Armidale Animal Breeding Summer Course 2020

Venue: University of New England, Armidale, NSW Australia

Course Audience: Postgraduate students and other professionals




The Search for Selection



Professor Bruce Walsh                      University of Arizona (USA)

Dr Michael Morrissey            University of St Andrews (UK)


Dates:     Monday 3 February 2020 (9am) – Friday 7 February 2020 (4pm)

Content:         The search for selection

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) for ecological data. 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 material covered comes from Chapters 8-10, 12, and 29-30 of Walsh and Lynch (2018) Evolution and Selection of Quantitative Traits (Oxford).

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.

Intended Audience

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 particular traits.  Given the breadth of this topic, the material would be 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.


Program 2020 (Feb 3-7)


Intro/refresher on Matrix Algebra


 Day 1: Tests of neutral trait divergence (WL Chapter 12)


Lecture 1:  Introduction and overview

Lecture 2:  Drift in the mean of Quantitative Traits: Rate-based and time-series based tests

Lecture 3:  QST vs FST

Lecture 4:  Orr QTL tests and their extensions with applications to genomic data


Day 2: Tests based on Molecular Data I (WL Chapters 8, 9)


Lecture 5:  Background: The neutral theory (WL Chapters 2, 4)

Lecture 6:  Sweep theory

Lecture 7:  Detecting selection with markers.  I. Overview

Lecture 8:  Detecting selection with markers.  2. Polymorphism-based tests I


Day 3: Tests based on Molecular Data II (WL Chapters 9, 10)


Lecture 9: Detecting selection with markers.  3. Polymorphism-based tests II

Lecture 10: Selection scans in humans and domesticated organisms

Lecture 11:  Divergence-based tests 1: HKA and MK tests, codon models

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, Sexual Selection


Practical Tasks

Practical file 1 ramLambs

Practical file 2 eweLambsWithLRS

Practical Solutions


Day 5: Multivariate trait-fitness associations (WL Chapter 30)


Lecture 17:  Multivariate selection 1: Basics

Lecture 18:  Multivariate selection 2: Fitness surfaces and path analysis


WL = Walsh and Lynch, Evolution and Selection of Quantitative Traits, Oxford (2018)


Photos (click on photo to download)










Material of previous years:


Armidale Genetics Summer Course 2019    Materials

·         Introduction to Graphical Models with Applications to Quantitative Genetics and Genomics: Guilherme Rosa and Francisco Peñagaricano


Armidale Genetics Summer Course 2018    Materials

·         Mathematical modeling of infection dynamics in genetically diverse livestock populations: Andrea Doeschl-Wilson and Osvaldo Anacleto          


Armidale Genetics Summer Course 2017    Materials

·         Genotype by environment interaction in breeding programs: Piter Bijma and Han Mulder           


Armidale Genetics Summer Course 2016    Materials


Investigating the Genetic Architecture of Complex Traits  & Prediction of Phenotype

from Genome-wide SNPs - Doug Speed and David Balding


Armidale Animal Breeding Summer Course 2015   Materials

                    Primer to genomic analysis using R:    Cedric Gondro

                    From Sequence Data to Genomic Prediction:   Ben Hayes and Hans Daetwyler


Armidale Animal Breeding Summer Course 2014    Materials

Breeding Program Design with Genomic Selection: Jack Dekkers, Julius van der Werf


Armidale Animal Breeding Summer Course 2012    Materials

Statistical Methods for Genome-Enabled Selection: Daniel Gianola, Gustavo de los Campos 


Armidale Animal Breeding Summer Course 2011    Materials

·         Statistical methods and design in plant breeding and genomics: Ian Mackay

·        IBD inference in genome association studies: Elizabeth Thompson


Armidale Animal Breeding Summer Course 2010    Materials

·         Application of evolutionary algorithms to solve complex problems in quantitative genetics

and bioinformatics:   Brian Kinghorn, Cedric Gondro

·         Bayesian methods in genome association studies:  Dorian Garrick,  Rohan Fernando


Armidale Animal Breeding Summer Course 2009    Materials

·        Quantitative Genetic Theory and Analysis- Selection Theory:    Bruce Walsh

·         Quantitative Genetic Models for social interaction and inherited variability: Piter Bijma


Armidale Animal Breeding Summer Course 2008      Materials 

·         Genomic Selection:       Ben Hayes


Armidale Animal Breeding Summer Course 2007      Materials

·         Generalized Linear Mixed Models:        Steve Kachman


Armidale Animal Breeding Summer Course 2006    Materials

·         Gene Expression:          Toni Reverter

·         Breeding Program Design:         Graser, James, Van der Werf

Armidale Animal Breeding Summer Course 2005    Materials
·         Breeding Objectives: Gibson, Van der Werf, Kinghorn
·         Scientific Writing:          David Lindsay
·         ASReml:           Arthur Gilmour
Armidale Animal Breeding Summer Course 2004    Materials
·         Bayesian for Beginners               Kerrie Mengersen
·         Bayesian Models for QTL analysis        Michel Perez-Enciso
·         Bioinformatics   John McEwan

Armidale Animal Breeding Summer Course 2003    Materials

·         Scientific Writing:  David Lindsay
·         Linear Models for animal breeding:   Julius van der Werf, Mike Goddard
·         QTL mapping for practitioners, from linkage to gene: Ben Hayes, Julius van der Werf
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