TY - JOUR

T1 - Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species

AU - Li, Shengbin

AU - Li, Bo

AU - Cheng, Cheng

AU - Xiong, Zijun

AU - Liu, Qingbo

AU - Lai, Jianghua

AU - Carey, Hannah V.

AU - Zhang, Qiong

AU - Zheng, Haibo

AU - Wei, Shuguang

AU - Zhang, Hongbo

AU - Chang, Liao

AU - Liu, Shiping

AU - Zhang, Shanxin

AU - Yu, Bing

AU - Zeng, Xiaofan

AU - Hou, Yong

AU - Nie, Wenhui

AU - Guo, Youmin

AU - Chen, Teng

AU - Han, Jiuqiang

AU - Wang, Jian

AU - Wang, Jun

AU - Chen, Chen

AU - Liu, Jiankang

AU - Stambrook, Peter J

AU - Xu, Ming

AU - Zhang, Guojie

AU - Gilbert, M. Thomas P.

AU - Yang, Huanming

AU - Jarvis, Erich D

AU - Yu, Jun

AU - Yan, Jianqun

PY - 2014

Y1 - 2014

N2 - BackgroundNearly a quarter of all avian species is either threatened or nearly threatened. Of these, 73 species are currently being rescued from going extinct in wildlife sanctuaries. One of the previously most critically-endangered is the crested ibis, Nipponia nippon. Once widespread across North-East Asia, by 1981 only seven individuals from two breeding pairs remained in the wild. The recovering crested ibis populations thus provide an excellent example for conservation genomics since every individual bird has been recruited for genomic and demographic studies.ResultsUsing high-quality genome sequences of multiple crested ibis individuals, its thriving co-habitant, the little egret, Egretta garzetta, and the recently sequenced genomes of 41 other avian species that are under various degrees of survival threats, including the bald eagle, we carry out comparative analyses for genomic signatures of near extinction events in association with environmental and behavioral attributes of species. We confirm that both loss of genetic diversity and enrichment of deleterious mutations of protein-coding genes contribute to the major genetic defects of the endangered species. We further identify that genetic inbreeding and loss-of-function genes in the crested ibis may all constitute genetic susceptibility to other factors including long-term climate change, over-hunting, and agrochemical overuse. We also establish a genome-wide DNA identification platform for molecular breeding and conservation practices, to facilitate sustainable recovery of endangered species.ConclusionsThese findings demonstrate common genomic signatures of population decline across avian species and pave a way for further effort in saving endangered species and enhancing conservation genomic efforts.

AB - BackgroundNearly a quarter of all avian species is either threatened or nearly threatened. Of these, 73 species are currently being rescued from going extinct in wildlife sanctuaries. One of the previously most critically-endangered is the crested ibis, Nipponia nippon. Once widespread across North-East Asia, by 1981 only seven individuals from two breeding pairs remained in the wild. The recovering crested ibis populations thus provide an excellent example for conservation genomics since every individual bird has been recruited for genomic and demographic studies.ResultsUsing high-quality genome sequences of multiple crested ibis individuals, its thriving co-habitant, the little egret, Egretta garzetta, and the recently sequenced genomes of 41 other avian species that are under various degrees of survival threats, including the bald eagle, we carry out comparative analyses for genomic signatures of near extinction events in association with environmental and behavioral attributes of species. We confirm that both loss of genetic diversity and enrichment of deleterious mutations of protein-coding genes contribute to the major genetic defects of the endangered species. We further identify that genetic inbreeding and loss-of-function genes in the crested ibis may all constitute genetic susceptibility to other factors including long-term climate change, over-hunting, and agrochemical overuse. We also establish a genome-wide DNA identification platform for molecular breeding and conservation practices, to facilitate sustainable recovery of endangered species.ConclusionsThese findings demonstrate common genomic signatures of population decline across avian species and pave a way for further effort in saving endangered species and enhancing conservation genomic efforts.

U2 - 10.1186/s13059-014-0557-1

DO - 10.1186/s13059-014-0557-1

M3 - Journal article

C2 - 25496777

VL - 15

JO - Genome Biology (Online Edition)

JF - Genome Biology (Online Edition)

SN - 1474-7596

M1 - 557

ER -