(updated December 20, 2024)
Course Format
The Recent Advances in Conservation Genetics (ConGen Global) course is an intensive 9-day practicum dedicated to the application of genomic technologies towards the conservation of biodiversity. Through a combination of lectures, discussions, and hands-on training tutorials, participants will learn the theory and practical application of evolutionary and population genomic analyses to conservation science. The course faculty represents an amazing group of people from around the world who will teach and share their current research and conservation stories, as well as interact with the course participants. The course has been running since 1996, with editions being held at different locations worldwide. The 2025 edition is being held at the Cheetah Conservation Fund in Otjiwarongo, Namibia.
Course Description
This course surveys the theory, methods, and software used in conservation genomics research. Through lectures and hands-on computer tutorials, participants will learn how to handle bioinformatics pipelines and algorithms for analyzing next-generation sequencing data. Topics to be covered include:
– Study design for conservation genomic projects
– Overview of genome sequencing and other next-generation sequencing methods
– Read mapping and variant discovery
– Analysis of genetic structure
– Analysis of genetic diversity and inbreeding
– Identification of deleterious variants
– Estimation of demographic history
– Phylogenomic analysis
Each evening will feature a keynote-style open lecture by guest faculty on their seminal research advances and interpretations in conservation biology and genomics.
Daily Schedule
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
Suggested Readings
Allendorf, F. W., Funk, W. C., Aitken, S. N., Byrne, M., & Luikart, G. (2022). Conservation and the Genomics of Populations, Third Edition. Oxford University Press, Oxford, United Kingdom, 750 pages.
Bertorelle, G., Raffini, F., Bosse, M., Bortoluzzi, C., Iannucci, A., Trucchi, E., Morales, H. E., & van Oosterhout, C. (2022). Genetic load: genomic estimates and applications in non-model animals. Nature Reviews Genetics 23(8), 492–503. https://doi.org/10.1038/s41576-022-00448-x
Ceballos, F. C., Joshi, P. K., Clark, D. W., Ramsay, M., & Wilson, J. F. (2018). Runs of homozygosity: windows into population history and trait architecture. Nature Reviews. Genetics, 19(4), 220–234. https://doi.org/10.1038/nrg.2017.109
Díez-Del-Molino, D., Sánchez-Barreiro, F., Barnes, I., Gilbert, M. T. P., & Dalén, L. (2018). Quantifying Temporal Genomic Erosion in Endangered Species. Trends in ecology & evolution, 33(3), 176–185. https://doi.org/10.1016/j.tree.2017.12.002
Fuentes-Pardo, A. P., Ruzzante, D. E. (2017). Whole-genome sequencing approaches for conservation biology: advantages, limitations and practical recommendations. Molecular Ecology 26(20): 5368-5406. https://doi.org/10.1111/mec.14264
Hendricks, S., Anderson, E. C., Antao, T., Bernatchez, L., Forester, B. R., Garner, B., Hand, B. K., Hohenlohe, P. A., Kardos, M., Koop, B., Sethuraman, A., Waples, R. S., & Luikart, G. (2018). Recent advances in conservation and population genomics data analysis. Evolutionary Applications, 11(8), 1197–1211. https://doi.org/10.1111/eva.12659
Kardos, M., Armstrong, E. E., Fitzpatrick, S. W., Hauser, S., Hedrick, P. W., Miller, J. M., Tallmon, D. A., & Funk, W. C. (2021). The crucial role of genome-wide genetic variation in conservation. Proceedings of the National Academy of Sciences of the United States of America, 118(48), e2104642118. https://doi.org/10.1073/pnas.2104642118
Lou, R. N., Jacobs, A., Wilder, A. P., & Therkildsen, N. O. (2021). A beginner’s guide to low-coverage whole genome sequencing for population genomics. Molecular Ecology, 30(23), 5966–5993. https://doi.org/10.1111/mec.16077.
O’Brien, S.J.: Tears of the Cheetah and Other Tales from the Genetic Frontier, St. Martin’s Press, New York, 2003, pp 273.
Robinson, J., Kyriazis, C. C., Yuan, S. C., & Lohmueller, K. E. (2023). Deleterious Variation in Natural Populations and Implications for Conservation Genetics. Annual Review of Animal Biosciences, 11, 93–114. https://doi.org/10.1146/annurev-animal-080522-093311
Segelbacher, G., Bosse, M., Burger, P., Galbusera, P., Godoy, J. A., Helsen, P., Hyilsom, C., Iacolina, L., Kahric, A., Manfrin, C., Nonic, M., Thizy, D., Tsvetkov, I., Veličković, N., Vilà, C., Wisely, S. M., & Buzan, E. (2022).New developments in the field of genomic technologies and their relevance to conservation management. Conservation Genetics 23, 217–242 https://doi.org/10.1007/s10592-021-01415-5
Theissinger, K., Fernandes, C., Formenti, G., Bista, I., Berg, P. R., Bleidorn, C., Bombarely, A., Crottini, A., Gallo, G. R., Godoy, J. A., Jentoft, S., Malukiewicz, J., Mouton, A., Oomen, R. A., Paez, S., Palsbøll, P. J., Pampoulie, C., Ruiz-López, M. J., Secomandi, S., Svardal, H., … European Reference Genome Atlas Consortium (2023). How genomics can help biodiversity conservation. Trends in Genetics 39(7),545–559. https://doi.org/10.1016/j.tig.2023.01.005