ConGen2025 CCF Namibia
The Recent Advances in Conservation Genetics 2024 is an intensive 9-day practicum focused on applying genomic technologies to biodiversity conservation. Through lectures, discussions, and hands-on tutorials, participants will learn the theory and practice of evolutionary and population genomic analyses for conservation science.
Some of the best conservation genetics faculty from all around the world will interact, teach, and share their research, interact with participants, and contribute their unique perspectives. This course has been running since 1996, with each edition in a different country, engaging diverse groups of students and faculty and a variety of conservation issues. In this way, ConGen tries to address the global scale of conservation issues by bringing it to different regions and countries worldwide. Over the decades, Congen has been to North and South America, the Caribbean, Europe, and Africa. The 2025 edition will be hosted at the Cheetah Conservation Fund in Otjiwarongo, Namibia.
Course Description
This course comprehensively surveys 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 Jan 6)
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, Part 1; Lightning talks by students: 2-minutes + 2 slides per
student (22 students)
Monday, January 6, 2025
8:00 – 9:00 am BREAKFAST
9:00 – 9:15 am Opening of CONGEN2025: Ms. Seimy Shidute, Deputy Executive
9:15 – 9:30 am Director for Tourism Planning and Administration, Namibia 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: Klaus Koepfli – “Conservation Genomics: Next-Gen Sequencing & Study Design”
12:00 – 1:00 pm LUNCH
1:00 – 2:30 pm Tutorial: Introduction to Unix and HPC (Henrique Figueiró)
2:30 – 3:00 pm BREAK
3:00 – 4:30 pm 4:30 – 5:00 pm Tutorial: Next-generation sequencing data and quality control (Henrique Figueiró)
Introductions, Part 2; Lightning talks by students: 2-minutes + 2 slides per student (6 students)
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 10:00 – 10:55 am Lecture: Anne Schmidt-Küntzel – “A Brief History of Genetic Advances and Natural History of the Cheetah”
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 (Lauren Hennelly)
2:30 – 3:00 pm BREAK
3:00 – 4:00 pm 4:00 – 4:30 pm Tutorial: Read mapping and variant calling 2 (Lauren Hennelly)
Lecture: Henrique Figueiró – “Conservation Genomics in the Neotropics”
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 (Lauren Hennelly)
2:30 – 3:00 pm BREAK
3:00 – 5:00 pm Tutorial: Population Structure 2 (Lauren Hennelly)
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 – Peter Dratch and others
12:00 – 1:00 pm LUNCH
1:00 – 2:30 pm Tutorial: Genome-wide heterozygosity, SNV density, visualization 1 (Larissa Arantes)
2:30 – 3:00 pm BREAK
3:00 – 5:00 pm Tutorial: Genome-wide heterozygosity, SNV density, visualization 2 (Henrique Figueiró)
5:30 – 6:30 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 am Cheetah Run demonstration
8:30 – 9:30 am BREAKFAST
9:30 am – 12:30 pm Break into 4 groups, with each group rotating in the following activities: Tour of CCF Veterinary Clinic (~30 minutes); Scat dogs for cheetah detection (~30 minutes)
12:30 – 1:30 pm LUNCH
1:30 pm – 4:00 pm Free time
4:30 – 9:00 pm SUNDOWNER & GAME DRIVE – Drinks and Dinner
Saturday, January 11, 2025
8:00 – 9:00 am BREAKFAST
9:00 – 9:55 AM 10:00 – 10:55 am Lecture: Stephen O’Brien – “Zoobiquity and Infectious Disease Outbreaks”
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 (Larissa Arantes)
2:30 – 3:00 pm BREAK
3:00 – 4:30 pm Tutorial: Runs of homozygosity 2 (Larissa Arantes)
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 (Larissa Arantes)
2:30 – 3:00 pm BREAK
3:00 – 4:30 pm 4:30 – 5:00 pm Tutorial: Deleterious variants 2 (Larissa Arantes)
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 (Henrique Figueiró)
2:30 – 3:00 pm BREAK
3:00 – 5:00 pm Tutorial: Demographic inference 2 (Henrique Figueiró)
5:30 – 6:30 pm DINNER
7:30 – 8:30 pm Keynote Evening Lecture Shu-Jin Luo – Perspective” The World’s Tiger Conservation Crisis: A Genomics
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 (Henrique Figueiró)
2:30 – 3:00 pm BREAK
3:00 – 430 pm Tutorial: Phylogenomic analysis 2 (Henrique Figueiró)
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
11:15 am – 12:00 pm Check-out and departure: Shuttles depart CCF for Hosea Kutako International Airport (WDH), Windhoek, Namibia