The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA: A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda

Frontiers in Ecology and Evolution

Jesús E. Maldonado¹  John Bosco Nkurunungi²  Molly M. McDonough⁵  Morgan Andama⁶  Tobias Goldhammer⁷  René Dommain⁹  Richard Potts⁹  Michael G. Campana^1,11  Natalia A. Prado^1,11 

[1] 0Department of Biology, George Mason University, Fairfax, VA, United States;1Department of Biology, Faculty of Science, Mbarara University of Science and Technology, Mbarara, Uganda;Center for Conservation Genomics, Smithsonian National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC, United States;Center for Species Survival, Smithsonian National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Front Royal, VA, United States;Department of Biological Sciences, Chicago State University, Chicago, IL, United States;Department of Biology, Faculty of Science, Muni University, Arua, Uganda;Department of Chemical Analytics and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany;Department of Environmental Science and Public Policy, George Mason University, Fairfax, VA, United States;Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States;Institute of Geosciences, University of Potsdam, Potsdam, Germany;School of Systems Biology, George Mason University, Fairfax, VA, United States;

关键词: sedimentary ancient DNA;    tropical biodiversity;    DNA preservation;    sediment;    tropical swamp;    shotgun sequencing;   

DOI  :  10.3389/fevo.2020.00218

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown