Exam 2 - Evolution

What parts of Genetic Variance is difficult to interpret? What parts are easy?

*Difficult* (b/c context dependent) Vd - because heterozyotes display the full trait so you don't know where they fall on the curve Vi - because you must examine multiple genes and there are complex things controlling an epistatic gene. *Easy* Va - because it's straight forward.

Why would you compare Non-synonymous to synonymous

*Faster evolution* than synonymous sites indicates *positive selection* (new mutations good) *Slower evolution* than synonymous sites indicates *purifying selection* (new mutations bad)

What are the four common methods on building a phylogentic tree?

*Maximum parsimony* - Simplest explanation favored *Distance matrix* (e.g. neighbor joining) - Clusters taxa based on genetic distance *Maximum likelihood* - Finds most likely tree given specific model of molecular evolution *Bayesian methods* - Looks at probability that a tree is correct given a specific model of molecular evolution

distinction between substitution and mutation

*Mutation* any change in a DNA sequence A *substitution* is a mutation that got fixed in a population or a species (that reached 100% freq) In other words, a *substitution* is mutation that survived the action of selection and drift

Reproductive barriers. Main types and subtypes. Big picture

*Prezygotic* 1) Premating • Behavioral • Ecological - Temporal, Habitat, Pollinator • Mechanical 2) Postmating • Copulatory behavioral • Gametic isolation *Postzygotic* 1) Intrinsic • Hybrid inviability (die shortly before or after birth) • Hybrid Sterility - physiological (no balls - mule) + behavioral 2) Extrinsic • Ecological inviability (cant make it in the niche) • Behavioral sterility (cant find a mate)

How can discrete alleles shape continuous traits? (2) reasons

*Reason 1:* multiple genes control a trait *Reason 2:* the trait should also take discrete values but it looks continuous due to the environmental variance Environmental variance (Ve) fills in the gaps to make it smoother looking

Selection differential (S)

*Selection differential measures the strength of selection*. It is the value between, i.e., the mean size of reproducing individual and the distance from the mean size of the entire population The larger the S the stronger the selection

What are the two versions of selection differential

*Strong Selection* - only the biggest individuals reproduce *Weak Selection* - big and medium individuals reproduce

Two types of isolating barriers

1) Geography: extrinsic properties of landscape that prevent gene flow (Allopatry) 2) Reproductive: features of organisms that prevent interbreeding (Barriers effective even in sympatry)

Why has selection not favored better repair mechanisms? (1)

1) Most organisms don't die due to aging but ecological pressures. (accidents, getting eaten) "Means that later-life reductions in fertility or survival rates are selected against more weakly selected against." AND "Mutations that have a positive affect on longevity doesn't have a chance to be selected for because organisms die too early. " Mutation-selection balance will thus be less efficient at eliminating mutations occurring later in life.

Long term bacteria experiment regarding natural selection.

12 genetically identical lines in separate flask bacteria have to complete for glucose morning new glucose afternoon all glucose gone small amount of survivors put into new flasks freeze the sample every 500 generations compared generations to original line Over time, the fitness of bacteria increased when compared to the original strain of E. coli Shows that bacteria are adapting to their situation

What is the estimated new mutations in humans?

9.8 billion

Bootstrapping results. What's considered good and what's consider bad?

90+ @ nodes is good and supported Anything under 90 is less supported.

bottleneck effect

A change in allele frequency following a dramatic reduction in the size of a population. i.e. Natural disaster rare alleles are very likely to be lost during bottleneck

genetic drift

A change in the allele frequency of a population as a result of *chance events* rather than natural selection. This is because when something like a natural disaster happens and if a small % of the population survive then that portion is not going to represent the whole population that well. Expected to lose alleles Drift is an overarching concept. Bottlenecks and founder effect cause genetic drift.

methylation

A chemical modification of DNA that does not affect the nucleotide sequence of a gene but makes that gene less likely to be expressed. epigenetic mechanism

Grandmother hypothesis

A hypothesis stating that *menopause in older women is an adaptive trait* because it contributes to the *survival of grandchildren* by eliminating the possibility of childbirth and allowing older women to further their genetic interests by nurturing their grandchildren. Studies show increased survival for children whose grandmothers are still alive

Genome wide association studies

A large-scale analysis of the genomes of many people having a certain phenotype or disease, with the aim of finding genetic markers that correlate with that phenotype or disease.

chromosome crossover

A process occurring *during meiosis* wherein homologous chromosomes pair up and exchange segments of their genetic material

homoplasy

A similar (analogous) structure or molecular sequence that has evolved independently in two species.

Phenotypic plasticity

A single genotype produces different phenotypes depending on the environment makes it more difficult to identify relative impact of genetic and environmental variance

Life history trade off

A trade off between reproduction and survival. Processes that contribute to higher reproductive output result in reduced survivorship or longevity. Due to a presumed physiological constraint on the ability to process resources (nutrients, energy) into competing organismal functions. Can define the way an organism lives its life, or its life history: extreme cases are fast growth with rapid reproduction, vs. slow growth with delayed reproduction. Natural selection determines Life History. The strategy that is used is the most advantageous given the organism environment.

polygenic trait. common example of this?

A trait in which *A* phenotype is controlled by two or more genes *at different loci* on different chromosomes. multiple genes encoding for a *single trait* i.e. height. many genes control this trait. also known as complex trait

complex trait

A trait that is influenced by multiple genes as well as by the environment. complex traits are continuous traits. also known as polygenic trait

Speciation involves barriers to reproduction

After sexual isolation the two populations accumulate mutations independently and diverge from one another. Once a lot of mutations have accumulated, the two species can no longer reproduce

How are male parents different from female parents when it comes to taking care of offspring.

All parents want to maximize their offspring's success. BUT For males there is a trade off between 'making sure one clutch is sufficiently taken care of' and 'trying to start more clutches' It is usually Most beneficial for males to let the female spend time and energy on the progeny, while they fertilize other females.

Alleles that lower fitness experience *_____________ _____________ * Alleles that increase fitness experience *_____________ _____________ * Alleles that don't have an impact on fitness *_____________ _____________ *. only __________ can impact it.

Alleles that lower fitness experience *negative selection* Alleles that increase fitness experience *positive selection* Alleles that don't have an impact on fitness *evolve neutrally*. only drift can impact it.

What is likely to happen to alleles when there is a small population size?

Allelles can be lost.

Extremely fast case of speciation can occur through...

Allopolyploidy. Breeding between species can lead to uneven chromosome numbers The hybrids can only reproduce among themselves after whole genome duplication "instant speciation"

Recessive allele

An allele that is masked when a dominant allele is present

Dominant allele

An allele whose trait always shows up in the organism when the allele is present. Aa

Neighbor-joining + outgroup example.

An outgroup can be compared to determine which nucleotides/amino acids are ancestral or derived. Variable site #1: outgroup has trait "A", this is most likely the ancestral state and "T" is the derived state

Bacillus thuringiensis (BT) crops

Are crops that can produce their own pesticides (a bacteria that kills the insects that eat it.)

Incomplete lineage sorting in primates.

At first we thought chimps were more closely related to gorillas than us, but later we find chimps are more closely related to us than gorillas Problem was solved was when we *used multiple genes* instead a small amount. Increasing the sample size of genes solves the problem of incomplete lineage sorting.

What is unique about bacterial genome?

Bacteria of the same species has only 50% of the same gene (the core genome)

What is a reason why bacteria are hard to differentiate according to species?

Bacteria perform horizontal gene transfer and Bacteria of the same species has only 50% of the same gene (the core genome)

Prezygotic barriers

Barriers that impede mating or hinder fertilization.

Postzygotic barriers

Barriers that prevent the hybrid zygote from becoming a reproducing adult. • Intrinsic • Extrinsic

Genetic basis of postzyotic isolation

Bateson-Dobzhansky-Muller incompatibilIties arise from epistatic interactions at two or more loci (Many proteins interact with each other) a & b do not interact well or at all, therefore the protein is dysfunctional

Why/how can mutations be used as a molecular clock?

Because neutral substitutions are not selected for or against and they accrue in a clock-like fashion. Substitution rate *can be calibrated* based on mutation rate and/or fossil evidence to infer time since divergence with the graph you can determine how long ago the paired species diverged.

How was snake venom come to be?

Beta-defensin a protein that fights bacteria. It is expressed in the pancreas The gene that produced beta-defensin got duplicated and started to be expressed in the mouth. it became more complex over time. it became a venom gland.

Hermaphroditic life cycle strategy

Better to be female when small because cant compete. A lot of fish develop this life history. Turn into male when they grow bigger.

Stabilizing selection of gall size. how does this occur?

Biggest and smallest diameter galls negatively selected against. Biggest make them easily spotted by birds Smallest make them easily accessed by wasps (injecting their eggs to eat the other larvae)

Example of penduline tits

Both parents build and protect the nest together but the male bird dips out as soon as the female has laid the eggs. The female attacks the male for checking trying to prevent him from leaving.

Mechanical isolation

Cannot mate due to structural differences

Pollinator isolation

Closely related species that are capable of reproducing but have adapted to bees and humming birds respectively causing them to specialize significantly. They can mate but their *hybrids are ignored* by both humming and bees. sexually isolated. (maladadapted)

Two possible reasons lactase persistence evolved.

Development of dairy farming resulted in higher fitness for individuals with lactase persistence. *(cows came first)* Cultures with high frequency of lactase persistence were more likely to adopt dairy farming. *(lactase came first)*

diploid individuals ...

Diploid individuals carry two alleles at every locus

Domestic dog diversity generated by artificial selection in last *_____* years

Domestic dog diversity generated by artificial selection in last *15,000* years

Medium ground finches during 1977 drought example.

Drought resulted in more hard, woody seeds. This Favored larger beaked birds Natural selection is variable over time and can result in rapid evolutionary change Long-term studies reveal fluctuation in the direction and strength of natural selection

The case of sticklebacks

Each isolated population had low morph and high morph of the Eda locus which causes armor in high predation environments and no armor in low predation environments. This case showed that the sticklebacks went through parallel natural selection

What are the mechanisms that drive polygenic traits?

Epistasis & Phenotypic plasticity.

Runaway sexual selection

Female choosiness and male elaboration form a positive feedback loop Arbitrary female preferences can lead to sexual selection. fisher model: if there is any biases in the preference of females its going to lead to the evolution of male traits.

What could be a reason why males parental care is rare?

Females have certain paternity - they know its their kid Males have uncertain paternity - they don't know it's their kid.

maximum likelihood

Finds most likely tree given specific model of molecular evolution (statistical) Maximum likelihood methods are looking for the tree with highest likelihood "score"

If you have a lot of variance for a trait how does the distribution curve look?

Flat and wide. The shortest curve

Gall fly and gall.

Fly inject a plant with chemicals and the plant produces a gall. The size of the gall is determined by the fly. Gall diameter is variable and heritable. (by the fly) This phenotype is considered a *extended phenotype. * The fly then inject their larvae into the gall so it can be protected and eat the plant from inside out.

Behavioral isolation

Form of reproductive isolation in which two populations have *differences in courtship rituals* or *other types of behavior* that prevent them from interbreeding

Gametic isolation

Gamete incapability sperm or pollen from one species fails to penetrate and fertilize the egg of another species *This is because:* Fertilization requires specialized protein-protein interactions

Genetic drift can also significantly impact large populations through _____________ and ______________ effects

Genetic drift can also significantly impact large populations through *bottlenecks* and *founder* effects

What is the main conceptual addition to the theory of evolution?

Genetic drift.

Was the differences in the guppies genetic or environmental?

Genetic. When the high predation guppies were transplanted into low predation areas, over and 11 year span, they got bigger, had less offspring, and reached sexual maturity later.

Broad sense heritability equation

H^2 = Vg/Vp = Vg/(Vg + Ve) Vg + Ve is total phenotypic variance (Vp) So H^2 is a percentage of how much the genetics contributes to a trait. i.e. if H^2 = 20%, then that means 20% of the trait is genetic and 80% is environmental

The case of Charles II of Spain

He was considered to be the most inbred through inbreeding coefficient. The more inbred you are the more likely you are to have homozygous recessive genotypes

How much the population evolves depends on ... (2) (The magnitude of change)

Heritability and Selective differential (S)

The concept of homology can be applied to genes Gene sequences can be used to build phylogenies

Homologous genes can be aligned

Natural selection favors phenotypes less preferred by fishermen and hunters. example of ram horns.

Hunting pressure leads to shorter horns in wild sheep.

Reinforcement

Hybrids have lower fitness. Therefore selection favors individuals who mate with their own population natural selection favors prezygotic isolation mechanisms that prevent the formation of hybrids with reduced fitness

Nematodes (Caenorhabditis elegans) example of phenotypic plasticity

If all the genotypes are equally impacted (the graph on the left) then low Vgxe If the genotypes response differently to the environments then High Vgxe.

How does creation of *Bt-free refuges* help slow evolution?

If an insect is genetically programmed to put extra resources into resisting a pesticide, it has fewer resources to invest in other activities, such as growth and reproduction. In a field without Bt, a Bt-resistant insect is therefore at a disadvantage compared to susceptible insects. In a field with Bt, the cost of Bt resistance is outweighed by its benefits, and the resistant insects take over. Doesn't prevent evolution completely.

Story of HMS bounty

In 1789, a mutiny broke on the HMS Bounty The 25 mutineers settled in Norfolk island in the Pacific ocean (with 30 Tahitian men and women) Norfolk island has now a population of 1,748 inhabitants Descendants of the the Bounty mutineers have been impacted by genetic drift Several rare alleles are found at high frequency in Norfolk population

Natural selection can be variable across space like *in the case of coral and scarlet snakes*

In areas where coral snakes are not present, scarlet snake is more likely to be attacked. in areas where coral snakes are present scarlet snakes are less likely to be attacked and resemble coral snakes more closely than snakes further away from overlap region Is this due to aposematism mimicry Natural selection can lead variation over the geographic range of a species

Expected consequences of male-female asymmetries

In males, selection should favor maximizing the number of matings (competitiveness). In females, selection should favor producing the most successful offspring (choosiness).

Alterations in EPSPS enzyme leads to Roundup resistance

Independent evolution of same mutation in weeds.

What are conditions that need to be met use Coalescence for genetic analysis?

It assumes that the alleles evolve neutrally It depends on parameters such as population size With these conditions met the *time of divergence can be determined* mathematically.

What does bootstrapping do?

It consists in resampling the data multiple times with replacement to check how robust the result Typically 100 or 1000 resampling are performed and a tree is built for each resampling. Topologies of the bootstrap trees are compared to the real tree This helps identify which nodes in the tree are not well supported (when only a few sites in the alignment are causing this inference)

what is the consequence of Bateson-Dobzhansky-Muller incompatibilities?

It facilitates speciation because the hybrids of two populations have a lower fitness

Example of Rhagoletis (flies)

It is a case of ecological speciation. Originally this species of flies ate hawthorn fruit hung around it, but some of them started to prefer apples. Flies mated with other flies that hung around the same fruit. Also, the fruits fruited at different times of the year this caused them to adapt their life cycles according to this.

What is The Evolutionary response to selection (R)?

It is the evolutionary response to selection Depends on two variables: Narrow sense heritability & Selection differential. R = h^2 x S If h^2 = 1, and S is big then the R will be strong. If h^2 = 0.25, and S is big then the R will be smaller.

Case of caterpillars

It seemed like a particular caterpillar was present all across the entire continent of south America. They realized it was different species that probably recently speciated. example of cryptic species

Example of Atlantic and Gulf coast mice

Light coat color evolved independently in different populations Atlantic and Gulf coast populations both evolved white fur, but the specific mutations responsible are different

loci

Location of a gene on a chromosome

bayesian methods

Looks at probability that a tree is correct given a specific model of molecular evolution (statistical)

What did the opossum experiment determine?

Mainland (w/ predators) and island (w/o predators) possum populations were compared to determine max age. The experiment showed that mutations that would expand their life span were beneficial and selected for.

Coat color of mainland vs beach mice QTL analysis. Which genes were there? which genes were the strongest in determining the coat color?

Mainland mice had more dark color on the back. Beach mice were lighter in the back. Agouti, Mc1r, and Corin Agouti and Mc1r were the main mechanisms of variance. Corin explained a small amount.

Genomic imprinting and parental conflict

Male and female parents can compete on an epigenetic level through methylation. Each parent has a distinct methylation pattern which is passed on to the offspring.

collared willowbird example of "good genes" model

Male body condition in collared willowbirds predicts tail length. Tail clipping experiment demonstrates benefits and costs of long tails.

Sexual selection is typically stronger on males because...

Male-biased OSR

phenotypic variance

Measures the degree of phenotypic differences among a group of individuals; composed of genetic, environmental, and genetic-environmental interaction variances. (Vp) = TOTAL Phenotypic variance in a population

Natural selection is ________ powerful in large population Drift is _________ in large populations Drift can ______________ with selection (esp. in smaller populations)

More, weaker, interfere

Mosquito example

Mosquitoes became resistance to pesticides when pesticides were used on the coast of France Resistance was due to allele Ester1. Mosquitoes with the Ester1 allele produce more esterase. An enzyme that degrades the insecticide. The Ester1 allele spread to mosquitoes further away from the coast Despite this advantage, the Ester1 allele did not spread to the entire population. Researchers found that the Ester1 allele increased the chance of mosquitoes to be caught by predators This is a case of *antagonistic pleiotropy*: the allele is beneficial under certain conditions but detrimental in other conditions

Why does a duplicated gene get deleted most of the time?

Most of the time, having two copies of the same gene is not advantageous. There is no need for two copies of the same gene. Purifying selection is not conserving both copies, so one copy will accumulate mutations rapidly. Therefore, one copy will be lost (it will become a pseudogene or be deleted)

Triver-Willard Hypothesis

Mothers alter sex ratio depending on conditions. Produce more males in good conditions because they are likely to get large which helps them compete Produce more females in bad conditions because they will be fertilized regardless.

Difference between mutation and substitution

Mutation occurs in the nucleotide sequence. If a mutation changes the A.A. then it is considered a non-synonymous mutation. Synonymous mutation doesn't change the A.A. because multiple codons can represent a particular A.A. Now comes substitutions. If a non-synonymous mutation changes the A.A. to an A.A. that isn't similar to the original one THEN the non-synonymous mutation CAUSES a non-synonymous substitution! jeez

Four main evolutionary mechanisms

Natural selection Genetic drift Migration (enter - exit) Mutation

how has cod fishing influenced their physiology?

Natural selection has reduced age (and size) of sexual maturity.

Directional selection

Natural selection in which individuals at one end of the phenotypic range survive or reproduce more successfully than do other individuals.

Distruptive selection

Natural selection that *favor* individuals with either *extreme of traits.*

stabilizing selection

Natural selection that favors intermediate variants by acting *against extreme phenotypes*

Types of population subdivisions

No division, Extreme division, and Intermediate subdivision.

Can selection drive dominant alleles to fixation?

No. because of heterozygotes.

When looking at the molecular clock it is best to use neutral (non-functional) sequences. why? what about functional sequences?

Non-functional sequences are not constrained so they evolve faster. They aren't counter selected so they build up mutations. Functional sequences evolve slower because mutations impairing the function of the sequence will be *eliminated by selection* For this reason, each gene evolves as its own rate

What does the bacterial genetic tree look like? why?

Not bifurcated and looks like a network because horizontal gene transfer is very common in the context of billions of years.

Mother hypothesis

Offspring survivability decreases when the mother dies in child birth or before the children are raised completely. Thus, selection would favor early cessation of childbearing. Problems with this hypothesis: Studies show little effect of mother's death on children's survival. Extended family usually can provide needed care.

polyandry

One female, several males.

Polygyny

One male, several females.

heritable variation

Organisms have different variations of traits which are passed down from parents to offspring

Example where baby birds compete (2)

Parents will feed the offspring with the best coloration in their mouth. American coots with the brightest color got fed more

Asexual reproduction consists of

Parthenogenesis (no fertilization) - no meiosis - chromosomes become embryos Self fertilization - self explanatory

Positive frequency dependent selection. Example.

Phenotypes are favored only when the phenotype is common. Example is warning coloration

Negative frequency dependent selection. Example

Phenotypes favored only when rare. Example is left-handed fighting ability i.e. flowers being trolls The flower doesn't have nectar. so if the purple is common and bees know for sure purple doesn't have nectar they will start going to yellow. vice versa. (balancing selection is conserving diversity)

Multiregional model vs Out-of-Africa model

Phylogeny points to Out-of-Africa model All human populations are derived from recent African ancestry

convergent evolution (independent evolution)

Process by which unrelated organisms independently evolve similarities when adapting to similar environments

Genetic bottlenecks often go hand in hand with inbreeding and selection

Recessive alleles exposed to selection this is because the gene pool is very limited usually after a bottleneck event.

anisogamy

Refers to a difference in gamete size in males and females. Eggs large and costly, sperm small and cheap Male vs. female reproduction are asymmetric

How can asexual reproduction have an advantage over sexual reproduction?

Reproducing asexually means you contribute both gametes rather than just one to each offspring. two-fold advantage. if there is a beneficial trait then you can pass the whole trait on to your offspring. whereas if you reproduce sexually then the advantage gets diluted.

Reproductive barriers are ____________ features of organisms that reduce likelihood of _____________________

Reproductive barriers are *intrinsic* features of organisms that reduce likelihood of *interbreeding*

Sickle cell alleles

S = sickle cell A = wildtype SS = sickle cell disease SA = heterozygote AA = wildtype homozygous

Selection occurs when *________* differ in *___________*

Selection occurs when *genotypes* differ in *fitness*

Stable ecotype model

Selection periodically leads to the loss of variants, when a single clone reaches fixation. The periodic loss of diversity maintains genetic cohesion in the species (this is not favored among the scientific community.

purifying selection

Selection that lowers the frequency of or even eliminates *deleterious alleles.*

What results from sexual selection? has to do with form difference of male and females.

Sexual dimorphism: Armaments (antlers) vs Ornaments (peacock)

What does broccoli, kale, cauliflower show us?

Shows that selection can change phenotypes rapidly. Shows presence of heritable variation.

Multiple or single colonizations of Galapagos finches

Single. They are monophyletic. Not Cocos finch. Phylogenetic evidence supports single colonization from South America

Genes differ in rate of evolution

Slowly evolving genes useful for distantly related species Rapidly evolving genes useful for closely related lineages

How do new genes appear?

Solution #1: a single gene can have multiple functions (Promiscuous protein) Solution #2: genes can be duplicated

Mating is of the upmost importance in an evolutionary context. In extreme cases of male-biased OSR what happens to the male?

Sometimes, males compete to death

What does the speed of speciation experiment with fruit flies tell us?

Speciation can occur even when genetic distance is very low. This suggests that premating behaviors are responsible for that. Reproductive isolation occurs even though the genetic distance between two species of flies are very close because of subtle changes such as premating behaviors, timing, etc.

Darwin's thoughts on species

Speciation is a result of evolution.

Peripatric speciation

Speciation pattern in which populations speciate while out of contact and isolated. Due to entering a new niche

Example red queen in snails

Species of snails can reproduce sexually and asexually. Sexual reproduction is more frequent in populations more impacted by parasites. Asexual individuals less likely to survive.

How to perform a QTL analysis

Step 1: identify trait and generate purebred strains and identify the genetic markers of each strain Step 2: cross the two lines (parental lines) and analyze the offspring Step 3: determine which genetic markers are statistically associated with the trait. (In other words) Find where all of the large offspring have the same gene

Quantitative genetics. What are the goals of it?

Study of genetic mechanisms of continuous phenotypic traits. Which genes encode the trait of interest How much each gene determines the trait of interest

Population genetics

Study of the distribution of alleles in populations and causes of allele frequency changes Population genetics focuses mostly on microevolution (i.e. evolution of populations within the same species)

Maximum likelihood and Bayesian analysis methods rely on explicit evolutionary models such as... how does it do it?

Substitution rates spectrum The computer models take a tree and constantly shift it to improve certain parameters.

dS = dN meaning dS > dN dS < dN

Synonymous substitutions (dS) Non-synonymous substitutions (dN) dS = dN neutral evolution. no selection occuring. (non-functional pseudogene) dS > dN purifying selection. negative selection. selection prefers keeping the gene as it is(likely an important function) dS < dN positive selection. new mutations are good. (adapting to new condition)

Ecological isolation (prezygotic) types

Temporal, Habitat, Pollinator

problem with "good genes" model

The "good genes" model is not resilient to "cheaters". Cheaters are individuals that display attractive ornaments but are not the best mates.

pleiotropy

The ability of a single gene to have multiple effects.

Pleiotrophy

The ability of a single gene to have multiple effects/phenotypes. Example: genes that control the feathers on a peacock. bright feathers can cause antagonistic effect (easily seen by predators), but allow for better mate selection in this case we would look at the *net effect* (overall effect) mosquito example of pleiotrophy (ester1 and ester4)

When a gene is duplicated what is likely to occur? what is less likely to occur?

The duplicated copy is likely to get deleted. BUT preservation of both copies can happen. this will lead to Gene dosage, Subfunctionalization, OR Neofunctionalization

ancestral organization was maintained in the giraffe regarding the vagus nerve

The end result does not always produce the most logical/efficient structure Evolution proceeds by the modification of existing structures by successive steps Natural selection often retools the form and function of characters present in a population, leading to adaptations that are not perfect, but still provide fitness advantages

Allopatric speciation

The formation of new species in populations that are geographically isolated from one another.

Sympatric speciation

The formation of new species in populations that live in the same geographic area. Due to genetic polymorphism or just genetic factors. i.e. variant in sexual selection arises

How can organisms adjust the family? (2)

The goal is to maximize fitness of offspring. 1) Regulate the number of offspring • Miscarriage • Cannibalism 2) Regulate sex ratio of offspring

Trade off example of beetle ornaments.

The horns reduce the beetles vision. Also smaller wings.

mutation accumulation hypothesis

The hypothesis that senescence occurs because natural selection is not strong enough to purge deleterious mutations associated with traits that are expressed only late in life *mutation selection balance* cannot occur. where mutations are selected against but keep forming new mutations. They just stay.

H^2 = 0

The phenotypic variance is entirely due to *environmental variance* Trait is *only controlled by environment* No genetic component

H^2 = 1

The phenotypic variance is entirely due to *genetic variance* Trait is controlled by *only genetics* No environmental influence

selective sweep

The situation in which strong selection can "sweep" a favorable allele to fixation within a population really quickly Alleles present at close loci are linked, therefore can not be recombined in a short period of time In the absence of recombination, alleles in large stretches of DNA flanking the favorable allele will also reach high frequency. Selective sweep causes a reduction in genetic diversity around the sweeping allele.

Selective sweep will produce specific patterns of genetic linkage. Explain in the context of lactase persistence.

There is reduced diversity of genes around the lactase allele because *genetic hitchhiking* is occuring Mutations conferring lactase persistence show evidence of selective sweeps. The cow came first

Significance of Seychelles Warblers

They adjust the number of male to female offspring according to resource levels. The females offspring stick around and the males fly away asap. So in low resource environments more males are born.

Significance of sand gobies

They can cannibalize their eggs when oxygen levels get too low.

The case of polar and brown (grizzly) bears

They can produce hybrids and there has been gene flow but generally they are adapted to their own ecological niches. Polar bears predominately feed on seals which are high in fat and cholesterol. They have adapted to digest high amounts of fats compared to the brown bear.

Elk (of N. America) and red deer (of China) example

They were the same species. Shows an example of allopatry

Ester4

This allele is not as efficient at protecting against pesticides, but it does not increase the chance of mosquitoes to be caught by predators The overall fitness provided by Ester4 is higher than Ester1

gene dosage

This causes the gene to be expressed at higher rate than normal.

What is isolation by distance

This happens because populations tend to breed with those in close proximity (genetic structure is a gradient)

parallel evolution

Two related species that have made similar evolutionary adaptations after their divergence from a common ancestor similar to convergent evolution. i.e. cave fish losing eyes.

Species can be considered. what?

Units of taxonomy. Species are populations of individuals that share similar traits and similar history

Fst = 0.11

Variation between population 11% Variation within population 89%

The problem with H^2 (broad sense heritability) what are those variables?

Vg can be broken down into multiple variables. Va + Vd + Vi Additive, dominant, epistatic

what is the equation for phenotypic variance?

Vp = Vg + Ve

Case of Anolis Lizards

Was a statement of reproduction/survival trade off The reproductive organs were removed which caused them to *grow bigger* and *live longer*. BUT could the results be due to a change in hormones?

What is the basis for Trivers-Willard Hypothesis?

Weak males are unlikely to compete successfully. BUT weak females are still likely to be fertilized.

deep homology

When growth and development of traits in different lineages result from underlying mechanisms inherited from a common ancestor this may be why parallel evolution can happen.

continuous trait

When the phenotype for a given trait can take on any value between two extremes. i.e.Height. Continuous traits typically *follow a normal distribution*

What is the goal of quantitative genetics? (again)

Which genes encode the trait of interest How much each gene determines the trait of interest

Does color affect predation

Yes Color-mismatched models attacked by predators more often in both environments.

Can plasticity evolve?

Yes it is a trait that can evolve. Some genotypes can be more plastic than others.

Is homoplasy common?

Yes, because only four possible character states for DNA

Can selection occur without evolution?

Yes. No evolution if the selected traits are *non-heritable* No evolution if selected traits are not different from the average of the population

neighbor joining

a distance method for reconstructing phylogenies; identifies the tree topology with the shortest possible branch lengths given the data DNA or protein sequences can be used.

FOXP2

a gene that is important in language and speech production

polymorphic locus

a locus/gene that has more than one allele

Which type of alleles are most relevant for evolution? why?

additive alleles. because dominance & epistatic alleles depend on their interaction with other alleles and therefore *not as heritable* as *additive alleles*. additive alleles are faithfully transmitted from parent to offspring

What type of alleles are easily selected for?

additive.

discrete allele meaning

alleles are either 1 or 0. present or not present.

genetic hitchhiking

alleles can increase in frequency when they are present near a positively selected allele

Non-synonymous mutation

alter the amino acid sequence of the protein -more likely to be subject to selection

Additive allele

an allele that yields *twice the phenotypic effect* when two copies are present at a given locus than when only a single copy is present AA

additive allele

an allele that yields twice the phenotypic effect when two copies are present at a given locus than when only a single copy is present

mutation-selection balance

an equilibrium in the number of deleterious alleles in a population that occurs when the rate at which deleterious alleles are created by mutation equals the rate at which deleterious alleles are eliminated by selection

Selection is not very efficient at purging recessive deleterious (harmful) alleles because...

an individual with heterozygous will have a recessive allele.

Polyandry selects for male traits that increase paternity (2)

an insect that has a brush penis that removes previous males sperm in female. Sperm competition drives evolution of larger testes (bigger balls, more sperm, higher chance to successfully fertilize when female has sex with multiple partners)

if you modified the number of cervical vertebrae you will likely have ________________ affects

antagonistic antagonistic pleiotropy - beneficial for one trait but deleterious for multiple other traits. giraffe vertebrae example: vertebrae are so central to the organisms so if you modify it it will likely result in many more bad affects than good ones.

Quantitative Trait Locus (QTL)

are genomic loci that correlate with the variation in a phenotypic trait in question QTL analysis links traits with genes

Ornaments

attractive traits in males that increase mating success makes males better at successfully mating females.

Which organisms alter sex ratios? why?

bees, wasps, ants why? because only a few males are needed to fertilize. 1:1 ratio of male and female when clutch size is small as clutch size increases more females.

Copulatory behavioral isolation

behavior of an individual during copulation is insufficient to allow normal fertilization

Amount of gene flow varies with the biology of the organisms.

big horn sheep populations are more likely to be geographically divided Humans can alter population structures. (look at chart on pp)

Two methods that are used to infer the quality of a phylogenic tree.

bootstrapping (most common) & jackknifing

Ecological speciation can lead to

both prezygotic and postzygotic isolation. AND sympatric speciation

Founder effect

change in allele frequencies as a result of the migration of a small subgroup of a population Example: HMS Bounty - by chance some rare alleles ended up in high frequency causes high representation of those alleles compared to a normal population

Define evolution in terms of alleles

change in allele frequencies from one generation to the next

Non-synonymous substitution

change protein

Descent from __________ _______ is a major feature of evolution

common ancestor

How do you estimate heritability?

compare trait values between offspring and parent slope = heritability 1 = 100% heritable.

polyploidy

condition in which an organism has extra sets of chromosomes

counter selection

condition that kills or inhibits the DNA donor strain in context: sickle cell SS individuals are *counter selected* AND AA individuals are counter selected in areas where malaria is common.

Lactase persistence is a __________ _________ possessed by only ____% of humans

derived trait, 30

incomplete lineage sorting

describes the case when speciation happens very quickly and the *history of a gene* differs from the *history of the species* carrying the gene speciation can happen at separate times of coalescence split. Multiple speciation events occur in a very short period of time - this causes the right tree.

Average excess fitness

difference between average fitness of individuals with *a single particular allele* vs. those without

Modes of selection

directional, stabilizing, disruptive

Isolated populations become genetically ___________

distinct. Due to drift, smaller isolated sub-populations become more genetically distinct the rate of change in genetic distance increases as populations become smaller.

Synonymous mutation

do not alter the amino acid sequence of the protein

synonymous substitutions

do not change protein

neofunctionalization

duplicated genes diverge and one copy takes on new function one copy of the gene evolves a new function. (least likely)

Red Queen Hypothesis

each species has to run (evolve) as fast as possible just to stay in place -- because predators, competitors, and parasites also continue to evolve

What does a deviation from hardy-weinberg suggest?

evolutionary mechanism are in play

fecundity

fertility; fruitfulness;

Armaments

fight or compete other males. makes males better than other males.

Relative fitness

fitness of a genotype standardized by comparison to other genotypes

epistatis

gene at one locus on the chromosome alters the phenotypic expression of a gene at different locus

subfunctionalization

gene duplication produces gene copies that diverge and divide the work initially undertaken by the gene before duplication each copy becomes specialized to a specific task (e.g. expression in different tissues). this is usually case when the gene was already performing TWO functions.

phenotypic variance of a trait is determined by...

genetic component (Vg) environmental component (Ve)

Narrow sense heritability equation

h^2 = Va/Vp = Va/(Va + Vd + Vi + Ve)

gene flow counteracts subdivisions by _________________ allele frequencies

homogenizing

"Unofficial" sexual reproduction of prokaryotes

horizontal gene transfer and shit

Extrinsic isolation

hybrid is unfit because of environment hybrid develops normally and is fertile but has low fitness (maladaptation)

Intrinsic isolation

hybrid is unfit regardless of environment hybrid dies before birth or is sterile (case with mule)

Heterozygous

individual carries different allele

Homozygous

individual carries two copies of the same allele

Prezygotic premating barriers

individuals do not mate • Behavioral • Ecological - Temporal, Habitat, Pollinator • Mechanical

Prezygotic postmating barriers

individuals mate but no fertilization occurs • Copulatory behavioral • Gametic isolation

jackknifing

instead of resampling taxa/species instead of sites of the alignment (nodes)

Recessive allele are _____________ to selection Selection ____________ (can/cant) drive dominant to fixation

invisible cannot rare recessive alleles fly under the radar in heterozygotes therefore it cannot gotten rid of and therefore dominant allele cannot reach fixation.

Life history

is the pattern of investment an organism makes in growth, maintenance, and reproduction. (mostly determined by selective pressures)

How is hardy-weinberg useful in real world context

it is used as a null hypothesis where we can use it as a base to compare real world populations to determine if there is something going on that causes evolution?

Where did HIV come from?

it was a Simian Immunodeficiency Virus (SIV) found in great apes that mutated Probably transferred to humans in Africa because they hunted them.

What are restrictions of QTL analysis? what would be better?

its very tedious and small scale. GWAS - Genome Wide Association Studies

Genetic locust

location of a specific gene or sequence of DNA on a chromosome

Beneficial recessive alleles will stay at _______ frequency for a long time before reaching high frequency. why?

low because they are hidden in heterozygotes until enough of the homozygotes appear for them to increase in frequency

good genes model

male ornaments show females that they are strong viable mates. when it may not actually be the case this is unproven but there is some evidence like collared willowbirds

sexual conflict in ducts

males get can aggressive and hurt the female. The female has evolved anti-rape mechanisms and the male has evolved according to rape the female. (particularly shaped penis) Traits coevolve antagonistically

coalescence

mathematical model aiming at tracing the alleles of a gene back to a single ancestor "model the variation of alleles" (notice when the lines converge) red coalesce is two generations black is 6

What can decrease genetic divergence between two populations?

migration + sexual reproduction

Gene flow

migration and reproduction mediates the exchange of alleles between populations

How long can reproductive isolation take for mammals and birds?

millions of years.

Types of mating systems

monogamy, Polygyny, polyandry

the ______ inbred you are, the ______ homozygous alleles you have

more, more

Malaria is a ....

mosquito-borne disease caused by a unicellular eukaryote: Plasmodium

What is the source for selection and drift to act?

mutations

positive selection

natural selection that increases the frequency of a favorable allele

Balancing selection. Two example types of balancing selection.

natural selection that maintains two or more phenotypic forms in a population. Balancing selection maintains multiple alleles in populations *examples:* negative frequency dependent selection heterozygote advantage

what is a case when balancing selection is conserving diversity

negative frequency dependent selection.

most mutations are ____________ or _____________

neutral, harmful

clutch size

number of offspring produced at each reproductive event

heterozygote advantage. Example.

occurs when heterozygotes have a higher fitness than do both homozygotes sickle cell

parental conflict

occurs when parents have an evolutionary conflict of interest over the optimal strategy for parental care

monogamy

one male pairs with one female Sexual: partners mate with each other exclusively Social: partner pair but may cheat

Senescence

organisms decline in fertility and survival probability as they get older.

What is the Hardy-Weinberg equation?

p^2 + 2pq + q^2 = 1 p = AA q = aa q = 1 - p √p^2

Muller's ratchet

process by which the genomes of an asexual population accumulate deleterious mutations in an irreversible manner

Narrow sense heritability

proportion of the phenotypic variance that can be attributed to additive genetic variance

broad sense heritability

proportion of the phenotypic variance that can be attributed to genetic variance

Promiscuous protein

proteins capable of carrying out more than one function, such as catalyzing reactions of different substrates

Mutations rates are relatively ___________, but since the genome is huge they are ___________

rare, common

selection is not effective at purging ____________ alleles

recessive

Is sickle cell dominant or recessive? what is unique about it in regards to recessive and dominant?

recessive it is dominant in one trait (protection against malaria) but recessive in SS resulting in death. its pleiotropic (a gene that influences many traits)

Vgxe

represents the phenotypic variance due to the interaction between genes and environment

why is sexual selection advantageous over asexual?

reshuffles variance of the genome. much wider distribution of genotypes. more options that natural selection choose from. deleterious alleles can be deleted. "Hitchhiking" of deleterious alleles at other loci can be avoided. Red Queen hypothesis

Frequency dependent selection

selection in which the fitness of a phenotype depends on how common the phenotype is in a population

Phylogenetic species definition

smallest possible group descending from a common ancestor and recognizable by unique, *derived traits* (monophyletic clade)

Cryptic species

some species look almost identical but don't interbreed. They probably look so similar due to recent speciation events.

colonization leads to

speciation

Parapatric speciation

speciation pattern in which populations speciate while in contact along a common border(Some gene flow possible) Due to entering a new niche

Biological species definition

species are groups of interbreeding populations that are *reproductively isolated* from other such groups

General lineage species concept

species are metapopulations (group of different populations) that exchange alleles frequently enough to comprise the same gene pool

Linnaeus believed that? what were some of the problems with this belief?

species were fixed entities established at creation *problems:* Species that don't look like they can reproduce, reproduce. lines between species can be hard to draw.

extended phenotype

structures constructed by organisms that can influence their performance or success Phenotype of one organisms expressed in another organisms.

What are the two components of fitness?

survival and reproduction

phenotypic plasticity

the ability of an organism to change its phenotype in response to changes in the environment. (this is a response of a gene to the environment)

antagonistic pleiotropy

the allele is beneficial under certain conditions but detrimental in other conditions

Neighbor-joining example

the dots represent exactly the same amino acid. The one with the most dots are the most closely related.

Antagonistic pleiotropy hypothesis

the hypothesis that senescence is largely due to the evolutionary accumulation of antagonistic pleiotropic alleles that increase *survival OR reproduction* early in life at the cost of deleterious effects late in life organisms are engaging some of their resources into growth and some into reproduction and by favoring reproduction it has an impact on other somatic function of the organism

posterior probability

the probability that a hypothesis is true after consideration of the evidence

genetic divergence

the process in which *two or more populations* of an ancestral species accumulate independent genetic changes (mutations) through time, often after the populations have become *reproductively isolated* for some period of time.

operational sex ratio

the ratio of male to female individuals who are available for reproducing at any given time. Females get tied up with their offspring for a certain period of time. whereas males can just hit it and go. this causes the male to female ratio to increase. this creates competition and male sexual selection. not all males can mate.

Allele fixation

the removal of all alleles within a population at a particular genetic locus except one. The allele that remains has a frequency of 100%

Fitness? Components of fitness?

the reproductive success of an individual with a particular phenotype *components of fitness*: Survival to reproductive age Mating success fecundity (how well you can make offspring)

Fst = 1

the two populations are very different (they don't reproduce and don't exchange alleles) Variation between population 100% Fst - genetic distance

Fst = 0

the two populations have similar allele compositions (they reproduce and exchange alleles frequently) Variation between population 0%

How do beneficial dominant alleles act? and why?

they quickly increase in frequency but will take a long time to reach fixation. the recessive allele is hidden in heterozygotes Aa since they display beneficial phenotype with only one A

Why can monogamy be beneficial?

to take care of the progeny or to protect each other. Females might also select for males that will contribute to raise the progeny

sexual conflict

traits that confer a fitness benefit on one sex but cost to the other The best reproductive strategy for males can be detrimental to females (or the opposite) Traits coevolve antagonistically

evolution of novel trait in e.coli: citrate metabolism

usually bacteria can't metabolize citrate in the presence of oxygen but the gene got duplicated and the promoter that turns off citrate operon got turned on and can metabolize citrate.

aposematism

warning coloration

epistasis

when one gene locus masks or modifies the phenotype of a second gene locus (this is interaction between alleles)

that fitness equation and the meaning of its variables...

Δp = p x (aA1/ϖ) Δp is the change in allele frequency due to selection p is the frequency of the A 1 allele ϖ is the average fitness of the population (the mean relative fitness) aA1 is the average excess of fitness for the A1 allele

What factors into an organism's *life history*

• Age at first reproduction • number and timing of reproductive • number of offspring produced per event • survival patterns

What does "natural selection is a mechanistic process" mean? (4)

• Doesn't anticipate the future • Not directed toward some goal • Acts on individual phenotypes • Results in changes in populations

What are some constraints on adaptation?

• Laws of physics • Pleiotropy - Single gene affects expression of many traits. Pleitropic genes can't be modified without having consequences on multiple traits (changes are therefore unlikely)

Why do organisms age? (3)

• failure to repair metabolic-related oxidative damage completely • mutations to DNA • Telomere shortening

Assumptions of Hardy-Weinberg Equilibrium

• no selection, • no mutation, • no migration, • large population (infinitely) , • random mating these are rules that are needed to use the H-W Equilibrium. They are theoretical assumptions to analyze allele frequencies and genotypes.