Mol Biol Evol:中科院动物所张健旭研究组等利用全基因组比较揭示
2017年5月8日，国际分子生物学和进化领域的权威期刊《molecular Biology and Evolution》杂志在线发表了中国科学院动物所张健旭研究组与北京生科院孙中生，赵方庆两个研究组合作的一篇研究论文，论文题为Population genomics reveals speciation and introgression between Brown Norway rats and their sibling species。研究报道了我国褐家鼠及姊妹种—大足鼠的基因组比较研究的成果。研究组滕花景、张瑶华和石承民为论文共同第一作者、张健旭研究员、孙中生研究员和赵方庆研究员为论文通讯作者。
褐家鼠属于家栖性鼠类，生态适应性极强，分布几乎遍布全球，是地球上最为成功的入侵哺乳动物。由其驯化而来的实验室大鼠成为最早的实验动物，已被广泛地应用于生命科学研究，它也是全球危害最为普遍的鼠。我国东北地区和蒙古被认为是褐家鼠的重要起源地。 张健旭/张瑶华前期与英国科学家Peter Keightley合 作，发现我国东北地区的褐家鼠种群遗传多样性很低，仅仅是小家鼠的五分之一，大约在2万年前出现过一个种群瓶颈 (2012 G3. 2:1661-1664;2015 Mol. Biol. evol. 32,2547-2558 )。与小家鼠相比较，褐家鼠的野外生物学研究要少得多，它作为独立物种出现的时间以及能迅速适应环境的基因组特点更是知之甚少。
针对我国遗传多样性丰富的褐家鼠资源，研究人员进一步利用比较基因组学，对我国多个褐家鼠种群及其姊妹种大足鼠的群体进行了全基因组测序和比较，发现广布性褐家鼠的核苷酸多样性反而比狭布性大足鼠的低，褐家鼠的有效种群大小随历史波动比较大，在末次冰期存在一个遗传瓶颈，两个姊妹种的分化时间与东亚发生的最大一次冰川的时间是吻合的，据此推断剧烈的气候变化影响了褐家鼠的物种形成。
他们还发现分化后的两个姊妹种仍然发生过种间的杂交，通过种间交流保留下来的与化学通讯相关的一些基因组区间以及褐家鼠基因组上受到选择性清除的与食物代谢、免疫反应、警觉和焦虑相关的区间在褐家鼠生态适应中可能发挥了重要作用。
这项研究阐明了褐家鼠物种的成种时间，揭示了分化后的褐家鼠与其姊妹种的种群历史变化及种间杂交，为阐明物种适应性分化提供了重要例证，为揭示褐家鼠这一广布种生态适应的分子基础提供了重要证据。
原文链接：
Population genomics reveals speciation and introgression between Brown Norway rats and their sibling species
原文摘要：
Murine rodents are excellent models for study of adaptive radiations and speciation. Brown Norway rats (Rattus norvegicus) are successful global colonizers and the contributions of their domesticated laboratory strains to biomedical research are well established. To identify nucleotide-based speciation timing of the rat and genomic information contributing to its colonization capabilities, we analyzed 51 whole-genome sequences of wild-derived Brown Norway rats and their sibling species, R. nitidus, and identified over 20 million genetic variants in the wild Brown Norway rats that were absent in the laboratory strains, which substantially expand the reservoir of rat genetic diversity. We showed that divergence of the rat and its siblings coincided with drastic climatic changes that occurred during the Middle Pleistocene. Further, we revealed that there was a geographically-widespread influx of genes between Brown Norway rats and the sibling species following the divergence, resulting in numerous introgressed regions in the genomes of admixed Brown Norway rats. Intriguing, genes related to chemical communications among these introgressed regions appeared to contribute to the population-specific adaptations of the admixed Brown Norway rats. Our data reveals evolutionary history of the Brown Norway rat, and offers new insights into the role of climatic changes in speciation of animals and the effect of interspecies introgression on animal adaptation.
作者：张健旭
