Genome-Wide Evolutionary Analysis of Natural History and Adaptation in the World's Tigers

Yue Chen Liu, Xin Sun, Carlos Driscoll, Dale G. Miquelle, Xiao Xu, Paolo Martelli, Olga Uphyrkina, James L.D. Smith, Stephen J. O'Brien, Shu Jin Luo

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10 Scopus citations

Abstract

No other species attracts more international resources, public attention, and protracted controversies over its intraspecific taxonomy than the tiger (Panthera tigris) [1, 2]. Today, fewer than 4,000 free-ranging tigers survive, covering only 7% of their historical range, and debates persist over whether they comprise six, five, or two subspecies [3–6]. The lack of consensus over the number of tiger subspecies has partially hindered the global effort to recover the species from the brink of extinction, as both captive breeding and landscape intervention of wild populations increasingly require an explicit delineation of the conservation management units [7]. The recent coalescence to a late Pleistocene bottleneck (circa 110 kya) [5, 8, 9] poses challenges for detecting tiger subspecific morphological traits, suggesting that elucidating intraspecific evolution in the tiger requires analyses at the genomic scale. Here, we present whole-genome sequencing analyses from 32 voucher specimens that resolve six statistically robust monophyletic clades corresponding to extant subspecies, including the recently recognized Malayan tiger (P. tigris jacksoni). The intersubspecies gene flow is very low, corroborating the recognized phylogeographic units. We identified multiple genomic regions that are candidates for identifying the adaptive divergence of subspecies. The body-size-related gene ADH7 appears to have been strongly selected in the Sumatran tiger, perhaps in association with adaptation to the tropical Sunda Islands. The identified genomic signatures provide a solid basis for recognizing appropriate conservation management units in the tiger and can benefit global conservation strategic planning for this charismatic megafauna icon.

Original languageEnglish (US)
Pages (from-to)3840-3849.e6
JournalCurrent Biology
Volume28
Issue number23
DOIs
StatePublished - Dec 3 2018

Bibliographical note

Funding Information:
This paper is dedicated to the memory of tiger conservationists Ulysses Seal and Peter Jackson, who sought molecular genetic evidence for tiger subspecies classification years ago. All samples were recruited in compliance with the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) through permissions issued to the School of Life Sciences (PI: S.-J.L.), Peking University, by the State Forestry Administration of China. We are grateful to all of the collaborators, institutes, and zoos that provided the specimens upon which this study is based. This work was supported by the National Key Research and Development Program of China ( NQI 2017YFF0210303 ), the National Natural Science Foundation of China ( NSFC 31471179 ), and the Peking-Tsinghua Center for Life Sciences . S.J.O. was supported, in part, by the Russian Science Foundation grant (project no. 17-14-01138 ) and by St. Petersburg State University (Genome Russia Grant no. 1.52.1647.2016 ). Novogene and PKU-BIOPIC provided genome sequencing for the study. We thank N. Yamaguchi, Y. Zhuang, G. Sun, Z.-T. Zou, H.-R. Xue, H. Yu, X.-S. Hu, L. Miao, and R. Li for their technical assistance and helpful discussions.

Publisher Copyright:
© 2018 Elsevier Ltd

Keywords

  • adaptation
  • evolution
  • tiger
  • whole-genome sequencing

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