A dated molecular phylogeny for the Chironomidae (Diptera)

We provide the first highly sampled phylogeny estimate for the dipteran family Chironomidae using molecular data from fragments of two ribosomal genes (18S and 28S), one nuclear protein-coding gene (CAD), and one mitochondrial protein-coding gene (COI), analysed using mixed-model Bayesian and maximum likelihood inference methods. The most recently described subfamilies Chilenomyiinae and Usambaromyiinae proved elusive, and are unsampled. We confirm monophyly of all sampled subfamilies except Prodiamesinae, which contains Propsilocerus Kieffer, previously in Orthocladiinae. The semifamily Chironomoinae is confirmed only if Telmatogetoninae is included, which is closer to Brundin's original suggestion. Buchonomyiinae is excluded from Chironomoinae: it is a sister group to all remaining Chironomidae, conforming more to Murray and Ashe's argumentation. Semifamily Tanypodoinae is a grade and unsupported as monophyletic: the austral Aphroteniinae alone is sister to all Chironomidae (less Buchonomyiinae). Podonominae is weakly supported as the next sister group, in contrast to some estimates that place this subfamily as sister group to Tanypodinae alone. In Diamesinae, the southern African Harrisonini is confirmed as a member, but embedded within austral tribe Heptagiini, which is confirmed as sister to the undersampled Diamesini. Tribe Pentaneurini and ‘non-Pentaneurini’ taxa are reciprocally monophyletic in Tanypodinae. Recent molecular findings concerning Podonominae are substantiated, with a monophyletic tribe Podonomini, Boreochlini forming a grade and Lasiodiamesa Kieffer placed as sister to all other Podonominae, but with uncertainty. In Orthocladiinae, a postulated two-tribe system of Orthocladiini and Metriocnemini can be supported after exclusion of a Corynoneura group and a Brillia group, which is revealed as sister to Stictocladius Edwards. The marine Clunio Haliday and Thalassosmittia Strenzke & Remmert (given high rank in the past) are clearly embedded deep in Orthocladiinae. The finding of Shangomyia Saether & Wang + Xyiaomyia Saether & Wang as sister group to all other Chironominae justifies high rank, as their authors suggested. Pseudochironomini (untested by sampling shortfall) is sister to a monophyletic Tanytarsini (with a weakly supported inclusion of the enigmatic Nandeva Wiedenbrug, Reiss & Fittkau). The tribe Chironomini can be supported only by excluding Shangomyia + Xyiaomyia, and a postulated monophyletic clade comprising several taxa such as Microtendipes Kieffer, with six-segmented larval antennae and alternate Lauterborn organs, that is sister group to Pseudochironomini + Tanytarsini. The tempo of diversification of the family, deduced by divergence time analysis (beast), shows Permian origination with subfamily stem-group origination from the mid–late Triassic to the early Cretaceous. Crown-group origination ranged from Podonominae on a short stem originating in the mid Jurassic to long-stemmed Aphroteninae from the late Cretaceous. Node dates allow inference of some vicariance via Gondwanan fragmentation, including certain nodes involving southern Africa.