Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome.
Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome.
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DOI：
10.1371/journal.pcbi.0020038
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发表时间：
2006-04
影响因子：
4.3
通讯作者：
Dopazo H
中科院分区：
文献类型：
--
作者：
Arbiza L;Dopazo J;Dopazo H
多年来，进化生物学家一直对寻找人类特性的遗传基础感兴趣。近期已经在大规模或全基因组范围内努力寻找人类和黑猩猩中的正选择基因。然而，可以采用最近开发的能够以更灵敏且可控的方法检测正选择的方法。在此，我们利用13198个基因，推断出了自与鼠类分化以来，人类、黑猩猩及其祖先谱系中涉及速率加速、正选择和选择约束放松的基因集。在469个人类基因和651个黑猩猩基因中观察到与严格分子钟的显著偏离。更严格的分支位点正选择检验检测到108个人类正选择基因和577个黑猩猩正选择基因。很大一部分正选择基因没有显示出速率的显著加速，同样，许多加速基因也没有显示出正选择的显著信号。除了与G蛋白偶联受体和感觉感知相关的术语外，人类和黑猩猩之间在速率加速、正选择和放松情况下的基因功能分化在统计学上并不显著。在人类相对于黑猩猩的放松情况下，这两者都表现过度。比较衍生谱系和祖先谱系之间的差异，一种更明显的趋势变化似乎有利于人类谱系中的正选择。由于在这些物种之间相同功能类别下大多数正选择基因是不同的，我们认为不同的正选择基因的个体作用可能是这些物种之间生物学差异的一个重要因素。
自人类和黑猩猩基因组公布以来，进化生物学中的一个主要挑战已经开始被解读：即寻找塑造人类特性的正选择基因。阿尔比扎及其同事在基因组规模上寻找在人类、黑猩猩及其共同祖先谱系中被正选择的基因。他们得出结论，黑猩猩中正选择事件的频率是人类的六倍，尽管它们没有归入在任一物种中被优先选择的特定功能类别。然而，在比较祖先谱系和后代谱系之间的进化趋势时，他们发现共同类别中的大多数相对差异显示人类分支上正选择丰富。通过区分正选择和选择约束的放松（这两者在基因组中产生相似的痕迹），他们证明许多先前被认为是正选择的基因可能是放松的情况。最后，他们量化了使用基于平均速率的方法在这些物种中集中适应性进化案例所产生的偏差。
For years evolutionary biologists have been interested in searching for the genetic bases underlying humanness. Recent efforts at a large or a complete genomic scale have been conducted to search for positively selected genes in human and in chimp. However, recently developed methods allowing for a more sensitive and controlled approach in the detection of positive selection can be employed. Here, using 13,198 genes, we have deduced the sets of genes involved in rate acceleration, positive selection, and relaxation of selective constraints in human, in chimp, and in their ancestral lineage since the divergence from murids. Significant deviations from the strict molecular clock were observed in 469 human and in 651 chimp genes. The more stringent branch-site test of positive selection detected 108 human and 577 chimp positively selected genes. An important proportion of the positively selected genes did not show a significant acceleration in rates, and similarly, many of the accelerated genes did not show significant signals of positive selection. Functional differentiation of genes under rate acceleration, positive selection, and relaxation was not statistically significant between human and chimp with the exception of terms related to G-protein coupled receptors and sensory perception. Both of these were over-represented under relaxation in human in relation to chimp. Comparing differences between derived and ancestral lineages, a more conspicuous change in trends seems to have favored positive selection in the human lineage. Since most of the positively selected genes are different under the same functional categories between these species, we suggest that the individual roles of the alternative positively selected genes may be an important factor underlying biological differences between these species. Since the publication of the human and the chimp genomes, one of the major challenges in evolutionary biology has begun to be deciphered: namely, the search for positively selected genes that have shaped humanness. Arbiza and colleagues undertake a genomic-scale search for the genes that have been positively selected in human, in chimp, and in their common ancestral lineage. They conclude that events of positive selection were six times more frequent in chimp than in human, although they do not group under specific functional classes that have been preferentially selected in either species. However, in the comparisons of the evolutionary trends between the ancestral and the descendant lineages, they found that most of the relative differences in common classes show an abundance of positive selection on the human branch. By differentiating positive selection from a relaxation of selective constraints, both producing analogous footprints in the genome, they demonstrate that many of the genes previously thought to have been positively selected correspond to likely cases of relaxation. Finally, they quantify the bias produced by the use of average rate–based approaches to concentrate cases of adaptive evolution in these species.
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影响因子：
10.7
作者：
Ding, KY;Zhou, K;Shen, Y
通讯作者：
Shen, Y
影响因子：
11
作者：
Adams, J;Crosbie, J;Barr, CL
通讯作者：
Barr, CL
影响因子：
5.8
作者：
Al-Shahrour, F;Díaz-Uriarte, R;Dopazo, J
通讯作者：
Dopazo, J
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
5.8
作者：
Amato, F;Warnes, GM;Norman, RJ
通讯作者：
Norman, RJ