# Genetic legacy and recent cross of two ancient lineages underlie the rebound of the world’s rarest primate

## TL;DR

This study explores how Hainan gibbons rebounded from near extinction using genomic data from fecal samples and museum specimens.

## Contribution

The study reveals cryptic lineages and genetic mechanisms that enabled recovery despite low genetic diversity.

## Key findings

- Hainan gibbons have low inbreeding and genetic load despite small population size.
- Millennial expansion and high recombination helped mitigate genetic bottlenecks.
- Recent crosses between cryptic lineages increased heterozygosity in new family groups.

## Abstract

Despite a recent mass extinction, a few species have bounced back from the brink, but little is known about their intrinsic mechanisms. Hainan gibbons (Nomascus hainanus) feature a mysterious rebound, from ~13 individuals in 2003 to 42 currently. Using reliable genomic data from the fecal samples of 18 gibbons, generated through a systematically established pipeline, and from four museum specimens, our analyses reveal that Hainan gibbons have the smallest effective population size and low genetic diversity but, unexpectedly, low inbreeding and genetic load among threatened primates assessed thus far. This results from a millennial expansion mitigating bottleneck effects and a high local recombination maintaining selection efficiency. Notably, we uncover two cryptic lineages, whose recent crosses led to new family groups with increased heterozygosity. Our study reveals the importance of demographic history, genome architecture, and behavioral regulation in the recovery of endangered species and highlights the great potential of fecal genomic research in conservation biology.

Fecal genomic analysis of Hainan gibbon reveals roles of demography, recombination, and behavioral regulation during its recovery.