Raw Data Files

Genepop files for simulated and empirical dataset

A Comparison of Neutral and Immune Genetic Variation in Atlantic Salmon, <i>Salmo salar</i> L. in Chilean Aquaculture Facilities

<div><p>Genetic diversity was assessed in samples of cultured Atlantic salmon, <i>Salmo salar</i> L., obtained from facilities in Chile between 2005 and 2010, a period of time during which the infectious pathogens Infectious Salmon Anemia (ISA) virus, <i>Caligus rogercresseyi</i> (sea lice), and <i>Piscirickettsia salmonis</i> (salmon rickettsial syndrome) were common. Two panels of microsatellite markers were utilized: one with microsatellites with no known gene associations (neutral) and one featuring microsatellites linked to putative immune-related genes (immune-related). Allelic richness and gene diversity across samples were significantly greater in neutral loci as compared to immune-related loci. Both diversity measures were homogeneous among samples for immune-related loci and heterogeneous among samples for neutral loci. Immune-related loci were identified as <i>F_ST</i> outliers in pairwise comparisons of samples at a 10-fold higher frequency than neutral loci. These results indicate that neutral and immune-related portions of the Atlantic salmon genome may have differed in response to the gauntlet of pathogens and that monitoring of specific, well characterized immune-related loci as well as neutral loci in cultured species could be useful when disease control and prevention is a goal.</p></div

MasterMSATmegacephalusOrderedLoci_11B

Microsatellite data for Microdipodops megacephlaus - 11 loci, 4 population

MasterMSATpallidusOrderLoci_11B

Microdipodops pallidus raw microsatellite data - 10 loci, 2 populations

Immune microsatellites that were significant positive outliers, at α = 0.01, in pairwise comparisons of samples.

<p>Coding genes, and their putative function, to which immune-related markers are potentially linked are indicated.</p

Allele frequency distributions (bars, left axis) and unbiased gene diversity (triangles, right axis) for two immune loci that were significant positive outliers and for two neutral loci.

<p>Allele frequency distributions (bars, left axis) and unbiased gene diversity (triangles, right axis) for two immune loci that were significant positive outliers and for two neutral loci.</p

Panels of neutral loci and immune-related loci used to screen samples of Atlantic salmon, <i>Salmo salar</i>, from the salmon industry in Chile.

a<p>Motif indicates repeat motif.</p>b<p>Range refers to alleles thus far uncovered (may include the 21 bp 50-tail-sequence).</p>c<p>T_A is optimized annealing temperature. For loci amplified with the tail protocol, a step-down protocol was used so annealing temperature is not applicable (NA).</p>d<p>Label refers to dye (6-Fam, Ned, or Hex) used to label forward primer. Tail refers to loci that were amplified using the tail protocol.</p>e<p>Primer sequences are forward (F and reverse (R).</p>f<p>Citations describing putative function.</p

Comparisons of mean allelic richness ± standard error for neutral loci (a) and immune loci (b) for samples taken during the epizootic (square) and sample taken during recovery (triangle).

<p>Locus names (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099358#pone-0099358-t001" target="_blank">Table 1</a>) are abbreviated. Figure created using R v.2.1.3.1 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099358#pone.0099358-R1" target="_blank">[57]</a>, using dotplots.errors <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099358#pone.0099358-Kozak1" target="_blank">[58]</a>.</p

Full data, finetooth sharks, haplotypes

Mitochondrial DNA haplotypes observed in the stud

SampleCollectionInfo

Spreadsheet with Sample_Name, Collection Date, Location Code, Locality, Sex, Weight (kg), and Total Length (cm) for each individual used in the study