Class Note for ECOL 320 at UA
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Date Created: 02/06/15
Forces Determining Amount of Genetic Diversity The following are major factors or forces that determine the amount of diversity in a population They also determine the rate and pattern of evolutionary base substitution factor parameter 1 mutation rate 2 natural selection kind and strength 3 random drift effective population size rnutatien M genetic variance eeieetian m gene F ng ranaarn drift Mutation Mutation is the ultimate source of genetic variation and differences between species All other things being equal the higher the mutation rate the greater the genetic variance in the population and the larger the differences between spec1es u mutation rate probability that a particular base pair will undergo mutation u is very low on the order of 10398 to 10399 per base pair or 10394 to 10396 per gene We are interested in the total number of mutations that enter the gene pool in one generation mutation 5 genetic variance seieetien in gene pea randam driftquot In a diploid organism if there are N individuals in the population 2N gametes must be produced each generation The total mutation rate in the population is the rate per base pair or gene per gamete times the number of copies of the gene in the population The number of copies is the number of individuals population size N times 2 for a diploid organism M2Nu M 2Nu Mutations per gene 2 Number of gametes x mutations per gene per gamete dimensional analysis mutations gametes x mutations genes genes x gametes M is usually very large If N is 105 the population will contain on the average of 2 new mutations in each gene in each generation Clearly most of these must be eliminated otherwise genetic variation will accumulate until species identity is lost If use DNA sequences to identify mutations u is in mutations per bp per gamete or mutations per site per gamete If N 105 and u 10399 and there are 3 X 109 bp per human genome will have 3 X 106 new mutations in gene pool in each generation n39nJ Latth a genetic variance eeleetinn I 1n gene pun randem drift 3 X 106 new mutations 3 X 106 new and old mutations Random genetic drift Nondirectional force Acts equally to increase or decrease frequencies Eliminates or fixes new mutations Happens because different individuals have different numbers of offspring by chance The probability that an allele will be fixed by drift is equal to its frequency Why drift happens Not all individuals in a population produce the same number of offspring Not all genes leave the same number of offspring Some of difference due to selection some to pure dumb luck Eg Mutation happens in one of the 6 million primary oocytes in your germ line when you were a fetus Only a few hundred survive and ovulate But you only have two children Probability that a child will have the mutation is about 2 6 million or 13 million Eg Three bdelloid rotifers belonging to same clone dry up and blow around Each one lands in a tiny pothole just after a rain and starts to reproduce Each one produces 5000 offspring A deer comes along and drinks the other pothole dry so that bdelloid has no offspring Any allele of any gene carried by it only leaves no offspring o a Q Bad things can happen even to good genes S happens Drift leads to fixation or loss of alleles Even in the absence of selection allele frequencies are not constant they undergo random walks If the frequency of an allele drifts to 0 it is lost if it drifts to 1 it is fixed and all other alleles of that gene are lost 1 1 ferr i llElEi E a ffI p xj I15 freq 39 H l quot392lquotl 39 390quot I u IF H I H J lH39H 1 t1r r ue gt mutatth Probability of fixation of an allele is equal to its frequency Pfix neutral allele of frequency x x 0 Section 18 divided into 18a b 0 18a and b on web Another homework assignment on population and evolutionary genetics Will be posted soon hopefully on Friday 1 KAPPA IF 5119120 5 I I m1 15 Iraq I PE rl39x l r r y 1x 2N 0 quotFM Ira N l r w t T time gt mutation Probability of fixation of an allele is equal to its frequency Pfix neutral allele of frequency X X Random drift is much more likely to eliminate a new mutation than to fix it New mutation X 12N Pfix new mutation 12N Plose new mutation 1 12N eg N 5000 Pfix 1 10000 00001 Ploss 09999 New mutation begins with frequency very close to 0 and very likely to hit 0 and be lost Conversely it is very far from 1 and very unlikely to get there Proof that random drift actually occurs has been obtained repeatedly in laboratory experiments Done with very small population size to make it go fast Fig 1730 and adjacent text describe an experiment in Drosophila Read it The strength of random drift depends on the population size works faster in smaller populations Eg Haploid population with N 5 or 10 Me 5 we 10 allele frequeIicy Tlme Iigenera ensj What is important is the effective population size Ne N 3 depends on N but also on the sex ratio and other factors that determine the variance in offspring number In nearly all cases Ne lt N Often Ne ltlt N eg elk harems In diploids the important number is 2Ne because each indiVidual has 2 genomes Play with a simple model of drift to understand it Go to bottom of web site then go either to URL for simulation or better download stuff and do manual simulation Best is to do both Another program available on web is PopG program which tracks changes in gene frequencies under mutation drift and or selection We will use it later Combined effects of mutation and drift neutral model Drift always happens Mutation always happens 80 add mutation to simulation This model is realistic it ts many real situations in which most genetic diversity is due to neutral alleles Some people think that it ts the majority of molecular data 4N u H z m 4Neu E Haploids and asexuals substitute 2Neu e Animal mitochondrial genes substitute Nfu 4Neu n z m 4Neu E but now u is in mutations per Site per gamete e sometimes symbolized by u Intuitive explanation for these equations Higher mutation rate more mutations pumped into the population Larger Ne drift is slower so mutations tend to linger in population longer Directional selection If mutation and drift were all that happened there would be no adaptation of organisms to different habitats Differences in N6 and u can t explain synonymous gt nonsynonymous or introns gt exons because all these are in same genome in same organism and have same Ne and u Directional selection is a directional force that tends to increase frequencies of advantageous alleles and decrease frequencies of detrimental alleles By itself directional selection will fix advantageous alleles and eliminate detrimental alleles Directional selection is the basis for most cases of Darwinian adaptive evolution because it results in a phenotypic change that increases the fitness of the organism Drosophila experimental results usually not as neat as those cases we use in class Did three factor cross in genetics lab course All mutant genotypes e g while eye present in fewer than the expected numbers All Visible mutants all at least slightly detrimental If they were not detrimental they would be more common in nature If they were advantageous they would have become the wild type Adaptive Melanism in Lava Flow Mice Hopi Hoekstra now at Harvard Michael Nachman EEB et al See Hopi39s web site htt wwwbiolo ucsdedu facult hoekstrahtml Follow the link to Projects Melanism seen in mice lizards and snakes living on desert lava flows Earlier work showed that melanism reduces owl predation on mice on dark lava rock and dark mice have reduced fitness on light rock Rock pocket mouse Chaeootdipus intermedius living in Arizona New Mexico and northern Sonora Hair color matches rock color Due to natural selection acting over lt 500000 years Requires strong selection This is shortterm evolution within a species Mouse populations on lava are not completely isolated from mouse populations on light rock in adjacent desert Therefore selection must be very strong to counteract effects of migration Melanism in Pinacate population in Arizona is due to a single point mutation in the melanocolrtin1 receptor gene Mair that is responsible for melanism Melanism in New Mexico populations due to different gene 2 2 independent origins of adaptive melanism in pocket mice Selection intensity is measured by relative fitness or by selection coefficient s of mutant allele mutant wild type S offspring number relative fitness 0 50 100 100 50 0 1 quot9 0 quot9 1 lethal detrimental neutral advantageous lethal mutant wild typle The majority of mutants have selection coefficients with small absolute values Isl lt 01 Combined Effects of Selection and Drift Probability of fixation of a new mutant allele with selection coefficients in population with effective size N6 is given by Kimura s equation 2N N 4N F 1 e es 1 e es Solving equation for various values of N Ne and s leads to the following conclusions 0 Even detrimental mutations can be fixed by drift 0 Even advantageous mutations can be lost by drift 0 Relative strength of selection and drift depends on the product Nelsl Nelsl gtgt 1 selection dominates Nelsl ltlt 1 drift dominates mutation is ejj eclively neutral If Nelsl gtgt 1 then either N6 is very large so drift works very slowly or s is very large so selection is very strong or both If Nelsl ltlt 1 then either N6 is very small so drift is strong or s is very small so selection is very weak or both Analogy selection is signal drift is noise Balancing Selection Balancing selection is any kind of selection that maintains two or more alleles in a population Sicklecell anemia Sicklecell gene has been maintained in fairly high frequency even though it is detrimental Heterozygotes are more resistant to malaria than homozygous normal Heterozygotes have selective advantage where malaria is endemic effects of anemia malaria HbA HbA none severe HbA HbS mild less severe Hbs HbS severe Example of overdominance heterozygotes are more fit than either homozygote There are a number of other kinds of balancing selection eg different alleles are adapted to different habitats Deer mice in western US live from sea level to 14000 feet Polymorphic for two variants of ocglobin protein one more efficient at binding oxygen at high altitude and the other at low altitude Only a few cases of balancing selection have been clearly demonstrated Probably less important than directional selection but this is still being debated Balancing selection delays the fixation or loss of alleles which increases heterozygosity Cnmbined Effects nf Muminn mm and Selenium Simple Mn dels nf meme Cases Fach am rzprzsmts 3 gm Tum guts mm ugh Fach mm column m am presan a gmzs m an gmmmn generatvuns Ltttt runnnm nnn Drennmlnnles generatvuns LLLLL lrecllnnnl selecllnn Drennmlnnles generatvuns g m E n m E Q h nurrmrw s hnlnnclng selecunn nrennmlnnles generatiuns mu 9 a a 5 2 a a quot3 q my so 39 runnnm arm prennmlnnles generatiuns mu u a a 7 2 quot i n a a b s a II EE Innnl selecllnn nrennmlnnles generatiuns a a M 2 am 2 J 4 man i s a hnlnnclng selecllnn nrennmlnnles Directional selection reduces genetic variability relative in neutral case by accelemdng die xation or loss of murau39ons Balancing selection increases genetic variability relative in neutral case Directional Selection Mutations stay in population average H 0ch neutral z 4Ne generations z 4Neu detrimental pushed to loss lt 4Ne generations lt 4Neu advantageous pushed to fixation lt 4Ne generations lt 4Neu balanced maintained gt 4Ne generations gt 4Neu Balancing selection is not very common Therefore if we look at a large segment of DNA we will find that H lt 4Neu A few genes have H gt 4Neu showing balancing selection Analogy Gene pool is bathtub with water molecules as alleles Mutation is faucet Drift is drain Directional selection is pump Balancing selection is 2 or more rubber duckies which can t fit out the drain or pump Evidence for directional and balancing selection from population genetics of Drolsophila Adh Directional selection 1 There is more polymorphism in introns than in exons 2 In the exons there is much more polymorphism in DNA sequence than in amino acid sequence 4 The left end of exon 4 is an exception The F S site is polymorphic and regions close to it on both sides have a higher polymorphism than other exons The F S difference is maintained by balancing selection This selection also tends to maintain heterozygosity for mutations closely linked to F or S Further away recombination tends to separate new mutations from F or S and directional selection acts to reduce polymorphism Explaining patternsphenomena Different species have different diversities Could be due to differences in u Ne or 8 Why are Cheetahs so uniform 0 No reason to believe mutation rate different from other animals 0 Some markers probably nearly neutral so probably not due to very strong selection 0 Probably mainly small N and Ne lingering effects of population bottleneck Different genomes have different diversities Hominids mitochondrial gene diversity gt nuclear gene diversity 2Nfum gt lNeun where Nf number of females we know 2Nf lt 4Ne therefore 11m gt 1111 Mitochondria have different DNA polymerase less effective repair systems and more exposure to mutagens Different genes or regions of genome have different diversity Eg fibrinopeptides gt orglobin All nuclear genes in same species so difference not due to N6 or to u ls due to selection fibrinopeptides work With a Wide range of amino acid sequences so new mutations are only slightly detrimental globin mutations more detrimental Why are conserved sequences lower in variation than others Not low u which is same on average for all segments of a genome Not N and N which are same for all genes in an organism Conserved sequences have arge negative s on average larger proportion of mutations are detrimental fewer are neutral Why are VNTRs so useful for forensic work N e is same for VNTRs and other genes Most nearly neutral so high variation partly due to lack of directional selection Mutation rate u is high due to replication slippage and changes in repeat numbers not to singlebase mutations One Implication for Conservation Endangered species have small N This means small Ne and Nelsl Which means less effective selection Which includes more accumulation of detrimental mutations leading to reduced fitness and further reduction in N Vicious circle smaller N reduced fitness Smaller Ne and NeISI less effective selection
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