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.2015 May-Jun;106(3):247-57.
doi: 10.1093/jhered/esv002. Epub 2015 Mar 8.

Genetic ancestry of the extinct Javan and Bali tigers

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Genetic ancestry of the extinct Javan and Bali tigers

Hao-Ran Xue et al. J Hered.2015 May-Jun.

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.

Keywords: Panthera tigris balica; Panthera tigris sondaica; mtDNA; phylogeny.

© The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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Figures

Figure 1.
Figure 1.
Geographic distribution of mtDNA haplotypes among tigers from the islands of Sumatra, Java, and Bali. Only tiger specimens with confirmed geographic origins from Java (N = 9) and Bali (N = 2) are used (Table 1). Haplotypes are color-coded. SUM includes 8 mtDNA haplotypes represented by voucher Sumatran tigers (N = 16) (Luoet al. 2004). SON and BAL are 2 haplotypes exclusively found in Java and Bali different from the most closely related SUM haplotype by 1 or 2bp only (Table 2). No haplotype is shared among voucher Sumatran, Javan and Bali tigers. The size of a circle corresponds to the number of specimens from the island and sectors of the pie chart are proportional to haplotype frequencies.
Figure 2.
Figure 2.
Phylogeny ofPanthera tigris mtDNA sequences. (a) Phylogenetic relationships among tiger mtDNA haplotypes based on 4078bp of concatenated sequences from all 9 subspecies rooted withP. uncia,P. pardus, andN. nebulosa. Fragments obtained from Sundaic historic tiger specimens are concatenated into mtDNA haplotypes of 1750bp in SON and BAL, and 1629bp in SUMx, respectively, and analyzed jointly with other previously published voucher haplotypes (Luoet al. 2004; Driscollet al. 2009). Haplotype designations are color-coded by subspecies. Eleven closely related haplotypes fromP. t. sumatrae,P. t. sondaica, andP. t. balica form a monophyletic group with strong statistical support. Phylogenetic trees derived from maximum parsimony (MP), neighbor-joining (NJ), maximum likelihood (ML), and Bayesian analyses have similar topologies and only the MP tree is shown. Numbers above branches represent bootstrap support in percent using the MP (from 2000 replicates), NJ (from 2000 replicates), and ML (from 100 replicates) methods, followed by posterior probabilities using Bayesian analyses (only those over 50% are indicated). Numbers below branches show the number of changes. (b) Statistical parsimony network of 29 mtDNA haplotypes (4078bp) as represented by circles from all 9 tiger subspecies. Circle size is proportional to the number of samples sharing the haplotype. BAL is shared by both voucher tiger specimens from Bali, and is one step away from SUM2. SON is 2 nucleotides different from SUM2 and found in tigers from Java only.
Figure 3.
Figure 3.
Bayesian skyline plot of mtDNA sequences of tigers from the islands of Sumatra, Java, and Bali. Thex-axis is time in KYA (thousand years ago). The last glacial period (c. 110 000–12 000 years ago) and last glacial maximum (LGM, c. 20 000 years ago) are marked. They-axis represents effective population sizeNe, assuming a generation time of 5 years for the tiger (Smith and McDougal 1991). The solid black line shows estimate of the posterior median and the shading denotes 95% highest posterior density limits.
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