animals Article Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region Emel Özkan Ünal 1,* , Fulya Özdil 2,* , Selçuk Kaplan 3, Eser Kemal Gürcan 1, Serdar Genç 4 , Sezen Arat 2 and Mehmet Ihsan˙ Soysal 1 1 Faculty of Agriculture, Department of Animal Science, Tekirda˘gNamık Kemal University, Tekirda˘g59030, Turkey;
[email protected] (E.K.G.);
[email protected] (M.I.S.)˙ 2 Faculty of Agriculture, Department of Agricultural Biotechnology, Tekirda˘gNamık Kemal University, Tekirda˘g59030, Turkey;
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[email protected] 4 Faculty of Agriculture, Department of Agricultural Biotechnology, Kır¸sehirAhi Evran University, Kır¸sehir40100, Turkey;
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[email protected] (E.Ö.Ü.);
[email protected] (F.Ö.); Tel.: +90-282-250-2185 (E.Ö.Ü.); +90-282-250-2233 (F.Ö.) Received: 25 September 2020; Accepted: 22 October 2020; Published: 27 October 2020 Simple Summary: This paper represents the first fundamental report of mtDNA diversity in Turkish indigenous donkey breeds and presents findings for the origin and genetic characterization of donkey populations dispersed in seven geographical regions in Turkey, and thus reveals insights into their genetic history. The median-joining network and phylogenetic tree exhibit two different maternal lineages of the 16 Turkish indigenous donkey populations. Abstract: In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey.