Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study.

摘要: Determining phylogenetic relationships among recently diverged species has long been a challenge in evolutionary biology. Cytoplasmic markers, which have widely used notably the context of molecular barcoding, not always proved successful resolving such phylogenies, but phylogenies for closely related resolved at much higher detail last couple years with advent next-generation-sequencing technologies and associated techniques reduced genome representation. Here we examine potential limitations one - Restriction-site Associated DNA (RAD) sequencing, method that produces thousands (mostly) anonymous nuclear disentangling phylogeny fly genus Chiastocheta (Diptera: Anthomyiidae). This encompasses seven described seed predators, studied their ecological interactions plant Trollius europaeus (Ranunculaceae). So far, analyses using mitochondrial markers failed to resolve monophyly most from this diversified genus, suggesting taxonomy may need be revised. However, relying on single, non-recombining molecule ignoring incongruences between loci provide incomplete account lineage history. In study, apply both classical Sanger sequencing three mtDNA regions RAD-sequencing, reconstructing genus. Contrasting results based RAD-sequencing retrieved all species, agreement morphological assignment. We found robust nuclear-based assignment individual samples, low levels estimated contemporary gene flow them. despite recovering species' monophyly, interspecific varied depending set RAD considered, producing contradictory topologies. Moreover, coalescence-based revealed supports relationships. Our indicate performance terms trees resolution compared cytoplasmic inter-specific lie beyond possibilities offered by large sets cases strong tree incongruence.