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Research data keyboard_double_arrow_right Dataset 2018Embargo end date: 13 Mar 2018 Spain EnglishPublisher:Dryad Funded by:EC | 100 Archaic Genomes, ARC | Australian Laureate Fello..., ARC | ARC Future Fellowships - ... +1 projectsEC| 100 Archaic Genomes ,ARC| Australian Laureate Fellowships - Grant ID: FL130100116 ,ARC| ARC Future Fellowships - Grant ID: FT140100384 ,ARC| ARC Future Fellowships - Grant ID: FT150100138Slon, Viviane; Hopfe, Charlotte; Weiss, Clemens L.; Mafessoni, Fabrizio; de la Rasilla, Marco; Lalueza-Fox, Carles;doi: 10.5061/dryad.m2dk7
handle: 10261/278288
Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples we detect Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility to detect the presence of hominin groups at sites and in areas where no skeletal remains are found. Multiple sequence alignment files This submission contains multiple sequence alignment files used for phylogenetic reconstructions. Sequences reconstructed from sediments are denominated by the site and layer of origin. The comparative data (identical in all files) is identified by the name of the individual and the accession code of its mtDNA sequence. MSA_sedimentDNA.zip Peer reviewed
DRYAD; ZENODO; NARCI... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICDataset . 2022 . 2018 . Peer-reviewedadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!visibility 33visibility views 33 download downloads 4 Powered bymore_vert DRYAD; ZENODO; NARCI... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICDataset . 2022 . 2018 . Peer-reviewedadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2013Embargo end date: 01 Mar 2013 EnglishPublisher:Dryad Funded by:ARC | An inventory of past biod..., ARC | Ancient DNA as a tool to ..., EC | HYRAXARC| An inventory of past biodiversity in Western Australia using ancient DNA. ,ARC| Ancient DNA as a tool to study Australia's paleome: exploring climatic change, past biodiversity, extinctions and long-term survival of DNA. ,EC| HYRAXMurray, Dáithí C.; Pearson, Stuart G.; Fullagar, Richard; Chase, Brian M.; Houston, Jayne; Atchison, Jennifer; White, Nicole E.; Bellgard, Matthew I.; Clarke, Edward; Macphail, Mike; Gilbert, M. Thomas P.; Haile, James; Bunce, Michael;doi: 10.5061/dryad.7334t
The study of arid palaeoenvironments is often frustrated by the poor or non-existent preservation of plant and animal material, yet these environments are of considerable environmental importance. The analysis of pollen and macrofossils isolated from herbivore middens has been an invaluable source of information regarding past environments and the nature of ecological fluctuations within arid zones. The application of ancient DNA (aDNA) techniques to hot, arid zone middens remains unexplored. This paper attempts to retrieve and characterise aDNA from four Southern Hemisphere fossil middens; three located in hot, arid regions of Australia and one sample from South Africa’s Western Cape province. The middens are dated to between 30,490 (±380) and 710 (±70) cal yr BP. The Brockman Ridge midden in this study is potentially the oldest sample from which aDNA has been successfully extracted in Australia. The application of high-throughput sequencing approaches to profile the biotic remains preserved in midden material has not been attempted to date and this study clearly demonstrates the potential of such a methodology. In addition to the taxa previously detected via macrofossil and palynological analyses, aDNA analysis indentified unreported plant and animal taxa, some of which are locally extinct or endemic. The survival and preservation of DNA in hot, arid environments is a complex and poorly understood process that is both sporadic and rare, but the survival of DNA through desiccation may be important. Herbivore middens now present an important source of material for DNA metabarcoding studies of hot, arid palaeoenvironments and can potentially be used to analyse middens in these environments throughout Australia, Africa, the Americas and the Middle East. CR_plant_trnLPlant trnL sequences from the midden located at Cavenagh Range, Western AustraliaTK_plant_trnLPlant trnL sequences from the midden located at Truitjes Kraal, Western Cape, South AfricaYR_plant_trnLPlant trnL sequences from the midden located at Young Range, Western AustraliaBR_mammal_16SMammalian 16S sequences from the midden located at Brockman Ridge, Western AustraliaBR_plant_trnLPlant trnL sequences from the midden located at Brockman Ridge, Western AustraliaCR_mammal_16SMammalian 16S sequences from the midden located at Cavenagh Range, Western AustraliaTK_mammal_16SMammalian 16S sequences from the midden located at Truitjes Kraal, South AfricaYR_mammal_16SMammalian 16S sequences from the midden located at Young Range, Western AustraliaBR_mammal_12SMammalian 12S sequences from the midden located at Brockman Ridge, Western AustraliaCR_mammal_12SMammalian 12S sequences from the midden located at Cavenagh Range, Western AustraliaTK_mammal_12SMammalian 12S sequences from the midden located at Truitjes Kraal, South AfricaYR_mammal_12SMammalian 12S sequences from the midden located at Young Range, Western Australia
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!visibility 40visibility views 40 download downloads 20 Powered bymore_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.5061/dryad.7334t&type=result"></script>'); --> </script>
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Research data keyboard_double_arrow_right Dataset 2018Embargo end date: 13 Mar 2018 Spain EnglishPublisher:Dryad Funded by:EC | 100 Archaic Genomes, ARC | Australian Laureate Fello..., ARC | ARC Future Fellowships - ... +1 projectsEC| 100 Archaic Genomes ,ARC| Australian Laureate Fellowships - Grant ID: FL130100116 ,ARC| ARC Future Fellowships - Grant ID: FT140100384 ,ARC| ARC Future Fellowships - Grant ID: FT150100138Slon, Viviane; Hopfe, Charlotte; Weiss, Clemens L.; Mafessoni, Fabrizio; de la Rasilla, Marco; Lalueza-Fox, Carles;doi: 10.5061/dryad.m2dk7
handle: 10261/278288
Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples we detect Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility to detect the presence of hominin groups at sites and in areas where no skeletal remains are found. Multiple sequence alignment files This submission contains multiple sequence alignment files used for phylogenetic reconstructions. Sequences reconstructed from sediments are denominated by the site and layer of origin. The comparative data (identical in all files) is identified by the name of the individual and the accession code of its mtDNA sequence. MSA_sedimentDNA.zip Peer reviewed
DRYAD; ZENODO; NARCI... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICDataset . 2022 . 2018 . Peer-reviewedadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.5061/dryad.m2dk7&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!visibility 33visibility views 33 download downloads 4 Powered bymore_vert DRYAD; ZENODO; NARCI... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICDataset . 2022 . 2018 . Peer-reviewedadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.5061/dryad.m2dk7&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2013Embargo end date: 01 Mar 2013 EnglishPublisher:Dryad Funded by:ARC | An inventory of past biod..., ARC | Ancient DNA as a tool to ..., EC | HYRAXARC| An inventory of past biodiversity in Western Australia using ancient DNA. ,ARC| Ancient DNA as a tool to study Australia's paleome: exploring climatic change, past biodiversity, extinctions and long-term survival of DNA. ,EC| HYRAXMurray, Dáithí C.; Pearson, Stuart G.; Fullagar, Richard; Chase, Brian M.; Houston, Jayne; Atchison, Jennifer; White, Nicole E.; Bellgard, Matthew I.; Clarke, Edward; Macphail, Mike; Gilbert, M. Thomas P.; Haile, James; Bunce, Michael;doi: 10.5061/dryad.7334t
The study of arid palaeoenvironments is often frustrated by the poor or non-existent preservation of plant and animal material, yet these environments are of considerable environmental importance. The analysis of pollen and macrofossils isolated from herbivore middens has been an invaluable source of information regarding past environments and the nature of ecological fluctuations within arid zones. The application of ancient DNA (aDNA) techniques to hot, arid zone middens remains unexplored. This paper attempts to retrieve and characterise aDNA from four Southern Hemisphere fossil middens; three located in hot, arid regions of Australia and one sample from South Africa’s Western Cape province. The middens are dated to between 30,490 (±380) and 710 (±70) cal yr BP. The Brockman Ridge midden in this study is potentially the oldest sample from which aDNA has been successfully extracted in Australia. The application of high-throughput sequencing approaches to profile the biotic remains preserved in midden material has not been attempted to date and this study clearly demonstrates the potential of such a methodology. In addition to the taxa previously detected via macrofossil and palynological analyses, aDNA analysis indentified unreported plant and animal taxa, some of which are locally extinct or endemic. The survival and preservation of DNA in hot, arid environments is a complex and poorly understood process that is both sporadic and rare, but the survival of DNA through desiccation may be important. Herbivore middens now present an important source of material for DNA metabarcoding studies of hot, arid palaeoenvironments and can potentially be used to analyse middens in these environments throughout Australia, Africa, the Americas and the Middle East. CR_plant_trnLPlant trnL sequences from the midden located at Cavenagh Range, Western AustraliaTK_plant_trnLPlant trnL sequences from the midden located at Truitjes Kraal, Western Cape, South AfricaYR_plant_trnLPlant trnL sequences from the midden located at Young Range, Western AustraliaBR_mammal_16SMammalian 16S sequences from the midden located at Brockman Ridge, Western AustraliaBR_plant_trnLPlant trnL sequences from the midden located at Brockman Ridge, Western AustraliaCR_mammal_16SMammalian 16S sequences from the midden located at Cavenagh Range, Western AustraliaTK_mammal_16SMammalian 16S sequences from the midden located at Truitjes Kraal, South AfricaYR_mammal_16SMammalian 16S sequences from the midden located at Young Range, Western AustraliaBR_mammal_12SMammalian 12S sequences from the midden located at Brockman Ridge, Western AustraliaCR_mammal_12SMammalian 12S sequences from the midden located at Cavenagh Range, Western AustraliaTK_mammal_12SMammalian 12S sequences from the midden located at Truitjes Kraal, South AfricaYR_mammal_12SMammalian 12S sequences from the midden located at Young Range, Western Australia
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.5061/dryad.7334t&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!visibility 40visibility views 40 download downloads 20 Powered bymore_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.5061/dryad.7334t&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu