The Hainan gibbon (Nomascus hainanus), one of the world's rarest primates, saw its population plummet starting in the 1950s, reaching a near-extinction point with only around 13 individuals remaining in the wild by 2003. Since then, the population has steadily recovered to around 42 individuals by 2024. While this rebound is often credited to conservation efforts, the role of genetic factors in the gibbon's recovery remains unknown. A major challenge is the difficulty in obtaining high-quality DNA samples without disturbing these elusive animals. Although fecal samples are one of the few noninvasive options, their use in genomic studies has been limited by concerns over low quantity and degraded host DNA.

A new study led by Prof. Xiangjiang Zhan at the Institute of Zoology, Chinese Academy of Sciences, solves this problem, demonstrates that fecal samples can provide reliable genomic data and uncover genetic mechanisms underlying the recovery of this critically endangered species. This study was published in Science Advances on February 11.

The study's key innovation is a rigorous workflow for fecal-based genomics that accurately quantifies errors in fecal genomic data and reveals, for the first time, a low error rate, ensuring reliable downstream genetic analyses.

By analyzing high-quality fecal genomic data from 18 gibbon individuals, approximately 40% of the entire Hainan gibbon population, the study reveals that the species' recovery is not solely attributed to recent conservation efforts, but is also owed to its evolutionary 'genetic legacy.' They find the species had undergone a population expansion over the past millennium, which helped mitigate genetic impacts of a prolonged bottleneck during the Last Glacial Maximum (LGM) and provided enough genetic variations to withstand the recent population decline in the end of 20 century. Furthermore, regions of high local recombination across the genome play a key role in buffering genetic load and preserving functional genetic variants critical for survival.

The study further reveals the surprising presence of two ancient genetic lineages within the extant Hainan gibbon population, with individuals from these lineages having already undergone natural crossbreeding. Modelling simulations indicate that such natural cross, if continue, will lead to a higher population growth potential and a lower extinction risk in the future.

The study highlights the power of integrating demographic history, genome architecture, and behavioral regulation in our understanding of the recovery of endangered species. The 'benchmark' workflow and low error rate of fecal genomics lay a foundation for broader and large-scale use of fecal samples in wildlife conservation.

This work was supported by the National Natural Science Foundation of China, the Hainan Tropical Rainforest Conservation Research Project, and the International Partnership Program of the Chinese Academy of Sciences.

https://www.science.org/doi/10.1126/sciadv.adw3298

Contact:

ZHAN Xiangjiang

Professor, Deputy Director

Institute of Zoology, Chinese Academy of Sciences

Tel: 8610-64807803

E-mail: zhanxj@ioz.ac.cn

Web: http://english.ioz.cas.cn

A male Hainan gibbon living in the rain forest (Image by Ping Li)