DOI: 10.5061/dryad.p85m5
title: Data from: Population transcriptomics in Daphnia: the role of thermal selection

description: The complex interplay of forces influencing genetic divergence among
 populations complicates the discovery of the genetic basis underlying
 local adaptation. Here, we utilized for the first time a combined reverse
 ecology and population transcriptomic approach to assess the contribution
 of thermal selection to population differentiation, thereby considering
 transcriptome-wide variation in both gene expression profiles and DNA
 sequences. We compared transcriptomes among four Daphnia galeata
 populations and identified transcripts potentially responding to local
 thermal selection based on an extensive literature search for candidate
 genes possibly under thermal selection in arthropods. Overrepresentation
 of temperature-relevant candidate genes among transcripts strongly
 contributing to sequence divergence among two populations indicates that
 local thermal selection acted on the coding sequence level. We identified
 a large number of transcripts which may contribute to local thermal
 adaptation based on outlier tests and distinctive expression profiles.
 However, among these, temperature-relevant candidate genes were not
 overrepresented compared to the global gene set; suggesting that thermal
 selection played a minor role in divergence among Daphnia populations.
 Interestingly, although the majority of genes contributing strongly to
 sequence divergence did not contribute strongly to divergence at the
 expression level and vice versa, the affected gene functions were largely
 consistent between the two data sets. This suggests that genetic and
 regulatory variation constitute alternative routes for responses to
 natural selection. Our combined utilization of a population
 transcriptomics approach and literature-based identification of
 ecologically informative candidate genes represents a useful and powerful
 methodology with a wide range of applications in evolutionary biology.
description: SI_1Supplementary file 1
 Tables S1-S8 accompanying the publication Population transcriptomics in
 Daphnia: the role of thermal selection, Maike Herrmann, Suda Parimala
 Ravindran, Klaus Schwenk and Mathilde Cordellier. For the Table of
 Contents please refer to the README file.SI_2Supplementary file 2
 Tables S9-S11 accompanying the publication Population transcriptomics in
 Daphnia: the role of thermal selection, Maike Herrmann, Suda Parimala
 Ravindran, Klaus Schwenk and Mathilde Cordellier. For the Table of
 Contents please refer to the README file.SI_3Supplementary file 3
 Tables S12-S19 accompanying the publication Population transcriptomics in
 Daphnia: the role of thermal selection, Maike Herrmann, Suda Parimala
 Ravindran, Klaus Schwenk and Mathilde Cordellier. For the Table of
 Contents please refer to the README file.SI_4Supplementary file 4
 accompanying the publication Population transcriptomics in Daphnia: the
 role of thermal selection, Maike Herrmann, Suda Parimala Ravindran, Klaus
 Schwenk and Mathilde Cordellier. Amino acid sequence translations of D.
 galeata transcripts and the reference candidate genesFig_S1Supplementary file 5
 Figure S1 accompanying the publication Population transcriptomics in
 Daphnia: the role of thermal selection, Maike Herrmann, Suda Parimala
 Ravindran, Klaus Schwenk and Mathilde Cordellier. Sample to sample
 distances heat map created with DESeq2, based on read counts after
 regularized-logarithm transformation. Each row/column corresponds to a
 single biological replicate.