ConGen-2026 OnLine (8 weeks: Sept. 24– Nov. 11th)
*We provide Pre-ConGen Video lectures to help you prepare for ConGen, and see ** below
*Most lectures below have hands-on exercises with worksheets and practice datasets
Lecture topics/titles:
Course welcome and introductions of students & instructors. Gordon Luikart, Sept. 24
The role of genomics in conservation – an overview, Keynote Lecture. Marty Kardos, Sept. 28
Basic R, Linus, fastq file format, and basics of next-gen sequence data. Will Hemstrom, Sept. 30
Scripting, data handling, & organizing bioinformatics projects. Rena Schweizer, G. Thomas, Oct. 2
Pop genomics: Concepts & tools to answer eco-evo questions. Paul Hohenlohe, Oct. 5
Probability, Bayesian stats, MCMC, genotype likelihoods. Eric Anderson, Oct. 7
The Coalescent: theory and applications. Arun Sethuraman, Oct. 9
Raw sequence reads to genotypes with vs. without a reference genome. Will Hemstrom, Oct. 12
Filtering (QC) best-practices & effects on downstream analyses, Hemstrom et al. 2024, Oct. 14
Inbreeding and runs of homozygosity (RoH), Marty Kardos, Oct. 16
Genome sequencing & assembly: Conceptual and practical aspects. Ellie Armstrong, Oct. 19
Effective population size estimation. Robin Waples, Oct. 21
Parentage assignment. Jared Grummer, Oct. 23
Inferring population structure & units (ESUs) using genomics. Chris Funk, Brenna Forester, Oct. 26
Assignment tests for ecology & conservation (WGSassign, GeneClass), Matt DeSaix, Oct. 2
Detecting local adaptation (Landscape Genomics), Brenna Forester, Oct. 28
PPPr and gene flow or hybridization (IMA) Arun Sethuraman, Arun Sethuraman, Oct. 30
BayesAss and contemporary gene flow (m) estimation, Bruce Rannala, Nov 2
Phylogeny and phylogenomics, Schuyler Liphardt, Nov. 4
eDNA Metabarcoding (biodiversity monitoring, diet analysis, microbiomes…), Steve Spear, Nov. 6
Genomic basis of adaptation: Example from mice and lagomorphs. Jeff Good, Nov. 9,
Final Discussion: Final discussion, future research, & publishing a ConGen note, Nov. 11
Other Lectures (or breakout groups) possible if students request them:
Relatedness, kinship, & parentage assignment
Gene flow estimation (current and historical via BayesAss and Migrate)
Hybridization detection, quantification, and testing for adaptive invasive alleles
GWAS Genome wide association testing (or GWAA)
Population abundance estimation, e.g., Close-Kin Mark-Recapture (CKMR), non-invasive sampling
Selection tests: Fst-outlers (Bayscan, OutFlank), Allele Frequency Spectrum (AFS), etc.
**Please LET US KNOW a lecture topic you’d like added to ConGen as we will consider it!
**This course provides lectures and exercises introducing you to R, Linux, and coding, during Week 1. Before Week 2, you will be able to write a BASH script to automate components of your bioinformatics analyses. Also, a month before the course, we provide links to video lectures introducing you to R, Linux, and reviewing concepts (nucleotide diversity, site frequency spectra, etc.). For coding, you can also consider doing the “DataCamp” at https://www.datacamp.com/courses/introduction-to-bash-scripting. Also: see “Learning the Shell” at LinuxCommand.org: Learning the shell. The data camp is free and lasts up to 3-4 hours.