PRJDB2148
Application of RAD-Based Phylogenetics to Complex Relationships among Variously Related Taxa in a Species Flock
Restriction site-associated DNA (RAD) sequencing produces a vast number of sequences from entire genomes of organisms that can be used to resolve complex phylogenetic problems. However, the resulting data matrix can vary depending on the strategies used to determine orthologous loci among species and to filter loci according to the number of taxa that share orthologous loci, and often contains missing data. To explore the utility of RAD sequencing for elucidating the phylogenetics of variously related species, we conducted RAD sequencing for the species flock of Ohomopterus ground beetles and attempted maximum-likelihood phylogenetic analyses using 42 data matrices ranging from ~103 informative single-nucleotide polymorphisms (SNPs) and 11% missing data to ~3 ? 105 informative SNPs and 60% missing data. We demonstrate that robust topologies, in terms of bootstrap values, do not necessarily result from larger data matrices containing missing data, as previously suggested. Robust topologies for distantly related and closely related taxa resulted from different data matrices due to their varying data composition. In addition, larger data matrices with much missing data strongly supported topologies that are partly incompatible with morphological evidence, which could be caused by some phylogenetic signals in variable sequence portions being shared due to introgressive hybridization. Practically, exploring variously prepared data matrices is an effective way to propose important alternative phylogenetic hypotheses for this study group.