DOI: 10.5061/dryad.3gr233c
title: Data from: Transcriptomic analysis of skin pigmentation variation in the Virginia opossum (Didelphis virginiana).

description: Skin and coat pigmentation are two of the best-studied examples of traits
 under natural selection given their quantifiable fitness interactions with
 the environment (e.g. camouflage) and signaling with other organisms (e.g.
 warning coloration). Previous morphological studies have found that skin
 pigmentation variation in the Virginia opossum (Didelphis virginiana) is
 associated with variation in precipitation and temperatures across its
 distribution range following Gloger’s rule (lighter pigmentation in
 temperate environments). To investigate the molecular mechanism associated
 with skin pigmentation variation, we used RNA-Seq and quantified gene
 expression of wild opossums from tropical and temperate populations. Using
 differential expression analysis and a coexpression network approach, we
 found that expression variation in genes with melanocytic and immune
 functions are significantly associated with the degree of skin
 pigmentation variation and may be underlying this phenotypic difference.
 We also found evidence suggesting that the Wnt/β-catenin signaling pathway
 might be regulating the depigmentation observed in temperate populations.
 Based on our study results, we present several alternative hypotheses that
 may explain Gloger’s rule pattern of skin pigmentation variation in
 opossum, including changes in pathogen diversity supporting a pathogen
 resistant hypothesis, thermal stress associated with temperate
 environments, pleiotropic and epistatic interactions between melanocytic
 and immune genes.
description: PCA input. cqn
 normalized and log2 transformed countsTab-delimited text file
 containing the cqn normalized and log2 transformed gene expression counts
 (using the conditional quantile normalization method) for 14,289 genes in
 13 virginia opossum individuals. This normalized-transformed counts were
 used as input for the principal component analysis
 (PCA).Nigenda-Morales_normalized_transfomed_counts_PCA_input.txtPCA resultsTab-delimited text file containing the results of the principal component analysis (PCA). It shows the loadings of 13 principal components (PC) for 14,289 genes. The genes are ordered by the loadings of PC1 from most negative to most positive.Nigenda-Morales_PCA_results.txtWGCNA input. Phenotypic traits of Virginia opossum individualsTab-delimited text file with phenotypic trait measurements fro 13 Virginia opossum specimens that was used as input for the weighted gene coexpression network analysis (WGCNA). The traits that were used in the WGCNA analysis were PTP (proportion of tail pigmentation), PEP (proportion of ear pigmentation) and PTO (proportion of toe pigmentation).Nigenda-Morales_Opossum_traits_WGCNAinput.txtRaw sequenceing data, raw expression counts per gene after filtering, normalized counts and metadataThis links to the Gene Expression Omnibus (GEO) series accession number GSE112562, which contains the following data files that can be divided in 4 sections: 1) 26 raw sequencing data files (gzipped fastq files; two files per individual due to the pair-end sequencing strategy used), 2) a tab-delimited text file containing raw expression counts for 14,289 genes (HTSeq output) after filtering for low count numbers and muscle genes removal, 3) a tab-delimited text file containing the cqn normalized and log2 transformed counts for the 14,289 genes, and 4) associated metadata (excel file) for 13 Virginia opossum individuals with pigmented and depigmented phenotypesWGCNA input. Normalized-transformed counts for the differentially expressed genesTab-delimited text file containing the cqn normalized and log2 transformed counts (using the conditional quantile normalization method) for the 1,186 differentially expressed genes between pigmented and depigmented opossums. This normalized-transformed counts were used as input for the weighted gene coexpression network analysis (WGCNA).Nigenda-Morales_DEgenes_normalized-transformed_WGCNAinput.txtDifferential expression results and qvalue for multiple testing correctionTab-delimited text file containing the results of the differential gene expression test (limma-voom results) between pigmented and depigmented Virginia opossums. To account for multiple hypothesis testing the false discovery rate (FDR) method was used as implemented in the qvalue package in R. Genes were considered differentially expressed if they had a qvalue &lt; 0.1. In this file the genes are order by qvalue from lower to higher.Nigenda-Morales_Differential_expression_results_qvalue.txt