NCBI BioProject PRJNA280774

Raw sequence reads for all 144 individuals are available at NCBI BioProject Accession: PRJNA280774 ID: 280774

Sailfin_Molly_total_Hapmap

Initial unfiltered SNP (18,255 SNP) for 144 individual Sailfin Mollies (Poecilia latipinna) were collected from five populations in the spring of 2014. Of the 144 individual sequenced, 122 (thirty per site) were had sufficient sequences and depth of reads for analyses (see filter data set

SF_955_hapmap

Filter SNP (955 SNP) for 122 collected from five populations in the spring of 2014. These 955 SNP in 122 individual were used for all analyze because they had sufficient sequences and depth of reads

Concentrations of Cy3 and Cy5 dye labeled RNA used for hybridization.

<p>Concentrations of Cy3 and Cy5 dye labeled RNA used for hybridization.</p

Number of genes and corresponding R² for various ranges of RNA concentrations.

<p>Number of genes and corresponding R² for various ranges of RNA concentrations.</p

Individuals sampled over time.

<p>Heat map for one individual (00) sampled 4 times over a total of 6 weeks. Numbers above the heat map are time points (0, 2, 4 & 6 weeks) and the “P” is for p-value (−log₁₀). P-values are from the ANOVA that tested for differences among separate blood isolations within an individual (4 isolations and 8 replicates per isolation). For gene expression, red is greater and green is lower expression than the mean expression for each gene. Table provides number of significant genes and percent (rounded up) out of the total of 304. Color bar gives fold difference for log₂ gene expression (e.g., 2 = 4×) and negative log₁₀ p-value (e.g., 2 = p-value of 0.01).</p

Gene expression for Single Blood isolate.

<p>Heat map for single blood isolate that was divided into four. RNA was purified, labeled and hybridized separately for each sample. Red is greater and green is less than the average gene specific fluorescence. First column (P) is the p-value from a one-way ANOVA. Only 6 genes (2.3%) out of 252 are significant at a critical p-value of 0.01. P-values (−log₁₀) shown in the heat map are from an ANOVA for significant differences among samples using the 8 replicates for each separate RNA isolation. Color bar gives fold difference for log₂ gene expression (e.g., 2 = 4×) and negative log₁₀ p-value (e.g., 2 = p-value of 0.01).</p

384 Array Metabolic Pathways.

<p>384 Array Metabolic Pathways.</p

Filtered Hapmap

Hapmap of SNPs after initial filtering. SNPs have been filtered to include 30% of all taxa, 80% of all sites. Individuals are identified as: MB - Mantoloking Basin, MC - Mantoloking Creek, MP - Mantoloking Pond, RB - Rutgers Basin, RC - Rutgers Creek, RP - Rutgers Pond, SB - Stone Harbor Basin, SC - Stone Harbor Creek, SP - Stone Harbor Pon

Final Hapmap

Hapmap of SNPs used in final analyses. SNPs have been filtered to include 30% of all taxa, 80% of all sites, and a 5% minimum allele frequency. SNPs in significant LD (p < 0.01) have also been removed. Individuals are identified as: MB - Mantoloking Basin, MC - Mantoloking Creek, MP - Mantoloking Pond, RB - Rutgers Basin, RC - Rutgers Creek, RP - Rutgers Pond, SB - Stone Harbor Basin, SC - Stone Harbor Creek, SP - Stone Harbor Pon