DSpace Repository

Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?

Show simple item record

dc.contributor.author Cho, Soowon en
dc.contributor.author Zwick, Andreas en
dc.contributor.author Regier, Jerome C. en
dc.contributor.author Mitter, Charles en
dc.contributor.author Cummings, Michael P. en
dc.contributor.author Yao, Jianxiu en
dc.contributor.author Du, Zaile en
dc.contributor.author Zhao, Hong en
dc.contributor.author Kawahara, Akito Y. en
dc.contributor.author Weller, Susan en
dc.contributor.author Davis, Donald R. en
dc.contributor.author Baixeras, Joaquin en
dc.contributor.author Brown, John W. en
dc.contributor.author Parr, Cynthia Sims en
dc.date.accessioned 2013-09-27T20:29:24Z
dc.date.available 2013-09-27T20:29:24Z
dc.date.issued 2011
dc.identifier.citation Cho, Soowon, Zwick, Andreas, Regier, Jerome C., Mitter, Charles, Cummings, Michael P., Yao, Jianxiu, Du, Zaile, Zhao, Hong, Kawahara, Akito Y., Weller, Susan, Davis, Donald R., Baixeras, Joaquin, Brown, John W., and Parr, Cynthia Sims. 2011. "<a href="https://repository.si.edu/handle/10088/21486">Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?</a>." <em>Systematic Biology</em>. 60 (6):782&ndash;796. <a href="https://doi.org/10.1093/sysbio/syr079">https://doi.org/10.1093/sysbio/syr079</a> en
dc.identifier.issn 1063-5157
dc.identifier.uri http://hdl.handle.net/10088/21486
dc.description.abstract This paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly-understood deeper relationships in the large clade Ditrysia (&gt;150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly non-synonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78-85% bootstrap) was weak or non-existent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A â more-genes-onlyâ data set (41 taxa Ã- 26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses. en
dc.relation.ispartof Systematic Biology en
dc.title Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)? en
dc.type Journal Article en
dc.identifier.srbnumber 103963
dc.identifier.doi 10.1093/sysbio/syr079
rft.jtitle Systematic Biology
rft.volume 60
rft.issue 6
rft.spage 782
rft.epage 796
dc.description.SIUnit NH-Entomology en
dc.description.SIUnit NMNH en
dc.description.SIUnit Peer-reviewed en
dc.description.SIUnit NH-EOL en
dc.citation.spage 782
dc.citation.epage 796

Files in this item

This item appears in the following Collection(s)

Show simple item record

Search DSpace


My Account