Heteroplasmy in the mitochondrial D-loop region in Turkish domestic pigeon breeds (Columba livia domestica) obfuscates their phylogeny

Columba livia domestica , the domesticated version of the rock pigeon, has long accompanied people for various purposes or activities for thousands of years. Nowadays, pigeon breeding is mostly done as a hobby and it is estimated that domestic pigeons have more than 350 breeds throughout the world. Because of the strong artificial selection applied to them, these different breeds exhibit dramatically diverse phenotypic traits. In this study, partial mitochondrial D-loop sequences from 96 different individuals, mainly from western Turkey, were used to uncover genetic diversity, the presence of heteroplasmy, and phylogenetic relationships within and among local and foreign breeds. It was discovered that the partial D-loop regions of domestic pigeon breeds vary in length, ranging from 714 to 1020 bp, due to heteroplasmy in the 61 bp long VNTR found at the end of the D-loop. The number of VNTR repeats changes from 2 to 7, with a T stretch between locations 382 and 391, containing 10 or 9 thymines. Although the D-loop is a promising marker for animal phylogenetic research due to its high polymorphism and high haplotype diversity, and despite the discovery of 30 different D-loop haplotypes, Bayesian phylogenetic analysis was not sufficient to separate different pigeon breeds in Turkey, except for the Modern Oriental Frill breed. In conclusion, mainly due to the heteroplasmy and possible introgression among distinct breeds, it is hard to use the D-loop as an informative marker for getting valid phylogenetic results and to distinguish morphologically distinct Turkish domestic pigeon breeds.