High phylogenetic utility of an ultraconserved element probe set designed for Arachnida
High phylogenetic utility of an ultraconserved element probe set designed for Arachnida
复制标题
为蛛形纲动物设计的超保守元件探针组的高系统发育效用
DOI：
10.1111/1755-0998.12621
复制
发表时间：
2016
影响因子：
7.7
通讯作者：
Faircloth, Brant C.
中科院分区：
文献类型：
--
作者：
Starrett, James;Derkarabetian, Shahan;Hedin, Marshal;Bryson, Jr., Robert W.;McCormack, John E.;Faircloth, Brant C.
蛛形纲动物是一个古老的、多样的、具有重要生态意义的动物类群，其中包含许多在医学、农业和工程应用方面具有重要意义的物种。尽管它们的重要性，蜘蛛生命树的许多方面仍然没有解决，阻碍了蜘蛛生物学的比较方法。生物学家已经做出了相当大的努力来解决蛛形纲动物的生殖;然而，有限的和具有挑战性的形态特征，以及缺乏遗传资源，阻碍了进展。在这里，我们提出了一个蛛形纲动物的基因组工具包，具有数百个保守的DNA区域（ultraconserved元件或UCE），允许在蛛形纲动物生命树中的任何物种的靶向测序。我们使用最近开发的捕获探针设计的保守区域的蜘蛛基因组，以丰富样品的基因座从32个不同的蜘蛛。序列捕获返回了所有物种的平均487个UCE位点，范围从170到722。这些UCE的系统发育分析产生了一个高度分辨率的蜘蛛树，其关系与最近基于转录组的系统发育基本一致。我们还测试了UCE探针在蜘蛛，蝎子和收获者目中的系统发育信息，证明了这些标记在较浅的分类尺度上的实用性，并表明这些位点将有助于物种水平的差异。这套探针将打开大门，在整个蛛形纲动物的生命树，使系统学，物种划界，物种发现和保护这些不同的节肢动物的基因组和人口基因组研究。
Arachnida is an ancient, diverse and ecologically important animal group that contains a number of species of interest for medical, agricultural and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved regions of available arachnid genomes to enrich a sample of loci from 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome‐based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales and suggesting that these loci will be useful for species‐level differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery and conservation of these diverse arthropods.