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Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee

Citation

Pimsler, Meaghan et al. (2020), Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee, Dryad, Dataset, https://doi.org/10.5061/dryad.tmpg4f4wx

Abstract

Global temperature changes have emphasized the need to understand how species adapt to thermal stress across their ranges. Genetic mechanisms may contribute to variation in thermal tolerance, providing evidence for how organisms adapt to local environments. We determine physiological thermal limits and characterize genome-wide transcriptional changes at these limits in bumble bees using laboratory-reared Bombus vosnesenskii workers. We analyze bees reared from latitudinal (35.7–45.7°N) and altitudinal (7–2154 m) extremes of the species’ range to correlate thermal tolerance and gene expression among populations from different climates. We find that critical thermal minima (CTMIN) exhibit strong associations with local minimums at the location of queen origin, while critical thermal maximum (CTMAX) was invariant among populations. Concordant patterns are apparent in gene expression data, with regional differentiation following cold exposure, and expression shifts invariant among populations under high temperatures. Furthermore, we identify several modules of co-expressed genes that tightly correlate with critical thermal limits and temperature at the region of origin. Our results reveal that local adaptation in thermal limits and gene expression may facilitate cold tolerance across a species range, whereas high temperature responses are likely constrained, both of which may have implications for climate change responses of bumble bees.

Methods

The datasets include read-count data generated by processing the raw poly-A amplified directional 50 bp paired-end RNAseq reads (see SRA accession below) using TrimGalore v0.4.2, aligning them to the Bombus impatiens genome v2.0 (BIMP2.0) with TopHat v2.1.1, and counting read alignments to the transcripts on a gene_name basis with HTSeq v0.9.1. 

Also included are: 

  • Bombus impatiens genome v2.0 (BIMP2.0) and Drosophila melanogaster (Release_6_plus_ISO1_MT) genomic.gff and protein.faa files for reciprocal best blast hit annotation.
  • WorldClim data relevant to the samples
  • Critical thermal test results
  • Alignment results
  • Pheontype tables for samples
  • a D. melanogaster GO file for use in R
  • Filtering files
  • Analytical R scripts

Usage Notes

To repeat the analyses in the paper, please go to the 'Scripts' folder. Please run the following scripts in R in this order.

  1. In a new session: WCGNA_complete_script.R
  2. Close session (all relevant results will be saved)
  3. In a new session: Limma_BlockedAnalysis_complete_script.R
  4. In the same session: DGE_WCGNA.comparison.R

Funding

National Science Foundation, Award: DEB-1457645/1457659

National Science Foundation, Award: EF-1921585