Vallender Eric J, Lahn Bruce T
Department of Human Genetics, Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637, USA.
Genomics. 2004 Oct;84(4):757-61. doi: 10.1016/j.ygeno.2004.07.005.
Many chromosomes are rearranged between humans and chimpanzees while others remain colinear. It was recently observed, based on over 100 genes, that the rates of protein evolution are substantially higher on rearranged than on colinear chromosomes during human-chimpanzee evolution. This finding led to the conclusion, since debated in the literature, that chromosomal rearrangements had played a key role in human-chimpanzee speciation. Here we re-examine this important conclusion by employing larger a data set (over 7000 genes), as well as alternative analyses. We show that the higher rates of protein evolution on rearranged chromosomes observed in the earlier study are not reproduced by our survey of the larger data set. We further show that the conclusion of the earlier study is likely confounded by two factors introduced by the relatively limited sample size: (1) nonuniform distribution of genes in the genome, and (2) stochastic noise in substitution rates inherent to short lineages such as the human-chimpanzee lineage. Our results offer a general cautionary note on the importance of controlling for hidden factors in studies involving bioinformatic surveys.
人类和黑猩猩之间的许多染色体发生了重排，而其他染色体则保持共线性。最近基于100多个基因观察到，在人类-黑猩猩进化过程中，重排染色体上的蛋白质进化速率显著高于共线性染色体上的。这一发现得出了一个结论，即染色体重排在人类-黑猩猩物种形成中起关键作用，该结论自提出以来一直在文献中受到争论。在这里，我们通过使用更大的数据集（超过7000个基因）以及其他分析方法，重新审视这一重要结论。我们表明，早期研究中观察到的重排染色体上较高的蛋白质进化速率，在我们对更大数据集的调查中并未重现。我们进一步表明，早期研究的结论可能受到样本量相对有限所引入的两个因素的混淆：（1）基因组中基因的不均匀分布，以及（2）人类-黑猩猩谱系等短线谱系中替代率固有的随机噪声。我们的结果对在涉及生物信息学调查的研究中控制隐藏因素的重要性提出了一般性的警示。
