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Neutral or Selectionist? One way to test these theories is to look at th number of silent vs. non-synonymous substitutions over a given region of DNA are silent point mutations in DNA (no effect on phenotype) more common or less common than non-synonymous changes? Negative selection: amino acid substitutions are less common than silent DNA substitutions (change is bad) Positive selection: non-synonymous amino acid substitutions are more common than silent substitutions Polymorphic sites 1: DNA changes Some positions are polymorphic (different nucleotides are found) between some of the species - a single nucleotide is fixed within each species E. papillosa a E. papillosa b GGTGCAGTAAACTTTATTACTACTATTTTTAATATACGGTCACCTGGTATAAGAATGGAACGTTTAAGATTATTTGTTTGATCAGTTTTA .....G.................................................................................... E. patina 06Jam11 E. patina 07Dom05 .....G..........................C..G.....T.....G..G.C...............T...........G......C.C .....G..........................C..G.....T.....G..G.C.........C.....T...........G......C.C E. zuleicae 04Ber03 E. zuleicae 04SSal11 .....G...........C..A...........C..G..C..T.....A..G.C...............T..................C.. .....G..............A.G.........C..G..C..T.....A..G.C...............T........C.........C.. Other positions are polymorphic within one species, but are otherwise fixed among species Polymorphic sites 2: amino acid changes S or T V or F E. papillosa a E. papillosa b VYPPLSGPIGHGGASVDLAIFSLHLAGMSSILGAVNFITTIFNMRSPGMSMERLSLFVWSVLVTAVLLLLSLPVLAGAITMLLTDRNFNTSF .................................................S...............V.......................... E. patina 06Jam11 E. patina 07Dom05 .................................................T...............F.......................... .................................................T...............F.......................... E. E. E. E. E. E. E. E. E. E. E. E. E. E. E. E. E. .................................................T...............F.......................... .................................................T...............F.......................... .................................................T...............F.......................... .................................................T...............F...................G...... .................................................T...............F.......................... .................................................T...............F.......................... .................................................T...............F.......................... .................................................T...............F.......................... .................................................T...............F.......................... .......................................S.........T...............F.......................... .................................................T...............F.......................... .................................................T...............F.......................... .................................................T...............F.......................... .......S.........................................T...............F.......................... .................................................T...............F.......................... .................................................T...............F.......................... .................................................T...............F.......................... zuleicae zuleicae zuleicae zuleicae zuleicae zuleicae zuleicae zuleicae zuleicae zuleicae zuleicae zuleicae zuleicae zuleicae zuleicae zuleicae zuleicae 04Ber04 04Ber06 04Boc102 06Jam07 07LSS02 04SSal03 04Boc101 07SSal01 06Jam03 04SSal11 04Bocas103 04SSal06 09Cur105 09Cur09 07Cur12 09Cur13 09Cur14 different amino acids can occur at a site within one species different amino acids can be fixed between species Normally, most substitutions that survive to be detected are silent 1. DNA – 17 polymorphic sites E. papillosa a E. papillosa b GGTGCAGTAAACTTTATTACTACTATTTTTAATATACGGTCACCTGGTATAAGAATGGAACGTTTAAGATTATTTGTTTGATCAGTTTTA .....G.................................................................................... E. patina 06Jam11 E. patina 07Dom05 .....G..........................C..G.....T.....G..G.C...............T...........G......C.C .....G..........................C..G.....T.....G..G.C.........C.....T...........G......C.C E. zuleicae 04Ber03 E. zuleicae 04SSal11 .....G...........C..A...........C..G..C..T.....A..G.C...............T..................C.. .....G..............A.G.........C..G..C..T.....A..G.C...............T........C.........C.. 2. amino acid – 4 polymorphic sites (= non-synonymous changes) E. papillosa a E. papillosa b VYPPLSGPIGHGGASVDLAIFSLHLAGMSSILGAVNFITTIFNMRSPGMSMERLSLFVWSVLVTAVLLLLSLPVLAGAITMLLTDRNFNTSF .................................................S...............V.......................... E. patina 06Jam11 E. patina 07Dom05 .................................................T...............F.......................... .................................................T...............F.......................... E. zuleicae 06Jam07 E. zuleicae 04SSal11 .................................................T...............F...................G...... .......................................S.........T...............F.......................... When non-synonymous changes pile up faster than silent changes (given that codons differ in whether one mutation can change the amino acid), it indicates positive selection is acting to quickly fix mutations before they get lost to drift Neutral or Selectionist? Evidence for positive selection suggests selection is driving the rate at which mutations are fixed as proteins evolve Smith & Ayre-Walker (2002) compared ratio of non-synonymous (dN) to synonymous (dS) substitutions within 2 Drosophila species, and between the two species, over the whole genome - found many sites where there were more non-synonymous changes between the species than within either species - indicates that selection favored differences between species - they estimated 45% of amino acid differences between the 2 species had been fixed by positive selection Neutral or Selectionist? Begun et al. (2007) found amount of polymorphism was correlated with recombination rate across Drosophila simulans genome Different regions of the genome can differ in how often crossing over occurs – some places have more, others less Some genes are more polymorphic than others (have more alleles) Neutral theory predicts no relationship between amount of genetic polymorphism (# of alleles) and how often crossing over happens Why does selectionist theory predict a correlation?... Neutral or Selectionist? Selection favoring one allele will also tend to drag alleles at nearby or linked loci to high frequency if selection strongly favors “big C” allele of the C gene... A B C D E F a b c d e f ...it will also tend to favor “B” and “D” alleles, if they happen to be linked to “C” on a chromosome Neutral or Selectionist? Selection favoring one allele will also tend to drag alleles at nearby or linked loci to high frequency if selection strongly favors “big C” allele of the C gene... A B C D E F a b c d e f ...all these alleles will be lost, unless they can get onto the “winning team” i.e., any chromosome with a C allele Neutral or Selectionist? in regions of high recombination, linked loci can escape the effects of selection on nearby genes crossing over “breaks up the team” Even if selection strongly favors C allele... alleles of other genes can cross over onto C chromosomes A B C D E F a b c d e f a b C d e In regions of high recombination, many alleles at linked loci can “hitchhike” onto chromosomes with favorable alleles, and thus survive selection greater overall polymorphism f Neutral or Selectionist? Begun et al. (2007) found amount of polymorphism was correlated with recombination rate across Drosophila simulans genome in regions of low recombination, linked loci can’t escape the effects of selection on nearby genes if selection strongly favors “big C” allele of the C gene... A B C D E F a b c d e f ...all these alleles get lost The correlation is strong evidence that selection acts on alleles all the time, across the whole genome Supports selectionist theory, not neutral theory Non-random mating: Inbreeding Violates one of the assumptions of Hardy-Weinberg Can affect genotype frequencies without affecting allele frequencies Selfing (not the same as cloning) - many plants and some animals can self-fertilize - homozygotes always give rise to homozygotes - heterozygotes produce 1/2 homozygotes and 1/2 heterozygotes Aa AA 1 Aa : 2 aa : 1 Non-random mating: Inbreeding Result: in every generation of selfing, the # of heterozygotes is halved - however, the allele frequencies are unchanged thus, inbreeding also causes loss of heterozygosity, and has a strong evolutionary impact - Inbreeding and loss of heterozygosity Case study: malaria parasite - most people in New Guinea are infected by only one mosquito - most reproduction occurs between brother and sister offspring when another mosquito bites an infected person (inbreeding) prediction: there should be an excess of homozygotes at loci that are polymorphic - in other words, even when there are a lot of alleles out there, selfing should result in few heterozygotes Inbreeding and loss of heterozygosity very polymorphic loci Coefficient of inbreeding Inbreeding among more distant relatives has the same effect, but less drastic Degree of relatedness is reflected in a measure called the coefficient of inbreeding, F F is the probability that the two alleles in an individual are related by descent from a common ancestor F = 0.5 for selfing: there’s a 50/50 chance selfing will produce an offspring with both alleles derived from the same parental allele Coefficient of inbreeding F is the probability that the two alleles in an individual are related by decent from a common ancestor Coefficient of inbreeding Ordinary genotype frequencies predicted by Hardy-Weinberg: AA Aa aa p2 2pq q2 In an inbred population, genotype frequencies are given by: AA p2(1-F) + pF Aa 2pq(1-F) aa q2(1-F) + qF -- why? odds of getting a homozygote = sum of 2 possible ways way #1 - p x (odds of an unrelated p), which is p x p(1-F) way #2 - p x (odds of a related p), which is pF Coefficient of inbreeding In an inbred population, genotype frequencies are given by: AA p2(1-F) + pF Aa 2pq(1-F) aa q2(1-F) + qF test: insert the value F = 0 - this is true for unrelated gametes - gives you the Hardy-Weinberg genotype odds Inbreeding depression Although inbreeding doesn’t change allele frequencies, it creates an excess of homozygotes This exposes loss-of-function alleles, which are normally masked in heterozygotes - creates lower fitness among offspring of relatives Inbreeding depression inbreeding coefficient population size Keller et al. (1994) followed a population of sparrows (small birds) on a Canadian island for 15 years Two population crashes, in 1980 (27 survivors) and 1989 (11 survivors) Inbreeding coefficient of survivors (those still alive in the crash year) was much lower than the average value in the year before the crash ones who survived the terrible winters were the least inbred; inbreeding lowers survival chances when environment goes bad