Klaus Koepfli

Senior Research Scientist, Smithsonian-Mason School of Conservation

Research Interests

  • Conservation genomics
  • Comparative genomics
  • Phylogenomics
  • Molecular evolution

Education

  • BA, Whitman College, USA
  • PhD, University of California, Los Angeles, USA

Experience

Dr. Koepfli is a Senior Research Scientist in the Smithsonian-Mason School of Conservation at George Mason University specializing in genomics and its application to the conservation of biodiversity. He and his students and collaborators generate and analyze whole genome sequencing data to assess genetic diversity relative to demographic history, dissect the underlying causes of inbreeding depression, and inform conservation management strategies of species at risk for extinction. His research also focuses on comparing the genomes of different species in order to understand the processes that create and maintain biological diversity. Dr. Koepfli also serves on the council of the Vertebrate Genomes Project Consortium, which aims to generate and assemble high quality chromosome-level genomes for more than 70,000 vertebrate species to address fundamental questions in biology, evolution and biodiversity conservation.

Current projects include:

  • Understanding the genetic and epigenetic causes of decreased reproductive fitness in the endangered black-footed ferret (Mustela nigripes) using genomic tools.
  • Empowering ex situ conservation management of the critically endangered southern black rhinoceros (Diceros bicornis minor) through sequencing and analysis of whole genomes.
  • Applying genomic data to enhance the conservation management of sable antelope (Hippotragus niger), dama gazelles (Nanger dama) and scimitar-horned oryx (Oryx dammah) in zoos and private ranches in North America.
  • Comparative genomics of otters and martens.
Koepfli serves on the council of the Genome 10K Consortium and Vertebrate Genomes Project, which aims to generate and assemble high quality chromosome-level genomes for more than 70,000 vertebrate species to address fundamental questions in biology, evolution and biodiversity conservation. He is a member of the IUCN/SSC Otter Specialist Group and SmalI Carnivore Specialist Group. He is also a member of the Association of Zoos and Aquariums Molecular Data for Population Management Scientific Advisory Group.

Selected Publications

Derežanin, L, A Blažytė, P Dobrynin, DA Duchêne, JH Grau, S Jeon, S Kliver, K-P Koepfli, D Meneghini, M Preick, A Tomarovsky, A Totikov, J Fickel DW Förster. 2022. Genome assembly of the tayra (Eira barbara, Mustelidae) and comparative genomic analysis reveal adaptive genetic variation in the subfamily Guloninae. Molecular Ecology. 31(10): 2898-2919. https://doi.org/10.1111/mec.16443

Stephan, T, SM Burgess, H Cheng, CG Danko, CM Gill, ED Jarvis, K-P Koepfli, JE Koltes, E Lyons, PC Ronald, OA Ryder, L Schriml, PS Soltis, S VandeWoude, H Zhou, EA Ostrander, EK Karlsson. 2022. Darwinian Genomics and Diversity in the Tree of Life. Proceedings of the National Academy of Science USA. 119(4): e2115644119. https://doi.org/10.1073/pnas.2115644119

Wold, J, K-P Koepfli, S Galla, D Eccles, CJ Hogg, MF Le Lec, J Guhlin, AW Santure, TE Steeves. 2021. Expanding the conservation genomics toolbox: incorporating structural variants to enhance genomic studies for species of conservation concern. Molecular Ecology. 30(23): 5949-5965. https://doi.org/10.1111/mec.16141

Coimbra, RTF, S Winter, V Kumar, K-P Koepfli, RM Gooley, P Dobrynin, J Fennessy, A Janke. 2021. Whole-genome analysis of giraffe supports four distinct species. Current Biology. 31(13): 2929-2938. https://doi.org/10.1016/j.cub.2021.04.033

Humble, E, P Dobrynin, H Senn, J Chuven, AF Scott, DW Mohr, O Dudchenko, AD Omer, Z Colaric, E Lieberman Aiden, SS Al Daheri, D Wildt, S Oliaji, G Tamazian, B Pukazhenthi*, R Ogden*, K-P Koepfli. 2020. Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild. Molecular Ecology Resources. 20: 1668-1681. https://doi.org/10.1111/1755-0998.13181

Genereux, DP, A Serres, J Armstrong, J Johnson, VD Marinescu, E Murén, D Juan, G Bejerano, NR Casewell, LG Chemnick, J Damas, F Di Palma, M Diekhans, IT Fiddes, M Garber, L Goodman, W Haerty, ML Houck, R Hubley, T Kivioja, K-P Koepfli, LFK Kuderna, ES Lander, JRS Meadows, WJ Murphy, W Nash, HJ Noh, M Nweeia, AR Pfenning, KS Pollard, D Ray, B Shapiro, A Smit, M Springer, CC Steiner, R Swofford, J Taipale, EC Teeling, J Turner-Maier, J Alfoldi, B Birren, OA Ryder, H Lewin, B Paten, T Marques-Bonet, K Lindblad-Toh, EK Karlsson. 2020. A comparative genomics multitool for scientific discovery and conservation. Nature. 587: 240-245. https://doi.org/10.1038/s41586-020-2876-6

Damas, J, GM Hughes, KC Keough, CA Painter, NS Persky, M Corbo, M Hiller, K-P Koepfli, AR Pfenning, H Zhao, DP Genereux, R Swofford, KS Pollard, OA Ryder, MT Nweeia, K Lindblad-Toh, EC Teeling, EK Karlsson, HA Lewin. 2020. Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates.Proceedings of the National Academy of Sciences USA. 117: 22311-22322. https://doi.org/10.1073/pnas.2010146117

Gooley, R, G Tamazian, S Castañeda-Rico, KR Murphy, P Dobrynin, GM Ferrie, H Haefele, JE Maldonado, D Wildt, B Pukazhenthi*, CW Edwards*, K-P Koepfli. 2020. Comparison of genomic diversity and structure of sable antelope (Hippotragus niger) in zoos, breeding centers and private ranches in North America. Evolutionary Applications. 13: 2143-2154. https://doi.org/10.1111/eva.12976

Koepfli, K-P, G Tamazian, D Wildt, P Dobrynin, AA Yurchenko, A Komissarov, K Krasheninnikova, S Kliver, S Kolchanova, C Kim, R Godinho, M Gonçalves, M Carneiro, P Vaz Pinto, N Ferrand, J Maldonado, GM Ferrie, L Chemnick, OA Ryder, WE Johnson, P Comizzoli, SJ O’Brien, B Pukazhenthi. 2019. Whole genome sequencing and re-sequencing of the sable antelope (Hippotragus niger): A resource for monitoring diversity in ex situ and in situ populations. G3: Genes, Genomes, Genetics 9: 1785-1793. https://doi.org/10.1534/g3.119.400084

Nigenda-Morales S, ME Gompper, D Valenzuela-Galvan, AR Lay, KM Kapheim, C Hass, S Booth-Binczik, G Booth-Binczik, B Hirsch, K McFadden, RK Wayne, K-P Koepfli. 2019. Phylogeographic and diversification patterns of the white-nosed coati (Nasua narica): Evidence for south-to-north colonization of North America. Molecular Phylogenetics and Evolution 131: 149-163. https://doi.org/10.1016/j.ympev.2018.11.011

Koepfli, K-P, J Pollinger, R Godinho, J Robinson, A Lea, S Hendricks, RM Schweizer, O Thalmann, P Silva, Z Fan, AA Yurchenko, P Dobrynin, A Makunin, JA Cahill, B Shapiro, F Álvares, JC Brito, E Geffen, JA Leonard, KM Helgen, WE Johnson, SJ O’Brien, B Van Valkenburgh, RK Wayne. 2015. Genome-wide evidence reveals that African and Eurasian golden jackals are distinct species. Current Biology 25: 2158-2165. https://doi.org/10.1016/j.cub.2015.06.060

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