DOI: 10.5061/dryad.6p5t3
title: Data from: Divergent transcriptional responses to low temperature among populations of alpine and lowland species of New Zealand stick insects (Micrarchus)

description: In widespread and genetically-structured populations, temperature
 variation may lead to among-population differentiation of thermal biology.
 The New Zealand stick insect genus Micrarchus contains four species that
 inhabit different thermal environments, two of which are geographically
 widespread. RNA-Seq and quantitative PCR were used to investigate the
 transcriptional responses to cold-shock among lowland and alpine species
 to identify cold-responsive transcripts that differ between the species,
 and to determine if there is intraspecific geographic variation in gene
 expression. We also used mitochondrial DNA, nuclear 28S ribosomal DNA and
 transcriptome-wide SNPs to determine phylogeographic structure and the
 potential for differences in genetic backgrounds to contribute to
 variation in gene expression. RNA-Seq identified 2,160 unigenes that were
 differentially expressed as a result of low temperature exposure across
 three populations from two species (M. hystriculeus and M. nov. sp. 2),
 with a majority (68% ± 20%) being population-specific. This extensive
 geographic variation is consistent across years and is likely a result of
 background genetic differences among populations caused by genetic drift
 and possibly local adaptation. Responses to cold-shock shared among alpine
 M. nov. sp. 2 populations included the enrichment of cuticular
 structure-associated transcripts, suggesting that cuticle modification may
 have accompanied colonisation of low-temperature alpine environments and
 the development of a more cold-hardy phenotype.
description: Micrarchus nov. sp. 2
 from Mt. Arthur annotated transcriptome assemblyTrinity assembled
 illumina de novo trasncriptome for Micrarchus nov. sp. 2 from Mt. Arthur
 annotated using BLASTx against NCBI swissprot with e-value cutoff
 e-10Arthur_Annotated.fastaMicrarchus nov. sp. 2 from Sewell Peak annotated transcriptome assemblyTrinity assembled illumina de novo trasncriptome for Micrarchus nov. sp. 2 from Sewell Peak annotated using BLASTx against NCBI swissprot with e-value cutoff e-10Sewell_Annotated.fastaMicrarchus hystriculeus from paengaroa annotated transcriptome assemblyTrinity assembled illumina de novo trasncriptome for Micrarchus hystriculeus from paengaroa annotated using BLASTx against NCBI swissprot with e-value cutoff e-10Paengaroa_Annotated.fastaDifferential expression results for Micrarchus stick insectsDifferential expression results for Micrarhcus stick insects using edgeR, DESeq and baySeqMicrarchus_Differential_Expression_Results.xlsxMicrarchus raw qPCR dataraw qPCR dataMicrarchus_raw_qPCR_data.xlsxMicrarchus SNP dataMicrarchus SNP data used to determine population structureMicrarchus_SNP_data.vcf28S alignment28S alignment, for detail information for each sample or which sample belongs to which haplotype, please see supplementary information for the manuscript28S.nexmtDNA (COI/COII) alignmentmtDNA(COI/COII) alignment, for detail information for each sample or which sample belongs to which haplotype, please see supplementary information for the manuscriptCO.nex28S MrBayes tree file28S MrBayes tree file, for detail information for each sample or which sample belongs to which haplotype and parameters used to construct th tree please see the manuscript and supplementary information28S_Bayes.tremtDNA (COI/COII) MrBayes tree filemtDNA (COI/COII) MrBayes tree file, for detail information for each sample or which sample belongs to which haplotype and parameters used to construct th tree please see the manuscript and supplementary informationmtDNA_Bayes.tre