Thielsch et al. MER Discrimination of hybrid classes in Daphnia

Zipped archive contains text files including genotyping data, locality information, infiles for NewHybrids, Structure, Genetix, and Micro-Checker (xls) as well as an information file about the data packag

Genototypes of C vestalis females at 98 SNPs

SNP genotypes of 139 Cotesia vestalis females collected in Western Taiwan at 98 polymorphic SNP

Cotesia vestalis SNP information and sequences

From our list of putative SNPs across the C. vestalis genome, we selected 100 SNPs for genotyping assay development. We first selected the 200 largest scaffolds; they varied in length from 17-58Kb and contained a total of 7,878 SNPs. We then removed SNPs with a minor allele frequency (MAF) <0.2, SNPs that had another SNP within 50 bp up- or downstream, and SNPs with more than 2 alleles. The remaining SNPs were binned in MAF bins of 0.2-0.3 (1,908 SNPs), 0.3-0.4 (1,605 SNPs) and 0.4-0.5 (1,156 SNPs). Per MAF bin, SNPs were ranked by SNP quality score. We then selected the SNPs with the highest quality scores, picking 20 SNPs with a MAF between 0.2-0.3 and 40 each with a MAF between 0.3-0.4 and 0.4-0.5, all on different scaffolds. All selected SNPs had a quality score of more than 200 (based on SAMTOOLS), and an average read depth of 61. High-throughput genotyping assays based on allele-specific forward primers were developed for these 100 SNP sequences at KBioscience (now LGC Genomics, Hoddesdon, U.K.)

Putative SNPs discovered in genome of Cotesia vestalis

Individual paired-end reads were aligned against the artificial Cotesia vestalis reference genome obtained from the de novo genome assembly using BWA. The resulting BAM file was then used for the identification of putative SNPs using SAMTOOLS and varFilter from the samtools.pl utility. We only considered nucleotide substitutions and ignored small indels. SNPs were filtered that had a mapping quality higher than 20, a minimum read depth of 3 and a maximum read depth of 90 (3x the average read depth, a strategy to avoid orthologous SNPs, e.g. in multi copy genes

Detailed results of the genetic admixture for region EG. See Fig. 5 for details.

<p>Detailed results of the genetic admixture for region EG. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097619#pone-0097619-g005" target="_blank">Fig. 5</a> for details.</p

Detailed results of the genetic admixture for region BB. See Fig. 5 for details.

<p>Detailed results of the genetic admixture for region BB. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097619#pone-0097619-g005" target="_blank">Fig. 5</a> for details.</p

Detailed results of the genetic admixture for the study regions HE.

<p>Every bar symbolises one individual in the investigated areas (a). Colours indicate Structure population assignments. We also provide results of population assignments with DAPC (b), Structure (c) and NewHybrids (d). Shades of grey indicate assignment to one of the admixed hybrid classes, from light to dark grey: F₁ hybrid, F₂ hybrid, backcross to P₁, and backcross to P₂. Coloured dots show individual assignments to CR haplotypes (e) (green circle = <i>C. f. albicus</i> a₁, blue square = <i>C. f. galliae</i> g, red triangle = <i>C. f. sp. r₁</i>, yellow diamond = <i>C. f. fiber</i> f). For visual purposes samples found close to one another were slightly displaced. Exact coordinates and sample information can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097619#pone.0097619.s001" target="_blank">Table S1</a>.</p

Results of DAPC (I) and Structure (II) analyses.

<p>Panel a represents the results with <i>K</i> = 6 for <i>C. fiber</i> and <i>C. canadensis</i> samples (grey), b-f show results of the <i>C. fiber</i> samples for <i>K</i> = 2–6. Samples are sorted according to the five investigated regions.</p

TCS network of 235 analysed beavers using a 487–489 bp fragment of the mitochondrial CR.

<p>Eight haplotypes were detected in this study (coloured) and 13 additional haplotypes originate from GenBank (grey): DQ088701 (a₂), AY623634 (b₁), AY623633 (b₂), AY623632 (b₃), AY623642 (i₁), AY623641 (i₂), AY623643 (i₃), AY623635 (p₁), AY623636 (p₂), AY623637 (t₁), AY623638 (t₂), AY623639 (t₃), AY623640 (t₄). Sizes of circles are proportional to the number of samples bearing the haplotype. Colours of circles indicate the origin of the samples.</p

Mallard SNP genotypes

Plain text file holding genoytpes of all analysed mallards