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Biology 4250 Evolutionary Genetics Winter 2008 Dr. David Innes Dr. Dawn Marshall Course Webpage:

Evolutionary Genetics Goals: - to understand the impact that evolutionary processes have on the patterns of genetic variation within and among populations or species - to understand the consequences of these patterns of genetic variation for various evolutionary processes

Course Information Tentative Outline of topics: 1. Introduction/History of Interest in Genetic Variation 2. Types of Molecular Markers 3. Molecular Evolution 4. Individuality and Relatedness 5. Population Demography, Structure & Phylogeography 6. Phylogenetic Methods & Species Level Phylogenies 7. Speciation, Hybridization and Introgression 8. Sex and Evolution 9. Forensic Applications 10. Human Evolutionary Genetics 11. Conservation Genetics

Course Information Lecture format: Mon, Tues lectures, Fri Discussion Reading for Friday Jan. 11 From “Evolution” Labs: Mon. 2 – 5 pm starting Jan. 14 Computer labs require a LabNet account

Evaluation Midterm (Mon. Feb. 25) 20% Final 30% Laboratory exercises 20% Term paper 15% Presentation 10% Participation 5%

History of Genetic Variation Darwin and evolution: conversion of variation between individuals to variation between populations and species in time and space. Population genetics: - origin and dynamics of genetic variation within populations - changes or stability of genes within populations and the rate of divergence in genes between partially or wholly isolated populations

History of Genetic Variation Evolution: adaptation, speciation, extinction Contribution of population genetics to evolution G1 genetic description of population at time t =1 G1’ genetic description of population at time t =1+1 P1, P2, G2 phenotypic and genotypic states of population during transition T1 – T4 transformation processes Lewontin (1974) Figure 1 T1 T2 T3 T4 G > P >P >G >G1’

History of Genetic Variation T1 processes that determine the distribution of phenotypes that develop from various genotypes in various environments T2 processes of mating, migration and natural selection that transform the phenotypic array in a population within a generation T3 rules that translate the distribution of phenotypes (P2) into the associated distribution of genotypes T4 genetic rules (Mendel) that predict the array of genotypes in the next generation as a function of gametogenesis, mating and fertilization

History of Genetic Variation Population Genetic Theory (early-mid 1900): Mendelian Genetics - Genotypes (genes, alleles) Biometrical Genetics - Phenotypes

1. Mendelian Genetics: change in allele frequencies Genotypes Fitness A 1 A 1 w 11 A 1 A 2 w 12 A 2 A 2 w 22 Freq. (A 1 ) = p Freq. (A 2 ) = q

1. Mendelian Genetics: p = allele frequency in current generation p’ = allele frequency in next generation w = p 2 w pqw 12 + q 2 w 22 (population mean fitness) change in allele frequency: p’ = p(pw 11 +qw 12 ) w ie. change a function of allele frequency and fitness

2. Biometrical Genetics: (change in phenotypes) R = h 2 S R = Response = distribution of phenotypes in the next generation S = Selection differential = difference in total distribution of phenotypes and distribution of phenotypes that survive and reproduce h 2 = Heritability (V G / V P ) proportion of total phenotypic variation (V P ) that is due to genetic variation (V G )

2. Mendelian Genetics and Biometrical Genetics Therefore two approaches to studying evolutionary dynamics: Genotypic (Mendelian) Phenotypic (Biometrical) However, - fitnesses (w) a function of the phenotype - heritabilities a function of genetic and phenotypic variances. thus, an understanding evolutionary processes requires an understanding of the relationship between genetic and phenotypic variation.

2. Mendelian Genetics and Biometrical Genetics describing an evolutionary process within a population requires some information on the statistical distribution of genotypic frequencies. Therefore, empirical population genetics has centered around the characterization of genetic variation in populations. (Lewontin 1974)

Molecular Variation Molecular ecology and evolution developed as a field of research > 1953 (DNA structure, proteins, 1986 PCR) Research preoccupied with functional role and adaptive significance of genetic variation (functional molecular variation: natural selection at the level of proteins and DNA) However, molecular variation can also be used as genetic markers to study behaviour, natural history and phylogenetic relationships (ie. Neutral markers)

The role of Natural Selection in Maintaining Genetic variation History: Classical-Balanced debate (< 1966) Evolution: temporal change in genetic composition of populations Measuring genetic variation required to reveal the operation of natural selection, mutation, genetic drift etc.

The role of Natural Selection in Maintaining Genetic variation Problem: difficult to measure genetic variation Theoretical population genetics being developed - limited opportunity to apply theory to natural populations Empirical Population genetics: - colour polymorphisms - chromosome variation

Natural Populations Genetic variation: 1. Classical - low 2. Balanced - high Source of genetic variation (new genotypic combinations)

Natural Populations What fraction of genes is heterozygous in an individual and polymorphic in a population? Answer requires an unbiased assay for polymorphic and monomorphic gene loci

Protein Electrophoresis 1966 Lewontin and Hubby 20 – 50 loci Variant and invariant loci Fruit flies and Humans ~ 30 % of loci polymorphic ~ 10 % of loci heterozygous

Protein Electrophoresis

Protein Genetic Variation Allele frequency data easily fit into existing population genetic theory Refined techniques showed high levels of DNA sequence variation Empirical data rejects the classical school

Genetic Variation Does natural selection explain the observed high levels of genetic variation? Could be determined by processes other than selection ie. neutral Neutralist-Selectionist debate

Neutralists - Selectionists Alternative alleles  no differential fitness effects Most molecular polymorphisms maintained by mutation input and random allelic extinction

Neutralists - Selectionists Neutral theory became the “Null Hypothesis” Neutral theory a simpler explanation than natural selection Requires only mutation rate, gene flow, population size