鸟类基因组及演化生物学研究

濒危鸟类研究

文章引用

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).

英文摘要

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.

文章解读

重新闪耀的“东方宝石”
——濒危朱鹮的基因组解读与保护

文/成诚

朱鹮,古称朱鹭、红朱鹭,唐代诗人张籍曾作一首《朱鹭诗》:翩翩起舞兮朱鹭,来泠春塘栖绿树,羽毛如剪色如染,远飞欲下双翅敛。这是诗人在游历秦岭时所作,朱鹮的摇曳身姿和华美羽翼可见一斑。朱鹮也因它的美貌也被人们誉为“东方宝石”,是中国的四大国宝(大熊猫、朱鹮、金丝猴、羚牛)之一。

自二十世纪以来,人类活动对大自然的干预越来越多,物种的灭绝成为了全球性问题。鸟类作为生态平衡中的重要角色,很多物种都面临濒危或灭绝,其中朱鹮就是濒危鸟类的一个典型例子。1960年,第十二届世界鸟类学会议将其列为“国际重点保护鸟”,中国也把朱鹮列为国家一类保护动物。最近,西安交通大学与华大基因联合主导的一个研究团队,完成了对濒危鸟类朱鹮的全基因组测序和解读,相关研究成果发表在Genome Biology上。

朱鹮群体经历了严重的瓶颈效应 朱鹮历史上广泛分布在东亚,二十世纪初,由于工业、战争、狩猎等因素,朱鹮数目迅速减少,濒于灭绝。1981年,科学家们在秦岭深处发现了仅存的7只朱鹮,从此开始了人工保护,至今增加到2000多只。朱鹮是一个罕见的”起死回生”的案例,是一个很有价值的研究模型。

基因组杂合度低是濒危的特点 朱鹮的基因组杂合度,尤其是免疫相关的MHC基因的杂合度,远低于与它近亲但并不濒危的白鹭。其它濒危鸟类,比如白头海雕、啄羊鹦鹉等,也都呈现出基因组杂合度低的特点。这意味着它们对复杂环境的适应能力降低。

濒危鸟类有更多的有害突变,影响大脑、代谢、解毒功能 二十世纪中期是DDT等农药和化肥使用的高峰期,也正是这些濒危鸟类数量骤减的时期。研究发现,因为朱鹮种群数目减少,遗传漂变的作用使得基因组上与神经系统、解毒相关基因的区域积累了大量有害突变,因此影响其正常功能。与此类似,在其它几个濒危鸟类基因组中,一些参与代谢、解毒过程中的重要基因成为假基因的频率也更大。

现在的朱鹮种群是否健康 通过对比洋县、宁陕、楼观台、华阳四个种群的样本发现,虽然它们的遗传距离异常偏大,而杂合度仍然是逐渐降低的。换句话说,虽然朱鹮数目上升了,但从遗传学角度讲,朱鹮仍然是不健康的,如果保护措施不当,仍然有灭绝的危险。

基于基因组的保护策略 研究者利用朱鹮基因组的信息为朱鹮设计了基于DNA分子标记的个体识别系统,这就好像给每只朱鹮都做了个“基因身份证”。通过这个“基因身份证”,在以后的育种中饲养员可以更科学的帮助朱鹮配对繁殖,从而得到更好的保护。

如今越来越多的物种被测序和解读,研究者希望在以后的濒危动物评定中,应该把全基因组的遗传信息作为考量因素之一,而不是仅仅评估其现存数目。同时这项研究中基于全基因组信息保护朱鹮的策略,可以应用到更多的濒危动物保护中,从而提高濒危动物保护的成功率。

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