Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study

dc.contributor.authorBazinet, Adam L.
dc.contributor.authorCummings, Michael P.
dc.contributor.authorMitter, Kim T.
dc.contributor.authorMitter, Charles W.
dc.descriptionFunding for Open Access provided by the UMD Libraries Open Access Publishing Fund.
dc.description.abstractRecent molecular phylogenetic studies of the insect order Lepidoptera have robustly resolved family-level divergences within most superfamilies, and most divergences among the relatively species-poor early-arising superfamilies. In sharp contrast, relationships among the superfamilies of more advanced moths and butterflies that comprise the mega-diverse clade Apoditrysia (ca. 145,000 spp.) remain mostly poorly supported. This uncertainty, in turn, limits our ability to discern the origins, ages and evolutionary consequences of traits hypothesized to promote the spectacular diversification of Apoditrysia. Low support along the apoditrysian “backbone” probably reflects rapid diversification. If so, it may be feasible to strengthen resolution by radically increasing the gene sample, but case studies have been few. We explored the potential of next-generation sequencing to conclusively resolve apoditrysian relationships. We used transcriptome RNA-Seq to generate 1579 putatively orthologous gene sequences across a broad sample of 40 apoditrysians plus four outgroups, to which we added two taxa from previously published data. Phylogenetic analysis of a 46-taxon, 741-gene matrix, resulting from a strict filter that eliminated ortholog groups containing any apparent paralogs, yielded dramatic overall increase in bootstrap support for deeper nodes within Apoditrysia as compared to results from previous and concurrent 19-gene analyses. High support was restricted mainly to the huge subclade Obtectomera broadly defined, in which 11 of 12 nodes subtending multiple superfamilies had bootstrap support of 100%. The strongly supported nodes showed little conflict with groupings from previous studies, and were little affected by changes in taxon sampling, suggesting that they reflect true signal rather than artifacts of massive gene sampling. In contrast, strong support was seen at only 2 of 11 deeper nodes among the “lower”, non-obtectomeran apoditrysians. These represent a much harder phylogenetic problem, for which one path to resolution might include further increase in gene sampling, together with improved orthology assignments.en_US
dc.description.sponsorshipFinancial support was provided by the U.S. National Science Foundation’s Assembling the Tree of Life program, award numbers 0531626 and 0531769; U.S. National Science Foundation grant DEB 0515699 to D. H. Janzen; U.S. National Science Foundation award DBI-0755048; and the Hatch funds of the Maryland Agricultural Experiment Station. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en_US
dc.identifier.citationBazinet AL, Cummings MP, Mitter KT, Mitter CW (2013) Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study. PLoS ONE 8(12): e82615. doi:10.1371/journal.pone.0082615en_US
dc.publisherPLoS Oneen_US
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtCollege of Computer, Mathematical & Natural Sciencesen_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectAnimal phylogeneticsen_US
dc.subjectDNA sequence analysisen_US
dc.subjectMoths and butterfliesen_US
dc.subjectPhylogenetic analysisen_US
dc.subjectRNA extractionen_US
dc.subjectSequence alignmenten_US
dc.titleCan RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Studyen_US


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