title: Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species.
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.
authors.forename: Shengbin
authors.initials: S
authors.lastname: Li
authors.forename: Bo
authors.initials: B
authors.lastname: Li
authors.forename: Cheng
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authors.lastname: Cheng
authors.forename: Zijun
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authors.lastname: Xiong
authors.forename: Qingbo
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authors.lastname: Liu
authors.forename: Jianghua
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authors.lastname: Lai
authors.forename: Hannah V
authors.initials: HV
authors.lastname: Carey
authors.forename: Qiong
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authors.lastname: Zhang
authors.forename: Haibo
authors.initials: H
authors.lastname: Zheng
authors.forename: Shuguang
authors.initials: S
authors.lastname: Wei
authors.forename: Hongbo
authors.initials: H
authors.lastname: Zhang
authors.forename: Liao
authors.initials: L
authors.lastname: Chang
authors.forename: Shiping
authors.initials: S
authors.lastname: Liu
authors.forename: Shanxin
authors.initials: S
authors.lastname: Zhang
authors.forename: Bing
authors.initials: B
authors.lastname: Yu
authors.forename: Xiaofan
authors.initials: X
authors.lastname: Zeng
authors.forename: Yong
authors.initials: Y
authors.lastname: Hou
authors.forename: Wenhui
authors.initials: W
authors.lastname: Nie
authors.forename: Youmin
authors.initials: Y
authors.lastname: Guo
authors.forename: Teng
authors.initials: T
authors.lastname: Chen
authors.forename: Jiuqiang
authors.initials: J
authors.lastname: Han
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Chen
authors.initials: C
authors.lastname: Chen
authors.forename: Jiankang
authors.initials: J
authors.lastname: Liu
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Stambrook
authors.forename: Ming
authors.initials: M
authors.lastname: Xu
authors.forename: Guojie
authors.initials: G
authors.lastname: Zhang
authors.forename: M Thomas P
authors.initials: MT
authors.lastname: Gilbert
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.forename: Erich D
authors.initials: ED
authors.lastname: Jarvis
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.forename: Jianqun
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authors.lastname: Yan
mesh_terms: D000818:Animals; D030161:Avian Proteins / Q000235:genetics*; D001717:Birds / Q000145:classification* / Q000235:genetics*; D001947:Breeding; D057231:Climate Change; D056727:Endangered Species; D019143:Evolution, Molecular; D053476:Extinction, Biological; D017353:Gene Deletion; D014644:Genetic Variation; D016678:Genome; D011156:Population Density; D017422:Sequence Analysis, DNA
chemical_list: D030161:Avian Proteins