10.5061/DRYAD.CQ63M
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
Data from: Taxon sampling to address an ancient rapid radiation: a
supermatrix phylogeny of early brachyceran flies (Diptera)
Dryad
dataset
2018
Early brachycera
Diptera
National Science Foundation
https://ror.org/021nxhr62
DEB1257960
2018-09-29T00:00:00Z
2018-09-29T00:00:00Z
en
https://doi.org/10.1111/syen.12275
7452793 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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,
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