DOI: 10.5061/dryad.cq63m
title: Data from: Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera)

description: 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.
description: Supplementary Fig.
 S1.Best ML tree with branch
 support from 100 thorough bootstrap replicates for dataset i,
 ALLSI_FIG_1_100BT_data_i.pdfSupplementary Fig. S2.Best ML tree with branch support from 100 thorough bootstrap replicates for dataset ii, MISSINGSI_FIG_2_100BT_data_ii_p.pdfSupplementary Fig. S3.Best ML tree with branch support from 100 thorough bootstrap replicates for dataset iii, COVERAGESI_FIG_3_100BT_data_iii_p.pdfSupplementary Fig. S4.Best ML tree with branch support from 100 thorough bootstrap replicates for dataset iv, ALL_ROGUESI_FIG_4_100BT_data_iv_p.pdfSupplementary Fig. S5.Best ML tree with branch support from 100 thorough bootstrap replicates for dataset v, MISSING_ROGUESI_FIG_5_100BT_data_v.pdfSupplementary Fig. S6.Best ML tree with branch support from 100 thorough bootstrap replicates for dataset vi, COVERAGE_ROGUESI_FIG_6_100BT_data_vi.pdfSupplementary Fig. S7.Best ML tree with branch support from 100 rapid bootstrap replicates with outgroup NematoceraSI_Fig_7_all.pdfTable_S1Gene and taxon coverage for dataset ‘i’ with species name, rogue taxa selection list for all 6 datasets.ML_tree_filesMaximum Likelihood bipartitions tree files for Supplementary Figs. S1-S7.phylip files for each datasetPhylip format files for all 6 datasets.Phylip_data.zip