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Research Interests

  • Conservation genomics
  • Population genetics
  • Comparative genomics
  • Evolutionary biology
  • Molecular evolution


  • BS, Whitman College
  • PhD, University of California


Dr. Koepfli is a broadly trained biologist specializing in genomics and its application to the conservation of biodiversity. He and his students and collaborators develop and apply state-of-the-art genomic tools to inform conservation management strategies of species at risk for extinction and to dissect the underlying causes of inbreeding depression, particularly with regard to deleterious variation. Analyses based on whole genome sequences, or reduced representations of these, provide a fertile ground for investigating the interplay of population size and fitness, which have the potential to revolutionize how endangered species are managed under human care. Koepfli’s research also includes comparing the genomes of different species in order to gain insights into the evolution and maintenance of biological diversity.

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

Gooley R.M., Tamazian G., Castaneda-Rico S., Murphy K.R., Dobrynin P., Ferrie G.M., Haefele H., Maldonado J.E., Wildt D., Pukazhenthi B.S., Edwards C.W., Koepfli K-P. 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.  DOI:

Damas J., Hughes G.M., Keough K.C., Painter C.A., Persky N.S., Corbo M., Hiller M., Koepfli K-P., Pfenning A.R., Zhao H., Genereux D.P., Swofford R., Pollard K.S., Ryder O.A., Nweeia M.T., Lindblad-Toh K., Teeling E.C., Karlsson E.K., Lewin H.A. 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. DOI:

Humble E., Dobrynin P., Senn H., Chuven J., Scott A.F., Mohr D.W., Dudchenko O., Omer A.D., Colaric Z., Lieberman Aiden E., Al Daheri S.S., Wildt D., Oliaji S., Tamazian G., Pukazhenthi B., Ogden R., Koepfli K-P. 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. DOI:

de Manuel M., Barnett R., Sandoval-Velasco M., Yamaguchi N., Garrett V., Filipe, Mendoza M.L.Z., Liu, S., Martin M.D., Sinding M-H.S., Mak S.S.T., Carøe C., Liu S., Guo C., Zheng J., Zazula, G., Baryshnikov G., Eizirik E., Koepfli, K-P., Johnson, Warren E.,  Antunes A., Sicheritz-Ponten T., Gopalakrishnan S., Larson G., Yang H., O’Brien S.J., Hansen A.J., Zhang G., Marques-Bonet, T., Gilbert, M.T.P. 2020. The evolutionary history of extinct and living lions. Proceedings of the National Academy of Sciences USA

Yang C., Li F., Xiong Z., Koepfli K-P., Ryder O.A., Perelman P., Li Q., Zhang G. 2020. A draft genome assembly of spotted hyena, Crocuta crocuta. Scientific Data. 7: 126. DOI:

Noskova E., Ulyantsev V., Koepfli K-P., O’Brien S.J., Dobrynin P. 2020. GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data. GigaScience 9: giaa005. DOI:

Koepfli K-P., Gooley R.M. 2020. A modern synthesis of mammal conservation genetics. In: Ortega, J., Maldonado, J.E. (Eds.), Conservation Genetics in Mammals. Springer International Publishing, Cham, Switzerland, pp. 3-11.

Koepfli K-P., Tamazian G., Wildt D.E., Dobrynin P., Kim C., Frandsen P.B., Godinho R., Yurchenko A.A., Komissarov A., Krasheninnikova K., Kliver S., Kolchanova S., Gonçalves M., Carneiro, M., Vaz Pinto P., Ferrand N., Maldonado J.E., Ferrie G.M., Chemnick L., Ryder O.A., Johnson W.E., Comizzoli P., O’Brien S.J.. Pukazhenthi B.S. 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.  9:1785-1793. DOI: