Genetics：基因代谢速度决定哺乳动物进化
通常认为人类和黑猩猩之间仅有1%～2%的基因差异，但事实上，区分人类和黑猩猩的基因比科学家预料的要多。一项新的研究表明，把人类和近亲——黑猩猩区分开的是人类获得新基因、抛弃旧基因的速率。
人类和黑猩猩这两个物种500万年以前还是一家，通常认为现在只有1%～2%的基因差异。但是这个百分比指的是基因中核糖的不同。然而，进化不仅仅能够修补基因序列，即使基因本身不变，不同物种基因副本的数量也是可变的。基因有时增加，有时丢失。然而，定量计算这种得失很难，要求知道许多物种完整的基因组序列。
A leg up.
The human species is turning over genes much faster than chimps and other mammals.
Credit: Michael K. Nichols/NGS/Getty Images
现在，由于一些哺乳动物的基因组测序已经完成，并有了一套新的统计方法，美国印第安那大学的Matthew Hahn和同事进行了基因代谢（gene turnover）计算的研究。他们测量了6种哺乳动物基因组中基因复制和丢失的速度。在观察了1万个基因家族中的大约12万个基因后，研究人员发现哺乳动物的基因代谢比犬类和啮齿动物快。而人类基因代谢的速率更快，是猴子的1.6倍，非哺乳动物的2.8倍。由于这么快速的淘汰更新，人类22000余个基因中，有6.4%没有在黑猩猩中表达出来，这导致两者表现出来的差别更加大了。
“你可以把基因组想象成旋转门——基因通过它进进出出。”Hahn的这一成果10月18号在线发表在《基因》上。他表示，基因代谢为自然选择提供了“燃料”，迅速扩张的基因家族显示出DNA的适应性变化。其中一支异军突起的基因家族是一组脑基因，它们在人类中扩大了一倍多。
美国科罗拉多大学的基因组生物学家James Sikela表示，该研究强调了“基因代谢在哺乳动物进化过程中的重要作用”。但是他警告说，研究人员使用的最近“完成”的基因组序列可能会存在所谓的装配误差（assembly errors），并且很难证明一个基因完全缺失，另外，基因多余的副本可能被忽视。这些因素都会导致速率估计不准确。不过Hahn表示，他们测试了误差的影响，在考虑误差的情况下，所得数据还是可以解释人类快速的基因代谢率对进化的影响。
原始出处:
Genetics. Published Articles Ahead of Print: October 18, 2007, Copyright © 2007
doi:10.1534/genetics.107.080077
Accelerated rate of gene gain and loss in primates
Matthew W. Hahn 1*, Jeffery P. Demuth 1 and Sang-Gook Han 1
1 Indiana University
* To whom correspondence should be addressed. E-mail: mwh@indiana.edu
.
Submitted on August 6, 2007
Revised on September 4, 2007
Accepted on 4 September 2007
The molecular changes responsible for the evolution of modern humans have primarily been discussed in terms of individual nucleotide substitutions in regulatory or protein coding sequences. However, rates of nucleotide substitution are slowed in primates, and thus humans and chimpanzees are highly similar at the nucleotide level. We find that a third source of molecular evolution, gene gain and loss, is accelerated in primates relative to other mammals. Using a novel method that allows estimation of rate heterogeneity among lineages, we find that the rate of gene turnover in humans is more than 2.5X faster than in other mammals and may be due to both mutational and selective forces. By reconciling the gene trees for all of the gene families included in the analysis, we are able to independently verify the numbers of inferred duplications. We also use two methods based on the genome assembly of rhesus macaque to further verify our results. Our analyses identify several gene families that have expanded or contracted more rapidly than is expected even after accounting for an overall rate acceleration in primates, including brain-related families that have more than doubled in size in humans. Many of the families showing large expansions also show evidence for positive selection on their nucleotide sequences, suggesting that selection has been important in shaping copy-number differences among mammals. These findings may help explain why humans and chimpanzees show high similarity between orthologous nucleotides yet great morphological and behavioral differences.
Key Words: comparative genomics, duplication, gene family, positive selection, segmental duplication
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