Additional file 1 of Seascape genomics of common dolphins (Delphinus delphis) reveals adaptive diversity linked to regional and local oceanography
Creators: name: Barceló, Andrea
name: Sandoval-Castillo, Jonathan
name: Brauer, Chris J.
name: Bilgmann, Kerstin
name: Parra, Guido J.
name: Beheregaray, Luciano B.
name: Möller, Luciana M.
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Ecology

description: Additional file 1: Table S1. Filtering steps and number of SNPs retained after each step for common dolphins (Delphinus delphis) in southern Australia. FDR: false discovery rate. Table S2. Summary of environmental variables included in the genotype-environment association multivariable analyses, datasets were retrieved from BioOracle. Table S3. (A) Significance of the RDA and the proportion explained by each component of the full model selection. (B) Significance of the environmental variables selected, with an overall significance of the model and variables at p = 0.0001. Table S4. Pairwise FST values between sites based on putatively adaptive (this study) and neutral (1) datasets for southern Australian common dolphins (Delphinus delphis). Upper right, neutral FST values, and lower left adaptive FST values, with their significance of the p-values by the B-Y method corrected represented by ***0.0001, **0.001. Acronyms for sites as in Fig. 1. Table S5. Significance of Gene Ontology (GO) terms for southern Australian common dolphins (Delphinus delphis), comparing the full dataset with the putative candidate loci by Fisher’s exact test. Biological Process (BP), Molecular Function (MF), Cellular Component (CC). Table S6. Function of the candidate genes found in exonic regions, which were over enriched by the Gene Ontology analyses, for the 747 putatively adaptive SNPs discovered by the RDA of southern Australian common dolphins (Delphinus delphis). Figure S1. Multicollinearity between the five environmental variables used for the RDA. Salinity maximum (BO2_salinitymax_ss), primary productivity maximum (BO2_ppmax_ss), sea surface temperature minimum (BO_sstmin), current velocity maximum (BO2_curvelmax_ss) and current velocity range (BO2_curvelrange_ss). Numbers in the upper right matrix are the correlation values of each comparison; the smaller the number gets, the closest to zero the correlation between the variables is. Variables were standardised from 0-1. Figure S2. Akaike Information Criterion (AIC) used to determine the best-supported number of clusters in the PCA, based on the putative adaptive dataset of southern Australian common dolphins (Delphinus delphis). Figure S3. Population genomic structure analysis using Admixture based on the putatively adaptive SNPs for southern Australian common dolphins (Delphinus delphis) (labelled by sampling site and individual). K represents the number of populations tested (A to F), in which K4* and K5* are both correctly assigned as they are the most supported and highly likely number of local populations suggested by the analyses. Acronyms for sites as in Fig. 1. Figure S4. Principal Component Analysis (PCA) based on 747 candidate adaptive loci for southern Australian common dolphins (Delphinus delphis). (A) Explanatory axes PC1 vs PC2. (B) Explanatory axes PC1 vs PC3. (C) Explanatory axes PC2 vs PC3. Acronyms for sites as in Fig. 1. Figure S5. Heatmap of pairwise FST values between sites based on the adaptive (this study) and neutral (1) SNP datasets for southern Australian common dolphins (Delphinus delphis). Upper right, neutral dataset, and lower left, adaptive dataset. Acronyms for sites as in Fig. 1. Figure S6. Allele frequency changes for the candidate gene variants found in exonic regions of common dolphins (Delphinus delphis) across sampling sites in southern Australia. (A) NR2F6/NR2F2 was associated with maximum salinity, (B) ZFP57, with primary productivity maximum, and (C) MAN2B1, with primary productivity maximum. Figure S7. Minor allele frequencies of 26 SNPs selected by a gene enrichment test, with variants in coding or non-coding regions.