Data from: Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera)
Shin, Seunggwan, University of Memphis, North Carolina State University
Bayless, Keith M., North Carolina State University, California Academy of Sciences
Winterton, Shaun L., California Department of Food and Agriculture
Dikow, Torsten, Smithsonian Institution
Lessard, Bryan D., Commonwealth Scientific and Industrial Research Organisation
Yeates, David K., Commonwealth Scientific and Industrial Research Organisation
Wiegmann, Brian M., North Carolina State University
Trautwein, Michelle D., California Academy of Sciences
Published Sep 29, 2018 on Dryad.
Cite this dataset
Shin, Seunggwan et al. (2018). Data from: Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera) [Dataset]. Dryad. https://doi.org/10.5061/dryad.cq63m
Early diverging brachyceran fly lineages underwent a rapid radiation approximately 180 million years ago, coincident in part with the origin of flowering plants. This region of the fly tree includes 25,000 described extant species with diverse ecological roles such as blood feeding (haematophagy), parasitoidism, predation, pollination, and wood feeding (xylophagy). Early diverging brachyceran lineages were once considered a monophyletic group of families called Orthorrhapha, based on the shared character of a longitudinal break in the pupal skin made during the emergence of the adult. Yet other morphological and molecular evidence generally supports a paraphyletic arrangement of ‘Orthorrhapha,’ with strong support for one orthorrhaphan lineage — dance flies and relatives — as the closest relative to all higher flies (Cyclorrhapha), together called Eremoneura. In order to establish a comprehensive estimate of the relationships among orthorrhaphan lineages using a thorough sample of publicly available data we compiled and analyzed a dataset including 1,217 taxa representing major lineages and 20 molecular markers. Our analyses suggest that ‘Orthorrhapha’ excluding Eremoneura is not monophyletic; instead, we recover two main lineages of early brachyceran flies— Homeodactyla and Heterodactyla. Homeodactyla includes Nemestrinoidea (uniting two parasitic families Acroceridae + Nemestrinidae) as the closest relatives to the large SXT clade, comprised of Stratiomyomorpha, Xylophagidae and Tabanomorpha. Heterodactyla includes Bombyliidae with a monophyletic Asiloidea (exclusive of Bombyliidae) as the closest relatives to Eremoneura. Reducing missing data, modifying the distribution of genes across taxa, and, in particular, removing rogue taxa significantly improved tree resolution and statistical support. Although relying on dense taxonomic sampling and substantial gene coverage, our analyses pinpoint the limited resolving power of Sanger sequencing-era molecular phylogenetic datasets in respect to ancient, hyperdiverse radiations.
Supplementary Fig. S1.
Best ML tree with branch support from 100 thorough bootstrap replicates for dataset i, ALL
Supplementary Fig. S2.
Best ML tree with branch support from 100 thorough bootstrap replicates for dataset ii, MISSING
Supplementary Fig. S3.
Best ML tree with branch support from 100 thorough bootstrap replicates for dataset iii, COVERAGE
Supplementary Fig. S4.
Best ML tree with branch support from 100 thorough bootstrap replicates for dataset iv, ALL_ROGUE
Supplementary Fig. S5.
Best ML tree with branch support from 100 thorough bootstrap replicates for dataset v, MISSING_ROGUE
Supplementary Fig. S6.
Best ML tree with branch support from 100 thorough bootstrap replicates for dataset vi, COVERAGE_ROGUE
Supplementary Fig. S7.
Best ML tree with branch support from 100 rapid bootstrap replicates with outgroup Nematocera
Gene and taxon coverage for dataset ‘i’ with species name, rogue taxa selection list for all 6 datasets.
Maximum Likelihood bipartitions tree files for Supplementary Figs. S1-S7.