A critical evaluation of how ancient DNA bulk bone metabarcoding complements traditional morphological analysis of fossil assemblages

Grealy, Alicia; McDowell, Matthew C.; Scofield, R. Paul; Murray, Dáithí C.; Fusco, Diana A.; Haile, James; Prideaux, Gavin J.; Bunce, Michael

doi:10.1016/j.quascirev.2015.09.014

Cited by 37 publications

(38 citation statements)

References 61 publications

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“…(unpublished); Table S2). The purpose of targeting two different sized amplicons from different barcoding regions is two‐fold: it allows us to gauge the fragment length of amplifiable target DNA, as well as to independently verify taxonomic IDs, potentially resolve taxonomic ambiguities or identify more taxa than could be identified by using only one region (Grealy et al ., ). Extraction controls and three template‐free PCR controls were included, and unique indexes were used to eliminate the possibility of sequence contamination arising from previously amplified DNA.…”

Section: Methodsmentioning

confidence: 99%

“…Dilutions exhibiting the least inhibition were then amplified via qPCR (in triplicate) using uniquely indexed Illumina fusion primers specific for a small, diagnostic barcoding region of the mitochondrial 12S rRNA gene in mammals and birds (12SAO, a 150-bp amplicon or 103 bp without primers; Cooper, 1994; Table S2), as well as an additional region specific for marsupials (12SMarsMini, an 85-bp amplicon or 41 bp without primers; D. Haouchar et al (unpublished); Table S2). The purpose of targeting two different sized amplicons from different barcoding regions is two-fold: it allows us to gauge the fragment length of amplifiable target DNA, as well as to independently verify taxonomic IDs, potentially resolve taxonomic ambiguities or identify more taxa than could be identified by using only one region (Grealy et al, 2015). Extraction controls and three templatefree PCR controls were included, and unique indexes were used to eliminate the possibility of sequence contamination arising from previously amplified DNA.…”

Section: Amplicon Sequencingmentioning

confidence: 99%

“…Only reads flanked either side by sequences matching indexes and primers with 100% identity were accepted. Quality control was performed using the web-based workflow Galaxy (usegalaxy.org; Giardine et al, 2005;Blankenberg et al, 2010;Goecks et al, 2010), and chimera filtering and abundance filtering were performed using USEARCH v. 6.1 (Edgar, 2010;Edgar et al, 2011) in QIIME v. 1.8.0 (Caporaso et al, 2010), as per Grealy et al (2015): reads were required to have an average quality score above 25 (i.e. !Q25), 100% of bases over Q10, 98% of bases over Q15, and 90% of bases of Q20 to be accepted; chimeric reads and low-abundance reads (comprising <0.1% of the total number of reads) were discarded.…”

Section: Bioinformatics and Data Analysismentioning

confidence: 99%

“…Furthermore, the use of aDNA has had implications for the conservation and management of endangered animal populations (Shepherd and Lambert, 2008). With advances in DNA sequencing techniques, aDNA is being extracted from increasingly older fossil material in increasingly poor preservation conditions (Orlando et al, 2011;Murray et al, 2012), including the relatively warm, moist microclimates of many Australian cave systems (Murray et al, 2013;Haouchar et al, 2014;Llamas et al, 2014;Grealy et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Methodsmentioning

confidence: 99%

Section: Amplicon Sequencingmentioning

confidence: 99%

Section: Bioinformatics and Data Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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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“…1). A brief description of the site and its sediments was provided by Grealy et al (2015). Finsch's folly tomo contains rich and diverse late Holocene fauna and the site is the subject of continuing excavation and research.…”

Section: Study Sites and Specimensmentioning

confidence: 99%

Bone stable isotopes indicate a high trophic position for New Zealand’s extinct South Island adzebill (Aptornis defossor) (Gruiformes: Aptornithidae)

Wood¹,

Scofield²,

Hamel³

et al. 2017

NZ J Ecol

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Abstract:The adzebills (Aptornithidae) were an ancient endemic lineage of large flightless Gruiformes that became extinct shortly after Polynesian settlement of New Zealand. The diet and ecology of these enigmatic birds has long been a matter for conjecture, but recent stable isotope analyses of bones of the North Island adzebill (Aptornis otidiformis) have indicated that adzebills may have been predatory. Here, we add to our understanding of adzebill ecology by providing the first stable isotope analyses of South Island adzebill (A. defossor) bones from two Holocene deposits. We interpret the results within frameworks of stable isotope measurements on bones of faunal species with known diets and from the same deposits (thereby mitigating regional effects on isotope values). Our results strongly support the hypothesis that adzebills had a high trophic position. Considered alongside the unique skeletal adaptations of adzebills and the distribution of the species during the Holocene, we suggest that adzebills were most likely terrestrial predators restricted to dry podocarp forests and may have specialised in dismantling rotting logs to obtain invertebrates and/or excavating burrowing animals such as tuatara or the chicks of burrow-nesting birds.

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Identifying marsupials from Australian archaeological sites: current methodological challenges and opportunities in zooarchaeological practice

Mein

Manne

2021

Archaeology in Oceania

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We review current zooarchaeological practice in Australia, identifying major research themes and key methodological gaps where opportunities exist for the development of Australian zooarchaeology as a discipline. We demonstrate that marsupial remains form a significant component of Australian zooarchaeological assemblages, yet high resolution taxonomic identification of these remains continues to prove challenging, owing to a combination of high species diversity and few resources which provide diagnostic criteria for discriminating morphologically similar, but ecologically variable taxa. The lack of robust protocols for discriminating marsupial taxa significantly impacts our ability to effectively integrate zooarchaeological data into broader narratives of Aboriginal colonisation, resilience and adaptation across Australia. Publication of identification protocols would help refine and standardise diagnostic criteria used between analysts, improve the methodological transparency of zooarchaeological analysis and provide resources for the training of a new generation of specialists. A range of opportunities currently exist, utilising qualitative and quantitative techniques, to significantly contribute towards the methodological robustness of zooarchaeological practice in Australia.

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A critical evaluation of how ancient DNA bulk bone metabarcoding complements traditional morphological analysis of fossil assemblages

Cited by 37 publications

References 61 publications

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

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

Bone stable isotopes indicate a high trophic position for New Zealand’s extinct South Island adzebill (Aptornis defossor) (Gruiformes: Aptornithidae)

Identifying marsupials from Australian archaeological sites: current methodological challenges and opportunities in zooarchaeological practice

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