Genomes of endangered birds


Shengbin Li, Bo Li, Cheng Cheng, Zijun Xiong, Qingbo Liu, Jianghua Lai, Hannah V. Carey, Qiong Zhang, Haibo Zheng, Shuguang Wei, Hongbo Zhang, Liao Chang, Shiping Liu, Shanxin Zhang, Bing Yu, Xiaofan Zeng, Yong Hou, Wenhui Nie, Youmin Guo, Teng Chen, Jiuqiang Han, Jian Wang, Jun Wang, Chen Chen, Jiankang Liu, Peter J. Stambrook, Ming Xu, Guojie Zhang, M. Thomas P. Gilbert, Huanming Yang, Erich D. Jarvis, Jun Yu, and Jianqun Yan, 'Genomic Signatures of near-Extinction and Rebirth of the Crested Ibis and Other Endangered Bird Species', Genome Biology (2014).


Background: Nearly one quarter (2,300) of all avian species is either threatened or nearly-threatened, and 73 of them are currently being rescued from going extinct in wildlife sanctuaries. One of the most previous critically endangered is the crested ibis (Nipponia nippon). Once widespread across North-East Asia, by 1981, only seven individuals from 2 breeding pairs remained in the wild, and they have now been successfully rescued both in the wild and in captivity. The crested ibis and its recovering populations thus provide an excellent example for conservation genomics since every individual of the populations has been tagged and recruited for biological 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 in association with environmental and behavioral attributes of species’ near extinction events in birds. We confirm that both loss of genetic diversity and enrichment of deleterious mutations of protein-coding genes are responsible for the major genetic defects of the endangered species. Selective sweeps or allelic drift, and loss-of-function genes reveal reasons and major events leading to the severe population reduction, which include population segregation, long-term climate change and periodic temperature drops, over-hunting, and agrochemical overuse. We also establish a genome-wide DNA identification platform for molecular breeding and conservation practices, to ensure sustainable recovery of endangered species.
Conclusion: These findings demonstrate that large-scale genomic signatures provide molecular clues for population decline, paving a way for further effort in saving endangered species and enhancing conservation genomics.

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