title: Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock.
abstract: Restriction site-associated DNA (RAD) sequences from entire genomes can be used to resolve complex phylogenetic problems. However, the processed data matrix varies depending on the strategies used to determine orthologous loci and to filter loci according to the number of taxa with sequence data for the loci, and often contains plenty of missing data. To explore the utility of RAD sequences for elucidating the phylogenetics of variously related species, we conducted RAD sequencing for the Ohomopterus ground beetles and attempted maximum-likelihood phylogenetic analyses using 42 data matrices ranging from 1.6×10(4) to 8.1×10(6) base pairs, with 11-72% missing data. We demonstrate that robust phylogenetic trees, in terms of bootstrap values, do not necessarily result from larger data matrices, as previously suggested. Robust trees for distantly related and closely related taxa resulted from different data matrices, and topologically different robust trees for distantly related taxa resulted from various data matrices. For closely related taxa, moderately large data matrices strongly supported a topology that is incompatible with morphological evidence, possibly due to the effect of introgressive hybridization. Practically, exploring variously prepared data matrices is an effective way to propose important alternative phylogenetic hypotheses for this study group.
authors.affiliation: Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
authors.forename: Tetsumi
authors.initials: T
authors.lastname: Takahashi
authors.affiliation: Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba, Sendai 980-8578, Japan.
authors.forename: Nobuaki
authors.initials: N
authors.lastname: Nagata
authors.affiliation: Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan. Electronic address: sota@terra.zool.kyoto-u.ac.jp.
authors.forename: Teiji
authors.initials: T
authors.lastname: Sota
mesh_terms: D000818:Animals; D001483:Base Sequence; D001517:Coleoptera / Q000145:classification* / Q000235:genetics; D006824:Hybridization, Genetic; D016013:Likelihood Functions; D008297:Male; D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods
keywords: Carabus; Maximum-likelihood analysis; Missing data; Ohomopterus; Orthologous sequence