It's still possible to register - if you hurry! but the course is almost full. 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 RADseq, genome sequencing & assembly, & SNP typing from raw reads to genotypes and many analyses to prepare you for future genomics data analyses. Instructors include experts: Eric Anderson, Ellie Armstrong, Jessica Da Silva, Marty Kardos, Brenna Forester, Paul Grobler, Will Hemstrom, Gordon Luikart, Monica Mwale, Rena Schweizer, Lisette Waits, Robin Waples, and more. When: December 7 - 12, 2025. Plus an optional December 13 -16 field trip to Kruger National Park Where: University of Pretoria, South Africa (https://www.up.ac.za/ ). Details and registration: see 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. Emphasis is on next-generation sequence data analysis (RADs, whole-genome sequence analyses) and interpretation of output from common and new statistical approaches, software, and bioinformatic pipelines. We teach how work from raw reads to produce quality genotypes and the crucial steps of filtering (Hemstrom et al. 2024). The course teaches the coalescent, Bayesian, and likelihood-based approaches. Special lectures and hands-on exercises are conducted on population structure, detecting selection, effective population size, landscape genomics, inbreeding detection (RoH), genome assembly, and more. Evening sessions allow hands-on analyses of your data with instructors. 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 and Linux (see below). BEFORE the course: Tutorials are given on Zoom 2-4 weeks before the course to help you learn Linux & R. Links to video recordings of past ConGen lectures. A field trip to amazing Kruger National Park is the 4 days after the course to learn wildlife and habitat ecology, and local research. Publication: We will likely publish together a meeting review (as 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. Additions/changes will be made following student requests. ConGen-Dec 2025, Pretoria, Africa (in-person, except the first five pre-course meeting) Nov 5th (Wednesday): Pre-ConGen Zoom introductions of instructor & students. Start networking! Nov. 12th: Pre-ConGen Zoom lecture on Basic R Studio & Linux Keynote lecturer: Will Hemstrom (with Rena Schweizer). Video-recorded for re-viewing. Nov 19th: Pre-ConGen Zoom Lecture: Bioinformatics concepts, technical skills Keynote lecturers: Rena Schweizer (USDA), G. Thomas (Harvard U). Recorded for re-viewing. Nov 26th: Pre-ConGen Zoom Lecture: The Coalescent. Video-recorded for re-viewing. Keynote lecturer: M. Miller, Will Hemstrom or Eric Anderson. Hands-on: Using your laptop: Coalescent simulations, and the Site Freq Spectrum Dec 3rd Pre-ConGen Zoom Lecture: Probability, Bayesian stats, MCMC, genotype likelihoods Keynote lecturer: Eric Anderson: Bayesian data analysis, MCMC, genotype likelihoods Hands-on: Using your laptop: Understanding genotype likelihoods, propagating uncertainty... Day 1 (Sunday, Dec. 7) - Arrival, move-in, computer testing, welcome & overview 5:00 - 6:15 PM Mixer and dinner 6:30-6:45 PM Welcome, course business, and introduction, Gordon Luikart and Monica Mwale 7:00-8:15 PM Introduction & overview of conservation genetics/omics Keynote address: Marty Kardos Day 2 (Monday, Dec. 8) - Topics: Markers, data filtering, Bayesian stats & genotype calling Markers in Conservation: microsats-to-WG-seq Keynote lecturer: Laura Bertola (with others) The F-word: Filtering best-practices, effects of F choices - on PCAs, etc. Keynote lecturer: Will Hemstrom Hands-on: Raw reads to genotypes without a reference, PCR duplicates, MAF, missing data Genotype calling without a reference genome: Raw reads to genotypes Keynote lecturer: TBA Hands-on: Raw reads to genotypes without a reference Conservation/Population genomics: Concepts & Tools to answer Eco-Evo questions Keynote lecturer: Paul Hohenlohe, (via Zoom) Day 3 (Tuesday, Dec. 9) - Filtering, HW, Ne, inbreeding & runs of homozygosity 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 Hands-on: Raw reads to genotypes - mapping to a reference genome Effective population size estimation Keynote lecturer: Robin Waples (via Zoom?) Hands-on: Effects sample size & Wahlund effects on Ne estimators? Day 4 (Wednesday, Dec. 10) - Forensics, Ne, Structure & Cons Units, Ne inference PID, Match probability Keynote lecturer: Paul Grobler Hands-on: Using DNA data, with Anri Assignment tests for forensics, conservation, and ecology (3:30 - 5:00 & evening) Keynote lecturers: Will Hemstrom, Andy Lee, C Bossu Hands-on: Microsatellites (Rubias), NG-seq data (WGSassign, OriGen msats or NGS) Inferring population structure and conservation units using genetics & omics Keynote lecturer: Brenna Forester, Chris Funk? Hands-on with background information: Delineating conservation units Inferring Ne from indicators (proxies) - overview & concepts Keynote lecturer: Jessica da Silva Hands-on: Infer Ne for several species (without using genetic data; Mtn Zebra, Buffalo) Day 5 (Thursday, Dec. 11) - Genome assembly, Landscape Genomics & Local Adaptation Genome sequencing & assembly: Conceptual and practical aspects Keynote lecturer: Ellie Armstrong, U of California Riverside, & Gregg Thomas, Harvard Hands-on: Genome sequencing & assembly, with Natalie Molea... Detecting local adaptation using genotype-environment associations Keynote lecturer: Brenna Forester Hands-on: Genotype-environment association analysis using RDA and LFMM - all instructors + regional managers. What to publish? Sharing resources: grant collaborations (Africa-USA-EU-etc.), markers, databases, reference individuals, data sharing, how to make it cheaper to run samples locally rather than overseas? Oxford NanoPore demonstration - assembly, amplicon seq Day 6 (Friday, Dec. 12) - multispecies analyses and eDNA Phylogenomics for research and conservation Keynote lecturer: Martin xxx Hands-on: Interpreting program outputs eDNA and Metabarcoding for conservation & biodiversity research Keynote lecturer: Sandi Willows-Munro. U KwaZulu-Natal. Hands-on: Lineage sorting, interpreting outputs. Filtering out non-target spp. Hands-on: diversity estimates, etc. Final 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 13-16). gordon.luikart@mso.umt.edu (to subscribe/unsubscribe the EvolDir send mail to golding@mcmaster.ca)