The Time Scale of Recombination Rate Evolution in Great Apes.
The Time Scale of Recombination Rate Evolution in Great Apes.
复制标题
类人猿重组率进化的时间尺度。
DOI：
10.1093/molbev/msv331
复制
发表时间：
2016
影响因子：
10.7
通讯作者：
Wall,JeffreyD
中科院分区：
文献类型：
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作者：
Stevison,LaurieS;Woerner,AugustE;Kidd,JeffreyM;Kelley,JoannaL;Veeramah,KrishnaR;McManus,KimberlyF;GreatApeGenomeProject;Bustamante,CarlosD;Hammer,MichaelF;Wall,JeffreyD
我们提出了三个基于连锁不平衡（LD）的重组图，这些重组图使用来自10只尼日利亚黑猩猩、13只倭黑猩猩和15只西部大猩猩的全基因组序列数据生成，这些数据是作为巨猿基因组计划的一部分收集的（Prado-Martinez J等人，2013年）。Great ape genetic diversity and population history. Nature499：471-475）.我们还确定了物种特异性重组热点，在每组使用修改的LDhot框架，这大大提高了统计能力，以检测热点在不同的强度。我们发现黑猩猩亚种之间共享的热点比人类种群内共享的热点少，进一步缩小了完整热点转换的时间尺度。此外，使用物种特异性PRDM 9序列来预测潜在的结合位点（PBS），我们显示出更高的预测PRDM 9结合在重组热点相比，匹配的冷点区域在多个类人猿物种，包括至少一个黑猩猩亚种。我们发现，大规模重组率之间的相关性下降得比物种之间的核苷酸分歧更快。我们还比较了物种间着丝粒和端粒重组率的偏斜，并显示了从染色体末端延伸至10-15 Mb的染色体平均值的偏斜。此外，我们研究了大猩猩易位附近的大规模重组率变化，发现与其他类人猿物种相比差异很小，这可能是因为相对于染色体末端的坐标不受影响。最后，在多元线性回归分析的基础上，我们发现，重组率的各种相关性持续存在于整个非洲类人猿，包括重复，多样性和分歧。我们的研究是第一个分析几个近亲的种内和种间全基因组重组率变异的研究。
We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history.Nature499:471–475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10–15 Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- and between-species genome-wide recombination rate variation in several close relatives.