inb 370 exam 3 learning objectives

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what is facultative sexual reproduction?

many plants and animals reproduce sexually AND asexually

t/f: obligate asexual linkages are mostly old and have been around for many generations

false; mostly young & may go extinct rapidly; tippy

sex in eukaryotes is likely _____

ancestral

what are hill-robertson effects?

fate of an allele depends on its genetic background

what is genetic hitchhiking?

allele’s frequency changes due to selection at a closely linked locus

what is genetic load?

reduction in population fitness due to deleterious alleles

how can hill-robertson effects and genetic hitchhiking lead to deleterious alleles remaining in the population or beneficial alleles being purged?

deleterious alleles may be kept if they are in the same genetic background as beneficial alleles

• opposite effect happens to beneficial alleles if it is near a very deleterious allele

what is linkage disequilibrium (LD)?

-0.25 < d < 0.25; statistical measure of how often alleles at different loci co-occur

in general, how does the D statistic between two loci relate to their physical proximity on a chromosome (distance)?

negative linear relationship; D decreases as distance increases

what is clonal interference?

in asexual populations, beneficial mutations “interfere” with each other unless they happen to arise on the same genetic background, while recombination can bring beneficial alleles together faster

what is muller’s ratchet?

• in asexual populations, once the most fit genotype is lost, it’s gone and the ratchet “clicks”; cannot be recovered unless a mutation recreates

• in sexual populations, the most fit genotype can be recreated by recombination, so sex “breaks” muller’s ratchet

why might a deleterious mutation be selected against so late (3)?

1. deleterious alleles increase because they are linked

2. recombination event separates the allele from its background

3. selection can “see” it and act against it (not hiding in a heterozygote, etc.)

what are selective sweeps?

selection causes areas of reduced diversity in the genome because nearby alleles are “swept” to fixation along with the beneficial allele (or swept away with purging of a deleterious allele)

when is sex most beneficial?

when the environment changes & selection comes into play

why might facultative sexual reproduction switch to asexual reproduction?

rapid increase in sex that levels off after a few generations because all beneficial alleles are fixed

what is the arms race & the red queen hypothesis?

constant evolution of two entities to take advantage of each other; must be able to respond to each other to keep up

what is an example of the arms race/red queen hypothesis?

virus and its host; recombination can create new/rare allelic combinations that may fare better against pathogens or competitors, so viruses must constantly be evolving to keep up 

B; lots of sex leads to high recombination and breaks up linked alleles

characteristics of sex in prokaryotes (3)?

1. can also exchange genetic info with other mechanisms then undergo recombination

2. not genome wide

3. generation time is short and can get new genetic information via recombination within a generation (think conjugation, transformation, horizontal gene transfer)

what mechanism of evolution is the most important in the evolution of molecules?

sex & recombination; makes selection efficient & works on alleles independently instead of linked

how did the neutral theory of molecular evolution develop?

• kimura studied dna sequences in horses & estimated a substitution every two years based on fossil record

• too many amino acid substitutions have occurred for all of them to be beneficial

• rates of molecular change are often clocklike → constant accumulation of divergence between species

what is the neutral theory of molecular evolution (3)?

1. most mutations are deleterious and quickly purged (negative selection)

2. beneficial mutations are rare, so won’t be fixed often (can basically ignore them) (positive selection)

3. most mutations that have been fixed between lineages (substitutions) therefore must be neutral and the product of drift

what are pseudogenes?

nonfunctional copies of a gene expected to evolve neutrally since all mutations have the same fitness

• accumulates all the frameshifts, etc; no selective constraints on how to evolve

what is dN vs. dS? which one is more prone to selective pressures?

rate of nonsynonymous vs. rate of synonymous changes; dN more prone to selective pressures & dS doesn’t change aa

what would the dN/dS ratios look like for functional vs. pseudogenes?

functional: dN < dS; lots of synonymous changes while the nonsynonymous changes have to be weeded out

pseudogene: dN = dS; doesn’t matter if the aa changes

what would the dN/dS ratio look like for important genes that are conserved?

dN << dS, even more so than just a normal gene

what types of genes would have the greatest difference between dN and dS?

immune system; changes in response to environment under selection

what does dN/dS < 1 mean as a metric for molecular evolution (3)?

• most mutations are deleterious

• negative (purifying) selection dominates

• most functional genes

what does a dN/dS = 1 mean as a metric for molecular evolution in terms of:

i. mutation benefit

ii. the mechanism of evolution that dominates

iii. types of genes this ratio is found in

• mutations are neutral

• drift dominates

• pseudogenes

what does dN/dS > 1 mean as a metric for molecular evolution in terms of:
i. mutation benefit

ii. type of selection dominating

iii. types of changes getting fixed

iv. fixation pattern

• mutations are beneficial

• positive selection dominates

• more functional changes are getting fixed than expected by change/than neutral allele

• change in aa being driven to fixation faster than neutral mutation

what is the mcdonald-kreitman (MK) test (3)?

• looks at the number of synonymous & nonsynonymous changes both within & among a species

• beneficial changes will spread to fixation quickly, so they don’t appear within species, but appear between species

• more sensitive at detecting positive selection than dN/dS

what is codon bias (4)?

nonrandom usage of codons

• degree of bias depends on expression level of gene 

• codons corresponding to most abundant tRNA are used most (allow for mRNA to be made at a faster rate)

• selection for increased translational speed and efficiency

how has neutral theory of molecular evolution been disproved?

selection plays an important role in molecular evolution, and much of the variation is likely due directly/indirectly  to selection

what is the current status of neutral theory of molecular evolution?

• much variation can also be explained by neutral evolution and drift

• mostly used as a null-model to tell when selection has happened (things predicted from neutral theory as a measure for selection strength)

in a donor/recipient relationship, describe the following:

• altruism

• spite

• cooperation

• selfishness

altruism: -/+

spite: -/-

cooperation: +/+

selfishness: +/-

what is kin selection?

an inclusive fitness where an individual is more likely to act altruistically towards related individuals

what is the equation for Hamilton’s rule?

Br - C > 0; benefit to the recipient times the relatedness between the actor and recipient minus the cost to the actor

what does it mean when Br - C > 0?

an individual should do an altruistic action because the benefits of doing it outweigh the costs

what are the three properties of a greenbeard allele when it comes to identifying kin?

1. allele that produces a phenotype

2. allele allows for recognition of other phenotype in others

3. allele initiates altruistic behavior towards them

what is the idea of a selfish gene?

you are just a vehicle for your genes, and genes don’t always get along

selfish genes - enhance their transmission at the expense of other gene

what is the selfish mitochondria?

mitochondria is inherited maternally, so it will select for daughters & some encoded alleles will result in low son fitness but are good for daughters

• mitochondria have their own genomes and the genes that are passed down are not always in the best interest of the nuclear genome

what is eusociality?

foregoing reproduction entirely to help someone else, such as a queen, reproduce

what is the haplodiploidy hypothesis, & is it largely supported?

sister are more closely related than they would be to offspring, so there’s higher fitness for helping raise sisters than making your own offspring (haploid = male, diploid = female)

• largely refuted

what is the monogamy hypothesis, & is it largely supported?

if you know your siblings are full siblings, they are as closely related to you as your own offspring, so it makes sense to help parents reproduce due to having similar relatedness

• similar problems as haplodiploidy

how is altruism explained by the ecology & life history hypothesis?

all eusocials have “fortress” nests and larvae that require lots of care. because it’s hard to go about it alone, allele that causes fortress building & is advantageous for all living in the nest is selected for

what is the most widely held hypothesis for explaining altruism in nature?

ecology & life history

what is reciprocity?

non-kin selection with punishment, where the moochers get punished/kicked from the social group

how does hamilton’s rule explain spite (2)?

• if both B (hurts recipient) & r (in a relative sense) are negative

• if it’s better for the average to reproduce than the recipient

what are some controversies surrounding hamilton’s rule (3)?

• eugenics

• lack of natural selection in modern humans

• does society determine what a beneficial allele is?

what are the three main species concepts?

phenetic, evolutionary, biological

what is the phenetic species concept?

• species have a particular type with key/defining features

• modern approaches use morphometrics, many measures & PCA clustering approaches

what are the downsides to the phenetic species concept (2)?

• how different do species have to be?

• hard to find objective criteria for key features

what is the evolutionary species concept?

• species is a lineage of ancestral descendant populations which maintains its identity from other such lineages & has its own evolutionary tendencies & historical fate

• focused on the products of evolution

t/f: the evolutionary species concept describes a monophyletic clade

true

what is the biological species concept?

species are groups of actually or potentially interbreeding populations, which are reproductively isolated from other such groups

what are three problems with the biological species concepts?

1. doesn’t apply to asexual species (prokaryotes don’t have sex but do exchange dna)

2. “potentially interbreeding” is hard to evaluate

3. hybridization between species to different degrees, but is much more common than originally thought

are hawaiian shrimps distinct species by the evolutionary/phylogenetic species concept?

several distinct genetic lineages across the island, some of which will never hybridize (good species)

are hawaiian shrimps distinct species by the phenetic species concept?

morphologically indistinguishable or very similar (not good species)

are hawaiian shrimps distinct species by the biological species concept?

will reproduce with each other somewhat, but it’s unclear about later generations and in the wild (not sure)

speciation exists on a _____ (1 word)

continuum

what causes reproductive isolation (2)?

prezygotic & postzygotic barriers

what are prezygotic barriers?

features preventing transfer of gametes between populations

what are the five prezygotic barriers?

temporal isolation, habitat isolation, behavioral isolation, mechanical isolation, gametic isolation

what does prezygotic barriers encourage?

assortative mating

what is temporal isolation?

mating happens at different points in time for different species. due to the lack of overlap in mating seasons, they won’t reproduce

what is habitat isolation?

reproduction between two species not happening due to not being in the same place/habitat

what is behavioral isolation?

ie sexual selection; different mating behaviors lead to species isolating and mating among each other

what is mechanical isolation?

two species physically cannot have sex

what is gametic isolation?

two gametes can physically interact with each other but the sperm cannot fertilize the egg or get its dna in the egg

what are postzygotic barriers?

a zygote is created but has relatively low fitness compared to the parental

what are dobzhansky-muller incompatibilities?

epistatic interactions between two genes that act fine in each species, but in hybrids, the genes don’t interact properly

what are magic traits & genes?

phenotypes/genes that cause immediate speciation through divergent selection & reproductive isolation

which type of barriers are most important?

prezygotic barriers will preempt (natural) postzygotic ones, but the pre/post barriers are not mutually exclusive

what is the grey zone of speciation?

species can be distinguished between having

i. high migration & low synonymous substitution rates or

ii. low migration & high synonymous substitution rates, but there is a grey area for species that have a medium area of both

what is allopatric speciation?

diverging populations are entirely geographically separate

what two types of allopatric speciation are there?

vicariance, dispersal

what is island endemism?

a form of dispersal in peripatric speciation, where a random founder event occurs and the large/small population don’t interact anymore

what factors influence allopatric speciation?

geography; how species diverge will be driven by drift & selection (population size & environment are important!)

what is peripatric speciation?

a founding event occurs in which a smaller population migrates away from a larger population and is isolated on an island, and results in speciation over time

what is sympatric speciation?

diverging populations remain in the same location

how common is sympatric speciation?

not uncommon as previously thought but harder

in what ways could sympatric speciation manifest in (2)?

resource/host switching, especially if a parasitic species; mating time

what is parapatric speciation?

diverging populations are right next to each other and may interbreed in the middle

what are hybrid zones?

areas where two species may interbreed and produce hybrids

what type of species show more prezygotic isolation?

sympatric (overlap & share the same range)

what is hybrid speciation?

hybridization happened in the distant past OR it is ongoing& hybrids are not going back to their parents, instead are reproducing within its own population

how can reproductive isolation be reinforced between two species?

when two species come back into contact with each other, reproductive isolation can be reinforced via low fitness hybrids or prezygotic barriers