title: Genetic ancestry of the extinct Javan and Bali tigers.
abstract: The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct tiger subspecies that went extinct in the 1940s and 1980s, respectively. Yet their genetic ancestry and taxonomic status remain controversial. Following ancient DNA procedures, we generated concatenated 1750bp mtDNA sequences from 23 museum samples including 11 voucher specimens from Java and Bali and compared these to diagnostic mtDNA sequences from 122 specimens of living tiger subspecies and the extinct Caspian tiger. The results revealed a close genetic affinity of the 3 groups from the Sunda Islands (Bali, Javan, and Sumatran tigers P. t. sumatrae). Bali and Javan mtDNA haplotypes differ from Sumatran haplotypes by 1-2 nucleotides, and the 3 island populations define a monophyletic assemblage distinctive and equidistant from other mainland subspecies. Despite this close phylogenetic relationship, no mtDNA haplotype was shared between Sumatran and Javan/Bali tigers, indicating little or no matrilineal gene flow among the islands after they were colonized. The close phylogenetic relationship among Sunda tiger subspecies suggests either recent colonization across the islands, or else a once continuous tiger population that had subsequently isolated into different island subspecies. This supports the hypothesis that the Sumatran tiger is the closest living relative to the extinct Javan and Bali tigers.
authors.affiliation: From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India.
authors.forename: Hao-Ran
authors.initials: HR
authors.lastname: Xue
authors.affiliation: From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India.
authors.forename: Nobuyuki
authors.initials: N
authors.lastname: Yamaguchi
authors.affiliation: From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India.
authors.forename: Carlos A
authors.initials: CA
authors.lastname: Driscoll
authors.affiliation: From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India.
authors.forename: Yu
authors.initials: Y
authors.lastname: Han
authors.affiliation: From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India.
authors.forename: Gila Kahila
authors.initials: GK
authors.lastname: Bar-Gal
authors.affiliation: From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhuang
authors.affiliation: From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India.
authors.forename: Ji H
authors.initials: JH
authors.lastname: Mazak
authors.affiliation: From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India.
authors.forename: David W
authors.initials: DW
authors.lastname: Macdonald
authors.affiliation: From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: O'Brien
authors.affiliation: From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India. luo.shujin@pku.edu.cn.
authors.forename: Shu-Jin
authors.initials: SJ
authors.lastname: Luo
mesh_terms: D000818:Animals; D003247:Conservation of Natural Resources; D004272:DNA, Mitochondrial / Q000235:genetics; D053476:Extinction, Biological; D051456:Gene Flow; D005828:Genetics, Population; D006239:Haplotypes; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D046010:Tigers / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial
keywords: Panthera tigris balica; Panthera tigris sondaica; mtDNA; phylogeny