Investigating the footprint of post-domestication dispersal on the diversity of modern European, African and Asian goats

Abstract

Background: Goats were domesticated in the Fertile Crescent about 10,000 years before present (YBP) and subsequently spread across Eurasia and Africa. This dispersal is expected to generate a gradient of declining genetic diversity with increasing distance from the areas of early livestock management. Previous studies have reported the existence of such genetic cline in European goat populations, but they were based on a limited number of microsatellite markers. Here, we have analyzed data generated by the AdaptMap project and other studies. More specifically, we have used the geographic coordinates and estimates of the observed (H_o) and expected (H_e) heterozygosities of 1077 European, 1187 African and 617 Asian goats belonging to 38, 43 and 22 different breeds, respectively, to find out whether genetic diversity and distance to Ganj Dareh, a Neolithic settlement in western Iran for which evidence of an early management of domestic goats has been obtained, are significantly correlated.

Results: Principal component and ADMIXTURE analyses revealed an incomplete regional differentiation of European breeds, but two genetic clusters representing Northern Europe and the British-Irish Isles were remarkably differentiated from the remaining European populations. In African breeds, we observed five main clusters: (1) North Africa, (2) West Africa, (3) East Africa, (4) South Africa, and (5) Madagascar. Regarding Asian breeds, three well differentiated West Asian, South Asian and East Asian groups were observed. For European and Asian goats, no strong evidence of significant correlations between H_o and H_e and distance to Ganj Dareh was found. In contrast, in African breeds we detected a significant gradient of diversity, which decreased with distance to Ganj Dareh.

Conclusions: The detection of a genetic cline associated with distance to the Ganj Dareh in African but not in European or Asian goat breeds might reflect differences in the post-domestication dispersal process and subsequent migratory movements associated with the management of caprine populations from these three continents.

Fig. 1

ADMIXTURE analysis of African, European Asian goat breeds included in our study. Each bar represents the percentages of global ancestries from one or more of K = 2–15 genetically distinct sources for each individual. Continental subregions in Africa include the following countries: (1) Northern Africa: Morocco, Algeria, Tunisia, and Egypt, (2) Western Africa: Burkina Faso, Mali, Nigeria, Cameroon, and Canary Islands, (3) Eastern Africa: Sudan, Ethiopia, Uganda, Burundi, Kenya, Tanzania, and Malawi, (4) Southern Africa: Mozambique, Zimbabwe, and South Africa, and (5) Madagascar. Continental subregions in Europe include the following countries: (1) Northern Europe: Denmark, Finland, and The Netherlands, (2) Central Europe: Switzerland, (3) Western Europe: France, (4) Eastern Europe: Romania, (5) Southern Europe: Italy and Spain, and (6) United Kingdom and Ireland. Continental subregions in Asia include the following countries: (1) West Asia: Iran and Turkey, (2) Pakistan and (3) China. African, European and Asian breeds and subregions names are reported

Fig. 1

ADMIXTURE analysis of African, European Asian goat breeds included in our study. Each bar represents the percentages of global ancestries from one or more of K = 2–15 genetically distinct sources for each individual. Continental subregions in Africa include the following countries: (1) Northern Africa: Morocco, Algeria, Tunisia, and Egypt, (2) Western Africa: Burkina Faso, Mali, Nigeria, Cameroon, and Canary Islands, (3) Eastern Africa: Sudan, Ethiopia, Uganda, Burundi, Kenya, Tanzania, and Malawi, (4) Southern Africa: Mozambique, Zimbabwe, and South Africa, and (5) Madagascar. Continental subregions in Europe include the following countries: (1) Northern Europe: Denmark, Finland, and The Netherlands, (2) Central Europe: Switzerland, (3) Western Europe: France, (4) Eastern Europe: Romania, (5) Southern Europe: Italy and Spain, and (6) United Kingdom and Ireland. Continental subregions in Asia include the following countries: (1) West Asia: Iran and Turkey, (2) Pakistan and (3) China. African, European and Asian breeds and subregions names are reported

Fig. 2

Principal Component Analysis plot of European, African and Asian breeds. Principal components 1 and 2 and percentages of variance explained by them. The figure shows the centroids of principal components 1 and 2 for each breed. Samples are coloured according to their continental subregion of sampling and represented by breed acronyms. The list of complete breed names can be found in Tables 1, 2 and 3

Fig. 3

Graphs depicting the relationships between observed and expected heterozygosities of European, African and Asian goat populations and distance between their sampling locations and Ganj Dareh. Graphs depicting the relationships (expressed as Pearson correlations and their P-values) between observed heterozygosity and expected heterozygosity and distance from Ganj Dareh (early Neolithic settlement in the Zagros Mountains representative of the geographic coordinates of the areas of early goat management in the Fertile Crescent) to sampling locations of a European breeds, including and not including insular populations, b African breeds, including and not including insular populations, c Asian populations. In all plots, country of origin is indicated with specific colours. Breed acronyms are listed in Tables 1, 2 and 3

Fig. 4

Interpolation maps showing the geographic distribution of observed and expected heterozygosities in African, European and Asian breeds. Interpolation maps showing the distribution of genetic diversity in African, European and Asian breeds. a Observed heterozygosity, H_o. b Expected heterozygosity, H_e. Blue points represent sampling localities in a and b, respectively. In Europe, a reduction of diversity is evident in goats from the United Kingdom and Ireland, while in Africa low diversity coincides with the Tsetse fly belt (a geographic area comprised between latitudes 14° N and 20° S) and Madagascar. In Asia, low variation is detected in Pakistan and Southern China