Strepsiptera, phylogenomics and the long branch attraction problem.

Bastien Boussau,Laura Beani,Zaak Walton,Peter W.H Holland,Isaac J Stewart,Jeyaraney Kathirithamby,Doris Bachtrog,Sydney A Cameron,James B Whitfield,John P Huelsenbeck,Juan A Delgado,J Spencer Johnston,Francisco Collantes

doi:10.1371/journal.pone.0107709

Abstract

Insect phylogeny has recently been the focus of renewed interest as advances in sequencing techniques make it possible to rapidly generate large amounts of genomic or transcriptomic data for a species of interest. However, large numbers of markers are not sufficient to guarantee accurate phylogenetic reconstruction, and the choice of the model of sequence evolution as well as adequate taxonomic sampling are as important for phylogenomic studies as they are for single-gene phylogenies. Recently, the sequence of the genome of a strepsipteran has been published and used to place Strepsiptera as sister group to Coleoptera. However, this conclusion relied on a data set that did not include representatives of Neuropterida or of coleopteran lineages formerly proposed to be related to Strepsiptera. Furthermore, it did not use models that are robust against the long branch attraction artifact. Here we have sequenced the transcriptomes of seven key species to complete a data set comprising 36 species to study the higher level phylogeny of insects, with a particular focus on Neuropteroidea (Coleoptera, Strepsiptera, Neuropterida), especially on coleopteran taxa considered as potential close relatives of Strepsiptera. Using models robust against the long branch attraction artifact we find a highly resolved phylogeny that confirms the position of Strepsiptera as a sister group to Coleoptera, rather than as an internal clade of Coleoptera, and sheds new light onto the phylogeny of Neuropteroidea.

Highlights

Phylogenomic analysis — the application of dozens to many hundreds of alignments to phylogenetic problems — provides a better understanding of the phylogenetic relationships of species, by leveraging vast amounts of data
Parsimony analyses Early molecular analyses of ribosomal RNAs supported a close proximity between Diptera and Strepsiptera [12]
This result was found due to the use of parsimony where the assumption of an absence of multiple substitutions is violated by the data, and to be consistent with LBA [11]

Summary

Introduction

Phylogenomic analysis — the application of dozens to many hundreds of alignments to phylogenetic problems — provides a better understanding of the phylogenetic relationships of species, by leveraging vast amounts of data. Parsimony analyses of ribosomal DNA sequences resulted in a tree with Diptera and Strepsiptera as sister groups [12,13]. [36] sequenced the nuclear genome of a species of Strepsiptera and compared it to genomic or transcriptomic data from 12 other insect species, including two Coleoptera (beetles).

Results

Conclusion