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
Teachers:
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 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 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
file 2 eweLambsWithLRS
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 2003 Materials