Short course: The Search for Selection
Venue: Roslin Institute, University of Edinburgh
Dates: Oct 15-19 2018,
Instructor: J. Bruce Walsh, Ecology & Evolutionary Biology, Univ. of Arizona
Biologists are obsessed (indeed, seduced) by the search for signatures of selection in organismal features of interest, ranging from specific traits to genome-wide signatures. A vast number of approaches have been suggested in this search for selection, including genomic-based signatures of recent or ongoing selection, tests based on either excessive amounts or nonrandom patterns of divergence (in both fossil sequences and functional genomics data) and the more classical Lande-Arnold fitness estimates (direct association of phenotypic values with fitness estimates) and their modern extensions (such as aster models). Given the breadth of such searches, a large amount of machinery has been developed, but is rarely presented in a unified fashion. This course presents an integrated overview of all these approaches, highlighting common themes and divergent assumptions.
The goal of this course is to expose investigators from all branches of biology to this rich menagerie of tests, applicable for population geneticists, genome biologists, evolutionary ecologists, paleontologists, functional morphologists, and just about any biologist who ponders on how to formally demonstrate that a feature (or features) of interest might have been shaped by selection.
The intended audience is advanced graduate students, postdocs, and faculty with an interest in searching for targets of selection, be they particular genomic sequences or specific traits. Given the breadth of this topic, the material is of interest to students from functional genomics, population and evolutionary genetics, ecology, paleobiology, functional morphology, and statistics (as well as other fields). Background required: some basic introduction to population and/or quantitative genetics.
This course is based on material from Chapters 8-10, 12, and 29-30 in Walsh and Lynch (2018) Evolution and Selection of Quantitative Traits (Oxford). While this text is not required, it does present much more detail discussion (with detailsed references) of the material to be covered.
Day 1: Tests of neutral trait divergence (WL Chapter 12)
Lecture 1: Drift in the mean of Quantitative Traits
Lecture 2: Rate-based and time-series based tests
Lecture 3: Qst vs Fst
Lecture 4: Orr QTL tests (and their extensions)
Day 2: Tests based on Molecular Data I (WL Chapters 8, 9)
Lecture 5: Sweep theory
Lecture 6: Genome-wide Signatures from repeated past selection
Lecture 7: Polymorphism-based tests 1: Allele frequency changes and Lewontin-Krakauer tests
Lecture 8: Polymorphism-based tests 2: Genome pattern-based tests and SFS tests
Day 3: Tests based on Molecular Data II (WL Chapters 9, 10 )
Lecture 9: Polymorphism-based tests 3: Haplotype-based tests
Lecture 10: Polymorphism-based tests 4: Domestication genes and other examples Lecture 11: Divergence-based tests 1: HKA and MK tests
Lecture 12: Divergence-based tests 2: Rate of adaptive substitutions, Poisson random field models
Day 4: Estimating Individual fitness (WL Chapter 29)
Lecture 13: Episodes of Selection and the Assignment of Fitness
Lecture 14: Variance in Individual Fitness, Bateman gradients, Trait-fitness associations I
Lecture 15: Descriptions of Phenotypic Selection 1: Basics
Lecture 16: Descriptions of Phenotypic Selection 2: Fitness surfaces
Day 5: Trait-fitness associations II (WL Chapter 30)
Lecture 17: Multivariate selection 1: Basics
Lecture 18: Multivariate selection 2: Fitness surfaces
Lecture 19: Final topics and wrap-up