{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T17:33:52Z","timestamp":1785346432313,"version":"3.55.0"},"reference-count":44,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2023,10,19]],"date-time":"2023-10-19T00:00:00Z","timestamp":1697673600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Department of Wildlife Protection"},{"name":"Jammu and Kashmir Government and the Ministry of Environment"},{"name":"Forests and Climate Change, Government of India"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:sec>\n<jats:title>Background<\/jats:title>\n<jats:p>The Kashmir red deer or Hangul (<jats:italic>Cervus hanglu hanglu<\/jats:italic>) is the only Tarim red deer species endemic to India. With a current estimated population size of fewer than 200 individuals, this critically endangered species is confined to the greater Dachigam landscape in Jammu and Kashmir. Poaching, habitat loss and fragmentation, resource competition with livestock, and small population size are the major conservation challenges for this species.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Methods<\/jats:title>\n<jats:p>Blood sampling was conducted from two wild Hangul individuals during radio-collaring operations at Dachigam National Park, Kashmir in 2013 and 2020, respectively. Using next-generation sequencing approach, we sequenced the 16,351 bp long mitogenome of two wild-caught Hangul individuals (1 M:1 F at ~14\u00d7 and ~10\u00d7 coverage, respectively) from Dachigam National Park.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>The annotated sequences were identical with an AT-rich composition, including 13 protein-coding genes (11,354 bp), 22 tRNA genes (1,515 bp), two ribosomal genes (2,526 bp) and a non-coding control region (917 bp) in a conserved order like other red deer species. Bayesian phylogenetic reconstruction of the red deer complex revealed two major groups: the elaphoid and the wapitoid clades. Hangul formed a distinct clade with its other subspecies <jats:italic>C. hanglu yarkandensis<\/jats:italic> and is sister to the Hungarian red deer (<jats:italic>C. elaphus hippelaphus<\/jats:italic>). Divergence time analyses suggested that the Tarim deer species group separated ~1.55 Mya from their common ancestors and Hangul diverged ~0.75 Mya from closely related <jats:italic>C. yarkandensis<\/jats:italic>, corroborating with the known paleobiogeographic events related to refugia during glaciations in the Pleistocene era. This study provides baseline information on Hangul mitogenome for further research on phylogeography and other population parameters and helps in developing suitable conservation plans for this species.<\/jats:p>\n<\/jats:sec>","DOI":"10.7717\/peerj.15746","type":"journal-article","created":{"date-parts":[[2023,10,19]],"date-time":"2023-10-19T07:23:42Z","timestamp":1697700222000},"page":"e15746","source":"Crossref","is-referenced-by-count":2,"title":["Evolutionary insights on critically endangered Kashmir red deer or hangul (<i>Cervus hanglu hanglu<\/i>) through a mitogenomic lens"],"prefix":"10.7717","volume":"11","author":[{"given":"Khursheed","family":"Ahmad","sequence":"first","affiliation":[{"name":"Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7979-4223","authenticated-orcid":true,"given":"Ankit","family":"Shankar Pacha","sequence":"additional","affiliation":[{"name":"Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, Uttarakhand, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rashid","family":"Yahya Naqash","sequence":"additional","affiliation":[{"name":"Department of Wildlife Protection, Jammu & Kashmir Government, Srinagar, Jammu and Kashmir, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sathish","family":"Kumar Peddamma","sequence":"additional","affiliation":[{"name":"Nucleome Informatics Pvt. Ltd., Hyderabad, Telangana, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5412-4717","authenticated-orcid":true,"given":"Srinivas","family":"Yellapu","sequence":"additional","affiliation":[{"name":"Nucleome Informatics Pvt. Ltd., Hyderabad, Telangana, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shenu","family":"Hudson","sequence":"additional","affiliation":[{"name":"Nucleome Informatics Pvt. Ltd., Hyderabad, Telangana, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dushyant","family":"Singh Baghel","sequence":"additional","affiliation":[{"name":"Nucleome Informatics Pvt. Ltd., Hyderabad, Telangana, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Parag","family":"Nigam","sequence":"additional","affiliation":[{"name":"Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, Uttarakhand, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3034-9396","authenticated-orcid":true,"given":"Samrat","family":"Mondol","sequence":"additional","affiliation":[{"name":"Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, Uttarakhand, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"4443","published-online":{"date-parts":[[2023,10,19]]},"reference":[{"issue":"1","key":"10.7717\/peerj.15746\/ref-1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12983-020-00379-5","article-title":"Whole-genome sequencing of Tarim red deer (Cervus elaphus yarkandensis) reveals demographic history and adaptations to an arid-desert environment","volume":"17","author":"Ababaikeri","year":"2020","journal-title":"Frontiers in Zoology"},{"key":"10.7717\/peerj.15746\/ref-2","first-page":"37","article-title":"Kashmir red deer or Hangul Cervus elaphus hanglu at the brink of Extinction-Conservation Action, the need of an Hour","volume":"26","author":"Ahmad","year":"2014","journal-title":"DSG Newsletter IUCN-DSG Newsletter"},{"issue":"3","key":"10.7717\/peerj.15746\/ref-3","first-page":"245","article-title":"Conservation status of the last surviving wild population of hangul or Kashmir deer Cervus elaphus hanglu in Kashmir, India","volume":"106","author":"Ahmad","year":"2009","journal-title":"Journal of the Bombay Natural History Society"},{"issue":"5","key":"10.7717\/peerj.15746\/ref-4","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"Journal of Computational Biology"},{"issue":"2","key":"10.7717\/peerj.15746\/ref-5","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1016\/j.ympev.2012.08.023","article-title":"MITOS: improved de novo metazoan mitochondrial genome annotation","volume":"69","author":"Bernt","year":"2013","journal-title":"Molecular Phylogenetics and Evolution"},{"key":"10.7717\/peerj.15746\/ref-6","article-title":"Cervus hanglu ssp. hanglu. The IUCN red list of threatened species 2017: e.T113259123A113281791","author":"Brook","year":"2017"},{"issue":"17","key":"10.7717\/peerj.15746\/ref-7","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ pre-processor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"issue":"8","key":"10.7717\/peerj.15746\/ref-8","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1038\/nmeth.2109","article-title":"jModelTest 2: more models, new heuristics and parallel computing","volume":"9","author":"Darriba","year":"2012","journal-title":"Nature Methods"},{"issue":"1","key":"10.7717\/peerj.15746\/ref-9","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1093\/zoolinnean\/zlx065","article-title":"The history of Crimean red deer population and Cervus phylogeography in Eurasia","volume":"183","author":"Doan","year":"2018","journal-title":"Zoological Journal of the Linnean Society"},{"issue":"2","key":"10.7717\/peerj.15746\/ref-10","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1093\/zoolinnean\/zlab025","article-title":"Phylogenetics and phylogeography of red deer mtDNA lineages during the last 50,000 years in Eurasia","volume":"194","author":"Doan","year":"2022","journal-title":"Zoological Journal of the Linnean Society"},{"issue":"1","key":"10.7717\/peerj.15746\/ref-11","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1186\/1471-2148-7-214","article-title":"BEAST: bayesian evolutionary analysis by sampling trees","volume":"7","author":"Drummond","year":"2007","journal-title":"BMC Evolutionary Biology"},{"issue":"2","key":"10.7717\/peerj.15746\/ref-12","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1556\/018.67.2016.2.2","article-title":"Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae","volume":"67","author":"Frank","year":"2016","journal-title":"Acta Biologica Hungarica"},{"issue":"W1","key":"10.7717\/peerj.15746\/ref-13","doi-asserted-by":"publisher","first-page":"W59","DOI":"10.1093\/nar\/gkz238","article-title":"OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes","volume":"47","author":"Greiner","year":"2019","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"10.7717\/peerj.15746\/ref-14","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1016\/j.crvi.2011.11.002","article-title":"Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes","volume":"335","author":"Hassanin","year":"2012","journal-title":"Comptes Rendus Biologies"},{"issue":"1\u20133","key":"10.7717\/peerj.15746\/ref-15","doi-asserted-by":"publisher","first-page":"e8114","DOI":"10.7717\/peerj.8114","article-title":"The systematics of the Cervidae: a total evidence approach","volume":"8","author":"Heckeberg","year":"2020","journal-title":"PeerJ"},{"key":"10.7717\/peerj.15746\/ref-16","article-title":"TREEANNOTATOR: versatile visual annotation of hierarchical text relations","author":"Helfrich","year":"2018"},{"issue":"1","key":"10.7717\/peerj.15746\/ref-17","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12864-019-5785-z","article-title":"Genome-wide study on genetic diversity and phylogeny of five species in the genus Cervus","volume":"20","author":"Hu","year":"2019","journal-title":"BMC Genomics"},{"key":"10.7717\/peerj.15746\/ref-18","doi-asserted-by":"crossref","first-page":"95","DOI":"10.2307\/20094864","article-title":"Evaluation of medetomidine and ketamine induced immobilization in markhors (Capra falconeri megaceros) and its reversal by atipamezole","volume":"19","author":"Jalanka","year":"1988","journal-title":"Journal of Zoo Animal Medicine"},{"key":"10.7717\/peerj.15746\/ref-19","first-page":"259","article-title":"The use of medetomidine, medetomidine-ketamine combinations, and atipamezole in nondomestic mammals: a review","volume":"21","author":"Jalanka","year":"1990","journal-title":"Journal of Zoo and Wildlife Medicine"},{"issue":"1","key":"10.7717\/peerj.15746\/ref-20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-020-02154-5","article-title":"GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes","volume":"21","author":"Jin","year":"2020","journal-title":"Genome Biology"},{"issue":"7","key":"10.7717\/peerj.15746\/ref-21","doi-asserted-by":"publisher","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Molecular Biology and Evolution"},{"issue":"6","key":"10.7717\/peerj.15746\/ref-22","doi-asserted-by":"publisher","first-page":"835","DOI":"10.1080\/24701394.2016.1197217","article-title":"Resolving the phylogenetic status and taxonomic relationships of the Hangul (Cervus elaphus hanglu) in the family Cervidae","volume":"28","author":"Kumar","year":"2017","journal-title":"Mitochondrial DNA Part A"},{"key":"10.7717\/peerj.15746\/ref-23","first-page":"317","volume-title":"Pleistocene mammals of Europe","author":"Kurten","year":"1968"},{"issue":"1","key":"10.7717\/peerj.15746\/ref-24","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1006\/mpev.1999.0731","article-title":"Phylogenetic relationships among European red deer, wapiti, and sika deer inferred from mitochondrial DNA sequences","volume":"15","author":"Kuwayama","year":"2000","journal-title":"Molecular Phylogenetics and Evolution"},{"issue":"4","key":"10.7717\/peerj.15746\/ref-25","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nature Methods"},{"issue":"1","key":"10.7717\/peerj.15746\/ref-26","doi-asserted-by":"publisher","first-page":"620","DOI":"10.3109\/19401736.2014.908373","article-title":"Complete mitochondrial genome of Cervus elaphus songaricus (Cetartiodactyla: Cervinae) and a phylogenetic analysis with related species","volume":"27","author":"Li","year":"2016","journal-title":"Mitochondrial DNA Part A"},{"issue":"4","key":"10.7717\/peerj.15746\/ref-27","doi-asserted-by":"publisher","first-page":"340","DOI":"10.1111\/jzs.12104","article-title":"Insights into the evolutionary history of Cervus (Cervidae, tribe Cervini) based on Bayesian analysis of mitochondrial marker sequences, with first indications for a new species","volume":"53","author":"Lorenzini","year":"2015","journal-title":"Journal of Zoological Systematics and Evolutionary Research"},{"issue":"3","key":"10.7717\/peerj.15746\/ref-28","doi-asserted-by":"publisher","first-page":"1064","DOI":"10.1016\/j.ympev.2003.10.003","article-title":"Mitochondrial DNA phylogeography of red deer (Cervus elaphus)","volume":"31","author":"Ludt","year":"2004","journal-title":"Molecular Phylogenetics and Evolution"},{"issue":"1","key":"10.7717\/peerj.15746\/ref-29","doi-asserted-by":"publisher","first-page":"16381","DOI":"10.1038\/s41598-022-20763-x","article-title":"Phylogeny and evolution of the genus Cervus (Cervidae, Mammalia) as revealed by complete mitochondrial genomes","volume":"12","author":"Mackiewicz","year":"2022","journal-title":"Scientific Reports"},{"issue":"4","key":"10.7717\/peerj.15746\/ref-30","doi-asserted-by":"publisher","first-page":"485","DOI":"10.2108\/zsj.19.485","article-title":"Molecular phylogeography of the red deer (Cervus elaphus) populations in Xinjiang of China: comparison with other Asian, European, and North American populations","volume":"19","author":"Mahmut","year":"2002","journal-title":"Zoological Science"},{"issue":"2","key":"10.7717\/peerj.15746\/ref-31","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1111\/jbi.13124","article-title":"Subspecies dynamics in space and time: a study of the red deer complex using ancient and modern DNA and morphology","volume":"45","author":"Meiri","year":"2018","journal-title":"Journal of Biogeography"},{"issue":"2","key":"10.7717\/peerj.15746\/ref-32","doi-asserted-by":"publisher","first-page":"e0117069","DOI":"10.1371\/journal.pone.0117069","article-title":"Pragmatic perspective on conservation genetics and demographic history of the last surviving population of Kashmir Red Deer (Cervus elaphus hanglu) in India","volume":"10","author":"Mukesh","year":"2015","journal-title":"PLOS ONE"},{"issue":"7","key":"10.7717\/peerj.15746\/ref-33","doi-asserted-by":"publisher","first-page":"e100136","DOI":"10.1371\/journal.pone.0100136","article-title":"Positioning the red deer (Cervus elaphus) hunted by the Tyrolean Iceman into a mitochondrial DNA phylogeny","volume":"9","author":"Olivieri","year":"2014","journal-title":"PLOS ONE"},{"issue":"2","key":"10.7717\/peerj.15746\/ref-34","doi-asserted-by":"publisher","first-page":"1995","DOI":"10.1007\/s11033-021-06165-8","article-title":"Sequencing and annotation of the endangered wild buffalo (Bubalus arnee) mitogenome for taxonomic assessment","volume":"48","author":"Pacha","year":"2021","journal-title":"Molecular Biology Reports"},{"issue":"2","key":"10.7717\/peerj.15746\/ref-35","doi-asserted-by":"publisher","first-page":"85","DOI":"10.3109\/19401736.2013.784748","article-title":"The complete mitochondrial genome of sika deer Cervus nippon (Cetartiodactyla: Cervinae) South Anhui population","volume":"25","author":"Pan","year":"2014","journal-title":"Mitochondrial DNA"},{"key":"10.7717\/peerj.15746\/ref-36","first-page":"19","article-title":"Restoration of Bukhara deer (Cervus elaphus bactrianus Lydd.) in Central Asia in 2000-2011","volume":"25","author":"Pereladova","year":"2013","journal-title":"Deer Specialist Members Welcome to the New Quadrienium"},{"key":"10.7717\/peerj.15746\/ref-37","article-title":"FigTree v1. 3.1","author":"Rambaut","year":"2009"},{"key":"10.7717\/peerj.15746\/ref-38","article-title":"Tracer","author":"Rambaut","year":"2007"},{"issue":"3","key":"10.7717\/peerj.15746\/ref-39","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1093\/sysbio\/syw095","article-title":"The impact of the tree prior on molecular dating of data sets containing a mixture of inter-and intraspecies sampling","volume":"66","author":"Ritchie","year":"2017","journal-title":"Systematic Biology"},{"issue":"3","key":"10.7717\/peerj.15746\/ref-40","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1093\/sysbio\/sys029","article-title":"MrBayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space","volume":"61","author":"Ronquist","year":"2012","journal-title":"Systematic Biology"},{"issue":"1","key":"10.7717\/peerj.15746\/ref-41","doi-asserted-by":"publisher","first-page":"1","DOI":"10.4404\/hystrix-00252-2019","article-title":"Phylogeny and diversity of moose (Alces alces, Cervidae, Mammalia) revealed by complete mitochondrial genomes","volume":"31","author":"\u015awis\u0142ocka","year":"2020","journal-title":"Hystrix"},{"issue":"2","key":"10.7717\/peerj.15746\/ref-42","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1007\/s10592-017-1011-1","article-title":"Genetic variation of complete mitochondrial genome sequences of the Sumatran rhinoceros (Dicerorhinus sumatrensis)","volume":"19","author":"Steiner","year":"2018","journal-title":"Conservation Genetics"},{"issue":"1\u20133","key":"10.7717\/peerj.15746\/ref-43","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1016\/j.smallrumres.2005.12.002","article-title":"The complete nucleotide sequence of mitochondrial genome in the Japanese Sika deer (Cervus nippon), and a phylogenetic analysis between Cervidae and Bovidae","volume":"69","author":"Wada","year":"2007","journal-title":"Small Ruminant Research"},{"issue":"1","key":"10.7717\/peerj.15746\/ref-44","doi-asserted-by":"publisher","first-page":"628","DOI":"10.4238\/2012.March.14.6","article-title":"Phylogeny and evolution of Cervidae based on complete mitochondrial genomes","volume":"11","author":"Zhang","year":"2012","journal-title":"Genetics and Molecular Research"}],"container-title":["PeerJ"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/peerj.com\/articles\/15746.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/15746.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/15746.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/15746.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,19]],"date-time":"2023-10-19T07:23:58Z","timestamp":1697700238000},"score":1,"resource":{"primary":{"URL":"https:\/\/peerj.com\/articles\/15746"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,10,19]]},"references-count":44,"alternative-id":["10.7717\/peerj.15746"],"URL":"https:\/\/doi.org\/10.7717\/peerj.15746","archive":["CLOCKSS","LOCKSS","Portico"],"relation":{},"ISSN":["2167-8359"],"issn-type":[{"value":"2167-8359","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,10,19]]},"article-number":"e15746"}}