Data from: Genetic homogenization of indigenous sheep breeds in Northwest Africa

Northwest-African sheep represent an ideal case-study for assessing the
potential impact of genetic homogenization as a threat to the future of
traditional breeds that are adapted to local conditions. We studied ten
Algerian and Moroccan breeds of sheep, including three transboundary
breeds, distributed over a large part of the Maghreb region, which
represents a geographically and historically coherent unit. Our analysis
of the dataset that involved carrying out Genome-wide SNP genotyping,
revealed a high level of homogenization (ADMIXTURE, NetView, fineSTRUCTURE
and IBD segments analyses), in such a way that some breeds from different
origins appeared genetically undistinguished: by grouping the eight most
admixed populations, we obtained a mean global FST value of 0.0024. The
sPCA analysis revealed that the major part of Morocco and the Northern
part of Algeria were affected by the phenomenon, including most of the
breeds considered. Unsupervised cross-breeding with the popular
Ouled-Djellal breed was identified as a proximate cause of this
homogenization. The issue of transboundary breeds was investigated, and
the Hamra breed in particular was examined via ROH fragments analysis.
Genetic diversity was considered in the light of historical archives and
anthropological works. All of these elements taken together suggest that
homogenization as a factor affecting the Maghrebin sheep stock, has been
particularly significant over the last few decades, although this process
probably started much earlier. In particular, we have identified the
policies set by the French administration during the colonial period of
the region’s history as a causal factor that probably contributed
significantly to this process. The genetic homogenization that we have
observed calls into question the integrity of the farm animal genomic
resources represented by these local breeds, whose conservation is of
critical importance to the future of the livestock sector.