Population genomics reveals deep diversification in Malayan pangolins
Archipelagos and oceanic islands have remarkably high levels of endemism, which is associated with rapid speciation. The Malayan pangolin (Manis javanica), one of critically endangered Asia pangolin species, occurs in southern Yunnan, China, and on oceanic islands via the Malay peninsula. The question of whether the distribution of Malayan pangolins between the mainland and nearby marine islands has led to deep population differentiation is not well addressed. In-depth investigation of population structure and genetic consequences is of vital importance for protection and conservation of Malayan pangolins. Here we carried out a large-scale population genomic analysis for Malayan pangolins, which revealed three highly distinct genetic populations. The largest population was found to be distributed over a wide area extending from mainland China to almost the whole of South East Asia. The other two smaller populations reported in this study were inferred from Borneo. In addition, based on multiple lines of genomic and skull morphological evidences, we confirmed the existence of a fifth Asian pangolin species (M. mysteria). Genetic diversity and genome-wide inbreeding were at moderate levels, indicating that anthropogenic factors did not significantly weaken the basis of genetic sustainability for Malayan pangolins. However, Malayan pangolins from northeastern Borneo exhibited low genetic diversity, high levels of inbreeding and mutational load, thereby necessitating attention to their protection.
Authors
- Yiyi Wang (ORCID: https://orcid.org/0000-0001-6896-6432)
- Shangchen Yang
- Yinping Tian (ORCID: https://orcid.org/0000-0002-6998-0612)
- Suying Bai (ORCID: https://orcid.org/0000-0001-9686-3342)
- Hua Yan (ORCID: https://orcid.org/0000-0002-9992-2026)
- Jiayi Wang
- Huixin Li (ORCID: https://orcid.org/0000-0002-2634-6486)
- Boyang Liu (ORCID: https://orcid.org/0000-0001-7378-3454)
- Hyeon Jeong Kim (ORCID: https://orcid.org/0009-0006-9941-5688)
- Jinyao Lu
- Lei Han
- Huabing Guo
- Hui Xie (ORCID: https://orcid.org/0000-0002-5293-4118)
- Kristen N. Finch (ORCID: https://orcid.org/0000-0003-2098-7546)
- Yuan Fu (ORCID: https://orcid.org/0000-0001-8082-4090)
- Xilong Zhao (ORCID: https://orcid.org/0009-0000-6444-8777)
- Jiahao Li (ORCID: https://orcid.org/0000-0001-7006-4470)
- Shasha Liu (ORCID: https://orcid.org/0000-0002-7727-2296)
- Yu Lin (ORCID: https://orcid.org/0000-0001-5650-8899)
- Dahui Li (ORCID: https://orcid.org/0000-0003-2050-6618)
- Chen Jin (ORCID: https://orcid.org/0009-0005-2453-6912)
- Yuze Jiang
- Hou YinMeng
- Qiye Li
- Bo Li
- Yanchun Xu
- Liangyu Cui
- ShiQing Wang
- Tianming Lan
- Minhui Shi
- Kai Wang
- Haorong Lu
- Li Yu
- Wei Zhang
- Zhangwen Deng
- Chuan Jiang
- Yan Yao
- Qing Wang
- Zhaowen Qiu
- Chen Wang
- Jun Li
- Li Li
- Jiale Fan
- Haimeng Li
- Samuel K Wasser
- Ce Guo
- Yue Ma
- Jingyang Hu
Institutions
- South China Agricultural University (CN)
- Nanjing University of Chinese Medicine (CN)
- Central South University (CN)
- Yunnan University (CN)
- Chinese Academy of Sciences (CN)
- University of Washington (US)
- Huazhong Agricultural University (CN)
- Institute for Biodiversity (DE)
- Guangxi Zhuang Autonomous Region Health and Family Planning (CN)
- Botswana Geoscience Institute (BW)
- Chinese Academy of Forestry (CN)
- Research Institute of Forestry Policy and Information (CN)
- Guangdong Academy of Forestry (CN)
- Central Botanical Garden (BY)
- Jiangxi Province Forestry Survey Planning Institute (CN)
- Xiangya Hospital Central South University (CN)
- Northeast Forestry University (CN)
- Henan Normal University (CN)
- Zhejiang University (CN)
Publication Details
- Journal
- Molecular Biology and Evolution
- Published
- 2026-01-14
- DOI
- https://doi.org/10.1093/molbev/msag016
- Citations
- 1
- Primary Topic
- Genetic diversity and population structure
- Type
- article
- Field-Weighted Citation Impact
- 30.93