TASK 4: Phylochronological mitochondrial DNA analysis of Bos
AIM: To perform a finescale phylochronological analysis of maternal lineages in cattle from Iberia/North Africa to capture ancestral variation/trace genetic changes over time. We will disclose novel polymorphisms for the analysis of peripheral Bos.
Progress in ancient DNA techniques together with lowered sequencing costs have recently made it possible to target complete ancient mitogenomes instead of short regions. By using a combination of shotgun sequencing coupled with targeted capture we will be able to generate highcoverage ancient mtgenomes from ~150 ancient Bos (Milestone2).
Well-preserved samples as identified in Task 3 and specimens with distinct maternal lineages (as determined from the PI’s previous ancient DNA research) will be selected for sequencing of mtgenomes.
We will generate libraries and screen 10 aDNA samples per lane for sequencing with the Illumina HiSeq2000 platform (coverage of >20 million reads/sample) through service acquisition (SciLife, Sweden). Sequence reads will be validated and mapped against reference NCBI sequences. Remaining gaps and expected repetitive regions will be completed by targeted sequencing.
Stringent criteria for ancient DNA analysis and sequence authentication, such as damage patterns consistent with ancient DNA, will be followed. Consensus sequences will be produced and phylogenetic analysis will be carried out following standard procedures (Task 6).
We will work in close cooperation with Bioinformatics researchers (A. Merida, L. Perez-Pardal, and consultant J. Archer to analyze NGS data. We will integrate novel and publicly available genetic data (Task 2) to perform phylochronological population genetic analyses (Task 6), compare genetic affinities among Iberian cattle and their local wild counterparts, and ultimately reveal signatures of introduction into Iberia of new lineages of cattle (Milestone3).