Genetic diversity and population structure of African village dogs based on microsatellite and immunity-related molecular markers

Abstract

The village and street dogs represent a unique model of canine populations. In the absence of selective breeding and veterinary care, they are subject mostly to natural selection. Their analyses contribute to understanding general mechanisms governing the genetic diversity, evolution and adaptation. In this study, we analyzed the genetic diversity and population structure of African village dogs living in villages in three different geographical areas in Northern Kenya. Data obtained for neutral microsatellite molecular markers were compared with those computed for potentially non-neutral markers of candidate immunity-related genes. The neutral genetic diversity was similar to other comparable village dog populations studied so far. The overall genetic diversity in microsatellites was higher than the diversity of European pure breeds, but it was similar to the range of diversity observed in a group composed of many European breeds, indicating that the African population has maintained a large proportion of the genetic diversity of the canine species as a whole. Microsatellite marker diversity indicated that the entire population is subdivided into three genetically distinct, although closely related subpopulations. This genetical partitioning corresponded to their geographical separation and the observed gene flow well correlated with the communication patterns among the three localities. In contrast to neutral microsatellites, the genetic diversity in immunity-related candidate SNP markers was similar across all three subpopulations and to the European group. It seems that the genetic structure of this particular population of Kenyan village dogs is mostly determined by geographical and anthropogenic factors influencing the gene flow between various subpopulations rather than by biological factors, such as genetic contribution of original migrating populations and/or the pathogen-mediated selection. On the other hand, the study of oldest surviving dogs suggested a biological mechanism, i.e. a possible advantage of the overal heterozygosity marked by the the microsatellite loci analyzed.

Fig 1. The region around the southern tip of the Lake Turkana in Northern Kenya.

(A) Mt. Kulal. (B) Mt. Ngyiro. (C) Lake Turkana.

Fig 2. Phenotype of sampled dogs.

Upper row—dogs of Samburu people from Mt. Kulal area, lower row–Turkana dogs from Lake Turkana (Loyiangalani) area.

Fig 3. Estimation of the population substructure across microsatellite loci in the Kenyan village dogs (K = 3) using Structure software.

A different pattern was identified for Mt. Ngyiro.

Fig 4. Principal coordinates analysis (PCoA) of the Kenyan village dogs.

(A) PCoA with the 27 microsatellite loci (n = 150). (B) PCoA with the 3 MHC loci (n = 135). (C) PCoA with the 3 MHC and 16 SNP loci (n = 135). (D) PCoA with the 16 SNP loci (n = 150).

Fig 5. DLA three locus haplotype frequency profiles for the different subpopulations of the Kenyan dogs.

Fig 6. Estimation of the population substructure across SNP loci in the Kenyan village dogs (K = 3) using structure software.

No substructure was identified.