Population Genomics Data Analysis Course & Workshop Themes: Conservation Genetics, Population Genomics, and Molecular Ecology. Understanding Population Structure and Environmental Influences on Genomic Variation - using Next Gen Sequencing Data & key computational approaches. Includes filtering from raw reads to genotypes and many analyses to prepare you for future genomics data analyses. When: December 7 - 13, 2025. First Lecture Sunday night (7th), last lecture Saturday 13th Where: University of Pretoria, South Africa (https://www.up.ac.za/ ). Details and registration: see below and https://www.umt.edu/congen/africa/ Course Objective: To teach conceptual and practical aspects of data analysis to understand the evolutionary and ecological genomics of natural and managed populations. Who should apply: Advanced Undergrads, M.S. & Ph.D. students, post-docs, PIs (agency biologists), and faculty who have understanding of population genetics & population ecology, R Linux. What you receive: 3 Lectures a day (video-recorded) by >12 expert instructors with question & answer sessions, copies of PowerPoints, hands-on exercise worksheets. Trip: Kruger National Park Publication: We will likely publish together a meeting review (e.g., below) to help advance the field and improve your ability to publish. Schweizer et al. 2021: doi.org/10.1093/jhered/esab019; Stahlke et al. 2020: doi.org/10.1093/jhered/esaa001; Hendricks et al. 2018: doi.org/10.1111/eva.12659 Tentative Course Agenda - see also https://www.umt.edu/congen/africa/ ConGen-December 2025, Pretoria, Africa (in-person, not on-line) Nov. 5th (Wednesday): Pre-ConGen Zoom lecture on Basic R Studio & Linux Keynote lecturer: Will Hemstrom (with Rena Schweizer). Video-recorded for re-viewing. Nov 12th (Wednesday): Pre-ConGen Zoom Lecture: Bioinformatics concepts & skills Keynote: Rena Schweizer (USDA), Gregg Thomas (Harvard U). Recorded for re-viewing. Nov 19th (Wednesday): Pre-ConGen introductions of instructors & students. Networking! *note: daily sessions allow you to analyze your data, network, and discuss ideas with instructors Day 1 (Sunday, Dec. 7) - Arrival, move-in, welcome, overview lecture 5:00 - 6:30 PM Mixer and dinner 6:30-6:45 PM Welcome, course business, and introduction, Gordon Luikart, Monica Mwale 7:00-8:15 PM Introduction & overview of conservation genetics/omics Keynote address: Marty Kardos, formerly of NOAA, National Marine Fisheries Service, USA Day 2 (Monday, Dec. 8) - Topics: Coalescent, stats, data filtering, genotype calling The Coalescent Keynote lecturer: Eric Anderson, formerly of National Marine Fisheries Service, California Hands-on: Using your laptop: Coalescent simulations, and the Site Freq Spectrum Bayesian statistics, probability, MCMC, genotype likelihoods for Next Gen seq data Keynote lecturer: Eric Anderson: Bayesian data analysis, MCMC, genotype likelihoods Hands-on: Using your laptop: understanding genotype likelihoods, propagating uncertainty The F-word: Filtering best practices, effects of F choices - on PCAs, etc. Keynote lecturer: Will Hemstrom, Colorado State Univ. Hands-on: Raw reads to genotypes without a reference, PCR duplicates, MAF, missing data Conservation/Population genomics: Tools to answer Ecological/Evolutionary questions Keynote lecturer: Paul Hohenlohe, University of Idaho, Moscow. (via Zoom) Day 3 (Tuesday, Dec. 9) - Filtering, HW, Ne, inbreeding, RoH, genotyping Hardy-Weinberg testing & filtering effects on selection detection Keynote lecturer: Will Hemstrom Hands-on: Testing for deviations from HWP. Filtering effects on selection signal detection Inbreeding, runs of homozygosity, LD distributions, & Identification of deleterious alleles Keynote lecturer: Marty Kardos Hands-on: Inbreeding estimation and RoH data analysis with R Raw reads to genotypes: Reference-based genotyping with the GATK pipeline Keynote lecturer: Rena Schweitzer, USDA, USA Hands-on: Raw reads to genotypes - mapping to a reference genome Effective population size estimation Keynote lecturer: Robin Waples?, NOAA, NMFS, U Washington, Seattle (via Zoom?) Hands-on: Effects sample size & Wahlund effects on Ne estimators? Day 4 (Wednesday, Dec. 10) - Forensics, Ne-estimation, Structure & Conservation Units Forensics, PID, Match probability Keynote lecturer: Paul Grobler, UFS, Bloemfontein, Free State, South Africa Hands-on: Using DNA data Inferring Ne from indicators (proxies) - overview & concepts Keynote lecturer: Jessica da Silva Hands-on: Infer Ne for several species (without using genetic data) Inferring population structure and conservation units using genetics & omics Keynote lecturer: Brenna Forester, US Fish & Wildlife Service Hands-on with background information: Delineating conservation units Assignment tests for forensics, conservation, and dispersal ecology Keynote lecturers: Will Hemstrom with Natalie Molea (U Montana) & Matthew DeSaix, USDA Hands-on: Microsatellites, NG-seq data Applications including GTseq Keynote lecturer: Lisette Waits, U Idaho Day 5 (Thursday, Dec. 11) - Structure & ESUs, Genome sequencing and assembly Detecting local adaptation using genotype-environment associations Keynote lecturer: Brenna Forester, U.S. Fish and Wildlife Service Hands-on: Genotype-environment association analysis using RDA and LFMM Conceptual and practical aspects of genome sequencing & assembly Keynote lecturer: Ellie Armstrong, U of California Riverside, & Gregg Thomas, Harvard Hands-on: Genome sequencing & assembly Discussion: Improving use of genetics for management - all instructors + regional managers Day 6 (Friday, Dec. 12) - multispecies analyses and eDNA Phylogenomics for research and conservation Keynote lecturer: Sandi Willows-Munro, U KwaZulu-Natal. Hands-on: Lineage sorting, interpreting program outputs eDNA and Metabarcoding for conservation & biodiversity research Keynote lecturer: Steven Spear(?), US Geological Survey. Hands-on: diversity estimates, etc. Discussion: Future directions, final questions, advice, and publishing a ConGen Review! Day 7 (Saturday, Dec. 13) - All depart, or Field trip to Kruger National Park (Dec. 13-17). Dec. 17 - field trip folks depart (e.g., from Jo-Berg Airport) gordon.luikart@mso.umt.edu (to subscribe/unsubscribe the EvolDir send mail to golding@mcmaster.ca)