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The<jats:italic>Aptostichus atomarius<\/jats:italic>species complex (family Euctenizidae) includes two coastal dune endemic members, each with inland sister species \u2013 affording exploration of dune adaptation associated patterns at the transcriptomic level. We apply an RNAseq approach to examine gene family conservation across the species complex and test for patterns of positive selection along branches leading to dune endemic species.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>An average of ~\u200944,000 contigs were assembled for eight spiders representing dune (<jats:italic>n<\/jats:italic>\u2009=\u20092), inland (<jats:italic>n<\/jats:italic>\u2009=\u20094), and<jats:italic>atomarius<\/jats:italic>species complex outgroup taxa (<jats:italic>n<\/jats:italic>\u2009=\u20092). Transcriptomes were estimated to be 64% complete on average with 77 spider reference orthologs missing from all taxa. Over 18,000 orthologous gene clusters were identified within the<jats:italic>atomarius<\/jats:italic>complex members, &gt;\u20095000 were detected in all species, and ~\u20094700 were shared between species complex members and outgroup<jats:italic>Aptostichus<\/jats:italic>species. Gene family analysis with the FUSTr pipeline identified 47 gene families appearing to be under selection in the<jats:italic>atomarius<\/jats:italic>ingroup; four of the five top clusters include sequences strongly resembling other arthropod venom peptides. The COATS pipeline identified six gene clusters under positive selection on branches leading to dune species, three of which reflected the preferred species tree. Genes under selection were identified as Cytochrome P450 2c15 (also recovered in the FUSTr analysis), Niemann 2 Pick C1-like, and Kainate 2 isoform X1.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>We have generated eight draft transcriptomes for a closely related and ecologically diverse group of trapdoor spiders, identifying venom gene families potentially under selection across the<jats:italic>Aptostichus atomarius<\/jats:italic>complex and chemosensory-associated gene families under selection in dune endemic lineages.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12862-020-01606-7","type":"journal-article","created":{"date-parts":[[2020,6,15]],"date-time":"2020-06-15T11:04:28Z","timestamp":1592219068000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Shifting evolutionary sands: transcriptome characterization of the Aptostichus atomarius species complex"],"prefix":"10.1186","volume":"20","author":[{"given":"Nicole L.","family":"Garrison","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael S.","family":"Brewer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason E.","family":"Bond","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,6,15]]},"reference":[{"key":"1606_CR1","doi-asserted-by":"publisher","unstructured":"Vera Opatova, Chris A Hamilton, Marshal Hedin, Laura Montes De Oca, Ji\u0159i Kr\u00e1l, Jason E Bond, Phylogenetic Systematics and Evolution of the Spider Infraorder Mygalomorphae Using Genomic Scale Data, Systematic Biology, syz064, https:\/\/doi.org\/10.1093\/sysbio\/syz064.","DOI":"10.1093\/sysbio\/syz064"},{"key":"1606_CR2","unstructured":"World Spider Catalog 2018. https:\/\/wsc.nmbe.ch\/. 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