Variation Chapter 9 10/6/2014. Some terms. Variation in phenotype can be due to genes AND environment: Is variation genetic, environmental, or both?

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1 Frequency 10/6/2014 Variation Chapter 9 Some terms Genotype Allele form of a gene, distinguished by effect on phenotype Haplotype form of a gene, distinguished by DNA sequence Gene copy number of copies of a given gene, used without distinguishing allele or sequence differences Allele copies Variation in phenotype can be due to genes AND environment: Phenotype (trait) V pheno. = V geno. + V env. + V G *V E Is variation genetic, environmental, or both? Cross phenotypes and use Mendelian ratio predictions Greater resemblance among siblings than among related individuals points towards genetic contribution Common garden experiment See if differences persist over two generations 1

2 Epigenetic inheritance Both often important Norms of reaction Genotype frequency is proportion of a genotype A population has a frequency of alleles AA AA Aa aa Aa Allele frequency is the relative commonness or rarity of an allele Aa AA AA aa Aa aa AA AA AA 2

3 Hypothetical population If Individuals mate at random and each genotype is equally represented by males and females then.. Hardy Weinberg Equilibrium After one generation of random mating, genotype frequencies and allele frequencies in a population will remain constant from generation to generation Has a set of 5 assumptions H-W can be modified for sex-linked loci and segregation other than 1:1 H-W assumptions Random mating Large population No gene flow No mutation Each individual has an equal chance of survival and reproduction (No natural selection) H-W Equilibrium p and q are allele frequencies Genotype frequencies are predicted with a binomial expansion (p+q) 2 = p 2 + 2pq + q 2 p = individuals homozygous for first allele 2pq = individuals heterozygous for alleles q = individuals homozygous for second allele 3

4 Genetic Evolution Asks what happens when one or more of the assumptions are relaxed Violations of H-W are the major factors the cause evolutionary change Frequencies of alleles Frequency of heterozygotes are highest when p = q When an allele is rare, almost all its carriers are heterozygotes This can cause concealed genetic variation in a population Hardy Weinberg Exercise Inbreeding Inbreeding occurs when individuals are more likely to mate with relatives that with non-relatives or when gene copies are more likely to be identical by descent Genes are identical by descent if they have descended from a common ancestor relative to other gene copies in the population 4

5 Inbreeding As inbreeding proceeds, the frequency of each homozygote increases Frequency of heterozygotes is H = H 0 (1-F) H 0 is frequency of heterozygotes under HW F is the inbreeding coefficient F increases as inbreeding continues F can be calculated by the deficiency of heterozygotes from HW equilibrium Selffertilization is the most extreme form of inbreeding Inbreeding Polymorphism Polymorphism is the presence in a population of two or more variants, either alleles or haplotypes vs. monomorphism Can be controlled by one to more than one locus One loci Two loci Genetic variation in viability Can perform crosses in flies to determine recessive lethal alleles 10% of alleles on chromosome 2 in Drosophila pseudoobscura are lethal when homozygous, half reduce viability Average person carries 3-5 lethal recessive alleles in heterozygote form Confirms that there is a great deal of concealed genetic variation 5

6 Inbreeding depression Because of these recessive alleles, inbreeding, when increasing the number of homozygotes, reduces survival and fecundity Inbreeding Inbreeding with selection over many generations can purge deleterious alleles Many mechanisms for inbreeding avoidance: behavioral and genetic Endangered species Genetic variation in proteins Enzymes are run through electrophoresis Electrophoretically distinguishable forms of an enzyme are called allozymes Not all amino acid substitutions alter electrophoretic mobility 6

7 Heterozygosity in proteins Measured by average heterozygosity Average heterozygosity was 12% in Drosophila pseudoobscura Average heterozygosity in humans was 7% Almost every individual in a sexuallyreproducing population is unique Variation in DNA Variation determined by DNA sequencing Nucleotide diversity per site (π) Drosophila melanogaster has 5% average diversity Humans have.15% average diversity Multiple loci More than one loci can affect fitness Linkage Genes are physically associated with other genes on the same chromosome Changes in allele frequencies at one allele can cause changes in a linked allele 7

8 Linkage Recombination Two loci in a population are in linkage equilibrium when the genotype of a chromosome at one locus is independent of its genotype at the other locus Two loci are in linkage disequilibrium when there is nonrandom association between a chromosome s genotype at one locus and its genotype at the other locus Recombination reduces the level of linkage disequilibrium Tighter linkages take longer to break down from recombination Linkage disequilibrium is common in asexual populations due to little recombination 8

9 Determining linkage equilibrium Use modified HW Frequency of A 1 B 1 /A 1 B 1 in next population should be p A2 p B 2 if population is in linkage equilibrium Most populations are in linkage equilibrium Quantitative traits Continuous variation - vary because of both polygenic control, as well as environmental factors Estimating variation Use variance, which measures the spread of values around the mean V P = V G + V E Heritability is the proportion of the phenotypic variance that is genetic h 2 = V G /(V G + V E ) Heritability Two ways to measure parent-offspring regression selection experiments Parent-offspring regression If variation among individuals due to genes, then offspring resemble parents Plot midparent value against midoffspring value Slope of line = heritability 9

10 mid-offspring height 10/6/2014 Parent-offspring regression mid-parent height Selection experiments Selection experiments Only particular individuals allowed to breed Difference between mean phenotype of population and mean of selected group = selection differential, S Selection experiments The change in offspring phenotype between selected group and unselected population is the response to selection, R Heritability estimates 10

11 How do populations vary from one another? There is variation in species characters from place to place Geographic variation Some terms Sympatric populations Parapatric populations Allopatric populations Subspecies or geographic race Recognizable distinct population or group of populations Controversy when more than one character does not match up Discordant pattern Flicker subspecies Discordant pattern Human races Cline A gradual change in character or allele frequencies over geographic distance is called a cline 11

12 Bergmann s Rule Example of adaptive geographic variation Adaptive geographic variation Alcohol dehydrogenase allozyme F gradually increases in frequency with increase in latitude May be related to rainfall Allen s rule Gloger s rule Ecotypes Phenotypes associated with particular habitats 12

13 Common garden experiments Gene flow Gene flow homogenizes a population if not countered by natural selection or genetic drift Rate of gene flow (m) Determined by two methods Indirectly by genetic differences between populations Directly by following the dispersal of individuals Gene flow varies with distance Allele frequency Differences among populations (for one locus with two alleles) is measured by F ST or G ST Both measures vary from 0 (no variation) to 1 (populations are fixed for different alleles) Variation in allele frequency F ST = V q /q*1-q q is mean frequency of one allele V q is variation among populations in its frequency 13

14 Subdivided population F ST Subpopulations H S = Average H e in subpopulations HT HS FST H T Total population H T = Total H e Mosquitos and glaciation As distance increased, genetic variation increased (isolation by distance) Greater variation in southern region (more time to evolve) variation in allele frequencies among (sub)populations Nei s genetic difference 14