The Recent Advances in Conservation Genetics (ConGen Global) 2024 is an intensive 9-day practicum focused on applying genomic technologies to the conservation of biodiversity. Through lectures, discussions, and hands-on tutorials, participants will learn the theory and practice of evolutionary and population genomic analyses for conservation science.
Faculty from around the world will teach and share their research, interact with participants, and contribute their unique perspectives. This course has been running since 1996, with each edition held in different global locations. The 2025 edition will be hosted at the Cheetah Conservation Fund in Otjiwarongo, Namibia.
Course Description
This course provides a comprehensive survey of the theories, methods, and software used in conservation genomics. Participants will learn bioinformatics pipelines and algorithms for analyzing next-generation sequencing data. Key topics covered include:
- Study design for conservation genomics projects
- Genome sequencing and next-generation sequencing methods
- Genome assembly and annotation
- Read mapping and variant discovery
- Genetic structure analysis
- Genetic diversity and inbreeding
- Identifying deleterious variants
- Demographic history estimation
Each evening will feature keynote-style lectures by guest faculty on their cutting-edge research in conservation biology and genomics.
Daily Schedule (Updated Dec 15)
Morning lectures, afternoon tutorials, and keynote evening lectures will be held in the CCF Lecture Hall
NOTE: All times are Central Africa Time (CAT) in Namibia
Sunday, January 5, 2025
12:00 – 6:00 pm Arrival and check-in: Pick up participants and faculty by shuttle from
Hosea Kutako International Airport (WDH), Windhoek, Namibia
6:00 – 7:30 pm DINNER
7:30 – 9:30 pm Introductions; Lightning talks by students: 3-minutes + 2 slides per student
Monday, January 6, 2025
8:00 – 9:00 am BREAKFAST
9:00 – 9:15 am Opening of CONGEN2025: Hon. Heather Sibungo, Deputy Minister, Ministry of Environment, Tourism and Forestry, Namibia
9:15 – 9:30 am Welcome and overview: Steve O’Brien & faculty
9:30 – 10:00 am Walk-through of course topics: Koepfli, Oleksyk, Schmidt-Küntzel
10:00 – 10:55 am Lecture: Steve O’Brien – “Perspectives of ConGen Global: Then and Now”
11:00 – 11:55 am Lecture: Theresa Sethusa – TBD
12:00 – 1:00 pm LUNCH
1:00 – 2:30 pm Tutorial: Introduction to Galaxy(?) and HPC
2:30 – 3:00 pm BREAK
3:00 – 4:30 pm Tutorial: Next-generation sequencing data and quality control
4:30 – 5:00 pm CCF Demo: Eveline Iikondja – Scat dogs for cheetah detection
5:30 – 6:30 pm DINNER
7:30 – 8:30 pm Keynote Evening Lecture
Laurie Marker – “The Global Cheetah Conservation Program”
Tuesday, January 7, 2025
8:00 – 9:00 am BREAKFAST
9:00 – 9:55 am Lecture: Anne Schmidt-Kuntzel – “A Brief History of Genetic Advances and Natural History of the Cheetah”
10:00 – 10:55 am Lecture: Al Roca – “African Elephants and Their Natural History”
11:00 – 11:55 am Lecture: Audrey Majeske – “Reef Royalty: Protecting the Royal Crown of the Reef”
12:00 – 1:00 pm LUNCH
1:00 – 3:00 pm Tutorial: Read mapping and variant calling 1
2:30 – 3:00 pm BREAK
3:00 – 4:00 pm Tutorial: Read mapping and variant calling 2
4:00 – 4:30 pm Lecture: Henrique Figueiró – TBD
4:30 – 5:00 pm CCF Demo: Calum O’Flaherty – Livestock Guarding Dogs
5:30 – 6:30 pm DINNER
7:30 – 8:30 pm Keynote Evening Lecture
Cindy Harper – “DNA individualization Forensics of Rhinos of Southern Africa”
Wednesday, January 8, 2025
8:00 – 9:00 am BREAKFAST
9:00 – 9:55 am Lecture: Bill Murphy – “Why high-quality genomes matter for evolutionary studies: lessons from cats.”
10:00 – 10:55 am Lecture: Anne Schmidt-Küntzel – “Non-invasive Genetics and Field Applications”
11:00 – 11:55 am Lecture: Taras Oleksyk – “Parrots of The Caribbean”
12:00 – 1:00 pm LUNCH
1:00 – 2:30 pm Tutorial: Population structure 1
2:30 – 3:00 pm BREAK
3:00 – 5:00 pm Tutorial: Population structure 2
5:30 – 6:30 pm DINNER
7:30 – 8:30 pm Keynote Evening Lecture
Bill Murphy – “The Natural History of the Mammalian Radiations”
Thursday, January 9, 2025
8:00 – 9:00 am BREAKFAST
9:00 – 9:55 am Lecture: Abigail Guerier – “Management of Black and White
Rhinoceros Populations at the Ongava Game Reserve Using Complementary Genetic and Observational Monitoring Tools”
10:00 – 10:55 am Lecture: Peter Dratch – “Policy for Sample/DNA Transport – Overview
Then and Now”
11:00 – 11:55 am Discussion of CITES restrictions – Dratch and others
12:00 – 1:00 pm LUNCH
1:00 – 2:30 pm Tutorial: Genome-wide heterozygosity, SNV density, visualization 1
2:30 – 3:00 pm BREAK
3:00 – 5:00 pm Tutorial: Genome-wide heterozygosity, SNV density, visualization 2
7:30 – 9:00 pm DINNER
7:30 – 8:30 pm Keynote Evening Lecture
Julian Fennessy – “Saving giraffe: using science and management to conserve all four species across Africa”
Friday, January 10, 2025
8:00 – 9:00 am BREAKFAST
9:00 am – 1:00 pm FIELD DAY – Game drive CCF with bag lunch
4:30 – 9:00 pm SUNDOWNER – Drinks and Dinner
Saturday, January 11, 2025
8:00 – 9:00 am BREAKFAST
9:00—9:55 AM Lecture: Stephen Obrien – “Zoobiquity and Infectious Disease Outbreaks”
10:00 – 10:55 am Lecture: Laurie Goodman – “How to Write a Scientific Manuscript
and Appropriate Use of Generative AI”
11:00 – 11:55 am Lecture: Justin Merry – “Undergraduate Education and Conservation Science”
12:00 – 1:00 pm LUNCH
1:00 – 2:30 pm Tutorial: Runs of homozygosity 1
2:30 – 3:00 pm BREAK
3:00 – 4:30 pm Tutorial: Runs of homozygosity 2
4:30 – 5:00 pm Lecture: Larissa Souza Arantes – “From Sloths to Sea Turtles: Genomic
Insights into Conservation Challenges and Evolutionary History”
5:30 – 6:30 pm DINNER
7:30 – 8:30 pm Keynote Evening Lecture
Klaus Koepfli – “Decoding Survival: Comparative and Population
Genomics Informs the Conservation of the Endangered Black-footed Ferret”
Sunday, January 12, 2025
8:00 – 9:00 am BREAKFAST
9:00 – 9:55 am: Lecture: Laurie Goodman – “A Guide to Publishing Ethics: From
Mistakes to Misrepresentation to Fraud”
10:00 – 10:55 am Lecture: Eduardo Eizirik – “Evolutionary and Conservation Genomics
of Neotropical Carnivores”
11:00 – 11:55 am Lecture: Agostinho Antunes – “Functional Genomics of Whole Genome
Sequences”
12:00 – 1:00 pm LUNCH
1:00 – 2:30 pm Tutorial: Deleterious variants 1
2:30 – 3:00 pm BREAK
3:00 – 4:30 pm Tutorial: Deleterious variants 2
4:30 – 5:00 pm Lecture: Lauren Hennelly – “How genomics informs the conservation
status and management of wolves in Asia”
5:30 – 6:30 pm DINNER
7:30 – 8:30 pm Keynote Evening Lecture
Harris Lewin – “The Earth BioGenome Project: An Enabler of the Coming Revolution in Conservation Genetics” (via Zoom)
Monday, January 13, 2025
8:00 – 9:00 am BREAKFAST
9:00 – 9:55 am Lecture: Jhala Yadvendradev – “The Cheetah Restoration Project”
10:00 – 10:55 am Lecture: Carlos Driscoll – “History of Domestications: The Lever That Founded All Civilizations”
11:00 – 11:55 am Lecture: Jose Lopez – “Global Invertebrate Genome Alliance – A Genomic Perspective for Marine Invertebrate Species”
12:00 – 1:00 pm LUNCH
1:00 – 2:30 pm Tutorial: Demographic inference 1
2:30 – 3:00 pm BREAK
3:00 – 5:00 pm Tutorial: Demographic inference 2
5:30 – 6:30 pm DINNER
7:30 – 8:30 pm Keynote Evening Lecture
Shu-Jin Luo – “The world’s tiger conservation crisis: a genomics perspective”
Tuesday, January 14, 2025
8:00 – 9:00 am BREAKFAST
9:00 – 9:55 am Lecture: Rainer Hassel – Rabies in Kudu revisited”
10:00 – 10:55 am Lecture: Matti Nghikembua – “Ecology of Southern African Cheetahs”
11:00 – 11:55 am Wrap Up with ConGen Board: O’Brien, Eizirik, Koepfli, Marker, Oleksyk, Schmidt-Küntzel
12:00 – 1:00 pm LUNCH
1:00 – 2:30 pm Tutorial: Phylogenomic analysis 1
2:30 – 3:00 pm BREAK
3:00 – 430 pm Tutorial: Phylogenomic analysis 2
4:30 – 5:30 pm Discussion: Students ask questions about their own projects
6:00 – 10:00 pm DINNER and CLOSING PARTY
Wednesday, January 15, 2025
8:00 – 9:00 am BREAKFAST
9:00 – 10:00 am Group Discussion: Career paths – Faculty
10:00 – 11:00 am Course evaluation and discussion- student comments
11:00 – 11:15 am Group photo
11:15am – 12:00 pm Check-out and departure: Shuttles depart CCF for Hosea Kutako
International Airport (WDH), Windhoek, Namibia