Complete Mitogenomes of the Critically Endangered Hainan Gibbon (Nomascus hainanus) Reveal Very Low Mitochondrial Diversity and Two Major Maternal Clades.
4 affiliations
- 1Laboratory 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.
- 2Hainan International One Health Institute, Hainan University, Haikou 570228, China.
- 3Wuzhishan 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.
- 4Institute of Hainan National Park, Haikou 570100, China.
Abstract
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 (π = 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): 11.9-45.7 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.
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BibTeX
@article{yu2026complete,
title = {{Complete Mitogenomes of the Critically Endangered Hainan Gibbon (Nomascus hainanus) Reveal Very Low Mitochondrial Diversity and Two Major Maternal Clades.}},
author = {Zhonghao Yu and Ren Xiahou and Meng Nie and Xiaoyi Cai and Dingfeng Duan and Yanjiao Zhou and Yuan Chen and Wenxing Long and Chenghong Liao},
journal = {Animals : an open access journal from MDPI},
year = {2026},
month = oct,
doi = {10.3390/ani16193091},
url = {https://europepmc.org/article/MED/42883060},
note = {CC BY},
}
RIS
TY - JOUR
TI - Complete Mitogenomes of the Critically Endangered Hainan Gibbon (Nomascus hainanus) Reveal Very Low Mitochondrial Diversity and Two Major Maternal Clades.
AU - Zhonghao Yu
AU - Ren Xiahou
AU - Meng Nie
AU - Xiaoyi Cai
AU - Dingfeng Duan
AU - Yanjiao Zhou
AU - Yuan Chen
AU - Wenxing Long
AU - Chenghong Liao
PY - 2026
DA - 2026/10/01
JO - Animals : an open access journal from MDPI
DO - 10.3390/ani16193091
UR - https://europepmc.org/article/MED/42883060
AB - 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 (π = 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): 11.9-45.7 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.
SN - 2076-2615
ER -