reproductive investments that species make over the course of their lives We have to look at other data to tell if that variation is genetic or environmental (average life expectancy within a species is often environmental)

What was a major evolutionary innovation in our own lineage during the Silurian? How did this influence vertebrate diversification in the Devonian?

Jaws! Placoderms came from the Silurian which evolved gnathostomes which dominated and started the Devonian without a major extinction event

What is the difference between lifespan and life expectancy?

Lifespan is how long an organism (a specific individual) survives (a bit more useful) Life expectancy is a statistically derived (an average (based on demographics)) figure that serves as how much time one is likely to have left given their current age Even though the human life expectancy was 30 for a long time, the lifespan of plenty of individuals was around 70 or 80. It was because many died before 30 so 30 was the average

What are some complications to straight forward heredity based on interactions - among alleles in the same locus and among alleles at different loci?

Linkage is any breakdown of independent assortment That is- alleles at different loci are inherited together more often than expected by chance Often due to physical linkage(close proximity on the same chromosome) Also translocation? (transposons)

What are some of the major events of the Proterozoic? What are banded iron formations and what do they signify about major changes during the Proterozoic?

Lots of fossils from this time that resemble contemporary microbes Banded iron formations were the result of the great oxygenation event, oxygen entering the atmosphere as a result of photosynthesis from algae and cyanobacteria between 2.4 bya and 1.8 bya. Oxygen would be dissolved in the ocean until it reached a threshold, at which it would bind with the iron in the oceans until all the oxygen was used up, leaving a layer of iron oxide on the sea floor. The oxygen would then be replenished and this process would repeat until there was no more iron in the oceans. This caused successive bands of iron oxide from these cycles. Without iron to bind the oxygen, oxygen was eventually able to fill the atmosphere (this went on for about 500 million years) At about this time, 1.8 bya, we start to see eukaryotes 100x the size of bacteria, which matches theories of endosymbiosis event greater than 1.5 bya (mitochondria acquisition likely only happened once in the common ancestor to all eukaryotes) Multicellularity came about in algae around 1.6 bya, but animal-like multicellularity wouldn't come about until another billion years Ediacaran fauna showing up at the tail end of the Proterozoic 600 mya

How does Malthus fit into pre-Darwinian thought? How do his contributions relate to specific postulates for natural selection?

Malthus - even with increases in production, agricultural surpluses would still inevitably lead to famine (due to exponential growth) - A high level of background mortality Postulate 3 - Variation in survivorship and reproductive success This view of a struggle for existence as intrinsic to all populations was critical to theformation of Darwin's ideas for a mechanism The importance of Darwin's work was in coupling the process with the pattern -widening the scope of selection to encompass all of the living world

What are Dobzhansky-Muller incompatibilities? How do they evolve?

Mechanism for allopatric speciation that kind of became a model for all speciation. A separated subpopulation develops an allele that is favorable in its environment and it goes to fixation in that subpopulation. Since it is reproductively isolated (by physical space and geological structures, in cases of allopatry), it never enters the other subpopulation. The same thing happens in the other subpopulation for a different allele. It turns out that those two alleles have a epistatic interaction that causes some kind of reproductive isolation, so one way or another the two subpopulations cannot produce viable offspring. They are now distinct species. It is more difficult for epistatic incompatibilities to develop if there is a lot of gene flow, but it happens

What is the difference between metaphysical and methodological naturalism? What does this have to do with our roles as scientists?

Metaphysical Naturalism - An extension of materialism: The physical world is the entirety of existence and that all of reality is the result of natural phenomenon (there is no such thing as the supernatural) Methodological Naturalism - There may well be something to existence beyond nature, but that is entirely outside the bounds of science. Without this principle, science grinds to a halt. It allows us to give up when we encounter something we don't understand.

How are micro- and macroevolution typically distinguished? In what way is speciation important in this discussion?

Microevolution concerns evolutionary processes within populations (same species) Macroevolution concerns evolutionary change above the species level Speciation is the link between microevolution and macroevolution as it is one species --> two

What is the effect of migration through time? How does its strength compare to other evolutionary forces?

Migration acts to decrease genetic differentiation between populations Strength depends how far away the allele frequencies are from each other and the migration rate (?)

What does this have to do with some of the broader themes of the course?

Misconception --> natural selection does not result in perfection

What is the punctuated equilibria model? What does it attempt to describe? What other concepts from class does it relate to?

Morphological change associated with new lineages appears to occur very abruptly in geological time and then remain constant for long stretches of time In the 1970s Gould and Eldredge proposed a model to explain this pattern of morphological stasis followed by leaps of divergence (before them, it was thought as environmental equilibrium, but that's not right) The equilibrium in Gould and Eldredge's model is essentially a genomic equilibrium (caused by epistasis, and species being stuck on high adaptive peaks surrounded by extremely low valleys) Speciation and morphology are linked, and speciation is evoking super strong drift. We have super strong drift (caused by founder effect or bottleneck) knocking them off of these adaptive topographies during peripatric (allopatric, colonizing a new spot with little migration) speciation (Wright's shifting balance theory on steroids) - then after developing a well adapted phenotype along with reproductive incompatibility (new species), some migrants do make it back and cause the original population to go extinct This is not always the case, but sometimes is useful (particularly in marine systems)

Can you describe the species concepts we went over in class? What are some circumstances under which some of them might be useful? What are some of their major limitations?

Morphospecies concept - t's only potentially useful for long extinct organisms (fossils), it can be extremely misleading as unrelated organisms can look similar and related organisms can vary widely in appearance Phylogenetic species concept - Species are the smallest recognizable monophyletic groups in a phylogeny - sometimes genetic data is insufficient to determine actual lineages - different genes offer different lineages especially when looking at recently split populations - sometimes reveals that populations are more separated than previously thought, revealing speciation - good for classification Ecological species concept - Species are co-occurring organisms that occupy different niches (or "adaptive zones") - It's impossible to define a niche extrinsically of the population occupying it - according to this concept, if a species drives another to extinction due to competition, they were the same species, and that is stupid - However, the utility here comes from it's application to asexual organisms Biological Species Concept - Species are groups of interbreeding populations that are reproductively isolated from other such groups - If populations aren't reproducing with each other, they become evolutionarily independent - This concept (in it's original incarnation) requires complete reproductive isolation - that is different species are incapable of producing fertile offspring with each other in the wild (doesn't really happen) - Species designations are always relative - we need another group to say that this group is different or the same - If we're basing this on the potential for interbreeding, it's hard to say anything about populations that aren't actually in contact - mostly reproductively isolated becomes the norm - hybrids are sterile Genotypic Clustering Species Concept - Species are genetically distinguishable groups of individuals, with few or no intermediates when in contact with other such groups - This is still relative - we have to compare a group to another group and it's still somewhat wishy-washy to say "few or no" - If populations are able to maintain discrete genotypic space, even if some reproduction is still going on, migration is no longer consequential - hybrids have such low fitness that they're genes never make much ground

What are the two branches of evolutionary explanations for aging?

Mutation accumulation in the germ line that get passed down, if the mutations only have an effect later in life, then selection will act on them weakly trying to remove them from the population Antagonistic pleiotropy occurs when the fitness consequences of the affected traits run in opposite directions - alleles benefitting one trait are detrimental to another

Why don't universally "good" alleles necessarily go to fixation in populations?

Natural selection is deterministic - not omnipotent If the average population fitness would have to go down so that it could later go much higher, it will never happen

What do these topographies tell us about the outcome of natural selection in a given system?

Natural selection will act to send allele frequencies in the direction of maximizing fitness

What types of mutations result in new alleles - what type result in new loci? Where are evolutionarily important point mutations likely to occur? Coding regions? Regulatory regions?

New alleles - Point mutations, SNPS, indels New loci - Gene duplications, Chromosomal rearrangements - inversions, Fissions/fusions Anywhere including coding regions, regulatory regions, and introns could all be important

How might sex increase the tempo of adaptive evolution?

New genotypes occurs more frequently, and selection can act on these phenotypes if they're beneficial or not.

What are the assumptions underlying the basic Hardy-Weinberg model?

No selection No mutation No migration (in or out) Infinite population size Mate choice occurs at random

What are the basic postulates for Darwinian natural selection? What kind of data would we look for to support each one in nature?

Number 1 - Populations are Variable - Morphology • Color• Physiology• Behavior• Life history traits• Immunity• Genetics (alleles) Number 2 - Traits are heritable - phenotypic distribution of generation 2 is at least partially a function of the phenotypic distribution of their parents Number 3 - Variation in survivorship and reproductive success - This is the one postulate that is almost universally true in natural populations - r = investment optimized to number of offspring • K = investment optimized for care and/or development of offspring - One exception for universality -cases where populations are actually in the midst of exponential growth (everyone born is having babies) Number 4 -Survivorship and reproductive vary as a function of traits (phenotypes) - On a trait vs. prop. survivorship curve, there would not be a straight line Uniform distribution - probability of y does not vary as a function of x - everyone in the population has the same chance of surviving and reproducing, regardless of phenotype (flat line on a trait vs. prop. survivorship curve) (not compliant with postulate 4)

What does the earliest evidence of our own bauplan look like in the fossil record? How old is it?

One Bauplan that certainly dates back to the Cambrian explosion is our own - Chordates They are little fish that seems to have notochords and bilateral symmetry similar to us Chengjang Lagerstatte - more recently discovered but older than Burgess by ~15 million years. This puts it at about 520 mya - this fish is definitive proof that our bauplan existed in the cambrian period

How is heritability measured in populations? What are some of the pitfalls associated with measuring heredity?

One of the most straightforward ways to estimate h2 is through midparent regressions (h2 is the slope of the regression (best fit) line) t's often hard to know who the father is. We can also measure h2 using a single-parent/offspring regression - which is going to underestimate heritability by exactly half Parents and offspring are also likely to share environmental variation. h2 is thus the upper limit of heritability in populations.

Who were the first members of the genus Homo and where did they live?

Organisms that we can start refering to as human appear 2.1 mya ago - Homo habilis Used tools, even though now we know that tools were being used about 3 mya Homo habilis was contemporary with Homo rudolphensis - these two seem to show a smaller version of the "gracile vs robust" ecological divergence in Paranthropus

What have the underlying patterns of human evolution been? Are we the result of a smooth, continuous "improvement" of a single lineage?

Our lineage was a complex, diverse radiation

Why is the reality of species even an issue?

Our other levels of Linnaean classification are rather arbitrary There are many ways to distinguish species from each other

What happens if you "start" an overdominant system at a certain allele frequency? What happens if you do this with an underdominant system? What do their adaptive topographies look like? Can you draw one given the fitness values or survival table?

Overdominant will always move toward equilibrium point Underdominant will always move away from equilibrium point to fixation of whichever allele is closest without lowering mean population fitness

Why is there potential evolutionary tension between the within-host and among-hosts parts of parasites lifecycles and what are some possible outcomes resolving this?

Parasites have two main components of fitness, growth an reproduction within host and transmission between hosts. If a parasite is able to use more of the host's resources, it will have a growth and reproduction advantage within the host, but making the host too sick or killing it too quickly can negatively affect the parasite's chances of passing offspring to a new host - making the current host a dead end Possible outcomes: 1. Evolutionary changes in the parasite influence the phenotype of the host --> extended phenotype (when your phenotype is influenced by genes that you don't hold). This is often used to increase transmission capabilities (often one way or another influences the host to commit a certain behavior that increases submission) 2. Utilization of transmission vectors (organisms that don't experience directly nourish the parasite, but transmit the parasite to a suitable host (strictly transportation purposes)) 3. Attenuation of virulence - become less virulent, you can survive longer in the host to be transmitted before killing the host or the host killing you

How are mutual and parasitism related?

Parasitism and Mutualism exist on the same continuum Our coevolutionary framework predicts that many specialized interactions exist in this ambiguous zone between parasite and mutualist

How do parasitic relationships fundamentally differ from predation, and how does that affect the potential outcomes of coevolution?

Parasitism does not kill the host, it exploits the host. Parasites can evolve to get along better with its host, predators cannot.

Darwin's argument can be divided into two areas: pattern and process. What did I mean by this?

Pattern - Descent with modification - what is observed Process - Mechanisms - how it happens

What determines the diversification rate of lineages?

Patterns in diversification are driven by the balance between the speciation rate (𝛼) and the extinction rate (Ω) of lineages.

What major change was associated with the Phanerozoic when it was initially designated?

Phanerozoic literally means 'visible life', this is the age of multicellulars

What are some of the mechanisms behind the existence of continuous variation in populations?

Polygenic or quantitative traits Traits are going to be the result of both polygenic effects and environmental effects

How does population genetics relate to Mendelian genetics?

Population genetics - The mathematical and empirical study of allelic variation within and among populations, **including the dynamics of changes in allelic variation through time** <-- Mendel

What do Sahelopithecus and Ardipithecus tell us about the order of some trait changes in the transition from ape-like bodies to our current form?

Potential precursor to Australopithecus Sahelanthropus - suggests very early shift to upright posture and bipedalism based on one skull Oldest well studied Hominin precusor - Aridpithecus ~4.4 mya - also upright posture/bipedal (not an ancestor to humans, but we share a common ancestor more recently than we do with chimps/bonobos)

How can we classify mechanisms of reproductive isolation along the life cycle of organisms? Can you imagine some examples of barriers that may act at those different point.

Premating -Behavioral isolation - organisms fail to attract each other as mates -Mechanical isolation - reproductive structures are incompatible for mating -Ecological isolation -divergent adaptation leads to decreased mating events across populations --different pollinators --different mating areas --different mating seasons Postmating/Prezygotic -Gametic isolation - Gametes are transferred but fail to form a zygote --Sperm fail to survive in female's reproductive tract --Sperm or pollen fail to react properly with eggs Postzygotic -Postzygotic isolation can result from either sterility or inviability (bad at reproducing or surviving) (intrinsic or extrinsic (independent of the environment or dependent on the environment))

Do human pathogens fit into the geographic mosaic framework for coevolution?

R0 > 1 - leading toward an epidemic R0 < 1 - the pathogen would have to evolve first an evolving parasite can increase R0 by increasing tranmission rate, decreasing parasite mediated death, or increasing rate of recovery Since the parameters that make up the R0 value are all dependent on the context of specific human populations, yes, that is a geographic mosaic. Differing interspecies conditions across space

What is the rate-of-living hypothesis for aging and what are some predictions that it makes? How do those predictions align with empirical evidence?

Rate-of-living theory - contends that senescence is simply the result of wear and tear at the metabolic level - replication errors, misfolded proteins, damaging metabolites (free radicals) all build up until we can't carry on If this was solely responsible for aging, then longer living organisms should have really different (and better) metabolisms and every organism that dies of "natural causes" should be metabolizing equal amounts of energy - sometimes there is a relationship between metabolic rate and lifespan, but not always. and there is huge variance in the overall amount of metabolism that organisms perform over their lives, so it doesn't really work If this was solely the only factor than natural selection would be able to act on these metabolic difficulties and organisms would be progressively be living longer and longer - we can put organisms in the lab and select them for longer lifespans and it works, which shows that there is genetic components to it, but natural selection isn't optimizing these organisms in terms of lifespan as predicted This tells us that rate of living might be part of the story, but it cannot explain everything

How might we test these predictions in the lab or in natural populations?

Replacing genes in drosophila that increase fecundity but decrease life span (antagonistic pleiotropy), also (deleterious) inbreeding effects in drosophila are more prevalent and act later in life (mutation accumulation) Opossums are big, but only live to be about two (that is weird for North American mammals (but not so weird for marsupials)). They also have large litters and large mortality as they are not well defended against predators (extrinsic mortality is high). Because they are likely to die young, we expect opossums' late acting deleterious traits to be even less susceptible to selection (more mutation accumulation). Also investment in reproduction early in life is more favored by selection and this will likely cause one to age faster (more antagonistic pleiotropy). Opossums on a predator free island live longer, age slower, invest less in early reproduction, and produce milk more consistently throughout subsequent litters (more higher quality offspring)

What kind of fish are we?

Sarcopterygians (lobe- finned fish) - we are sarcopterygians bony fish that gave rise to all terrestrial life on Earth, aquatic mammals, and lungfish

What are Mendel's first two "laws" of inheritance? What are some circumstances when they break down?

Segregation - Homologous chromosomes separate during meiosis so that only one copy of each gene (one allele per locus) occurs in each gamete. Breakdown - non-disjunction Independent assortment - allelic variation at different loci are passed to offspring independently Probability of two independent events happening --> p1 *p2 = p(1&2) Breakdown - linkage (recombination combats this to an extent)

What are the effects of directional selection on deleterious alleles? What are the effects of mutation on the same?

Selection gets rid of deleterious alleles Mutation adds them

How do they interact in cases of deleterious alleles?

Selection weeds out deleterious alleles as mutation adds new copies These evolutionary forces are working against each other

Which evolutionary forces are deterministic? Which are stochastic? What's the difference?

Selection, mutation, migration --> deterministic drift --> stochastic

How do the basic pairwise interactions among forces play out? Thinking specifically about adaptive topographies, how do the forces other than selection act to move populations on these theoretical surfaces? How does the shape of the adaptive topography affect the balance of evolutionary forces?

Selection-mutation --> q^ (number of deleterious alleles) = sqrt(𝜇/s) mutation-drift --> Mutation creates variation and drift turns some of it into substitutions at a constant rate v migration-drift --> F^st (genetic differentiation that exists as a result of two opposing forces) drift sends allele frequency, and therefore mean population fitness, in random directions mutation (almost) always brings allele frequency down (which brings mean population fitness in terms of a deleterious mutation) Migration wouldn't change the adaptive topography of both subpopulations, if we considered the populations separately, it would might bring fitness down as we're introducing migrants from a different environments (migration load) Of course, drift and mutation can act on one subpopulation and then migration can bring that new genetic diversity to the other subpopulation If the change puts the population on a steeper incline, the stronger selection will act to raise mean population fitness to an optimum

What do we mean by "theory" in science? How does evolution relate to this?

Set of overarching mechanisms and principles that explain a major aspect of of the natural world...supported by independent lines of evidence A theory in this sense is a system that organizes facts (well-confirmed, objective observations) and laws (describing relationships in science)in a well-reasoned and empirically supported way that allows us to makes sense of the world

Synapomorphy

Shared derived traits which serve as the basis for cladistics homologous traits resulting from common ancestry

What does this have to do with the "molecular clock?," and in general terms, how can predictions from the process be used to detect natural selection in the genome?

Since neutral substitution is not a function of population size, it is a function of linear time. We have an expected ratio of neutral synonymous to neutral non-synonymous substitutions building up across the genome Selection favoring nonsynonymous mutations should throw things off of this neutral expectation with higher than expected nonsynonymous substitution rates being driven by natural selection

Why do some lineages become numerically dominant following mass extinctions? What does this say about the deterministic nature of macroevolution? Was the evolution of human inevitable?

Some species happen to already have adaptations that allow them to survive in the world post mass extinction I don't know lol --> I'd say no, and it is not super deterministic since it is based on kind of stochastic change that is altering the environment and selection pressures can't be predicted too well Convergent evolution kind of hints that there may be some deterministic factors to macroevolution (flight, dolphin phenotypes, wolves, saber tooth tigers, moles, desert plants.

How can natural selection lead to the persistence of delitarious traits like hemolygic anemia?

Sometimes heterozygotes are beneficial

What are the two models for patterns of biodiversity presented in the text book? What predictions do they make?

Special Creation • Species are immutable • Lineages do not diverge • Species created separately • Species created independently Descent with modification • Species change through time • Single lineages give rise to many • Old forms beget new forms • Species are genealogically related • Requires the Earth to be vastly older than recorded human history

What are extinction rates and (in basic terms) how are they calculated?

Species (and higher taxa) have geological lifespans and extinction rates are calculated as the proportion of those lifespans that end over a given time interval The proportion of species that stop being in a given timeframe Average - 25% every million years - 4 million year averge for a species

What are some of the major intellectual trends that paved the way for Darwin's ideas? What were the most important contributions made by the central historical figures discussed in class to these intellectual trends?

Steno - STRATIGRAPHY - Study of of the layering of rocks in terms of chronology Smith - index fossils - fossils that serve as diagnostics for particular geological periods Hutton & Lyell - UNIFORMITARIANISM - Natural laws observable around us now are also responsible for events in the past Linnaeus - Father of Taxonomy and binomial nomenclature - classified and named over 12,000 species of plants and animals Buffon - biogeography - the study of the distribution of species across space (one of first to say species change) Lamarck - Described how traits of organisms are matched to their environments and habits (First to develop a cohesive theory how organisms evolve) Cuvier - Greatest contribution was the realization of extinction and recognized that geological history was characterized by waves of very different fauna Malthus - even with increases in production, agricultural surpluses would still inevitably lead to famine (due to exponential growth) - A high level of background mortality

What is Wright's Shifting Balance Theory? What kind of adaptive evolution does it help explain? What is the progression of "shifts" in this model?

Step 1 - in individual subpopulations - drift can predominate if population sizes are small (relative to "height" of fitness peak) Step 2 - When drift brings the population in contact with a steep fitness slope, the strength of selection starts to outweigh the effect of drift - selection pushes the population up the peak (As mean population fitness increases, population size is likely also increasing) Step 3 involves a shift toward dynamics among populations - large high fitness populations are likely to produce a lot of migrants. These migrants can influence the evolution of other subpopulations. Step 4 occurs when this push from migration (migration load) allows selection to take over in the 2nd population - driving it towards the global optimum This explains rugged topographies, where epistatic interactions between loci create multiple local fitness optima

What are some ways of dividing up fitness into different components?

Survival Mating success -competition -locating a mate -copulation -fertilization Fecundity - number of offspring produced -number of offspring -parenting success

What are some ways that fitness might be counterintuitive at times?

The biggest, strongest, fastest, fiercest, etc, isn't necessarily the fittest. (seagulls with higher muscle mass were more easily killed by raptors, same with low muscule mass (stabilizing selection) (pug and husky) Dung beetles - strong and bulky individuals and tiny and sneaky individuals have comparable reproductive success --> extremely different phenotypes in the same species have the same fitness

Are the relative fitness values of genotypes enough to know the outcome of natural selection?

The effect of natural selection doesn't just depend on these values alone, it depends on the context of the allelic variation in the population too. Specifically, whether an allele will decrease or increase in a populations depends on these genotype fitness values and the current allele frequencies in the population. We need to calculate the average fitness across the population which takes both of these factor into account. **Natural selection affects those that vary most from the average population fitness**

What is the fitness distribution like of random mutations? What does this say about the plausibility of adaptation by natural selection?

The majority are either bad or neutral (no effect on fitness) Beneficial mutations are rarer, but they certainly still occur Thismixtureofmostlybadbutsomegood mutations still provides ample fodder for natural selection In the absence of selection, deleterious mutations accumulate and drive fitness down Return of selection: rapidly sort out the good from the bad and fitness bounces back (plausibility is high for adaptation by natural selection)

What were some of the causes and consequences of the two mass extinctions we discussed specifically?

The most famous of these was the K-Pg extinction - that brought the Cretaceous Period (and age of the dinosaurs) to a close Ended 160 million years of terrestrial vertebrate dominance - but it was actually the smallest of the big 5 mass extinctions Caused by extraterrestrial impact of an asteroid (along with other minor changes such as climate that paled in comparison) The largest ended the Permian about 252 million years ago - 55% of families when extinct which was 96% of all genera - occured over 200,000 years Likely due to volcanic activity (the siberian traps) (insane amounts of lava) causing widespread and severe climate change and atmostpheric change (massive warming and anoxia) During recovery during the triassic - for millions of years, >90% of terrestrial vertebrates were a single burrowing genus, all marine life moved to the poles

What were the gaps in knowledge that prevented Darwin's idea of Natural Selection fromgaining widespread acceptance in the 19th century? What's the problem with blending inheritance?

The nature of novel variation (mutation) & The nature of inheritance (genetics) were unknown Dilution of minority phenotypes

What is the relationship between "effective population size" and "census population size"?

The population size expected to match the realized rate of drift is called the "effective population size" or Ne Ne = 4(males)(females)/(males + females) These are males and females that are actually reproducing Effective population size is the adjusted number of individuals that are actually contributing to the population and thus the actual population that drift will have an effect on Census population size is the actual total number of individuals whether they mate or not

What was the Modern Synthesis? What ideas came together during this time?

The reconciliation between the Mendelian and Biometric ways of thinking with Darwinian Evolution Reframed Evolution explicitly around population genetics

In what way is homology a major underpinning of a lot of biological research?

The shared derived traits, which serve as the basis for cladistics Understanding evolutionary relationships, using data from homology, is important to just about every field of biology, as previously discussed

What is the Cambrian Explosion? Why are Cambrian fossil assemblages different from the diverse communities of the Ediacaran fauna?

The very beginning of the Phanerozoic At this point, about 520 mya, all major extant phyla are not only present, but abundant throughout the fossil record The explosion is of crazy animal morphological diversity and abundance that seems to have appeared in a very small amount of time due to oxygen reaching a certain threshold (also possibly temperature stabilization) Ediacaran fauna was kind of scarce and we cannot trace them to modern animals

What the earliest signs of life and how far back do they date?

There are fossils that are undisputed evidence (in Greenland maybe) from about 3.2 bya Biologically favored isotope ratios place some controversial evidence at 3.7 bya Controlversial fossils (stromatolites) date to 3.5 bya

What did the coevolutionary trend story tell us about the potential constraints on driven trends? What does this have to do with the connection between micro- and macroevolution?

There is a noticable driven trend for speed in ungulates, but cursorial predators do not seem to be evolving speed at the same rate. Option #1 - a stable population would need to have a larger number of herbivores than carnivores, so slower predators had more food to eat Option #2 - antagonistic pleiotropy - speed adaptation in predators causing more detrimental effects than it would in ungulates, so ungulate evolve more speed than predators (ungulates don't do much with their feet so they can specialize them to be really good at running, predators need their feet to do other things so they can't develop hooves) Option #3 - selection may be weaker on predators - an evolutionary change in ungulates increases mean population fitness and in turn population density, predators might find that even though prey have increased fitness, their fitness stays the same as they have more food now. So there is less selection pressure to become faster, if they are eating just as many fast ungulate as slow ones (this can explain the surprising lack of coevolutionary arms races between predators and prey in nature) If we look at the trends that influence species interactions today, we can apply those concepts to interactions the entirety of evolutionary history

What was hominin diversity like for most of the time that anatomically modern humans have been around?

There were Neanderthals which lived in Europe decended likely from Homo erectus as well, much better cold tempered There were hobbits as well in Asia, they were short

Why have marine invertebrates been important to this field?

These fossils are extremely abundant, providing the most complete sequences in the fossil record Therefore we can map biodiversity in this group over time pretty well

What do telomeres or mitochondria have to do with mechanisms of senescence?

These were explanations for rate-of-living effects, how these processes over time can cause critical damage Telomeres are the ends of chromosomes that get shorter with every replication. Eventually they get eaten up and coding genes go away. Telomere length can be indicative of lifespan within a species but the argument falls apart between species Mitochondria have high mutation rates and are the sight of high metabolism in an oxygen rich environment (much damage)

Why do terms like p2 and 2pq show up in Hardy-Weinberg - what do they really mean?

They are the probabilities that two gametes carrying specific alleles will fertilize each other and give rise to an organism of the next generation

How do mutation and drift function to drive neutral nucleotide substitutions?

They both collide based on population sized to cancel population size effect altogether (stronger drift with smaller population, stronger mutation with larger population) --> this gives us v (neutral mutation rate due to drift and migration

What are some of the earliest evidence for metazoan life?

This is pre-Ediacaran in the Proterozoic Sponge fossils > 600 mya Trace fossils (tunnels and tracks) of motile animals 585 mya 575 mya gives us large animals --> Ediacaran fauna

Why is the coevolutionary process difficult to study in practice?

Time is a limiting factor for studying coevolution. The reciprocal, dynamic nature of coevolution plays out over many, many generations Often studying systems for a small amount of time only presents a snapshot of the processes going on and it can be hard to determine a reciprocal evolutionary relationship We have to look at measurements taken at different times to determine that both groups are changing

What are mass extinctions and why are they important in understanding macroevolutionary patterns?

Time periods where a large percent of the species on Earth went extinct (about 70 to 80 percent) 5 largest mass extinctions were associated not just identifiable shifts in faunas, but major restructuring of the biosphere (the composition of life was drastically changed)

What is the basic premise of our "two island" model of migration?

Two otherwise isolated equally sized subpopulations live in separate "islands" with a set rate of migrants moving from each island to the other, equally each generation

Why might whole genome duplications been important in evolutionary history?

Typically due to meiotic errors Very common in some groups of organisms- particularly plants Currently involved in speciation and adaptation But may have been very important in early history of life - providing fodder for protein diversity (more duplications allow for spot where loci can be changed (potentially better) and the original copy is still present to provide a vital gene product)

How can genes be duplicated through mutation events?

Unequal crossing over • Meiotic error When unequal crossing over occurs, there is one chromosome with extra DNA. If that is passed down to the offspring and it isn't fatal, it will continue to be passed on Retroposition • mRNA processed by viral or retrotransponson (reverse transcriptase) machinery and integrated back in the genome

What does phenotypic "variance" mean specifically?

Variance is a metric of how far away the population is away from the mean In this case, it is how far the population is generally away from the phenotypic average and this has to do with genetic (polygenic) and environmental variances

How can phenotypic variance be broken down into different components? Why is this important for understanding the effect of natural selection?

Vp = Vg + Ve = Va + Vd + Vi + Ve Because natural selection can only work on heritable variation, some of these components contribute to a trait's heritability If we know the heritability of a trait, we can predict how natural selection will affect it h2 = 𝑉a / 𝑉p

How does the breeder's equation work? What are the parameters that go into it? What do they mean?

We can predict the response a particular strength of selection. R = h2S Where R is the response to selection in the offspring generation --> offspring mean - overall parental mean R is the change in the population mean from one generation to the next And S is the selection differential in the parental generation --> S is equal to the difference between mean trait value of survivors and the overall mean of the starting population (surviving parental mean - overall parental mean) The response to selection R, is smaller than S because h2 is the less than one

How has the discovery of the Ediacaran fauna complicated our view of the history of animal life?

We cannot connect these fossils to modern phyla for some reason Weird body plans They might be so weird that they actually aren't early animals at all, but an entirely different kingdom altogether, Vendobionata

I mentioned a statement from two prominent aging researchers (Mueller and Rose) that the question of aging was now "biologically solved" - what does this mean and what are the implications for aging from a health care perspective?

We know the biological reasons why people get old and die, and it is very complicated. This means that the medical intervention to aging is going to be very complicated. For every method of aging that we combat, there will always be another to work on after, so it won't be some kind of silver bullet. It is going to be multidimensional and very nuanced.

Why do we need to know the average population fitness? What types of data does this metric combine? What does it really mean? How do we calculate it?

We need to know how far our fitnesses vary from the average population to know how strongly natural selection will act It combines allele frequency and relative fitness This is the all the fitness values of every individual added up and divided by the total 𝜔avg =𝑝^2𝜔AA +2𝑝𝑞𝜔Aa +𝑞^2𝜔𝑎𝑎

In what way does speciation serve as the interface between micro- and macroevolution?

We see how speciation can cause two population to diverge from each other more and more until they are completely geographically isolated, and so we can apply the same principle to a broader scope that speciation can produce numerous species and these numerous species interact with the environment and other species and these interactions further drive evolution It starts with speciation at the lowest level, but a lot at the same time

Why are ecological population models of species interactions useful in the context of understanding what traits are likely to be shaped by coevolution?

We see in the Lotka-Volterra equations that c (capture rate) affects both predators and prey phenotypes evolution of traits that affect "capture rate" are going to alter the fitness dynamics of the interaction species traits involved in predation are under selection, but coevolution involves reciprocal evolution: Evolutionary response to evolution in another population (it HAS to go both ways)

Specifically, what do we mean allele frequency?

We simply need to count the allele in question and determine the proportion it makes up of all the copies of that locus in the population alleles/totall alleles

Why is specialization an important concept for coevolution?

We suspect that increased specialization in interactions results in more coevolution to either become adapted to embrace the interaction as much as possible, or adapt to attempt to escape the interaction. If either species has other options, there is a less powerful selection regime to adapt for an interaction

What is convergent evolution and what does it potentially tell us about the long-term role of natural selection in macroevolution?

When two species exhibit similar phenotypes by evolving them independently of each other and the common ancestor of these species did not exhibit the phenotype Convergent evolution kind of hints that there may be some deterministic factors to macroevolution (flight, dolphin phenotypes, wolves, saber tooth tigers, moles, desert plants) This tells us that natural selection might be limited in the solutions it can provide animals (or at least vertebrates) to assume ecological niches

What is an extended phenotype, and what does this have to do with parasitism?

When your phenotype is influenced by genes that you don't hold, either directly or indirectly. This is often used to increase transmission capabilities of parasites through one way or another influencing the host to commit a certain behavior that increases submission

Are switches between the two likely to evolve in nature? What did the Jeon amoeba example tell us about this?

Yes they are. Depending of the situation it can be beneficial for a mutualist to stop contributing can become purely parasitic. Or it can be more beneficial for a parasite to become a mutualist to continue indefinite living with the host or increase transmission to new hosts The amoebas showed that organisms can go from being parasitic to obligate mutalists in as short as 5 years The switch between parasitic relationship to an endosymbiosis is present in many protists and is thought to be the origin of chloroplasts and mitochondria in eukaryotes Horizontal gene transfer is what allows hosts to make sure that endosymbiotes do not turn parasitic

What is migration load? How does it work? How can migration enhance adaptive evolution?

a lower average population fitness than predicted given selection regime due to migrants from populations with different selection regimes If populations are well adapted in one subpopulation's environment, they might send out migrants to other subpopulations in different environments where selection acts a bit differently and now it is affecting allele frequency by given good alleles from one environment to a different one (they might not be good in the new environment) Migration can bring in new alleles, bringing a specific allele frequency down off of a local mean population fitness optimum. It could push it so far off the optimum, that it is now downhill from a new better optimum, and selection will now act on the population to send it to the global optimum. Thanks immigrants!

What is a Lagerstätte? Why have they been important is our understanding of the history of life?

a particularly rich fossil deposit including organisms (or parts of organisms) that don't typically fossilize well the Burgess shale (505 mya, Canada) was the first thoroughly studied assemblage of animal life from this early on

What is an idealized population? Why are idealized populations useful?

a simplified model of a population that meets certain assumptions - allowing us to isolate the effects of interest We can also compare data from real populations to expectations from idealized populations to test hypotheses

What is coevolution?

an evolutionary change in a trait of the individuals in one population in response to a trait of the individuals of a second population, followed by an evolutionary response by the second population to the change in the first Reciprocal evolutionary change across species interactions

What is homoplasy?

analogous traits, for which similarity is not due to shared ancestry the major confounding factor in reconstructing evolutionary relationships "coincidental" similarities resultant of convergent evolution evolved independently

What is the attenuation of virulence and when would we expect evolution to lead to this outcome? How does this concept relate to emerging pathogens?

become less virulent, you can survive longer in the host to be transmitted before killing the host or the host killing you When density of hosts decreases it becomes more beneficial for viruses to keep the host alive longer so they will have more opportunity to infect other host This is indicative of general dynamics that we expect with emerging pathogens, in the long term, attenuation of virulence is a very likely outcome to increase R0 (a metric of the ability of a pathogen to transmit to new hosts (how many people are likely to be infected by an infected person)) and reach more dispersed individuals R0 > 1 - leading toward an epidemic R0 < 1 - the pathogen would have to evolve first an evolving parasite can increase R0 by increasing tranmission rate, decreasing parasite mediated death, or increasing rate of recovery

What's the difference between broad-sense and narrow-sense heritability?

broad in that it encompasses all of the genetic input to the trait Narrow --> This is the proportion of phenotypic variation that is passed between parents and offspring in a straight forward, easily predictable way, due to additive genetic variation

What are homologous traits?

characteristics shared among organisms because they were inherited from a common ancestor

What is senescence, and why is it an inherently evolutionary issue?

deteriorative changes (damaging to survival and reproductive ability) that occur in an individual with increasing age Senescence is by definition decrease in survival and reproductive fitness as time goes on, which is a basis for selection to act (or not)

What is phenotypic plasticity? How does the term polyphenism fit into this?

discrete or continuous changes in the phenotype exhibited by the same genotype due to environmental differences Polyphenism - only discrete phenotypic variation arising from the same genotype in different environments

How do we calculate an equilibrium between these opposing evolutionary forces?

for a purely recessive allele: q(hat) = sqrt(𝜇/s)

How do we use dominance coefficients to define a single selection coefficient in a two allele system?

h = 0 The deleterious allele is purely recessive h = 1 The deleterious allele is purely dominant h tells us about the degree of similarity between heterozygote fitness and homozygote fitness 1 - (relative fitness value of the heterozygote) = hs Because s = 1 means relative fitness is bad, so large s means deleterious, so large h means dominant deleterious effect in heterozygote

What does heritability represent in terms of phenotypic variance?

h2 = 𝑉a / 𝑉p = (additive genetic variance) / (overall phenotypic variance)

I've told you multiple times that natural selection is a deterministic process. What do I mean by that?

if we know what the conditions are, we know what the outcome will be With natural selection acting alone, the outcome is very predictable - increasing fitness until an allele is fixed (or the allele frequency reaches equivalence point)

How can the concept of coevolution be framed in terms of adaptive topographies?

in coevolution, adaptive topographies necessarily become dynamic Evolution in one species (movement along the topography) changes the shape of the other species' topography The position of species isn't changing, the peaks and valleys that represent the most beneficial/deleterious genotypes are changing. Therefore selection will act in response to the changing peaks and valleys

What do monophyly, paraphyly, and polyphyly mean? Can you identify those patterns given an evolutionary tree?

monophyletic - proper clades - an ancestor and all of its descendants -birds - the first bird gave rise to all birds and all of its descendants are birds -mammals - all the descendants of the first mammal are mammals paraphyletic - an incomplete clade - an ancestor and only some of its descendants (the common ancestor of all reptiles also gave rise to birds (non-reptiles)) polyphyly - grouped by homoplasies - the last common ancestor was not in their group (social structures in insects (ants and termites both have social structures but their most recent common ancestor did not)

What are the two recent hypotheses for the transition from H. erectus to H. sapiens. Which one is best supported by data? What are some implications of this for relationships among current human populations?

multiregional hypothesis - If Homo erectus occured around the world so early, did modern human evolve gradually from these populations in each different region? African replacement - Or did modern humans evolve in one location and subsequently displace H. erectus? The advent of DNA sequencing data strongly support a single, African origin of Homo sapiens

What are the mechanisms underlying each? What predictions do they make? What kind of empirical evidence supports those predictions?

mutation accumulation - Inbreeding effects that show up later in life are more common and stronger in Drosophila - Late acting alleles with stronger phenotypic effects are maintained at higher frequencies antagonistic pleiotropy - genes that affect lifespan (make it shorter) tend to have a large effect on increasing fitness when they act early in life. Also many genes that cause long life, make you have less kids (actually discussed) - involves energy allocation at different stages of life These are not mutually exclusive

How do we calculate the expected change in allele frequencies Δp? If we're given the equation, do we know how to get the numbers to plug into it? How do p, p' and Δp relate to each in this context?

p is the sqrt of the frequency of the homozygote pp q is the sqrt of the frequency of the homozygote qq or the frequency of the heterozygote divided by 2p or 1-p We do survivor tables if we're not given relative fitnesses of each genotype We use the average population fitness equation for 𝜔avg We only use the homozygote and the heterozygote because we're only concerned with p ∆𝑝= (𝑝/𝜔avg)(𝑝𝜔AA +𝑞𝜔Aa −𝜔avg) p' = p + ∆𝑝

In underdominant and overdominant situations, how do we calculate equilibrium points? What is the crucial difference between these two equilibria?

phat = t / (t + s) In overdominance - t & s are positive and equilibrium is a max In underdominance - t & s are negative and equilibrium is a min

How does the Red Queen Hypothesis fit into this?

populations are constantly evolving to changing biological challenges (interactions with other species or the abiotic environment) and sex is a crucial way for populations to keep pace with their enemies

What is taphonomic bias?

processes relating to the fate of organism's remains some animals, for one reason or another, might be better at making fossils and leaving evidence of their existence than others

What is parthenogenesis? How is this trait distributed in nature?

reproduction by females of other females via eggs Parthenogenesis is sometimes just occasional in species Other times, particular species are fixed for asexual reproduction These obligate parthenogens tend to be single species or very small clades... not large radiations of diversity. They also tend to be young.

Which population genetic parameters affect this process and why?

stronger drift with smaller population (1/(2N)) stronger mutation with larger population (2Nv) Multiply these affects --> v • In small populations, each allele has a higher chance of going to fixation In large populations, more alleles come into existence

What is different about the outcome of these dynamics when the alleles aren't purely recessive?

the equilibrium for mutation-selection balance (q(hat)) is much, much lower as soon as you move off of the case of purely recessive mutations.

What does heterozygosity really represent?

the expected frequency of heterozygotes given the allele frequency and assuming HWE it represents not just the total allele variation in the overall population, but the amount of differing alleles that exist together in interbreeding populations. It represents genetic variation in subdivided populations Drift working alone (going toward fixation) will driv heterozygosity down

What are vestigial structures and atavistic traits? How do they fit in here?

vestigial structures - a useless, rudimentary version of a trait that is functional in related taxa (pelvic bones in whales) --pseudogenes - non functional copies of coding genes - can also be thought of as vestigial (e.g. vitamin C synthesis) in primates Atavistic traits - Reappearance of ancestral traits in individuals If we have the instructions to produce things that we don't need, that is evidence that we needed them at some point (we changed over time)

Demonstrate the basic dynamics of unchecked population growth over a few generations.

y(t) = y0 * x^t y(t) is the number of females in a population y0 is the starting number of females x is the average number of females a female has t is number of generations

How do we calculate their effect over time?

∆𝑝 = −𝜇𝑝 and 𝑝(n) =𝑝(0)𝑒^(−𝜇𝑛) 𝜇 is the mutation rate of p turning into q

Can you calculate the expected change in allele frequency across generations due to migration acting in isolation of other evolutionary forces?

𝑝′1 = (1−𝑚)(𝑝1) + (𝑚)(𝑝2) 𝑝′2 = (1−𝑚)(𝑝2) + (𝑚)(𝑝1) ∆𝑝1 =𝑚(𝑝2 − 𝑝1)