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Özdoğan KT, Gelabert P, Hammers N, Altınışık NE, de Groot A, Plets G. Archaeology meets environmental genomics: implementing sedaDNA in the study of the human past. ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES 2024; 16:108. [PMID: 38948161 PMCID: PMC11213777 DOI: 10.1007/s12520-024-01999-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/20/2024] [Indexed: 07/02/2024]
Abstract
Sedimentary ancient DNA (sedaDNA) has become one of the standard applications in the field of paleogenomics in recent years. It has been used for paleoenvironmental reconstructions, detecting the presence of prehistoric species in the absence of macro remains and even investigating the evolutionary history of a few species. However, its application in archaeology has been limited and primarily focused on humans. This article argues that sedaDNA holds significant potential in addressing key archaeological questions concerning the origins, lifestyles, and environments of past human populations. Our aim is to facilitate the integration of sedaDNA into the standard workflows in archaeology as a transformative tool, thereby unleashing its full potential for studying the human past. Ultimately, we not only underscore the challenges inherent in the sedaDNA field but also provide a research agenda for essential enhancements needed for implementing sedaDNA into the archaeological workflow.
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Affiliation(s)
- Kadir Toykan Özdoğan
- Department of History and Art History, Utrecht University, Drift 6, Utrecht, 3512 BS Netherlands
- Animal Ecology, Wageningen Environmental Research, P.O box 47, Wageningen, Gelderland 6700 AA The Netherlands
| | - Pere Gelabert
- Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, Vienna, 1030 Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Djerassiplatz 1, Vienna, 1030 Austria
| | - Neeke Hammers
- Environmental Archaeology, ADC ArcheoProjecten, Nijverheidsweg-Noord 114, Amersfoort, Utrecht, 3812 PN Netherlands
| | - N. Ezgi Altınışık
- Human-G Laboratory, Department of Anthropology, Hacettepe University, Ankara, 06800 Türkiye
| | - Arjen de Groot
- Animal Ecology, Wageningen Environmental Research, P.O box 47, Wageningen, Gelderland 6700 AA The Netherlands
| | - Gertjan Plets
- Department of History and Art History, Utrecht University, Drift 6, Utrecht, 3512 BS Netherlands
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2
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Fordham DA, Brown SC, Canteri E, Austin JJ, Lomolino MV, Haythorne S, Armstrong E, Bocherens H, Manica A, Rey-Iglesia A, Rahbek C, Nogués-Bravo D, Lorenzen ED. 52,000 years of woolly rhinoceros population dynamics reveal extinction mechanisms. Proc Natl Acad Sci U S A 2024; 121:e2316419121. [PMID: 38830089 PMCID: PMC11181021 DOI: 10.1073/pnas.2316419121] [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] [Received: 09/24/2023] [Accepted: 04/29/2024] [Indexed: 06/05/2024] Open
Abstract
The extinction of the woolly rhinoceros (Coelodonta antiquitatis) at the onset of the Holocene remains an enigma, with conflicting evidence regarding its cause and spatiotemporal dynamics. This partly reflects challenges in determining demographic responses of late Quaternary megafauna to climatic and anthropogenic causal drivers with available genetic and paleontological techniques. Here, we show that elucidating mechanisms of ancient extinctions can benefit from a detailed understanding of fine-scale metapopulation dynamics, operating over many millennia. Using an abundant fossil record, ancient DNA, and high-resolution simulation models, we untangle the ecological mechanisms and causal drivers that are likely to have been integral in the decline and later extinction of the woolly rhinoceros. Our 52,000-y reconstruction of distribution-wide metapopulation dynamics supports a pathway to extinction that began long before the Holocene, when the combination of cooling temperatures and low but sustained hunting by humans trapped woolly rhinoceroses in suboptimal habitats along the southern edge of their range. Modeling indicates that this ecological trap intensified after the end of the last ice age, preventing colonization of newly formed suitable habitats, weakening stabilizing metapopulation processes, triggering the extinction of the woolly rhinoceros in the early Holocene. Our findings suggest that fragmentation and resultant metapopulation dynamics should be explicitly considered in explanations of late Quaternary megafauna extinctions, sending a clarion call to the fragility of the remaining large-bodied grazers restricted to disjunct fragments of poor-quality habitat due to anthropogenic environmental change.
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Affiliation(s)
- Damien A. Fordham
- The Environment Institute, School of Biological Sciences, University of Adelaide, AdelaideSA, 5005, Australia
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø2100, Denmark
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen Ø2100, Denmark
| | - Stuart C. Brown
- The Environment Institute, School of Biological Sciences, University of Adelaide, AdelaideSA, 5005, Australia
- Globe Institute, University of Copenhagen, Copenhagen K1350, Denmark
| | - Elisabetta Canteri
- The Environment Institute, School of Biological Sciences, University of Adelaide, AdelaideSA, 5005, Australia
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø2100, Denmark
| | - Jeremy J. Austin
- The Environment Institute, School of Biological Sciences, University of Adelaide, AdelaideSA, 5005, Australia
| | - Mark V. Lomolino
- Department of Environmental and Forest Biology, College of Environmental Science, Syracuse, NY13210
| | - Sean Haythorne
- The Environment Institute, School of Biological Sciences, University of Adelaide, AdelaideSA, 5005, Australia
- Centre of Excellence for Biosecurity Risk Analysis, School of Biosciences, University of Melbourne, Melbourne, VIC3010, Australia
| | - Edward Armstrong
- Department of Geosciences and Geography, University of Helsinki, Helsinki, FI-00014, Finland
| | - Hervé Bocherens
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Tübingen72074, Germany
- Department of Geosciences, Biogeology, University of Tübingen, Tübingen72074, Germany
| | - Andrea Manica
- Department of Zoology, University of Cambridge, CB23EJCambridge, United Kingdom
| | - Alba Rey-Iglesia
- Globe Institute, University of Copenhagen, Copenhagen K1350, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø2100, Denmark
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen Ø2100, Denmark
- Institute of Ecology, Peking University, Beijing100871, China
- Danish Institute for Advanced Study, University of Southern Denmark, Odense M5230, Denmark
| | - David Nogués-Bravo
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø2100, Denmark
| | - Eline D. Lorenzen
- Globe Institute, University of Copenhagen, Copenhagen K1350, Denmark
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Alsos IG, Boussange V, Rijal DP, Beaulieu M, Brown AG, Herzschuh U, Svenning JC, Pellissier L. Using ancient sedimentary DNA to forecast ecosystem trajectories under climate change. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230017. [PMID: 38583481 PMCID: PMC10999269 DOI: 10.1098/rstb.2023.0017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 10/22/2023] [Indexed: 04/09/2024] Open
Abstract
Ecosystem response to climate change is complex. In order to forecast ecosystem dynamics, we need high-quality data on changes in past species abundance that can inform process-based models. Sedimentary ancient DNA (sedaDNA) has revolutionised our ability to document past ecosystems' dynamics. It provides time series of increased taxonomic resolution compared to microfossils (pollen, spores), and can often give species-level information, especially for past vascular plant and mammal abundances. Time series are much richer in information than contemporary spatial distribution information, which have been traditionally used to train models for predicting biodiversity and ecosystem responses to climate change. Here, we outline the potential contribution of sedaDNA to forecast ecosystem changes. We showcase how species-level time series may allow quantification of the effect of biotic interactions in ecosystem dynamics, and be used to estimate dispersal rates when a dense network of sites is available. By combining palaeo-time series, process-based models, and inverse modelling, we can recover the biotic and abiotic processes underlying ecosystem dynamics, which are traditionally very challenging to characterise. Dynamic models informed by sedaDNA can further be used to extrapolate beyond current dynamics and provide robust forecasts of ecosystem responses to future climate change. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.
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Affiliation(s)
- Inger Greve Alsos
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Victor Boussange
- Department of Environmental System Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Dilli Prasad Rijal
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Marieke Beaulieu
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Antony Gavin Brown
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Ulrike Herzschuh
- Alfred Wegener Institute for Polar and Marine Research, Telegraphenberg A43, 14473 Potsdam, Germany
- Institute of Environmental Sciences and Geography, Potsdam University, 14479 Potsdam, Germany
| | - Jens-Christian Svenning
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) & Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Loïc Pellissier
- Department of Environmental System Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
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4
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Liu S, Stoof-Leichsenring KR, Harms L, Schulte L, Mischke S, Kruse S, Zhang C, Herzschuh U. Tibetan terrestrial and aquatic ecosystems collapsed with cryosphere loss inferred from sedimentary ancient metagenomics. SCIENCE ADVANCES 2024; 10:eadn8490. [PMID: 38781339 PMCID: PMC11114237 DOI: 10.1126/sciadv.adn8490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024]
Abstract
Glacier and permafrost shrinkage and land-use intensification threaten mountain wildlife and affect nature conservation strategies. Here, we present paleometagenomic records of terrestrial and aquatic taxa from the southeastern Tibetan Plateau covering the last 18,000 years to help understand the complex alpine ecosystem dynamics. We infer that steppe-meadow became woodland at 14 ka (cal BP) controlled by cryosphere loss, further driving a herbivore change from wild yak to deer. These findings weaken the hypothesis of top-down control by large herbivores in the terrestrial ecosystem. We find a turnover in the aquatic communities at 14 ka, transitioning from glacier-related (blue-green) algae to abundant nonglacier-preferring picocyanobacteria, macrophytes, fish, and otters. There is no evidence for substantial effects of livestock herding in either ecosystem. Using network analysis, we assess the stress-gradient hypothesis and reveal that root hemiparasitic and cushion plants are keystone taxa. With ongoing cryosphere loss, the protection of their habitats is likely to be of conservation benefit on the Tibetan Plateau.
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Affiliation(s)
- Sisi Liu
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam 14473, Germany
- Institute of Environmental Science and Geography, University of Potsdam, Potsdam 14469, Germany
| | - Kathleen R. Stoof-Leichsenring
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam 14473, Germany
| | - Lars Harms
- Computing and Data Centre, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven 27570, Germany
| | - Luise Schulte
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam 14473, Germany
| | - Steffen Mischke
- Institute of Earth Sciences, University of Iceland, Reykjavík 102, Iceland
| | - Stefan Kruse
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam 14473, Germany
| | - Chengjun Zhang
- School of Earth Sciences, Lanzhou University, Lanzhou 73000, China
| | - Ulrike Herzschuh
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam 14473, Germany
- Institute of Environmental Science and Geography, University of Potsdam, Potsdam 14469, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
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5
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Bell KL, Campos M, Hoffmann BD, Encinas-Viso F, Hunter GC, Webber BL. Environmental DNA methods for biosecurity and invasion biology in terrestrial ecosystems: Progress, pitfalls, and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171810. [PMID: 38513869 DOI: 10.1016/j.scitotenv.2024.171810] [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: 12/21/2023] [Revised: 03/13/2024] [Accepted: 03/16/2024] [Indexed: 03/23/2024]
Abstract
Analysis of environmental DNA (eDNA) enables indirect detection of species without the need to directly observe and sample them. For biosecurity and invasion biology, eDNA-based methods are useful to address biological invasions at all phases, from detecting arrivals to confirming eradication of past invasions. We conducted a systematic review of the literature and found that in biosecurity and invasion biology, eDNA has primarily been used to detect new incursions and monitor spread in marine and freshwater ecosystems, with much slower uptake in terrestrial ecosystems, reflecting a broader trend common to the usage of eDNA tools. In terrestrial ecosystems, eDNA research has mostly focussed on the use of eDNA metabarcoding to characterise biodiversity, rather than targeting biosecurity threats or non-native populations. We discuss how eDNA-based methods are being applied to terrestrial ecosystems for biosecurity and managing non-native populations at each phase of the invasion continuum: transport, introduction, establishment, and spread; across different management options: containment, control, and eradication; and for detecting the impact of non-native organisms. Finally, we address some of the current technical issues and caveats of eDNA-based methods, particularly for terrestrial ecosystems, and how these might be solved. As eDNA-based methods improve, they will play an increasingly important role in the early detection and adaptive management of biological invasions, and the implementation of effective biosecurity controls.
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Affiliation(s)
- Karen L Bell
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.
| | - Mariana Campos
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; Harry Butler Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
| | | | - Francisco Encinas-Viso
- CSIRO Centre of Australian National Biodiversity Research, Black Mountain, Australian Capital Territory 2601, Australia
| | - Gavin C Hunter
- CSIRO Health & Biosecurity, Black Mountain, Australian Capital Territory 2601, Australia
| | - Bruce L Webber
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
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6
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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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7
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Karabanina E, Lansink GMJ, Ponnikas S, Kvist L. A renewed glance at the Palearctic golden eagle: Genetic variation in space and time. Ecol Evol 2024; 14:e11109. [PMID: 38469039 PMCID: PMC10925523 DOI: 10.1002/ece3.11109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
Anthropogenic pressures on nature have been causing population declines for centuries. Intensified persecution of apex predators, like the golden eagle, resulted in population bottlenecks during the 19th and 20th centuries. To study population genetics and demographic history of the golden eagle throughout its distribution, we collected museum samples from previously underrepresented regions, such as Russia and Central Asia. We used 12 microsatellite loci and a fragment of the mitochondrial DNA control region to re-evaluate phylogeography of Eurasian golden eagles and study the impacts of the population bottleneck. Our results revealed a north-south genetic gradient, expressed by the difference between Mediterranean and Holarctic lineages, as well as genetically distinct Northern Europe and Central Asia and Caucasus regions. Furthermore, Northern Europe exhibited the lowest, whereas Central Asia and Caucasus had the highest genetic diversity. Although golden eagles maintained relatively high genetic diversity, we detected genetic signatures of the recent bottleneck, including reduced genetic diversity and a decline in the effective female population size around the year 1975. Our study improves the knowledge of the genetic composition of Eurasian golden eagles and highlights the importance of understanding their historical population dynamics in the face of ongoing and future conservation efforts.
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Affiliation(s)
| | | | - Suvi Ponnikas
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Laura Kvist
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
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8
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Bernatchez L, Ferchaud AL, Berger CS, Venney CJ, Xuereb A. Genomics for monitoring and understanding species responses to global climate change. Nat Rev Genet 2024; 25:165-183. [PMID: 37863940 DOI: 10.1038/s41576-023-00657-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2023] [Indexed: 10/22/2023]
Abstract
All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.
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Affiliation(s)
- Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada.
- Parks Canada, Office of the Chief Ecosystem Scientist, Protected Areas Establishment, Quebec City, Quebec, Canada.
| | - Chloé Suzanne Berger
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Amanda Xuereb
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
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9
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Rowe AG, Bataille CP, Baleka S, Combs EA, Crass BA, Fisher DC, Ghosh S, Holmes CE, Krasinski KE, Lanoë F, Murchie TJ, Poinar H, Potter B, Rasic JT, Reuther J, Smith GM, Spaleta KJ, Wygal BT, Wooller MJ. A female woolly mammoth's lifetime movements end in an ancient Alaskan hunter-gatherer camp. SCIENCE ADVANCES 2024; 10:eadk0818. [PMID: 38232155 DOI: 10.1126/sciadv.adk0818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024]
Abstract
Woolly mammoths in mainland Alaska overlapped with the region's first people for at least a millennium. However, it is unclear how mammoths used the space shared with people. Here, we use detailed isotopic analyses of a female mammoth tusk found in a 14,000-year-old archaeological site to show that she moved ~1000 kilometers from northwestern Canada to inhabit an area with the highest density of early archaeological sites in interior Alaska until her death. DNA from the tusk and other local contemporaneous archaeological mammoth remains revealed that multiple mammoth herds congregated in this region. Early Alaskans seem to have structured their settlements partly based on mammoth prevalence and made use of mammoths for raw materials and likely food.
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Affiliation(s)
- Audrey G Rowe
- Alaska Stable Isotope Facility, University of Alaska Fairbanks, AK, USA
- Department of Marine Biology, University of Alaska Fairbanks, AK, USA
| | - Clement P Bataille
- Department of Earth and Environmental Sciences, University of Ottawa, Ontario, Canada
- Department of Biology, University of Ottawa, Ontario, Canada
| | - Sina Baleka
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
| | | | - Barbara A Crass
- University of Alaska Museum of the North, Fairbanks, AK, USA
| | - Daniel C Fisher
- Museum of Paleontology, University of Michigan, Ann Arbor, MI, USA
| | - Sambit Ghosh
- Alaska Stable Isotope Facility, University of Alaska Fairbanks, AK, USA
| | - Charles E Holmes
- Department of Anthropology, University of Alaska Fairbanks, AK, USA
| | | | - François Lanoë
- Bureau of Applied Research in Anthropology, University of Arizona, Tucson, AZ, USA
| | - Tyler J Murchie
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Hendrik Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
- Departments of Biochemistry and Biology, McMaster University, Hamilton, Ontario, Canada
| | - Ben Potter
- Department of Anthropology, University of Alaska Fairbanks, AK, USA
| | | | - Joshua Reuther
- University of Alaska Museum of the North, Fairbanks, AK, USA
- Department of Anthropology, University of Alaska Fairbanks, AK, USA
| | - Gerad M Smith
- Department of Anthropology and Geography, University of Alaska Anchorage, AK, USA
| | - Karen J Spaleta
- Alaska Stable Isotope Facility, University of Alaska Fairbanks, AK, USA
| | - Brian T Wygal
- Department of Anthropology, Adelphi University, Garden City, NY, USA
| | - Matthew J Wooller
- Alaska Stable Isotope Facility, University of Alaska Fairbanks, AK, USA
- Department of Marine Biology, University of Alaska Fairbanks, AK, USA
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10
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Fracasso I, Zaccone C, Oskolkov N, Da Ros L, Dinella A, Belelli Marchesini L, Buzzini P, Sannino C, Turchetti B, Cesco S, Le Roux G, Tonon G, Vernesi C, Mimmo T, Ventura M, Borruso L. Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168159. [PMID: 37923262 DOI: 10.1016/j.scitotenv.2023.168159] [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: 07/12/2023] [Revised: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Natural and human-induced environmental changes deeply affected terrestrial ecosystems throughout the Holocene. Paleoenvironmental reconstructions provide information about the past and allow us to predict/model future scenarios. Among potential records, peat bogs are widely used because they present a precise stratigraphy and act as natural archives of highly diverse organic remains. Over the decades, several techniques have been developed to identify debris occurring in peat, including their morphological description. However, this is strongly constrained by the researcher's ability to distinguish residues at the species level, which typically requires many years of experience. In addition, potential contamination hampers using these techniques to obtain information from organisms such as fungi or bacteria. Environmental DNA metabarcoding and shotgun metagenome sequencing could represent a solution to detect specific groups of organisms without any a priori knowledge of their characteristics and/or to identify organisms that have rarely been considered in previous investigations. Moreover, shotgun metagenomics may allow the identification of bacteria and fungi (including both yeast and filamentous life forms), ensuring discrimination between ancient and modern organisms through the study of deamination/damage patterns. In the present review, we aim to i) present the state-of-the-art methodologies in paleoecological and paleoclimatic studies focusing on peat core analyses, proposing alternative approaches to the classical morphological identification of plant residues, and ii) suggest biomolecular approaches that will allow the use of proxies such as invertebrates, fungi, and bacteria, which are rarely employed in paleoenvironmental reconstructions.
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Affiliation(s)
- Ilaria Fracasso
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy.
| | - Claudio Zaccone
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 221 00 Lund, Sweden
| | - Luca Da Ros
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Anna Dinella
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Luca Belelli Marchesini
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06123 Perugia, Italy
| | - Ciro Sannino
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06123 Perugia, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Science, University of Perugia, 06123 Perugia, Italy
| | - Stefano Cesco
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Gael Le Roux
- Laboratoire Ecologie Fonctionnelle et Environnement (UMR5245 CNRS/UPS/INPT), Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Giustino Tonon
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all'Adige, Italy
| | - Tanja Mimmo
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Maurizio Ventura
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy
| | - Luigimaria Borruso
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy.
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11
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Venkatachalam S, Vipindas PV, Jabir T, Jain A, Krishnan KP. Metagenomic insights into novel microbial lineages with distinct ecological functions in the Arctic glacier foreland ecosystems. ENVIRONMENTAL RESEARCH 2024; 241:117726. [PMID: 37984782 DOI: 10.1016/j.envres.2023.117726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
Land-terminating glaciers are retreating globally, resulting in the expansion of the ice-free glacier forelands (GFs). These GFs act as a natural laboratory to study microbial community succession, soil formation, and ecosystem development. Here, we have employed gene-centric and genome-resolved metagenomic approaches to disseminate microbial diversity, community structure, and their associated biogeochemical processes involved in the carbon, nitrogen, and sulfur cycling across three GF ecosystems. Here, we present a compendium of draft Metagenome Assembled Genomes (MAGs) belonging to bacterial (n = 899) and archaeal (n = 4) domains. These MAGs were reconstructed using a total of 27 shotgun metagenomic datasets obtained from three different GFs, including Midtre Lovénbreen glacier (Svalbard), Russell glacier (Greenland), and Storglaciaren (Sweden). The taxonomic classification revealed that 98% of MAGs remained unclassified at species levels, suggesting the presence of novel microbial lineages. The abundance of metabolic genes associated with carbon, nitrogen, and sulfur cycling pathways varied between and within the samples collected across the three GF ecosystems. Our findings indicate that MAGs from different GFs share close phylogenetic relationships but exhibit significant differences in abundance, distribution patterns, and metabolic functions. This compendium of novel MAGs, encompassing autotrophic, phototrophic, and chemolithoautotrophic microbial groups reconstructed from GF ecosystems, represents a valuable resource for further studies.
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Affiliation(s)
- Siddarthan Venkatachalam
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India.
| | - Puthiya Veettil Vipindas
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
| | - Thajudeen Jabir
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
| | - Anand Jain
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
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12
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Mitka J, Wróblewska A, Boroń P, Kucharzyk S, Stachurska-Swakoń A. Perhaps there were northern refugia in LGM? The phylogeographic structure of the thermophilic tree Carpinus betulus in the Carpathian region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167214. [PMID: 37730049 DOI: 10.1016/j.scitotenv.2023.167214] [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: 05/30/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
Carpinus betulus L., the hornbeam, is a component of lowland and highland forests in Europe. By examining the postglacial migratory history of thermophilic tree species, the study aimed to unravel their putative glacial microrefugia in the Carpathian region. The present study points to the two distinct genetic AFLP groups of C. betulus in the Carpathian region that represent different genetic lineages based on Bayesian analysis. They differed in Nei's gene diversity index h, and the analysis of molecular variance AMOVA showed a percentage variation of the populations between the groups of 13.74 %. Principal coordinate analysis (PCoA) of 368 AFLP tree samples confirmed the presence of two genetic groups. Ninety-five populations underwent principal component analysis (PCA) to show the main correlations between genetic diversity indices and bioclimatic/climate variables (WorldClim and Carpatclim). The generalized logistic model (GLM) showed the significance of Nei's genetic index h in delimiting genetic groups. The results of population-genetic and multivariate analyses determined that the two genetic groups nowadays are spatially diffused and do not show a clear geographic pattern, pointing to a genetic melting pot. We found ecological links between genetic diversity and bioclimatic characteristics, especially the precipitation in the coldest quarter - Bio19. The refugial Maxent model indicates a significant contribution of the Bio7 variable (both linked with a continental type of climate) to the occurrence of the species during the LGM in Europe. We suggest the relict character of hornbeam populations in a specific climatic-terrain niche in the northern part of the Carpathian Basin.
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Affiliation(s)
- Józef Mitka
- Jagiellonian University in Kraków, Faculty of Biology, ul. Gronostajowa 3, 30-387 Kraków, Poland.
| | - Ada Wróblewska
- University of Bialystok, Faculty of Biology, ul. K. Ciołkowskiego 1J, 15-245 Białystok, Poland
| | - Piotr Boroń
- University of Agriculture in Kraków, Department of Forest Ecosystems Protection, 29 Listopada 46, 31-425 Kraków, Poland
| | - Stanisław Kucharzyk
- Bieszczady National Park, Ecological Education Unit, Bełska 7, 38-700 Ustrzyki Dolne, Poland
| | - Alina Stachurska-Swakoń
- Jagiellonian University in Kraków, Faculty of Biology, ul. Gronostajowa 3, 30-387 Kraków, Poland
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13
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Petr M, Haller BC, Ralph PL, Racimo F. slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes. PEER COMMUNITY JOURNAL 2023; 3:e121. [PMID: 38984034 PMCID: PMC11233137 DOI: 10.24072/pcjournal.354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
One of the goals of population genetics is to understand how evolutionary forces shape patterns of genetic variation over time. However, because populations evolve across both time and space, most evolutionary processes also have an important spatial component, acting through phenomena such as isolation by distance, local mate choice, or uneven distribution of resources. This spatial dimension is often neglected, partly due to the lack of tools specifically designed for building and evaluating complex spatio-temporal population genetic models. To address this methodological gap, we present a new framework for simulating spatially-explicit genomic data, implemented in a new R package called slendr (www.slendr.net), which leverages a SLiM simulation back-end script bundled with the package. With this framework, the users can programmatically and visually encode spatial population ranges and their temporal dynamics (i.e., population displacements, expansions, and contractions) either on real Earth landscapes or on abstract custom maps, and schedule splits and gene-flow events between populations using a straightforward declarative language. Additionally, slendr can simulate data from traditional, non-spatial models, either with SLiM or using an alternative built-in coalescent msprime back end. Together with its R-idiomatic interface to the tskit library for tree-sequence processing and analysis, slendr opens up the possibility of performing efficient, reproducible simulations of spatio-temporal genomic data entirely within the R environment, leveraging its wealth of libraries for geospatial data analysis, statistics, and visualization. Here, we present the design of the slendr R package and demonstrate its features on several practical example workflows.
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Affiliation(s)
- Martin Petr
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Denmark
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Denmark
| | - Benjamin C Haller
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Peter L Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Denmark
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Denmark
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14
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Collins G, Schneider C, Boštjančić LL, Burkhardt U, Christian A, Decker P, Ebersberger I, Hohberg K, Lecompte O, Merges D, Muelbaier H, Romahn J, Römbke J, Rutz C, Schmelz R, Schmidt A, Theissinger K, Veres R, Lehmitz R, Pfenninger M, Bálint M. The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution. Commun Biol 2023; 6:1241. [PMID: 38066075 PMCID: PMC10709333 DOI: 10.1038/s42003-023-05621-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Soil invertebrates are among the least understood metazoans on Earth. Thus far, the lack of taxonomically broad and dense genomic resources has made it hard to thoroughly investigate their evolution and ecology. With MetaInvert we provide draft genome assemblies for 232 soil invertebrate species, representing 14 common groups and 94 families. We show that this data substantially extends the taxonomic scope of DNA- or RNA-based taxonomic identification. Moreover, we confirm that theories of genome evolution cannot be generalised across evolutionarily distinct invertebrate groups. The soil invertebrate genomes presented here will support the management of soil biodiversity through molecular monitoring of community composition and function, and the discovery of evolutionary adaptations to the challenges of soil conditions.
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Affiliation(s)
- Gemma Collins
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Clément Schneider
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Ljudevit Luka Boštjančić
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Landau, Germany
| | | | - Axel Christian
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Peter Decker
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Ingo Ebersberger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
| | - Karin Hohberg
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
| | - Dominik Merges
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hannah Muelbaier
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
| | - Juliane Romahn
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Jörg Römbke
- ECT Oekotoxikologie GmbH, Flörsheim, Germany
| | - Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
| | | | - Alexandra Schmidt
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Kathrin Theissinger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Landau, Germany
| | - Robert Veres
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Ricarda Lehmitz
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Johannes Gutenberg University, Mainz, Germany
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany.
- Department of Insect Biotechnology, Justus-Liebig University, Gießen, Germany.
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15
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Molnár ÁP, Demeter L, Biró M, Chytrý M, Bartha S, Gantuya B, Molnár Z. Is there a massive glacial-Holocene flora continuity in Central Europe? Biol Rev Camb Philos Soc 2023; 98:2307-2319. [PMID: 37646107 DOI: 10.1111/brv.13007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
The prevailing paradigm about the Quaternary ecological and evolutionary history of Central European ecosystems is that they were repeatedly impoverished by regional extinctions of most species during the glacial periods, followed by massive recolonizations from southern and eastern refugia during interglacial periods. Recent literature partially contradicts this view and provides evidence to re-evaluate this Postglacial Recolonization Hypothesis and develop an alternative one. We examined the long-term history of the flora of the Carpathian (Pannonian) Basin by synthesising recent advances in ecological, phylogeographical, palaeoecological and palaeoclimatological research, and analysing the cold tolerance of the native flora of a test area (Hungary, the central part of the Carpathian Basin). We found that (1) many species have likely occurred there continuously since before the Last Glacial Maximum (LGM); (2) most of the present-day native flora (1404 species, about 80%) can occur in climates as cold as or colder than the LGM (mean annual temperature ≤+3.5°C); and (3) grasslands and forests can be species-rich under an LGM-like cold climate. These arguments support an alternative hypothesis, which we call the Flora Continuity Hypothesis. It states that long-term continuity of much of the flora in the Carpathian Basin is more plausible than regional extinctions during the LGM followed by massive postglacial recolonizations. The long-term continuity of the region's flora may have fundamental implications not only for understanding local biogeography and ecology (e.g. the temporal scale of processes), but also for conservation strategies focusing on protecting ancient species-rich ecosystems and local gene pools.
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Affiliation(s)
- Ábel Péter Molnár
- Hungarian University of Agriculture and Life Sciences, Institute for Wildlife Management and Nature Conservation, Páter Károly u. 1., Gödöllő, 2100, Hungary
- Doctoral School of Biological Sciences, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1., Gödöllő, 2100, Hungary
| | - László Demeter
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
| | - Marianna Biró
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
| | - Milan Chytrý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Sándor Bartha
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
| | - Batdelger Gantuya
- Botanic Garden and Research Institute, Mongolian Academy of Sciences, 13th Street, Peace Avenue 54a, Bayanzurkh district, Ulaanbaatar, 13330, Mongolia
- Doctoral School of Biology, Eötvös Lorand University, Budapest, Pázmány P. stny. 1/C., Budapest, 1117, Hungary
| | - Zsolt Molnár
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
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16
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Pochon Z, Bergfeldt N, Kırdök E, Vicente M, Naidoo T, van der Valk T, Altınışık NE, Krzewińska M, Dalén L, Götherström A, Mirabello C, Unneberg P, Oskolkov N. aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow. Genome Biol 2023; 24:242. [PMID: 37872569 PMCID: PMC10591440 DOI: 10.1186/s13059-023-03083-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 10/06/2023] [Indexed: 10/25/2023] Open
Abstract
Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.
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Affiliation(s)
- Zoé Pochon
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Nora Bergfeldt
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Emrah Kırdök
- Department of Biotechnology, Faculty of Science, Mersin University, Mersin, Turkey
| | - Mário Vicente
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Ancient DNA Unit, Science for Life Laboratory, Stockholm, Sweden
- Ancient DNA Unit, Science for Life Laboratory, Uppsala, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - N Ezgi Altınışık
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800, Beytepe, Ankara, Turkey
| | - Maja Krzewińska
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Claudio Mirabello
- Department of Physics, Chemistry and Biology, Science for Life Laboratory, National Bioinformatics Infrastructure Sweden, Linköping University, Linköping, Sweden
| | - Per Unneberg
- Department of Cell and Molecular Biology, Science for Life Laboratory, National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Nikolay Oskolkov
- Department of Biology, Science for Life Laboratory, National Bioinformatics Infrastructure Sweden, Lund University, Lund, Sweden.
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17
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Pittman M, Wang Y. Paleoecology of extinct species. BMC Ecol Evol 2023; 23:59. [PMID: 37803274 PMCID: PMC10557349 DOI: 10.1186/s12862-023-02170-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023] Open
Abstract
Recent developments, including new imaging and ancient environmental DNA (aeDNA) technologies, are providing unprecedented insights into the past, which can also help researchers predict future ecological change. BMC Ecology and Evolution has launched a new article Collection on the "Paleoecology of extinct species" to provide an open-access resource for all interested in this multidisciplinary field.
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Affiliation(s)
- Michael Pittman
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Yucheng Wang
- Department of Zoology, University of Cambridge, Cambridge, UK.
- Group of Alpine Paleoecology and Human Adaptation (ALPHA), State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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18
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Williams JW, Spanbauer TL, Heintzman PD, Blois J, Capo E, Goring SJ, Monchamp ME, Parducci L, Von Eggers JM. Strengthening global-change science by integrating aeDNA with paleoecoinformatics. Trends Ecol Evol 2023; 38:946-960. [PMID: 37230884 DOI: 10.1016/j.tree.2023.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/27/2023]
Abstract
Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.
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Affiliation(s)
- John W Williams
- Department of Geography, University of Wisconsin-Madison, Madison, WI 53704, USA.
| | - Trisha L Spanbauer
- Department of Environmental Science and Lake Erie Center, University of Toledo, Toledo, OH 43606, USA
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway; Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-10691 Stockholm, Sweden; Department of Geological Sciences, Stockholm University, SE-10691, Stockholm, Sweden
| | - Jessica Blois
- Department of Life and Environmental Sciences, University of California -Merced, Merced, CA 95343, USA
| | - Eric Capo
- Department of Ecology and Environmental Science, Umeå University, Linnaeus väg 4-6, 907 36 Umeå, Sweden
| | - Simon J Goring
- Department of Geography, University of Wisconsin-Madison, Madison, WI 53704, USA
| | | | - 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, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Jordan M Von Eggers
- Department of Geology and Geophysics, University of Wyoming, Laramie, WY 82071, USA
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19
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Tan HZ, Jansen JJFJ, Allport GA, Garg KM, Chattopadhyay B, Irestedt M, Pang SEH, Chilton G, Gwee CY, Rheindt FE. Megafaunal extinctions, not climate change, may explain Holocene genetic diversity declines in Numenius shorebirds. eLife 2023; 12:e85422. [PMID: 37549057 PMCID: PMC10406428 DOI: 10.7554/elife.85422] [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] [Received: 12/07/2022] [Accepted: 06/27/2023] [Indexed: 08/09/2023] Open
Abstract
Understanding the relative contributions of historical and anthropogenic factors to declines in genetic diversity is important for informing conservation action. Using genome-wide DNA of fresh and historic specimens, including that of two species widely thought to be extinct, we investigated fluctuations in genetic diversity and present the first complete phylogenomic tree for all nine species of the threatened shorebird genus Numenius, known as whimbrels and curlews. Most species faced sharp declines in effective population size, a proxy for genetic diversity, soon after the Last Glacial Maximum (around 20,000 years ago). These declines occurred prior to the Anthropocene and in spite of an increase in the breeding area predicted by environmental niche modeling, suggesting that they were not caused by climatic or recent anthropogenic factors. Crucially, these genetic diversity declines coincide with mass extinctions of mammalian megafauna in the Northern Hemisphere. Among other factors, the demise of ecosystem-engineering megafauna which maintained open habitats may have been detrimental for grassland and tundra-breeding Numenius shorebirds. Our work suggests that the impact of historical factors such as megafaunal extinction may have had wider repercussions on present-day population dynamics of open habitat biota than previously appreciated.
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Affiliation(s)
- Hui Zhen Tan
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | | | | | - Kritika M Garg
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholmSweden
| | - Sean EH Pang
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Glen Chilton
- Department of Biology, St. Mary's UniversityCalgaryCanada
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Frank E Rheindt
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
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20
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Winker K, Withrow JJ, Gibson DD, Pruett CL. Beringia as a high-latitude engine of avian speciation. Biol Rev Camb Philos Soc 2023; 98:1081-1099. [PMID: 36879465 DOI: 10.1111/brv.12945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023]
Abstract
Beringia is a biogeographically dynamic region that extends from northeastern Asia into northwestern North America. This region has affected avian divergence and speciation in three important ways: (i) by serving as a route for intercontinental colonisation between Asia and the Americas; (ii) by cyclically splitting (and often reuniting) populations, subspecies, and species between these continents; and (iii) by providing isolated refugia through glacial cycles. The effects of these processes can be seen in taxonomic splits of shallow to increasing depths and in the presence of regional endemics. We review the taxa involved in the latter two processes (splitting-reuniting and isolation), with a focus on three research topics: avian diversity, time estimates of the generation of that diversity, and the regions within Beringia that might have been especially important. We find that these processes have generated substantial amounts of avian diversity, including 49 pairs of avian subspecies or species whose breeding distributions largely replace one another across the divide between the Old World and the New World in Beringia, and 103 avian species and subspecies endemic to this region. Among endemics, about one in three is recognised as a full biological species. Endemic taxa in the orders Charadriiformes (shorebirds, alcids, gulls, and terns) and Passeriformes (perching birds) are particularly well represented, although they show very different levels of diversity through evolutionary time. Endemic Beringian Charadriiformes have a 1.31:1 ratio of species to subspecies. In Passeriformes, endemic taxa have a 0.09:1 species-to-subspecies ratio, suggesting that passerine (and thus terrestrial) endemism might be more prone to long-term extinction in this region, although such 'losses' could occur through their being reconnected with wider continental populations during favourable climatic cycles (e.g. subspecies reintegration with other populations). Genetic evidence suggests that most Beringian avian taxa originated over the past 3 million years, confirming the importance of Quaternary processes. There seems to be no obvious clustering in their formation through time, although there might be temporal gaps with lower rates of diversity generation. For at least 62 species, taxonomically undifferentiated populations occupy this region, providing ample potential for future evolutionary diversification.
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Affiliation(s)
- Kevin Winker
- University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
| | - Jack J Withrow
- University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
| | - Daniel D Gibson
- University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK, 99775-6960, USA
| | - Christin L Pruett
- Department of Biology, Ouachita Baptist University, 410 Ouachita St, Arkadelphia, AR, 71998, USA
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21
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Barrio IC, Rapini A. Plants under pressure: the impact of environmental change on plant ecology and evolution. BMC Ecol Evol 2023; 23:13. [PMID: 37081378 PMCID: PMC10116802 DOI: 10.1186/s12862-023-02115-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 04/17/2023] [Indexed: 04/22/2023] Open
Abstract
Plants have demonstrated tremendous resilience through past mass extinction events. However, anthropogenic pressures are rapidly threatening plant survival. To develop our understanding of the impact of environmental change on plant ecology and evolution and help solve the current biodiversity crisis, BMC Ecology and Evolution has launched a new article Collection titled "Plants under Pressure".
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Affiliation(s)
- Isabel C Barrio
- Faculty of Environmental and Forest Sciences, Agricultural University of Iceland, Reykjavík, Iceland.
| | - Alessandro Rapini
- Department of Biological Sciences, The State University of Feira de Santana, Feira de Santana, Brazil
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22
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Abstract
This perspective draws on the record of ancient pathogen genomes and microbiomes illuminating patterns of infectious disease over the course of the Holocene in order to address the following question. How did major changes in living circumstances involving the transition to and intensification of farming alter pathogens and their distributions? Answers to this question via ancient DNA research provide a rapidly expanding picture of pathogen evolution and in concert with archaeological and historical data, give a temporal and behavioral context for heath in the past that is relevant for challenges facing the world today, including the rise of novel pathogens.
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23
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Hoffecker JF, Elias SA, Scott GR, O'Rourke DH, Hlusko LJ, Potapova O, Pitulko V, Pavlova E, Bourgeon L, Vachula RS. Beringia and the peopling of the Western Hemisphere. Proc Biol Sci 2023; 290:20222246. [PMID: 36629115 PMCID: PMC9832545 DOI: 10.1098/rspb.2022.2246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Did Beringian environments represent an ecological barrier to humans until less than 15 000 years ago or was access to the Americas controlled by the spatial-temporal distribution of North American ice sheets? Beringian environments varied with respect to climate and biota, especially in the two major areas of exposed continental shelf. The East Siberian Arctic Shelf ('Great Arctic Plain' (GAP)) supported a dry steppe-tundra biome inhabited by a diverse large-mammal community, while the southern Bering-Chukchi Platform ('Bering Land Bridge' (BLB)) supported mesic tundra and probably a lower large-mammal biomass. A human population with west Eurasian roots occupied the GAP before the Last Glacial Maximum (LGM) and may have accessed mid-latitude North America via an interior ice-free corridor. Re-opening of the corridor less than 14 000 years ago indicates that the primary ancestors of living First Peoples, who already had spread widely in the Americas at this time, probably dispersed from the NW Pacific coast. A genetic 'arctic signal' in non-arctic First Peoples suggests that their parent population inhabited the GAP during the LGM, before their split from the former. We infer a shift from GAP terrestrial to a subarctic maritime economy on the southern BLB coast before dispersal in the Americas from the NW Pacific coast.
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Affiliation(s)
- John F. Hoffecker
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO 80309, USA,Department of Anthropology, University of Kansas, 622 Fraser Hall, 1415 Jayhawk Blvd, Lawrence, KS 66045, USA
| | - Scott A. Elias
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO 80309, USA
| | - G. Richard Scott
- Department of Anthropology, University of Nevada-Reno, 1664 N. Virginia Street, Reno, NV 89557, USA
| | - Dennis H. O'Rourke
- Department of Anthropology, University of Kansas, 622 Fraser Hall, 1415 Jayhawk Blvd, Lawrence, KS 66045, USA
| | - Leslea J. Hlusko
- Human Evolution Research Center, University of California-Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720-3140, USA,Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Olga Potapova
- Pleistocene Park Foundation, Philadelphia, PA 19006, USA,Department of Mammoth Fauna Studies, Academy of Sciences of Sakha, Yakutsk, Russia,The Mammoth Site of Hot Springs, Hot Springs, SD 57747, USA
| | - Vladimir Pitulko
- Institute of the History of Material Culture, Russian Academy of Sciences, Dvortsovaya nab., 18, 191186 St Petersburg, Russia,Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, 3, Universitetskaya nab., St Petersburg 199034, Russian Federation
| | - Elena Pavlova
- Arctic and Antarctic Research Institute, Russian Federal Service for Hydrometeorology and Environmental Monitoring, 38 Bering Street, 199397 St Petersburg, Russia
| | - Lauriane Bourgeon
- Kansas Geological Survey, University of Kansas, 1930 Constant Ave., Lawrence, KS 66047, USA
| | - Richard S. Vachula
- Department of Geosciences, Auburn University, 2050 Beard Eaves Coliseum, Auburn, AL 36849-5305, USA
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24
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Vasar M, Davison J, Moora M, Sepp SK, Anslan S, Al-Quraishy S, Bahram M, Bueno CG, Cantero JJ, Fabiano EC, Decocq G, Drenkhan R, Fraser L, Oja J, Garibay-Orijel R, Hiiesalu I, Koorem K, Mucina L, Öpik M, Põlme S, Pärtel M, Phosri C, Semchenko M, Vahter T, Doležal J, Palacios AMV, Tedersoo L, Zobel M. Metabarcoding of soil environmental DNA to estimate plant diversity globally. FRONTIERS IN PLANT SCIENCE 2023; 14:1106617. [PMID: 37143888 PMCID: PMC10151745 DOI: 10.3389/fpls.2023.1106617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/03/2023] [Indexed: 05/06/2023]
Abstract
Introduction Traditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. Methods We sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. Results Large-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. Discussion eDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.
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Affiliation(s)
- Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- *Correspondence: Martti Vasar,
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Siim-Kaarel Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - C. Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Juan José Cantero
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, CONICET, Córdoba, Argentina
- Departamento de Biología Agrícola, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | | | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR CNRS 7058), Jules Verne, University of Picardie, Amiens, France
| | - Rein Drenkhan
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Roberto Garibay-Orijel
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Perth, WA, Australia
- Department of Geography & Environmental Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sergei Põlme
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Jiři Doležal
- Institute of Botany, The Czech Academy of Sciences, Třeboň, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Aida M. Vasco Palacios
- Grupo de Microbiología Ambiental y Grupo BioMicro, Escuela de Microbiología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Leho Tedersoo
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Botany, University of Tartu, Tartu, Estonia
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25
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DNA reveals that mastodons roamed a forested Greenland two million years ago. Nature 2022:10.1038/d41586-022-03626-3. [PMID: 36476763 DOI: 10.1038/d41586-022-03626-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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26
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Kjær KH, Winther Pedersen M, De Sanctis B, De Cahsan B, Korneliussen TS, Michelsen CS, Sand KK, Jelavić S, Ruter AH, Schmidt AMA, Kjeldsen KK, Tesakov AS, Snowball I, Gosse JC, Alsos IG, Wang Y, Dockter C, Rasmussen M, Jørgensen ME, Skadhauge B, Prohaska A, Kristensen JÅ, Bjerager M, Allentoft ME, Coissac E, Rouillard A, Simakova A, Fernandez-Guerra A, Bowler C, Macias-Fauria M, Vinner L, Welch JJ, Hidy AJ, Sikora M, Collins MJ, Durbin R, Larsen NK, Willerslev E. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature 2022; 612:283-291. [PMID: 36477129 PMCID: PMC9729109 DOI: 10.1038/s41586-022-05453-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/18/2022] [Indexed: 12/12/2022]
Abstract
Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago1 had climates resembling those forecasted under future warming2. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11-19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare5. Here we report an ancient environmental DNA6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.
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Affiliation(s)
- Kurt H Kjær
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Binia De Cahsan
- Section for Molecular Ecology and Evolution, The Globe Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Thorfinn S Korneliussen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christian S Michelsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Karina K Sand
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stanislav Jelavić
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, IRD, Université Gustave Eiffel, ISTerre, Grenoble, France
| | - Anthony H Ruter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Astrid M A Schmidt
- Nordic Foundation for Development and Ecology (NORDECO), Copenhagen, Denmark
- DIS Study Abroad in Scandinavia, University of Copenhagen, Copenhagen, Denmark
| | - Kristian K Kjeldsen
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Alexey S Tesakov
- Geological Institute, Russian Academy of Sciences, Moscow, Russia
| | - Ian Snowball
- Department of Earth Sciences, Uppsala University, Uppsala, Sweden
| | - John C Gosse
- Department of Earth and Environmental Sciences, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Inger G Alsos
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Yucheng Wang
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Ana Prohaska
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Jeppe Å Kristensen
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
- Geological Survey of Denmark and Greenland, (GEUS), Copenhagen, Denmark
| | - Morten Bjerager
- Department of Geophysics and Sedimentary Basins, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Eric Coissac
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
- University of Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Alexandra Rouillard
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Geosciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | | | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM Université PSL, Paris, France
| | - Marc Macias-Fauria
- School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alan J Hidy
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Matthew J Collins
- Department of Archaeology, University of Cambridge, Cambridge, UK
- Section for GeoBiology, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Nicolaj K Larsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM, University of Bremen, Bremen, Germany.
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27
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Miller JH, Simpson C. When did mammoths go extinct? Nature 2022; 612:E1-E3. [DOI: 10.1038/s41586-022-05416-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 10/06/2022] [Indexed: 12/02/2022]
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Wang Y, Prohaska A, Dong H, Alberti A, Alsos IG, Beilman DW, Bjørk AA, Cao J, Cherezova AA, Coissac E, De Sanctis B, Denoeud F, Dockter C, Durbin R, Edwards ME, Edwards NR, Esdale J, Fedorov GB, Fernandez-Guerra A, Froese DG, Gusarova G, Haile J, Holden PB, Kjeldsen KK, Kjær KH, Korneliussen TS, Lammers Y, Larsen NK, Macleod R, Mangerud J, McColl H, Merkel MKF, Money D, Möller P, Nogués-Bravo D, Orlando L, Owens HL, Pedersen MW, Racimo F, Rahbek C, Rasic JT, Rouillard A, Ruter AH, Skadhauge B, Svendsen JI, Tikhonov A, Vinner L, Wincker P, Xing Y, Zhang Y, Meltzer DJ, Willerslev E. 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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Yucheng Wang
- Department of Zoology, University of Cambridge, Cambridge, UK
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- ALPHA, State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research (ITPCAS), Chinese Academy of Sciences (CAS), Beijing, China
| | - Ana Prohaska
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Haoran Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Science, Lanzhou University, Lanzhou, China
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Inger Greve Alsos
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - David W Beilman
- Department of Geography and Environment, University of Hawaii, Honolulu, HI, USA
| | - Anders A Bjørk
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Jialu Cao
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Anna A Cherezova
- Institute of Earth Sciences, St Petersburg State University, St Petersburg, Russia
- Arctic and Antarctic Research Institute, St Petersburg, Russia
| | - Eric Coissac
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
- Université Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Mary E Edwards
- School of Geography and Environmental Science, University of Southampton, Southampton, UK
- Alaska Quaternary Center, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Neil R Edwards
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, UK
| | - Julie Esdale
- Center for the Environmental Management of Military Lands, Colorado State University, Fort Collins, CO, USA
| | - Grigory B Fedorov
- Institute of Earth Sciences, St Petersburg State University, St Petersburg, Russia
- Arctic and Antarctic Research Institute, St Petersburg, Russia
| | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Duane G Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Galina Gusarova
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
- Faculty of Biology, St Petersburg State University, St Petersburg, Russia
| | - James Haile
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Philip B Holden
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, UK
| | - Kristian K Kjeldsen
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen K, Denmark
| | - Kurt H Kjær
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Youri Lammers
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Nicolaj Krog Larsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ruairidh Macleod
- Department of Zoology, University of Cambridge, Cambridge, UK
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jan Mangerud
- Department of Earth Science, University of Bergen, Bergen, Norway
- Bjerknes Centre for Climate Research, Bergen, Norway
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Daniel Money
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Per Möller
- Department of Geology, Quaternary Sciences, Lund University, Lund, Sweden
| | - David Nogués-Bravo
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø, Denmark
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, Faculté de Médecine Purpane, Université Paul Sabatier, Toulouse, France
| | - Hannah Lois Owens
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø, Denmark
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø, Denmark
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jeffrey T Rasic
- Gates of the Arctic National Park and Preserve, US National Park Service, Fairbanks, AK, USA
| | - Alexandra Rouillard
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Geosciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Anthony H Ruter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - John Inge Svendsen
- Department of Earth Science, University of Bergen, Bergen, Norway
- Bjerknes Centre for Climate Research, Bergen, Norway
| | - Alexei Tikhonov
- Zoological Institute, Russian academy of sciences, St Petersburg, Russia
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Yingchun Xing
- Resource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing, China
| | - Yubin Zhang
- College of Plant Science, Jilin University, Changchun, Jilin, China
| | - David J Meltzer
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Anthropology, Southern Methodist University, Dallas, TX, USA
| | - Eske Willerslev
- Department of Zoology, University of Cambridge, Cambridge, UK.
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- MARUM, University of Bremen, Bremen, Germany.
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29
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Simulations of human migration into North America are more sensitive to demography than choice of palaeoclimate model. Ecol Modell 2022. [DOI: 10.1016/j.ecolmodel.2022.110115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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Canteri E, Brown SC, Schmidt NM, Heller R, Nogués‐Bravo D, Fordham DA. Spatiotemporal influences of climate and humans on muskox range dynamics over multiple millennia. GLOBAL CHANGE BIOLOGY 2022; 28:6602-6617. [PMID: 36031712 PMCID: PMC9804684 DOI: 10.1111/gcb.16375] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Processes leading to range contractions and population declines of Arctic megafauna during the late Pleistocene and early Holocene are uncertain, with intense debate on the roles of human hunting, climatic change, and their synergy. Obstacles to a resolution have included an overreliance on correlative rather than process-explicit approaches for inferring drivers of distributional and demographic change. Here, we disentangle the ecological mechanisms and threats that were integral in the decline and extinction of the muskox (Ovibos moschatus) in Eurasia and in its expansion in North America using process-explicit macroecological models. The approach integrates modern and fossil occurrence records, ancient DNA, spatiotemporal reconstructions of past climatic change, species-specific population ecology, and the growth and spread of anatomically modern humans. We show that accurately reconstructing inferences of past demographic changes for muskox over the last 21,000 years require high dispersal abilities, large maximum densities, and a small Allee effect. Analyses of validated process-explicit projections indicate that climatic change was the primary driver of muskox distribution shifts and demographic changes across its previously extensive (circumpolar) range, with populations responding negatively to rapid warming events. Regional analyses show that the range collapse and extinction of the muskox in Europe (~13,000 years ago) was likely caused by humans operating in synergy with climatic warming. In Canada and Greenland, climatic change and human activities probably combined to drive recent population sizes. The impact of past climatic change on the range and extinction dynamics of muskox during the Pleistocene-Holocene transition signals a vulnerability of this species to future increased warming. By better establishing the ecological processes that shaped the distribution of the muskox through space and time, we show that process-explicit macroecological models have important applications for the future conservation and management of this iconic species in a warming Arctic.
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Affiliation(s)
- Elisabetta Canteri
- The Environment Institute and School of Biological SciencesUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Center for Macroecology, Evolution and ClimateGlobe Institute, University of CopenhagenCopenhagenDenmark
| | - Stuart C. Brown
- The Environment Institute and School of Biological SciencesUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Section for Molecular Ecology and EvolutionGlobe Institute, University of CopenhagenCopenhagenDenmark
| | - Niels Martin Schmidt
- Department of Ecoscience and Arctic Research CentreAarhus UniversityRoskildeDenmark
| | - Rasmus Heller
- Department of Biology, Section of Computational and RNA BiologyUniversity of CopenhagenCopenhagenDenmark
| | - David Nogués‐Bravo
- Center for Macroecology, Evolution and ClimateGlobe Institute, University of CopenhagenCopenhagenDenmark
| | - Damien A. Fordham
- The Environment Institute and School of Biological SciencesUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Center for Macroecology, Evolution and ClimateGlobe Institute, University of CopenhagenCopenhagenDenmark
- Center for Global Mountain BiodiversityGlobe Institute, University of CopenhagenCopenhagenDenmark
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31
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Boulygina E, Sharko F, Cheprasov M, Gladysheva-Azgari M, Slobodova N, Tsygankova S, Rastorguev S, Grigorieva L, Kopp M, Fernandes JMO, Novgorodov G, Boeskorov G, Protopopov A, Hwang WS, Tikhonov A, Nedoluzhko A. Ancient DNA Reveals Maternal Philopatry of the Northeast Eurasian Brown Bear ( Ursus arctos) Population during the Holocene. Genes (Basel) 2022; 13:1961. [PMID: 36360198 PMCID: PMC9689912 DOI: 10.3390/genes13111961] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/08/2022] [Accepted: 10/25/2022] [Indexed: 09/14/2023] Open
Abstract
Significant palaeoecological and paleoclimatic changes that took place during Late Pleistocene-Early Holocene transition are considered important factors that led to megafauna extinctions. Unlike many other species, the brown bear (Ursus arctos) has survived this geological time. Despite the fact that several mitochondrial DNA clades of brown bears became extinct at the end of the Pleistocene, this species is still widely distributed in Northeast Eurasia. Here, using the ancient DNA analysis of a brown bear individual that inhabited Northeast Asia in the Middle Holocene (3460 ± 40 years BP) and comparative phylogenetic analysis, we show a significant mitochondrial DNA similarity of the studied specimen with modern brown bears inhabiting Yakutia and Chukotka. In this study, we clearly demonstrate the maternal philopatry of the Northeastern Eurasian U. arctos population during the several thousand years of the Holocene.
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Affiliation(s)
- Eugenia Boulygina
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Fedor Sharko
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Limited Liability Company ELGENE, 109029 Moscow, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Maksim Cheprasov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
| | - Maria Gladysheva-Azgari
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Natalia Slobodova
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Svetlana Tsygankova
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Sergey Rastorguev
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Limited Liability Company ELGENE, 109029 Moscow, Russia
| | - Lena Grigorieva
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
| | - Martina Kopp
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Jorge M. O. Fernandes
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Gavril Novgorodov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
| | - Gennady Boeskorov
- Institute of Diamond and Precious Metals Geology, Siberian Branch of Russian 5 Academy of Sciences, 677007 Yakutsk, Russia
| | - Albert Protopopov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
- Academy of Sciences of Sakha (Yakutia), 677007 Yakutsk, Russia
| | - Woo-Suk Hwang
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
- UAE Biotech Research Center, Abu Dhabi 30310, United Arab Emirates
| | - Alexei Tikhonov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
- Zoological Institute Russian Academy of Sciences, 190121 Saint-Petersburg, Russia
| | - Artem Nedoluzhko
- Limited Liability Company ELGENE, 109029 Moscow, Russia
- Paleogenomics Laboratory, European University at Saint Petersburg, 191187 Saint-Petersburg, Russia
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32
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Wang Y, Korneliussen TS, Holman LE, Manica A, Pedersen MW.
ngs
LCA
—A toolkit for fast and flexible lowest common ancestor inference and taxonomic profiling of metagenomic data. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.14006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yucheng Wang
- Department of Zoology University of Cambridge Cambridge UK
- Lundbeck Foundation GeoGenetics Centre, Globe Institute University of Copenhagen Copenhagen K Denmark
- ALPHA, State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER) Institute of Tibetan Plateau Research (ITPCAS), Chinese Academy of Sciences (CAS) Beijing China
- BGI BGI‐Shenzhen Shanghai China
| | | | - Luke E. Holman
- School of Ocean and Earth Science, National Oceanography Centre Southampton University of Southampton Southampton UK
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Andrea Manica
- Department of Zoology University of Cambridge Cambridge UK
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute University of Copenhagen Copenhagen K Denmark
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33
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Alsos IG, Rijal DP, Ehrich D, Karger DN, Yoccoz NG, Heintzman PD, Brown AG, Lammers Y, Pellissier L, Alm T, Bråthen KA, Coissac E, Merkel MKF, Alberti A, Denoeud F, Bakke J. Postglacial species arrival and diversity buildup of northern ecosystems took millennia. SCIENCE ADVANCES 2022; 8:eabo7434. [PMID: 36170372 PMCID: PMC9519041 DOI: 10.1126/sciadv.abo7434] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/12/2022] [Indexed: 05/31/2023]
Abstract
What drives ecosystem buildup, diversity, and stability? We assess species arrival and ecosystem changes across 16 millennia by combining regional-scale plant sedimentary ancient DNA from Fennoscandia with near-complete DNA and trait databases. We show that postglacial arrival time varies within and between plant growth forms. Further, arrival times were mainly predicted by adaptation to temperature, disturbance, and light. Major break points in ecological trait diversity were seen between 13.9 and 10.8 calibrated thousand years before the present (cal ka BP), as well as break point in functional diversity at 12.0 cal ka BP, shifting from a state of ecosystem buildup to a state where most habitat types and biotic ecosystem components were in place. Trait and functional diversity stabilized around 8 cal ka BP, after which both remained stable, although changes in climate took place and species inflow continued. Our ecosystem reconstruction indicates a millennial-scale time phase of formation to reach stable and resilient levels of diversity and functioning.
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Affiliation(s)
- Inger Greve Alsos
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
| | - Dilli Prasad Rijal
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
- Institute of Marine Research, Tromsø, Norway
| | - Dorothee Ehrich
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Dirk Nikolaus Karger
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Nigel Gilles Yoccoz
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Peter D. Heintzman
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
| | - Antony G. Brown
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
| | - Youri Lammers
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
| | - Loïc Pellissier
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Department of Environmental System Science, ETH Zurich, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Torbjørn Alm
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kari Anne Bråthen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Eric Coissac
- Université Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000 Grenoble, France
| | | | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - France Denoeud
- Department of Environmental System Science, ETH Zurich, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Jostein Bakke
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Bergen, Norway
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34
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De Sanctis B, Money D, Pedersen MW, Durbin R. A theoretical analysis of taxonomic binning accuracy. Mol Ecol Resour 2022; 22:2208-2219. [PMID: 35285150 DOI: 10.1111/1755-0998.13608] [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] [Received: 05/25/2021] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 11/28/2022]
Abstract
Many metagenomic and environmental DNA studies require the taxonomic assignment of individual reads or sequences by aligning reads to a reference database, known as taxonomic binning. When a read aligns to more than one reference sequence, it is often classified based on sequence similarity. This step can assign reads to incorrect taxa, at a rate which depends both on the assignment algorithm and on underlying population genetic and database parameters. In particular, as we move towards using environmental DNA to study eukaryotic taxa subject to regular recombination, we must take into account issues concerning gene tree discordance. Though accuracy is often compared across algorithms using a fixed data set, the relative impact of these population genetic and database parameters on accuracy has not yet been quantified. Here, we develop both a theoretical and simulation framework in the simplified case of two reference species, and compute binning accuracy over a wide range of parameters, including sequence length, species-query divergence time, divergence times of the reference species, reference database completeness, sample age and effective population size. We consider two assignment methods and contextualize our results using parameters from a recent ancient environmental DNA study, comparing them to the commonly used discriminative k-mer-based method Clark (Current Biology, 31, 2021, 2728; BMC Genomics, 16, 2015, 1). Our results quantify the degradation in assignment accuracy as the samples diverge from their closest reference sequence, and with incompleteness of reference sequences. We also provide a framework in which others can compute expected accuracy for their particular method or parameter set. Code is available at https://github.com/bdesanctis/binning-accuracy.
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Affiliation(s)
- Bianca De Sanctis
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Daniel Money
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
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35
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Wang Y. Ancient environmental DNA reveals Arctic ecosystem dynamics in last 50,000 years. Sci Bull (Beijing) 2022; 67:1304-1306. [PMID: 36546258 DOI: 10.1016/j.scib.2022.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yucheng Wang
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen K1350, Denmark; BGI, BGI-Shenzhen, Shanghai 201321, China; Group of Alpine Paleoecology and Human Adaptation (ALPHA), State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.
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36
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Schwörer C, Leunda M, Alvarez N, Gugerli F, Sperisen C. The untapped potential of macrofossils in ancient plant DNA research. THE NEW PHYTOLOGIST 2022; 235:391-401. [PMID: 35306671 PMCID: PMC9322452 DOI: 10.1111/nph.18108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/07/2022] [Indexed: 05/26/2023]
Abstract
The rapid development of ancient DNA analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high-throughput sequencing, and bioinformatics, ancient genome-scale data for a rapidly growing variety of taxa are now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of paleogenomic studies still focus on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for paleogenomic analyses: plant remains, such as needles, leaves, wood, seeds, or fruits, that are deposited in natural archives, such as lake sediments, permafrost, or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state-of-the-art, address important challenges, and highlight new research avenues to inspire future research.
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Affiliation(s)
- Christoph Schwörer
- Institute of Plant Sciences & Oeschger Centre for Climate Change ResearchUniversity of Bern3013BernSwitzerland
| | - Maria Leunda
- Institute of Plant Sciences & Oeschger Centre for Climate Change ResearchUniversity of Bern3013BernSwitzerland
- WSL Swiss Federal Research Institute8903BirmensdorfSwitzerland
| | - Nadir Alvarez
- Natural History Museum of Geneva1208GenevaSwitzerland
- Department of Genetics and EvolutionUniversity of Geneva1205GenevaSwitzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute8903BirmensdorfSwitzerland
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37
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Scharn R, Negri IS, Sundqvist MK, Løkken JO, Bacon CD, Antonelli A, Hofgaard A, Nilsson RH, Björk RG. Limited decadal growth of mountain birch saplings has minor impact on surrounding tundra vegetation. Ecol Evol 2022; 12:e9028. [PMID: 35784030 PMCID: PMC9219107 DOI: 10.1002/ece3.9028] [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: 02/01/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 11/11/2022] Open
Abstract
Temperatures over the Arctic region are increasing at three times the rate of the global average. Consequently, Arctic vegetation is changing and trees are encroaching into the tundra. In this study, we examine the establishment and growth of mountain birch (Betula pubescens ssp. tortuosa), which forms the treeline in subarctic Europe, and its impact on community composition across the treeline ecotone nearby Abisko, Sweden. Birch advancement along elevational gradients was studied by comparing data collected in 2016 with data collected 10 and 15 years previously. Species identity, cover, and phylogenetic relatedness were used to assess the impact of birch encroachment on community composition. Our results show that birch occurrence above the treeline did not affect plant community composition, probably owing to the observed lack of significant growth due to herbivore browsing, nitrogen limitation, or a reduction in snow cover. Independent of birch performance, the tundra community structure shifted toward a novel community dissimilar from the forest plant community found below the treeline. Taken together, our findings are explained by species-specific responses to climate change, rather than by a linear forest advance. Future treeline advancements are likely more restricted than previously expected.
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Affiliation(s)
- Ruud Scharn
- Department of Earth SciencesUniversity of GothenburgGothenburgSweden
- Gothenburg Global Biodiversity CentreGothenburgSweden
| | - Isabel S. Negri
- Department of Earth SciencesUniversity of GothenburgGothenburgSweden
- School of BiosciencesCardiff UniversityCardiffUK
| | - Maja K. Sundqvist
- Department of Earth SciencesUniversity of GothenburgGothenburgSweden
- Department of Forest Ecology and ManagementSwedish University of Agricultural SciencesUmeåSweden
| | - Jørn O. Løkken
- Norwegian Institute for Nature ResearchTrondheimNorway
- Department of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Christine D. Bacon
- Gothenburg Global Biodiversity CentreGothenburgSweden
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity CentreGothenburgSweden
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
- Royal Botanical Gardens KewRichmondUK
- Department of Plant SciencesUniversity of OxfordOxfordUK
| | | | - R. Henrik Nilsson
- Gothenburg Global Biodiversity CentreGothenburgSweden
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
| | - Robert G. Björk
- Department of Earth SciencesUniversity of GothenburgGothenburgSweden
- Gothenburg Global Biodiversity CentreGothenburgSweden
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38
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Stojak J, Jędrzejewska B. Extinction and replacement events shaped the historical biogeography of Arctic mammals in Europe: new models of species response. Mamm Rev 2022. [DOI: 10.1111/mam.12298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joanna Stojak
- Mammal Research Institute, Polish Academy of Sciences ul. Stoczek 1, 17‐230 Białowieża Poland
- Department of Ecology and Evolutionary Biology, Paleogenomics Laboratory University of California Santa Cruz Santa Cruz CA 95064 USA
| | - Bogumiła Jędrzejewska
- Mammal Research Institute, Polish Academy of Sciences ul. Stoczek 1, 17‐230 Białowieża Poland
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39
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Ariza M, Fouks B, Mauvisseau Q, Halvorsen R, Alsos IG, de Boer H. Plant biodiversity assessment through soil
eDNA
reflects temporal and local diversity. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- María Ariza
- Universitetet i Oslo, Naturhistorisk Museum Oslo Norway
| | - Bertrand Fouks
- Westfälische Wilhelms‐Universität Institute for Evolution and Biodiversity Molecular Evolution and Bioinformatics. Hüfferstraße 1 Münster Germany
| | | | | | - Inger Greve Alsos
- The Arctic University Museum of Norway UiT ‐ The Arctic University of Norway Norway
| | - Hugo de Boer
- Universitetet i Oslo, Naturhistorisk Museum Oslo Norway
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40
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Shadrina EG, Volpert YL, Okhlopkov IM. Introduction of Mammals in Yakutia: Analysis of Effectiveness, Prospects, and Negative Impacts. RUSSIAN JOURNAL OF BIOLOGICAL INVASIONS 2022. [DOI: 10.1134/s2075111722010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Stunz E, Fetcher N, Lavretsky P, Mohl JE, Tang J, Moody ML. Landscape Genomics Provides Evidence of Ecotypic Adaptation and a Barrier to Gene Flow at Treeline for the Arctic Foundation Species Eriophorum vaginatum. FRONTIERS IN PLANT SCIENCE 2022; 13:860439. [PMID: 35401613 PMCID: PMC8987161 DOI: 10.3389/fpls.2022.860439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Global climate change has resulted in geographic range shifts of flora and fauna at a global scale. Extreme environments, like the Arctic, are seeing some of the most pronounced changes. This region covers 14% of the Earth's land area, and while many arctic species are widespread, understanding ecotypic variation at the genomic level will be important for elucidating how range shifts will affect ecological processes. Tussock cottongrass (Eriophorum vaginatum L.) is a foundation species of the moist acidic tundra, whose potential decline due to competition from shrubs may affect ecosystem stability in the Arctic. We used double-digest Restriction Site-Associated DNA sequencing to identify genomic variation in 273 individuals of E. vaginatum from 17 sites along a latitudinal gradient in north central Alaska. These sites have been part of 30 + years of ecological research and are inclusive of a region that was part of the Beringian refugium. The data analyses included genomic population structure, demographic models, and genotype by environment association. Genome-wide SNP investigation revealed environmentally associated variation and population structure across the sampled range of E. vaginatum, including a genetic break between populations north and south of treeline. This structure is likely the result of subrefugial isolation, contemporary isolation by resistance, and adaptation. Forty-five candidate loci were identified with genotype-environment association (GEA) analyses, with most identified genes related to abiotic stress. Our results support a hypothesis of limited gene flow based on spatial and environmental factors for E. vaginatum, which in combination with life history traits could limit range expansion of southern ecotypes northward as the tundra warms. This has implications for lower competitive attributes of northern plants of this foundation species likely resulting in changes in ecosystem productivity.
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Affiliation(s)
- Elizabeth Stunz
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, United States
| | - Ned Fetcher
- Institute for Environmental Science and Sustainability, Wilkes University, Wilkes-Barre, PA, United States
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, United States
| | - Jonathon E. Mohl
- Department of Mathematical Sciences, Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States
| | - Jianwu Tang
- Marine Biological Laboratory, The Ecosystems Center, Woods Hole, MA, United States
| | - Michael L. Moody
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, United States
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42
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Abstract
Joint phylogenetic analysis of ancient DNA (aDNA) with modern phylogenies is hampered by low sequence coverage and post-mortem deamination, often resulting in overconservative or incorrect assignment. We provide a new efficient likelihood-based workflow, pathPhynder, that takes advantage of all the polymorphic sites in the target sequence. This effectively evaluates the number of ancestral and derived alleles present on each branch and reports the most likely placement of an ancient sample in the phylogeny and a haplogroup assignment, together with alternatives and supporting evidence. To illustrate the application of pathPhynder, we show improved Y chromosome assignments for published aDNA sequences, using a newly compiled Y variation data set (120,908 markers from 2,014 samples) that significantly enhances Y haplogroup assignment for low coverage samples. We apply the method to all published male aDNA samples from Africa, giving new insights into ancient migrations and the relationships between ancient and modern populations. The same software can be used to place samples with large amounts of missing data into other large non-recombining phylogenies such as the mitochondrial tree.
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Affiliation(s)
- Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Bianca De Sanctis
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Pille Hallast
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
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43
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Fordham DA, Brown SC, Akçakaya HR, Brook BW, Haythorne S, Manica A, Shoemaker KT, Austin JJ, Blonder B, Pilowsky J, Rahbek C, Nogues-Bravo D. Process-explicit models reveal pathway to extinction for woolly mammoth using pattern-oriented validation. Ecol Lett 2021; 25:125-137. [PMID: 34738712 DOI: 10.1111/ele.13911] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/18/2021] [Accepted: 10/05/2021] [Indexed: 12/01/2022]
Abstract
Pathways to extinction start long before the death of the last individual. However, causes of early stage population declines and the susceptibility of small residual populations to extirpation are typically studied in isolation. Using validated process-explicit models, we disentangle the ecological mechanisms and threats that were integral in the initial decline and later extinction of the woolly mammoth. We show that reconciling ancient DNA data on woolly mammoth population decline with fossil evidence of location and timing of extinction requires process-explicit models with specific demographic and niche constraints, and a constrained synergy of climatic change and human impacts. Validated models needed humans to hasten climate-driven population declines by many millennia, and to allow woolly mammoths to persist in mainland Arctic refugia until the mid-Holocene. Our results show that the role of humans in the extinction dynamics of woolly mammoth began well before the Holocene, exerting lasting effects on the spatial pattern and timing of its range-wide extinction.
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Affiliation(s)
- Damien A Fordham
- The Environment Institute and School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stuart C Brown
- The Environment Institute and School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - H Reşit Akçakaya
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Barry W Brook
- School of Natural Sciences and ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania, Australia
| | - Sean Haythorne
- The Environment Institute and School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, England
| | - Kevin T Shoemaker
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, Nevada, USA
| | - Jeremy J Austin
- The Environment Institute and School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Benjamin Blonder
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Julia Pilowsky
- The Environment Institute and School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Life Sciences, Imperial College London, Ascot, England.,Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark.,Institute of Ecology, Peking University, Beijing, China
| | - David Nogues-Bravo
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
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