Tentative Course Agenda. Additions/changes will be made following student requests.
ConGen-Dec 2025, Pretoria, Africa (in-person, except the first five pre-course meetings)
Nov 5th (Wednesday): Pre-ConGen Zoom introductions of instructors & 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, Gene Flow/Connectivity
PID, Match probability
Keynote lecturer: Paul Grobler
Hands-on: Using DNA data, with Anri
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 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 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) – Structure & ESUs, Genome sequencing and assembly
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, U.S. Fish and Wildlife Service (w/ C Funk)
Hands-on: Genotype-environment association analysis using RDA and LFMM
Discussion: Improving use of genetics for management – 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).