Course Materials
Fred Allendorf
please watch the video found here:
http://www.crafoordprize.se/events.4.2f692b3510dbfce339680003497.html
Jim Seeb
- Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncohynchus tshawytscha)
- Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in shim salmon (Oncorhynchus keta)
- Single-nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing improve genetic stock identification of Chinook salmon (Oncorhynchus tsawytscha) from western Alaska
Mike Miller
1st lecture
2nd lecture
pages to visit:
http://korflab.ucdavis.edu/Unix_and_Perl/
Paul Hohenlohe
1st lecture
- Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences
- Using Population Genomics to Detect Selection in Natural Populations: Key Concepts and Methodological Considerations
2nd lecture
- Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing
- Neandertals and Moderns Made Imperfect Mates
- The Genetic Structure of Admixed Populations
Long Test (and other downstream analyses) for detecting admixture outliers
http://webpages.uidaho.edu/hohenlohe/2015_ConGen_1.pptx
http://webpages.uidaho.edu/hohenlohe/2015_ConGen_2.pptx
Lisa Seeb
- BayeScan v2.0 User Manual
- Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations
- Temporally Isolated Lineages of Pink Salmon Reveal Unique Signatures of Selection on Distinct Pools of Standing Genetic Variation
Tiago Antao
https://wiki.galaxyproject.org/Learn
Pleae visit the above webpage for assigned readings.
Robin Waples
1st lecture
- Effects of Overlapping Generations on Linkage Disequilibrium Estimates of Effective Population Size
- Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tsawytscha)
- Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution
2nd lecture
- Environmental selection of transciptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)
- Harnessing genomics for delineating conservation units
- What is population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity
Johnathon Pritchard
- Clonal Origin and Evolution of a Transmissible Cancer
- Documentation for structure software: Version 2.
- Muriga et al. 2006
- http://pritchardlab.stanford.edu/teaching/congen/readme
- http://pritchardlab.stanford.edu/teaching/congen/all_dogs_and_CTVT.str
- http://pritchardlab.stanford.edu/teaching/congen/asiandogs_wolves_CTVT.str
2015 Nature Fine Structure British Genomics
Brian Hand
- Disentangling the Effects of Evolutionary, Demographic, and Environmental Factors Influencing Genetic Structure of Natureal Populations: Atlantic Herring as a Case Study
- Ten years of landscape genetics
pages to visit:
Gordon Luikart
Kate Kendall
Likely hike to Stanton Lake (photo)
Brice Sarver
High-Throughput Sequencing: from Raw Reads to Variants
Molecular Ecology, Killy Whale Phylogeny
Jeff Good
Joanna Kelley
Tabatha Graves
A practical guide to environmental association analysis in landscape genomics
General
Bernatchez Worlflow Presentation