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

Dommain, René; Andama, Morgan; McDonough, Molly M.; Prado, Natalia A.; Goldhammer, Tobias; Potts, Richard; Maldonado, Jesús E.; Nkurunungi, John Bosco; Campana, Michael G.

doi:10.3389/fevo.2020.00218

Cited by 30 publications

(26 citation statements)

References 138 publications

(220 reference statements)

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“…Other se-daDNA studies have focused on the effects of soil evolution, climate change and pastoral activities on plant communities e.g., [32]. Based on the current body of literature, we know that sedaDNA can also trace vegetation changes over millennia in environments at cold high-latitude regions, including tropical regions from high-altitude sites with lower temperatures and warmer lowland sites [52][53][54]. At the same time, some of the above-cited works highlighted confounding methodological issues related to accelerated degradation of sedaDNA with temperature, which may result in less informative historical DNA signals in lake sediments from moderate to hot temperature environments e.g., [53].…”

Section: Sedadna To Study Past Vegetation Changes From Lake Catchmentmentioning

confidence: 99%

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

et al. 2021

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The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

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Section: Sedadna To Study Past Vegetation Changes From Lake Catchmentmentioning

confidence: 99%

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

et al. 2021

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“…Oftentimes, the organic fraction is extracted from a certain sedimentary sub-fraction only, like the suspended load (e.g., Galy et al, 2008;Ponton et al, 2014), bedload (e.g., Galy et al, 2008;Galy and Eglinton, 2011), or from flood deposits (Hoffmann et al, 2016). To investigate past biodiversity, recent efforts advanced the analyses of ancient DNA preserved in sediments (Dommain et al, 2020), which may be transported together with silt and clay. For a detailed discussion on sediment generation and composition we refer to the recent review by Caracciolo (2020).…”

Section: Definition Of Signal and Hydraulic Grain Size Fractionsmentioning

confidence: 99%

Times Associated With Source-to-Sink Propagation of Environmental Signals During Landscape Transience

et al. 2021

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Sediment archives in the terrestrial and marine realm are regularly analyzed to infer changes in climate, tectonic, or anthropogenic boundary conditions of the past. However, contradictory observations have been made regarding whether short period events are faithfully preserved in stratigraphic archives; for instance, in marine sediments offshore large river systems. On the one hand, short period events are hypothesized to be non-detectable in the signature of terrestrially derived sediments due to buffering during sediment transport along large river systems. On the other hand, several studies have detected signals of short period events in marine records offshore large river systems. We propose that this apparent discrepancy is related to the lack of a differentiation between different types of signals and the lack of distinction between river response times and signal propagation times. In this review, we (1) expand the definition of the term ‘signal’ and group signals in sub-categories related to hydraulic grain size characteristics, (2) clarify the different types of ‘times’ and suggest a precise and consistent terminology for future use, and (3) compile and discuss factors influencing the times of signal transfer along sediment routing systems and how those times vary with hydraulic grain size characteristics. Unraveling different types of signals and distinctive time periods related to signal propagation addresses the discrepancies mentioned above and allows a more comprehensive exploration of event preservation in stratigraphy – a prerequisite for reliable environmental reconstructions from terrestrially derived sedimentary records.

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“…These contrasting strengths were exemplified in recent studies where ancient sedaDNA, when compared with pollen, was able to detect a higher diversity of plant taxa, achieve higher taxonomic resolution (especially for grasses, which is a known limitation of pollen) and distinguish different plant assemblages (Clarke et al, 2020;Liu et al, 2020;Parducci et al, 2019;Zimmermann et al, 2017). Although some technical limitations persist (e.g., Dommain et al, 2020), linking ancient sedaDNA records with disturbance events in the palaeorecord could provide a much clearer picture of how disturbance impacts plant biodiversity and community composition, which is of crucial importance given the intensifying disturbance trends on the modern landscape.…”

Section: Improving the Re Soluti On Of Dis Turban Ce And Veg E Tation Dynamic Smentioning

confidence: 99%

Emerging palaeoecological frameworks for elucidating plant dynamics in response to fire and other disturbance

Napier

Chipman

2021

Global Ecol. Biogeogr.

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Motivation: Rapid climate change is altering plant communities around the globe fundamentally. Despite progress in understanding how plants respond to these climate shifts, accumulating evidence suggests that disturbance could not only modify expected plant responses but, in some cases, have larger impacts on compositional shifts than climate change. Climate-driven disturbances are becoming increasingly common in many biomes and are key drivers of vegetation dynamics at both species and community levels. Palaeoecological records provide valuable observational windows for elucidating the long-term impacts of these disturbances on plant dynamics; however, sparse resolution and difficulty in disentangling drivers of change limit our ability to understand the impact of disturbance on plant communities. In this targeted review, we highlight emerging opportunities in palaeoecology to advance our understanding about how disturbance, especially fire, impacts the ecological and evolutionary dynamics of terrestrial plant communities. Location:Global examples, with many from North America. Conclusions:We propose a set of palaeoecological and integrative approaches that could greatly enhance our understanding of how disturbance regimes influence global plant dynamics. Specifically, we identify four future study areas: (1) focus on palaeoecological disturbance proxies beyond fire and leverage multi proxy research to examine the influence of interacting disturbances on plant community dynamics;(2) use advances in disturbance and vegetation reconstructions, including ancient sedimentary DNA, to provide the spatial, temporal and taxonomic resolution needed to resolve the relationship between changing disturbance regimes and corresponding shifts in plant community composition; (3) integrate palaeoecological, archaeological and Indigenous knowledge to disentangle the complex interplay between climate, human land use, fire and vegetation structure; and (4) apply "functional palaeoecology" and the synergy between palaeoecology and genetics to understand how fire disturbance has served as a long-standing selective agent on plants. These frameworks could increase the resolution of disturbance-driven plant dynamics, potentially providing valuable information for future management.

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

Cited by 30 publications

References 138 publications

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

Times Associated With Source-to-Sink Propagation of Environmental Signals During Landscape Transience

Emerging palaeoecological frameworks for elucidating plant dynamics in response to fire and other disturbance

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