|Background: Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical
space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds.
Whole genome data is key to understand the consequences of historic breed formation and the putative role of
earlier admixture events in the observed diversity patterns.
Results: We sequenced 48 genomes belonging to eight Iberian native breeds and found that the individual breeds
are genetically very distinct with FST values ranging from 4 to 16% and have levels of nucleotide diversity similar or
larger than those of their European counterparts, namely Jersey and Holstein. All eight breeds display significant
gene flow or admixture from African taurine cattle and include mtDNA and Y-chromosome haplotypes from
multiple origins. Furthermore, we detected a very low differentiation of chromosome X relative to autosomes
within all analyzed taurine breeds, potentially reflecting male-biased gene flow.
Conclusions: Our results show that an overall complex history of admixture resulted in unexpectedly high levels of
genomic diversity for breeds with seemingly limited geographic ranges that are distantly located from the main
domestication center for taurine cattle in the Near East. This is likely to result from a combination of trading
traditions and breeding practices in Mediterranean countries. We also found that the levels of differentiation of
autosomes vs sex chromosomes across all studied taurine and indicine breeds are likely to have been affected by
widespread breeding practices associated with male-biased gene flow.|