TY  - GEN
A1  - Dommain, René
A1  - Andama, Morgan
A1  - McDonough, Molly M.
A1  - Prado, Natalia A.
A1  - Goldhammer, Tobias
A1  - Potts, Richard
A1  - Maldonado, Jesús E.
A1  - Nkurunungi, John Bosco
A1  - Campana, Michael G.
T1  - The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA
BT  - A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - Sedimentary ancient DNA has been proposed as a key methodology for reconstructing biodiversity over time. Yet, despite the concentration of Earth’s biodiversity in the tropics, this method has rarely been applied in this region. Moreover, the taphonomy of sedimentary DNA, especially in tropical environments, is poorly understood. This study elucidates challenges and opportunities of sedimentary ancient DNA approaches for reconstructing tropical biodiversity. We present shotgun-sequenced metagenomic profiles and DNA degradation patterns from multiple sediment cores from Mubwindi Swamp, located in Bwindi Impenetrable Forest (Uganda), one of the most diverse forests in Africa. We describe the taxonomic composition of the sediments covering the past 2200 years and compare the sedimentary DNA data with a comprehensive set of environmental and sedimentological parameters to unravel the conditions of DNA degradation. Consistent with the preservation of authentic ancient DNA in tropical swamp sediments, DNA concentration and mean fragment length declined exponentially with age and depth, while terminal deamination increased with age. DNA preservation patterns cannot be explained by any environmental parameter alone, but age seems to be the primary driver of DNA degradation in the swamp. Besides degradation, the presence of living microbial communities in the sediment also affects DNA quantity. Critically, 92.3% of our metagenomic data of a total 81.8 million unique, merged reads cannot be taxonomically identified due to the absence of genomic references in public databases. Of the remaining 7.7%, most of the data (93.0%) derive from Bacteria and Archaea, whereas only 0–5.8% are from Metazoa and 0–6.9% from Viridiplantae, in part due to unbalanced taxa representation in the reference data. The plant DNA record at ordinal level agrees well with local pollen data but resolves less diversity. Our animal DNA record reveals the presence of 41 native taxa (16 orders) including Afrotheria, Carnivora, and Ruminantia at Bwindi during the past 2200 years. Overall, we observe no decline in taxonomic richness with increasing age suggesting that several-thousand-year-old information on past biodiversity can be retrieved from tropical sediments. However, comprehensive genomic surveys of tropical biota need prioritization for sedimentary DNA to be a viable methodology for future tropical biodiversity studies.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 970 
KW  - sedimentary ancient DNA
KW  - tropical biodiversity
KW  - DNA preservation
KW  - sediment
KW  - tropical swamp
KW  - shotgun sequencing
KW  - metagenomic analysis
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-474305
SN  - 1866-8372
IS  - 970
ER  - 
TY  - GEN
A1  - Cohen, Abby
A1  - Campisano, Christopher
A1  - Arrowsmith, J. Ramon
A1  - Asrat, Asfawossen
A1  - Behrensmeyer, A. K.
A1  - Deino, A.
A1  - Feibel, C.
A1  - Hill, A.
A1  - Johnson, R.
A1  - Kingston, J.
A1  - Lamb, Henry F.
A1  - Lowenstein, T.
A1  - Noren, A.
A1  - Olago, D.
A1  - Owen, Richard Bernhart
A1  - Potts, R.
A1  - Reed, Kate
A1  - Renaut, R.
A1  - Schäbitz, F.
A1  - Tiercelin, J.-J.
A1  - Trauth, Martin  H.
A1  - Wynn, J.
A1  - Ivory, S.
A1  - Brady, K.
A1  - O’Grady, R.
A1  - Rodysill, J.
A1  - Githiri, J.
A1  - Russell, Joellen
A1  - Foerster, Verena
A1  - Dommain, René
A1  - Rucina, J. S.
A1  - Deocampo, D.
A1  - Russell, J.
A1  - Billingsley, A.
A1  - Beck, C.
A1  - Dorenbeck, G.
A1  - Dullo, L.
A1  - Feary, D.
A1  - Garello, D.
A1  - Gromig, R.
A1  - Johnson, T.
A1  - Junginger, Annett
A1  - Karanja, M.
A1  - Kimburi, E.
A1  - Mbuthia, A.
A1  - McCartney, Tannis
A1  - McNulty, E.
A1  - Muiruri, V.
A1  - Nambiro, E.
A1  - Negash, E. W.
A1  - Njagi, D.
A1  - Wilson, J. N.
A1  - Rabideaux, N.
A1  - Raub, Timothy
A1  - Sier, Mark Jan
A1  - Smith, P.
A1  - Urban, J.
A1  - Warren, M.
A1  - Yadeta, M.
A1  - Yost, Chad
A1  - Zinaye, B.
T1  - The Hominin Sites and Paleolakes Drilling Project
BT  - inferring the environmental context of human evolution from eastern African rift lake deposits
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - The role that climate and environmental history may have played in influencing human evolution has been the focus of considerable interest and controversy among paleoanthropologists for decades. Prior attempts to understand the environmental history side of this equation have centered around the study of outcrop sediments and fossils adjacent to where fossil hominins (ancestors or close relatives of modern humans) are found, or from the study of deep sea drill cores. However, outcrop sediments are often highly weathered and thus are unsuitable for some types of paleoclimatic records, and deep sea core records come from long distances away from the actual fossil and stone tool remains. The Hominin Sites and Paleolakes Drilling Project (HSPDP) was developed to address these issues. The project has focused its efforts on the eastern African Rift Valley, where much of the evidence for early hominins has been recovered. We have collected about 2 km of sediment drill core from six basins in Kenya and Ethiopia, in lake deposits immediately adjacent to important fossil hominin and archaeological sites. Collectively these cores cover in time many of the key transitions and critical intervals in human evolutionary history over the last 4 Ma, such as the earliest stone tools, the origin of our own genus Homo, and the earliest anatomically modern Homo sapiens. Here we document the initial field, physical property, and core description results of the 2012-2014 HSPDP coring campaign.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 611 
KW  - Turkana-Basin
KW  - Adar formation
KW  - climate-change
KW  - olorgesailie formation
KW  - Southern Ethiopia
KW  - global climate
KW  - Kenya Rift
KW  - Pleistocene
KW  - variability
KW  - patterns
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-412498
IS  - 611
ER  - 
TY  - JOUR
A1  - Dommain, René
A1  - Andama, Morgan
A1  - McDonough, Molly M.
A1  - Prado, Natalia A.
A1  - Goldhammer, Tobias
A1  - Potts, Richard
A1  - Maldonado, Jesús E.
A1  - Nkurunungi, John Bosco
A1  - Campana, Michael G.
T1  - The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA
BT  - A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda
JF  - Frontiers in Ecology and Evolution
N2  - Sedimentary ancient DNA has been proposed as a key methodology for reconstructing biodiversity over time. Yet, despite the concentration of Earth’s biodiversity in the tropics, this method has rarely been applied in this region. Moreover, the taphonomy of sedimentary DNA, especially in tropical environments, is poorly understood. This study elucidates challenges and opportunities of sedimentary ancient DNA approaches for reconstructing tropical biodiversity. We present shotgun-sequenced metagenomic profiles and DNA degradation patterns from multiple sediment cores from Mubwindi Swamp, located in Bwindi Impenetrable Forest (Uganda), one of the most diverse forests in Africa. We describe the taxonomic composition of the sediments covering the past 2200 years and compare the sedimentary DNA data with a comprehensive set of environmental and sedimentological parameters to unravel the conditions of DNA degradation. Consistent with the preservation of authentic ancient DNA in tropical swamp sediments, DNA concentration and mean fragment length declined exponentially with age and depth, while terminal deamination increased with age. DNA preservation patterns cannot be explained by any environmental parameter alone, but age seems to be the primary driver of DNA degradation in the swamp. Besides degradation, the presence of living microbial communities in the sediment also affects DNA quantity. Critically, 92.3% of our metagenomic data of a total 81.8 million unique, merged reads cannot be taxonomically identified due to the absence of genomic references in public databases. Of the remaining 7.7%, most of the data (93.0%) derive from Bacteria and Archaea, whereas only 0–5.8% are from Metazoa and 0–6.9% from Viridiplantae, in part due to unbalanced taxa representation in the reference data. The plant DNA record at ordinal level agrees well with local pollen data but resolves less diversity. Our animal DNA record reveals the presence of 41 native taxa (16 orders) including Afrotheria, Carnivora, and Ruminantia at Bwindi during the past 2200 years. Overall, we observe no decline in taxonomic richness with increasing age suggesting that several-thousand-year-old information on past biodiversity can be retrieved from tropical sediments. However, comprehensive genomic surveys of tropical biota need prioritization for sedimentary DNA to be a viable methodology for future tropical biodiversity studies.
KW  - sedimentary ancient DNA
KW  - tropical biodiversity
KW  - DNA preservation
KW  - sediment
KW  - tropical swamp
KW  - shotgun sequencing
KW  - metagenomic analysis
Y1  - 2019
U6  - https://doi.org/10.3389/fevo.2020.00218
SN  - 2296-701X
VL  - 8
PB  - Frontiers Media
CY  - Lausanne
ER  -