1
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Wang X, Ganzert L, Bartholomäus A, Amen R, Yang S, Guzmán CM, Matus F, Albornoz MF, Aburto F, Oses-Pedraza R, Friedl T, Wagner D. The effects of climate and soil depth on living and dead bacterial communities along a longitudinal gradient in Chile. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:173846. [PMID: 38871316 DOI: 10.1016/j.scitotenv.2024.173846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Soil bacterial communities play a critical role in shaping soil stability and formation, exhibiting a dynamic interaction with local climate and soil depth. We employed an innovative DNA separation method to characterize microbial assemblages in low-biomass environments such as deserts and distinguish between intracellular DNA (iDNA) and extracellular DNA (eDNA) in soils. This approach, combined with analyses of physicochemical properties and co-occurrence networks, investigated soil bacterial communities across four sites representing diverse climatic gradients (i.e., arid, semi-arid, Mediterranean, and humid) along the Chilean Coastal Cordillera. The separation method yielded a distinctive unimodal pattern in the iDNA pool alpha diversity, increasing from arid to semi-arid climates and decreasing in humid environments, highlighting the rapid feedback of the iDNA community to increasing soil moisture. In the arid region, harsh surface conditions restrict bacterial growth, leading to peak iDNA abundance and diversity occurring in slightly deeper layers than the other sites. Our findings confirmed the association between specialist bacteria and ecosystem-functional traits. We observed transitions from Halomonas and Delftia, resistant to extreme arid environments, to Class AD3 and the genus Bradyrhizobium, associated with plants and organic matter in humid environments. The distance-based redundancy analysis (dbRDA) analysis revealed that soil pH and moisture were the key parameters that influenced bacterial community variation. The eDNA community correlated slightly better with the environment than the iDNA community. Soil depth was found to influence the iDNA community significantly but not the eDNA community, which might be related to depth-related metabolic activity. Our investigation into iDNA communities uncovered deterministic community assembly and distinct co-occurrence modules correlated with unique bacterial taxa, thereby showing connections with sites and key environmental factors. The study additionally revealed the effects of climatic gradients and soil depth on living and dead bacterial communities, emphasizing the need to distinguish between iDNA and eDNA pools.
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Affiliation(s)
- Xiuling Wang
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Lars Ganzert
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Alexander Bartholomäus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Rahma Amen
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; Department of Zoology, Faculty of Science, Aswan University, 81528 Aswan, Egypt
| | - Sizhong Yang
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Carolina Merino Guzmán
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, BIOREN, Universidad de La Frontera, Temuco 4780000, Chile
| | - Francisco Matus
- Laboratory of Conservation and Dynamics of Volcanic Soils, Department of Chemical Sciences and Natural Resources, Universidad de La Frontera, Temuco 4780000, Chile; Network for Extreme Environmental Research (NEXER), Universidad de La Frontera, Temuco 4780000, Chile
| | - Maria Fernanda Albornoz
- Laboratorio de Investigación de Suelos, Aguas y Bosques (LISAB), Universidad de Concepción, Concepción, Chile
| | - Felipe Aburto
- Pedology and Soil Biogeochemistry Lab, Soil and Crop Sciences Department, Texas A&M University, College Station, TX, USA
| | - Rómulo Oses-Pedraza
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama, Universidad de Atacama (CRIDESAT UDA), Copayapu 484, Copiapó 1530000, Chile
| | - Thomas Friedl
- Department of Experimental Phycology and Culture Collection of Algae (EPSAG), Albrecht-von-Haller-Institute for Plant Sciences, Georg August University, 37073 Göttingen, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; Institute of Geosciences, University of Potsdam, 14476 Potsdam, Germany.
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2
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Aldeias V, Stahlschmidt MC. Sediment DNA can revolutionize archaeology-if it is used the right way. Proc Natl Acad Sci U S A 2024; 121:e2317042121. [PMID: 38900796 PMCID: PMC11214044 DOI: 10.1073/pnas.2317042121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024] Open
Affiliation(s)
- Vera Aldeias
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour, Universidade do Algarve, Faro8005-139, Portugal
| | - Mareike C. Stahlschmidt
- Department of Evolutionary Anthropology, University of Vienna, Vienna1010, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna1010, Austria
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3
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Boilard A, Walker SJ, Lødøen TK, Henriksen M, Takken Beijersbergen LM, Star B, Robu M, Tøssebro C, Albrektsen CM, Soleng Y, Aksnes S, Jørgensen R, Hufthammer AK, van Kolfschoten T, Lauritzen SE, Boessenkool S. Ancient DNA and osteological analyses of a unique paleo-archive reveal Early Holocene faunal expansion into the Scandinavian Arctic. SCIENCE ADVANCES 2024; 10:eadk3032. [PMID: 38552017 PMCID: PMC10980262 DOI: 10.1126/sciadv.adk3032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 02/23/2024] [Indexed: 04/01/2024]
Abstract
Paleo-archives are essential for our understanding of species responses to climate warming, yet such archives are extremely rare in the Arctic. Here, we combine morphological analyses and bulk-bone metabarcoding to investigate a unique chronology of bone deposits sealed in the high-latitude Storsteinhola cave system (68°50' N 16°22' E) in Norway. This deposit dates to a period of climate warming from the end of the Late Glacial [~13 thousand calibrated years before the present (ka cal B.P.)] to the Holocene thermal maximum (~5.6 ka cal B.P.). Paleogenetic analyses allow us to exploit the 1000s of morphologically unidentifiable bone fragments resulting in a high-resolution sequence with 40 different taxa, including species not previously found here. Our record reveals borealization in both the marine and terrestrial environments above the Arctic Circle as a naturally recurring phenomenon in past periods of warming, providing fundamental insights into the ecosystem-wide responses that are ongoing today.
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Affiliation(s)
- Aurélie Boilard
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Samuel J. Walker
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Trond Klungseth Lødøen
- Department of Cultural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Mona Henriksen
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | | | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Marius Robu
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Karstonomy, Karst Inventory and Protection, Emil Racoviţă Institute of Speleology, Bucharest, Romania
| | - Christine Tøssebro
- Department of Cultural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | | | - Yvonne Soleng
- Department of Cultural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Sverre Aksnes
- Department of Earth Sciences, University of Bergen, Bergen, Norway
| | - Roger Jørgensen
- The Arctic University Museum of Norway, University of Tromsø, Tromsø, Norway
| | - Anne Karin Hufthammer
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Thijs van Kolfschoten
- Faculty of Archaeology, Leiden University, Leiden, Netherlands
- Joint International Research Laboratory of Environment and Social Archaeology, Shandong University, Qingdao, China
| | - Stein-Erik Lauritzen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Earth Sciences, University of Bergen, Bergen, Norway
- Department of Earth Science, Bjerknes Centre for Climate Research, University of Bergen, Bergen, Norway
- Centre for Early Sapiens Behaviour (SapienCE), University of Bergen, Bergen, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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4
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Seeber PA, Batke L, Dvornikov Y, Schmidt A, Wang Y, Stoof-Leichsenring K, Moon K, Vohr SH, Shapiro B, Epp LS. Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes. eLife 2024; 12:RP89992. [PMID: 38488477 PMCID: PMC10942779 DOI: 10.7554/elife.89992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Abstract
Ancient environmental DNA (aeDNA) from lake sediments has yielded remarkable insights for the reconstruction of past ecosystems, including suggestions of late survival of extinct species. However, translocation and lateral inflow of DNA in sediments can potentially distort the stratigraphic signal of the DNA. Using three different approaches on two short lake sediment cores of the Yamal peninsula, West Siberia, with ages spanning only the past hundreds of years, we detect DNA and identified mitochondrial genomes of multiple mammoth and woolly rhinoceros individuals-both species that have been extinct for thousands of years on the mainland. The occurrence of clearly identifiable aeDNA of extinct Pleistocene megafauna (e.g. >400 K reads in one core) throughout these two short subsurface cores, along with specificities of sedimentology and dating, confirm that processes acting on regional scales, such as extensive permafrost thawing, can influence the aeDNA record and should be accounted for in aeDNA paleoecology.
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Affiliation(s)
| | - Laura Batke
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Yury Dvornikov
- Agroengineering Department/Department of Landscape Design and Sustainable Ecosystems, Agrarian and Technological Institute, RUDN University, Moscow, Russian Federation
- Laboratory of Carbon Monitoring in Terrestrial Ecosystems, Institute of Physicochemical and Biological Problems of Soil Science of the Russian Academy of Sciences, Pushchino, Russian Federation
| | | | - Yi Wang
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Kathleen Stoof-Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Potsdam, Germany
| | - Katie Moon
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, United States
| | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, United States
| | - Laura S Epp
- Department of Biology, University of Konstanz, Konstanz, Germany
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5
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Johnson MD, Freeland JR, Parducci L, Evans DM, Meyer RS, Molano-Flores B, Davis MA. Environmental DNA as an emerging tool in botanical research. AMERICAN JOURNAL OF BOTANY 2023; 110:e16120. [PMID: 36632660 DOI: 10.1002/ajb2.16120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single-species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost-effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems.
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Affiliation(s)
- Mark D Johnson
- Engineering Research and Development Center, Construction Engineering Research Laboratory (CERL), Champaign, IL, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Joanna R Freeland
- Department of Biology, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
| | - Laura Parducci
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-75236, Uppsala, Sweden
| | - Darren M Evans
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Brenda Molano-Flores
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Mark A Davis
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
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6
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Seeber PA, Epp LS. Environmental
DNA
and metagenomics of terrestrial mammals as keystone taxa of recent and past ecosystems. Mamm Rev 2022. [DOI: 10.1111/mam.12302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Peter A. Seeber
- Limnological Institute University of Konstanz Konstanz Germany
| | - Laura S. Epp
- Limnological Institute University of Konstanz Konstanz Germany
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7
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Verry AJF, Lubbe P, Mitchell KJ, Rawlence NJ. Thirty years of ancient DNA and the faunal biogeography of Aotearoa New Zealand: lessons and future directions. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2093227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Alexander J. F. Verry
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
- Centre for Anthropobiology and Genomics of Toulouse, Faculté de Médecine Purpan, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Pascale Lubbe
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Kieren J. Mitchell
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Nicolas J. Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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8
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Lunghi E, Valle B, Guerrieri A, Bonin A, Cianferoni F, Manenti R, Ficetola GF. Environmental DNA of insects and springtails from caves reveals complex processes of eDNA transfer in soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154022. [PMID: 35202680 DOI: 10.1016/j.scitotenv.2022.154022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/01/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Subterranean environments host a substantial amount of biodiversity, however assessing the distribution of species living underground is still extremely challenging. Environmental DNA (eDNA) metabarcoding is a powerful tool to estimate biodiversity in poorly known environments and has excellent performance for soil organisms. Here, we tested 1) whether eDNA metabarcoding from cave soils/sediments allows to successfully detect springtails (Hexapoda: Collembola) and insects (Hexapoda: Insecta); 2) whether eDNA mostly represents autochthonous (cave-dwelling) organisms or it also incorporates information from species living in surface environments; 3) whether eDNA detection probability changes across taxa with different ecology. Environmental DNA metabarcoding analyses detected a large number of Molecular Operational Taxonomic Units (MOTUs) for both insects and springtails. For springtails, detection probability was high, with a substantial proportion of hypogean species, suggesting that eDNA provides good information on the distribution of these organisms in caves. Conversely, for insects most of MOTUs represented taxa living outside caves, and the majority of them represented taxa/organisms living in freshwater environments (Ephemeroptera, Plecoptera and Trichoptera). The eDNA of freshwater insects was particularly abundant in deep sectors of caves, far from the entrance. Furthermore, average detection probability of insects was significantly lower than the one of springtails. This suggests that cave soils/sediments act as "conveyer belts of biodiversity information", possibly because percolating water lead to the accumulation of eDNA of organisms living in nearby areas. Cave soils hold a complex mix of autochthonous and allochthonous eDNA. eDNA provided unprecedented information on the understudied subterranean cave organisms; analyses of detection probability and occupancy can help teasing apart local eDNA from the eDNA representing spatially-integrated biodiversity for whole landscape.
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Affiliation(s)
- Enrico Lunghi
- Division of Molecular Biology Ruđer Bošković Institute, Zagreb, Croatia; Natural Oasis, Prato, Italy.
| | - Barbara Valle
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy; Unità di Climatologia ed Ecologia, MUSE-Museo delle Scienze di Trento, Italy
| | - Alessia Guerrieri
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Aurélie Bonin
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Fabio Cianferoni
- Istituto di Ricerca sugli Ecosistemi Terrestri (IRET), Consiglio Nazionale delle Ricerche (CNR), Sesto Fiorentino (Firenze), Italy; Zoologia, La Specola, Museo di Storia Naturale, Università degli Studi di Firenze, Firenze, Italy
| | - Raoul Manenti
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy; Laboratorio di Biologia Sotterranea "Enrico Pezzoli", Parco Regionale del Monte Barro, Galbiate, Italy
| | - Gentile Francesco Ficetola
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy; Laboratoire d'Écologie Alpine (LECA), Université Grenoble Alpes, CNRS, Grenoble, France
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9
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Tsugeki N, Nakane K, Doi H, Ochi N, Kuwae M. Reconstruction of 100-year dynamics in Daphnia spawning activity revealed by sedimentary DNA. Sci Rep 2022; 12:1741. [PMID: 35110566 PMCID: PMC8810866 DOI: 10.1038/s41598-021-03899-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/10/2021] [Indexed: 11/09/2022] Open
Abstract
Environmental DNA (eDNA) is currently developing as a powerful tool for assessing aquatic species dynamics. However, its utility as an assessment tool for quantification remain under debate as the sources of eDNA for different species is not always known. Therefore, accumulating information about eDNA sources from different species is urgently required. The objective of our study was to evaluate whether sedimentary DNA targeting two Daphnia species, D. galeata and D. pulicaria, could track Daphnia population dynamics and resting egg production. Applying a quantitative PCR targeting the mitochondrial 12S rRNA gene on sediment cores collected in Lake Biwa, Japan, we compared sedimentary DNA concentration of Daphnia with the abundance of remains and ephippia, reflecting their abundance and resting egg production, respectively. We found that the sedimentary DNA concentrations of Daphnia for the past century were inconsistent with their population abundance. However, the concentration was highly correlated with the resting egg production. Our results provide evidence that ephippia with resting eggs, released during spawning activities, was a significant source of Daphnia DNA archived in sediments. Our work provides critical insights for using sedimentary DNA as a monitoring tool for egg production dating back 100 years.
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Affiliation(s)
- Narumi Tsugeki
- Faculty of Law, Matsuyama University, Matsuyama, 790-8578, Ehime, Japan.
| | - Kai Nakane
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Ehime, Japan
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, Kobe, 650-0047, Hyogo, Japan
| | - Natsuki Ochi
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Ehime, Japan
| | - Michinobu Kuwae
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Ehime, Japan
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10
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Murchie TJ, Karpinski E, Eaton K, Duggan AT, Baleka S, Zazula G, MacPhee RDE, Froese D, Poinar HN. Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments. Curr Biol 2022; 32:851-860.e7. [PMID: 35016010 DOI: 10.1016/j.cub.2021.12.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/20/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022]
Abstract
Traditionally, paleontologists have relied on the morphological features of bones and teeth to reconstruct the evolutionary relationships of extinct animals.1 In recent decades, the analysis of ancient DNA recovered from macrofossils has provided a powerful means to evaluate these hypotheses and develop novel phylogenetic models.2 Although a great deal of life history data can be extracted from bones, their scarcity and associated biases limit their information potential. The paleontological record of Beringia3-the unglaciated areas and former land bridge between northeast Eurasia and northwest North America-is relatively robust thanks to its perennially frozen ground favoring fossil preservation.4,5 However, even here, the macrofossil record is significantly lacking in small-bodied fauna (e.g., rodents and birds), whereas questions related to migration and extirpation, even among well-studied taxa, remain crudely resolved. The growing sophistication of ancient environmental DNA (eDNA) methods have allowed for the identification of species within terrestrial/aquatic ecosystems,6-12 in paleodietary reconstructions,13-19 and facilitated genomic reconstructions from cave contexts.8,20-22 Murchie et al.6,23 used a capture enrichment approach to sequence a diverse range of faunal and floral DNA from permafrost silts deposited during the Pleistocene-Holocene transition.24 Here, we expand on their work with the mitogenomic assembly and phylogenetic placement of Equus caballus (caballine horse), Bison priscus (steppe bison), Mammuthus primigenius (woolly mammoth), and Lagopus lagopus (willow ptarmigan) eDNA from multiple permafrost cores spanning the last 30,000 years. We identify a diverse metagenomic spectra of Pleistocene fauna and identify the eDNA co-occurrence of distinct Eurasian and American mitogenomic lineages.
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Affiliation(s)
- Tyler J Murchie
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada.
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Katherine Eaton
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Ana T Duggan
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Sina Baleka
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Grant Zazula
- Yukon Government, Palaeontology Program, Department of Tourism and Culture, Box 2703, Whitehorse, YT Y1A 2C6, Canada; Collections and Research, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, ON K1P 6P4, Canada
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB T6G 2E3, Canada.
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; CIFAR, Humans and the Microbiome Program, MaRS Centre, West Tower, 661 University Avenue, Suite 505, Toronto, ON M5G 1M1, Canada.
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11
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Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments. Proc Natl Acad Sci U S A 2022; 119:2113666118. [PMID: 34969841 PMCID: PMC8740756 DOI: 10.1073/pnas.2113666118] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 01/26/2023] Open
Abstract
DNA preserved in sediments has emerged as an important source of information about past ecosystems, independent of the discovery of skeletal remains. However, little is known about the sources of sediment DNA, the factors affecting its long-term preservation, and the extent to which it may be translocated after deposition. Here, we show that impregnated blocks of intact sediment are excellent archives of DNA. DNA distribution is highly heterogeneous at the microscale in the cave sediment we studied, suggesting that postdepositional movement of DNA is unlikely to be a common phenomenon in cases where the stratigraphy is undisturbed. Combining micromorphological analysis with microstratigraphic retrieval of ancient DNA therefore allows genetic information to be associated with the detailed archaeological and ecological record preserved in sediments. Ancient DNA recovered from Pleistocene sediments represents a rich resource for the study of past hominin and environmental diversity. However, little is known about how DNA is preserved in sediments and the extent to which it may be translocated between archaeological strata. Here, we investigate DNA preservation in 47 blocks of resin-impregnated archaeological sediment collected over the last four decades for micromorphological analyses at 13 prehistoric sites in Europe, Asia, Africa, and North America and show that such blocks can preserve DNA of hominins and other mammals. Extensive microsampling of sediment blocks from Denisova Cave in the Altai Mountains reveals that the taxonomic composition of mammalian DNA differs drastically at the millimeter-scale and that DNA is concentrated in small particles, especially in fragments of bone and feces (coprolites), suggesting that these are substantial sources of DNA in sediments. Three microsamples taken in close proximity in one of the blocks yielded Neanderthal DNA from at least two male individuals closely related to Denisova 5, a Neanderthal toe bone previously recovered from the same layer. Our work indicates that DNA can remain stably localized in sediments over time and provides a means of linking genetic information to the archaeological and ecological records on a microstratigraphic scale.
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12
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Jensen EL, Díez-del-Molino D, Gilbert MTP, Bertola LD, Borges F, Cubric-Curik V, de Navascués M, Frandsen P, Heuertz M, Hvilsom C, Jiménez-Mena B, Miettinen A, Moest M, Pečnerová P, Barnes I, Vernesi C. Ancient and historical DNA in conservation policy. Trends Ecol Evol 2022; 37:420-429. [DOI: 10.1016/j.tree.2021.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 12/15/2022]
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13
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Reply to: When did mammoths go extinct? Nature 2022; 612:E4-E6. [PMID: 36450908 PMCID: PMC9712097 DOI: 10.1038/s41586-022-05417-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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14
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Abstract
Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computational analyses. Furthermore, researchers often work with finite sample sizes, which impedes optimal experimental design and control of confounding factors, and with ethically sensitive samples necessitating the consideration of additional guidelines. In September 2020, early career researchers in the field of ancient metagenomics met (Standards, Precautions & Advances in Ancient Metagenomics 2 [SPAAM2] community meeting) to discuss the state of the field and how to address current challenges. Here, in an effort to bridge the gap between ancient and modern metagenomics, we highlight and reflect upon some common misconceptions, provide a brief overview of the challenges in our field, and point toward useful resources for potential reviewers and newcomers to the field.
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15
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Ancient DNA diffuses from human bones to cave stones. iScience 2021; 24:103397. [PMID: 34988387 PMCID: PMC8710462 DOI: 10.1016/j.isci.2021.103397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 11/22/2022] Open
Abstract
Recent studies have demonstrated the potential to recover ancient human mitochondrial DNA and nuclear DNA from cave sediments. However, the source of such sedimentary ancient DNA is still under discussion. Here we report the case of a Bronze Age human skeleton, found in a limestone cave, which was covered with layers of calcite stone deposits. By analyzing samples representing bones and stone deposits from this cave, we were able to: i) reconstruct the full human mitochondrial genome from the bones and the stones (same haplotype); ii) determine the sex of the individual; iii) reconstruct six ancient bacterial and archaeal genomes; and finally iv) demonstrate better ancient DNA preservation in the stones than in the bones. Thereby, we demonstrate the direct diffusion of human DNA from bones into the surrounding environment and show the potential to reconstruct ancient microbial genomes from such cave deposits, which represent an additional paleoarcheological archive resource.
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16
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Murchie TJ, Monteath AJ, Mahony ME, Long GS, Cocker S, Sadoway T, Karpinski E, Zazula G, MacPhee RDE, Froese D, Poinar HN. Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA. Nat Commun 2021; 12:7120. [PMID: 34880234 PMCID: PMC8654998 DOI: 10.1038/s41467-021-27439-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 11/22/2021] [Indexed: 12/30/2022] Open
Abstract
The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record.
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Affiliation(s)
- Tyler J Murchie
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada. .,Department of Anthropology, McMaster University, Hamilton, Canada.
| | - Alistair J Monteath
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada.,School of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom
| | - Matthew E Mahony
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - George S Long
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada
| | - Scott Cocker
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - Tara Sadoway
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,The Hospital for Sick Children, Toronto, Canada
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada
| | - Grant Zazula
- Yukon Government, Palaeontology Program, Department of Tourism and Culture, Whitehorse, Canada.,Collections and Research, Canadian Museum of Nature, Ottawa, Canada
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, New York, United States
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada.
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada. .,Department of Anthropology, McMaster University, Hamilton, Canada. .,Department of Biochemistry, McMaster University, Hamilton, Canada. .,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada. .,CIFAR Humans and the Microbiome Program, Toronto, Canada.
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17
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Badania kopalnego DNA – możliwości i ograniczenia. POSTEP HIG MED DOSW 2021. [DOI: 10.2478/ahem-2021-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Abstrakt
Ostatnie cztery dekady przyniosły znaczący rozwój archeologii molekularnej i badania nad kopalnym DNA (aDNA). Nowatorskie metody uwzględniają szeroki zakres badań, począwszy od sekwencjonowania niewielkich fragmentów mitochondrialnego DNA po wielkoskalowe badania całych populacji, łączące sekwencjonowanie genomów mitochondrialnych, genów podlegających doborowi naturalnemu, jak i całych genomów jądrowych. Postęp, zwłaszcza w dziedzinie technologii sekwencjonowania DNA, umożliwił pozyskanie informacji ze szczątków paleontologicznych i materiału archeologicznego, umożliwiając zbadanie związków filogenetycznych między wymarłymi i współczesnymi gatunkami. Dzięki zastosowaniu technologii sekwencjonowania nowej generacji możliwe stało się poznanie sekwencji DNA nie tylko bezpośrednio ze szczątków ludzkich lub zwierzęcych, ale także z osadów sedymentacyjnych z głębin jezior oraz jaskiń. W artykule przedstawiono możliwości i ograniczenia występujące w badaniach nad kopalnym DNA ludzi, zwierząt czy bakterii z podkreśleniem wkładu polskich badaczy w rozwój tej dziedziny nauki.
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18
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Dussex N, Bergfeldt N, de Anca Prado V, Dehasque M, Díez-Del-Molino D, Ersmark E, Kanellidou F, Larsson P, Lemež Š, Lord E, Mármol-Sánchez E, Meleg IN, Måsviken J, Naidoo T, Studerus J, Vicente M, von Seth J, Götherström A, Dalén L, Heintzman PD. Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics. Proc Biol Sci 2021; 288:20211252. [PMID: 34428961 PMCID: PMC8385357 DOI: 10.1098/rspb.2021.1252] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.
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Affiliation(s)
- Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Nora Bergfeldt
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Marianne Dehasque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Erik Ersmark
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Foteini Kanellidou
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Petter Larsson
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Špela Lemež
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Emilio Mármol-Sánchez
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ioana N Meleg
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,'Emil Racoviță' Institute of Speleology of the Romanian Academy, Calea 13 Septembrie, nr. 13, 050711, Sector 5, Bucharest, Romania.,Emil. G. Racoviță Institute, Babeș-Bolyai University, Clinicilor 5-7, 400006 Cluj-Napoca, Romania
| | - Johannes Måsviken
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Ancient DNA Unit, SciLifeLab, Stockholm and Uppsala, Sweden
| | - Jovanka Studerus
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Mário Vicente
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Peter D Heintzman
- The Arctic University Museum of Norway, The Arctic University of Norway, 9037 Tromsø, Norway
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19
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Abstract
Researchers in the ancient DNA community have suspected for well over a decade that ancient whole genomes can be found in sediments. Three new studies now provide such evidence and, with it, endless possibilities for future studies of sedimentary ancient DNA.
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Affiliation(s)
- Anna Linderholm
- Centre for Palaeogenetics, Stockholm University, 10691 Stockholm, Sweden; Department of Geological Sciences, Stockholm University, 10691 Stockholm, Sweden.
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20
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Zavala EI, Jacobs Z, Vernot B, Shunkov MV, Kozlikin MB, Derevianko AP, Essel E, de Fillipo C, Nagel S, Richter J, Romagné F, Schmidt A, Li B, O'Gorman K, Slon V, Kelso J, Pääbo S, Roberts RG, Meyer M. Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave. Nature 2021; 595:399-403. [PMID: 34163072 PMCID: PMC8277575 DOI: 10.1038/s41586-021-03675-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/27/2021] [Indexed: 12/31/2022]
Abstract
Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals1–4. The dozen hominin remains recovered from the deposits also include Neanderthals5,6 and the child of a Neanderthal and a Denisovan7, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages5,8–11. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly—possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments. Ancient mitochondrial DNA from sediments reveals the sequence of Denisovan, Neanderthal and faunal occupation of Denisova Cave, and evidence for the appearance of modern humans at least 45,000 years ago.
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Affiliation(s)
- Elena I Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia. .,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Fillipo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Richter
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frédéric Romagné
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Schmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Bo Li
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Kieran O'Gorman
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Viviane Slon
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Shmunis Family Anthropology Institute, The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Richard G Roberts
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia. .,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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21
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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. QUATERNARY 2021. [DOI: 10.3390/quat4010006] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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22
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Kévin R, Nicolas C, Elsa P, Paolo L, Pasquino P, Raffaella B, Matthieu LB. Gastrointestinal parasite burden in 4th-5th c. CE Florence highlighted by microscopy and paleogenetics. INFECTION GENETICS AND EVOLUTION 2021; 90:104713. [PMID: 33429070 DOI: 10.1016/j.meegid.2021.104713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/25/2020] [Accepted: 01/06/2021] [Indexed: 10/22/2022]
Abstract
The study of ancient parasites, named paleoparasitology, traditionally focused on microscopic eggs disseminated in past environments and archaeological structures by humans and other animals infested by gastrointestinal parasites. Since the development of paleogenetics in the early 1980s, few paleoparasitological studies have been based on the ancient DNA (aDNA) of parasites, although such studies have clearly proven their utility and reliability. In this paper, we describe our integrative approach for the paleoparasitological study of an ancient population from Florence in Italy, dated to the 4th-5th c. CE. The first stage consisted in the study of sediment samples from the pelvic area of 18 individuals under light microscopy. This allowed us to detect Ascarid-type eggs belonging very probably to the human-infesting roundworm Ascaris lumbricoides. Ten subsamples were selected corresponding to five individuals, and we extracted their whole DNA following sediment aDNA protocols. A targeted approach allowed us to detect two nematodes and one trematode aDNA fragments, namely Ascaris sp., Trichuris trichiura, and Dicrocoelium dendriticum. Among the five individuals tested for microscopic eggs and aDNA, three of them showed the remains of eggs (only Ascarid-type), but all of them tested positive to the presence of at least one parasite aDNA. Microscopic diagnosis first guided our research for the selection of promising samples while the targeted aDNA approach significantly improved our knowledge in terms of parasitic diversity and frequency in this population subgroup. These results enabled us to discuss the possible impact of latent parasitism in this past population at the time of an epidemic, as suggested in Florence. In particular, the singular case of D. dendriticum detection is discussed in light of the present-day scarcity of genuine human infections. Nevertheless, actual infections are known in the paleoparasitological record, and food habits may have led to false parasitism in this historical context. aDNA leaching from overlying strata may also explain this detection. This study strongly pleads for a systematic integrative approach combining microscopy and aDNA in paleoparasitology.
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Affiliation(s)
- Roche Kévin
- Université Bordeaux Montaigne, CNRS UMR 5607 Ausonius, France; Université de Bourgogne Franche-Comté, CNRS UMR 6249 Chrono-Environnement, France.
| | - Capelli Nicolas
- Université de Bourgogne Franche-Comté, CNRS UMR 6249 Chrono-Environnement, France
| | - Pacciani Elsa
- Soprintendenza Archeologia, Belle Arti e Paesaggio of Firenze, Pistoia and Prato, Italy
| | | | - Pallecchi Pasquino
- Soprintendenza Archeologia, Belle Arti e Paesaggio of Firenze, Pistoia and Prato, Italy
| | - Bianucci Raffaella
- Legal Medicine Section, Department of Public Health and Paediatric Sciences, University of Turin, Italy; Warwick Medical School, Biomedical Sciences, University of Warwick, United Kingdom; ADES (UMR 7268), Laboratoire d'Anthropologie bio-culturelle, Droit, Ethique & Santé (Adés), Faculté de Médecine de Marseille, France
| | - Le Bailly Matthieu
- Université de Bourgogne Franche-Comté, CNRS UMR 6249 Chrono-Environnement, France.
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23
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Using environmental DNA methods to survey for rare groundwater fauna: Detection of an endangered endemic cave crayfish in northern Alabama. PLoS One 2020; 15:e0242741. [PMID: 33301442 PMCID: PMC7728221 DOI: 10.1371/journal.pone.0242741] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/06/2020] [Indexed: 11/25/2022] Open
Abstract
The conservation and management of subterranean biodiversity is hindered by a lack of knowledge on the true distributions for many species, e.g., the Wallacean shortfall. In recent years, several studies have demonstrated the potential of environmental DNA (eDNA) as an effective approach to detect and monitor biodiversity, including rare, threatened, and endangered taxa. However, there are few eDNA studies of groundwater fauna. Here we report the results of the development and implementation of an eDNA assay targeting a short fragment of the mitochondrial CO1 locus of a critically imperiled cave crayfish, the Sweet Home Alabama Cave Crayfish (Cambarus speleocoopi), known from just four cave systems in the Interior Plateau karst region of northern Alabama. We detected C. speleocoopi DNA from water samples collected at 5 of 16 sites sampled (caves and springs), including two historical sites as well as three additional and potentially new sites in Marshall County, Alabama. All three of these sites were within 2 km of historical sites. Our study is the first to detect a groundwater crustacean in the Interior Plateau karst region. Additionally, our study contributes to the growing literature that eDNA is a viable complementary tool for detection and monitoring of a fauna that is difficult to survey and study using traditional approaches.
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24
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Researchers using environmental DNA must engage ethically with Indigenous communities. Nat Ecol Evol 2020; 5:146-148. [PMID: 33184485 DOI: 10.1038/s41559-020-01351-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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25
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Kuwae M, Tamai H, Doi H, Sakata MK, Minamoto T, Suzuki Y. Sedimentary DNA tracks decadal-centennial changes in fish abundance. Commun Biol 2020; 3:558. [PMID: 33033377 PMCID: PMC7546629 DOI: 10.1038/s42003-020-01282-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 09/09/2020] [Indexed: 01/28/2023] Open
Abstract
Far too little is known about the long-term dynamics of populations for almost all macro-organisms. Here, we examined the utility of sedimentary DNA techniques to reconstruct the dynamics in the “abundance” of a species, which has not been previously defined. We used fish DNA in marine sediments and examined whether it could be used to track the past dynamics of pelagic fish abundance in marine waters. Quantitative PCR for sedimentary DNA was applied on sediment-core samples collected from anoxic bottom sediments in Beppu Bay, Japan. The DNA of three dominant fish species (anchovy, sardine, and jack mackerel) were quantified in sediment sequences spanning the last 300 years. Temporal changes in fish DNA concentrations are consistent with those of landings in Japan for all three species and with those of sardine fish scale concentrations. Thus, sedimentary DNA could be used to track decadal-centennial dynamics of fish abundance in marine waters. Michinobu Kuwae et al. reconstruct the past dynamics of pelagic fish abundance in Beppu Bay of Japan, using sedimentary DNA. This study demonstrates the utility of sedimentary DNA in investigating the history of fish abundance in marine waters.
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Affiliation(s)
- Michinobu Kuwae
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Japan.
| | - Hiromichi Tamai
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Japan
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, Kobe, 650-0047, Japan
| | - Masayuki K Sakata
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan
| | - Yoshiaki Suzuki
- Research Institute of Geology and Geoinformation, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8567, Japan
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26
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Jacobson DK, Honap TP, Monroe C, Lund J, Houk BA, Novotny AC, Robin C, Marini E, Lewis CM. Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190586. [PMID: 33012230 PMCID: PMC7702801 DOI: 10.1098/rstb.2019.0586] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human microbiome studies are increasingly incorporating macroecological approaches, such as community assembly, network analysis and functional redundancy to more fully characterize the microbiome. Such analyses have not been applied to ancient human microbiomes, preventing insights into human microbiome evolution. We address this issue by analysing published ancient microbiome datasets: coprolites from Rio Zape (n = 7; 700 CE Mexico) and historic dental calculus (n = 44; 1770–1855 CE, UK), as well as two novel dental calculus datasets: Maya (n = 7; 170 BCE-885 CE, Belize) and Nuragic Sardinians (n = 11; 1400–850 BCE, Italy). Periodontitis-associated bacteria (Treponema denticola, Fusobacterium nucleatum and Eubacterium saphenum) were identified as keystone taxa in the dental calculus datasets. Coprolite keystone taxa included known short-chain fatty acid producers (Eubacterium biforme, Phascolarctobacterium succinatutens) and potentially disease-associated bacteria (Escherichia, Brachyspira). Overlap in ecological profiles between ancient and modern microbiomes was indicated by similarity in functional response diversity profiles between contemporary hunter–gatherers and ancient coprolites, as well as parallels between ancient Maya, historic UK, and modern Spanish dental calculus; however, the ancient Nuragic dental calculus shows a distinct ecological structure. We detected key ecological signatures from ancient microbiome data, paving the way to expand understanding of human microbiome evolution. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
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Affiliation(s)
- David K Jacobson
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Tanvi P Honap
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Cara Monroe
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Justin Lund
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Brett A Houk
- Department of Sociology, Anthropology, and Social Work, Texas Tech University, Lubbock, TX, USA
| | - Anna C Novotny
- Department of Sociology, Anthropology, and Social Work, Texas Tech University, Lubbock, TX, USA
| | - Cynthia Robin
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Elisabetta Marini
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Sardinia, Italy
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
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Dommain R, Andama M, McDonough MM, Prado NA, Goldhammer T, Potts R, Maldonado JE, Nkurunungi JB, Campana MG. The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA: A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00218] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Shillito LM, Whelton HL, Blong JC, Jenkins DL, Connolly TJ, Bull ID. Pre-Clovis occupation of the Americas identified by human fecal biomarkers in coprolites from Paisley Caves, Oregon. SCIENCE ADVANCES 2020; 6:eaba6404. [PMID: 32743069 PMCID: PMC7363456 DOI: 10.1126/sciadv.aba6404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
When and how people first settled in the Americas is an ongoing area of research and debate. The earliest sites typically only contain lithic artifacts that cannot be directly dated. The lack of human skeletal remains in these early contexts means that alternative sources of evidence are needed. Coprolites, and the DNA contained within them, are one such source, but unresolved issues concerning ancient DNA taphonomy and potential for contamination make this approach problematic. Here, we use fecal lipid biomarkers to demonstrate unequivocally that three coprolites dated to pre-Clovis are human, raise questions over the reliance on DNA methods, and present a new radiocarbon date on basketry further supporting pre-Clovis human occupation.
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Affiliation(s)
- Lisa-Marie Shillito
- School of History, Classics and Archaeology, Armstrong Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Helen L. Whelton
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - John C. Blong
- School of History, Classics and Archaeology, Armstrong Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Dennis L. Jenkins
- Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA
| | - Thomas J. Connolly
- Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA
| | - Ian D. Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
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Smith O, Dunshea G, Sinding MHS, Fedorov S, Germonpre M, Bocherens H, Gilbert MTP. Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival. PLoS Biol 2019; 17:e3000166. [PMID: 31361744 PMCID: PMC6667121 DOI: 10.1371/journal.pbio.3000166] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/25/2019] [Indexed: 01/31/2023] Open
Abstract
While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here, we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but it also shows evidence of biologically relevant tissue specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data’s authenticity. By performing independent technical library replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues but also that it has potential for tissue identification. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology. Ancient DNA is known to survive in cold environments for tens of millennia, but it is assumed that ancient RNA could not persist in such a way due to its relative instability. However, this study shows that under permafrost conditions, ancient RNA can survive well enough to show tissue specificity even in mammalian soft tissues.
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Affiliation(s)
- Oliver Smith
- Section for Evogenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Glenn Dunshea
- Section for Evogenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel-Holger S. Sinding
- Section for Evogenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Sergey Fedorov
- Mammoth Museum, Institute of Applied Ecology of the North of the North-Eastern Federal University, Yakutsk, Russia
| | - Mietje Germonpre
- Directorate Earth and History of Life, Royal Belgian Institute of Natural Science, Brussels, Belgium
| | - Hervé Bocherens
- Department of Geosciences, Palaeobiology, University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - M. T. P. Gilbert
- Section for Evogenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
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Espunyes J, Espunya C, Chaves S, Calleja JA, Bartolomé J, Serrano E. Comparing the accuracy of PCR-capillary electrophoresis and cuticle microhistological analysis for assessing diet composition in ungulates: A case study with Pyrenean chamois. PLoS One 2019; 14:e0216345. [PMID: 31116750 PMCID: PMC6530829 DOI: 10.1371/journal.pone.0216345] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/18/2019] [Indexed: 11/18/2022] Open
Abstract
The study of diet composition is required to understand the interactions between animal and plant ecosystems. Different non-invasive techniques applied on faecal samples have commonly been used for such purposes, with cuticle microhistological analysis (CMA) and emerging DNA-based methods being the most relevant. In this work, we refined and optimized a qualitative DNA-based approach combining PCR amplification of long trnL(UAA) and ITS2 fragments and capillary electrophoresis (PCR-CE), instead of short trnL(UAA) fragments and massive sequencing technologies commonly reported. To do so, we developed a controlled diet assay using a stabled Pyrenean chamois specimen (Rupicapra pyrenaica pyrenaica), which included representative herbaceous and shrubby plant species. We also assessed the impact of sample freshness on the diet determination of this mountain caprinae by exposing faecal samples to the outdoor environment for three weeks. Faecal samples from both experiments were analysed by qualitative PCR-CE and semi-quantitative CMA in order to compare the pros and cons of both approaches. Our results show that all of the offered plant species were detected by both methodologies although CMA over-detected shrubs compared to herbaceous species. At the same time, sample degradation due to sustained climate exposure is a limiting factor for molecular analysis, but not for CMA. Taken all together, our results suggest that the qualitative information obtained by CMA and PCR-CE can be interchangeable when faecal samples are fresh (less than one week after deposition) but, afterwards, molecular analysis underestimates diet composition probably due to DNA degradation. CMA, however, can accurately be used at least three weeks after defecation. Moreover, by combining the results of simultaneous PCR amplification of two complementary genes, this optimized PCR-CE methodology provides a reliable, feasible and more affordable alternative for multiple and routine analyses of complex samples. Neither CMA nor PCR-CE seems to solve comprehensively the quatification of herbivore diets and thus further research needs to be done.
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Affiliation(s)
- Johan Espunyes
- Wildlife Ecology & Health Group (WE&H) and Servei d’Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i de Cirurgia Animals, Universitat Autònoma de Barcelona UAB, Bellaterra, Spain
| | - Carme Espunya
- Departament de Bioquímica i de Biologia Molecular, UAB, Bellaterra, Spain
| | - Sara Chaves
- Wildlife Ecology & Health Group (WE&H) and Servei d’Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i de Cirurgia Animals, Universitat Autònoma de Barcelona UAB, Bellaterra, Spain
| | - Juan Antonio Calleja
- Centre de Recerca Ecològica i Aplicacions Forestals (CREAF), Cerdanyola del Vallès, Spain
| | - Jordi Bartolomé
- Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, UAB, Bellaterra, Spain
| | - Emmanuel Serrano
- Wildlife Ecology & Health Group (WE&H) and Servei d’Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i de Cirurgia Animals, Universitat Autònoma de Barcelona UAB, Bellaterra, Spain
- Dipartimento di Scienze Veterinarie, Universitá di Torino, Grugliasco, Torino, Italy
- * E-mail:
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31
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Del Carmen Gomez Cabrera M, Young JM, Roff G, Staples T, Ortiz JC, Pandolfi JM, Cooper A. Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA. Mol Ecol 2019; 28:2636-2652. [PMID: 30723959 DOI: 10.1111/mec.15038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 01/10/2019] [Accepted: 01/18/2019] [Indexed: 11/30/2022]
Abstract
Marine environments face acute pressures from human impacts, often resulting in substantial changes in community structure. On the inshore Great Barrier Reef (GBR), palaeoecological studies show the collapse of the previously dominant coral Acropora from the impacts of degraded water quality associated with European colonization. Even more dramatic impacts can result in the replacement of corals by fleshy macroalgae on modern reefs, but their past distribution is unknown because they leave no fossil record. Here, we apply DNA metabarcoding and high-throughput sequencing of the 18S rDNA gene on palaeoenvironmental DNA (aeDNA) derived from sediment cores at two sites on Pandora Reef (GBR), to enhance palaeoecological studies by incorporating key soft-bodied taxa, including macroalgae. We compared temporal trends in this aeDNA record with those of coral genera derived from macrofossils. Multivariate analysis of 12 eukaryotic groups from the aeDNA community showed wide variability over the past 750 years. The occurrence of brown macroalgae was negatively correlated only with the dominant coral at both sites. The occurrence of coralline and green macroalgae was positively correlated with only the dominant coral at one of the sites, where we also observed a significant association between the whole coral community and the occurrence of each of the three macroalgae groups. Our results demonstrate that reef sediments can provide a valuable archive for understanding the past distribution and occurrence of important soft-bodied reef dwellers. Combining information from fossils and aeDNA provides an enhanced understanding of temporal changes of reefs ecosystems at decadal to millennial timescales.
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Affiliation(s)
- Maria Del Carmen Gomez Cabrera
- Australian Research Council Centre of Excellence for Coral Reef Studies, Centre for Marine Science and School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Jennifer M Young
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - George Roff
- Australian Research Council Centre of Excellence for Coral Reef Studies, Centre for Marine Science and School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Timothy Staples
- Australian Research Council Centre of Excellence for Coral Reef Studies, Centre for Marine Science and School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Juan Carlos Ortiz
- Australian Research Council Centre of Excellence for Coral Reef Studies, Centre for Marine Science and School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Institute for Marine Science, Townsville, Queensland, Australia
| | - John M Pandolfi
- Australian Research Council Centre of Excellence for Coral Reef Studies, Centre for Marine Science and School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
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32
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Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia. Sci Rep 2019; 9:6628. [PMID: 31036834 PMCID: PMC6488622 DOI: 10.1038/s41598-019-43147-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/15/2019] [Indexed: 11/08/2022] Open
Abstract
Metagenomic analysis is a highly promising technique in paleogenetic research that allows analysis of the complete genomic make-up of a sample. This technique has successfully been employed to archaeological sediments, but possible leaching of DNA through the sequence limits interpretation. We applied this technique to the analysis of ancient DNA (aDNA) from Late Quaternary stalagmites from two caves in Western Georgia, Melouri Cave and Solkota. Stalagmites form closed systems, limiting the effect of leaching, and can be securely dated with U-series. The analyses of the sequence data from the Melouri Cave stalagmite revealed potential contamination and low preservation of DNA. However, the two Solkota stalagmites preserved ancient DNA molecules of mammals (bear, roe deer, bats) and plants (chestnut, hazelnut, flax). The aDNA bearing layers from one of the two Solkota stalagmites were dated to between ~84 ka and ~56 ka BP by U-series. The second Solkota stalagmite contained excessive detrital clay obstructing U-series dating, but it also contained bear bones with a minimum age of ~50 BP uncalibrated years and ancient DNA molecules. The preservation of authentic ancient DNA molecules in Late Quaternary speleothems opens up a new paleogenetic archive for archaeological, paleontological and paleoenvironmental research.
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Bálint M, Pfenninger M, Grossart HP, Taberlet P, Vellend M, Leibold MA, Englund G, Bowler D. Environmental DNA Time Series in Ecology. Trends Ecol Evol 2018; 33:945-957. [DOI: 10.1016/j.tree.2018.09.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/28/2018] [Accepted: 09/05/2018] [Indexed: 12/13/2022]
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Cristescu ME, Hebert PD. Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062306] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The study of environmental DNA (eDNA) has the potential to revolutionize biodiversity science and conservation action by enabling the census of species on a global scale in near real time. To achieve this promise, technical challenges must be resolved. In this review, we explore the main uses of eDNA as well as the complexities introduced by its misuse. Current eDNA methods require refinement and improved calibration and validation along the entire workflow to lessen false positives/negatives. Moreover, there is great need for a better understanding of the “natural history” of eDNA—its origins, state, lifetime, and transportation—and for more detailed insights concerning the physical and ecological limitations of eDNA use. Although eDNA analysis can provide powerful information, particularly in freshwater and marine environments, its impact is likely to be less significant in terrestrial settings. The broad adoption of eDNA tools in conservation will largely depend on addressing current uncertainties in data interpretation.
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Affiliation(s)
| | - Paul D.N. Hebert
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Ontario N1G 2W1, Canada
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35
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Kisand V, Talas L, Kisand A, Stivrins N, Reitalu T, Alliksaar T, Vassiljev J, Liiv M, Heinsalu A, Seppä H, Veski S. From microbial eukaryotes to metazoan vertebrates: Wide spectrum paleo-diversity in sedimentary ancient DNA over the last ~14,500 years. GEOBIOLOGY 2018; 16:628-639. [PMID: 30035382 DOI: 10.1111/gbi.12307] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/09/2018] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
Most studies that utilize ancient DNA have focused on specific groups of organisms or even single species. Instead, the whole biodiversity of eukaryotes can be described using universal phylogenetic marker genes found within well-preserved sediment cores that cover the post-glacial period. Sedimentary ancient DNA samples from Lake Lielais Svētiņu, eastern Latvia, at a core depth of 1,050 cm in ~150 year intervals were used to determine phylotaxonomy in domain Eukaryota. Phylotaxonomic affiliation of >1,200 eukaryotic phylotypes revealed high richness in all major eukaryotic groups-Alveolata, Stramenopiles, Cercozoa, Chlorophyta, Charophyta, Nucletmycea, and Holozoa. The share of organisms that originate from terrestrial ecosystems was about one third, of which the most abundant molecular operational taxonomic units were Fungi and tracheal/vascular plants, which demonstrates the usefulness of using lake sediments to reconstruct the terrestrial paleoecosystems that surround them. Phylotypes that originate from the lake ecosystem belonged to various planktonic organisms; phyto-, proto,- and macrozooplankton, and vascular aquatic plants. We observed greater richness of several planktonic organisms that can be associated with higher trophic status during the warm climate period between 4,000 and 8,000 years ago and an increase in eukaryotic richness possibly associated with moderate human impact over the last 2,000 years.
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Affiliation(s)
- Veljo Kisand
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Liisi Talas
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Anu Kisand
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Normunds Stivrins
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
- Department of Geography, Faculty of Geography and Earth Sciences, University of Latvia, Riga, Latvia
| | - Triin Reitalu
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Tiiu Alliksaar
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Jüri Vassiljev
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Merlin Liiv
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Atko Heinsalu
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Heikki Seppä
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Siim Veski
- Department of Geology, Tallinn University of Technology, Tallinn, Estonia
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Sand KK, Jelavić S. Mineral Facilitated Horizontal Gene Transfer: A New Principle for Evolution of Life? Front Microbiol 2018; 9:2217. [PMID: 30319562 PMCID: PMC6167411 DOI: 10.3389/fmicb.2018.02217] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/30/2018] [Indexed: 11/22/2022] Open
Abstract
A number of studies have highlighted that adsorption to minerals increases DNA longevity in the environment. Such DNA-mineral associations can essentially serve as pools of genes that can be stored across time. Importantly, this DNA is available for incorporation into alien organisms through the process of horizontal gene transfer (HGT). Here we argue that minerals hold an unrecognized potential for successfully transferring genetic material across environments and timescales to distant organisms and hypothesize that this process has significantly influenced the evolution of life. Our hypothesis is illustrated in the context of the evolution of early microbial life and the oxygenation of the Earth's atmosphere and offers an explanation for observed outbursts of evolutionary events caused by HGT.
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Affiliation(s)
- Karina Krarup Sand
- Department of Geography and Earth Sciences, Aberystwyth University, Aberystwyth, United Kingdom
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Stanislav Jelavić
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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Fernandes K, van der Heyde M, Bunce M, Dixon K, Harris RJ, Wardell-Johnson G, Nevill PG. DNA metabarcoding-a new approach to fauna monitoring in mine site restoration. Restor Ecol 2018. [DOI: 10.1111/rec.12868] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kristen Fernandes
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
| | - Mieke van der Heyde
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
| | - Kingsley Dixon
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
| | - Richard J. Harris
- School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
| | - Grant Wardell-Johnson
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
| | - Paul G. Nevill
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
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38
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Nichols RV, Vollmers C, Newsom LA, Wang Y, Heintzman PD, Leighton M, Green RE, Shapiro B. Minimizing polymerase biases in metabarcoding. Mol Ecol Resour 2018; 18:927-939. [PMID: 29797549 DOI: 10.1111/1755-0998.12895] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/12/2018] [Accepted: 03/01/2018] [Indexed: 01/24/2023]
Abstract
DNA metabarcoding is an increasingly popular method to characterize and quantify biodiversity in environmental samples. Metabarcoding approaches simultaneously amplify a short, variable genomic region, or "barcode," from a broad taxonomic group via the polymerase chain reaction (PCR), using universal primers that anneal to flanking conserved regions. Results of these experiments are reported as occurrence data, which provide a list of taxa amplified from the sample, or relative abundance data, which measure the relative contribution of each taxon to the overall composition of amplified product. The accuracy of both occurrence and relative abundance estimates can be affected by a variety of biological and technical biases. For example, taxa with larger biomass may be better represented in environmental samples than those with smaller biomass. Here, we explore how polymerase choice, a potential source of technical bias, might influence results in metabarcoding experiments. We compared potential biases of six commercially available polymerases using a combination of mixtures of amplifiable synthetic sequences and real sedimentary DNA extracts. We find that polymerase choice can affect both occurrence and relative abundance estimates and that the main source of this bias appears to be polymerase preference for sequences with specific GC contents. We further recommend an experimental approach for metabarcoding based on results of our synthetic experiments.
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Affiliation(s)
- Ruth V Nichols
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California
| | - Lee A Newsom
- Department of Social Sciences, Flagler College, St. Augustine, Florida
| | - Yue Wang
- Department of Geography, University of Wisconsin-Madison, Madison, Wisconsin
| | - Peter D Heintzman
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California
- Tromsø University Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - McKenna Leighton
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California
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Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol 2018; 66:e1-e29. [PMID: 28173586 PMCID: PMC5410953 DOI: 10.1093/sysbio/syw059] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 12/02/2022] Open
Abstract
Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.
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Affiliation(s)
- Michela Leonardi
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, Toulouse, France
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40
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Buxton AS, Groombridge JJ, Griffiths RA. Seasonal variation in environmental DNA detection in sediment and water samples. PLoS One 2018; 13:e0191737. [PMID: 29352294 PMCID: PMC5774844 DOI: 10.1371/journal.pone.0191737] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/10/2018] [Indexed: 11/18/2022] Open
Abstract
The use of aquatic environmental DNA (eDNA) to detect the presence of species depends on the seasonal activity of the species in the sampled habitat. eDNA may persist in sediments for longer than it does in water, and analysing sediment could potentially extend the seasonal window for species assessment. Using the great crested newt as a model, we compare how detection probability changes across the seasons in eDNA samples collected from both pond water and pond sediments. Detection of both aquatic and sedimentary eDNA varied through the year, peaking in the summer (July), with its lowest point in the winter (January): in all seasons, detection probability of eDNA from water exceeded that from sediment. Detection probability of eDNA also varied between study areas, and according to great crested newt habitat suitability and sediment type. As aquatic and sedimentary eDNA show the same seasonal fluctuations, the patterns observed in both sample types likely reflect current or recent presence of the target species. However, given the low detection probabilities found in the autumn and winter we would not recommend using either aquatic or sedimentary eDNA for year-round sampling without further refinement and testing of the methods.
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Affiliation(s)
- Andrew S. Buxton
- Durrell Institute for Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, Kent, United Kingdom
- * E-mail:
| | - Jim J. Groombridge
- Durrell Institute for Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, Kent, United Kingdom
| | - Richard A. Griffiths
- Durrell Institute for Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, Kent, United Kingdom
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41
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Raemy M, Ursenbacher S. Detection of the European pond turtle (Emys orbicularis) by environmental DNA: is eDNA adequate for reptiles? AMPHIBIA-REPTILIA 2018. [DOI: 10.1163/15685381-17000025] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Recent studies have demonstrated the potential of combining molecular technologies with environmental sampling to detect various vertebrate species in aquatic ecosystems. The European pond turtle (Emys orbicularis) is a threatened and elusive aquatic reptile with shy behaviour. We aimed to develop and evaluate a methodology to detect the presence of this secretive aquatic reptile in ponds from environmental water samples. First, we determined that reptilian DNA can be isolated and amplified from water samples in artificial and natural ponds with known turtle density. Then we compared the potential of two water sampling methods (through filtration or precipitation) and found no significant differences between these approaches. Finally, we demonstrated that the eDNA concentration detected is not correlated with the number of E. orbicularis individuals or biomass. Detection of eDNA was higher in artificial ponds with small volumes of water or in the shallow waters of natural ponds. The eDNA-based methodology aims to detect the presence of specific species, even at low density, with better accuracy than visual observation. However, our study indicates that this method of population monitoring should be applied with caution to aquatic reptiles.
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Affiliation(s)
- Matthieu Raemy
- Department of Environmental Sciences, Section of Conservation Biology, University of Basel, St. Johanns-Vorstadt 10, CH-4056 Basel, Switzerland
| | - Sylvain Ursenbacher
- Department of Environmental Sciences, Section of Conservation Biology, University of Basel, St. Johanns-Vorstadt 10, CH-4056 Basel, Switzerland
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42
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43
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Environmental DNA as a tool for ecological monitoring of fungal communities. UKRAINIAN BOTANICAL JOURNAL 2017. [DOI: 10.15407/ukrbotj74.05.442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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44
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Cole TL, Wood JR. The ancient DNA revolution: the latest era in unearthing New Zealand’s faunal history. NEW ZEALAND JOURNAL OF ZOOLOGY 2017. [DOI: 10.1080/03014223.2017.1376690] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Theresa L. Cole
- Department of Zoology, University of Otago, Dunedin, New Zealand
- Long Term Ecology Lab, Landcare Research, Lincoln, New Zealand
| | - Jamie R. Wood
- Long Term Ecology Lab, Landcare Research, Lincoln, New Zealand
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45
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Olajos F, Bokma F, Bartels P, Myrstener E, Rydberg J, Öhlund G, Bindler R, Wang X, Zale R, Englund G. Estimating species colonization dates using
DNA
in lake sediment. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12890] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fredrik Olajos
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Folmer Bokma
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Pia Bartels
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Erik Myrstener
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Johan Rydberg
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Gunnar Öhlund
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Richard Bindler
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Xiao‐Ru Wang
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Rolf Zale
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
| | - Göran Englund
- Department of Ecology & Environmental ScienceUmeå University Umeå Sweden
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46
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Andruszkiewicz EA, Sassoubre LM, Boehm AB. Persistence of marine fish environmental DNA and the influence of sunlight. PLoS One 2017; 12:e0185043. [PMID: 28915253 PMCID: PMC5600408 DOI: 10.1371/journal.pone.0185043] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/04/2017] [Indexed: 11/23/2022] Open
Abstract
Harnessing information encoded in environmental DNA (eDNA) in marine waters has the potential to revolutionize marine biomonitoring. Whether using organism-specific quantitative PCR assays or metabarcoding in conjunction with amplicon sequencing, scientists have illustrated that realistic organism censuses can be inferred from eDNA. The next step is establishing ways to link information obtained from eDNA analyses to actual organism abundance. This is only possible by understanding the processes that control eDNA concentrations. The present study uses mesocosm experiments to study the persistence of eDNA in marine waters and explore the role of sunlight in modulating eDNA persistence. We seeded solute-permeable dialysis bags with water containing indigenous eDNA and suspended them in a large tank containing seawater. Bags were subjected to two treatments: half the bags were suspended near the water surface where they received high doses of sunlight, and half at depth where they received lower doses of sunlight. Bags were destructively sampled over the course of 87 hours. eDNA was extracted from water samples and used as template for a Scomber japonicus qPCR assay and a marine fish-specific 12S rRNA PCR assay. The latter was subsequently sequenced using a metabarcoding approach. S. japonicus eDNA, as measured by qPCR, exhibited first order decay with a rate constant ~0.01 hr -1 with no difference in decay rate constants between the two experimental treatments. eDNA metabarcoding identified 190 organizational taxonomic units (OTUs) assigned to varying taxonomic ranks. There was no difference in marine fish communities as measured by eDNA metabarcoding between the two experimental treatments, but there was an effect of time. Given the differences in UVA and UVB fluence received by the two experimental treatments, we conclude that sunlight is not the main driver of fish eDNA decay in the experiments. However, there are clearly temporal effects that need to be considered when interpreting information obtained using eDNA approaches.
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Affiliation(s)
- Elizabeth A. Andruszkiewicz
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
| | - Lauren M. Sassoubre
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
- * E-mail:
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47
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Time to Spread Your Wings: A Review of the Avian Ancient DNA Field. Genes (Basel) 2017; 8:genes8070184. [PMID: 28718817 PMCID: PMC5541317 DOI: 10.3390/genes8070184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/27/2017] [Accepted: 07/10/2017] [Indexed: 01/16/2023] Open
Abstract
Ancient DNA (aDNA) has the ability to inform the evolutionary history of both extant and extinct taxa; however, the use of aDNA in the study of avian evolution is lacking in comparison to other vertebrates, despite birds being one of the most species-rich vertebrate classes. Here, we review the field of “avian ancient DNA” by summarising the past three decades of literature on this topic. Most studies over this time have used avian aDNA to reconstruct phylogenetic relationships and clarify taxonomy based on the sequencing of a few mitochondrial loci, but recent studies are moving toward using a comparative genomics approach to address developmental and functional questions. Applying aDNA analysis with more practical outcomes in mind (such as managing conservation) is another increasingly popular trend among studies that utilise avian aDNA, but the majority of these have yet to influence management policy. We find that while there have been advances in extracting aDNA from a variety of avian substrates including eggshell, feathers, and coprolites, there is a bias in the temporal focus; the majority of the ca. 150 studies reviewed here obtained aDNA from late Holocene (100–1000 yBP) material, with few studies investigating Pleistocene-aged material. In addition, we identify and discuss several other issues within the field that require future attention. With more than one quarter of Holocene bird extinctions occurring in the last several hundred years, it is more important than ever to understand the mechanisms driving the evolution and extinction of bird species through the use of aDNA.
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48
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Niemeyer B, Epp LS, Stoof-Leichsenring KR, Pestryakova LA, Herzschuh U. A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline. Mol Ecol Resour 2017; 17:e46-e62. [DOI: 10.1111/1755-0998.12689] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 04/13/2017] [Accepted: 04/25/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Bastian Niemeyer
- Periglacial Research Section; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research; Potsdam Germany
- Institute of Earth and Environmental Science; University of Potsdam; Potsdam-Golm Germany
| | - Laura S. Epp
- Periglacial Research Section; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research; Potsdam Germany
| | | | - Luidmila A. Pestryakova
- Department for Geography and Biology; North-Eastern Federal University of Yakutsk; Yakutsk Russia
| | - Ulrike Herzschuh
- Periglacial Research Section; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research; Potsdam Germany
- Institute of Earth and Environmental Science; University of Potsdam; Potsdam-Golm Germany
- Institute of Biochemistry and Biology; University of Potsdam; Potsdam-Golm Germany
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49
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Philips A, Stolarek I, Kuczkowska B, Juras A, Handschuh L, Piontek J, Kozlowski P, Figlerowicz M. Comprehensive analysis of microorganisms accompanying human archaeological remains. Gigascience 2017; 6:1-13. [PMID: 28609785 PMCID: PMC5965364 DOI: 10.1093/gigascience/gix044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/09/2017] [Accepted: 06/11/2017] [Indexed: 02/01/2023] Open
Abstract
Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that the vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains. DNA samples were isolated from the teeth of human skeletons dated from 100 AD to 1200 AD. The skeletons were collected from 7 archaeological sites in Central Europe and stored under different conditions. The majority of identified microbes were ubiquitous environmental bacteria that most likely contaminated the host remains not long ago. We observed that the composition of microbial communities was sample-specific and not correlated with its temporal or geographical origin. Additionally, traces of bacteria and archaea typical for human oral/gut flora, as well as potential pathogens, were identified in two-thirds of the samples. The genetic material of human-related species, in contrast to the environmental species that accounted for the majority of identified bacteria, displayed DNA damage patterns comparable with endogenous human ancient DNA, which suggested that these microbes might have accompanied the individual before death. Our study showed that the microbiome observed in an individual sample is not reliant on the method or duration of sample storage. Moreover, shallow sequencing of DNA extracted from ancient specimens and subsequent bioinformatics analysis allowed both the identification of ancient microbial species, including potential pathogens, and their differentiation from contemporary species that colonized human remains more recently.
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Affiliation(s)
- Anna Philips
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Ireneusz Stolarek
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Bogna Kuczkowska
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty
of Biology, Adam Mickiewicz University in Poznan, Poznan, 61-614, Poland
| | - Luiza Handschuh
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Department of Hematology and Bone Marrow Transplantation, University of
Medical Sciences, Poznan, 60-569, Poland
- Institute of Technology and Chemical Engineering, Poznan University of
Technology, Poznan, 60-965, Poland
| | - Janusz Piontek
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty
of Biology, Adam Mickiewicz University in Poznan, Poznan, 61-614, Poland
| | - Piotr Kozlowski
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Institute of Technology and Chemical Engineering, Poznan University of
Technology, Poznan, 60-965, Poland
| | - Marek Figlerowicz
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan,
60-965, Poland
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50
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Parducci L, Bennett KD, Ficetola GF, Alsos IG, Suyama Y, Wood JR, Pedersen MW. Ancient plant DNA in lake sediments. THE NEW PHYTOLOGIST 2017; 214:924-942. [PMID: 28370025 DOI: 10.1111/nph.14470] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/07/2016] [Indexed: 05/14/2023]
Abstract
Contents 924 I. 925 II. 925 III. 927 IV. 929 V. 930 VI. 930 VII. 931 VIII. 933 IX. 935 X. 936 XI. 938 938 References 938 SUMMARY: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
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Affiliation(s)
- Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Keith D Bennett
- Department of Geography & Sustainable Development, School of Geography & Geosciences, University of St Andrews, St Andrews, Fife, KY16 9AL, UK
- Marine Laboratory, Queen's University Belfast, Portaferry, BT22 1LS, UK
| | - Gentile Francesco Ficetola
- CNRS, Université Grenoble-Alpes, Laboratoire d'Ecologie Alpine (LECA), Grenoble, F-38000, France
- Department of Biosciences, Università degli Studi di Milano, Milan, 20133, Italy
| | - Inger Greve Alsos
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, NO-9037, Norway
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Jamie R Wood
- Long-term Ecology Lab, Landcare Research, PO Box 69040, Lincoln Canterbury, 7640, New Zealand
| | - Mikkel Winther Pedersen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
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