The Lusitano horse maternal lineage based on mitochondrial D-loop sequence variation.

The analysis of mitochondrial D-loop sequences (408 bp) from 145 Lusitano founder mares yielded a total of 27 different haplotypes. The distribution of these mtDNA sequences was quite unequal, with the three most frequent ones representing 56.5% of all the Lusitano founder mares and 14 haplotypes (51.9%) being rare variants found only once in the sampling. Four main haplotype clusters were present in the Lusitano breed. The comparison of these sequences with other equine haplotypes shows that they fall in groups shared with other horse breeds. These data support the hypothesis of multiple domestication events in many distinct geographic areas over a broad time span. However, the analysis of 145 Lusitano, 55 Pura Raza Espanola and 18 Sorraia sequences indicates that half of the samples (50.9%) fall in one specific-cluster (A), which has previously been described as characteristic of the Iberian and Northern African horse breeds. The presence of a phylogeographic structure in cluster A associated with its star-like structure was interpreted as suggestive of a centre of horse domestication in the Iberia Peninsula.