The domestic dog was the one of the main companion animals of the Roman people. We applied a zooarchaeogenetic approach to describe the morphological and genetic variability of dogs in Roman Iberia and North Africa. Osteometry was used to confirm the domesticated status of the Canis remains and to understand the extent of morphological variability of dogs in Roman times in Mauretania Tingitana, Lusitania and Tarraconensis provinces. High-throughput 454-DNA sequencing technology was used to obtain mitochondrial DNA (mtDNA) sequences from 15 samples. Five dog haplotypes were identified, as well as a matriline not yet observed in extant dogs from these geographic regions. MtDNA haplotypes were grouped in two of the major clades found in present day dogs. We detected dog clade A haplotypes in 12 samples from Portugal, Spain and Morocco, and a dog clade D haplotype in 3 samples from Spain. So far, this is the oldest evidence for the presence of dog clade D in Iberia and which is dated to the late Roman times. This result may echo the consolidation of distinct dog breeds in this period carrying more divergent genetic lineages. From our data, it is evident that there is a long-term continuity, since at least 1,600 years ago, for local breeding involving dog clades A and D in the Iberian Peninsula. Also, the sharing of matrilines between dogs from Spain and North Africa may suggest gene flow. Dogs could have been easily transported between these regions by humans following maritime trading routes.
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