Publications by authors named "Klaus-Peter Koepfli"

48Publications

Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens.

Curr Biol 2020 Dec 15;30(24):5018-5025.e5. Epub 2020 Oct 15.

Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark; Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1352, Denmark. Electronic address:

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December 2020

GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data.

Gigascience 2020 03;9(3)

Computer Technologies Laboratory, ITMO University, 49 Kronverkskiy Pr., St. Petersburg 197101, Russian Federation.

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March 2020

Characteristics of the complete mitochondrial genome of the monotypic genus (Family: Viverridae) and its phylogenetic implications.

PeerJ 2019 25;7:e8033. Epub 2019 Nov 25.

Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India.

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November 2019

Comparative genomics provides new insights into the remarkable adaptations of the African wild dog (Lycaon pictus).

Sci Rep 2019 06 6;9(1):8329. Epub 2019 Jun 6.

Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, 90095, USA.

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June 2019

Phylogeographic and diversification patterns of the white-nosed coati (Nasua narica): Evidence for south-to-north colonization of North America.

Mol Phylogenet Evol 2019 02 20;131:149-163. Epub 2018 Nov 20.

Smithsonian Conservation Biology Institute, National Zoological Park, Washington, D.C. 20008, USA; Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg 199034, Russian Federation. Electronic address:

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February 2019

Improving draft genome contiguity with reference-derived in silico mate-pair libraries.

Gigascience 2018 05;7(5)

Faculty of Mathematics and Life Sciences, Institute of Biochemistry and Biology, Unit of General Zoology-Evolutionary Adaptive Genomics, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany.

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May 2018

Robust forensic matching of confiscated horns to individual poached African rhinoceros.

Curr Biol 2018 01;28(1):R13-R14

Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004; Guy Harvey Oceanographic Center, Nova Southeastern University, 8000 North Ocean Drive, Ft Lauderdale, FL 33004, USA.

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January 2018

Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences.

Gigascience 2016 08 22;5(1):38. Epub 2016 Aug 22.

Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Sredniy Prospekt 41A, St. Petersburg, 199004, Russia.

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August 2016

Response to Comment by Faurby, Werdelin and Svenning.

Genome Biol 2016 May 5;17:90. Epub 2016 May 5.

Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia.

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May 2016

The Population Origins and Expansion of Feral Cats in Australia.

J Hered 2016 03 7;107(2):104-14. Epub 2015 Dec 7.

From the School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia (Spencer); Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russian Federation (Yurchenko and O'Brien); Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MA 21702 (David, Scott, Driscoll, and Menotti-Raymond); University of Maryland, College Park, MA 20742 (Scott and Driscoll); NIAAA, National Institutes of Health, Bethesda, MA 20892 (Koepfli); Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL (O'Brien); and 5115 Westridge Road, Bethesda, MA (Menotti-Raymond).

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March 2016

The Genome 10K Project: a way forward.

Annu Rev Anim Biosci 2015 ;3:57-111

Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russian Federation; email:

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January 2016

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Authors:
Erich D Jarvis Siavash Mirarab Andre J Aberer Bo Li Peter Houde Cai Li Simon Y W Ho Brant C Faircloth Benoit Nabholz Jason T Howard Alexander Suh Claudia C Weber Rute R da Fonseca Jianwen Li Fang Zhang Hui Li Long Zhou Nitish Narula Liang Liu Ganesh Ganapathy Bastien Boussau Md Shamsuzzoha Bayzid Volodymyr Zavidovych Sankar Subramanian Toni Gabaldón Salvador Capella-Gutiérrez Jaime Huerta-Cepas Bhanu Rekepalli Kasper Munch Mikkel Schierup Bent Lindow Wesley C Warren David Ray Richard E Green Michael W Bruford Xiangjiang Zhan Andrew Dixon Shengbin Li Ning Li Yinhua Huang Elizabeth P Derryberry Mads Frost Bertelsen Frederick H Sheldon Robb T Brumfield Claudio V Mello Peter V Lovell Morgan Wirthlin Maria Paula Cruz Schneider Francisco Prosdocimi José Alfredo Samaniego Amhed Missael Vargas Velazquez Alonzo Alfaro-Núñez Paula F Campos Bent Petersen Thomas Sicheritz-Ponten An Pas Tom Bailey Paul Scofield Michael Bunce David M Lambert Qi Zhou Polina Perelman Amy C Driskell Beth Shapiro Zijun Xiong Yongli Zeng Shiping Liu Zhenyu Li Binghang Liu Kui Wu Jin Xiao Xiong Yinqi Qiuemei Zheng Yong Zhang Huanming Yang Jian Wang Linnea Smeds Frank E Rheindt Michael Braun Jon Fjeldsa Ludovic Orlando F Keith Barker Knud Andreas Jønsson Warren Johnson Klaus-Peter Koepfli Stephen O'Brien David Haussler Oliver A Ryder Carsten Rahbek Eske Willerslev Gary R Graves Travis C Glenn John McCormack Dave Burt Hans Ellegren Per Alström Scott V Edwards Alexandros Stamatakis David P Mindell Joel Cracraft Edward L Braun Tandy Warnow Wang Jun M Thomas P Gilbert Guojie Zhang

Science 2014 Dec;346(6215):1320-31

China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.

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December 2014

Evolution: a new cat species emerges.

Curr Biol 2013 Dec;23(24):R1103-5

Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199004, Russia.

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December 2013

Phylogeography and demographic history of the neotropical otter (Lontra longicaudis).

J Hered 2012 Jul 15;103(4):479-92. Epub 2012 May 15.

Departamento de Genética, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, prédio 43323, Porto Alegre, Rio Grande do Sul, Brazil.

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July 2012

Evolution of a major drug metabolizing enzyme defect in the domestic cat and other felidae: phylogenetic timing and the role of hypercarnivory.

PLoS One 2011 Mar 28;6(3):e18046. Epub 2011 Mar 28.

Comparative and Molecular Pharmacogenomics Laboratory, Department of Molecular Physiology and Pharmacology, Tufts University School of Medicine, Boston, Massachusetts, United States of America.

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March 2011

Evolutionary history of the Falklands wolf.

Curr Biol 2009 Nov;19(20):R937-8

Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 90095-1606, USA.

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November 2009

Extensive population genetic structure in the giraffe.

BMC Biol 2007 Dec 21;5:57. Epub 2007 Dec 21.

Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.

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December 2007

Phylogeny of the Procyonidae (Mammalia: Carnivora): molecules, morphology and the Great American Interchange.

Mol Phylogenet Evol 2007 Jun 11;43(3):1076-95. Epub 2006 Oct 11.

Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-1606, USA.

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June 2007

Molecular systematics of the Hyaenidae: relationships of a relictual lineage resolved by a molecular supermatrix.

Mol Phylogenet Evol 2006 Mar;38(3):603-20

Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-1606, USA.

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March 2006

Genome sequence, comparative analysis and haplotype structure of the domestic dog.

Authors:
Kerstin Lindblad-Toh Claire M Wade Tarjei S Mikkelsen Elinor K Karlsson David B Jaffe Michael Kamal Michele Clamp Jean L Chang Edward J Kulbokas Michael C Zody Evan Mauceli Xiaohui Xie Matthew Breen Robert K Wayne Elaine A Ostrander Chris P Ponting Francis Galibert Douglas R Smith Pieter J DeJong Ewen Kirkness Pablo Alvarez Tara Biagi William Brockman Jonathan Butler Chee-Wye Chin April Cook James Cuff Mark J Daly David DeCaprio Sante Gnerre Manfred Grabherr Manolis Kellis Michael Kleber Carolyne Bardeleben Leo Goodstadt Andreas Heger Christophe Hitte Lisa Kim Klaus-Peter Koepfli Heidi G Parker John P Pollinger Stephen M J Searle Nathan B Sutter Rachael Thomas Caleb Webber Jennifer Baldwin Adal Abebe Amr Abouelleil Lynne Aftuck Mostafa Ait-Zahra Tyler Aldredge Nicole Allen Peter An Scott Anderson Claudel Antoine Harindra Arachchi Ali Aslam Laura Ayotte Pasang Bachantsang Andrew Barry Tashi Bayul Mostafa Benamara Aaron Berlin Daniel Bessette Berta Blitshteyn Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Adam Brown Patrick Cahill Nadia Calixte Jody Camarata Yama Cheshatsang Jeffrey Chu Mieke Citroen Alville Collymore Patrick Cooke Tenzin Dawoe Riza Daza Karin Decktor Stuart DeGray Norbu Dhargay Kimberly Dooley Kathleen Dooley Passang Dorje Kunsang Dorjee Lester Dorris Noah Duffey Alan Dupes Osebhajajeme Egbiremolen Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Patricia Ferreira Sheila Fisher Mike FitzGerald Karen Foley Chelsea Foley Alicia Franke Dennis Friedrich Diane Gage Manuel Garber Gary Gearin Georgia Giannoukos Tina Goode Audra Goyette Joseph Graham Edward Grandbois Kunsang Gyaltsen Nabil Hafez Daniel Hagopian Birhane Hagos Jennifer Hall Claire Healy Ryan Hegarty Tracey Honan Andrea Horn Nathan Houde Leanne Hughes Leigh Hunnicutt M Husby Benjamin Jester Charlien Jones Asha Kamat Ben Kanga Cristyn Kells Dmitry Khazanovich Alix Chinh Kieu Peter Kisner Mayank Kumar Krista Lance Thomas Landers Marcia Lara William Lee Jean-Pierre Leger Niall Lennon Lisa Leuper Sarah LeVine Jinlei Liu Xiaohong Liu Yeshi Lokyitsang Tashi Lokyitsang Annie Lui Jan Macdonald John Major Richard Marabella Kebede Maru Charles Matthews Susan McDonough Teena Mehta James Meldrim Alexandre Melnikov Louis Meneus Atanas Mihalev Tanya Mihova Karen Miller Rachel Mittelman Valentine Mlenga Leonidas Mulrain Glen Munson Adam Navidi Jerome Naylor Tuyen Nguyen Nga Nguyen Cindy Nguyen Thu Nguyen Robert Nicol Nyima Norbu Choe Norbu Nathaniel Novod Tenchoe Nyima Peter Olandt Barry O'Neill Keith O'Neill Sahal Osman Lucien Oyono Christopher Patti Danielle Perrin Pema Phunkhang Fritz Pierre Margaret Priest Anthony Rachupka Sujaa Raghuraman Rayale Rameau Verneda Ray Christina Raymond Filip Rege Cecil Rise Julie Rogers Peter Rogov Julie Sahalie Sampath Settipalli Theodore Sharpe Terrance Shea Mechele Sheehan Ngawang Sherpa Jianying Shi Diana Shih Jessie Sloan Cherylyn Smith Todd Sparrow John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Sabrina Stone Sean Sykes Pierre Tchuinga Pema Tenzing Senait Tesfaye Dawa Thoulutsang Yama Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Vijay Venkataraman Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Shuli Yang Xiaoping Yang Geneva Young Qing Yu Joanne Zainoun Lisa Zembek Andrew Zimmer Eric S Lander

Nature 2005 Dec;438(7069):803-19

Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA.

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December 2005

Type I STS markers are more informative than cytochrome B in phylogenetic reconstruction of the Mustelidae (Mammalia: Carnivora).

Syst Biol 2003 Oct;52(5):571-93

Department of Organismic Biology, Ecology and Evolution, 621 Charles E. Young Drive South, University of California, Los Angeles, California 90095-1606, USA.

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October 2003

A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships.

Mol Phylogenet Evol 2003 Aug;28(2):225-40

Department of Biology, University of California, Riverside 92521, USA.

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August 2003