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dc.contributor.author Wiegmann, Brian M.
dc.contributor.author Trautwein, Michelle D.
dc.contributor.author Winkler, Isaac S.
dc.contributor.author Barr, Norman B.
dc.contributor.author Kim, Jung-Wook
dc.contributor.author Lambkin, Christine
dc.contributor.author Bertone, Matthew A.
dc.contributor.author Cassel, Brian K.
dc.contributor.author Bayless, Keith M.
dc.contributor.author Heimberg, Alysha M.
dc.contributor.author Wheeler, Benjamin M.
dc.contributor.author Peterson, Kevin J.
dc.contributor.author Pape, Thomas
dc.contributor.author Sinclair, Bradley J.
dc.contributor.author Skevington, Jeffrey H.
dc.contributor.author Blagoderov, Vladimir
dc.contributor.author Caravas, Jason
dc.contributor.author Kutty, Sujatha Narayanan
dc.contributor.author Schmidt-Ott, Urs
dc.contributor.author Kampmeier, Gail E.
dc.contributor.author Thompson, F. Christian
dc.contributor.author Grimaldi, David A.
dc.contributor.author Beckenbach, Andrew T.
dc.contributor.author Courtney, Gregory W.
dc.contributor.author Friedrich, Markus
dc.contributor.author Meier, Rudolf
dc.contributor.author Yeates, David K.
dc.date.accessioned 2012-11-21T20:40:18Z
dc.date.available 2012-11-21T20:40:18Z
dc.date.issued 2011-03-14
dc.identifier doi:10.5061/dryad.21nf3
dc.identifier.citation Wiegmann BM, Trautwein MD, Winkler IS, Barr NB, Kim J-W, Lambkin C, Bertone MA, Cassel BK, Bayless KM, Heimberg AM, Wheeler BM, Peterson KJ, Pape T, Sinclair BJ, Skevington JH, Blagoderov V, Caravas J, Kutty SN, Schmidt-Ott U, Kampmeier GE, Thompson FC, Grimaldi DA, Beckenbach AT, Courtney GW, Friedrich M, Meier R, Yeates DK (2011) Episodic radiations in the fly tree of life. Proceedings of the National Academy of Sciences of the United States of America 108(14): 5690-5695.
dc.identifier.uri http://hdl.handle.net/10255/dryad.43593
dc.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.
dc.relation.ispartofseries 108;14;2011
dc.relation.haspart doi:10.5061/dryad.21nf3/1
dc.relation.haspart doi:10.5061/dryad.21nf3/2
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dc.relation.haspart doi:10.5061/dryad.21nf3/37
dc.relation.isreferencedby doi:10.1073/pnas.1012675108
dc.relation.isreferencedby PMID:21402926
dc.subject molecular systematics
dc.subject phylogenetics
dc.subject adaptive radiation
dc.title Data from: Episodic radiations in the fly tree of life
dc.type Article *
dwc.ScientificName Insecta
dwc.ScientificName Diptera
dc.contributor.correspondingAuthor Wiegmann, Brian M.
prism.publicationName Proceedings of the National Academy of Sciences of the United States of America

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Title FLYTREEmitoGeneAln
Downloaded 38 times
Description Nucleotide 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)
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Title FLYTREENuclearGenes_ALN
Downloaded 25 times
Description Nucleotide 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)
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Title 18SrDNA_alnFLYTREE
Downloaded 42 times
Description Alignment of dipteran 18S ribosomal RNA gene sequences from the FLYTREE project in fasta format.
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Title 28SrDNA_alnFLYTREE
Downloaded 43 times
Description Alignment of dipteran 28S ribosomal RNA gene sequences from the FLYTREE project in fasta format.
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Title AATS_Exon1alnFLYTREE
Downloaded 38 times
Description Alignment of dipteran AATS1 gene sequences from the FLYTREE project in fasta format.
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Title CAD_noIntrons.alnFLYTREE
Downloaded 34 times
Description Alignment of dipteran CAD (= CPSase, rudimentary) gene sequences from the FLYTREE project in fasta format.
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Title G6PD_alnFLYTREE
Downloaded 40 times
Description Alignment of dipteran G6PD gene sequences from the FLYTREE project in fasta format.
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Title GART_alnFLYTREE
Downloaded 41 times
Description Alignment of dipteran GART gene sequences from the FLYTREE project in fasta format.
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Title PEPCK_alnFLYTREE
Downloaded 33 times
Description Alignment of dipteran PEPCK gene sequences from the FLYTREE project in fasta format.
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Title PER_NoIntrons_alnFLYTREE
Downloaded 40 times
Description Alignment of dipteran period (per) gene sequences from the FLYTREE project in fasta format.
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Title PGDintrons_alnFLYTREE
Downloaded 32 times
Description Alignment of dipteran PGD gene sequences, with introns included in the alignment,from the FLYTREE project in fasta format.
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Title PGDnointrons_alnFLYTREE
Downloaded 33 times
Description Alignment of dipteran PGD gene sequences from the FLYTREE project in fasta format.
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Title PUG_C1THFsynthase_alnFLYTREE
Downloaded 37 times
Description Alignment of dipteran CH1-THF synthase (pug) gene sequences from the FLYTREE project in fasta format.
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Title SINA_alnFLYTREE
Downloaded 38 times
Description Alignment of dipteran SINA gene sequences from the FLYTREE project in fasta format.
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Title SNF_alnFLYTREE
Downloaded 34 times
Description Alignment of dipteran sans fille (snf) gene sequences from the FLYTREE project in fasta format.
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Title SYX1A_alnFLYTREE
Downloaded 39 times
Description Alignment of dipteran SYX1A gene sequences from the FLYTREE project in fasta format.
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Title TPI_noIntrons_alnFLYTREE
Downloaded 35 times
Description Alignment of dipteran TPI gene sequences from the FLYTREE project in fasta format.
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Title mtAtp6-alnFLYTREE
Downloaded 37 times
Description Alignment of dipteran mitochondrial ATP6 gene sequences from the FLYTREE project in fasta format.
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Title mtAtp8-alnFLYTREE
Downloaded 39 times
Description Alignment of dipteran mitochondrial ATP8 gene sequences from the FLYTREE project in fasta format.
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Title Cox1-alnFLYTREE
Downloaded 33 times
Description Alignment of dipteran mitochondrial CO1 gene sequences from the FLYTREE project in fasta format.
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Title Cox2-alnFLYTREE
Downloaded 44 times
Description Alignment of dipteran mitochondrial COII (cox2) gene sequences from the FLYTREE project in fasta format.
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Title Cox3-alnFLYTREE
Downloaded 43 times
Description Alignment of dipteran mitochondrial CO-III (Cox3) gene sequences from the FLYTREE project in fasta format.
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Title Cytb-alnFLYTREE
Downloaded 41 times
Description Alignment of dipteran mitochondrial cyt-b gene sequences from the FLYTREE project in fasta format.
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Title Large_rRNA16S-alnFLYTREE
Downloaded 39 times
Description Alignment of dipteran mitochondrial 16S ribosomal RNA gene sequences from the FLYTREE project in fasta format.
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Title Small_rRNA12S-alnFLYTREE
Downloaded 33 times
Description Alignment of dipteran mitochondrial 12S ribosomal RNA gene sequences from the FLYTREE project in fasta format.
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Title Nad1-alnFLYTREE
Downloaded 41 times
Description Alignment of dipteran mitochondrial NADH1 gene sequences from the FLYTREE project in fasta format.
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Title Nad2-alnFLYTREE
Downloaded 40 times
Description Alignment of dipteran mitochondrial NADH2 gene sequences from the FLYTREE project in fasta format.
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Title Nad3-alnFLYTREE
Downloaded 32 times
Description Alignment of dipteran mitochondrial NADH3 gene sequences from the FLYTREE project in fasta format.
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Title Nad4-alnFLYTREE
Downloaded 41 times
Description Alignment of dipteran mitochondrial NADH4 gene sequences from the FLYTREE project in fasta format.
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Title Nad4L-alnFLYTREE
Downloaded 37 times
Description Alignment of dipteran mitochondrial NADH4L gene sequences from the FLYTREE project in fasta format.
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Title Nad5-alnFLYTREE
Downloaded 35 times
Description Alignment of dipteran mitochondrial NADH5 gene sequences from the FLYTREE project in fasta format.
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Title Nad6-alnFLYTREE
Downloaded 39 times
Description Alignment of dipteran mitochondrial NADH6 gene sequences from the FLYTREE project in fasta format.
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Title Small_rRNA12S-alnFLYTREE
Downloaded 37 times
Description Alignment of dipteran mitochondrial 12S ribosomal RNA gene sequences from the FLYTREE project in fasta format.
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Title Textnames
Downloaded 63 times
Description This 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.php
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Title FLY dataset annotations
Downloaded 36 times
Description this 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'.
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Title 28S.aln5.22.09
Downloaded 55 times
Description This 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).
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Title fly2.28s
Downloaded 41 times
Description 28S rDNA alignment for phylogenetic analysis with ambiguous alignment regions The cut version of 28s.aln.5.22.09.nex
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