European Genotype Samples
During the Late Pleistocene Era, all of the wild horse fossils that were sampled had the Phenotype of a Bay. All of the fossils were found to have two copies of the dominant Extension Allele (E/E), with all but one fossil having two dominant Agouti Alleles (A/A). Because all of the horses had a least one functional agouti gene and one functional extension gene, all of the horses had the base color of a Bay.
None of the horse fossils showed any evidence of having the Overo (EDNRB), Tobiano (KIT13), Sabino (KIT16), Cream (MATP), or either variation of the Silver Gene (SILV9 and SILV11). This shows that the fossils had no variation to their base color.
One fossil,” PET5″, had a single mutation at the Agouti Locus (AS1P) showing the emergence of the recessive Agouti Allele (a) in the horse population. Because there was only a small sample of fossils found and genotyped, it is likely that other horses in the total population experienced the same mutation, allowing the allele to increase in frequency as the following generations inherited the allele.