Tentative (near final) Course Agenda.
ConGen-Dec 2025, Pretoria, Africa (in-person, except the first five pre-course meetings)
NOTE: lecture lengths below are approximate & might go longer, e.g. if a hands-on or discussions require more time.
Nov 12th (Wednesday, 3 PM Pretoria time, 6 AM USA Mountain time): Pre-ConGen Zoom: course business, and Introductions of instructors & students. Students start networking! Video-recorded, ~1.5 hours. Recommended reading: Schiebelhut et al. 2023 – Mol. Ecol. Res
Nov. 17th: (3 PM Pretoria time) Pre-ConGen Zoom lecture on Basic R Studio & Linux
Keynote lecturer: Will Hemstrom (with Laura Bertola). Video-recorded, ~1.5 hours.
You will be sent online login info when the cloud server is ready and available.
You can email congen.it.help@gmail.com and Ted, Leif, Will or Laura for advice.
Nov 19th: Before this Lecture, watch the video-lecture on “Bioinformatics concepts, technical skills” by Rena Schweizer (USDA) & G. Thomas (Harvard U) at: . https://drive.google.com/file/d/1TQlqT5RrVQgnm9sFAjgIHj836jAbOvFy/view?usp=sharing Keynote lecturers: Laura Bertola, Will Hemstrom, Arun Sethuraman. “Q & A and advice on Bioinformatics for this course”. We’ll conduct a brief hands-on activity to get you ready for the course.…Please know at least several Bash Shell commands before Nov 19th. Consider doing the “DataCamp” at https://www.datacamp.com/courses/introduction-to-bash-scripting, and/or “Learning the Shell” at http://linuxcommand.org/lc3_learning_the_shell.php. The data camp is free and lasts up to 3-4 hours.
Nov 24th (4 PM Pretoria time) NanoPore sequencing & genotyping for conservation.
Keynote: Shane Murray, Diplomics of South Africa, Video-recorded, ~1 hour
Applications of NanoPore technologies, the 1K genomes project across South Africa.
Nov 26th: (3 PM Pretoria time) Pre-ConGen Zoom Lecture: The Coalescent. Recorded, ~2 hours.
Keynote lecturer: Arun Sethuraman
Hands-on: Using your laptop: Coalescent simulations, and the Site Freq Spectrum
Recommended reading: TBD
Dec 3rd (3 PM Pretoria time, 6 AM USA MT) Pre-ConGen Zoom Lecture: Probability, Bayesian stats, MCMC, genotype likelihoods. Recorded, 2 hours.
Keynote lecturer: Eric Anderson
Hands-on: Using your laptop: Understanding genotype likelihoods, propagating uncertainty…
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Day 1 (Sunday, Dec. 7) – Arrival, move-in, computer testing, welcome & overview
5:00 – 6:30 PM Mixer and dinner
6:30 - 6:45 PM Welcome, course business, and introduction, Gordon Luikart
7:00 - 8:00 PM Introduction & overview of conservation genetics/omics
Keynote address: “The expanding role of genomics in conservation”, Marty Kardos
Recommended reading: TBD
Day 2 (Monday, Dec. 8) – Topics: Markers, data filtering, genotype calling w/ next gen data
8:00 - 9:00 AM Markers in Conservation: microsats-to-WG-seq
Keynote lecturer: Laura Bertola
Recommended reading: Schiebelhut et al. (2023 – section 1.2.1). Chap 4 in Allendorf book
9:00 - *12:00 AM The F-word: Filtering best-practices, effects of F choices - on PCAs, etc.
Keynote lecturer: Will Hemstrom (with Laura)
Hands-on: Raw reads to genotype calling without a reference (STACKS), PCR dups, MAF, etc.
*coffee break around 10:30
Recommended reading: Hemstrom et al. 2024-NRG
1:00-4:30 PM Genotype calling with a reference genome: Raw reads to genotypes
Keynote lecturer: Rena Schweitzer
Hands-on: Raw reads to genotypes without a reference
*coffee break around 2:30
Recommended reading: TBD
4:00- 5:00 PM Q & A with all instructors (genotype calling, questions on your data, etc.)
7:00- 8:00 PM Conservation/Pop genomics: Concepts & tools to answer eco-evo questions
Keynote lecturer: Paul Hohenlohe (via Zoom)
Recommended reading: TBD
8:00- 9:00 PM Q & A with all instructors in person (or via a brief Zoom call for with an instructor if
you/we schedule it in advance)
Day 3 (Tuesday, Dec. 9) – Filtering, HW, Ne, inbreeding & runs of homozygosity
8:00- 10:00 AM 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
Recommended reading: TBD
10:00-10:30-ish Coffee Break
10:30-12:00 Continued: Hardy-Weinberg & filtering effects, forensics, Ne
1:00- 4:00 PID, Match probability, forensics applications
Keynote lecturer: Paul Grobler
1:00- *4:00 PID continued
Hands-on: Using DNA data for computing PID, detecting poaching, etc.
*Coffee break around 2:30
Recommended reading: TBD
4:00- 5:00 PM Q & A with instructors (HW, filtering, genotyping, ask about your data or research)
7:00- 8:30 PM (11 AM MT USA): Inbreeding, runs of homozygosity, LD distributions,
& identification of deleterious alleles
Keynote lecturer: Marty Kardos
Hands-on: Inbreeding estimation and RoH data analysis with R
Recommended reading: TBD
8:30- 9:00 PM Q & A with all instructors in person (or Zoom if you/we schedule it)
Day 4 (Wednesday, Dec. 10) – Genome assembly, Structure & Cons Units, Ne inference
8:00- 9:15 AM Genome sequencing & assembly: Conceptual and practical aspects
Keynote lecturer: Inqaba Biotec
9:15- 10:00 Demonstration of the1kSA pipeline, & discussions of pipelines & technologies
Keynote lecturer: Tina Meiring
Recommended reading: TBD
10:00 Coffee break
10:30- 12:00 Hands-on with background information: Assembling the Hornbill genome
Keynote lecturers: Ellie Armstrong (with Natalie Molea)
Recommended reading: TBD
1:00- 2:00 continued: Hands-on with background information: Assembling the Hornbill genome
2:30- *5:00 Inferring population structure and conservation units using genetics & omics
Keynote lecturer: Chris Funk (Zoom), Brenna Forester
*Coffee break if needed
Hands-on with background information: Delineating conservation units
Recommended reading: TBD
7:00- 9:00 PM (10 -12 AM in Seattle) Effective population size estimation
Keynote lecturer: Robin Waples (via Zoom)
Hands-on: Effects sample size & Wahlund effects on Ne estimators?
Recommended reading: TBD
Day 5 (Thursday, Dec. 11) – Assignment Tests, Landscape Genomics & Adaptation
8:00-8:30 Inferring Ne from indicators (proxies) – overview & concepts
Keynote lecturer: Jessica da Silva.
8:30-9:30 Hands-on: Infer Ne for several species (without using genetic data; Mtn Zebra, Buffalo)
Recommended reading: TBD
9:30- *12:00 Population assignment tests for forensics, conservation, and ecology
Keynote lecturers: Will Hemstrom, Andy Lee, C Bossu
*Coffee break around 10:30
Hands-on: Microsatellites (Rubias), NG-seq data (WGSassign, OriGen msats or NGS)
Recommended reading: TBD
1:00- *4:00 Detecting local adaptation using genotype-environment associations
Keynote lecturer: Brenna Forester
*Coffee break around 2:30 PM
Hands-on: Genotype-environment association analysis using RDA and LFMM
Recommended reading: TBD
4:00- 5:00 PM Q & A with instructors in person
6:00-8:00 Dinner & Discussion – with all instructors + regional managers?
What is the greatest barrier to the immediate use of genetics for conservation? How to spark grant collaborations (Africa-USA-EU-etc.)? How to promote resource sharing (markers, databases, etc.), and genotyping samples regionally and internationally?
Recommended reading: Chap 24 in Allendorf et al. 2022 book; Helen Taylor’s Video-Lecture
8:00- 9:00 PM Q & A with all instructors in person (or via Zoom in you/we arrange it)
Day 6 (Friday, Dec. 12) – multispecies analyses and eDNA
8:30- *12:00 Phylogenomics for research and conservation
Keynote lecturer: Martin Coetzee
*Coffee break
Hands-on: Interpreting program outputs
Recommended reading: TBD
1:00-2:00 eDNA Metabarcoding for conservation & biodiversity research (concepts &
examples)
Keynote lecturers: Sandi Willows-Munro
Recommended reading: TBD
2:30-3:30 PM FINAL Q & A with all instructors
3:30-4:30 Final Discussion: Future research & teaching directions, questions, advice, and publishing a ConGen Review.
Recommended reading: Schiebelhut et al. 2023; Schweizer et al. 2021; Hendricks et al 2016
5:30 PM final dinner (please sign up); some leave/fly out
Day 7 8:00AM (Sat., Dec. 13) – All depart, or Field trip to Kruger National Park, Dec 13-16