DOI: 10.5061/dryad.21nf3
title: Data from: Episodic radiations in the fly tree of life

description: Flies are one of four superradiations of insects (along with beetles,
 wasps, and moths) that account for the majority of animal life on Earth.
 Diptera includes species known for their ubiquity (Musca domestica house
 fly), their role as pests (Anopheles gambiae malaria mosquito), and their
 value as model organisms across the biological sciences (Drosophila
 melanogaster). A resolved phylogeny for flies provides a framework for
 genomic, developmental, and evolutionary studies by facilitating
 comparisons across model organisms, yet recent research has suggested that
 fly relationships have been obscured by multiple episodes of rapid
 diversification. We provide a phylogenomic estimate of fly relationships
 based on molecules and morphology from 149 of 157 families, including 30
 kb from 14 nuclear loci and complete mitochondrial genomes combined with
 371 morphological characters. Multiple analyses show support for
 traditional groups (Brachycera, Cyclorrhapha, and Schizophora) and
 corroborate contentious findings, such as the anomalous Deuterophlebiidae
 as the sister group to all remaining Diptera. Our findings reveal that the
 closest relatives of the Drosophilidae are highly modified parasites
 (including the wingless Braulidae) of bees and other insects. Furthermore,
 we use micro-RNAs to resolve a node with implications for the evolution of
 embryonic development in Diptera. We demonstrate that flies experienced
 three episodes of rapid radiation—lower Diptera (220 Ma), lower Brachycera
 (180 Ma), and Schizophora (65 Ma)—and a number of life history transitions
 to hematophagy, phytophagy, and parasitism in the history of fly evolution
 over 260 million y.
description: FLYTREEmitoGeneAlnNucleotide alignments in FASTA format for mitochondrial genes sequenced in the FLYTREE PROJECT. These sequences were used in Wiegmann et al. 2011 PNAS 108:5690 (doi:10.1073/pnas.1012675108) and in Caravas and Friedrich 2012 Syst. Ent. (doi: 10.1111/j.1365-3113.2012.00657.x)FLYTREENuclearGenes_ALNNucleotide alignments in FASTA format for all nuclear genes sequenced in the FLYTREE PROJECT. These sequences were used in Wiegmann et al. 2011 PNAS 108:5690 (doi:10.1073/pnas.1012675108) and in Caravas and Friedrich 2012 Syst. Ent. (doi: 10.1111/j.1365-3113.2012.00657.x)18SrDNA_alnFLYTREEAlignment of dipteran 18S ribosomal RNA gene sequences from the FLYTREE project in fasta format.28SrDNA_alnFLYTREEAlignment of dipteran 28S ribosomal RNA gene sequences from the FLYTREE project in fasta format.AATS_Exon1alnFLYTREEAlignment of dipteran AATS1 gene sequences from the FLYTREE project in fasta format.CAD_noIntrons.alnFLYTREEAlignment of dipteran CAD (= CPSase, rudimentary) gene sequences from the FLYTREE project in fasta format.G6PD_alnFLYTREEAlignment of dipteran G6PD gene sequences from the FLYTREE project in fasta format.GART_alnFLYTREEAlignment of dipteran GART gene sequences from the FLYTREE project in fasta format.PEPCK_alnFLYTREEAlignment of dipteran PEPCK gene sequences from the FLYTREE project in fasta format.PER_NoIntrons_alnFLYTREEAlignment of dipteran period (per) gene sequences from the FLYTREE project in fasta format.PGDintrons_alnFLYTREEAlignment of dipteran PGD gene sequences, with introns included in the alignment,from the FLYTREE project in fasta format.PGDnointrons_alnFLYTREEAlignment of dipteran PGD gene sequences from the FLYTREE project in fasta format.PUG_C1THFsynthase_alnFLYTREEAlignment of dipteran CH1-THF synthase (pug) gene sequences from the FLYTREE project in fasta format.SINA_alnFLYTREEAlignment of dipteran SINA gene sequences from the FLYTREE project in fasta format.SNF_alnFLYTREEAlignment of dipteran sans fille (snf) gene sequences from the FLYTREE project in fasta format.SYX1A_alnFLYTREEAlignment of dipteran SYX1A gene sequences from the FLYTREE project in fasta format.TPI_noIntrons_alnFLYTREEAlignment of dipteran TPI gene sequences from the FLYTREE project in fasta format.mtAtp6-alnFLYTREEAlignment of dipteran mitochondrial ATP6 gene sequences from the FLYTREE project in fasta format.Atp6-alnFLYTREE.fastamtAtp8-alnFLYTREEAlignment of dipteran mitochondrial ATP8 gene sequences from the FLYTREE project in fasta format.Atp8-alnFLYTREE.fastaCox1-alnFLYTREEAlignment of dipteran mitochondrial CO1 gene sequences from the FLYTREE project in fasta format.Cox2-alnFLYTREEAlignment of dipteran mitochondrial COII (cox2) gene sequences from the FLYTREE project in fasta format.Cox3-alnFLYTREEAlignment of dipteran mitochondrial CO-III (Cox3) gene sequences from the FLYTREE project in fasta format.Cytb-alnFLYTREEAlignment of dipteran mitochondrial cyt-b gene sequences from the FLYTREE project in fasta format.Large_rRNA16S-alnFLYTREEAlignment of dipteran mitochondrial 16S ribosomal RNA gene sequences from the FLYTREE project in fasta format.Small_rRNA12S-alnFLYTREEAlignment of dipteran mitochondrial 12S ribosomal RNA gene sequences from the FLYTREE project in fasta format.Nad1-alnFLYTREEAlignment of dipteran mitochondrial NADH1 gene sequences from the FLYTREE project in fasta format.Nad2-alnFLYTREEAlignment of dipteran mitochondrial NADH2 gene sequences from the FLYTREE project in fasta format.Nad3-alnFLYTREEAlignment of dipteran mitochondrial NADH3 gene sequences from the FLYTREE project in fasta format.Nad4-alnFLYTREEAlignment of dipteran mitochondrial NADH4 gene sequences from the FLYTREE project in fasta format.Nad4L-alnFLYTREEAlignment of dipteran mitochondrial NADH4L gene sequences from the FLYTREE project in fasta format.Nad5-alnFLYTREEAlignment of dipteran mitochondrial NADH5 gene sequences from the FLYTREE project in fasta format.Nad6-alnFLYTREEAlignment of dipteran mitochondrial NADH6 gene sequences from the FLYTREE project in fasta format.Small_rRNA12S-alnFLYTREEAlignment of dipteran mitochondrial 12S ribosomal RNA gene sequences from the FLYTREE project in fasta format.TextnamesThis file resolves the identity of taxon name codes used in the phylogenetic data sets below. You can also find information about all of these name codes at : http://www.inhs.uiuc.edu/research/flytreephp/flytree/index.phpFLY dataset annotationsthis is an EXCEL file that gives annotations by position numbers for the combined datasets (see below). Note.. the mitochondrial genes are just annotated as 'mito'.28S.aln5.22.09This is the uncut 28S rDNA file for T2+T1, with annotations about included regions. Ribosomal genes are complex to align across deep divergences (240 million years for flies). That means that divergent domains (expansion regions are excluded in most phylogenetic analyses of this gene.), so the annotations in this file (at the bottom) correspond to positions that are cut-out (excluded) in our phylogenetic analysis. If you sequenced 28S this will allow you to fit your sequence into our alignment without confusion about missing pieces. Brachyceran or only Schizophoran sequences were separated from lower Diptera for some regions in this alignment, in order to include alignable regions within these sections for just higher flies. The cut version of this file is FLY2.28s.nex (not annotated).fly2.28s28S rDNA alignment for phylogenetic analysis with ambiguous alignment regions The cut version of 28s.aln.5.22.09.nex