Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life.
Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life.
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DOI：
10.1186/s12862-016-0769-y
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发表时间：
2016-10-13
影响因子：
3.4
通讯作者：
Bond JE
中科院分区：
文献类型：
--
作者：
Hamilton CA;Lemmon AR;Lemmon EM;Bond JE
尽管付出了相当大的努力，蜘蛛分子系统学的进展已经落后于许多其他可比的节肢动物组，从而阻碍了家庭水平的分辨率，分类和测试的重要宏观进化假说。最近，替代的靶向序列捕获技术为分子系统学提供了一个强大的工具，用于解决整个生命之树的关系。其中一种方法，锚定杂交富集（AHE），旨在从整个基因组中恢复数百个独特的正向同源基因座，以解决非模型系统中的浅层和深层进化关系。在这里，我们提出了一个修改的AHE方法，扩大其在蜘蛛中的应用，特别强调的下目Mygalomorphae。我们的目的是设计一套探针，有效地捕捉位点信息的多样性系统发育的时间尺度。在确定了假定的节肢动物全基因座后，我们利用了所有蜘蛛中17个物种的同源转录组序列来确定外显子边界。然后在蜱基因组、三个已发表的蜘蛛形蜘蛛基因组和两个菌形分类群的原始基因组读数中寻找具有可变侧翼区的保守区。在蜘蛛探针试剂盒中的585个目标位点的开发之后，我们应用AHE跨越三个分类学深度来评估性能：深层蜘蛛家族关系（33个分类群，327个位点）;在mygalomorph家族Eucentenizidae（25个分类群，403个位点）内的家族和属的关系;以及在北美狼蛛属Aponopelma（83个分类群，581个位点）中的种的关系。在最深层次上，所有三个主要的蜘蛛谱系（Mesothelae，Mygalomorphae和Araneomorphae）都得到了高自助支持。强有力的支持也发现整个Eutenizidae，包括属内的家庭和属内Aptostichus种的关系。在Ectenizidae，几乎相同的拓扑推断与整个Aponopelma的支持率很高。蜘蛛探针工具包，AHE方法在蛛形纲的第一个实施，具有很大的希望，通过提供一种机制，使不同的研究人员可以自信和有效地使用相同的基因座独立的项目，但允许跨独立的研究小组的数据合成，收集所需的分子数据的类型和数量，以加速对蜘蛛生命树的理解。本文的在线版本（doi：10.1186/s12862-016-0769-y）包含补充材料，可供授权用户使用。
Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae. Our aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus. As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma. The Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups. The online version of this article (doi:10.1186/s12862-016-0769-y) contains supplementary material, which is available to authorized users.
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影响因子：
1.3
作者：
Bond JE
通讯作者：
Bond JE
影响因子：
3.4
作者：
Brandley, Matthew C.;Bragg, Jason G.;Moritz, Craig
通讯作者：
Moritz, Craig
影响因子：
3.4
作者：
Eytan, Ron I.;Evans, Benjamin R.;Near, Thomas J.
通讯作者：
Near, Thomas J.
影响因子：
3.7
作者：
Bond JE;Hendrixson BE;Hamilton CA;Hedin M
通讯作者：
Hedin M
影响因子：
3.7
作者：
Faircloth BC;Sorenson L;Santini F;Alfaro ME
通讯作者：
Alfaro ME