Ancient wolf population dynamics and ancestry of dogs in Southern Europe

Wolves have walked alongside humans for millennia, first as competitors for territories and prey and then, following the process of domestication, as their most faithful friends. However, the geographic and temporal origins of dog domestication remain controversial. In Europe, especially in the South, almost no data are available on the genetic diversity of wolves prior to their domestication and on early dog DNA variability. Using mitochondrial genomes from ancient wolf and dog remains from Italy, we investigated two fundamental aspects of their evolutionary narrative: (1) the genetic diversity and structure of the ancient wolf populations and (2) the spatiotemporal dynamics of mitochondrial haplogroups in early dogs. Through shotgun approach and mitochondrial capture, we obtained complete mitogenomes of 39 samples, of which 22 wolves and 17 dogs ranging in age from ~40 to 3 thousand years ago and in depths from 1.1 to 869.9-fold coverage (mean 108.9 x). The results provided an overview of the temporal patterns of the Italian wolf population dynamics, revealing a high variability and a pronounced connection with Eurasian coeval samples. Dynamics of dog populations highlighted the occurrence of the main dog haplogroups (A, B, C, D), with a greater presence of haplogroup A, followed by C and D. These results will surely contribute to clarifying the population changes and current morphological and genetic uniqueness of the Italian wolf population while shedding light on local domestication dynamics.