Population Genetics I. Evolution: process of change in allele
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1 Population Genetics I. Evolution: process of change in allele frequenciesNatural Selection: the mechanismEcological genetics: study of genes innatural populationsWhat are the forces that maintain geneticdiversity? Is that genetic diversityselectively neutral, or activelymaintained by natural selection?
2 What IS natural selection, anyway? Individuals within a population are differentfrom each other in various characteristicsThese differences are heritableSome individuals survive and reproduce moresuccessfully than others, based on theseheritable differencesOver time, this differential survival andreproduction leads to altered genefrequencies
3 “Descent with modification” An Evolutionary Tree…“Descent with modification”Macroevolution:
4 Example: Galapagos Finches Micro-evolution:changes in the geneticcomposition of a populationfrom generation to generation
5 Another Example of Changing Selection I’iwi(Vestiaria coccinea)Bill shape has changed since the extinctionof several of its original food plants, based onmeasurements of museum skins comparedto birds caught recently(Smith, Freed, Lepson, and Carothers Cons. Biol. 9: )
6 Population Genetics Changes in gene frequency in populations Consequences of gene flowConsequences of small population sizeGenetic drift, inbreeding, other factorsUnderstanding evolutionary relationships
7 Some Basic Terms and Concepts Genes: a sequence of DNA that encodesfor a proteinLocus: position on a chromosome; may ormay not code for a proteinAllele: Alternative DNA sequence at a locusA locus is monomorphic if there is only oneallele in the population. A locus ispolymorphic if there is more than one allele
8 Some Basic Terms and Concepts Genotype: The overall genetic makeup of anindividualPhenotype: The expression of the genotype.Gene expression influenced by theenvironmentGenetic drift: Changes in allele frequenciesdue to chance eventsIf the same alleles are present at a locus, theindividual is homozygous. If the alleles aredifferent, the individual is heterozygous.
9 Measures of genetic diversity General diversity, HeHe = 1 - Σpi2 where pi is the frequencyof the allele typeNote that when the frequency of pi isclose to or equal to 1, then He is essentiallyzero.This is a measure of locus variability- noassumptions on mating, etc.
10 If this is not the case, the interesting question is: No Selection or Drift?If population large, randomly mating...Offspring gene frequencies depend onlyon gene frequencies of parent generationFrequencies will be at equilibriumIf this is not the case, the interesting question is:WHY NOT?
11 Hardy-Weinberg Equilibrium Gene frequencies will reach an equilibriumwhen the following conditions are met:Diploid organism (copy of gene from each parent)Sexual reproductionNon-overlapping generationsRandom matingLarge populationEqual allele frequencies in the sexesNO migration, mutation, or selection
12 Forces that can account for non-Hardy- Weinberg Equilibrium Non-random matingactive sexual selection of mates“isolation by distance”Geographic structure in population(can lead to non-random mating throughout)Natural selectionSome genotypes have better reproductivesuccess and survival than others
13 Inbreeding Plant populations in particular may show a great deal of inbreedingUsually not considered advantageous*leads to a loss of genetic diversity and*increases expression of deleteriousrecessive genesWhen inbreeding causes a drop in demographicrates, it is termed “inbreeding depression”
14 Measuring the extent of inbreeding Inbreeding leads to a loss of heterozygosityThe inbreeding coefficient, F, is a measuremeasures probability that an individual’s2 alleles are identical by descentAA: p2 + FpqAa: 2pq(1-F)aa: q2 + FpqComplete self-fertilization:F = 1.
15 Measuring the extent of inbreeding The coefficient of inbreeding for a selfingpopulation can be calculated as:F = S/(2-S) S is the selfing rateIF we have information on the frequency ofheterozygous individuals, AND we assumethat the population is in equilibrium,we can calculate the selfing rate
16 F-statistics for inbreeding FIS:Inbreeding of individuals relative totheir subpopulationValue is high in inbreeding populationsFST:Measures whether individuals more similarto subpopulation than total set ofsubpopulationsIncreases with increasing isolation
17 Genetic Drift Defined as the random fluctuation in allele frequencies Survival of new mutations can fail due tochance eventsParticularly important in small populations:elimination or fixation of alleles possiblesolely due to chance
18 Genetic Drift Time needed to fix or eliminate allele a function of population sizeEffective population size (Ne)size of idealized popn that loses geneticdiversity at same rate as real populationNe almost always smaller than real N
19 Consequences of population subdivision Consequences of population subdivision and movement of genetic materialDiscrete patches, or demes, of genetic structureform when populations are isolatedAssociated with limited dispersal capabilities,even in continuous populationsIsolation by distanceMovements of individuals or pollen amongpopulations break down formation ofdemes
20 Gene Flow: animals Animals: dispersal is the key; isolation by distance still appliesNon-sessile animals: any age or stage couldstart new populationConservation biology: concerned with popnseither too small, or too isolated,to maintain gene flow and genetic diversity
21 Gene Flow: plants Genetic mixing occurs through both seed and pollen dispersalGene flow therefore dependent on dispersalmechanisms: wind patterns, animalbehavior (both pollination and seeddispersal)Only seeds can start new populations
22 Those rare events…. What if a few individuals- or even a single seed- founds a new population far out-side the original range, or survives acatastrophe where all other populationsof the species are lost?The new population will have greatly reducedgenetic diversity compared to the largerpopulations
23 Bottlenecks and Founder Events A bottleneck:population reduced to a tiny fractionof its former size, thus eliminatingmuch of its former genetic diversity.
24 Bottlenecks and Founder Events A founder event occurs when one or a fewindividuals establish an isolated populationThis is of particular concern in conservationbiology, and captive breeding programsBritish field cricket:12 individualsSnow Leopard:7 individualsPuerto Rican Parrot:13 individuals(Frankham et al. 2002)