DOI: 10.5061/dryad.rq3sp
title: Data from: Comparative transcriptomics support evolutionary convergence of diapause responses across Insecta

description: Diapause is a common phenotype that is broadly phylogenetically dispersed
 across Insecta and appears to have multiple evolutionary origins.
 Nevertheless, there are clear commonalities in diapause regulation across
 insect taxa. In the present study, we report a meta-analysis of diapause
 whole transcriptomic data sets from 11 different insect species that
 addresses three questions: (i) how similar are whole-transcriptome
 diapause responses across species within and across different diapause
 life-cycle stages; (ii) do the most closely-related species demonstrate
 the most similar diapause responses within and across diapause life-cycle
 stages (the existence of phylogenetic signal); and (iii) is there a core
 set of regulatory genes that universally associate with insect diapause at
 the transcript level? The included species are mostly Dipterans (n = 9),
 plus one species each from Lepidoptera and Hymenoptera. The group includes
 multiple species that enter diapause as either larvae, pupae or adults. We
 establish a set of 4791 orthologous transcript sequences with expression
 data acquired from published studies of diapause transcriptomes. We find
 no support for phylogenetic signal. Transcriptomic responses of
 nondipterans clustered within rather than outside of Dipteran responses.
 However, expression profiles do tend to cluster with the diapause stage of
 developmental arrest, although this pattern is only moderately supported.
 We identify a statistically significant set of 542 orthologues (11% of all
 orthologues) that are commonly differentially regulated during diapause
 across all included species. From this core set, we identify candidate
 genes participating in circadian rhythmicity, insulin signalling and Wnt
 signalling, which are pathways previously associated with insect diapause
 development. Clustering relationships among species are most consistent
 with evolutionary convergence of the shared transcriptomic response,
 although we are unable to determine whether this reflects convergence of
 the diapause initiation, maintenance or termination phases.
description: Species_Orthologs.tar.gzArchive containing files for target species-to-Drosophila melanogaster pairwise ortholog models. Each file maps ids from a transcriptome assembly to D. melanogaster flyabase IDs. Methods for orthology assignment and references for each transcriptome assembly available in Ragland and Keep, and in the 'MetaData' data file also contained in this archive.MetaDataDryadMeta data for transcriptomic data sets used in the comparative analysis to generate gene expression matrix 'UnFilteredExpressionAllOrthos' also included in this archive.UnFilteredExpressionAllOrthos.txt.gzMatrix of diapause expression data across included insect species. Each row of expression data is associated with a single gene orthologous across all species, designated with the flyabase id for the gene in Drosophila melanogaster. Each data value is a log2 fold change: log2(diapause) - log2(non-diapause) for each included species. See Ragland and Keep for methods. Species codes are described in the first metadata line of the file.