Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species
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- 作者：Shengbin Li (1)
Bo Li (2)
Cheng Cheng (1) (2) (4)
Zijun Xiong (2)
Qingbo Liu (1)
Jianghua Lai (1)
Hannah V Carey (5)
Qiong Zhang (2) (6)
Haibo Zheng (1)
Shuguang Wei (1)
Hongbo Zhang (1)
Liao Chang (1) (2)
Shiping Liu (2)
Shanxin Zhang (1)
Bing Yu (1)
Xiaofan Zeng (2)
Yong Hou (2)
Wenhui Nie (7)
Youmin Guo (1)
Teng Chen (1)
Jiuqiang Han (1)
Jian Wang (2) (8)
Jun Wang (10) (2) (9)
Chen Chen (11)
Jiankang Liu (1) (4)
Peter J Stambrook (12)
Ming Xu (13)
Guojie Zhang (2) (9)
M Thomas P Gilbert (14) (15)
Huanming Yang (16) (2) (6) (8)
Erich D Jarvis (17)
Jun Yu (1) (3)
Jianqun Yan (1)
1. Xi鈥檃n Jiaotong University ; Xi鈥檃n ; 710049 ; P. R. China
2. BGI-Shenzhen ; Shenzhen ; 518083 ; P. R. China
4. Center for Mitochondrial Biology and Medicine ; The Key Laboratory of Biomedical Information Engineering of Ministry of Education ; School of Life Science and Technology and Frontier Institute of Science and Technology ; Xi鈥檃n Jiaotong University ; Xi鈥檃n ; 710049 ; China
5. University of Wisconsin School of Veterinary Medicine ; Madison ; Wisconsin ; USA
6. BGI-Northwest ; BGI-Shenzhen ; Xi鈥檃n ; 710000 ; P. R. China
7. Kunming Institute of Zoology ; Chinese Academy of Sciences ; Kunming ; Yunnan ; P. R. China
8. James D. Watson Institute of Genome Science ; Hangzhou ; China
10. King Abdulaziz University ; Jeddah ; Saudi Arabia
9. Department of Biology ; University of Copenhagen ; Copenhagen ; Denmark
11. School of Biomedical Sciences ; University of Queensland ; Queensland ; Australia
12. University of Cincinnati College of Medicine ; Cincinnati ; Ohio ; USA
13. College of medicine ; University of Chicago ; Chicago ; USA
14. Centre for GeoGenetics ; Natural History Museum of Denmark ; University of Copenhagen ; 脴sterVoldgade 5-7 ; 1350 ; Copenhagen ; Denmark
15. Department of Environment and Agriculture ; Trace and Environmental DNA Laboratory ; Curtin University ; Perth ; Western Australia ; 6845 ; Australia
16. Prince Aljawhra Center of Excellence in Research of Hereditary Disorders ; King Abdulaziz University ; Jeddah ; Saudi Arabia
17. Howard Hughes Medical Institute ; Duke University Medical Center ; Durham ; NC ; 27710 ; USA
3. CAS Key Laboratory of Genome Sciences and Information ; Beijing Institute of Genomics ; Chinese Academy of Sciences ; Beijing ; 100101 ; P.R. China - 刊名：Genome Biology
- 出版年：2014
- 出版时间：December 2014
- 年：2014
- 卷：15
- 期：12
- 全文大小：2,299 KB
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- 出版者：BioMed Central
- ISSN：1465-6906
文摘
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.