Prevalence of multinucleotide replacements in evolution of primates and Drosophila.
Prevalence of multinucleotide replacements in evolution of primates and Drosophila.
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DOI：
10.1093/molbev/mst036
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发表时间：
2013-06
影响因子：
10.7
通讯作者：
Seplyarskiy VB
中科院分区：
文献类型：
--
作者：
Terekhanova NV;Bazykin GA;Neverov A;Kondrashov AS;Seplyarskiy VB
序列的进化大多涉及不同位点的独立变化。然而，邻近位点的替换可能以多核苷酸替换事件(MNRs)的形式共同发生。在这里，我们比较了几种灵长类动物和三种果蝇的非编码序列，对发生在附近核苷酸位点的物种之间的替换进行了系统发育分析。在灵长类动物和果蝇中，单核苷酸替换的频率在同一谱系上发生的其他替换的10个核苷酸内显著增加，但在另一个谱系上没有。这些数据表明，灵长类基因组中2.3%的单核苷酸替换和果蝇基因组中5.6%的单核苷酸替换是由影响彼此之间长达10个核苷酸的位置的二核苷酸替换(DNRs)引起的。在这些DNRs中，分别有26%和69%实际上是三个或三个以上三核苷酸替换(TNR)的一部分。多个MNRs影响附近的核苷酸，因此影响两个相邻核苷酸位点的DNRs至少是相隔10个核苷酸的位点的六倍。尽管如此，大约60%的DNR和大约90%的TNR跨越两个(或三个)以上的核苷酸。MNRs对观察到的替换集群做出了重大贡献：在人与黑猩猩的比较中，当观察到人类谱系上的两个邻近替换时，DNRs解释了50%的病例，而当观察到人类谱系上三个紧邻位置的三个替换时，TnRs解释了83%的病例。MNRs的流行与从头突变数据中观察到的一致，也在序列保守性最低的区域观察到，这表明MNRs主要有突变起源；然而，上位性选择和/或基因转换也可能起作用。
Evolution of sequences mostly involves independent changes at different sites. However, substitutions at neighboring sites may co-occur as multinucleotide replacement events (MNRs). Here, we compare noncoding sequences of several species of primates, and of three species of Drosophila fruit flies, in a phylogenetic analysis of the replacements that occurred between species at nearby nucleotide sites. Both in primates and in Drosophila, the frequency of single-nucleotide replacements is substantially elevated within 10 nucleotides from other replacements that occurred on the same lineage but not on another lineage. The data imply that dinucleotide replacements (DNRs) affecting sites at distances of up to 10 nucleotides from each other are responsible for 2.3% of single-nucleotide replacements in primate genomes and for 5.6% in Drosophila genomes. Among these DNRs, 26% and 69%, respectively, are in fact parts of replacements of three or more trinucleotide replacements (TNRs). The plurality of MNRs affect nearby nucleotides, so that at least six times as many DNRs affect two adjacent nucleotide sites than sites 10 nucleotides apart. Still, approximately 60% of DNRs, and approximately 90% of TNRs, span distances more than two (or three) nucleotides. MNRs make a major contribution to the observed clustering of substitutions: In the human–chimpanzee comparison, DNRs are responsible for 50% of cases when two nearby replacements are observed on the human lineage, and TNRs are responsible for 83% of cases when three replacements at three immediately adjacent sites are observed on the human lineage. The prevalence of MNRs matches that is observed in data on de novo mutations and is also observed in the regions with the lowest sequence conservation, suggesting that MNRs mainly have mutational origin; however, epistatic selection and/or gene conversion may also play a role.
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影响因子：
9.8
作者：
Hodgkinson A;Ladoukakis E;Eyre-Walker A
通讯作者：
Eyre-Walker A
种群基因组学：果蝇果蝇中多态性和差异的全基因组分析。
影响因子：
9.8
作者：
Begun, David J.;Holloway, Alisha K.;Stevens, Kristian;Hillier, LaDeana W.;Poh, Yu-Ping;Hahn, Matthew W.;Nista, Phillip M.;Jones, Corbin D.;Kern, Andrew D.;Dewey, Colin N.;Pachter, Lior;Myers, Eugene;Langley, Charles H.
通讯作者：
Langley, Charles H.
影响因子：
3.9
作者：
Keightley, Peter D.;Eyre-Walker, Adam
通讯作者：
Eyre-Walker, Adam
影响因子：
30.8
作者：
Jeffreys, AJ;May, CA
通讯作者：
May, CA
影响因子：
14.9
作者：
BIRD, AP
通讯作者：
BIRD, AP