Course Materials
Fred Allendorf
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
UC Davis page on Unix and Perl for Biologists
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
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
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
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
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