With Barbara Wohlfarth and Tanja Slotte from Stockholm University and SciLifeLab Genomics we tested the utility of shotgun metagenomics on ancient lake sediments in collaboration with people at the GeoGenetic Centre in Copenhagen. We worked on a Late Glacial sediment sequences from Hässeldala in southern Sweden covering a time interval documenting dramatic climatic changes characterizing the end of the last ice age and the transition into the present interglacial (14,000 - 11,000 years ago).
In our newly established aDNA laboratory in Uppsala, we have also used shotgun metagenomics and metabarcoding on Lago Grande Monticchio from Italy. Here we obtained a core in 2016 with people from the Research Centre for Geosciences (GFZ) in Potsdam. At Monticchio we are also testing the capture technique (see below) and the single-cell sequencing approach on single pollen grains using the Microbial single cell genomic resources at SciLifeLab. We think that the fossil sequences from Hässeldala and from Monticchio form excellent records to test the potential of metagenomics on sediments and to address climatic and ecological questions that we cannot resolve using classical paleoecological methods.
In collaboration with Cristiano Vernesi at the Edmund Mach Foundation in Italy. we are developing capture probes targeting a combination of the three plant barcoding loci matK, trnL and rbcL. We aim to design probes that capture all the diversity of plants and use them on shotgun sequencing data from Monticchio Lake.We base the design on ancestral sequences obtained using phylogenetic tools. This allows us to design probes equally different to all the species that share a common ancestor and a more equal capturing of our gene fragments of interest.
In this proejct we are investigating the hypothesis that spruce (Picea abies L. Karst.) survived at northern latitudes in Norway during the last ice age - the glacial survival hypothesis. We use qPCR to screen sediments from northern Europe to investigate where spruce trees may have been present during cold periods, and how populations moved after the ice melted.
A good explanation for how spruce moved in the past is important for guiding forecasts for tree movements in the future and we hope this information will be useful for researchers modeling species distributions in relation to anticipated climate changes. Our results can also help other researchers to understand the ecology of cold tolerant species and identify genetic genetic resources important for forest breeders who are interested in provenances with traits related to flexibility to changing climatic conditions.
Styrax officinalis is an Eurasian species with highly fragmented distribution in the Mediterranean regions with core range in the Aegeo-Anatolian districts, reaching Italy and the Near East. Populations in Italy have long been considered a human import from classic times, due to its very restricted local range close to Rome and the overall scanty and isolated populations occuring in this areas. In order to reconstruct patterns of geographical differentiation and demographic history of the italian populations we use using genome-wide sequencing markers and analyze population structure in samples selected from the whole range in the Mediterranean regions, from Italy to Lebanon and Provence. Our results support relictuality of the Italian populations rather than import all over the western European range of the species.
Jillian Pelto is an artist who likes to communicate science using art. She works since many years with extreme environmental issues to raise awareness about environmental topics and illustrate real climate change data (rising sea levels, decrease in glacier mass balance, increase fire occurrences. Jill recently visited our labs and had an art exhibition at Uppsala and Tromsø University showing her artworks and explained their association with climate change data. A large gallery of Jillian's artworks using researcher data can be found at Jill’s homesite.
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