No reliable evidence supports the presence of the Javan tiger: data issues related to theDNAanalysis of a recent hair sample ZHE NG-YAN S UI 1 ,NOBUYUKI YAMAG U C H I 2 , 3 ,YUE-CHE N L IU 4 , 5
HAO -RAN XUE 6 ,XIN SUN7 ,PHILIP NYH US 8 and SHU-J IN LUO* 1
Abstract A recent study published in Oryx proposed that the extinct Javan tiger Panthera tigris sondaica may still sur- vive on the Island of Java, Indonesia, based on mitochon- drial DNA analysis of a single hair sample collected from a location where a tiger was reportedly encountered. However, upon reanalysing the genetic data presented in that study, we conclude that there is little support for this claim. The sequences of the putative tiger hair and Javan tiger museum specimens generated are not from tiger cytoplasmic mito- chondrial DNA but more likely the nuclear pseudogene copies of mitochondrial DNA. In addition, the number of mismatches between the two Javan tiger sequences is un- usually high for homologous sequences that are both from tigers, suggesting potential issues with data reliability. The paper provides insufficient details on quality control mea- sures, making it impossible to rule out the possibility that errors were introduced during the analysis. Consequently, it is inappropriate to use the sequences presented in that study to infer the existence of the Javan tiger.
Keywords Extinct species, genetic analysis, Indonesia, Java, Javan tiger, mitochondrial DNA, Numt, Panthera tigris sondaica
cies has been declared extinct (Seidensticker, 1987; Jackson & Nowell, 1996, 2008). In 2019 a putative encounter with a tiger was reported near a community plantation in West
T
*Corresponding author,
luo.shujin@
pku.edu.cn 1The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced
Interdisciplinary Studies; Institute of Ecology, Peking University, Beijing, China 2Institute of Tropical Biodiversity and Sustainable Development, University of
Malaysia Terengganu, Kuala Nerus, Malaysia 3Wildlife Conservation Research Unit, Department of Biology, University of
Oxford, Oxford, UK 4Department of Human Evolutionary Biology, Harvard University, Cambridge,
Massachusetts, USA 5Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA 6Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm,
Germany 7Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and
Medical Sciences, University of Copenhagen, Copenhagen, Denmark 8Environmental Studies Department, Colby College, Waterville, Maine, USA
Received 17 April 2024. Revision requested 14 June 2024. Accepted 23 August 2024. First published online 6 December 2024.
here has been no confirmed sighting of the Javan tiger Panthera tigris sondaica since the 1970s and the subspe-
Java, and DNA from a single hair sample collected from a fence nearby was subsequently analysed (Wirdateti et al., 2024). Our re-examination of the genetic data from the paper raises concerns regarding the credibility of the data and hence the reliability of the conclusion. Wirdateti et al. amplified and sequenced a 1,043 bp cyto-
chrome b mitochondrial DNA (mtDNA) segment from the hair collected and compared it to those of leopards and tiger subspecies of known origin, including a Javan tiger museum specimen collected in 1930. Phylogenetic trees showed that the hair sample aligned most closely with the Javan tiger museum specimen, forming a clade distinct from other tiger subspecies and the Javan leopard. Based on the results the authors concluded that the hair belongs to the Javan tiger, implying that this tiger subspecies is not extinct. However, after reanalysing the data presented by Wirdateti et al., we conclude there is no support for the authors’ conclusions, for the following three reasons: (1) the sequences that the authors obtained are not genuine tiger mtDNA, (2) the sequences are probably nuclear pseudogene copies of mtDNA (Numt), and (3) the sequences generated from the putative and the control Javan tiger specimens are more divergent from one another than the mean difference between other tiger sequences, yet readers cannot evaluate the reliability of the original data because few details concerning quality control were provided in the paper. Firstly, the sequences that the authors obtained are not
tiger mtDNA segments. In the paper, the genetic clade in- cluding the hair sample in question (NCBI Accession OQ601561.1) and the Javan tiger museum specimen from 1930 (OQ601562.1) is an outgroup to the tiger mtDNA clade and is phylogenetically equidistant from both tigers and leopards, which is a pattern that was not observed in previous studies involving the Javan tiger (Xue et al., 2015; Sun et al., 2023). To investigate this issue, we conducted a phylogenetic analysis of the two putative Javan tiger se- quences produced by Wirdateti et al., along with published mtDNA sequences from Panthera species (28 Panthera ti- gris including one Panthera tigris sondaica museum speci- men, three Panthera pardus, three Panthera leo, three Panthera onca and three Panthera uncia; Table 1). We used MUSCLE 5.1 (Edgar et al., 2022) for multi-sequence alignment of the 42 sequences. We manually trimmed 72 bp from both sides of the alignment, resulting in a 971 bp nucleotide DNA sequence matrix without missing data.
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (
http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited. Oryx, 2025, 59(1), 69–74 © The Author(s), 2024. Published by Cambridge University Press on behalf of Fauna & Flora International doi:10.1017/S0030605324001248
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