EVE 100 Midterm 2

Dominance

• describes the effect of an allele on a phenotypic character when it is paired with another allele in a heterozygote condition —> higher fitness

• takes longer to reach fixation since the recessive alleles hide in the background

• Advantageous dominant alleles increase in frequency more rapidly since it is expressed in both homozygous and heterozygous genotypes

Recessive alleles

• Hide behind the dominant allele even when advantageous

• advantageous recessive alleles take a long time to increase in frequency since when at lowe frequencies, it is present in the heterozygous form → invisible to selection

• Advantageous recessive alleles can reach fixation since they hide in the background

• After the advantageous dominant allele attains high frequency, the alternative disadvantageous recessive allele is slowly eliminated → rare recessive alleles occur mostly in heterozygous forms -→ invisible to selection

Fitness

• Measure of the “relative success of a population, genotype, and alleles

• measures how often thinsg reproduces

• defined by the probability of survival and the avergae number of offspring

• best applied to a set of entities → all individuals in a population or individuals with a given genotype

• MOST fit genotype = relative fitness of 1

• LEAST fit genotype = relative fitness of 1-s (s = selection coefficient)

• HETEROZYGOUS genotype = relative fitness of 1- hs (h - dominance coefficient) → determines how far the heterozygous genotype is from the homozygous phenotypes

  • h = 0 → A1 is dominant

  • h = 0.5 → A1 is additive

  • h = 1 → A2 would be dominant (A1 is recessive)

Finding relative fitness

• absolute fitness/the highest absolute fitness —> needs to be ain a decimal form less than or equal to 1

Selection coefficient

• finds how fit something is from the MOST fit organism

  • most fit h and s coefficients help us understand how dominance affects fitness

Decent of modification

genetic changes in populations over timeM

Mutations

• Mutation rates per base pair are low —> but the number of new mutations per individual may be large

• humans have a mutation rate of ~2.5 × 10^-8 mutations per generation → BUT the number of new mutations PER individual may be large

  • Humans have around 160 new mutations per transmission (each of us has 160 unique mutations that other people do not have)

• Mutations are random but common

• Mutation types:

  • single base pair mutations

  • translocations

  • deletions/duplications

  • whole genome duplications

  • inversions

  • transposable elements

  • retrovirus insertions

  • chromosome fission and futsion

• Mutations can either be beneficial, deleterious or neutral —> they can also have small or large effects —> they can also be dominant or recessive

• most mutations are directly selected out of a population

Distribution of fitness effects (DFE)

• this looks like a continuous ditribution

• most effects of mutations are small —> most new mutations reduce fitness ( a little)

• fitness effects of mutations —> less than 1 = deleterious and decrease fitness and fitness greater than 1 are probably beneficial mutations

  

Heterozygosiry = H

• this is the fraction of sites that are heterozygous → more heterozygous genotypes = higher heterozygosity

• humans have a heterozygosity of 0.1 → therefore diversity within humans are low

• higher heterozygosity = lower offspring (ex., hybrids survive but rarely reproduce)

3 reasons for how genetic and phenotypic polymorphism is maintained

→ polymorphism: different phenotypes = different genotypes

1. balancing selection: selection sometimes acts to maintainvariation

2. Mutation selection balance: the rate of mutation and the rate of selection are both similar emough that the mutations are not gotten rid of due to the rate of new mutations being too fast

3. mutation-drift balance ( neutral theory): genetic drift

Balancing seelction

• when selection can maintain balanced polymophism in a population

  1. overdominance or heterzygote advantage: Heterozygotes for an allele have a higher fitness than either homozygote

  2. negative frequency-dependent selection: selction favors rare morphs —> states that it is better to be different → this increases trait diversity

  3. spatially or temporally variable selection: variation in selection across space or time maintains genetic variation

Overdominance and Underdominance

• Best genotype = combination of 2 different types of alleles

• over mean fitness when there is an intermediate frequency of alleles → p is in the middle → this maintains polymorphism for more favorable genotypes → heterozygote is the BEST

  

• Underdominance: when the heterozygote individual is the worst → the AA or aa genotype is the best

• Example: sickle cell anemia → the patient is less susceptable to malaria when they have a heterozygous genotype for those with mild anemia (Ss = mild anemia) → (SS = sickle cell anemia) → thisis because the RBCs have shorter life spans → this gives the plasmodium less time to reproduce

  If a heterozygote has the HIGHEST fitness = heterozygote advantage = overdominance

Negative frequency-dependent selection

• genotype/phenotype has a fitness advantage when it is rare, but its fitness decreases as it becomes more common

• fitness is negatively correlated with frequency → lower frequency = higher fitness

• rarity is an advantage

Spatially and temporally variable selection

• variation in a phenotype of genotype is maintained by variation in selection patterns across environments → one allele has a fitness advantage in one environment while another allele has a fitness advantage in another environment

• e.g. Bird beak shapes → change yearly based on drought → smaller or bigger → adapt to time and environmental conditions

• spatial and temporal selection can occur at the same time

• local adaptation = a form of variable selection

Things that determine the amount of variation in a population

• mutation selection balance

• mutation and inbreeding (gene flow) between populations

Ge

Gene flow

• homogenizes allele frequencies UNLESS selection prevents it → if it does then we get a migration selection balance → how gene flow (migration) and natural selection interact → equilibrium that forms when:

  • Migration brings alleles into a population → continuously introduces new variants to a population

  • Selection works against those alleles

  • two forces balance out so the allele stays at an intermediate frequency instead of being lost or fixed

• If selection eliminates deleterious variants, variation can be maintained

  

Mutation selection balance

• mutations continuously introduces new variants to a population → if selection eliminates the deleterious mutations → variation can be maintained

• mutation = MAIN SOURCE or genetic variation

• stronger selection = rate of taking away deleterious variatns in the population is faster

• Weaker selection = rate of taking away deleterious variants in the population is slower

Mutation selection equilibrium

• Deleterious alleles that dont have a too strong of an effect in the heterozygote can be maintained at low frequenes in the population → recessive deleterious alleles

1. Mutation introduces new variation into a population

2. Random genetic drift determines heather a neutral allele will be fixed or (usually) lost

3. At equilibrium, there is a balance between mutation and genetic drift

Inbreeding depression

• reduces fitness of inbred individuals due to deleterious mutations

• reduced fitness in offspring that results from mating between relatives.

• more recessive mutations should segregate at high frequencies under mutation-selection balance

1. Expression of deleterious recessive alleles

   • Normally, recessive harmful mutations are “hidden” in heterozygotes.

   • Inbreeding makes offspring more homozygous, so these bad alleles get expressed.

   • Example: genetic disorders in royal families with lots of cousin marriages.

2. Loss of heterozygote advantage (overdominance)

   • Some genotypes (heterozygotes) are fitter than either homozygote

   • nbreeding reduces heterozygosity, lowering this benefit

• The closer the parents are to each other (genetically) → the lower of the mean lifespan of children → this is due to everyone having these recessive negative deleterious mutations hiding in our genomes under our dominant alleles

Polymorphism

1. Overdominance 

   1.  Having A2 always better than A1 → directional selection

   2. Overdominance: heterozygous genotype is the most fit → aka heterozygous advantage

   3. Eg. sickle cell anemia → maintains variation of an allele in a population

2.  Mutation - selection balance → reasons we might see variation in a population

   1. “Giant sink of all of our alleles in a population” 

      1. → lots of allele variation = full sink

      2. → little allele variation = empty sink

      3. Need to induce mutations (faucet → fills the sink up)

      4. New alleles → everyone looks more different

      5. Selection: can remove alleles in our population (drain) → “directional selection” that is natural selection

      6. We can get an equilibrium of our variation → called the Mutation Selection Equilibrium

      7. We need to know μ: rate of mutation

      8. s = selection coefficient

      9. h = dominance coefficient

3. q(eq) = mutation rate (μ)/ ((selection rate(s) * dominance coefficient (h)))

4. Balance between mutation → Genetic drift

• we dont believe in selection → we believe in a more random process where we take variance outside of the population

• instead of selection we get drift

• mutation drift equilibrium

  • Ne = (N = number of things we see → E = means effective)

  • Ne = effective population size → if mutations add things to a small population → “size of an idealized population (one that follows Hardy–Weinberg assumptions perfectly) that would experience the same amount of genetic drift, inbreeding, or loss of diversity as the real population”

  • larger population size = more even probability of allele frequency

  • genetic drift → more effective in smaller populations

• neutral alleles are alleles that don’t impacts fitness → synonymous mutations and codons → change in third codon doesn’t change the fitness of an organism

• selection

Neutral theory of molecular evolution

• most mutations are deleterious and are lost immediately

• Most observed molecular polymorphism and genetic substitutions are neutral → consistent with high levels of genetic polymorphism and molecular clock

• Frequency of neutral alleles are controlled by:

  • Mutation rate

  • Genetic rate

Mutation - selection balance

• occurs when new mutations introduce deleterious alleles at the same rate that natural selection removes them

• new mutations create new alleles

• selection acts to remove deleterious alleles

• Definition: Frequency of deleterious alleles is controlled by:

  • mutation rate (μ or aka u)

  • selection coefficient (s) and dominace coefficient (h)

• qeq (equilibrium frequency) = u/(sh)

Mutation-drift balace (neutral theory)

• most mutations are deleterious and are lost immediately

• Most of the observed molecular polymorphisms (like enzyme amino acid sequence variation) and genetic substitutions are neutral

  • claimed to be consistent with high levels of genetic polymorphism and the molecular clock

Mutation drift quilibrium (MDE)

1. Mutation introduces new variation into a population

2. random genetic drift determines whether a neutral allele will be finzed or (usually) lost

3. at equilibrium, there is a balance between mutation and genetic drift

   • mew meutral alleles arise continually by mytation → many are usually lost by genetic drift while others drift to higher frequencies and persist for some time in a polymorphic state before they are lost or fixed

→ definition: under the MDE, the amount of variation introduced by mutation = the amount of variation lost due to drift → this is dependent on:

• Ne = effective population size

• Myu = mutation rate to new neutral alleles

• at equilibrium under MDE → heterozygosity = H = 4Ne*(myu)

→ in larger populations:

1. the rate of genetic drift is slower

2. The input of new mutations is higher

3. the level of neutral polymorphism is higher

Hardy-Weinberg assumptions

• diploid secual population with dicrete generations

• allele frequencies equal in both sexes

• mendelian segreghation of alleles

• random mating

• no natural selection

• no mutation

• no migration

• large population sizes → no drift

Genetic drift ( and selection )

• These are the two most important forces affecting allele frequency changes in a population

• genetic drift: fluctuations in allele frequencies that occur by chance → particularly in small populations as a result of sampling error

  • It can also change the frequency of neutral alleles (alleles with no effect on fitness)

  • can change the frequency of alleles under selection only if selection is WEAK

  • Changes by genetic drift are random in direction

  • results from a random sampling error → can be thought of as randomly sampling gametes to form the next generation → allele frequencies increase or decrease by chance

• rate of genetic drift is higher in smaller population → in large populations they drift slower

• droft leads to a loss of heterozygosity as it causes loss or fixation

• drift is higher when the variance for reproductive success is higher

Neutral allele

• an allele with no effect on fitness compared to other alleles at that locus

• only 2% of our genome encodes for proteins

• changes outside of exons (coding regions) can be completely neutral if they do not disript gene regulation

• examples

  1. synonymous change in a codon → the a.a doesnt change since the third base in a codon are usually neutral → the are more changed by drift than selection

  2. non-synonymous change → replaces one amino acid with a functionally similar one → produces a large change in a phenotype oin which selection no longer acts → can cause pseudogenes

Non-coding regions that make up most of the genome

• RNA genes

• pseudogenes

• mobile genetic elements

• repetative DNA

Population bottlenecks

• thisis when a popualtion size is dramatically reduces

  • can be caused by a widespread outbreak or diesease, high hunting pressure, extreme natural evcents, habitat shifts

• this can be a short-term reduction in population size with long-term effects on allele frequencies → rare alleles are likely to be lost

• some rare alleles can by chance, drift to high frequency within the population

• lowers heterozygosity

• this is a form of inbreeding

Inbreeding

• two alleles are identical by decent (IBD) if they are the same alleles due to inheritance from a very recent shared common ancestor

• inbreeding coefficient (F): thisis the probability an individual inherits two alleles identical by descent at a locus

  • F = 1 → completely inbred

  • F = 0 → completely unrelated

  • F = 0.25 → siblings

  • F = 0.125 → ½ siblings

  • F = 0.0625 → first cousins

  • F = 0.0156 → second cousins

• F = proportion of the genome that is homozygous due to inbreeding

• consequence of inbreeding:

  • The frequency of homozygotes is higher

  • The frequency of heterozygotes is lower

Effective population size

Ne = effective population size = the number of individuals in an idealized population that would produce the same amount of genetic drift as in the real (census) population

• Ne«N (census population size)

• The rate of genetic drift/ loss of heterozygosity is increases if:

  • The population often crashes to a small size

  • there is high variance in reproductive success among individuals

• Factors effecting population size

  • variation in the number of progeny among males, females, or both

    • sex ratio away from 1:1

  • Natural selection (variance in reproductive success)

  • inbreeding

  • fluctuations in population size

Probability of fixation for a new allele

• a new allele has just arisen by mutation that has a frequency (p) of: 1/2N

  • This is the probabilty that the new allele reaches fixation

  • fixation is when the alle frequency p = 1

  • loss is when the allele frequency p = 0

• Larger populations = longer time to reach fixation

Substitution rate per generation

substitution rate per generation = number of new mutations per generations * the chance of a mutation fixing

→ 2N*(myu) *(1/2N) = myu per generations → we can eliminate N → therefore mutation is independent of population size

Levels of contraint

• neutral theory claims that most new mutations are deleterious and are lost immediately → only neutral mutations contribute to substitution

• neutral mutation rate → myu - myu(t)(1-C)

• consistent with neutral theory → slower rate of substitution at more constrained sites

• contraint (C): the proportion of mutations that are too deleterious to contribute to polymorphism or substitution

• therefore: 1-C = the proportion of mutations that are neutral → in regiouns like pseudogenes → we expect the contraint to be low (1-C = ~1)

• dN = non-synonymous substitution/site = C

• dS = synonymous substitution/site = 1-C

• EXPECTED dN/dS for a typical gene = less thjan 1

  • A SLOWER rate of substitution at more CONTRAINED sites is seen

• effective population size will largely determine the levels of contraint

Nearly neutral alleles

• chance (genetic drift) plays a role in the fate of all allleles but matters more for neutral or very near to neutral alleles

• alleles that aren’t strictly neutral, but their effect on fitness is very small, so whether they behave like neutral alleles depends on population size

• Selection is weak: These alleles have tiny positive or negative fitness effects.

• Drift matters: Random genetic drift can override weak selection in small populations.

• Implication for molecular evolution:

  • Some slightly deleterious alleles can fix in small populations, contributing to molecular change.

  • Explains why the molecular clock isn’t perfectly constant across all species.

The dN/dS ratio

• most genes will be evolving slowly since they are under contraint

• expected dNdS for a gene encoding an uncontrainted protein = 1 (number of non-synonymous = number of synonymous substitutions)

• genes under consistent directional selection have a dNdS GREATER than 1 → this is rare → this is positive selection for a gene

• most non-synonymous mutations are deleterious and removed by negative selection

• larger Ne = selction is more effective at removing “nearly neutral” alleles ( weakly deleterious alleles) so the dN/dS ratio would be smaller

• only calculated for CODING REGIONS → need to use a condon chart to determinine they are synonymous or non-synonymous

• dN/dS → typically much smaller than 1

C-value paradox

c-value paradox: no direct correlation between phenotypic complexity of eukaryotic organisms and the size of the genome (larger genome size does not mean more complex)

• There is no consistent relationship between the genome size (C-value) and the organism’s complexity

Transposable elements

• this is a short DNA sequence that makes copies of themselves (they act like DNA parasits -→ AKA selfish DNA)

  • (a and b) DNA mediated transposition: transposition to a target site → this is followed by a loss or retention of the transposable elelment at the donor site

  • ( C ) retrotransposition: the element is transcribed into RNA which is then reverse-transcribed in to cDNA → the cDNA copy is either inserted or copied into the target site

  • TEs are not always neutral → they can lead to gene reverse transcription and random insertion

Neutral theory of genome evolution

• theory: genetic drift may be important in shaping genome features → Repetitive DNA, introns, TEs, and large tracts of non-coding DNA → may have accumulated not because of adaptive processes but rather the inability of selection to work

• smaller organisms = large Ne

• larger organisms = smaller Ne

• lower recombination rate and higher drift may lead to larger genome sizes → Multicellular organisms more likely to

  accumulate repetitive DNA (introns, transposable elements, and large tracts of non-coding DNA) through genetic drift →Transition to multi-cellularity led to

  - lower recombination rates

  - stronger drift

→ This increases the likelihood of mildly deleterious mutation accumulation → This reduces the efficacy of selection

→ Endosymbiotic bacteria accumulate mildly deleterious mutations

Recombination rate

• larger number of chromosomes = higher recombination rate

• lower number of chromosomes = lower recombination rate

• multicellular organisms are more likley to accumularte repetative DNA

  • transposable chromosomes have a higher recombination rate

Orgins of new genes

• histones: proteins with DNA wrapped around them

• the regulatory regions is upstream of the coding regions

• alternative splicing: different versions of our mRNA

-→ evolution of new genes is due to nuplication and co-option opf whole developmental pathways

Gene duplication

• This is how novel genes arise

• Subfunctionalization: functions become subdivided among copies

• Neofunctionalization: novel functions arrive

• orthologous genes: homologous genes in two or more species —> split copies of the duplicate genes

• paralogous genes: homologous genes (gene copies) that are related by gene duplication → 2 new duplicated versions of genes

→ two major mechanisms of gene duplication:

1. unequal crossing over: chromosomes are incorrectly alligned → this leads to tandem duplicates

2. retrotransposition of mRNA → loss of introns in the copu

→ most duplicated genes are deleterious and so are non-functional (dead on arrival)

• changes in gene dose

• retrotransposition

→ color blindness - result of gene duplication

→ majority of gene duplications are lost → only a small fraction that reach fixation are quickly pseudogenized

→ most gene duplicationsa re selected out of the population immediately lost and only a SMALL amount stick around

• Paralogs that are not lost and sbsequentially diverge may have 2 fates:

  1. suibfunctionalization

  2. neofunctionalization

Subfunctionalization

• both paralogs may diverge in sequence and in function

  • both paralogs may lose complementary components of the ancestral function → this may reduce the pleiotrophy of both paralogs

Neofunctionalization

• the second copy has a totally new function

• this is an example of convergent evolution

Cop

Copy number variation

• a type of genetic variation where sections of the genome are repeated or deleted, leading to differences in the number of copies of a particular DNA segment between individuals.

Gene Chimerism

• happens when a single gene (or transcript) is formed from two originally separate genes or gene fragments → encodes a hybrid protein with domains from different sources → It can be beneficial in evolution (new functions) or harmful in disease (like cancer fusions)

• exon shuffling: new chimeric genes originate through novel combinations of exons from non-homologous recombination between genes

• domain: small segment of proteins with specific functions

• hypothesis: many genes evolved though exon shuffling between genes

• Horizontal gene transfer: genes transferred from distant lineages

Inversions

• happen when a large chunk of the chromosom gets swapped or flipped → same gene but the orger is inverted in the chromosome → this creates new functions and regulatory programs → help lead to different phenotypes, mating, and bahavior (chromosome loops happen too)

  • example: bird ruff

Selective sweep

• definition: positive selection acting to fix a newly arisen advantageous mutation

• genetic diversity is reduced at the site of an advantageous mutation that have undergon selective sweep

• three factors that interact to determin ethe amount by which diversity is reduced at or near a selection locus:

  1. strength of selection

  2. recombination rate

  3. the time since the selective sweep

1. The selection sweep:

   • stronger selection makes the stretch of diversity wider

   • stronger selection leads to a reduction in diversity over larger genomic regions (makes the stretch of reduced diversity wider)

   • How much the beneficial allele increases fitness compared to alternatives

   • Strong selection (large s): allele rises to fixation fast → sharp reduction in genetic diversity

   • Weak selection (small s): allele rises slowly → more time for recombination and drift

2. Recombination rate:

   • Lower recombination leads to a reduction in diversity over larger genomic regions

   • haplotype: a set of alleles that physically link on a chromosome

   • new beneficial allele arises on haplotypes → this happenes to be a rare recombination → after the sweep, genetic variance is still reduced but not as strongly

   • heyterozygosity is reduces in regions of low recombination

   • How often crossing-over breaks linkage between the selected allele and nearby neutral alleles

   • Low recombination: large “hitchhiking” region → big chunk of genome around the beneficial allele shows reduced variation

   • High recombination: sweep effect is localized → only the immediate neighborhood of the selected site shows reduced diversity

3. Time since the selective sweep

   • Definition: How long ago the beneficial allele fixed

   • Effect on sweep:

     • Recent sweep: strong signature remains → reduced diversity, extended haplotype homozygosity (long stretches of identical DNA).

     • Old sweep: recombination and new mutations restore variation → signal becomes faint or erased over timeMutation arises -< advantageous mutation increases in frequency → later it is fixed and all chromnosomes coalese soon after it appears

   • This is the patterns of how many individuals/populations carry the mutation and the patterns of genetic linkage to indicate the history of that sweep

—> summary:

• Strong selection = faster, more dramatic sweep.

• Low recombination = larger genomic region affected.

• Recent sweep = stronger detectable signal.

Hitchhiking effect

• This is the indirect impact of selection on patterns of linked diversity

• a new beneficial mutation arises on a particular genetic background (haplotype) among chromosomes in a population and after a few generations → the most fit genotyupe has the most offspring → happens if there is no recombination

• reduces genetic diversity

• One beneficial afllele can sweep to fixation

• When a beneficial allele increases in frequency due to positive selection, the nearby neutral (or even slightly deleterious) alleles that are physically linked to it on the chromosome also rise in frequency → carried alomg the ride

• Creates long blocks of haplotype homozygosity

• Creates long blocks of haplotype homozygosity

Soft Sweeps

• maintains genetic variations

• beneficial allele is present in multiple copies in the population before selection

•  a few mutations that are close to each other and are both beneficial, and it takes a lot of time for these beneficial mutations to recombine before they add a lot of fitness to the genotype = more diversity in the genotypes that get swept 

Hard sweeps

• A single new mutation arises that is beneficial and sweeps to fixation

• neutral alleles dragged to fixation → the new advantageous mutation sweeps through a population very quickly → by the end of the sweep, everyone single individual has the exact same mutation
  

  

Background selection (reverse hitchhiking)

• decreases neutral genetic polymorphism

• the reduction of genetic variation at neutral sites due to purifying (negative) selection removing deleterious alleles from the population

• decreases genetic diversity

• stronger selection leasds to reduction in diversity over larger genomic regions

Gene Flow

• this is the mix of alleles from different populations (aka migration)

• new alleles are introduced into the population

• homogenious allele frequencies across populations

• results from dispersal = the movement of individuals and/or gametes

→ measuring gene flow:

• if populations are discrete → m = migration rate = the fraction of individuals in a population that are migrant

→ how gene flow homogenizes allele frequencies:

• Change in frequency = migration rate (m) (frequency in source population → where the migrants come from (pm) MINUS the frequency in the the present population → where the migrants have gone to (p))

• new p = present population MINUS the change in p

B

Barriers to gene flow permit diffrientiation (and drift)

• lower rates of miigration and/or smaller populations sizes increase drift rates

• Fst → measures genetic diffrientiation among populations → if Fst is higher → then there is MORE genetic differentiation among populations (ranges from 0-1)

• Fst = 1 → a lot of genetic variation

• Fst = 0 → no genetic variation between the 2 population (more similar)

• used to identify genes underlying adaptive traits

• this leads to Isolation by distance: Fst increases smoothly with physical distance between populations → further away means less likely to be more genetically related higher Fst value (Fst value is porportional to the distance → higher Fst = more distance)

-→ Isolation by distance (IBD) = MAIN driver of differences between human populations

Linkage disequilibriums (LD)

• when an allele at one locus is found together with an allele at a second locus in a population more often than expected by chance → no independent assortment → occurs when alleles at two (or more) loci are associated more (or less) often than expected by chance → knowing the allele at one locus gives you information about the allele at the other locus

• LD is influenced/caused by:

  • Recombination: breaks down LD over time → the higher it is the faster LD erodes → takes more than 1 generatrion

  • Selection: can increase LD if certain allele combinations are favored.

  • Genetic drift: random sampling can create or maintain LD in small populations.

  • genetic hitchhiking: may lead to LD

  • non-random mating: can maintain LD

• Heterostyly prevent inbreeding

Linkage equilibrium

alelles are inherited independently

Sexual recombination

• asexual → no recombination

• sexual → with recombination

What is sex?

• sexual reproduction is the fusion of 2 gametes and the subsequent segregation of chromosomes by meiosis

• usually accompanied by recombination

• it is very diverse:

  • hermaphroditic (can change to male or female sex )

  • sequential hermaphroditism (male to female)

  • cleisstogamous

  • conjugation

High costs of Sex

1. finding a mate: energetically costly and dangerous (STIS and vulnerability)

2. can break up winning genotypes →recombination can make new combinations of alleles that are worse or bad

3. two fold cost of sex →

   • sexual organism produce both males and females → only females produce offspring

   • ASEXUAL organisms only produce females → every offspring can reproduce → many reproducers

4. Cost of males: sexual organisms pass on ½ of their genome

   • In sexual populations, males don’t produce offspring themselves, so half the population (males) is not directly contributing copies of their genome to the next generation → every individual reproduces, passing on their entire genome

   • asexual organisms pass on whole genomes → genome fully inherited

   • in sexual populations, genes are diluted

Asexual reproduction

• colonal reproduction may only last for a few generations

• asexual species are associated with invations → Reproductive advantage (no mate needed) → A single individual can establish a new population because it doesn’t need a mate to reproduce → causes rapid population growth

• the entire genome has the same gene tree and is in LD since there is no recombination and they got their genome from colonial inheritance → high LD

Advantages of Sex

1. new combinations: suffling of alalles during recombination creates novel genotypes → some may be asaptive

2. efficient selection: recombination breaks up LD between beneficial and deleterious alleles

3. combine beneficial mutations: recombination allows beneficial; mutations to be combined ina single individual→ in asexual reproductionm the alleles are in compettion

4. Removed deleterious mutations: recombination allows deleterious mutations to be removed

→ advantage to sex = RECOMBINATION!!

Disadvantage to asexuality

1. asexual species accumulate deleterious mutations

   • hitchhiking of deleterious mutations

   • due to mullers ratchet

2. asexual species adapt slower

   • forced to fix advantageous mutaions sequentially

   • creation of novel haplotypes in asexuals is limited by the rate of mutations _> makes it hard to keep pace with rapidly evolving pathogens (red queen hypothesis)

Muller’s Ratchet

• talks about mutation accumulation → ONLY works in asexual organisms

• in asexuals → process in asexual populations where deleterious mutations accumulate irreversibly over generations

• no recombination → once the best or “least mutated” genotype is lost by genetic drift → you cannot recreate it or get it back

• this lowers the mean fitness

• in sexual organism → mullers ratchet is avoided since recombination can reform the haplotypwe that lacks deleterious mutations

• Experiemental evidence for the accumulation of deleterious mutations in asexual populations → yeast mutation trajectories

  • Sexual yeast removed deleterious mutations and only the beneficial alleles made it in the population

  • Asexual organisms accumulate more deleterious alleles

    • Higher number of dN/dS

Colonial interference hypothesis

• without sex/recombination → selected alleles must fix sequentially

• WITH sex/recombination → selected alleles can fix simultaneously

• the max rate of adaptation is limited in asexual specieies

• In asexual species: combinations of alleles are not formed until a second mutation occurs in a lineage that already has a first mutation

• in sexual populations: independent mutations are brought together un a lineage more rapidly by recombination → adaptation is more rapidly achieved

The red queen hypothesis

• to stay the same fitness you need to be constantly adapting to the changes in your environment → recombination allow sexual species to evolve more rapidly to resist parasites

• Sex is an advantage in constant co-evolutionalry arms races between hosts and parasites

• Arms race with parasites/pathogens

What are sexes

• anisogamy: gametes of different sizes

• male: small and mobile gamtes

• females: larger and less mobile gametes that provide maternal provisioning (nutritional input)

→ why have seperate sexes arose?

• selection for specialization

• inbreeding avoidance

• secondary sexuyal traits → showy or exagerated traits

Sexual selection

• diffferences among individuals in their reproductive success causes competition for access to mates or fertilization opportunitues

• fitness = fucunbdity * viability

  • diffrient traits or selective pressures trhat uncrease fucundity

Sexual dimophism

• viability selection may favor the reduction of showy traits in both sexes → but sexual selection can favor a stronger increase on one sex

  • exagerated traits = better reproductive success → can find mates better

How sex is determined

• some genes have hermaphrodites

• haploid, diploid

• most plants are hermaphroditic and dont really have a sex determination system

• sex determination = involves genes and the environement and also the [hysiology (hormones)

• one chromosome may be reduced in size and may not undergo recombination → gets very small

• Heteromorphic sex chromosomes have evolved independently many times

How the evolution of sex chromosomes work

1. they are apart of ancestral autosomes

2. they evolve a sex determining locus

3. spression of recombination between neo-X and neo-Y

4. degeneration of neo-Y due to muller’s ratchet and hitchkling of deleterious alleles

Sexually antigonistic allele

• this is an allele that has a benefit for one sex and cost for the other

  1. sex determining allele arises

  2. recombination between sexually antagonistic allele and male-determining allele lowers fitness

  3. selection for recombinmation is supressed between these loci

  4. this leads to shutting off recombination and no means that selection of proto-Y no longer recomines

  5. this leads to the degeneration of the Y sex chromosome and the accumulation of repeats and transposable elecments

  • old chromosomes can be longer due to TEs

Evolutionary strata

• specific chunks of our X and Y chromosomes stopped recomning due to differnt inversions and transpositions at specific times in history of our genus and species

  • most decay chromosome size = oldest strata → inversion of the Y chromosome

  • halting recombination leads to the decay of y chromosomes

  • Inversions can lead to the sudden reduction of recombination

Bateman gradient

• used to measure the strength of selection

• fertility gradient of multiple matings can differ

• this tells us the variation between individuals in males and females

• thisalso tells us the selection gradient between fertility and number or mates or mating events

• and tells us the variance in reproductive success and how it can differ between species

• Bateman gradient measures how strongly an individual’s reproductive success increases with the number of mates

• males usually have a steeper gradient slope since → stronger sexual selection:

  • Males: Reproductive success increases steeply with number of mates.

    • Each additional mating can directly add more offspring (since sperm is cheap and plentiful).

  • Females: Reproductive success increases much more slowly (or not at all after the first mate).

    • Egg production is limited, so having more mates doesn’t usually give more offspring.

Evolution for sexual dimorphism

• females are more showy

• males are more choosy

• males suffer less by mating with an inappropriate female but females’ fitness is significantly lowered if they mated with the wrong male since their developing sygot will almost always impacts the female parent fitness

• maternal parent prodive more or most of the care for their offspring

Measuring difference in slection pressures

I = the opportunity for selection → differnce of variance in fitness (number of offspring) between in males and females (males MINUS females = difference or change in these 2 measurments) → used to decide who has more variance in the offspring they have

• males often have great variance in reproductive success

• when males take care of their offspring then the females are more showy ( not very common but is still present)

Why it pays to be showy

1. intrasexual selection: competions between individuals of the SAME SEX for mating and fetelization opportunities →WITHIN one sex

2. intersexual selection: selection due to the choice by the OPPOSITE SEX → BETWEEN

Intrasexual selection

1. intrasexual selection: often male-male competitions

2. post copulatory intrasexual selection:

   • adaptations to ensure fertilization

   • removing rivals sperms, mucus plugs, etc

3. Female choice: bias towards males with particular chacters:

   • direct benefit

   • indirect benefits

     • good genes

     • fisharian runaway selection

   • sensory exploitation

1. Direct benefits by mate choice

1. Help raising offspring

2. Territory

3. “Nuptial” gifts

4. Greater fertility

5. Even if mates provide nothing there can still be direct benefits → spotting males from afar without having to wonder around getting eating by a predator looking for a mate and showy traits help determine with individual is healthy or have no parasites

2. Indirect benefits of intrasexual selection

• good genes hypothesis

  • male has female trait that attracts females and vis versa → caused by assortive mating

• Fisherian runaway sexual selection

  • attractive dads make attractive sons

  • posotbe feedback look

  • Initial variation:

    • Some males have a slightly longer tail, brighter feathers, louder calls, etc.

    • Some females prefer those traits.

  • Female choice spreads:

    • Females who prefer the trait mate with males that have it.

    • Their sons inherit the trait, and their daughters inherit the preference.

    • Now the trait and preference become genetically correlated.

  • Runaway process:

    • As both the preference and the trait spread, the trait becomes more and more extreme.

    • This “runaway” continues until the survival cost balances the mating advantage

Sex ratio

• usually 1:1 or 50/50

• when the sex ratio balance is off, some animals can change their sex to revert the balace back

• optimal sex ratio = more females than males → cost of males = disadvantageous to sexual reproduction

• thisis an example of evolutionary stable strategy (ESS)

• for an autosomal allele → 50/50 sex ration is an ESS but for an allele on a sex chromosome it is not → Y can only be passed to YX offspring

Sex ratio disorders

1. X chromosome of a father is not transmitted to his male offspring → therefore the X chromosome sin the males can benefit by evolving to damage or kill sperm carrying the Y → winters sex ratio distorter → after it preads → suppression of distorters can arise and spread → thi restores the sex ration back to 50/50

2. Autosomal killer systems (damage sperm or eggs) → less common → Chromosomes make extra centromeres on chromosome, → makes it more likely that a microtubule attaches and pulls the allele down → female gametes only the last bottom gamete survive → making these extra centromeres allows the gamete to have a higher survival rate -→ can kill all the eggs or all the sperm

Kin selection

• self sacrificing behaviro that benefits relatives

• inclusive fitness: it measures the transmission of alleles that are IBD and increases if individuals are alturistic → this is the idea that the fitnes is made up of direct+ indirect fitness

• B = beneit

• C = cost

• r = degree of relatedness between actor and recipient

• need to follow Hamilton’s rule to know that they havea shared relationship

• eusociality: offspring are nearly or completely sterile workers

Conflict and cooperation

1. conflict between siblings → bird can bully their sister out of the nest to gewt the full benefits from their parents → occurs when cooperation is not beneficial

2. Mother-offsping conflict: resource conflicts during pregnancy → fetus may try to keep mother’s blood glucose levels high to get more nutrients → too much nutrients = invasisve placental growth → can lead to fetal overgrowth and/or hut/kill the mother