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Klaus-Peter Koepfli

Conservation Biologist
B.A., Whitman College; Ph.D., University of California, Los Angeles

Klaus-Peter Koepfli is a broadly trained conservation biologist at the Smithsonian Conservation Biology Institute. He and his team 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.

Captive breeding is often the last hope for many endangered species facing extinction, but a number of genetic challenges can compromise their long-term sustainability. 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.

Koepfli’s 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
Koepfli serves on the council of the Genome 10K Consortium and Vertebrate Genome 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 also a member of the International Union for Conservation of Nature's otter and small carnivore specialist groups.
Koepfli majored in biology as an undergraduate at Whitman College and went on to earn his Ph.D. in biology at the University of California Los Angeles. He was a cancer research training fellow at the National Cancer Institute from 2009-2012. In 2016, he was awarded the Smithsonian’s prestigious George E. Burch Fellowship in Theoretic Medicine and Affiliated Theoretic Science. Koepfli has authored or co-authored more than 60 peer-reviewed scientific articles and book chapters. He is passionate about fostering and teaching the next generation of biodiversity scientists.
Recent Publications: 

Gooley, Rebecca M., Tamazian, Gaik, Castaneda-Rico, Susette, Murphy, Katherine R., Dobrynin, Pavel, Ferrie, Gina M., Haefele, Holly, Maldonado, Jesus E., Wildt, David, Pukazhenthi, Budhan S., Edwards, Cody W., Koepfli, Klaus-Peter. 2020. Comparison of genomic diversity and structure of sable antelope (Hippotragus niger) in zoos, breeding centers and private ranches in North America. Evolutionary Applications. https://doi.org/10.1111/eva.12976

Humble, Emily, Dobrynin, Pavel, Senn, Helen, Chuven, Justin, Scott, Alan F., Mohr, David W., Dudchenko, Olga, Omer, Arina D., Colaric, Zane, Lieberman Aiden, Erez, Al Daheri, Shaikha Salem, Wildt, David, Oliaji, Shireen, Tamazian, Gaik, Pukazhenthi, Budhan, Ogden, Rob, Koepfli, Klaus-Peter. 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. https://doi.org/10.1111/1755-0998.13181

de Manuel, Marc, Barnett, Ross, Sandoval-Velasco, Marcela, Yamaguchi, Nobuyuki, Garrett, Vieira, Filipe, Mendoza, M. Lisandra Zepeda, Liu, Shiping, Martin, Michael D., Sinding, Mikkel-Holger S., Mak, Sarah S. T., Carøe, Christian, Liu, Shanlin, Guo, Chunxue, Zheng, Jiao, Zazula, Grant, Baryshnikov, Gennady, Eizirik, Eduardo, Koepfli, Klaus-Peter, Johnson, Warren E.,  Antunes, Agostinho, Sicheritz-Ponten, Thomas, Gopalakrishnan, Shyam, Larson, Greger, Yang, Huanming, O’Brien, Stephen J.,  Hansen, Anders J., Zhang, Guojie, Marques-Bonet, Tomas, Gilbert, M. Thomas P. 2020. The evolutionary history of extinct and living lions. Proceedings of the National Academy of Sciences USA. DOI: 10.1073/pnas.1919423117

Yang, Chentao, Li, Fang, Xiong, Zijun, Koepfli, Klaus-Peter, Ryder, Oliver, Perelman, Polina, Li, Qiye, Zhang, Guojie. 2020. A draft genome assembly of spotted hyena, Crocuta crocuta. Scientific Data. 7: 126.

Noskova Ekaterina, Ulyantsev, Vladimir, Koepfli, Klaus-Peter, O’Brien, Stephen J., and Dobrynin, Pavel. 2020. GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data. GigaScience 9: giaa005.

Koepfli, Klaus-Peter, Gooley, Rebecca M. 2020. A modern synthesis of mammal conservation genetics. In: Ortega, Jorge, Maldonado, Jesus E. (Eds.), Conservation Genetics in Mammals. Springer International Publishing, Cham, Switzerland, pp. 3-11.

Koepfli, Klaus-Peter, Tamazian, Gaik, Wildt, David E., Dobrynin, Pavel, Kim, Changhoon, Frandsen, Paul B., Godinho, Raquel, Yurchenko, Andrey A., Komissarov, Aleksey, Krasheninnikova, Ksenia, Kliver, Sergei, Kolchanova, Sofia, Gonçalves, Margarida, Carneiro, Miguel, Vaz Pinto, Pedro, Ferrand, Nuno, Maldonado, Jesús E., Ferrie, Gina M., Chemnick, Leona, Ryder, Oliver A., Johnson, Warren E., Comizzoli, Pierre, O'Brien, Stephen J. and Pukazhenthi, Budhan 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. G3 (Bethesda, Md.), 1785-1793. https://doi.org/10.1534/g3.119.400084