ConGen-2026 OnLine (8 weeks: Sept. 24– Nov. 13th)
*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
Tentative Lecture topics/titles:
(8 to 9:50 AM Mountain time; some lectures run until 10:30 AM):
ConGen-2026 Online (7 weeks: Sept. 25 to Nov. 13th)
Draft 1 Sept. (subject to change)
Tentative Lecture Topics/Titles
(8 to 9:50 AM Mountain time; some lecture run until 10:30 AM-ish):
Course Welcome and Introductions of Students & Instructors. Gordon Luikart, Sept. 25
The Role of Genomics in Conservation – an Overview, Keynote Lecture. Marty Kardos, Sept. 28
Basic R, Linux, 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
Population genomics: Concepts & tools to answer eco-evo questions. Paul Hohenlohe, Oct. 5
Probability, Bayesian statistics, 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), TBD, Oct. 16
Inferring population structure & units (ESUs) using genomics. Chris Funk, Brenna Forester, Oct. 19
Effective population size estimation. Robin Waples, Oct. 21
PPPr and gene flow or hybridization. Arun Sethuraman, Oct. 23
Genome sequencing & assembly: Conceptual and practical aspects. Ellie Armstrong, Oct. 26
Assignment tests for ecology & conservation (WGSassign, GeneClass), Matt DeSaix, Oct. 28
Detecting local adaptation (Landscape Genomics), Brenna Forester, 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
Gene expression and adaptation. Joanna Kelley, Nov. 9
Testing for selection signatures, Nick Bermentelo, Nov 11
Final Discussion: Final discussion, future research, & publishing a ConGen note, Nov. 13
**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.