Additional file 1: of Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle

Note S1. Brief description of the Iberian native cattle breeds sampled in our study. Table S1. Iberian breeds databases. Table S2. Individual sample information. The Y-chromosome haplogroups in bold were determined in this study (n.a.: not applicable). Table S3. FST values between taurine breeds. The highest value is shown in bold and the lowest in italic. Figure S1. Average error rate per sample. Figure S2. Population structure plots determined by NGSadmix; each individual is represented by a stacked column for 3, 4, 6 and 8 proportions. Other K values are shown in Fig. 1b. Figure S3. Principal component analysis done with PCAngsd (components 1 and 2 are shown in Fig. 1c). Variance explained by each component is shown in parenthesis. Figure S4. Differences in Tajima’s D between autosomes and sex chromosome X (calculated using only the female individuals). Figure S5. D-statistics determined as in [4] using genome-wide data. Positive values indicate an excess of derived alleles shared by the breeds in H2 (ANG: Angus; HOL: Holstein; JER: Jersey) and the British Aurochs [5], as indicated by the tree depicted above. Figure S6. Approximately-maximum-likelihood phylogeny of cattle Y-chromosome sequences (sites with a minimum of two minor alleles) determined in FastTree [6] which uses the Jukes-Cantor distance [7]. Labels for the Iberian cattle are according to Table S2. JER: Jersey; ANG: Angus; BOR: Borana; KEN: Kenana. 50% missing data was allowed. The taurine haplogroups Y1 and Y2 are shown in green and red, respectively, and the indicine Y3 in grey. Figure S7. FST per chromosome for all pairwise comparisons within Iberian cattle and between Iberian cattle and the African taurine N’Dama and the African indicine Ogaden. The proportion of shared variation oscillates throughout the genome, reaching extreme values for chromosome 21 (the largest between Iberian and African taurine cattle) and sex chromosome X (shows the lowest differentiation within taurine breeds, while having a relatively large FST between Iberian and the African indicine cattle). (DOCX 1909 kb