Hamilton Chris A, Lemmon Alan R, Lemmon Emily Moriarty, Bond Jason E
Department of Biological Sciences, Auburn University & Auburn University Museum of Natural History, Auburn, AL, USA.
Department of Scientific Computing, Florida State University, Tallahassee, FL, USA.
BMC Evol Biol. 2016 Oct 13;16(1):212. doi: 10.1186/s12862-016-0769-y.
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.
尽管付出了巨大努力，但蜘蛛分子系统学的进展仍落后于许多其他类似的节肢动物类群，从而阻碍了科级分辨率、分类以及对重要宏观进化假说的检验。最近，替代性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，用于解析生命之树中的各种关系。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直系同源基因座，以解析非模式系统内的浅层和深层进化关系。在此，我们提出了对AHE方法的一种改进，扩展了其在蜘蛛中的应用，尤其侧重于原蛛亚目。
我们的目标是设计一组能在多种系统发育时间尺度上有效捕获信息丰富基因座的探针。在确定了假定的全节肢动物基因座后，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、三个已发表的新蛛亚目蜘蛛基因组以及两个原蛛亚目类群的原始基因组读数中寻找具有可变侧翼区域的保守区域。在开发出蜘蛛探针试剂盒中的585个目标基因座后，我们在三个分类深度上应用AHE来评估其性能：蜘蛛科级的深层关系（33个分类单元，327个基因座）；原蛛亚目真掘蛛科内的科级和属级关系（25个分类单元，403个基因座）；以及北美捕鸟蛛属阿氏蛛属的物种关系（83个分类单元，581个基因座）。在最深层次上，所有三个主要蜘蛛谱系（中纺亚目、原蛛亚目和新蛛亚目）都得到了高自展支持。在整个真掘蛛科中也发现了强有力的支持，包括科内的属级关系和阿氏蛛属内的物种关系。与真掘蛛科一样，在整个阿氏蛛属中也推断出了几乎相同的拓扑结构，并得到了高度支持。
蜘蛛探针试剂盒是AHE方法在蛛形纲中的首次应用，通过提供一种机制，使不同的研究人员能够自信且有效地将相同的基因座用于独立项目，同时允许跨独立研究小组的数据综合，对于收集加速理解蜘蛛生命之树所需的分子数据的类型和数量具有巨大潜力。
