TASK 5: Post-domestication changes in inheritable traits
AIM: To study the variability of nuclear genes linked to morphological traits likely to be associated with humandriven selection, and to date the emergence of specific mutations affecting morphology.
In Portugal Christians improved cattle in post-Medieval times as osteometry clearly indicates an increase in body size. We will follow a casestudy strategy to integrate results from zooarchaeological surveys of cattle specimens (see figure) with genetic data and compare from Roman, Moslem and post-Medieval cattle.
We will track post-domestication changes in inheritable traits as follows:
Case study 1 North Tagus – Conimbriga (10 Roman & 20 Moslem samples) and Santa Clara Monastery (20 post-Medieval samples, Christian);
Case study 2 South Tagus – Silves (16 Medieval samples, Moslem), Palmela (30 Medieval samples, Moslem), Santarém (35 Medieval samples, Moslem) and Beja (20 post-Medieval samples, Christian).
We will examine ~7 nuclear regions involved in: sex determination, coat colour, body size and disease resistance. Specific genes/SNPs of interest (validated in well-characterized phenotypes) will be identified from the literature. For example, three nuclear regions have proven useful to investigate phenotypic variation in past cattle from Northern Europe: melanocortin receptor1,
MC1R–coat colour; leptin,LEP gene–body fat deposition; and tolllike receptor4, TLR4–disease resistance. In cattle, polymorphisms in myostatin muscle development genes can also be useful to investigate improvement. The analysis of
Y-chromosome SNPs will be done to identify major haplogroups Y1/Y2. Sequence variability at Major Histocompatibility loci will also be analysed as it plays a key role in immune response/disease resistance/longterm survival of species.
For targeting specific genes we will use MYbaits sequence capture probe libraries that enable targeted next generation sequencing. Nuclear ancient DNA regions will be captured with complementary biotinylated RNA baits. This approach is recommended for ancient DNA target enrichment where capture is performed on highly contaminated and fragmented DNA. Indexed libraries generated in Task 4 will be used to capture these regions in ancient samples of good quality. Next, Illumina HiSeq2000 highthroughput sequencing, demultiplexing and mapping of these regions against reference NCBI sequences will be done. High-coverage/independent replicates will allow for accurate identification of polymorphisms. Laboratory analyses, sequence alignments and results validation will be done by the PI, A.E. Pires and I. Ureña in collaboration with A. Götherström and E. Svensson, and the bioinformatics team from InBIO/ICETA.
Contrasting SNPs data on extant Iberian/North African cattle with data on past populations will introduce a temporal dimension in demographic inferences. We will also genotype ~60 individuals representatives of 4 Iberian breeds (DNA samples guaranteed by the PI) with the Illumina BovineHD BeadChip (service acquisition). This will allow for an assessment of breed relationships and admixture along a transect Iberia-West Africa.
Genetic and zooarchaeological data will be integrated (Task 6) to reconstruct phenotypic traits of ancient Bos (Milestone4).