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Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry.
Mobile DNA ( IF 4.9 ) Pub Date : 2019-11-26 , DOI: 10.1186/s13100-019-0187-y
Jerilyn A Walker 1 , Vallmer E Jordan 1 , Jessica M Storer 1 , Cody J Steely 1 , Paulina Gonzalez-Quiroga 1 , Thomas O Beckstrom 1 , Lydia C Rewerts 1 , Corey P St Romain 1 , Catherine E Rockwell 1 , Jeffrey Rogers 2, 3 , Clifford J Jolly 4 , Miriam K Konkel 1, 5 , , Mark A Batzer 1
Affiliation  

Background Baboons (genus Papio) and geladas (Theropithecus gelada) are now generally recognized as close phylogenetic relatives, though morphologically quite distinct and generally classified in separate genera. Primate specific Alu retrotransposons are well-established genomic markers for the study of phylogenetic and population genetic relationships. We previously reported a computational reconstruction of Papio phylogeny using large-scale whole genome sequence (WGS) analysis of Alu insertion polymorphisms. Recently, high coverage WGS was generated for Theropithecus gelada. The objective of this study was to apply the high-throughput "poly-Detect" method to computationally determine the number of Alu insertion polymorphisms shared by T. gelada and Papio, and vice versa, by each individual Papio species and T. gelada. Secondly, we performed locus-specific polymerase chain reaction (PCR) assays on a diverse DNA panel to complement the computational data. Results We identified 27,700 Alu insertions from T. gelada WGS that were also present among six Papio species, with nearly half (12,956) remaining unfixed among 12 Papio individuals. Similarly, each of the six Papio species had species-indicative Alu insertions that were also present in T. gelada. In general, P. kindae shared more insertion polymorphisms with T. gelada than did any of the other five Papio species. PCR-based genotype data provided additional support for the computational findings. Conclusions Our discovery that several thousand Alu insertion polymorphisms are shared by T. gelada and Papio baboons suggests a much more permeable reproductive barrier between the two genera then previously suspected. Their intertwined evolution likely involves a long history of admixture, gene flow and incomplete lineage sorting.

中文翻译:

狒狒和 Theropithecus gelada 共有的 Alu 插入多态性揭示了一个相互交织的共同祖先。

背景 狒狒(狒狒属)和狒狒(Theropithecus gelada)现在通常被认为是近亲,尽管在形态上非常不同并且通常被分类为不同的属。灵长类动物特异性 Alu 反转录转座子是研究系统发育和种群遗传关系的成熟基因组标记。我们之前报道了使用 Alu 插入多态性的大规模全基因组序列 (WGS) 分析对 Papio 系统发育进行计算重建。最近,为 Theropithecus gelada 生成了高覆盖率 WGS。本研究的目的是应用高通量“poly-Detect”方法来计算确定 T. gelada 和 Papio 共享的 Alu 插入多态性的数量,反之亦然,每个单独的 Papio 物种和 T. gelada。第二,我们在不同的 DNA 面板上进行了位点特异性聚合酶链反应 (PCR) 测定,以补充计算数据。结果 我们确定了来自 T. gelada WGS 的 27,700 个 Alu 插入,这些插入也存在于六种 Papio 物种中,其中近一半 (12,956) 在 12 个 Papio 个体中仍未固定。同样,六种 Papio 物种中的每一种都具有指示物种的 Alu 插入,这些插入也存在于 T. gelada 中。一般来说,P. kindae 与 T. gelada 共享的插入多态性比其他五种 Papio 物种中的任何一种都多。基于 PCR 的基因型数据为计算结果提供了额外的支持。结论 我们发现 T. gelada 和狒狒共有数千个 Alu 插入多态性,这表明这两个属之间的生殖屏障比以前怀疑的要高得多。
更新日期:2019-11-26
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