分析承载59732个候选人类特异性调控序列的基因组位点的进化起源，识别大猿进化期间的遗传分化模式
Analysis of evolutionary origins of genomic loci harboring 59,732 candidate human-specific regulatory sequences identifies genetic divergence patterns during evolution of Great Apes
AI总结：
研究分析了承载59732个候选人类特异性调控序列的基因组位点的进化起源，发现人类通过继承和新创造调控序列实现了物种分化。
摘要：
近年来，我们对承载各种类型候选人类特异性调控序列（HSRS）的基因组区域的视界有了显著扩展。为了推断承载HSRS的位点的进化起源，对现代人类、黑猩猩、倭黑猩猩、大猩猩、orangutan、云豹和恒河猴基因组中59732个位点的保守模式进行了分析。已识别出两种主要的进化路径，包含成千上万个序列，这些序列要么继承自已灭绝的共同祖先（ECAs），要么在人类与黑猩猩分裂后在人类中新创造。成千上万个HSRS似乎继承自ECAs，但跳过了我们最近的进化近亲的基因组，可能是由于不完全的谱系排序和/或物种特异性丢失或调控DNA。跳过模式在与人类大脑发育和功能相关的HSRS上尤为突出。在大猿进化过程中可能促成物种分化的共同基因组位点包括248个非洲大猿特异性逆转录病毒PtERV1的插入位点（45.9%；p = 1.03E-44），这些位点与承载442个与人类特异性（HS）基因表达变化相关的HSRS的区域相交。这些HSRS在人类特异性（HS）变化的脑类器官中富集。在非人灵长类动物（NHP）中，大多数显著的候选HSRS，与兴奋性神经元（347个位点；67%）和放射状胶质细胞（683个位点；72%）的HS表达变化相关，高度保守于大猩猩基因组。现代人类获得了在六个分离了3000万年的NHP物种中高度保守的独特的调控序列组合。同时，这种独特的调控序列拼图，继承自ECAs，同时补充了12486个新创造的HSRS。这些观察支持了在大猿进化过程中复杂连续的物种形成过程模型，这种过程不太可能作为瞬间事件发生。
英文摘要：
Our view of the universe of genomic regions harboring various types of candidate human-specific regulatory sequences (HSRS) has been markedly expanded in recent years. To infer the evolutionary origins of loci harboring HSRS, analyses of conservations patterns of 59,732 loci in Modern Humans, Chimpanzee, Bonobo, Gorilla, Orangutan, Gibbon, and Rhesus genomes have been performed. Two major evolutionary pathways have been identified comprising thousands of sequences that were either inherited from extinct common ancestors (ECAs) or created de novo in humans after human/chimpanzee split. Thousands of HSRS appear inherited from ECAs yet bypassed genomes of our closest evolutionary relatives, presumably due to the incomplete lineage sorting and/or species-specific loss or regulatory DNA. The bypassing pattern is prominent for HSRS associated with development and functions of human brain. Common genomic loci that may contributed to speciation during evolution of Great Apes comprise 248 insertions sites of African Great Ape-specific retrovirus PtERV1 (45.9%; p = 1.03E-44) intersecting regions harboring 442 HSRS, which are enriched for HSRS associated with human-specific (HS) changes of gene expression in cerebral organoids. Among non-human primates (NHP), most significant fractions of candidate HSRS associated with HS expression changes in both excitatory neurons (347 loci; 67%) and radial glia (683 loci; 72%) are highly conserved in Gorilla genome. Modern Humans acquired unique combinations of regulatory sequences highly conserved in distinct species of six NHP separated by 30 million years of evolution. Concurrently, this unique mosaic of regulatory sequences inherited from ECAs was supplemented with 12,486 created de novo HSRS. These observations support the model of complex continuous speciation process during evolution of Great Apes that is not likely to occur as an instantaneous event.
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