1
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Lammers Y, Taberlet P, Coissac E, Elliott LD, Merkel MF, Pitelkova I, Alsos IG. Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA. Mol Ecol Resour 2024; 24:e13926. [PMID: 38189170 DOI: 10.1111/1755-0998.13926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/06/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
Sedimentary ancient DNA (sedaDNA) has rarely been used to obtain population-level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to retrieve population-level genetic data from sedaDNA samples. Vaccinium uliginosum (Ericaceae) is a widespread species with a circumpolar distribution and three lineages in present-day populations. We searched 18 plastid genomes for intraspecific variable regions and developed 61 primer sets to target these. Initial multiplex PCR testing resulted in a final set of 38 primer sets. These primer sets were used to analyse 20 lake sedaDNA samples (11,200 cal. yr BP to present) from five different localities in northern Norway, the Alps and the Polar Urals. All known V. uliginosum lineages in these regions and all primer sets could be recovered from the sedaDNA data. For each sample on average 28.1 primer sets, representing 34.15 sequence variants, were recovered. All sediment samples were dominated by a single lineage, except three Alpine samples which had co-occurrence of two different lineages. Furthermore, lineage turnover was observed in the Alps and northern Norway, suggesting that present-day phylogeographical studies may overlook past genetic patterns. Multiplexing primer is a promising tool for generating population-level genetic information from sedaDNA. The relatively simple method, combined with high sensitivity, provides a scalable method which will allow researchers to track populations through time and space using environmental DNA.
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Affiliation(s)
- Y Lammers
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - P Taberlet
- 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
| | - E Coissac
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - L D Elliott
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - M F Merkel
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - I Pitelkova
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - I G Alsos
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
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2
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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: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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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3
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Brown T, Rijal DP, Heintzman PD, Clarke CL, Blankholm HP, Høeg HI, Lammers Y, Bråthen KA, Edwards M, Alsos IG. Paleoeconomy more than demography determined prehistoric human impact in Arctic Norway. PNAS Nexus 2022; 1:pgac209. [PMID: 36712342 PMCID: PMC9802259 DOI: 10.1093/pnasnexus/pgac209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
Population size has increasingly been taken as the driver of past human environmental impact worldwide, and particularly in the Arctic. However, sedimentary ancient DNA (sedaDNA), pollen and archaeological data show that over the last 12,000 years, paleoeconomy and culture determined human impacts on the terrestrial ecology of Arctic Norway. The large Mortensnes site complex (Ceavccageađgi, 70°N) has yielded the most comprehensive multiproxy record in the Arctic to date. The site saw occupation from the Pioneer period (c. 10,000 cal. years BP) with more intensive use from c. 4,200 to 2,000 cal. years BP and after 1,600 cal. years BP. Here, we combine on-site environmental archaeology with a near-site lake record of plant and animal sedaDNA. The rich animal sedaDNA data (42 taxa) and on-site faunal analyses reveal switches in human dietary composition from early-Holocene fish + marine mammals, to mixed marine + reindeer, then finally to marine + reindeer + domesticates (sheep, cattle, pigs), with highest reindeer concentrations in the last millennium. Archaeological evidence suggests these changes are not directly driven by climate or variation in population densities at the site or in the region, but rather are the result of changing socio-economic activities and culture, probably reflecting settlers' origins. This large settlement only had discernable effects on its hinterland in the last 3,600 years (grazing) and more markedly in the last 1,000 years through reindeer keeping/herding and, possibly domestic stock. Near-site sedaDNA can be linked to and validate the faunal record from archaeological excavations, demonstrating that environmental impacts can be assessed at a landscape scale.
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Affiliation(s)
- Tony Brown
- To whom correspondence should be addressed:
| | - Dilli P Rijal
- The Arctic University Museum of Norway, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Charlotte L Clarke
- The Palaeolab., Geography and Environmental Science, University of Southampton, Southampton SO17 1BJ, UK
| | - Hans Peter Blankholm
- The Institute of Archaeology, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Helge I Høeg
- Department of Geosciences, University of Oslo, 0371 Oslo, Norway
| | - Youri Lammers
- The Arctic University Museum of Norway, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Kari Anne Bråthen
- The Department of Arctic and Marine Biology, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Mary Edwards
- The Palaeolab., Geography and Environmental Science, University of Southampton, Southampton SO17 1BJ, UK
| | - Inger G Alsos
- The Arctic University Museum of Norway, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
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4
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Schulte L, Meucci S, Stoof-Leichsenring KR, Heitkam T, Schmidt N, von Hippel B, Andreev AA, Diekmann B, Biskaborn BK, Wagner B, Melles M, Pestryakova LA, Alsos IG, Clarke C, Krutovsky KV, Herzschuh U. Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA. Commun Biol 2022; 5:570. [PMID: 35681049 PMCID: PMC9184489 DOI: 10.1038/s42003-022-03455-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/06/2022] [Indexed: 11/19/2022] Open
Abstract
Climate change is expected to cause major shifts in boreal forests which are in vast areas of Siberia dominated by two species of the deciduous needle tree larch (Larix). The species differ markedly in their ecosystem functions, thus shifts in their respective ranges are of global relevance. However, drivers of species distribution are not well understood, in part because paleoecological data at species level are lacking. This study tracks Larix species distribution in time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We discovered that Larix sibirica, presently dominating in western Siberia, likely migrated to its northern distribution area only in the Holocene at around 10,000 years before present (ka BP), and had a much wider eastern distribution around 33 ka BP. Samples dated to the Last Glacial Maximum (around 21 ka BP), consistently show genotypes of L. gmelinii. Our results suggest climate as a strong determinant of species distribution in Larix and provide temporal and spatial data for species projection in a changing climate. Using ancient sedimentary DNA from up to 50 kya, dramatic distributional shifts are documented in two dominant boreal larch species, likely guided by environmental changes suggesting climate as a strong determinant of species distribution.
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5
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Smyčka J, Roquet C, Boleda M, Alberti A, Boyer F, Douzet R, Perrier C, Rome M, Valay JG, Denoeud F, Šemberová K, Zimmermann NE, Thuiller W, Wincker P, Alsos IG, Coissac E, Lavergne S. Tempo and drivers of plant diversification in the European mountain system. Nat Commun 2022; 13:2750. [PMID: 35585056 PMCID: PMC9117672 DOI: 10.1038/s41467-022-30394-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 04/26/2022] [Indexed: 12/03/2022] Open
Abstract
There is still limited consensus on the evolutionary history of species-rich temperate alpine floras due to a lack of comparable and high-quality phylogenetic data covering multiple plant lineages. Here we reconstructed when and how European alpine plant lineages diversified, i.e., the tempo and drivers of speciation events. We performed full-plastome phylogenomics and used multi-clade comparative models applied to six representative angiosperm lineages that have diversified in European mountains (212 sampled species, 251 ingroup species total). Diversification rates remained surprisingly steady for most clades, even during the Pleistocene, with speciation events being mostly driven by geographic divergence and bedrock shifts. Interestingly, we inferred asymmetrical historical migration rates from siliceous to calcareous bedrocks, and from higher to lower elevations, likely due to repeated shrinkage and expansion of high elevation habitats during the Pleistocene. This may have buffered climate-related extinctions, but prevented speciation along elevation gradients as often documented for tropical alpine floras. Here, the authors use full-plastome phylogenomics and multiclade comparative models to reconstruct the tempo and drivers of six European Alpine angiosperm lineages before and during the Pleistocene. They find that geographic divergence and bedrock shifts drive speciation events, while diversification rates remained steady.
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Affiliation(s)
- Jan Smyčka
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, FR-38000, Grenoble, France. .,Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, CZ-11000, Prague, Czech Republic. .,Department of Botany, Faculty of Science, Charles University, CZ-12801, Prague, Czech Republic.
| | - Cristina Roquet
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, FR-38000, Grenoble, France.,Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, ES-08193, Bellaterra, Spain
| | - Martí Boleda
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, FR-38000, Grenoble, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, FR-91057, Evry, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), FR-91190, Gif-sur-Yvette, France
| | - Frédéric Boyer
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, FR-38000, Grenoble, France
| | - Rolland Douzet
- CNRS, Lautaret, Jardin du Lautaret, Université Grenoble Alpes, FR-38000, Grenoble, France
| | - Christophe Perrier
- CNRS, Lautaret, Jardin du Lautaret, Université Grenoble Alpes, FR-38000, Grenoble, France
| | - Maxime Rome
- CNRS, Lautaret, Jardin du Lautaret, Université Grenoble Alpes, FR-38000, Grenoble, France
| | - Jean-Gabriel Valay
- CNRS, Lautaret, Jardin du Lautaret, Université Grenoble Alpes, FR-38000, Grenoble, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, FR-91057, Evry, France
| | - Kristýna Šemberová
- Department of Botany, Faculty of Science, Charles University, CZ-12801, Prague, Czech Republic.,Czech Academy of Sciences, Institute of Botany, CZ-25243, Průhonice, Czech Republic
| | | | - Wilfried Thuiller
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, FR-38000, Grenoble, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, FR-91057, Evry, France
| | - Inger G Alsos
- UiT - The Arctic University of Norway, The Arctic University Museum of Norway, N-9037, Tromsø, Norway
| | - Eric Coissac
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, FR-38000, Grenoble, France
| | | | - Sébastien Lavergne
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, FR-38000, Grenoble, France
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6
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Rijal DP, Heintzman PD, Lammers Y, Yoccoz NG, Lorberau KE, Pitelkova I, Goslar T, Murguzur FJA, Salonen JS, Helmens KF, Bakke J, Edwards ME, Alm T, Bråthen KA, Brown AG, Alsos IG. Sedimentary ancient DNA shows terrestrial plant richness continuously increased over the Holocene in northern Fennoscandia. Sci Adv 2021; 7:eabf9557. [PMID: 34330702 PMCID: PMC8324056 DOI: 10.1126/sciadv.abf9557] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/15/2021] [Indexed: 05/22/2023]
Abstract
The effects of climate change on species richness are debated but can be informed by the past. Here, we generated a sedimentary ancient DNA dataset covering 10 lakes and applied novel methods for data harmonization. We assessed the impact of Holocene climate changes and nutrients on terrestrial plant richness in northern Fennoscandia. We find that richness increased steeply during the rapidly warming Early Holocene. In contrast to findings from most pollen studies, we show that richness continued to increase thereafter, although the climate was stable, with richness and the regional species pool only stabilizing during the past three millennia. Furthermore, overall increases in richness were greater in catchments with higher soil nutrient availability. We suggest that richness will increase with ongoing warming, especially at localities with high nutrient availability and assuming that human activity remains low in the region, although lags of millennia may be expected.
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Affiliation(s)
- Dilli P Rijal
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway.
- 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.
| | - Youri Lammers
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
| | - Nigel G Yoccoz
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kelsey E Lorberau
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Iva Pitelkova
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
| | - Tomasz Goslar
- Faculty of Physics, Adam Mickiewicz University, Poznań, Poland
- Poznań Park of Science and Technology, Poznań, Poland
| | - Francisco J A Murguzur
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - J Sakari Salonen
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Karin F Helmens
- Swedish Museum of Natural History, P.O. Box 50007, 10405 Stockholm, Sweden
- Värriö Research Station, Institute for Atmospheric and Earth System Research INAR/Physics, University of Helsinki, P.O. Box 64, 00014 Helsinki, Finland
| | - Jostein Bakke
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Mary E Edwards
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
- School of Geography and Environmental Science, University of Southampton, Southampton, UK
- Alaska Quaternary Center, University of Alaska, Fairbanks, AK 99775, USA
| | - 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
| | - Antony G Brown
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway
- School of Geography and Environmental Science, University of Southampton, Southampton, UK
| | - Inger G Alsos
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø, Norway.
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7
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Brown AG, Van Hardenbroek M, Fonville T, Davies K, Mackay H, Murray E, Head K, Barratt P, McCormick F, Ficetola GF, Gielly L, Henderson ACG, Crone A, Cavers G, Langdon PG, Whitehouse NJ, Pirrie D, Alsos IG. Ancient DNA, lipid biomarkers and palaeoecological evidence reveals construction and life on early medieval lake settlements. Sci Rep 2021; 11:11807. [PMID: 34083588 PMCID: PMC8175756 DOI: 10.1038/s41598-021-91057-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/04/2021] [Indexed: 11/17/2022] Open
Abstract
Direct evidence of ancient human occupation is typically established through archaeological excavation. Excavations are costly and destructive, and practically impossible in some lake and wetland environments. We present here an alternative approach, providing direct evidence from lake sediments using DNA metabarcoding, steroid lipid biomarkers (bile acids) and from traditional environmental analyses. Applied to an early Medieval Celtic settlement in Ireland (a crannog) this approach provides a site chronology and direct evidence of human occupation, crops, animal farming and on-site slaughtering. This is the first independently-dated, continuous molecular archive of human activity from an archeological site, demonstrating a link between animal husbandry, food resources, island use. These sites are under threat but are impossible to preserve in-situ so this approach can be used, with or without excavation, to produce a robust and full site chronology and provide direct evidence of occupation, the use of plants and animals, and activities such as butchery.
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Affiliation(s)
- A G Brown
- Tromsø Museum, Artic University of Norway, Tromsø, Norway. .,School of Geography and Environmental Science, University of Southampton, Southampton, UK.
| | - M Van Hardenbroek
- School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne, UK
| | - T Fonville
- School of Geography and Environmental Science, University of Southampton, Southampton, UK
| | - K Davies
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, UK.,IMSET, Bournemouth University, Poole, UK
| | - H Mackay
- School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne, UK.,Department of Geography, Durham University, Durham, UK
| | - E Murray
- Archaeology, Queens University, Belfast, Northern Ireland, UK
| | - K Head
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, UK
| | - P Barratt
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, UK
| | - F McCormick
- Archaeology, Queens University, Belfast, Northern Ireland, UK
| | - G F Ficetola
- Department of Environmental Science and Policy, University of Milan, Milan, Italy.,LECA, Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, Grenoble, France
| | - L Gielly
- LECA, Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, Grenoble, France
| | - A C G Henderson
- School of Geography, Politics and Sociology, Newcastle University, Newcastle upon Tyne, UK
| | - A Crone
- AOC Group Ltd., Edinburgh, Scotland, UK
| | - G Cavers
- AOC Group Ltd., Edinburgh, Scotland, UK
| | - P G Langdon
- School of Geography and Environmental Science, University of Southampton, Southampton, UK
| | - N J Whitehouse
- Department of Archaeology, School of Humanities, University of Glasgow, Glasgow, UK
| | - D Pirrie
- School of Applied Sciences, University of South Wales, Pontypridd, UK
| | - I G Alsos
- Tromsø Museum, Artic University of Norway, Tromsø, Norway
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8
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Chua PYS, Crampton-Platt A, Lammers Y, Alsos IG, Boessenkool S, Bohmann K. Metagenomics: A viable tool for reconstructing herbivore diet. Mol Ecol Resour 2021; 21:2249-2263. [PMID: 33971086 PMCID: PMC8518049 DOI: 10.1111/1755-0998.13425] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 04/08/2021] [Accepted: 05/04/2021] [Indexed: 11/28/2022]
Abstract
Metagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding. Metagenomic approaches to diet analysis have remained relatively unexplored, requiring validation of bioinformatic steps. Currently, no metagenomic herbivore diet studies have utilized both chloroplast and nuclear markers as reference sequences for plant identification, which would increase the number of reads that could be taxonomically informative. Here, we explore how in silico simulation of metagenomic data sets resembling sequences obtained from faecal samples can be used to validate taxonomic assignment. Using a known list of sequences to create simulated data sets, we derived reliable identification parameters for taxonomic assignments of sequences. We applied these parameters to characterize the diet of western capercaillies (Tetrao urogallus) located in Norway, and compared the results with metabarcoding trnL P6 loop data generated from the same samples. Both methods performed similarly in the number of plant taxa identified (metagenomics 42 taxa, metabarcoding 43 taxa), with no significant difference in species resolution (metagenomics 24%, metabarcoding 23%). We further observed that while metagenomics was strongly affected by the age of faecal samples, with fresh samples outperforming old samples, metabarcoding was not affected by sample age. On the other hand, metagenomics allowed us to simultaneously obtain the mitochondrial genome of the western capercaillies, thereby providing additional ecological information. Our study demonstrates the potential of utilizing metagenomics for diet reconstruction but also highlights key considerations as compared to metabarcoding for future utilization of this technique.
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Affiliation(s)
- Physilia Y S Chua
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Youri Lammers
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Inger G Alsos
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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9
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Clarke CL, Edwards ME, Gielly L, Ehrich D, Hughes PDM, Morozova LM, Haflidason H, Mangerud J, Svendsen JI, Alsos IG. Persistence of arctic-alpine flora during 24,000 years of environmental change in the Polar Urals. Sci Rep 2019; 9:19613. [PMID: 31873100 PMCID: PMC6927971 DOI: 10.1038/s41598-019-55989-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/03/2019] [Indexed: 12/18/2022] Open
Abstract
Plants adapted to extreme conditions can be at high risk from climate change; arctic-alpine plants, in particular, could "run out of space" as they are out-competed by expansion of woody vegetation. Mountain regions could potentially provide safe sites for arctic-alpine plants in a warmer climate, but empirical evidence is fragmentary. Here we present a 24,000-year record of species persistence based on sedimentary ancient DNA (sedaDNA) from Lake Bolshoye Shchuchye (Polar Urals). We provide robust evidence of long-term persistence of arctic-alpine plants through large-magnitude climate changes but document a decline in their diversity during a past expansion of woody vegetation. Nevertheless, most of the plants that were present during the last glacial interval, including all of the arctic-alpines, are still found in the region today. This underlines the conservation significance of mountain landscapes via their provision of a range of habitats that confer resilience to climate change, particularly for arctic-alpine taxa.
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Affiliation(s)
- C L Clarke
- School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.
| | - M E Edwards
- School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - L Gielly
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, C2 40700 38058, Grenoble, Cedex 9, France
| | - D Ehrich
- Department of Arctic and Marine Biology, UiT- The Arctic University of Norway, Tromsø, NO-9037, Norway
| | - P D M Hughes
- School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - L M Morozova
- Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences, Ekaterinburg, Russia
| | - H Haflidason
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, Bergen, 5007, Norway
| | - J Mangerud
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, Bergen, 5007, Norway
| | - J I Svendsen
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, Bergen, 5007, Norway
| | - I G Alsos
- Tromsø University Museum, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
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10
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Zinger L, Bonin A, Alsos IG, Bálint M, Bik H, Boyer F, Chariton AA, Creer S, Coissac E, Deagle BE, De Barba M, Dickie IA, Dumbrell AJ, Ficetola GF, Fierer N, Fumagalli L, Gilbert MTP, Jarman S, Jumpponen A, Kauserud H, Orlando L, Pansu J, Pawlowski J, Tedersoo L, Thomsen PF, Willerslev E, Taberlet P. DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions. Mol Ecol 2019; 28:1857-1862. [DOI: 10.1111/mec.15060] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 02/19/2019] [Accepted: 02/19/2019] [Indexed: 01/20/2023]
Affiliation(s)
- Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), Département de biologie Ecole normale supérieure, CNRS, INSERM, Université PSL Paris France
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine (LECA) CNRS, Université Grenoble Alpes Grenoble France
| | - Inger G. Alsos
- UiT – The Arctic University of Norway, Tromsø Museum Tromsø Norway
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG) Frankfurt Germany
| | - Holly Bik
- Department of Nematology University of California Riverside California
| | - Frédéric Boyer
- Laboratoire d'Ecologie Alpine (LECA) CNRS, Université Grenoble Alpes Grenoble France
| | - Anthony A. Chariton
- Department of Biological Sciences Macquarie University Sydney New South Wales Australia
| | - Simon Creer
- School of Natural Sciences Bangor University Gwynedd UK
| | - Eric Coissac
- Laboratoire d'Ecologie Alpine (LECA) CNRS, Université Grenoble Alpes Grenoble France
| | | | - Marta De Barba
- Laboratoire d'Ecologie Alpine (LECA) CNRS, Université Grenoble Alpes Grenoble France
| | - Ian A. Dickie
- School of Biological Sciences, BioProtection Research Centre University of Canterbury Christchurch New Zealand
| | | | - Gentile Francesco Ficetola
- Laboratoire d'Ecologie Alpine (LECA) CNRS, Université Grenoble Alpes Grenoble France
- Department of Environmental Science and Policy Università degli Studi di Milano Milano Italy
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology University of Colorado Boulder Colorado
- Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder Colorado
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics, Biological Institute University of Copenhagen Copenhagen Denmark
- Norwegian University of Science and Technology, University Museum Trondheim Norway
| | - Simon Jarman
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture Curtin University Perth Western Australia Australia
- Environomics Future Science Platform CSIRO National Collections and Marine Infrastructure Crawley Western Australia Australia
| | - Ari Jumpponen
- Division of Biology Kansas State University Manhattan Kansas
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE) University of Oslo Oslo Norway
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier Toulouse France
- Lundbeck Foundation GeoGenetics Center University of Copenhagen Copenhagen Denmark
| | - Johan Pansu
- Department of Biological Sciences Macquarie University Sydney New South Wales Australia
- Station Biologique de Roscoff CNRS UMR 7144, Sorbonne Université Roscoff France
- CSIRO Ocean & Atmosphere Lucas Heights New South Wales Australia
| | - Jan Pawlowski
- ID‐Gene Ecodiagnostics Geneva Switzerland
- Department of Genetics and Evolution University of Geneva Geneva Switzerland
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | | | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Center University of Copenhagen Copenhagen Denmark
- Department of Zoology University of Cambridge Cambridge UK
- Wellcome Trust Sanger Institute Cambridge UK
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine (LECA) CNRS, Université Grenoble Alpes Grenoble France
- UiT – The Arctic University of Norway, Tromsø Museum Tromsø Norway
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11
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Rijal DP, Alm T, Nilsen L, Alsos IG. Giant invasive Heracleum persicum: Friend or foe of plant diversity? Ecol Evol 2017; 7:4936-4950. [PMID: 28690820 PMCID: PMC5496559 DOI: 10.1002/ece3.3055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 11/12/2022] Open
Abstract
The impact of invasion on diversity varies widely and remains elusive. Despite the considerable attempts to understand mechanisms of biological invasion, it is largely unknown whether some communities’ characteristics promote biological invasion, or whether some inherent characteristics of invaders enable them to invade other communities. Our aims were to assess the impact of one of the massive plant invaders of Scandinavia on vascular plant species diversity, disentangle attributes of invasible and noninvasible communities, and evaluate the relationship between invasibility and genetic diversity of a dominant invader. We studied 56 pairs of Heracleum persicum Desf. ex Fisch.‐invaded and noninvaded plots from 12 locations in northern Norway. There was lower native cover, evenness, taxonomic diversity, native biomass, and species richness in the invaded plots than in the noninvaded plots. The invaded plots had nearly two native species fewer than the noninvaded plots on average. Within the invaded plots, cover of H. persicum had a strong negative effect on the native cover, evenness, and native biomass, and a positive association with the height of the native plants. Plant communities containing only native species appeared more invasible than those that included exotic species, particularly H. persicum. Genetic diversity of H. persicum was positively correlated with invasibility but not with community diversity. The invasion of a plant community by H. persicum exerts consistent negative pressure on vascular plant diversity. The lack of positive correlation between impacts and genetic diversity of H. persicum indicates that even a small founder population may cause high impact. We highlight community stability or saturation as an important determinant of invasibility. While the invasion by H. persicum may decrease susceptibility of a plant community to further invasion, it severely reduces the abundance of native species and makes them more vulnerable to competitive exclusion.
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Affiliation(s)
- Dilli P Rijal
- Department of Natural Sciences Tromsø Museum UiT-The Arctic University of Norway Tromsø Norway
| | - Torbjørn Alm
- Department of Natural Sciences Tromsø Museum UiT-The Arctic University of Norway Tromsø Norway
| | - Lennart Nilsen
- Department of Arctic and Marine Biology UiT-The Arctic University of Norway Tromsø Norway
| | - Inger G Alsos
- Department of Natural Sciences Tromsø Museum UiT-The Arctic University of Norway Tromsø Norway
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12
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Rämä T, Davey ML, Nordén J, Halvorsen R, Blaalid R, Mathiassen GH, Alsos IG, Kauserud H. Fungi Sailing the Arctic Ocean: Speciose Communities in North Atlantic Driftwood as Revealed by High-Throughput Amplicon Sequencing. Microb Ecol 2016; 72:295-304. [PMID: 27147245 DOI: 10.1007/s00248-016-0778-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/22/2016] [Indexed: 06/05/2023]
Abstract
High amounts of driftwood sail across the oceans and provide habitat for organisms tolerating the rough and saline environment. Fungi have adapted to the extremely cold and saline conditions which driftwood faces in the high north. For the first time, we applied high-throughput sequencing to fungi residing in driftwood to reveal their taxonomic richness, community composition, and ecology in the North Atlantic. Using pyrosequencing of ITS2 amplicons obtained from 49 marine logs, we found 807 fungal operational taxonomic units (OTUs) based on clustering at 97 % sequence similarity cut-off level. The phylum Ascomycota comprised 74 % of the OTUs and 20 % belonged to Basidiomycota. The richness of basidiomycetes decreased with prolonged submersion in the sea, supporting the general view of ascomycetes being more extremotolerant. However, more than one fourth of the fungal OTUs remained unassigned to any fungal class, emphasising the need for better DNA reference data from the marine habitat. Different fungal communities were detected in coniferous and deciduous logs. Our results highlight that driftwood hosts a considerably higher fungal diversity than currently known. The driftwood fungal community is not a terrestrial relic but a speciose assemblage of fungi adapted to the stressful marine environment and different kinds of wooden substrates found in it.
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Affiliation(s)
- Teppo Rämä
- Tromsø University Museum, UiT The Arctic University of Norway, Tromsø, Norway.
- Marbio, UiT The Arctic University of Norway, Tromsø, Norway.
| | - Marie L Davey
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
- University Centre in Svalbard (UNIS), Svalbard, Norway
| | - Jenni Nordén
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Natural History Museum, University of Oslo, Oslo, Norway
- Norwegian Institute for Nature Research, Oslo, Norway
| | - Rune Halvorsen
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Rakel Blaalid
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Haukeland University Hospital, Bergen, Norway
| | - Geir H Mathiassen
- Tromsø University Museum, UiT The Arctic University of Norway, Tromsø, Norway
| | - Inger G Alsos
- Tromsø University Museum, UiT The Arctic University of Norway, Tromsø, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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13
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Ware C, Berge J, Jelmert A, Olsen SM, Pellissier L, Wisz M, Kriticos D, Semenov G, Kwaśniewski S, Alsos IG. Biological introduction risks from shipping in a warming
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rctic. J Appl Ecol 2015. [DOI: 10.1111/1365-2664.12566] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Chris Ware
- UiT The Arctic University of Norway Tromsø University Museum Kvaløyvegen 30 Tromsø 9037 Norway
- School of Geography & Environmental Studies University of Tasmania Churchill Avenue Sandy Bay Tasmania 7005 Australia
- Land and Water Flagship Commonwealth Scientific and Industrial Research Organisation GPO Box 1700 Canberra Australian Capital Territory 2601 Australia
| | - Jørgen Berge
- Faculty of Biosciences, Fisheries & Economics UiT The Arctic University of Norway Tromsø 9037 Norway
- University Centre in Svalbard P.O Box 156 Longyearbyen 9171 Norway
| | - Anders Jelmert
- Institute of Marine Research Flødevign Research Station Nye Flødevign 25 N‐4817 Norway
| | - Steffen M. Olsen
- Danish Meteorological Institute Lyngbyvej 100 Copenhagen 2100 Denmark
| | - Loïc Pellissier
- Swiss Federal Research Institute WSL 8903 Birmensdorf Switzerland
- Landscape Ecology Institute of Terrestrial Ecosystems ETH Zürich Universitaetstrasse 22 8092 Zürich Switzerland
| | - Mary Wisz
- National Institute of Aquatic Resources Danish Technical University Jægersborg Allé 12920 Charlottenlund Denmark
| | - Darren Kriticos
- Biosecurity Flagship Commonwealth Scientific and Industrial Research Organisation GPO Box 1700 Canberra Australian Capital Territory 2601 Australia
| | - Georgy Semenov
- Institute of Systematics & Ecology of Animals Siberian Branch of the Russian Academy of Sciences Frunze St. 11 630091 Novosibirsk Russia
| | - Sławomir Kwaśniewski
- Institute of Oceanology Polish Academy of Sciences Powstańców Warszawy 55 Sopot 81‐712 Poland
| | - Inger G. Alsos
- UiT The Arctic University of Norway Tromsø University Museum Kvaløyvegen 30 Tromsø 9037 Norway
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14
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Rijal DP, Alm T, Jahodová Š, Stenøien HK, Alsos IG. Reconstructing the invasion history of Heracleum persicum (Apiaceae) into Europe. Mol Ecol 2015; 24:5522-43. [PMID: 26454010 DOI: 10.1111/mec.13411] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 10/03/2015] [Accepted: 10/06/2015] [Indexed: 01/15/2023]
Abstract
Sparse, incomplete and inappropriate historical records of invasive species often hamper invasive species management interventions. Population genetic analyses of invaders might provide a suitable context for the identification of their source populations and possible introduction routes. Here, we describe the population genetics of Heracleum persicum Desf. ex Fisch and trace its route of introduction into Europe. Microsatellite markers revealed a significantly higher genetic diversity of H. persicum in its native range, and the loss of diversity in the introduced range may be attributed to a recent genetic bottleneck. Bayesian cluster analysis on regional levels identified three and two genetic clusters in the native and the introduced ranges, respectively. A global structure analysis revealed two worldwide distinct genetic groups: one primarily in Iran and Denmark, the other primarily in Norway. There were also varying degrees of admixture in England, Sweden, Finland and Latvia. Approximate Bayesian computation indicated two independent introductions of H. persicum from Iran to Europe: the first one in Denmark and the second one in England. Finland was subsequently colonized by English populations. In contrast to the contemporary hypothesis of English origin of Norwegian populations, we found Finland to be a more likely source for Norwegian populations, a scenario supported by higher estimated historical migration from Finland to Norway. Genetic diversity per se is not a primary determinant of invasiveness in H. persicum. Our results indicate that, due to either pre-adaptations or rapid local adaptations, introduced populations may have acquired invasiveness after subsequent introductions, once a suitable environment was encountered.
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Affiliation(s)
- Dilli P Rijal
- Department of Natural Sciences, Tromsø Museum, University of Tromsø-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Torbjørn Alm
- Department of Natural Sciences, Tromsø Museum, University of Tromsø-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Šárka Jahodová
- Institute of Botany, The Czech Academy of Sciences, CZ-252 43, Průhonice, Czech Republic.,Department of Ecology, Faculty of Science, Charles University in Prague, Viničná 7, Prague, CZ-128 44, Czech Republic
| | - Hans K Stenøien
- Department of Natural History, Centre for Biodiversity Dynamics, NTNU University Museum, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Inger G Alsos
- Department of Natural Sciences, Tromsø Museum, University of Tromsø-The Arctic University of Norway, 9037, Tromsø, Norway
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15
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Ware C, Berge J, Sundet JH, Kirkpatrick JB, Coutts ADM, Jelmert A, Olsen SM, Floerl O, Wisz MS, Alsos IG. Climate change, non‐indigenous species and shipping: assessing the risk of species introduction to a high‐
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rctic archipelago. DIVERS DISTRIB 2013. [DOI: 10.1111/ddi.12117] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Chris Ware
- University of Tromsø Tromsø University Museum Kvaløyvegen 30 Tromsø 9037 Norway
- University of Tasmania Churchill Avenue Sandy Bay Tas. 7005 Australia
| | - Jørgen Berge
- Faculty of Biosciences, Fisheries, and Economics University of Tromsø Tromsø 9037 Norway
- University Centre on Svalbard PO Box 156 Longyearbyen 9171 Norway
| | - Jan H. Sundet
- Institute of Marine Research PO Box 6404 Tromsø 9294 Norway
| | | | | | - Anders Jelmert
- Institute of Marine Research PO Box 1870 Nordnes Bergen 5817 Norway
| | - Steffen M. Olsen
- Danish Meteorological Institute Lyngbyvej 100 Copenhagen 2100 Denmark
| | - Oliver Floerl
- SINTEF Fisheries & Aquaculture Brattørkaia 17C Trondheim 7010 Norway
| | - Mary S. Wisz
- Department of Bioscience Aarhus University Frederiksborgvej 399 4000 Roskilde Denmark
- Greenland Climate Research Centre Greenland Institute of Natural Resources Nuuk Greenland
| | - Inger G. Alsos
- University of Tromsø Tromsø University Museum Kvaløyvegen 30 Tromsø 9037 Norway
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16
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Westergaard KB, Alsos IG, Popp M, Engelskjøn T, Flatberg KI, Brochmann C. Glacial survival may matter after all: nunatak signatures in the rare European populations of two west-arctic species. Mol Ecol 2010; 20:376-93. [PMID: 21156004 DOI: 10.1111/j.1365-294x.2010.04928.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Abstract
To fully understand the contemporary genetic structure of plants, both nuclear and plastid markers are needed. Three chloroplast DNA (cpDNA) lineages, which probably diverged before the major Pleistocene glaciations, have been identified in the circumpolar/circumboreal Vaccinium uliginosum. Here we investigate its nuclear DNA variation using nuclear ribosomal internal transcribed spacer (ITS) sequences, DNA ploidy level measurements and amplified fragment length polymorphisms (AFLPs). We also extend the cpDNA dataset. Two ITS lineages, corresponding to diploids and tetraploids, respectively, were identified. However, both main sequence types apparently occurred in most individual plants but showed ploidy-biased homogenization and possibly reflect paralogy predating the origin of V. uliginosum. The ploidy levels were largely consistent with the cpDNA lineages, suggesting that the initial cpDNA divergence followed early polyploidizations. Five main AFLP groups were identified, consistent with recent glacial refugia in Beringia, western Siberia, the southern European mountains and areas south/east of the Scandinavian and Laurentide ice sheets. Except from the southern European mountains, there has been extensive expansion from all refugia, resulting in several contact zones. Surprisingly, the presumably older ploidy and cpDNA patterns were partly inconsistent with the main AFLP groups and more consistent with AFLP subgroups. A likely major driver causing the inconsistencies is recent nuclear gene flow via unreduced pollen from diploids to tetraploids. This may prevent cytoplasmic introgression and result in overlayed patterns formed by processes dominating at different time scales. The data also suggest more recent polyploidizations, as well as several chloroplast capture events, further complicating this scenario. This study highlights the importance of combining different marker systems to unravel intraspecific histories.
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Affiliation(s)
- P B Eidesen
- National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318 Oslo, Norway.
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18
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Abstract
We address the impact of the ice age cycles on intraspecific cpDNA diversity, for the first time on the full circumboreal-circumarctic scale. The bird-dispersed bog bilberry (or arctic blueberry, Vaccinium uliginosum) is a key component of northern ecosystems and is here used to assess diversity in previously glaciated vs. unglaciated areas and the importance of Beringia as a refugium and source for interglacial expansion. Eighteen chloroplast DNA haplotypes were observed in and among 122 populations, grouping into three main lineages which probably diverged before, and thus were affected more or less independently by, all major glaciations. The boreal 'Amphi-Atlantic lineage' included one haplotype occurring throughout northern Europe and one occurring in eastern North America, suggesting expansion from at least two bottlenecked, glacial refugium populations. The boreal 'Beringian lineage' included seven haplotypes restricted to Beringia and the Pacific coast of USA. The 'Arctic-Alpine lineage' included nine haplotypes, one of them fully circumpolar. This lineage was unexpectedly diverse, also in previously glaciated areas, suggesting that it thrived on the vast tundras during the ice ages and recolonized deglaciated terrain over long distances. Its largest area of persistence during glaciations was probably situated in the north, stretching from Beringia and far into Eurasia, and it probably also survived the last glaciation in southern mountain ranges. Although Beringia apparently was important for the initial divergence and expansion of V. uliginosum as well as for continuous survival of both the Beringian and Arctic-Alpine lineages during all ice ages, this region played a minor role as a source for later interglacial expansions.
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Affiliation(s)
- I G Alsos
- Tromsø Museum, University of Tromsø, NO-9037 Tromsø, Norway
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