Evolutionary Genetics: Part 0.2

Introduction to Population genetics

S. peruvianum

S. chilense

Winter Semester 2012-2013

Prof Aurélien TellierFG Populationsgenetik

Population genetics

Why study the genetics of populations?

� the population is the main unit at which selection acts !!!!!!!!!

Evolution = changes between generations of frequency of

characters, traits or alleles

Population genetics

Populations and species show variability:

� what type and how much genetic variation exist within

populations/species?

� what are the forces that influence the amount of variation

within populations?

Population genetics: 4 evolutionary forces

random genomic processes

(mutation, duplication, recombination, gene conversion)

natural

selection

random demographic

process (drift)

random spatial

process (migration)

molecular diversity

Population genetics investigates the laws governing the genetic structure of

populations, and changes in allele frequencies over time

Population genetics: 4 evolutionary forces

random genomic processes

(mutation, duplication, recombination, gene conversion)

natural

selection

random demographic

process (drift)

random spatial

process (migration)

molecular diversity

We want to infer the role of the evolutionary forces from sequence data

(very useful tool is the coalescent theory)

phenotypic

variability

Population genetics

Populations and species show variability:

� what type and how much genetic variation exist within

populations/species?

� what are the forces that influence the amount of variation

within populations?

� how can population genetics principles be used to

address questions in human health, environmental issues,

and evolution?

Population genetics: applications

Examples and case studies of population genetics applications

� E1: Study of Biodiversity

� E2: Conservation genetics

� E3: Interactions host-parasites

� E4: Genetic exchanges between species

� E5: Genetic exchanges between populations

� E6: Genetic barriers

� E7: Genetic exchanges between individuals

� E8: Legal medicine

� E9: Gene evolution

� E10: Localization of genes

� E11: Understanding mechanisms of adaptation

� E12: Reveal the demographic history of species

E1: Study of Biodiversity

� Counting species

� Characterizing the genetic diversity of endangered species in relation to group/population sizes, inbreeding

� Ex. Cheetah in Namibia, Elephants, Northern Spotted owls, Grizzli bears, …

E2: Conservation genetics

� Conservation genetics and reserve of genetic resources

� Animal breeding (Oysters), Fish farms (salmon, trouts)

� Newly re-introduced species (Alpine Ibex and Lynx in the Alps)

E2: Conservation genetics

� Conservation genetics and reserve of genetic resources

� Banks for seeds of endangered plant species

� Determine and assess the genetic diversity of crop ancestors => preserve source of new characters for crop improvements

E3: Interactions host-parasites

� Correlation between host and parasite genetic diversity

� Adaptation of parasites to hosts, how fast do parasites adapt?

� Transmission of resistance factors between strains (esp. antibiotics)

� Selection in virus (HIV) or bacteria during multiplication in hosts

E3: Interactions host-parasites

� Evolution of human/animal parasites

Tanabe et al. 2010: Origin and population structure of Plasmodium falciparum (malaria)

E3: Interactions host-parasites

� Evolution of human/animal parasites

Yalcindag et al. 2012: Origin and population structure of

Plasmodium falciparum in South-America

E3: Interactions host-parasites

� Examples of plant-parasite coevolution

Stuckenbrock et al. 2011, Evolution of Mycosphaerella graminicola pathogen of wheat

E3: Interactions host-parasites

� Examples of new emergent diseases on animals and plants

E4: Gene flow between species

� Study the existence of hybrid species (often in plants)

� Hybrid zones: for house mice (Mus musculus)

Bonhomme et al. 2007

E4: Gene flow between species

� Horizontal gene transfer from one species to another: ex of virulence factors in

parasite to favor host-jump

Gardiner et al. 2012: horizontal gene transfer between fungal pathogens on wheat and

barley

E5: Gene flow between populations

� Understand migration between populations, migration flow between human populations

� Reconstructing the history of colonization of new environment

� Reassign people to populations (recent migrants)

Alves et al. 2012 Admixture between

Neanderthals and recent hominids?

E6: Barriers to gene flow

� Reveal genetic barriers between species or sub-species (important in conservation)

� Behavioral barriers (mating avoidance,…)

� Cultural or social

E7: Genetic exchanges between individuals

� Choice of partner

� is this choice random? Studies show that in human, mice, fish, individuals

prefer complimentary individuals for their HLA/MHC system

� Inbreeding

� Tests for genetic diseases

Charles II inbreeding coefficient = 0.254

E8: Legal medicine

� Genetic prints

� identification of suspects

E9: Gene evolution

� More examples will come later

�Intraspecific

� Estimation of divergence between populations

� Interspecific

� Divergence time between species

� Molecular Taxonomy

� Intergenic

� divergence between duplicated genes

� rates of gene conversion

Wheeler et al. PNAS 2001

Marko and Hart Trends Evol 2011

E10: Gene localization

� Find genes for human diseases

� linkage analysis in a family

� linkage disequilibrium mapping

� Genome wide association studies (GWAs)

� Quantitative traits loci (QTLs)

E11: Mechanisms of adaptation

� Reveal mechanisms of adaptation

� clines in frequency of alleles

� selection at HLA/MHC alleles

� speciation processes: which mutations are involved?

E12: Demographic history of species

� Demographic expansions, Demographic bottlenecks

� Domestication of plants or animals (apples, wheat, maize, …)

� Expansion of viral or bacterial strains

� Effect of climatic changes on population sizes

�Mechanisms of colonization from a glacial refugia