0000000000617975
AUTHOR
Gregor Gorjanc
On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Background In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation. Results We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of commo…
Additional file 10 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 10: Figure S6. Spatial PCA of 507 domestic sheep without EFB, KCH and VBS, which were found to dominate the sPC2 and sPC3 just as for in the normal PCA (Additional file 8: Figure S4 left panels). The three methods of triangulation, indicated above the plots, give essentially the same results, which are similar to the supervised PCA pattern (see Additional file 8: Figure S4 right panels).
Additional file 11 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 11: Figure S7. Supervised PCA of 546 animals in which the PC (svPC1, svPC2) were calculated based on the indicated fat-tailed, Nordic and Spanish sheep.
Additional file 14 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 14: Figure S9. Neighbor-net graphs of 17 regional groups of breeds (Additional file 12 B) with (A) AMF, (B) EMF, (C, D) both AMF and EMF; (D, E) pattern obtained by increasing the AMF-EFM distance in order to suppress the EMF-AMF clustering and to show different affinities of EMF and AMF for European domestic sheep.
Additional file 6 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 6: Figure S2. Neighbour-joining tree visualizing the allele-sharing distances of the Balkan sheep (see Fig. 1) or (see Additional file 1: Table S1) for the breed codes). Breeds that are dispersed over different branches of the tree are indicated by colored lines.
Additional file 13 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 13: Figure S8. Neighbor-net graph of Reynolds’ distances between breeds or regional combinations of closely related breeds (see Additional file 12: Table S5).
Additional file 8 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 8: Figure S4. Left panels: normal PCA plots of 525 sheep (≤ 6 per breed) including the inbred EFB, KCH, VBS. Right panels: supervised PCA of 546 sheep, including three mouflon populations, in which EFB, KCH and VBS as well as the mouflons have been excluded for calculation of the principal components (svPC1, svPC2 and svPC3).
Additional file 16 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 16. Methodological comparisons and considerations [22, 50, 53, 54, 56, 64, 65, 77].
Additional file 5 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 5: Figure S1. Inverse linear relationship of observed heterozygosity and the total ROH coverage FROH, showing relatively low heterozygosity values for AMF, SMF and fat-tailed sheep.
Additional file 9 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 9: Figure S5. Supervised PCA of 546 animals as in Fig. 2b, showing svPC1 vs. svPC3 averaged per breed.
Additional file 15 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 15: Figure S10. TreeMix trees without and with 6, 10 and 20 migrations and plots of the proportions of the variance explained (f-indices) and likelihoods at different m values. Coloured lines indicate inferred migrations with a weight according to the color scale.
Additional file 7 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 7: Figure S3. FineStructure clustering of eastern and southeastern European sheep breeds. The color of each bin in the matrix indicates the number of “genomic chunks” copied from a donor (columns) to a recipient individual (rows).
Additional file 2 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 2: Table S2. Datasets used for analysis.
Additional file 1 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 1: Table S1. Sheep breeds analyzed in this study [16, 18, 20, 22, 31, 35, 47, 59, 76]. Colors indicate genetic clusters. Boxes indicate breeds combined in the 78-breed panel.
Additional file 3 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 3: Table S3. A 358 SNPs informative for Asian Mouflon ancestry used in BSAA. Only SNPs were considered with > 40 out of 42, > 55 out of 57 and > 67 out of 69 non-missing allele frequencies used for the pairwise AFM-PRMS, AMF-EMFM and EMFM-PRMS FST calculations, respectively. B 334 SNPs informative for Asian Mouflon ancestry used in BSAA. Only SNPs were considered with > 67 out of 69, > 55 out of 57 and > 40 out of 42 non-missing allele frequencies used for the pairwise EMFM-PRMS, AMF-EMFM and AFM-PRMS FST calculations, respectively. C 606 SNPs informative for Merino ancestry used in BSAA. Only SNPs were considered without missing allele frequencies used for…
Additional file 12 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 12: Table S5. Grouping of breeds for calculation of genetic distances. (A) Regional monophyletic groups of breeds for the Neighbor-net graph in Additional file 13: Figure S8. (B) 17 Regional groups of related breeds for the Neighbor-net graphs in Fig. 3 and Additional file 14: Figure S9.
Additional file 4 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 4: Table S4. ROH statistic per individual or averaged per breed. FROH is the total length of the ROH divided by the total length of the sheep autosomes (2452.06 Mb).