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Ice core genetics: Uncovering biodiversity from ancient ecosystems in Greenland and Antarctica

Ice core genetics: Uncovering biodiversity from ancient ecosystems in Greenland and Antarctica
Astrid M. Z. Schmidt

2011

Centre for Ice and Climate, Niels Bohr Institute AND Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1165 Copenhagen, DENMARK.

ABSTRACT

Reconstructions of palaeo-ecosystems have traditionally been approached by analysis of pollen and macrofossil remains from geological layers representing the past environments. These traditional methods are very specific in terms of the taxonomic level to which the fossil material can be assigned and can provide climatic and ecological details from the composition of the detected remains. However, the methods are inadequate when accessibility to sample material is limited or when the past biota did not leave a representative fossil record behind. Ancient DNA (aDNA) methods have the potential to detect past biodiversity in areas where sediments have adsorbed genetic degraded material from dead organisms and preserved it in a frozen state. Polar areas with low temperatures and dry climates offer optimal DNA and fossil preservation condition but access have only been possible on the margins of the ice sheets that cover Greenland and Antarctica. Amplification of ancient genetic material from ice cores can therefore contribute with details on past ecological characteristics, biodiversity and age of the periods where the ice sheets retreated in response to warming climates.

In this thesis I present a review of the major contributions and implications of studies on biological contents within ice. Then I present a study on the abiotic factors of basal ice from different deep drilling sites in Greenland that verify soil chemical characteristics of the sites producing aDNA results. Additionally, we find that within frozen basal ice, chemical factors that have formerly shown to increase the DNA degradation rate (non neutral pH and oxidation) are not of critical importance for DNA survival over a time scale of at least 400,000 years. The methods involved in analyzing aDNA sequence data through different filtering and assignment pipelines are evaluated and point to the critical importance of how to deal with possible false positive results. The major projects in this work have been the reconstruction of three ecosystems, one in Antarctica and two in Greenland. Ecological and climatic details were assessed from the composition of biodiversity detected by means of aDNA amplification of mini-barcodes and deep sequencing on the GS-FLX sequencing platform. Another side project has been the cross-disciplinary effort in age determination of the basal ice samples by three dating methods; cosmogenic 10Be/36Cl dating, recoil dating of 234U/238U and optical stimulated luminescence (OSL) dating.

Results from the thesis verified the existence of aDNA in the sample material and provided the following outcomes for each of the sites. Camp Century in Northwestern Greenland had a northern temperate to boreal ecosystem with indicator plant taxa constraining the mean annual temperature (MAT) conditions to 5 - 15°C. Moreover, the results from the Kap København formation in Northern Greenland supplemented and confirmed the climate defined from previous fossil findings and showed an overlap to the Camp Century taxa. Comparisons of the amplified biodiversity from the two sites in Greenland with fossil findings suggested a co-existence of these ecosystems and re-opened the discussion of when the Greenland Ice Sheet formed. We propose an age of around 1 million years (MY) for these sites. In Antarctica did the aDNA results from basal ice in Suess Glacier in the Dry Valleys point to a mixed boreal/taiga palaeo-ecosystem with MAT around –10°C and summer temperatures that allowed tree growth prior to cooling and ice coverage. The preservation conditions at this location are optimal with average temperatures below – 20°C. The results complemented a climate period suggested by fossil findings in the Transantarctic Mountains and thereby indirectly provide support for a debated warm climate period where the West Antarctic Ice Sheet was absent approximately 3MY.