High-throughput sequencing of ancient plant and mammal DNA preserved in herbivore middens

Murray, Dáithí C.; Pearson, Stuart; Fullagar, Richard; Chase, Brian M.; Houston, Jayne; Atchison, Jennifer; White, Nicole E.; Bellgard, M.; Clarke, Edwin; Macphail, Michael; Gilbert, M. Thomas P.; Haile, James; Bunce, Michael

doi:10.1016/j.quascirev.2012.10.021

Cited by 43 publications

(40 citation statements)

References 80 publications

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“…Past floras have been reconstructed from aDNA extracted from plant‐based diets using fossil coprolites, rodent middens, or cave earth in dry climates (e.g. Gypsum Cave, Nevada: Poinar et al ., ; Hofreiter et al ., ; Atacama Desert, Chile: Kuch et al ., ; western South Africa and central Australia: Murray et al ., ; Kangaroo Island, South Australia: Haouchar et al ., ). Some striking elevational or latitudinal range shifts in the last 30 kyr have been revealed, assuming that the aDNA in these materials originated locally.…”

Section: Adna As the Sole Basis For Floristic Reconstructionsmentioning

confidence: 99%

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How have studies of ancient DNA from sediments contributed to the reconstruction of Quaternary floras?

Birks

2015

New Phytologist

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499I.499II.500III.500IV.500V.500VI.501VII.502VIII.504504References505 Summary Ancient DNA (aDNA) from lake sediments, peats, permafrost soils, preserved megafaunal gut contents and coprolites has been used to reconstruct late‐Quaternary floras. aDNA is either used alone for floristic reconstruction or compared with pollen and/or macrofossil results. In comparative studies, aDNA may complement pollen and macrofossil analyses by increasing the number of taxa found. We discuss the relative contributions of each fossil group to taxon richness and the number of unique taxa found, and situations in which aDNA has refined pollen identifications. Pressing problems in aDNA studies are contamination and ignorance about taphonomy (transportation, incorporation, and preservation in sediments). Progress requires that these problems are reduced to allow aDNA to reach its full potential contribution to reconstructions of Quaternary floras.

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Section: Adna As the Sole Basis For Floristic Reconstructionsmentioning

confidence: 99%

“…Murray et al . () suggest, however, that this determination may result from inadequate coverage in the DNA databases used. The occurrence of Pinus aDNA in a central Australian midden, a continent where Pinaceae is not native, is interpreted by Murray et al .…”

Section: Adna As the Sole Basis For Floristic Reconstructionsmentioning

confidence: 99%

How have studies of ancient DNA from sediments contributed to the reconstruction of Quaternary floras?

Birks

2015

New Phytologist

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“…As each plant species currently inhabits a preferred temperature and precipitation range (determined mainly by elevation in this environment), the exact identification of the plants that lived in the desert through different time periods can provide information about past climate change (Díaz, Latorre, Maldonado, Quade, & Betancourt, ; Latorre, Betancourt, Rylander, & Quade, ). DNA metabarcoding is a molecular technique for identifying species using molecular markers (barcodes) obtained from a sample containing DNA of more than one organism (Hebert, Cywinska, & Ball, ; Taberlet, Coissac, Pompanon, Brochmann, & Willerslev, ) and combined with aDNA can be used to reconstruct past diversity from ancient or fossil samples like lake sediments and other substrates (Alsos et al., ; Murray et al., ; Willerslev et al., ).…”

Section: Introductionmentioning

confidence: 99%

Multiscale climate change impacts on plant diversity in the Atacama Desert

Díaz

Latorre

Carrasco‐Puga

et al. 2019

Global Change Biology

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Comprehending ecological dynamics requires not only knowledge of modern communities but also detailed reconstructions of ecosystem history. Ancient DNA (aDNA) metabarcoding allows biodiversity responses to major climatic change to be explored at different spatial and temporal scales. We extracted aDNA preserved in fossil rodent middens to reconstruct late Quaternary vegetation dynamics in the hyperarid Atacama Desert. By comparing our paleo‐informed millennial record with contemporary observations of interannual variations in diversity, we show local plant communities behave differentially at different timescales. In the interannual (years to decades) time frame, only annual herbaceous expand and contract their distributional ranges (emerging from persistent seed banks) in response to precipitation, whereas perennials distribution appears to be extraordinarily resilient. In contrast, at longer timescales (thousands of years) many perennial species were displaced up to 1,000 m downslope during pluvial events. Given ongoing and future natural and anthropogenically induced climate change, our results not only provide baselines for vegetation in the Atacama Desert, but also help to inform how these and other high mountain plant communities may respond to fluctuations of climate in the future.

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“…The absolute concentration of each shotgun library was quantified via qPCR using a synthetic standard of known molarity as per Murray et al . (; Appendix S2.8; Table S3) and the libraries were then pooled in approximately equimolar concentrations to create the final sequencing library. The absolute concentration of the sequencing library was quantified via qPCR as above to determine how much to add to the sequencing reaction (Appendix S2.8).…”

Section: Methodsmentioning

confidence: 97%

An assessment of ancient DNA preservation in Holocene–Pleistocene fossil bone excavated from the world heritage Naracoorte Caves, South Australia

Grealy

Macken²,

Allentoft

et al. 2016

J Quaternary Science

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Although there is a long history of research into the fossil deposits of the Naracoorte Caves (South Australia), ancient DNA (aDNA) has not been integrated into any palaeontological study from this World Heritage site. Here, we provide the first evidence of aDNA preservation in Holocene‐ and Pleistocene‐aged fossil bone from a deposit inside Robertson Cave. Using a combination of metabarcoding and shotgun next‐generation sequencing approaches, we demonstrate that aDNA from diverse taxa can be retrieved from bulk bone as old as 18 600 cal a BP. However, the DNA is highly degraded and contains a lower relative proportion of endogenous sequences in bone older than 8400 cal a BP. Furthermore, modelling of DNA degradation suggests that the decay rate is rapid, and predicts a very low probability of obtaining informative aDNA sequences from extinct megafaunal bones from Naracoorte (ca. 50 000 cal a BP). We also provide new information regarding the past faunal biodiversity of Robertson Cave, including families that have not been formerly described in the fossil record from here before. Collectively, these data demonstrate the potential for future aDNA studies to be conducted on material from Naracoorte, which will aid in the understanding of faunal turnover in southern Australia.

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High-throughput sequencing of ancient plant and mammal DNA preserved in herbivore middens

Cited by 43 publications

References 80 publications

How have studies of ancient DNA from sediments contributed to the reconstruction of Quaternary floras?

How have studies of ancient DNA from sediments contributed to the reconstruction of Quaternary floras?

Multiscale climate change impacts on plant diversity in the Atacama Desert

An assessment of ancient DNA preservation in Holocene–Pleistocene fossil bone excavated from the world heritage Naracoorte Caves, South Australia

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