TASK 6: Integrative genetic and zooarchaeological analyses

AIM: To perform comprehensive population genetic and phylochronological analyses; to integrate publicly available and novel genetic data from this project to assess genetic diversity and evaluate continuity/discontinuity through time and space for wild and domestic cattle in Iberia/North Africa. We will identify and date events of cattle dispersal, selection and improvement.

Mitochondrial DNA markers (Task 4) will be used to investigate the maternal history of Bos. Haplotype analysis will include genetic diversity measures, genetic distances and reconstruction of phylogenetic relationships. Investigation of paternal history will rely on analogous phylogenetic haplotype analysis of Y­chromosome data (Task 5), to explore sex-­biased events (e.g. selective reproduction & male­mediated gene flow). Investigation of demographic events and timing of sequence divergence will be done using both mt­ and nuclear markers. The analysis of nuclear genes (Task 5) will provide valuable clues on morphological traits variation. These markers will allow to detect changes in phenotypic traits over time. A decrease in heterozygosity can indicate directional breeding. We will apply a multi­marker genetic approach to recover signatures of human­driven selection and improvement.

Consensus profiles will be established using the following criteria: only haplotypes validated (high­-coverage) will be considered as endogenous; consensus haplotypes (replicates) must be congruent; miscoding lesions (due to ancient DNA degradation) will be identified and removed from consensus haplotypes.

We will use standard software: estimation of classical population genetics parameters; phylogenetic reconstruction, following selection of evolutionary models. By including heterochronous data, the phylochronological analysis will reconcile different models of interaction between ancestral and extant cattle populations. The dynamics of genetic variability will be captured to investigate domestication­-associated genetic changes, i.e. demographic events (e.g. bottlenecks and/or post­-domestication expansions), admixture between aurochs and domestic cattle, and changes in phenotypic traits.

We will test for genetic continuity and/or discontinuity between the pre­- and post­-domestication periods, and will compare ancient and extant populations; we will try to quantify the Near Eastern genetic ancestry in Iberian cattle at Neolithic times. Also, genetic connections between Iberia and North Africa will be investigated. We will integrate these data with published datasets from other regions/various periods (including the western fringe of Europe from England to Iberia, data contributed by C. Edwards and E. Wright and U. Albarella, and with results from our previous research on ancient cattle from these regions to track dispersion, and local domestication/introgression events.

Neolithic expansion modelling and coalescent simulation of genetic data will be performed using the program BayeSSC. Results will be analysed using the statistical software R to determine the best model and demographic parameters (e.g. population sizes, growth rate) to explain ancient DNA results. We will use Approximate Bayesian Computation in which R. Rasteiro and L. Chikhi (consultant) are experts.

Zooarchaeologists and archaeologists will contribute to interpretations of the genetic results. We will combine these with the most recent and sometimes contrasting theories that aim to explain animal and human movements as well as cultures in prehistoric and historic times. We will disclose relevant information on the origins, evolutionary trajectories and modes of improvement of cattle (Milestone5), merging and conciliating the evidences and hypotheses raised into a coherent framework.