{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T00:56:22Z","timestamp":1760057782025,"version":"build-2065373602"},"reference-count":28,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2025,2,25]],"date-time":"2025-02-25T00:00:00Z","timestamp":1740441600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42202014","2022YFC2601200","NABRI202203"],"award-info":[{"award-number":["42202014","2022YFC2601200","NABRI202203"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Key R&amp;D Program of China","award":["42202014","2022YFC2601200","NABRI202203"],"award-info":[{"award-number":["42202014","2022YFC2601200","NABRI202203"]}]},{"name":"Northeast Asia Biodiversity Research Center","award":["42202014","2022YFC2601200","NABRI202203"],"award-info":[{"award-number":["42202014","2022YFC2601200","NABRI202203"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background: The phylogenetic resolution within the Gloydius halys-intermedius Complex remains debatable due to the following reasons: loci selection in previous studies varied between authors; limited dataset (1\u22125 mitochondrial or nuclear gene fragments); lack of sampling density; and nodal supports at specific nodes remain weak, specifically within Gloydius cognatus, G. halys, and G. stejnegeri. Objectives: To revise the taxonomic and phylogenetic relationships within the G. halys-intermedius Complex, we reconstructed the molecular phylogeny and performed species delimitation based on the complete mitochondrial genomes. Methods: In this study, twelve nomenclatural groups of Gloydius species were involved in the computation of Bayesian phylogenomic inference, five of the twelve nomenclature groups were newly sequenced, while the rest were acquired from the National Center for Biotechnology Information (NCBI). The Bayesian phylogenomic inference was constructed based on 13 mitochondrial protein-coding genes. Species delimitation was performed by two distance-based methods (ABGD and ASAP) and two tree-based methods (GMYC and bPTP). Results: This research resolved the systematic relationship within the G. intermedius Complex with the support of mitogenome-based phylogenomics, while indicating cryptic diversity within the Gloydius halys-intermedius Complex: G. intermedius samples from South Korea show as paraphyletic to the cluster of the samples from northeastern China. Species delimitation results based on four models resemble each other, supporting Gloydius caucasicus, G. cognatus, G. halys, and G. stejnegeri, each representing full species. The species delimitation results of this research also resemble the nomenclatural species based on previous morphometrical results. This research indicates that species delimitation efforts based on the phylogenomic approach would likely resolve complex evolutionary relationships.<\/jats:p>","DOI":"10.3390\/genes16030276","type":"journal-article","created":{"date-parts":[[2025,2,25]],"date-time":"2025-02-25T10:55:48Z","timestamp":1740480948000},"page":"276","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Phylogeny and Specific Determination of Gloydius halys-intermedius Complex Based on Complete Mitochondrial Genes"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-4299-412X","authenticated-orcid":false,"given":"Lijie","family":"Jin","sequence":"first","affiliation":[{"name":"Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zuyao","family":"Xia","sequence":"additional","affiliation":[{"name":"Department of Evolution, Ecology & Biodiversity, University of California, Davis, CA 95616, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ning","family":"Liu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shengyue","family":"Hou","sequence":"additional","affiliation":[{"name":"Department of Wildlife, Fish and Conservation Biology, University of California, Davis, CA 95618, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chuandong","family":"Lv","sequence":"additional","affiliation":[{"name":"National Nature Conservation of Snake Island and Laotieshan Mountain, Dalian 116041, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lianyou","family":"Tang","sequence":"additional","affiliation":[{"name":"National Nature Conservation of Snake Island and Laotieshan Mountain, Dalian 116041, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuguang","family":"Feng","sequence":"additional","affiliation":[{"name":"National Nature Conservation of Snake Island and Laotieshan Mountain, Dalian 116041, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9168-1734","authenticated-orcid":false,"given":"Jingsong","family":"Shi","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"},{"name":"Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming","family":"Bai","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"},{"name":"Northeast Asia Biodiversity Research Center, Northeast Forestry University, Harbin 150040, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,2,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1163\/15685381-00003134","article-title":"A new moth-preying alpine pit viper species from Qinghai-Tibetan Plateau (Viperidae, Crotalinae)","volume":"38","author":"Shi","year":"2017","journal-title":"Amphib. 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