Molecular Structure of Portuguese dogs and their relationship to Sloughi, and Aidi dog breeds and Tunisian village dogs
Summary by Dr. Dominique de Caprona 
© de Caprona 2009 

This study entitled "Molecular structure in peripheral dog breeds: Portuguese native breeds as a case study" by A. E. Pires* and collaborators is a follow-up of the previous study about the Mitochondrial DNA of Portuguese dogs and their relationship to Sloughi, Aidi and Tunisian village dogs.  The same breeds of dogs were characterized using 16 microsatellites and 225 Amplified Fragment Length Polymorphism (AFLP)markers and their genetic differentiation was analyzed.

It is the first time that both microsatellites and AFLP markers are used together to compare patterns of genetic differentiation in Portuguese native dog breeds and other geographically neighboring breeds. The aim of the study was to analyze correlations between breed affiliation and molecular structure, phylogeographic structure and historical events, breeds and stray dogs of the same area, and to see whether breeds represent a distinct geographical distribution of alleles.
The use of AFLP markers in genetic studies of dog populations has been limited so far but they offer a higher statistically discriminatory power particularly in cases of weak differentiation.

Genetic differentiation:
Microsatellites: approximately 92% of the variation can be explained by individual differences, and no geographical structure was detected.
AFLP markers: with these markers the Castro Laboreiro Watchdog, Portuguese Sheepdog, Portuguese Water dog, Aidi and Sloughi were segregated from all other breeds. Further analysis differentiated these breeds from one another, and separated them in two groups, with the Castro Laboreiro Watchdog alone in its group.
For the remaining dog populations, the Estrela Mountain dog and Alentejo Shepherd dog clustered together, independent of other dog populations in the study. Further structure was detected differentiating the Spanish Mastiff, the Portuguese Pointer and the Azores Cattle Dog from one another. The Portuguese Warren Hound, Portuguese stray dogs and Tunisian stray dogs remained undifferentiated.

Breed Assignment:
Microsatellites: The overall percentage of individuals assigned correctly to their breed was 12 %. No individuals were classified within the Spanish Mastiff, Portuguese Pointer, Portuguese Sheepdog, Aidi, Sloughi and Tunisian village dogs. Only the Transmontano Mastiff showed the highest percentage of  67% correctly assigned individuals.
AFLP markers: In stark contrast to the microsatellites, the AFLP markers showed a strong percentage of correctly assigned individuals varying from 73.1 % to 93.9 %. All individuals were correctly assigned to their source population for the Spanish Mastiff, Portuguese Sheepdog, Portuguese Pointer, Portuguese Waterdog, Aidi and Tunisian village dogs. Percentage of individuals correctly assigned with AFLP ranged between 46.4 and 70 % for the Azores Cattle Dog, Portuguese Warren Dog, Sloughi and Portuguese stray dogs.

Genetic Diversity:
Values of genetic diversity based on microsatellites and AFLP markers cannot be compared directly. However the breeds did not rank in the same order using these markers. Microsatellites reveal recent or ongoing demographic processes. AFLP markers with their lower evolutionary rate and polymorphism, may differ in their sensitivity to population bottlenecks and demographic recovery, and retain the signal of past genetic structure more effectively.

Fine-scale population genetic patterning:
The AFLP data allowed higher resolution among the Spanish Mastiff, Aidi and Sloughi. 
There was no evidence of genetic differentiation between the Alentejo Shepherd Dog and Estrela Mountain Dog. The Estrela Mountain Dog is considered to be the ancestor of the Alentejo Shepherd Dog, and the two populations were in contact during transhumance in the past.

The distinctiveness of the Castro Laboreiro Watchdog found in the first study is confirmed here with AFLP markers. However, surprisingly, this breed shows no private microsatellites.

Conclusion

AFLP markers produced a very high percentage of breed affiliation, much higher than the microsatellites, reinforcing the suitability of the AFLP markers for population differentiation and breed assignment studies. 
AFLP markers also allowed a higher resolution of geographic genetic structure and detected significant genetic differentiation among the dogs of the regions of Portugal, Spain and North Africa.
Historically, the iberian Peninsula was closely connected to North Africa, mainly through the centuries long occupation by the Arabs and Berbers. This historical event explains the influence of North African mitochondrial DNA (mtDNA) in Iberian people, not detected elsewhere in Europe. During this occupation, animals from Africa were probably introduced into Iberia also. In fact, admixture based on mtDNA and casein haplotypes was detected in bovines and Iberian sheep.

An "African print" of African dogs in Portuguese dog breeds was not detected using mtDNA in the first study and the microsatellites and AFLP markers confirm this previous finding.

Aknowledgements

I thank A.E.Pires for fine tuning this text and all the photographers who provided pictures for this page.

References 

Pires A.E., I. R. Amorim, C. Ginja, M. Gomes, I. Godinho, F. Simoes M. Oom, F. Petrucci-Fonseca, J. Matos and M. W. Bruford (2009): "Molecular structure in peripheral dog breeds: Portuguese native breeds as a case study." International Society for Animal Genetics, Animal Genetics, doi:10.1111/j.1365-2052.2009.01849.x

The Portuguese and Spanish breeds in the study