Whole genome shotgun phylogenomics resolve the diving beetle tree of life

Abstract

Diving beetles (Dytiscidae) are important generalist predators in freshwater ecosystems that have been around since the Jurassic. Previous phylogenetic studies have identified a largely stable set of monophyletic named groups (subfamilies, tribes and subtribes); however, backbone relationships among these have remained elusive. Here we use whole genome sequencing to reconstruct the phylogeny of Dytiscidae. We mine de novo assemblies and combine them with others available from transcriptome studies of Adephaga to compile a dataset of 149 taxa and 5364 orthologous genes. Species tree and concatenated maximum likelihood methods provide largely congruent results, resolving in agreement all but two inter-subfamily nodes. All 11 subfamilies are monophyletic, supporting previous results; possibly also all tribes, but Hydroporini is recovered as paraphyletic with weak support and monophyly of Dytiscini is method dependent. One large clade includes eight of 11 subfamilies (excluding Laccophilinae, Lancetinae and Coptotominae). Matinae is sister to Hydrodytinae + Hydroporinae, in contrast with previous studies that have hypothesized Matinae as sister to the remaining Dytiscidae. Copelatinae belong in a clade with Cybistrinae, Dytiscinae, Agabinae and Colymbetinae. Strongly confirmed sister group relationships of subfamilies include Cybistrinae + Dytiscinae, Agabinae + Colymbetinae, Lancetinae + Coptotominae and Hydrodytinae + Hydroporinae. Remaining problems include resolving with confidence the basal ingroup trichotomy and relationships between tribes in Hydroporinae. Resolution of tribes in Dytiscinae is affected by methodological inconsistencies. Platynectini, new tribe, is described and Hydrotrupini redefined within subfamily Agabinae. This study is a step forward towards completely resolving the backbone phylogeny of Dytiscidae, which we hope will stimulate further work on remaining challenges.