Genomic signatures and evolutionary history of the endangered blue-crowned laughingthrush and other Garrulax species

The blue-crowned laughingthrush (Garrulax courtoisi) is a critically endangered songbird endemic to Wuyuan, China, with population of ~323 individuals. It has attracted widespread attention, but the lack of a published genome has limited research and species protection.

This study supplies the missing reference genome of laughingthrush, provides insight into the genetic variability, evolutionary potential, and molecular ecology of laughingthrush and provides a genomic resource for future research and conservation.

We report two laughingthrush genome assemblies and reveal the taxonomic status of laughingthrush species among 25 common avian species according to the comparative genomic analysis. The blue-crowned laughingthrush, black-throated laughingthrush, masked laughingthrush, white-browed laughingthrush, and rusty laughingthrush showed a close genetic relationship, and they diverged from a common ancestor between ~2.81 and 12.31 million years ago estimated by the population structure and divergence analysis using 66 whole-genome sequencing birds from eight laughingthrush species and one out group (Cyanopica cyanus). Population inference revealed that the laughingthrush species experienced a rapid population decline during the last ice age and a serious bottleneck caused by a cold wave during the Chinese Song Dynasty (960-1279 AD). The blue-crowned laughingthrush is still in a bottleneck, which may be the result of a cold wave together with human exploitation. Interestingly, the existing blue-crowned laughingthrush exhibits extremely rich genetic diversity compared to other laughingthrushes. These genetic characteristics and demographic inference patterns suggest a genetic heritage of population abundance in the blue-crowned laughingthrush. The results also suggest that fewer deleterious mutations in the blue-crowned laughingthrush genomes have allowed them to thrive even with a small population size. We believe that cooperative breeding behavior and a long reproduction period may enable the blue-crowned laughingthrush to maintain genetic diversity and avoid inbreeding depression. We identified 43 short tandem repeats that can be used as markers to identify the sex of the blue-crowned laughingthrush and aid in its genetic conservation. Conclusions: This study supplies the missing reference genome of laughingthrush, provides insight into the genetic variability, evolutionary potential, and molecular ecology of laughingthrush and provides a genomic resource for future research and conservation.