Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life

BMC Evolutionary Biology

Research Article

Emily Moriarty Lemmon¹  Chris A. Hamilton²  Jason E. Bond²  Alan R. Lemmon³ 

[1]Department of Biological Science, Florida State University, Tallahassee, FL, USA

[2]Department of Biological Sciences, Auburn University & Auburn University Museum of Natural History, Auburn, AL, USA

[3]Department of Scientific Computing, Florida State University, Tallahassee, FL, USA

关键词: Anchored Hybrid Enrichment;    Anchored phylogenomics;    Targeted sequence capture;    Conserved regions;    Ultraconserved elements;    Araneae;    Mygalomorphae;    Arachnida;   

DOI  :  10.1186/s12862-016-0769-y

 received in 2016-06-04, accepted in 2016-09-28,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundDespite 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.ResultsOur 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© The Author(s). 2016