African Village Dogs, their Relationships to each other, Other Breeds, including Basenji, Pharaoh Hound, Rhodesian Ridgeback, Saluki and Afghan hound
Summary by Dr. Dominique de Caprona 
© de Caprona 2009 
No Sloughi, Azawakh, Aidi or AfriCanis in this study

The study entitled "Complex population structure in African village dogs and its implications for inferring dog domestication history" by Adam R. Boyko et al. (2009) was carried out to ascertain the genetic diversity of African village dogs and compare it to the high sampling diversity of East Asian village dogs which is used to argue that domestication of the dog happened in East Asia. 

318 of semi-feral village dogs from 7 regions in Egypt, Uganda, and Namibia, were sampled and compared with 126 breeds of western bred dogs including Basenji, Afghan hounds, Salukis, Pharaoh hounds, Rhodesian Ridgebacks, Salukis, as well as with Puerto Rican street dogs, and mixed-breed dogs from the United States of America.

Egypt: dogs were sampled in three distinct locales:Giza (animal shelter), Luxor (animal shelter and surroundings), and Kharga (rural desert oasis). The geographic distance between Giza and Luxor is greater than that between Kharga and Luxor, but the desert could be a strong barrier to gene flow between Kharga and Luxor resulting in their populations being more genetically distinct.
Uganda: 100 dogs were sampled from a cluster of villages east of Kampala and 30 dogs from three neighboring isleands of the KomeIsland group in Lake Victoria. Although the islands are close to each other and just 20 km off the mainland, the authors expected the lake might act as a genetic dispersal barrier.
Namibia: Dogs from over a dozen villages and urban areas in the northern and central parts of the country were sampled. There are no natural barriers between sampling locations. However, a cordon fence exists which keeps livestock diseases from the North out of the southern part of the country. Dogs are not forbidden to go across the cordon and can get through the fence themselves. Dogs within 100 km of both sides of the cordon were sampled, as well as from populations within 10–20 km of the fence, to see whether this fence had any isolating effect.

To determine the degree of non-native admixture in African dogs the following populations were sampled
16 Dogs of two shelters in Puerto Rico, 
102 known mixed-breed dogs from the United States of America
Samples from dogs from previous studies (Parker et al.) representing 126 breeds, including 129 dogs of the following breeds (western bred): Afghan hounds, Basenjis, Pharaoh hounds, Rhodesian Ridgebacks, and Salukis were use for comparison.

Mitochondrial DNA (mtDNA), microsatellites, and SNP markers were used to characterize population structure and genetic diversity. 
Mitochondrial DNA:  680 bp of the mitochondrial D-loop were sequenced, including the 582-bp region described previously by P.Savolainen et al. (2002)
Microsatellites: 227 village dogs were typed on a 89-microsatellite panel. 
SNP markers: 300 SNP markers were analysed from 168 village dogs, 102 mixed-breed dogs, and 126 western bred breeds.

Microsatellites, and SNP markers:
The authors found that Puerto Rican street dogs clustered with the mixed-breed dogs from the United States, indicating these dogs are all breed admixtures. 
For the other populations five groupings were consistent for the African village dogs: the Egyptian dogs, the Ugandan mainland dogs, the Kome Island dogs, the Northern Namibian dogs, and admixed dogs in a few of the village dogs.
84% of African village dogs outside of central Namibia showed little or no evidence of non-native admixture, whereas all central Namibian dogs had more than 25% admixture, most with more than 60%. 
Central Namibian dogs show virtually no genetic differentiation from American mixed breed dogs.
Egyptian dogs from Giza and Luxor show little differentiation also.

A clear separation was found between Egyptian and sub-Saharan populations and between Ugandan and Namibian populations.
Dogs from Kharga were the most distinct whereas dogs from mainland Uganda and northern Namibia (2,900 km apart) show only moderate differentiation. 

Three breed groups were differentiated: Basenjis on their own, Salukis and Afghan hounds clustering close together*,Rhodesian Ridgeback clustering with the Pharaoh hound.

Mitochondrial Diversity:
47 haplotypes were found in the African dogs,  9 haplotypes in the Puerto Rican dogs, two of which found also in the United States mixed breeds All haplotypes were in the A (33 African haplotypes), B (6 African haplotypes), or C (8African haplotypes) clades, the 3 which are believed to contain 95% of domestic dogs.
18 of the African haplotypes haf not been described by Savolainen et al.: 14 in A clade, 1 in B clade, and 3 in C clade. The Puerto Rican and United States mixed-breed dogs had 8 A clade and one B clade haplotypes (1 haplotype, a Puerto Rican A clade haplotype, was not previously described) 
Local mtDNA diversity did not differ systematically between African regions and similarly sized regions in East Asia, the purported origin of domestic dogs.

Conclusions
This study shows that African village dogs have complex population structure resulting from geographic distance, local gene flow barriers, and the presence or absence of non-african DNA in some populations. Most importantly the vast majority of the African village dogs could be classified as indigenous (less than 25% of non-African ancestry) and some as non-native (more than 60% of non-African ancestry). Only 7 % showed intermediate level of African ancestry.
The authors state:"The lack of consistent levels of admixture within regions suggests that non-indigenous dog genes are quickly removed from village dog populations, or that admixture with non-indigenous dogs is a very recent phenomenon in these areas."

The populations with non-native ancestry were from central Namibia, where every dog had significant levels of non-african admixture, and Giza, where all dogs showed some, usually low, level of admixture. This background level of admixture in Giza is thought by the authors to reflect the relative proximity of Giza to Eurasia. Groupings were detected among the admixed dogs which could result from ancestral breeds being different in various individuals. 

The African village dogs grouped in a large cluster separated from the Basenji, Saluki/Afghan Hound, Rhodesian Ridgeback/Pharaoh Hound clusters. The  Egyptian village dogs were somewhat closer to the Saluki/Afghan, the Ugandan and North Namibian dogs closer to the Basenji. The Rhodesian Ridgebacks and Pharaoh hounds**were closer to mixed-bred dogs, suggesting these breeds have had admixture of non-African dogs.

Influence of barriers to gene flow:
The 230 km of desert separating the Kharga oasis from Luxor led to much stronger differentiation between the populations of village dogs in these areas, than the 500 km Nile corridor between Luxor and Giza. 
The dogs from the Kome islands which lie 10–20 km from the mainland in Lake Victoria were much more differentiated from mainland dogs in Uganda than were northern Namibian populations 2,900 km away. 
Heterozygosity was high across all genetic marker types in all village dog populations except those of the Kharga oasis and the Kome islands (populations which are more isolated and likely smaller, resulting in higher levels of inbreeding).
A surprising result: the samples taken at a 20–100 km distance between northern and central Namibian populations on each side of that country’s Red Line veterinary cordon fence showed a stark population boundary—dogs north of the cordon averaged 87% indigenous African ancestry while those south of the cordon were only 9%African. For the past 100 years, this fence under police watch has separated the indigenous human populations (to the north) from white settlers (to the south)***. This fence is now used to restrict livestock from crossing southward.

In their own words, the authors state: "African village dogs exhibited a similar level of mitochondrial D-loop diversity to that of the dogs sampled by P. Savolainen at al.(2002) in East Asia, the putative site of dog domestication. Although we do not suggest that Africa is actually the site of dog domestication, we do believe that an East Asian origin of dogs should be further scrutinized, especially as Africa also has numerous private haplotypes and East Asia has no private haplogroups, with the possible exception of clade E"

Aknowledgements

I thank A.R.Boyko for reviewing this text and for granting permission to use the photos of African village dogs, as well as all the other photographers who provided pictures for this page.

References

Adam R. Boyko, Ryan H. Boyko, Corin M. Boyko, Heidi G. Parker, Marta Castelhano, Liz Corey, Jeremiah D. Degenhardt, Adam Autona, Marius Hedimbi, Robert Kityo, Elaine A. Ostrander, Jeffrey Schoenebeck, Rory J. Todhunterd, Paul Jones, and Carlos D. Bustamante (2009):"Complex population structure in African village dogs and its implications for inferring dog domestication history" in Proceedings of the National Academy of Sciences.

P. Savolainen, Zhang Y, Luo J, Lundeberg J, Leitner T (2002): "Genetic evidence for an East Asian origin of domestic dogs." Science 298:1610–1613.

Author's notes:
 * Among the countries of origin of the Saluki (Arabian peninsula, Syria, Iran, Iraq) Iran shares borders with the country of origin of the Afghan Hound (Afghanistan).
** The Pharaoh Hound is indigenous to the island of Malta in the Mediterranean sea, not far from other European breeds. The Rhodesian Ridgeback is considered to have been developed by crossing the indigenous Hottentot ridged dogs with dogs imported by the Dutch, German and Huguenot settlers in the 16th and 17th centuries (Danes, Mastiffs, Greyhounds, Salukis, Bloodhounds).
*** The German settlers had imported European breeds.