454-sequence data of Iron Age cattle from Althiburos – Tunisia

The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on mitochondrial D-loop sequences obtained for 12 archaeological specimens of Iron Age (~2,800 cal BP–2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results corroborate the introgression of aurochs females into the domestic stock of cattle from Althiburos. , Analyses of ancient DNA were conducted in the dedicated ancient DNA (aDNA) facilities at the Centre for Palaeogenetics (CPG), Stockholm University, Sweden. The bone/tooth specimens were submitted to UV sterilisation and removal of ~1 mm from the outermost surfaces with a clean razor blade to eliminate potential surface contaminants.  We obtained approximately 90 mg of bone powder from each specimen using a multitool drill (DremelTM) at low rpm to avoid local heating. Following, we used the Yang et al. (1998) guanidinium/silica-based method for DNA extraction with modifications as in Svensson et al. (2007). Two negative extraction controls were included in every batch of 6 samples. We analysed two overlapping mitochondrial D-loop fragments of 157 bp and 139 bp with the oligonucleotide primer pairs AN2_F: 5’ - GCCCCATGCATATAAGCAAG - 3’/AN1_R: 5’ - CACGCGGCATGGTAATTAAG -3’ (Edwards et al. 2004) and KO1: 5’ - ACCATTAGATCACGAGCTTAA - 3’/KO2: 5’ - GAAGAAAGAACCAGATGCC - 3’ (Anderung et al. 200..., The GALAXY platform (http://galaxy.psu.edu/), a web-based genome analysis package (Afgan et al. 2018), was used to obtain sequence files for each sample. Sequence reads were identified through unique combinations of primers and tags for each sample and aligned against reference NCBI sequences. Stringent criteria for ancient DNA analysis and sequence authentication were followed (Afgan et al. 2018; Malmström et al. 2015). For multiple alignments, the Geneious Prime version 2019.0.4 (https://www.geneious.com) software was used, and consensus sequences were generated for each individual from independent amplifications. A neighbor-joining phylogeny of genetic distances was obtained using the same software with the HKY model of sequence evolution (Hasegawa et al. 1985) for determination of the maternal haplogroups of the Althiburos specimens.
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Afgan, E., Baker, D., Batut, B., Van Den Beek, M., Bouvier, D., Ech, M., Chilton, J., Clements, D., Coraor, N., Grüning, B.A., et al. (20...