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 (draft)

 

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

Introduction and overview; Drift; QST vs FST; Orr QTL tests and their extensions with applications to genomic data

 

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

The neutral theory; Sweep theory; Detecting selection with markers.

 

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

Detecting selection with markers (c’td); Selection scans in humans and domesticated organisms; Divergence-based tests; Rate of adaptive substitutions

 

Day 4: Estimating Individual fitness (WL Chapter 29)

Episodes of Selection and the Assignment of Fitness; Variance in Individual Fitness, Sexual Selection; Univariate trait-fitness associations; Descriptions of Phenotypic Selection

 

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

Multivariate selection

 

 

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

 

 

Course Fees:

 

 

 Students

Academics

Other

Fees in AU$

 440

605

825

Prices include GST (10%),

UNE personnel should not pay GST component

 

Register online:

 

            https://une.onestopsecure.com/onestopweb/aabcsummercourse20

 

                        UNE staff and students should not book online

 

 

Accommodation

                        On Campus at Mary White College    use Casual 2020 bookings:

 

This facility will become available later (~October 2019 )                  

 

MWC Accommodation is in standard student style rooms, shared bathroom facilities and is subject to availability at the time your booking request is submitted.

 

The nightly rate is ~$70.00 per person room only (meals are not available) linen is provided.

 

Please refer to the Armidale Tourism site for town accommodation options.

 

 http://www.armidaletourism.com.au/

            Note that the town is about 5 km from the campus

 

 

 

 

 

 

 

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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