Structure plot of the assignment probabilities in the African panel.

<p>Each accession is represented by a bar and the highest Q group membership defines cluster assignment. Asterisks mark the three modern varieties included (from left to right: Staha; TMV1, Longe 5). The plot is based on 26,900 SNPs and the highest probability run for K = 3.</p

SNP associations with maximum temperature during growing season.

<p>Manhattan plot of the log₁₀P-values for 43,963 SNPs along the chromosomes (Y-axis) for association with maximum temperature during the growing season. Dotted line indicates significance at 1% false discovery rate (FDR) threshold. Highlighted SNPs are described specifically in the main text.</p

Cluster membership for the African panel.

*<p>in addition to the number of assignments in agreement with the 26,900 PZE-prefix markers, two and one accessions were asigned to a different cluster in the 1% and 270 LP SNP datasets, respectively.</p><p>Comparison of number of accessions assigned to three clusters defined by STRUCTURE for the African panel based on three PZE-prefix SNP datasets (26,900 SNPs and subsets of 10% (2691) and 1% (270)), and one 270 non-PZE-prefix SNP dataset (the Landrace Panel SNPs). Assignment level refers to the Q group membership threshold for assignment of an accession to a cluster.</p

Structure results for the combined African panel and association panel.

<p>Plots of STRUCTURE results for the combined African panel and Association Panel showing: a) the Ln (probability of the data) for the values of K from 1 to 6; b) the similarity coefficient for nine different runs per K; and c) the delta K value.</p

Map of African maize in relation to American landraces.

<p>Population structure in the combined African panel and Landrace Panel based on STRUCTURE analysis with K = 10. Each geographic group from van Heerwaarden et al. [19 and each cluster in Africa is represented by a pie diagram whose composition shows admixture coefficients. The position of the pie diagrams on the map are defined by the average latitude and longitude of geographical group or cluster except for the North and Central US group where the pies were moved (indicated by lines) to avoid overlap. Like <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047832#pone.0047832-vanHeerwaarden1" target="_blank">[19]</a> we excluded the US-derived varieties in South America and we furthermore excluded the Zambian accessions clustering with the Western African cluster and the Spanish accession from the Sahelian cluster.</p

Diversity statistics for panels and clusters.

<p>Summary statistics, including gene diversity (expected heterozygosity) and observed heterozygosity calculated for the 259 common SNPs in the combined AP, LP and African panel dataset. The standard error of the mean for gene diversity and heterozygosity is given in parenthesis. All clusters within panels are defined by STRUCTURE; K = 3 both for the AP and the African panel and K = 5 for the LP. Statistics were calculated independently on panel- and cluster-level.</p>*<p>Inbred lines.</p

BergEtAl2017_AtlanticCod_TransatlanticDataset_PLINK-format

SNP array data for 316 individuals of Atlantic cod (Gadus morhua), genotyped at 8,165 loci in standard PLINK file format. The PLINK file format consists of two files, a map file and a ped file. In the map file, the first column defines the linkage group, the second column contains the loci names (dbSNP accession numbers), the third line describes the position within the linkage groups (here all are set to 0) and the fourth column defines the order of the SNPs within each linkage group. In the ped file, column one is used to separate the populations (pop-1 to pop-9), column 2 defines the individuals within each population (denoted as the population abbreviation followed by the individual number) where the populations are abbreviated as follows: Can-N_PB = Placentia Bay, Can-N_SG = Southern Gulf of St. Lawrence, Can-S_SB = Sambro, Can-S_GM = Gulf of Maine, Can-S_BB = Browns Bank, Ice_F = Iceland Frontal, Ice_C = Iceland Coastal, NEAC = Northeast Arctic cod, NCC = Norwegian coastal cod. The genotypes are given as numbers from column 7 and onwards, where 1=A, 2=C, 3=G, 4=T. (For a thorough description of the PLINK format, please see https://www.cog-genomics.org/plink). All SNPs are referred to by their database of Single Nucleotide Polymorphisms (dbSNP) accession numbers, available from: http://www.ncbi.nlm.nih.gov/SNP

Interchromosomal linkage disequilibrium between LG2 and LG7.

<p>(A) Heat map of interchromosomal linkage disequilibrium between LG2 and LG7, axis labels represent linkage map positions (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106380#pone.0106380-Borza1" target="_blank">[34]</a>), note that several SNPs share a common map location. Plots of population differentiation (<i>F</i>_ST) on the left and the bottom compare divergence between N and S types, in both the west (black line) and east Atlantic (grey line). Two main regions of ILD between previously identified adaptive genomic regions are highlighted by white rectangles. (B) Histogram of D’ values for all interchromosomal pairs of SNPs.</p

Bayesian assignment of simulated hybrid classes using (A) Structure with K = 2, and (B) New Hybrids with six possible hybrid classes of individuals (N type, S type, F1, F2, Backcross A, and Backcross B).

<p>Individuals simulated using HYBRIDLAB. Bayesian identification of hybrid classes of individuals present in wild Atlantic cod samples using (C) Structure, and (D) New Hybrids.</p

Clinal trends in allele frequency in Atlantic cod range-wide.

<p>Allele frequencies for outlier loci in linkage groups LG2, LG7 and LG12 from 23 locations. See Bradbury et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106380#pone.0106380-Bradbury1" target="_blank">[16]</a> for specific results of outlier tests. See Figure S1 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106380#pone.0106380.s001" target="_blank">File S1</a> for sample locations.</p