Summary of the demographic model and sampling from Freedman et al. [1].

<p>Their critical inclusion of data from the Australian Dingo illustrates that high copy number in <i>AMY2B</i> is not a basal trait in dogs. The reciprocal monophyly of wild and domestic suggests that, despite the geographical diversity of sampling, descendants of the wolf population that contributed to dog domestication are not represented and may only be accessible using ancient DNA.</p

Scatter plot of the p values on chromosome 22 and a 1 Mb region surrounding the three most significant SNPs.

<p>Significance (−log 10 of p-values) is plotted against position along the chromosome and the three SNPs above the threshold of chromosome wide significance (the red line) are indicated in red. The 1 Mb region surrounding these SNPs is shown in more detail and superimposed on the genes found in the region. One of the SNPs lies within the first intron of the gene SLC6A6 and the other two are upstream (plot generated using build Btau4.2 on animalgenome.org).</p

SNPs with chromosome wide (p<5.19×10⁻⁵) significant associations to TB EBV.

<p>BTA: Bos taurus Chromosome.Position: base pair on the chromosome. P-value: p-values with one degree of freedom. CallRate: proportion of samples in which SNP was successfully called. P11: number of samples with AA genotype. P.12: number of samples with AB genotype. P.22: number of samples with BB genotype.</p

Manhattan plot displaying the results (−log 10 of p-values) of the genome wide scan with respect to genomic position.

<p>Three SNPs on chromosome 22 attain chromosome wide significance and are indicated with red dots.</p

Q-Q plot of observed p-values against expected p values.

<p>Q-Q plot of observed p-values against expected p values.</p

Multidimensional scaling (MDS) analysis of an Identity by State (IBS) matrix of 986 samples, divided into two clusters which reflect differing proportions of Holstein and Friesian ancestry.

<p>Both phenotypes and genotypes were adjusted for the population structure before analysis.</p

Counts of BWA/GATK SNPs of each consequence within gene regions.

<p>Counts of BWA/GATK SNPs of each consequence within gene regions.</p

Whole mitochondrion consensus sequences

Fasta consensus sequences for 24 goat mitochondria published in the study

Principal components 2 and 3 of combined Irish and British coancestry matrix.

<p>(<b>A</b>) fineSTRUCTURE clustering dendrogram for combined Irish and British data, with cluster groups defined as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007152#pgen.1007152.g002" target="_blank">Fig 2</a>. Immediately following the principal inter-island split, Orkney and Wales branch in sequence, consistent with previous observations. (<b>B</b>) Principal component analysis (PCA) of haplotypic similarity based on the ChromoPainter coancestry matrix, coloured by cluster group with their median locations labelled. PC2 captures an Orkney split, while PC3 captures a Welsh split.</p

All-Ireland GLOBETROTTER admixture date estimates for European and British surrogate admixing populations.

<p>A summary of the date estimates and 95% confidence intervals for inferred admixture events into Ireland from European and British admixing sources is shown in (<b>A</b>), with ancestry proportion estimates for each historical source population for the two events and example coancestry curves shown in (<b>B</b>). In the coancestry curves <i>Relative joint probability</i> estimates the pairwise probability that two haplotype chunks separated by a given genetic distance come from the two modelled source populations respectively (i.e. FRA(8) and NOR-SG); if a single admixture event occurred, these curves are expected to decay exponentially at a rate corresponding to the number of generations since the event. The green fitted line describes this GLOBETROTTER fitted exponential decay for the coancestry curve. If the sources come from the same ancestral group the slope of this curve will be negative (as with FRA(8) vs FRA(8)), while a positive slope indicates that sources come from different admixing groups (as with FRA(8) vs NOR-SG). The adjacent bar plot shows the inferred genetic composition of the historical admixing sources modelled as a mixture of the sampled modern populations. A European admixture event was estimated by GLOBETROTTER corresponding to the historical record of the Viking age, with major contributions from sources similar to modern Scandinavians and northern Europeans and minor contributions from southern European-like sources. For admixture date estimates from British-like sources the influence of the Norman settlement and the Plantations could not be disentangled, with the point estimate date for admixture falling between these two eras and GLOBETROTTER unable to adequately resolve source and proportion details of admixture event (fit quality FQ_B< 0.985). The relative noise of the coancestry curves reflects the uncertainty of the British event. Cluster labels (for the European clustering dendrogram, see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007152#pgen.1007152.s004" target="_blank">S4 Fig</a>; for the PoBI clustering dendrogram, see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007152#pgen.1007152.s003" target="_blank">S3 Fig</a>): FRA(8), France cluster 8; NOR-SG, Norway, with significant minor representations from Sweden and Germany; SE_ENG, southeast England; N_SCOT(4) northern Scotland cluster 4.</p