Class Note for ECOL 600B at UA
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Date Created: 02/06/15
Spring 2003 ECOL 600A Evolution Core Birky Directional selection Directional selection is a directional force which tends to increase frequencies of advantageous alleles and decrease frequencies of detrimental alleles Classic example pepper moth Biston betularia in Great Britain 2 alleles C black carbonaria c peppered Before the industrial revolution fC low and fc high After the industrial revolution fC increased and fc decreased although it never disappeared f C remained the dominant form in industrial areas at least into the 197039s Explanation in terms of directional selection bird predation Directional selection is the basis for most cases of Darwinian adaptative evolution because it results in a phenotypic change that increases the fitness of the organism The strength of directional selection is expressed by two parameters fitness w and selection coefficient s Hard selection models population size changes according to fitness Soft selection population size constant In real life most organisms probably have periods of hard selection and periods of soft selection Soft selection model Haploid population N 200 constant lnitially all genes are Al wild type allele and AZ is a new mutation Fitnesses are WI and wZ number of offspring produced s selection coefficient of the mutant wZ 7 wlN it is negative 71 gt 0 for detrimental genes and positive 0 gt 1 for advantageous genes A1 A2 w w s g i 200 O 1 A2 is lethal detrimental mutation 150 50 O5 A2 is detrimental mutation s lt 0 W2 lt wL 100 100 0 A2 is neutral mutation s 0 W2 wL 50 150 05 A2 is advantageous mutation s gt 0 W2 gt wL O 200 1 A2 is advantageous mutation A1 is lethal There are many variants on the simple models we will discuss Mostly deal with features that are very important in many but not all cases eg o diploidy and sexuality with different kinds of dominance 0 selection on different life history stages 0 measuring fitness in terms of offspring over several generations Spring 2003 ECOL 600A Evolution Core Birky Fitness is a quantitative trait unless one is concerned only with lethal genotypes Fitness is a function of all genes that help determine fitness However we can often isolate a single gene for study eg 0 we choose to focus on effects of a single gene such as a new mutant allele 0 antibiotic resistance in bacteria where only one gene at a time has a significant effect on phenotype Directional selection by itself leads to fixation or loss of alleles Haploid deterministic model p fdetrimental allele q fadvantageous allele A10 7 WV 1 7 5101 Change in allele frequencies is greater for o greater s selection is stronger o p and q closer to equal frequencies Case of special interest is a new mutation Neutral mutation no selection Detrimental mutation purifying or negative selection Advantageous mutation positive or adaptive selection Combined effects of mutation and selection Mutationeselection equilibrium or balance Most new mutations are detrimental Case of some interest especially in human genetics is when mutation pumps new detrimental alleles into the population and selection removes them at the same rate If q frequency of detrimental mutation at equilibrium q N u s Combined effects of mutation drift and selection Here we consider the realistic situation in which all alleles are subject to drift some are neutral and of the remainder the vast majority are detrimental Time to fixation or loss and expected heterozygosity or nucleotide diversity are reduced when some sites are under selection With selection pushing a new detrimental mutation to loss or pushing a new advantageous mutation to fixation time to fixation or loss will be shorter than the neutral expectation 5pm 2am ECOL S A Evaluuan Care Buky Beeause mnauans that are mhjectta selemm darn stay In the papulauan as lung as neuua mutatmns naey emmhme less in awexsuy than da nzuu39a mmauans we Hltm 2t generatvuns Ltttt rnn nm arm Drennmlnnles generatvuns Ltttt lrecllnnnl selecunn Drennmlnnles generatvuns Ltttt g m m Q m Q mama hnlnnclng selecunn nrennmlnnles Fm example mnnder mesw lnn agene 1 Stan AUG caan dnemunal sdeman damnateS xnahxhtyta make naepmmaL mnseqeuendy dwemt 2 3m pasman m athex mdans am dummites heeause mast subsumuans dm t rharge amma aaas and heme are neuaas at nearly nzuual m hgdy Expressed genes 311st and 2nd pasmansm anaea cade amaaam selemm an amma and suhsmuuans aauses dwexmy ah lessthan nae nzuual sase althaughm same eases e g vzry we papulauanS 11 ea he effecuvely neutral because any mnaaan leads in Spring 2003 ECOL 600A Evolution Core Birky Probability of fixation or loss Kimura s equation diploid Pfix mutation of freq x F 1 ei4Nesx 1 7 ewes new mutation x 12N F 1 7 EVZNesN 1 7 ewes haploid F 1 eiNesxV 1 7 72Nes new mutation x 1N F 1 7 72NesN 1 7 EVZNES Solving equation for various values of N6 and 5 shows 0 Even an advantageous mutation is more likely to be lost due to drift than it is to be fixed unless the selective advantage is remarkably high This illustrates the power of drift It also shows that most new mutations will be lost regardless of the effects of selection 0 Even a detrimental mutation can be fixed This again illustrates the power of random drift Nevertheless even though these calculations emphasize the importance of drift directional selection often determines the ultimate fate of mutations It is important in two general ways it promotes the fixation of advantageous mutations that lead to greater fitness or adaptation to a new environment positive selection and it eliminates detrimental mutations that would otherwise decrease fitness purifying selection The distinction between neutral and selected mutations is not entirely clearcut If the population size is small even mutations with very large values of s or very small negative values may have nearly the same fixation probability as a neutral mutation Conversely if the population is very large even very small selection coefficients can substantially increase or decrease the fixation probability Note that Ne and s always appear together as Nes This expresses their antagonistic relationship Think of drift as noise that interferes with selection which is the signal 0 Natural selection is effective ie determines the fate of a new mutation when ZNe s Z 1 Signal is louder than noise 0 Random drift determines the fate of a new allele when ZNe s ltlt 1 Noise overwhelms the signal ZNe s S 01 may be small enough Some authors use 4Ne s ltlt 1 or Ne s ltlt 1 Therefore alleles with very small s or alleles with large s in very small population behave like neutral alleles These are said to be effectively neutral alleles or nearly neutral alleles Spring 2003 ECOL 600A Evolution Core Birky Balancing Selection Balancing selection any kind of selection that maintains 2 or more alleles in a population The classic example is sickleicell anemia in which the sickleicell gene has been maintained in fairly high frequency even though it is detrimental In countries where malaria is endemic the genotypes and phenotypes are effects of anemia malaria HbA HbA none severe HbA HbS mild less severe HbS HbS severe 7 Overdominance heterozygotes are more fit than either homozygote There are a number of kinds of balancing selection notably l overdominance 2 selection for different alleles in different environments selection varies over time or in different habitats 3 frequencyidependent selection alleles are advantageous when rare detrimental when common Only a few cases of balancing selection have been clearly demonstrated Many or most evolutionary biologists believe that it is less important in determining overall levels of diversity than directional selection but this is still being debated It is clearly of functional important in some specific cases e g major histocompatibility locus in hominids Balancing selection increases heterozygosity and delays the fixation of alleles lt favors high polymoprphism In the Adh locus of Drosophila the fast and slow alleles are probably maintained by some unidentified kind of balancing selection Genetic diversity for synonymous alleles is high in the vicinity of the fastislow site ie balancing selection acting on a single base pair difference delays fixation and increases heterozygosity at neighboring base pairs because they are closely linked to it Migration Gene Flow Many species and populations are subdivided by various factors e g o intrinsically low dispersal rates 0 physical bariers o habitat barriers Subdivided populations tend to become genetically different counteracted by migration Spring 2003 ECOL 600A Evolution Core Birky Drift is partially independent in each subpopulation so they may maintain or fix different alleles and increase variation in the population as a whole Handled theoretically by setting up models eg o continenteisland o steppingestone Whole population is a metapopulation Parameter is migration rate m Effect measured by Wright s F statistics or similar G statistics m 2 l migrant per generation can make metapopulation nearly identical to randomemating population with respect to some statistics Population subdivision important in many areas e g speciation Polymorphism as a Double Edged Sword Adapted vs Adaptable Fisher s Fundamental Theorem Fisher the rate of change in mean fitness due to selection equals the additive genetic variance in fitness Monomorphic population can t evolve except by selection on new mutations The more different alleles there are in the population the faster the population can adapt by selection for good alleles or genotypes Genetic Load H J Muller pointed out that if there is more than one genotype with different fitnesses all but one will be of less than optimal fitness and the mean population fitness will be lower than if the population was monomorphic for the the optimal genotype e g segregation load when alleles of different fitnesses are maintained by balancing selection recombination continually produces lessefit homozygotes eg mutation load mutation continually introduces detrimental mutations which aren t eliminated immediately etc load L wmax 7 wmeanv Wmean Mutation load is a function only of the total detrimental mutation rate per genome U and is independent of the magnitude of the selection coefficient Large genetic load with hard selection can reduce fitness of population so that it becomes extinct meltdown The population can in theory be rescued by back mutations very rare or compensating mutations more common Spring 2003 ECOL 600A Evolution Core Birky When molecular methods showed very large proportion of loci are polymorphic Jukes amp King and Kimura argued that if polymorphism is maintained by balancing selection the load would cause extinction Their solution most of the variation seen at the molecular level is selectively neutral Argument depends on specific kinds of selection there are other solutions involving different kinds of selection Sex and Variation within Species Sex putting genes from two individuals together in one and recombining them Meiotic also involves segregation of alleles which is important in organisms with a significant diploid phase One locus HardyeWeinberg equilibrium With random mating frequency of heterozygotes is given by qu Although the conditions for HeW equilibrium are stringent and probably very rarely met it turns out that this prediction is a good approximation in many cases Used to estimate frequency of carriers of recessive human hereditary diseases lnbreeding reduces the proportion of heterozygotes Measured by coefficient of inbreeding F probability that two copies of a gene in an individual are identical by descent F ranges 0 random mating to l lnbreeding can result from mechanics of fertilization eg in peas the flower is enclosed by the keel which favors selfing from behavior and mate choice eg preference for individuals of similar phenotype or from small effective population size Obligate inbreeding observed heterozygosity goes to 0 fastest with autogamy 1 generation fast with selfing slower with sib mating etc If some individuals self and others are outcrossing heterozygosity goes to a low level but not to zero in infinite populations One locus Selection on recessive detrimental mutations Most new mutations are recessive Consequently the mutant allele is subject to reduced or no selection in heterozygotes This greatly retards selection especially when the mutant allele is rare It is easy to reduce the frequency of a detrimental mutation by selection but very hard to completely eliminate it Two or more loci Linkage disequilibrium Effectiveness of sex commonly measured by linkage disequilibrium Two or more loci Hitchhiking and background selection Spring 2003 ECOL 600A Evolution Core Birky Consider the behavior of two loci A B each with two alleles 1 Z in a randomemating population Allele Gamete Gamete Zygote Zygote Allele Frequency Genotype Frequency Genotype Freqzuenzcy A1 PA A1131 PA PB A1 A1 B1 B1 PA PB A2 lA A1132 PA QB A1 A1 B1 132 PA22 PB QB B1 PB A2131 QA PB A1 A1 132 132 PA2 QBZ 132 QB A2 132 QA QB A1 A2 B1 B1 t 2 PA QAPBZ e c Zygotic and gametic disequilibrium refers to deviations from these values Note that at equilibrium the genes are behaving independently Anything that causes deviations from independence can result in disequilibrium o linkage o asexual reproduction o preferencial inbreeding or outbreeding 0 selection with epistasis interactions between loci in determining fitness Also anything that causes gene frequencies to change can cause linkage disequilibrium o mutation o drift eg founder effects Hitchhiking Hitchhiking means that an advantageous mutation driver goes to fixation and carries with it linked neutral mutations or even mutations that are detrimental hitchhikers Hitchhiking reduces genetic variation Variation slowly recovers due to new mutations Extreme case periodic selection in asexual organism in which an advantageous mutation is fixed so quickly that genetic variation goes to zero at all loci Background selection hitchhiking with lots of drivers going a little ways backward detrimental mutations are lost and carry with them neutral mutations If it happens at many loci variation is reduced
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