Thorough assessment of DNA preservation from fossil bone and sediments excavated from a late Pleistocene–Holocene cave deposit on Kangaroo Island, South Australia

Haouchar, Dalal; Haile, James; McDowell, Matthew C.; Murray, Dáithí C.; White, Nicole E.; Allcock, Richard; Phillips, Matthew J.; Prideaux, Gavin J.; Bunce, Michael

doi:10.1016/j.quascirev.2013.11.007

Cited by 39 publications

(32 citation statements)

References 51 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: 97%

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: 97%

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

Birks

2015

New Phytologist

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“…Mammal aDNA between 115 and 175 bp was amplified from bones preserved at this site that were ranged from ca. 6800 to over 20 000 cal a BP (Haouchar et al ., ). However, several layers between 6800 and 10 000 cal a BP, and over 20 000 cal a BP, did not yield mammal DNA (Haouchar et al ., ) and the mammalian diversity identified through aDNA was much lower than this study (see below) − about four families across 15 layers.…”

Section: Resultsmentioning

confidence: 97%

“…6800 to over 20 000 cal a BP (Haouchar et al ., ). However, several layers between 6800 and 10 000 cal a BP, and over 20 000 cal a BP, did not yield mammal DNA (Haouchar et al ., ) and the mammalian diversity identified through aDNA was much lower than this study (see below) − about four families across 15 layers. This may indicate that fragment length sizes were smaller than could be amplified with the primer sets used, i.e., shorter than 100 bp − similar to fragment lengths observed in this study.…”

Section: Resultsmentioning

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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“…In general, DNA preservation is site specific and heavily influenced by the thermal history of the material (Lindahl, , ; Smith et al ., , ; Sawyer et al ., ). The highest success rate for PalEnDNA isolation is achieved with specimens from frozen (Gould et al ., ), arid, or temperate areas rather than hot and humid areas (Poinar et al ., ; Thomsen et al ., ; Haouchar et al ., ). The current upper ages for replicable results from warm to cool, wet sites (including those containing lacustrine and marine deposits) are ca.…”

Section: Climatic and Temporal Limits Of Palendna‐based Researchmentioning

confidence: 99%

Using palaeoenvironmental DNA to reconstruct past environments: progress and prospects

Rawlence

Lowe

Wood

et al. 2014

J Quaternary Science

100

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Palaeoenvironmental DNA (PalEnDNA) is defined as ancient DNA (aDNA) originating from disseminated genetic material within palaeoenvironmental samples. Sources of PalEnDNA include marine and lake sediments, peat, loess, till, ice, permafrost, palaeosols, coprolites, preserved gut contents, dental calculus, tephras, and soils as well as deposits in caves/rockshelters and at archaeological sites. PalEnDNA analysis provides a relatively new tool for Quaternary and archaeological sciences and its applications have included palaeoenvironmental and palaeodietary reconstructions, testing hypotheses regarding megafaunal extinctions, human-environment interactions, taxonomic studies, and studies of DNA damage. Because PalEnDNA samples comprise markedly different materials, and represent wide-ranging depositional and taphonomic contexts, various issues must be addressed to achieve robust, reproducible findings. Such issues include climatic and temporal limitations, the biological origin and state (free versus bound) of PalEnDNA, stratigraphic reliability, sterile sampling, ability to distinguish modern from aDNA signals, DNA damage and PCR amplification, DNA extraction methods, and taxonomic resolution. In this review, we provide a non-specialist introduction to the use of PalEnDNA for Quaternary and archaeological researchers, assess attributes and limitations of this palaeoenvironmental tool, and discuss future prospects of using PalEnDNA to reconstruct past environments.

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Thorough assessment of DNA preservation from fossil bone and sediments excavated from a late Pleistocene–Holocene cave deposit on Kangaroo Island, South Australia

Cited by 39 publications

References 51 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?

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

Using palaeoenvironmental DNA to reconstruct past environments: progress and prospects

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