Extended longevity of DNA preservation in Levantine Paleolithic sediments, Sefunim Cave, Israel

Slon, Viviane; Clark, Jamie L.; Friesem, David E.; Orbach, Meir; Porat, Naomi; Meyer, Matthias; Kandel, Andrew W.; Shimelmitz, Ron

doi:10.1038/s41598-022-17399-2

Cited by 18 publications

(6 citation statements)

References 81 publications

(121 reference statements)

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“…However, eDNA-based studies suffer from limitations linked to the level of preservation of nucleotides in environmental matrices. Although it has been shown that DNA can be recovered from lacustrine and marine sediments as far back as the Holocene 32 , biases might still exist due to the degradation of eDNA, especially over geological times 33 and in warmer climates 34 . In addition, physio-chemical changes in sediment and soil may affect the assemblage and composition of prokaryotic communities that can survive in extreme conditions, including anoxic environments.…”

Section: Discussionmentioning

confidence: 99%

100 years of anthropogenic impact causes changes in freshwater functional biodiversity

Eastwood

Zhou

Derelle

et al. 2023

Preprint

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Despite efforts from scientists and regulators, biodiversity is declining at an alarming rate. Unless we find transformative solutions to preserve biodiversity, future generations may not be able to enjoy nature's services. We have developed a conceptual framework that establishes the links between biodiversity dynamics and abiotic change through time and space using artificial intelligence. Here, we apply this framework to a freshwater ecosystem with a known history of human impact and study 100 years of community-level biodiversity, climate change and chemical pollution trends. We apply explainable network models with multimodal learning to community-level functional biodiversity measured with multilocus metabarcoding, to establish correlations with biocides and climate change records. We observed that the freshwater community assemblage and functionality changed over time without returning to its original state, even if the lake partially recovered in recent times. Insecticides and fungicides, combined with extreme temperature events and precipitations, explained up to 90% of the functional biodiversity changes. Community-level biodiversity reliably explained freshwater ecosystem shifts whereas traditional quality indices (e.g. Trophic Diatom Index) and physicochemical parameters proved to be poor metrics for these shifts. Our study advocates the advantage of high throughput systemic approaches on long-term trends over species-focused ecological surveys to identify the environmental factors that cause loss of biodiversity and disrupt ecosystem functions.

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Section: Discussionmentioning

confidence: 99%

100 years of anthropogenic impact causes changes in freshwater functional biodiversity

Eastwood

Zhou

Derelle

et al. 2023

Preprint

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“…Rather than merging different extracts, we utilized a single (positive) extract and combined it with progressively larger volumes of another (negative) extract to attain higher pooling levels. This strategy was used to simulate the potential low success rate of sedaDNA samples (Massilani et al, 2022; Slon et al, 2022). However, it’s important to note that equal-volume pooling does not guarantee equal representation of each extract within the pool.…”

Section: Discussionmentioning

confidence: 99%

Maximizing Efficiency in SedaDNA Analysis: A Novel Extract Pooling Approach

Oberreiter,

Gelabert,

Brück

et al. 2023

Preprint

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In recent years, the field of ancient DNA (aDNA) has taken a new direction toward studying human population dynamics through sedimentary DNA (sedaDNA), enabling the study of past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing method. Our approach involves combining multiple extracts, allowing users to parallelize laboratory procedures early in the sample preparation pipeline while effectively screening for the presence of aDNA. Pooled samples that exhibit aDNA signals can then undergo detailed analysis, while empty pools are discarded. We have successfully applied our extract pooling method to various sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth.

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“…However, eDNA-based studies suffer from limitations linked to the level of preservation of nucleotides in environmental matrices. Although it has been shown that DNA can be recovered from lacustrine and marine sediments as far back as the Holocene ( Slon et al, 2022 ), biases might still exist due to the degradation of eDNA, especially over geological times ( Jia et al, 2022 ) and in warmer climates ( Mauvisseau et al, 2022 ). In addition, physio-chemical changes in sediment and soil may affect the assemblage and composition of prokaryotic communities that can survive in extreme conditions, including anoxic environments.…”

Section: Discussionmentioning

confidence: 99%

100 years of anthropogenic impact causes changes in freshwater functional biodiversity

Eastwood,

Zhou,

Derelle

et al. 2023

eLife

View full text Add to dashboard Cite

Despite efforts from scientists and regulators, biodiversity is declining at an alarming rate. Unless we find transformative solutions to preserve biodiversity, future generations may not be able to enjoy nature’s services. We have developed a conceptual framework that establishes the links between biodiversity dynamics and abiotic change through time and space using artificial intelligence. Here, we apply this framework to a freshwater ecosystem with a known history of human impact and study 100 years of community-level biodiversity, climate change and chemical pollution trends. We apply explainable network models with multimodal learning to community-level functional biodiversity measured with multilocus metabarcoding, to establish correlations with biocides and climate change records. We observed that the freshwater community assemblage and functionality changed over time without returning to its original state, even if the lake partially recovered in recent times. Insecticides and fungicides, combined with extreme temperature events and precipitations, explained up to 90% of the functional biodiversity changes. Community-level biodiversity reliably explained freshwater ecosystem shifts whereas traditional quality indices (e.g. Trophic Diatom Index) and physicochemical parameters proved to be poor metrics for these shifts. Our study advocates the advantage of high throughput systemic approaches on long-term trends over species-focused ecological surveys to identify the environmental factors that cause loss of biodiversity and disrupt ecosystem functions.

show abstract

Extended longevity of DNA preservation in Levantine Paleolithic sediments, Sefunim Cave, Israel

Cited by 18 publications

References 81 publications

100 years of anthropogenic impact causes changes in freshwater functional biodiversity

100 years of anthropogenic impact causes changes in freshwater functional biodiversity

Maximizing Efficiency in SedaDNA Analysis: A Novel Extract Pooling Approach

100 years of anthropogenic impact causes changes in freshwater functional biodiversity

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