Marques-Bonet Tomas, Kidd Jeffrey M, Ventura Mario, Graves Tina A, Cheng Ze, Hillier LaDeana W, Jiang Zhaoshi, Baker Carl, Malfavon-Borja Ray, Fulton Lucinda A, Alkan Can, Aksay Gozde, Girirajan Santhosh, Siswara Priscillia, Chen Lin, Cardone Maria Francesca, Navarro Arcadi, Mardis Elaine R, Wilson Richard K, Eichler Evan E
Department of Genome Sciences, University of Washington and the Howard Hughes Medical Institute, Seattle, Washington 98195, USA.
Nature. 2009 Feb 12;457(7231):877-81. doi: 10.1038/nature07744.
It is generally accepted that the extent of phenotypic change between human and great apes is dissonant with the rate of molecular change. Between these two groups, proteins are virtually identical, cytogenetically there are few rearrangements that distinguish ape-human chromosomes, and rates of single-base-pair change and retrotransposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. Studies of gene family evolution indicate that gene loss and gain are enriched within the primate lineage. Here, we perform a systematic analysis of duplication content of four primate genomes (macaque, orang-utan, chimpanzee and human) in an effort to understand the pattern and rates of genomic duplication during hominid evolution. We find that the ancestral branch leading to human and African great apes shows the most significant increase in duplication activity both in terms of base pairs and in terms of events. This duplication acceleration within the ancestral species is significant when compared to lineage-specific rate estimates even after accounting for copy-number polymorphism and homoplasy. We discover striking examples of recurrent and independent gene-containing duplications within the gorilla and chimpanzee that are absent in the human lineage. Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single-base-pair mutations, there has been a genomic burst of duplication activity at this period during human evolution.
人们普遍认为，人类与大猩猩之间的表型变化程度与分子变化速率不一致。在这两组之间，蛋白质实际上是相同的，从细胞遗传学角度来看，区分猿类和人类染色体的重排很少，而且与啮齿动物或猴子相比，单碱基对变化率和逆转座子活性在灵长类谱系中尤其减缓，特别是在人科谱系中。基因家族进化研究表明，基因的丢失和获得在灵长类谱系中更为丰富。在这里，我们对四个灵长类基因组（猕猴、猩猩、黑猩猩和人类）的重复内容进行了系统分析，以了解人科进化过程中基因组重复的模式和速率。我们发现，导致人类和非洲大猩猩的祖先分支在碱基对和事件方面的重复活性都有最显著的增加。即使在考虑了拷贝数多态性和同塑性之后，与谱系特异性速率估计相比，祖先物种内的这种重复加速也是显著的。我们在大猩猩和黑猩猩中发现了人类谱系中不存在的反复出现且独立的含基因重复的显著例子。我们的结果表明，拷贝数突变的进化特性与其他形式的基因突变有显著差异，并且与单碱基对突变在人科中的减缓相反，在人类进化的这一时期出现了基因组重复活性的爆发。
