Genetic analyses of extinct and recent forms of Saiga (family Bovidae) to determine their taxonomic variation and phylogeographic relationships in comparison with morphological and palaeoclimatic data (OPUS, NCN)

Climatic oscillations in the Pleistocene have significantly influenced the distribution and variation of present-day organisms. Temperate and thermophilic species retreated from cold regions to southern refugia, while arctic and subarctic species expanded to the regions of steppe tundra. One of such subarctic species is a small steppe antelope saiga (Saiga tatarica). This relic from the Ice Age is now critically endangered and is restricted to a few regions in Central Asia, so its studies are a priority. However, in the Pleistocene it was widely distributed across the central and northern Eurasia up to North America. This saiga is especially good taxon to analyse migrations because it is a nomadic herding species that migrates seasonally looking for areas with better food availability. Its geographic range probably expanded and contracted many times depending on the climatic conditions. However, the details about the migration routes of this mammal are still unclear. There is also no consensus on the saiga taxonomic differentiation and the phylogenetic relationship between its fossil forms, described only based on morphology under various names and taxonomic levels. Thus, to elucidate the evolutionary history of saiga, we will: (1) study the phylogeny and genetic variation in time and space of extant and Pleistocene saiga; (2) verify if the morphologically established forms are justified based on genetic analyses; (3) reconstruct migration routes including expansions and local extinctions of saiga populations; (4) determine causes behind changes in the natural environment and human impact on the population size and the distribution of saiga in the past to better protect this critically endangered species. We will analyse mitochondrial and nuclear genomes acquired not only from modern specimens but also 250 fossils collected from sites across the whole Eurasia. Using methods dedicated to ancient DNA, i.e. extraction, target enrichment, amplification and sequencing, we plan to obtain sequences of 150 mitochondrial genomes as well as 4 modern and 10 ancient nuclear genomes. We will apply all procedures to avoid sample contaminations. Selected specimens will be dated using radiocarbon and uranium-thorium methods. We will perform advanced phylogenetic, palaeographic, population analyses and molecular dating analyses, which will be compared with morphological results and palaeoclimatic data. We have already collected 1235 measurements from 200 skulls coming from 86 sites. We found significant differences between skulls assigned to: tatarica and borealis forms, Pleistocene and recent forms, and various geographical regions. It indicates that the saiga was subjected to temporal and spatial differentiation. To prove our ability to obtain DNA from fossil remains, we received sequences of mitogenomes from 5 present and 22 Pleistocene saiga specimens. Phylogenetic analyses confirmed their significant grouping with other mitogenomes of recent samples. It suggests that the modern saiga populations can be descendants of separated past populations. Since the saiga was a substantial component of cold-adapted Pleistocene faunal complex, our results can be a good reference point and working model for its other members as well as modern species that are also subjected to drastic changes in climate and environment. The project can provide important information about the development and disappearance of past ecosystems as well as verify the concept about different response of individual species to climatic and environmental changes. The comparison of the data with palaeoclimatic records will allow to better understand the relationship between climate change and population dynamics in general. The comparison of aDNA analyses with morphometrical study will check whether the diversified morphology of fossil forms has its genetic justification i.e. if these forms are separately evolving and genetically isolated lineages or represent a local or temporal response to a specific environment. Since there are many common factors influencing the saiga populations in the past and nowadays, this project can help in the prediction of future fate of saiga populations and their protection. The project is an interdisciplinary approach that show a fruitful integration of different disciplines: molecular and population genetics, palaeontology and palaeoecology. Such cooperation will accelerate the development of science and make new scientific discoveries.