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Genomics, epigenomics and transcriptomics of Yakutian horses, a unique domestic breed adapted to life in the Arctic

Periodic Reporting for period 1 - YAKUT (Genomics, epigenomics and transcriptomics of Yakutian horses, a unique domestic breed adapted to life in the Arctic)

Reporting period: 2015-09-15 to 2017-09-14

The YAKUT project had as main aim the analysis of fresh and ancient biological horse samples from Yakutia, Siberia. Unexpected problems did not allow the work to be conducted as planned meaning contingency measures had to be developed and implemented. The supervisor and the researcher together developed two modified projects and new Work Packages (nWP) as described below. The Work Packages had almost identical titles to those in the original application, with the difference being the samples used and, for example, Yakutian has been switched with Italian. This allowed full training to the researcher, in particular to the latest methodological advances in genomic sciences and spatial distribution modelling through the new Work Packages (nWP) described below.

The first project (nWP1 and nWP2) has been developed in order to ensure adequate training in the molecular methods required to obtain genetic data from ancient and modern biological material (as expected from WP1 and WP2 of the DoA), and the associated data analysis (as expected from WP3).

The second part of the modified project (nWP4 and nWP5) was designed in order to ensure adequate, additional training in a field, paleo-ecological modelling, that represents a novelty in association to ancient DNA analyses, even if it is commonly used in other fields of biological research. This corresponded to a novel set of skills and approaches for which the researcher developed increasing interest, with the specific long-term objective to develop research projects merging (ancient and modern) genome-scale data and ecological modelling. This second project thus broadened the range of skills for the researcher, opening her to spatial distribution modelling and climate niche projection and reinforcing her position as independent and mature professional.

nWP1 Characterisation of the past genomic diversity of Italian horses
nWP2 Characterizing the present genomic diversity within Italian horses
nWP3 Reconstruction of the demographic history of ancient (Italian) horses and their relationships to present-day (Italian) breeds
nWP4 Establishment and analysis of a spatially-explicit database of radiocarbon dates and relative frequencies associated to horse presence in Eurasian archaeological sites.
nWP5 Reconstruction of the Palaeoecology of the horse in Eurasia.
nWP 1 Characterisation of the past genomic diversity of Italian horses
The supervisor guided the researcher to achieve the full organisation of the network of scientists to be involved in the project. The sampling was organized in the Italian collections, in line with Italian regulations for accessing cultural and archaeological material. All tests performed at a later stage of the project excluded the presence of contamination, thereby validating the quality of the sampling, and the proficiency of the training in molecular tools.

nWP2 Characterizing the present genomic diversity within Italian horses
The supervisor guided the researcher in establishing contact with a large network of collaborators that could help access DNA material from modern Italian breeds. Amongst over 12 different contacts established, two proved extremely useful and provided access to DNA material and hair/blood samples from a total of 9 iconic Italian breeds.

nWP 3 Reconstruction of the demographic history of ancient Italian horses and their relationships with other ancient and modern populations
The researcher has been extensively trained in the molecular methods needed to successfully extract DNA from ancient specimens, and obtain reliable genomic and genetic data from them. The poor conservation of the samples resulted in a low quantity of ancient DNA retrieved that precluded the genome-wide analyses foreseen, but extensive quality checks demonstrated the good value of the training and of the researcher’s work. In terms of computational analyses of high-throughput DNA sequencing data, the researcher has been trained in the use of the software developed in the lab in order to process genomic data as well as on a range of complementary, state-of-the-art pipelines/packages in statistical genomics.

nWP4 Establishment and analysis of a spatially-explicit database of radiocarbon dates and relative frequencies associated to horse presence in Eurasian archaeological sites.
The supervisor and the researcher organised a large network of experts in the field, allowing to get access to the latest, unpublished results in the field and to obtain the best possible data. After merging the information received by the collaborators and collecting further dates, the resulting database represents by far the largest effort so far aimed at characterising the variation through time of the palaeoecology of a megafauna species.

nWP5 Reconstruction of the Palaeoecology of the horse in Eurasia.
The collaborative network opened access to the most complete palaeoclimatic reconstructions hitherto produced. The analysis of the radiocarbon dataset in conjunction with such extensive estimates allowed the characterisation of the climatic niche of the horse and its variations through space and time. The researcher underwent a training period to learn the state-of-art ecological methods to reconstruct the potential distribution of biological species on the basis of climatic and environmental information and implemented them on the collected database. This comprehensive analysis merging archaeozoology, archaeology, palaeoclimatology and palaeoecology allowed to reconstruct the relationship between horse populations and the environment, and their variation through time to unprecedented detail.
All products of the present project are intended to be published open-access and shared in repositories such as Academia.edu and ResearchGate, as has been done for the article published in Systematic Biology. The work performed following nWP 1 has been presented at the ISBA congress that was held in Oxford in September 2016 as part of a bigger project on horse palaeogenomics, and the results of the researcher work will be included in the forthcoming publication of a large dataset of ancient genomic horse data. Even if the quality of the DNA preserved in the Italian samples was not compatible with the characterization of the whole genome sequence of any of the samples analysed, pending analyses will reveal the publication potential of some findings.

The work performed following nWP 3 and nWP 4 had produced results only very recently, and for this reason has not been presented yet. The database of radiocarbon dates and frequency data for horses will be included in the open access supplementary material of the associated publication, and will be made available from the host website and/or published as an original publication in dedicated journals. It will represent the legacy of the project and will be used as a basis for further studies requiring the collection of radiocarbon dates and set as example for similar analyses.

The associated study, merging radiocarbon dates, archaeozoological analyses, ecological modelling and palaeoclimatic reconstructions, not only helps answering several questions about the population history of the horse species, but also represents the most comprehensive analysis of the palaeoecology of a macrofaunal species carried out so far. For this reason, it is expected to receive a lot of attention both because of its interdisciplinary nature and of its innovative approach