Reanalysis of sequences of alleged Javan tiger highlights the difficulties in studying big cats and the need for high-throughput sequencing
Big cats are of conservation concern throughout their range, and genetic tools are often employed to study them for various purposes. However, there are several difficulties in using genetic tools for big cat conservation that could be resolved by modern methods of DNA sequencing. Recent reports of...
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| author | Anubhab Khan Yulianto Yulianto Sabhrina Gita Aninta Wirdateti Wirdateti |
| author_facet | Anubhab Khan Yulianto Yulianto Sabhrina Gita Aninta Wirdateti Wirdateti |
| author_sort | Anubhab Khan |
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| description | Big cats are of conservation concern throughout their range, and genetic tools are often employed to study them for various purposes. However, there are several difficulties in using genetic tools for big cat conservation that could be resolved by modern methods of DNA sequencing. Recent reports of the sighting of a putative Javan tiger Panthera tigris sondaica in West Java, Indonesia, highlight some of the difficulties of studying the genetics of big cats. We reanalysed the data of the original reports and found that the conclusions were drawn based on incorrect copies of the genes. Specifically, the nuclear copy of the mitochondrial gene was analysed with the mitochondrial sequence, leading to discordance in the results. However, re-sequencing of the remaining DNA confirms that the sighting could have been that of a tiger, but the subspecies cannot be confirmed. This work highlights the urgency of developing high-throughput sequencing infrastructure in the tropics and the need for reliable databases for the study of big cats. |
| format | Article |
| id | doaj-art-f23d014bfb5d47f381c40ebf4ff4cc57 |
| institution | Kabale University |
| issn | 0030-6053 1365-3008 |
| language | English |
| publisher | Cambridge University Press |
| record_format | Article |
| series | Oryx |
| spelling | doaj-art-f23d014bfb5d47f381c40ebf4ff4cc572025-01-23T05:42:17ZengCambridge University PressOryx0030-60531365-30081610.1017/S0030605324001297Reanalysis of sequences of alleged Javan tiger highlights the difficulties in studying big cats and the need for high-throughput sequencingAnubhab Khan0https://orcid.org/0000-0002-6342-6522Yulianto Yulianto1Sabhrina Gita Aninta2https://orcid.org/0000-0002-0736-4750Wirdateti Wirdateti3https://orcid.org/0000-0002-9224-1017Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark Department of Biology, Pwani University, Kilifi, KenyaResearch Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong, IndonesiaSection for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, DenmarkResearch Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, IndonesiaBig cats are of conservation concern throughout their range, and genetic tools are often employed to study them for various purposes. However, there are several difficulties in using genetic tools for big cat conservation that could be resolved by modern methods of DNA sequencing. Recent reports of the sighting of a putative Javan tiger Panthera tigris sondaica in West Java, Indonesia, highlight some of the difficulties of studying the genetics of big cats. We reanalysed the data of the original reports and found that the conclusions were drawn based on incorrect copies of the genes. Specifically, the nuclear copy of the mitochondrial gene was analysed with the mitochondrial sequence, leading to discordance in the results. However, re-sequencing of the remaining DNA confirms that the sighting could have been that of a tiger, but the subspecies cannot be confirmed. This work highlights the urgency of developing high-throughput sequencing infrastructure in the tropics and the need for reliable databases for the study of big cats.https://www.cambridge.org/core/product/identifier/S0030605324001297/type/journal_articleCapacity buildingDNA analysisextinctJavan tigerLazarus speciesnext-generation sequencingSanger sequencingshed hair |
| spellingShingle | Anubhab Khan Yulianto Yulianto Sabhrina Gita Aninta Wirdateti Wirdateti Reanalysis of sequences of alleged Javan tiger highlights the difficulties in studying big cats and the need for high-throughput sequencing Oryx Capacity building DNA analysis extinct Javan tiger Lazarus species next-generation sequencing Sanger sequencing shed hair |
| title | Reanalysis of sequences of alleged Javan tiger highlights the difficulties in studying big cats and the need for high-throughput sequencing |
| title_full | Reanalysis of sequences of alleged Javan tiger highlights the difficulties in studying big cats and the need for high-throughput sequencing |
| title_fullStr | Reanalysis of sequences of alleged Javan tiger highlights the difficulties in studying big cats and the need for high-throughput sequencing |
| title_full_unstemmed | Reanalysis of sequences of alleged Javan tiger highlights the difficulties in studying big cats and the need for high-throughput sequencing |
| title_short | Reanalysis of sequences of alleged Javan tiger highlights the difficulties in studying big cats and the need for high-throughput sequencing |
| title_sort | reanalysis of sequences of alleged javan tiger highlights the difficulties in studying big cats and the need for high throughput sequencing |
| topic | Capacity building DNA analysis extinct Javan tiger Lazarus species next-generation sequencing Sanger sequencing shed hair |
| url | https://www.cambridge.org/core/product/identifier/S0030605324001297/type/journal_article |
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