Felis silvestris catus, the domestic cat, diverged ~ 10,000 years ago from populations of Felis silvestris lybica, the African wildcat. This result is supported by remains of cats inhumed with humans on the island of Cyprus and mtDNA phylogenies. More recently, within the last ~ 150 years, there has been development of "fancy" breeds such as the Persian. But there are gaps in the evolutionary history of the cat between the initial domestication events in the Middle East and the efforts of modern breed associations in developing specialized varieties.

To further explore variation in Felis silvestris with the aim of inferring historical dynamics, phylogenetic analyses were performed on over 3,000 individuals from 30 breeds and 30 regional populations using 38 autosomal microsatellites. These are inclusive of non-breed cats from six continents, breeds, wildcats, and hybrids. Genetic diversity and distance estimates were generated. Principle coordinate analysis was used to visualize distances. Analysis of population clustering utilizing the STRUCTURE package was performed. Finally, the TREEMIX package generated graphs of relationships across the populations, and migration events between lineages.

Over the data STRUCTURE analyses with > 20 explicit clusters were less informative. The initial bifurcation occurred between domestic lineages and wildcats. Subsequent splits occurred between European, Middle Eastern, and Asian lineages. Known breeds' attested histories were confirmed in terms of derivation from specific regional populations. Breed-specific admixture events were identified. Geopolitical contours were recapitulated by genetic population structure. The cats of Iran and Iraq formed a distinct cluster from those of the Levant, possibly reflecting ancient divisions in the Middle East. Other genetic relationships are only comprehensible through understanding of local histories of colonialism. The population structure of domestic cats reflects local interactions with humans. Finally, preliminary replications of some of these analyses using 150 and 63,000 SNP data sets were examined.