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

Li, Shengbin, Li, Bo, Cheng, Cheng, Xiong, Zijun, Liu, Qingbo, Lai, Jianghua, Carey, Hannah V., Zhang, Qiong, Zheng, Haibo, Zheng, Haibo, Wei, Shuguang, Zhang, Hongbo, Chang, Liao, Liu, Shiping, Zhang, Shanxin, Yu, Bing, Zeng, Xiaofan, Huo, Yong, Nie, Wenhui, Guo, Youmin, Chen, Teng, Han, Jiuqiang, Wang, Jian, Wang, Jun, Chen, Chen, Liu, Jiankang, Stambrook, Peter J., Xu, Ming, Zhang, Guojie, Gilbert, Thomas P., Yang, Huanming, Jarvis, Erich D., Yu, Jun and Yan, Jianqun (2014) Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species. Genome Biology, 15 557: 1-16. doi:10.1186/s13059-014-0557-1

Author Li, Shengbin
Li, Bo
Cheng, Cheng
Xiong, Zijun
Liu, Qingbo
Lai, Jianghua
Carey, Hannah V.
Zhang, Qiong
Zheng, Haibo
Zheng, Haibo
Wei, Shuguang
Zhang, Hongbo
Chang, Liao
Liu, Shiping
Zhang, Shanxin
Yu, Bing
Zeng, Xiaofan
Huo, Yong
Nie, Wenhui
Guo, Youmin
Chen, Teng
Han, Jiuqiang
Wang, Jian
Wang, Jun
Chen, Chen
Liu, Jiankang
Stambrook, Peter J.
Xu, Ming
Zhang, Guojie
Gilbert, Thomas P.
Yang, Huanming
Jarvis, Erich D.
Yu, Jun
Yan, Jianqun
Title Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species
Journal name Genome Biology   Check publisher's open access policy
ISSN 1465-6906
Publication date 2014-01-01
Year available 2014
Sub-type Article (original research)
DOI 10.1186/s13059-014-0557-1
Open Access Status DOI
Volume 15
Issue 557
Start page 1
End page 16
Total pages 16
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Formatted abstract
Background: Nearly one-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.

Results: Using 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.

Conclusions: These 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.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2015 Collection
School of Biomedical Sciences Publications
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Citation counts: TR Web of Science Citation Count  Cited 17 times in Thomson Reuters Web of Science Article | Citations
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Created: Wed, 14 Jan 2015, 21:55:19 EST by Professor Chen Chen on behalf of School of Biomedical Sciences