{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T04:49:09Z","timestamp":1791607749853,"version":"4.3.4"},"reference-count":43,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the Hainan Institute of National Park, HINP","award":["KY-24ZK02"],"award-info":[{"award-number":["KY-24ZK02"]}]},{"name":"the Hainan Province Science and Technology Special Fund","award":["ZDYF2023RDYL01"],"award-info":[{"award-number":["ZDYF2023RDYL01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>The Hainan gibbon (Nomascus hainanus) is one of the most threatened primates, yet its mitochondrial haplotype diversity and genealogy remain poorly understood. This study investigated mitochondrial haplotype structure, genealogical history, and selective constraints on mitochondrial protein-coding genes using complete mitochondrial genomes. We generated mitogenomic data from 13 wild individuals representing five of seven extant social groups, including the recently formed F and G groups, which were established through natural dispersal and had not previously been genetically characterized. Complete mitogenomes were obtained using a combination of Illumina and Sanger sequencing, followed by population genetic analyses, phylogenetic reconstruction, molecular dating, and mitochondrial selection tests. All mitogenomes were 16,481 bp in length and exhibited very low nucleotide diversity (\u03c0 = 0.000498), with four haplotypes forming two major maternal clades. Groups B, C, and E contained haplotypes from both major maternal clades, whereas F and G each showed a single sampled haplotype, a pattern consistent with maternal founder effects in these recently formed groups. The two major maternal clades had an estimated time to the most recent common ancestor (TMRCA) of ~27 ka (95% highest posterior density (HPD): 11.9\u201345.7 ka), placing their most recent common ancestor in the Late Pleistocene. Interspecific selection analyses were consistent with predominantly purifying selection across mitochondrial protein-coding genes, with no significant evidence of episodic positive selection or altered selection intensity. These findings complement previous nuclear genomic and partial mitochondrial DNA studies by providing a population-level view of complete-mitogenome haplotype distribution across five sampled social groups.<\/jats:p>","DOI":"10.3390\/ani16193091","type":"journal-article","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T09:38:16Z","timestamp":1790847496000},"page":"3091","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Complete Mitogenomes of the Critically Endangered Hainan Gibbon (Nomascus hainanus) Reveal Very Low Mitochondrial Diversity and Two Major Maternal Clades"],"prefix":"10.3390","volume":"16","author":[{"given":"Zhonghao","family":"Yu","sequence":"first","affiliation":[{"name":"Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan Province Key Laboratory of One Health, Collaborative Innovation Center of One Health, Hainan University, Haikou 570228, China"},{"name":"Hainan International One Health Institute, Hainan University, Haikou 570228, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ren","family":"Xiahou","sequence":"additional","affiliation":[{"name":"Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan Province Key Laboratory of One Health, Collaborative Innovation Center of One Health, Hainan University, Haikou 570228, China"},{"name":"Hainan International One Health Institute, Hainan University, Haikou 570228, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meng","family":"Nie","sequence":"additional","affiliation":[{"name":"Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan Province Key Laboratory of One Health, Collaborative Innovation Center of One Health, Hainan University, Haikou 570228, China"},{"name":"Hainan International One Health Institute, Hainan University, Haikou 570228, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyi","family":"Cai","sequence":"additional","affiliation":[{"name":"Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan Province Key Laboratory of One Health, Collaborative Innovation Center of One Health, Hainan University, Haikou 570228, China"},{"name":"Hainan International One Health Institute, Hainan University, Haikou 570228, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dingfeng","family":"Duan","sequence":"additional","affiliation":[{"name":"Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan Province Key Laboratory of One Health, Collaborative Innovation Center of One Health, Hainan University, Haikou 570228, China"},{"name":"Hainan International One Health Institute, Hainan University, Haikou 570228, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanjiao","family":"Zhou","sequence":"additional","affiliation":[{"name":"Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan Province Key Laboratory of One Health, Collaborative Innovation Center of One Health, Hainan University, Haikou 570228, China"},{"name":"Hainan International One Health Institute, Hainan University, Haikou 570228, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Chen","sequence":"additional","affiliation":[{"name":"Wuzhishan National Long-Term Forest Ecosystem Monitoring Research Station, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Forestry, Hainan University, Haikou 570228, China"},{"name":"Institute of Hainan National Park, Haikou 570100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenxing","family":"Long","sequence":"additional","affiliation":[{"name":"Wuzhishan National Long-Term Forest Ecosystem Monitoring Research Station, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Forestry, Hainan University, Haikou 570228, China"},{"name":"Institute of Hainan National Park, Haikou 570100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-9148-5985","authenticated-orcid":false,"given":"Chenghong","family":"Liao","sequence":"additional","affiliation":[{"name":"Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan Province Key Laboratory of One Health, Collaborative Innovation Center of One Health, Hainan University, Haikou 570228, China"},{"name":"Hainan International One Health Institute, Hainan University, Haikou 570228, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,10,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"932","DOI":"10.1007\/s10764-022-00309-8","article-title":"The critically endangered Hainan gibbon (Nomascus hainanus) population increases but not at the maximum possible rate","volume":"43","author":"Liu","year":"2022","journal-title":"Int. J. Primatol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1007\/s10764-005-2933-x","article-title":"Hainan black-crested gibbon is headed for extinction","volume":"26","author":"Zhou","year":"2005","journal-title":"Int. J. Primatol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"eadw3298","DOI":"10.1126\/sciadv.adw3298","article-title":"Genetic legacy and recent cross of two ancient lineages underlie the rebound of the world\u2019s rarest primate","volume":"12","author":"Hou","year":"2026","journal-title":"Sci. Adv."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"eadv4828","DOI":"10.1126\/sciadv.adv4828","article-title":"Science-based suggestions to save the world\u2019s rarest primate species Nomascus hainanus","volume":"11","author":"Zhong","year":"2025","journal-title":"Sci. Adv."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Guo, Y., Chang, J., Han, L., Liu, T., Li, G., Garber, P.A., Xiao, N., and Zhou, J. (2020). The genetic status of the critically endangered Hainan gibbon (Nomascus hainanus): A species moving toward extinction. Front. Genet., 11.","DOI":"10.3389\/fgene.2020.608633"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"3540","DOI":"10.1111\/mec.13716","article-title":"Assessing current genetic status of the Hainan gibbon using historical and demographic baselines: Implications for conservation management of species of extreme rarity","volume":"25","author":"Bryant","year":"2016","journal-title":"Mol. Ecol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"e70120","DOI":"10.1002\/ajp.70120","article-title":"Genetic diversity of the critically endangered Nomascus hainanus based on non-invasive sampling microsatellite analysis","volume":"88","author":"Li","year":"2026","journal-title":"Am. J. Primatol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"4541","DOI":"10.1111\/j.1365-294X.2009.04380.x","article-title":"Mitochondrial DNA as a marker of molecular diversity: A reappraisal","volume":"18","author":"Galtier","year":"2009","journal-title":"Mol. Ecol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1146\/annurev.es.18.110187.001413","article-title":"Evolution of animal mitochondrial DNA: Relevance for population biology and systematics","volume":"18","author":"Moritz","year":"1987","journal-title":"Annu. Rev. Ecol. Syst."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1080\/23802359.2021.1909432","article-title":"Mitochondrial DNA control region sequencing of the critically endangered Hainan gibbon (Nomascus hainanus) reveals two female origins and extremely low genetic diversity","volume":"6","author":"Guo","year":"2021","journal-title":"Mitochondrial DNA Part B Resour."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_12","doi-asserted-by":"crossref","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":"J. Comput. Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"3350","DOI":"10.1093\/bioinformatics\/btv383","article-title":"Bandage: Interactive visualization of de novo genome assemblies","volume":"31","author":"Wick","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1111\/1755-0998.13096","article-title":"PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies","volume":"20","author":"Zhang","year":"2020","journal-title":"Mol. Ecol. Resour."},{"key":"ref_15","doi-asserted-by":"crossref","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":"Mol. Phylogenetics Evol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-4939-9173-0_1","article-title":"tRNAscan-SE: Searching for tRNA genes in genomic sequences","volume":"1962","author":"Chan","year":"2019","journal-title":"Methods Mol. Biol."},{"key":"ref_17","doi-asserted-by":"crossref","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 Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"3299","DOI":"10.1093\/molbev\/msx248","article-title":"DnaSP 6: DNA sequence polymorphism analysis of large data sets","volume":"34","author":"Rozas","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: Molecular evolutionary genetics analysis across computing platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1111\/2041-210X.12410","article-title":"Popart: Full-feature software for haplotype network construction","volume":"6","author":"Leigh","year":"2015","journal-title":"Methods Ecol. Evol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1093\/molbev\/msx335","article-title":"Datamonkey 2.0: A modern web application for characterizing selective and other evolutionary processes","volume":"35","author":"Weaver","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1093\/molbev\/msv035","article-title":"Gene-wide identification of episodic selection","volume":"32","author":"Murrell","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1093\/molbev\/msu400","article-title":"RELAX: Detecting relaxed selection in a phylogenetic framework","volume":"32","author":"Wertheim","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_27","doi-asserted-by":"crossref","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":"Syst. Biol."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Drummond, A.J., and Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol., 7.","DOI":"10.1186\/1471-2148-7-214"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"674","DOI":"10.1111\/1749-4877.12878","article-title":"Mitogenomes of museum specimens provide new insight into species classification and recently reduced diversity of highly endangered Nomascus gibbons","volume":"20","author":"Liu","year":"2025","journal-title":"Integr. Zool."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Drummond, A.J., Ho, S.Y.W., Phillips, M.J., and Rambaut, A. (2006). Relaxed phylogenetics and dating with confidence. PLoS Biol., 4.","DOI":"10.1371\/journal.pbio.0040088"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1093\/sysbio\/syu089","article-title":"Calibrated birth\u2013death phylogenetic time-tree priors for bayesian inference","volume":"64","author":"Heled","year":"2015","journal-title":"Syst. Biol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior summarization in bayesian phylogenetics using Tracer 1.7","volume":"67","author":"Rambaut","year":"2018","journal-title":"Syst. Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1017\/S0016672300034455","article-title":"Effective population size\/adult population size ratios in wildlife: A review","volume":"66","author":"Frankham","year":"1995","journal-title":"Genet. Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1007\/s10329-022-00983-5","article-title":"Diverse grouping and mating strategies in the Critically Endangered Hainan gibbon (Nomascus hainanus)","volume":"63","author":"Li","year":"2022","journal-title":"Primates"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1093\/genetics\/141.1.413","article-title":"Properties of statistical tests of neutrality for DNA polymorphism data","volume":"141","author":"Simonsen","year":"1995","journal-title":"Genetics"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1046\/j.1365-294X.2003.02004.x","article-title":"Patterns of DNA sequence diversity and genetic structure after a range expansion: Lessons from the infinite-island model","volume":"13","author":"Excoffier","year":"2004","journal-title":"Mol. Ecol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"13390","DOI":"10.1073\/pnas.0701256104","article-title":"Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals","volume":"104","author":"Popadin","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"6551","DOI":"10.1038\/s41598-018-24497-7","article-title":"Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas","volume":"8","author":"Caillaud","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Dussex, N., von Seth, J., Robertson, B.C., and Dal\u00e9n, L. (2018). Full Mitogenomes in the Critically Endangered K\u0101k\u0101p\u014d Reveal Major Post-Glacial and Anthropogenic Effects on Neutral Genetic Diversity. Genes, 9.","DOI":"10.3390\/genes9040220"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Schenk, J.J. (2016). Consequences of Secondary Calibrations on Divergence Time Estimates. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0148228"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"lqaa089","DOI":"10.1093\/nargab\/lqaa089","article-title":"Characterization of nuclear mitochondrial insertions in the whole genomes of primates","volume":"2","author":"Dayama","year":"2020","journal-title":"NAR Genom. Bioinform."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1975","DOI":"10.1038\/s41598-018-20427-9","article-title":"Methylation-based enrichment facilitates low-cost, noninvasive genomic scale sequencing of populations from feces","volume":"8","author":"Chiou","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Wanner, N., Larsen, P.A., McLain, A., and Faulk, C. (2021). The mitochondrial genome and epigenome of the golden lion tamarin from fecal DNA using Nanopore adaptive sequencing. BMC Genom., 22.","DOI":"10.1186\/s12864-021-08046-7"}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/19\/3091\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T04:11:04Z","timestamp":1791605464000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/19\/3091"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,1]]},"references-count":43,"journal-issue":{"issue":"19","published-online":{"date-parts":[[2026,10]]}},"alternative-id":["ani16193091"],"URL":"https:\/\/doi.org\/10.3390\/ani16193091","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,1]]}}}