Population and Ecological Genetics

Timetable

The module consists of ten sessions of 2h (2 x 45 min) per week (lecture, in total 10 weeks x 2h = 20h) and five sessions (2h each) of computer exercises (in total 5 weeks x 2h = 10h). The exact time will be announced before the course starts.

Module aim (aims)

Explain the factors and processes that shape genetic variation, population structure, and gene flow, using molecular data.

Develop skills to formulate and evaluate hypotheses about evolutionary mechanisms in populations.

Understand the causes and consequences of microevolutionary processes.

Analyze and interpret genetic data to make inferences about population dynamics and evolution.

Pre-requisites in terms of knowledge, skills and social competences (where relevant)

General genetics; basic statistics 

Syllabus

Lecture

Week 1 – Populations, Genetic Variation & Evolution: Definition of populations; Genetic variation in natural populations; Microevolutionary forces overview; Ecological vs. evolutionary timescales

 Week 2 – Genetic Markers & Genomic Data: Dominant vs. codominant markers

Microsatellites, SNPs, reduced-representation genomics; Marker choice for ecological questions: How many loci are enough?

 Week 3 – Allele & Genotype Frequencies; Hardy–Weinberg Equilibrium: Estimating allele and genotype frequencies; Hardy–Weinberg equilibrium as a null model; Testing for HWE; Causes of HWE deviations

 Week 4 – Mutation, Recombination & Neutral Theory: Mutation as the source of variation; Mutation rate estimation; Recombination and linkage; Neutral theory and molecular evolution

 Week 5 – Genetic Drift & Effective Population Size: Genetic drift in finite populations; Census vs. effective population size (Ne); Estimating Ne from genetic data;

Week 6 – Gene Flow, Dispersal & Spatial Structure; Dispersal vs. gene flow;

Isolation by distance; Barriers to gene flow; Measuring migration

 Week 7 – Population Structure & Genetic Diversity: Measures of genetic diversity; F-statistics and population subdivision; Clonal vs. sexual populations

 Week 8 – Mating Systems & Natural Selection: Mating systems and inbreeding

Sexual vs. clonal reproduction; Types of selection; Measuring selection in natural populations; Drift–selection interactions

 Week 9 – Local Adaptation & Ecological Genetics: Genotype–environment interactions; Local adaptation; Detecting adaptive loci; Neutral vs. selective processes.

 Week 10 – Detecting Microevolutionary Processes: Statistical and genomic approaches; Case studies (conservation, climate change, invasions); Course synthesis and future directions.

Computer-based exercises will familiarise students with the use of GenAlEx and R packages for population genetics.

Reading list

For students who wish to explore the topics covered in this course in greater depth, additional references are provided below.

 Week 1 – Populations, Genetic Variation & Evolution

Core: Hartl, D. L., & Clark, A. G. Principles of Population Genetics, Ch. 1–2; Hedrick, P. W. (2011). Genetics of Populations, Ch. 1

Supplementary: Lewontin, R. C. (1974). The Genetic Basis of Evolutionary Change, Ch. 1; Endler, J. A. (1986). Natural Selection in the Wild, Introduction

Week 2 – Genetic Markers & Genomic Data

Core: Allendorf, F. W., Luikart, G., & Aitken, S. (2013). Conservation and the Genetics of Populations, Ch. 3; Schlötterer, C. (2004). The evolution of molecular markers. Nature Reviews Genetics

Supplementary: Davey et al. (2011). Genome-wide genetic marker discovery and genotyping using NGS. Nature Reviews Genetics; Morin, Luikart & Wayne (2004). SNPs in ecology and evolution. Trends in Ecology & Evolution

Week 3 – Allele & Genotype Frequencies; Hardy–Weinberg Equilibrium

Core: Hartl & Clark, Ch. 3; Wigginton, Cutler & Abecasis (2005). A note on exact tests of HWE. AJHG

Supplementary: Nielsen et al. (1998). Estimation of population allele frequencies from dominant markers. Genetics; Graffelman et al. (2017). HWE testing in structured populations. Heredity

Week 4 – Mutation, Recombination & Neutral Theory

Core: Hedrick, Ch. 4; Kimura, M. (1983). The Neutral Theory of Molecular Evolution, Ch. 1–2

Supplementary: Drake et al. (1998). Rates of spontaneous mutation. Genetics; Lynch et al. (2016). Mutation rate evolution. PNAS;

Week 5 – Genetic Drift & Effective Population Size

Core: Hartl & Clark, Ch. 4–5; Charlesworth, B. (2009). Effective population size and patterns of variation. Nature Reviews Genetics.

Supplementary: Wright, S. (1931). Evolution in Mendelian populations. Genetics; Waples (2005). Genetic estimates of Ne. Molecular Ecology.

Week 6 – Gene Flow, Dispersal & Spatial Structure

Core: Slatkin, M. (1987). Gene flow and population structure. Science; Rousset, F. (1997). Genetic differentiation and isolation by distance. Genetics

Supplementary: Bohonak (1999). Dispersal and gene flow. Evolution; Lowe & McPeek (2014). Is dispersal neutral? Trends in Ecology & Evolution.

Week 7 – Population Structure & Genetic Diversity

Core: Allendorf et al., Ch. 6; Weir & Cockerham (1984). Estimating F-statistics. Evolution

Supplementary: Jost (2008). GST and its relatives do not measure differentiation. Molecular Ecology

Pritchard, Stephens & Donnelly (2000). STRUCTURE. Genetics

 Week 8 – Mating Systems & Natural Selection

Core: Hedrick, Ch. 11–12; Endler (1986), Ch. 2–4

Supplementary: Charlesworth & Charlesworth (2010). Elements of Evolutionary Genetics, mating systems chapters; Kingsolver et al. (2001). Measuring selection in natural populations. American Naturalist.

Week 9 – Local Adaptation & Ecological Genetics

Core: Kawecki & Ebert (2004). Conceptual issues in local adaptation. Ecology Letters; Savolainen, Lascoux & Merilä (2013). Ecological genomics of local adaptation. Nature Reviews Genetics

Supplementary: Nosil et al. (2009). Divergent selection and genomic divergence. Molecular Ecology; Rellstab et al. (2015). Environmental association analysis. Molecular Ecology

 Week 10 – Detecting Microevolutionary Processes

Core: Allendorf et al., Ch. 12–14; Beaumont & Rannala (2004). Bayesian inference of population history. Genetics;

Supplementary: Excoffier et al. (2013). Robust demographic inference from genomic data. PNAS; Hendry et al. (2008). Human influences on adaptive evolution. Evolutionary Applications

Additional instructions will be provided during the lecture.