Topics of this course

Approaches to modeling a complex world

Laurence Loewe
To understand reality we have to represent it in simplified models that can be investigated. We will discuss (i) the tradeoff between complex realistic models that nobody understands and abstract models that are fully understood, but too simple to apply in any real situation, (ii) how to build high quality models and (iii) strengths and weaknesses of various approaches that allow us to simplify such models of reality. These approaches include deterministic - and stochastic - , top-down - and bottom up -, forward in time - and backward in time - as well as individual-based - and coalescent models.

The coalescent process

Laurence Loewe
Coalescent theory has been widely used to analyse molecular sequence data. After introducing the simplest basic coalescent model, we will discuss the impact of demography, recombination, population structure, strong selection and weak selection on the coalescent process. We will see how various population genetical parameters can be estimated from coalescent models and will consider limitations of this approach.

Inferring population structure from genetic data

Laurence Loewe
All biological populations have spatial structure and depending on their migration rates this structure can have a huge impact on the evolution of a population. We will discuss some elementary models of population structure and relevant parameters such as Fst that might be estimated assuming these models. One part will be devoted to population structure models without selection and another one to such models with selection. The latter are important to understand observable clines.

Detecting the effects of selection on DNA sequences

Laurence Loewe and Deborah Charlesworth
DNA sequences can vary within a species (diversity) and between species (divergence). Evolutionary theory can predict diversity and divergence, if the corresponding parameters are known. Using the null-hypothesis that all sequences are completely neutral, one can derive a number of statistical tests that allow detecting selection. We will look at tests based on measures of diversity, of divergence and of a combination of the two. Finally we will discuss balancing selection.

Phylogenetic methods

Andy Leigh-Brown
Ever since Darwin drew the first phylogenetic tree, many researchers have worked on estimating phylogenetic trees from features observed in extant organisms. The recent deluge of DNA sequences has lead to the development of rigorous methods for the construction of trees. Here we will discuss the strengths and weaknesses of various tree-constructing methods.

Evolutionary genetics of wild animal populations

Loeske Kruuk, Alastair Wilson and Josephine Pemberton
We describe studies of evolutionary genetics in the wild, using results from wild populations experiencing natural environments. We show how the pedigree information now available for several long-term studies of wild mammal and bird populations can be used to estimate: (i) heritabilities and genetic correlations, using the animal model; (ii) patterns of natural selection; (iii) inbreeding depression. Many of the results presented illustrate the impact of prevailing environmental conditions on microevolution, and hence underline the value for data from natural populations for a full understanding of evolutionary processes.

Background reading

• Page & Holmes (1998) Molecular evolution: a phylogenetic approach, Blackwell Science.
• Graur & Li (1999) Fundamentals of molecular evolution, Sinauer.
• Li (1997) Molecular evolution, Sinauer.
• Roff (1997) Evolutionary quantitative genetics, Chapman Hall.
• Revisit this list for updated recommendations.