1
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Haider M, Schilling MP, Moest MH, Steiner FM, Schlick‐Steiner BC, Arthofer W. Evolutionary history of an Alpine Archaeognath ( Machilis pallida): Insights from different variant. Ecol Evol 2023; 13:e10227. [PMID: 37404697 PMCID: PMC10316371 DOI: 10.1002/ece3.10227] [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: 07/29/2022] [Revised: 05/31/2023] [Accepted: 06/09/2023] [Indexed: 07/06/2023] Open
Abstract
Reconstruction of species histories is a central aspect of evolutionary biology. Patterns of genetic variation within and among populations can be leveraged to elucidate evolutionary processes and demographic histories. However, interpreting genetic signatures and unraveling the contributing processes can be challenging, in particular for non-model organisms with complex reproductive modes and genome organization. One way forward is the combined consideration of patterns revealed by different molecular markers (nuclear vs. mitochondrial) and types of variants (common vs. rare) that differ in their age, mode, and rate of evolution. Here, we applied this approach to RNAseq data generated for Machilis pallida (Archaeognatha), an Alpine jumping bristletail considered parthenogenetic and triploid. We generated de novo transcriptome and mitochondrial assemblies to obtain high-density data to investigate patterns of mitochondrial and common and rare nuclear variation in 17 M. pallida individuals sampled from all known populations. We find that the different variant types capture distinct aspects of the evolutionary history and discuss the observed patterns in the context of parthenogenesis, polyploidy, and survival during glaciation. This study highlights the potential of different variant types to gain insights into evolutionary scenarios even from challenging but often available data and the suitability of M. pallida and the genus Machilis as a study system for the evolution of sexual strategies and polyploidization during environmental change. We also emphasize the need for further research which will be stimulated and facilitated by these newly generated resources and insights.
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Affiliation(s)
- Marlene Haider
- Department of Ecology, Molecular Ecology GroupUniversity of InnsbruckInnsbruckAustria
| | - Martin P. Schilling
- Department of Ecology, Molecular Ecology GroupUniversity of InnsbruckInnsbruckAustria
| | - Markus H. Moest
- Department of Ecology, Molecular Ecology GroupUniversity of InnsbruckInnsbruckAustria
| | - Florian M. Steiner
- Department of Ecology, Molecular Ecology GroupUniversity of InnsbruckInnsbruckAustria
| | | | - Wolfgang Arthofer
- Department of Ecology, Molecular Ecology GroupUniversity of InnsbruckInnsbruckAustria
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2
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Jardim de Queiroz L, Doenz CJ, Altermatt F, Alther R, Borko Š, Brodersen J, Gossner MM, Graham C, Matthews B, McFadden IR, Pellissier L, Schmitt T, Selz OM, Villalba S, Rüber L, Zimmermann NE, Seehausen O. Climate, immigration and speciation shape terrestrial and aquatic biodiversity in the European Alps. Proc Biol Sci 2022; 289:20221020. [PMID: 35946161 PMCID: PMC9363983 DOI: 10.1098/rspb.2022.1020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Quaternary climate fluctuations can affect speciation in regional biodiversity assembly in two non-mutually exclusive ways: a glacial species pump, where isolation in glacial refugia accelerates allopatric speciation, and adaptive radiation in underused adaptive zones during ice-free periods. We detected biogeographic and genetic signatures associated with both mechanisms in the assembly of the biota of the European Alps. Age distributions of endemic and widespread species within aquatic and terrestrial taxa (amphipods, fishes, amphibians, butterflies and flowering plants) revealed that endemic fish evolved only in lakes, are highly sympatric, and mainly of Holocene age, consistent with adaptive radiation. Endemic amphipods are ancient, suggesting preglacial radiation with limited range expansion and local Pleistocene survival, perhaps facilitated by a groundwater-dwelling lifestyle. Terrestrial endemics are mostly of Pleistocene age and are thus more consistent with the glacial species pump. The lack of evidence for Holocene adaptive radiation in the terrestrial biome is consistent with faster recolonization through range expansion of these taxa after glacial retreats. More stable and less seasonal ecological conditions in lakes during the Holocene may also have contributed to Holocene speciation in lakes. The high proportion of young, endemic species makes the Alpine biota vulnerable to climate change, but the mechanisms and consequences of species loss will likely differ between biomes because of their distinct evolutionary histories.
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Affiliation(s)
- Luiz Jardim de Queiroz
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Carmela J Doenz
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Florian Altermatt
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8006 Zürich, Switzerland
| | - Roman Alther
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8006 Zürich, Switzerland
| | - Špela Borko
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jakob Brodersen
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Martin M Gossner
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland.,Department of Environmental Systems Science, Swiss Federal Institute of Technology in Zürich, 8092 Zürich, Switzerland
| | - Catherine Graham
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland
| | - Blake Matthews
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Ian R McFadden
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland.,Department of Environmental Systems Science, Swiss Federal Institute of Technology in Zürich, 8092 Zürich, Switzerland
| | - Loïc Pellissier
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland.,Department of Environmental Systems Science, Swiss Federal Institute of Technology in Zürich, 8092 Zürich, Switzerland
| | - Thomas Schmitt
- Senckenberg German Entomological Institute, 15374 Müncheberg, Germany.,Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Oliver M Selz
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland
| | - Soraya Villalba
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland
| | - Lukas Rüber
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Naturhistorisches Museum Bern, 3005 Bern, Switzerland
| | - Niklaus E Zimmermann
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland.,Department of Environmental Systems Science, Swiss Federal Institute of Technology in Zürich, 8092 Zürich, Switzerland
| | - Ole Seehausen
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
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3
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Daco L, Matthies D, Hermant S, Colling G. Genetic diversity and differentiation of populations of Anthyllis vulneraria along elevational and latitudinal gradients. Ecol Evol 2022; 12:e9167. [PMID: 35949527 PMCID: PMC9351329 DOI: 10.1002/ece3.9167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/09/2022] Open
Abstract
The abundant centre model (ACM) predicts that the suitability of environmental conditions for a species decreases from the centre of its distribution toward its range periphery and, consequently, its populations will become scarcer, smaller and more isolated, resulting in lower genetic diversity and increased differentiation. However, little is known about whether genetic diversity shows similar patterns along elevational and latitudinal gradients with similar changes in important environmental conditions. Using microsatellite markers, we studied the genetic diversity and structure of 20 populations each of Anthyllis vulneraria along elevational gradients in the Alps from the valleys to the elevational limit (2500 m) and along a latitudinal gradient (2500 km) from Central Europe to the range margin in northern Scandinavia. Both types of gradients corresponded to an 11.5°C difference in mean annual temperature. Genetic diversity strongly declined and differentiation increased with latitude in line with the predictions of the ACM. However, as population size did not decline with latitude and genetic diversity was not related to population size in A. vulneraria, this pattern is not likely to be due to less favorable conditions in the North, but due to serial founder effects during the post-glacial recolonization process. Genetic diversity was not related to elevation, but we found significant isolation by distance along both gradients, although the elevational gradient was shorter by orders of magnitude. Subarctic populations differed genetically from alpine populations indicating that the northern populations did not originate from high elevational Alpine ones. Our results support the notion that postglacial latitudinal colonization over large distances resulted in a larger loss of genetic diversity than elevational range shifts. The lack of genetic diversity in subarctic populations may threaten their long-term persistence in the face of climate change, whereas alpine populations could benefit from gene flow from low-elevation populations.
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Affiliation(s)
- Laura Daco
- Musée national d'histoire naturelleLuxembourgLuxembourg
- University of Marburg, Department of BiologyMarburgGermany
- Fondation faune‐floreLuxembourgLuxembourg
| | | | | | - Guy Colling
- Musée national d'histoire naturelleLuxembourgLuxembourg
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4
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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: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [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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5
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Discovery of cryptic plant diversity on the rooftops of the Alps. Sci Rep 2021; 11:11128. [PMID: 34045566 PMCID: PMC8159976 DOI: 10.1038/s41598-021-90612-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/04/2021] [Indexed: 11/08/2022] Open
Abstract
High elevation temperate mountains have long been considered species poor owing to high extinction or low speciation rates during the Pleistocene. We performed a phylogenetic and population genomic investigation of an emblematic high-elevation plant clade (Androsace sect. Aretia, 31 currently recognized species), based on plant surveys conducted during alpinism expeditions. We inferred that this clade originated in the Miocene and continued diversifying through Pleistocene glaciations, and discovered three novel species of Androsace dwelling on different bedrock types on the rooftops of the Alps. This highlights that temperate high mountains have been cradles of plant diversity even during the Pleistocene, with in-situ speciation driven by the combined action of geography and geology. Our findings have an unexpected historical relevance: H.-B. de Saussure likely observed one of these species during his 1788 expedition to the Mont Blanc and we describe it here, over two hundred years after its first sighting.
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6
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Moore AJ, Messick JA, Kadereit JW. Range and niche expansion through multiple interspecific hybridization: a genotyping by sequencing analysis of Cherleria (Caryophyllaceae). BMC Ecol Evol 2021; 21:40. [PMID: 33691632 PMCID: PMC7945309 DOI: 10.1186/s12862-020-01721-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 11/10/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Cherleria (Caryophyllaceae) is a circumboreal genus that also occurs in the high mountains of the northern hemisphere. In this study, we focus on a clade that diversified in the European High Mountains, which was identified using nuclear ribosomal (nrDNA) sequence data in a previous study. With the nrDNA data, all but one species was monophyletic, with little sequence variation within most species. Here, we use genotyping by sequencing (GBS) data to determine whether the nrDNA data showed the full picture of the evolution in the genomes of these species. RESULTS The overall relationships found with the GBS data were congruent with those from the nrDNA study. Most of the species were still monophyletic and many of the same subclades were recovered, including a clade of three narrow endemic species from Greece and a clade of largely calcifuge species. The GBS data provided additional resolution within the two species with the best sampling, C. langii and C. laricifolia, with structure that was congruent with geography. In addition, the GBS data showed significant hybridization between several species, including species whose ranges did not currently overlap. CONCLUSIONS The hybridization led us to hypothesize that lineages came in contact on the Balkan Peninsula after they diverged, even when those lineages are no longer present on the Balkan Peninsula. Hybridization may also have helped lineages expand their niches to colonize new substrates and different areas. Not only do genome-wide data provide increased phylogenetic resolution of difficult nodes, they also give evidence for a more complex evolutionary history than what can be depicted by a simple, branching phylogeny.
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Affiliation(s)
- Abigail J. Moore
- Department of Microbiology and Plant Biology and Oklahoma Biological Survey, University of Oklahoma, 770 Van Vleet Oval, Norman, OK 73019 USA
| | - Jennifer A. Messick
- Department of Biology, University of Central Oklahoma, Howell Hall, Room 220, Edmond, OK 73034 USA
| | - Joachim W. Kadereit
- Fachbereich Biologie, Institut Für Organismische Und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, Anselm-Franz-von-Bentzel-Weg 9a, 55099 Mainz, Germany
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7
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Kirschner P, Arthofer W, Pfeifenberger S, Záveská E, Schönswetter P, Steiner FM, Schlick-Steiner BC. Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework. Sci Rep 2021; 11:3978. [PMID: 33597550 PMCID: PMC7889850 DOI: 10.1038/s41598-020-79778-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 12/09/2020] [Indexed: 01/31/2023] Open
Abstract
Multi-locus genetic data are pivotal in phylogenetics. Today, high-throughput sequencing (HTS) allows scientists to generate an unprecedented amount of such data from any organism. However, HTS is resource intense and may not be accessible to wide parts of the scientific community. In phylogeography, the use of HTS has concentrated on a few taxonomic groups, and the amount of data used to resolve a phylogeographic pattern often seems arbitrary. We explore the performance of two genetic marker sampling strategies and the effect of marker quantity in a comparative phylogeographic framework focusing on six species (arthropods and plants). The same analyses were applied to data inferred from amplified fragment length polymorphism fingerprinting (AFLP), a cheap, non-HTS based technique that is able to straightforwardly produce several hundred markers, and from restriction site associated DNA sequencing (RADseq), a more expensive, HTS-based technique that produces thousands of single nucleotide polymorphisms. We show that in four of six study species, AFLP leads to results comparable with those of RADseq. While we do not aim to contest the advantages of HTS techniques, we also show that AFLP is a robust technique to delimit evolutionary entities in both plants and animals. The demonstrated similarity of results from the two techniques also strengthens biological conclusions that were based on AFLP data in the past, an important finding given the wide utilization of AFLP over the last decades. We emphasize that whenever the delimitation of evolutionary entities is the central goal, as it is in many fields of biodiversity research, AFLP is still an adequate technique.
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Affiliation(s)
- Philipp Kirschner
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria ,grid.5771.40000 0001 2151 8122Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Wolfgang Arthofer
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Stefanie Pfeifenberger
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Eliška Záveská
- grid.5771.40000 0001 2151 8122Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Peter Schönswetter
- grid.5771.40000 0001 2151 8122Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | | | - Florian M. Steiner
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Birgit C. Schlick-Steiner
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
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8
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Weng YM, Kavanaugh DH, Schoville SD. Drainage basins serve as multiple glacial refugia for alpine habitats in the Sierra Nevada Mountains, California. Mol Ecol 2020; 30:826-843. [PMID: 33270315 DOI: 10.1111/mec.15762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/19/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022]
Abstract
The evolutionary histories of alpine species are often directly associated with responses to glaciation. Deep divergence among populations and complex patterns of genetic variation have been inferred as consequences of persistence within glacier boundaries (i.e., on nunataks), while shallow divergence and limited genetic variation are assumed to result from expansion from large refugia at the edge of ice shields (i.e., massifs de refuge). However, for some species, dependence on specific microhabitats could profoundly influence their spatial and demographic response to glaciation, and such a simple dichotomy may obscure the localization of actual refugia. In this study, we use the Nebria ingens complex (Coleoptera: Carabidae), a water-affiliated ground beetle lineage, to test how drainage basins are linked to their observed population structure. By analysing mitochondrial COI gene sequences and genome-wide single nucleotide polymorphisms, we find that the major drainage systems of the Sierra Nevada Mountains in California best explain the population structure of the N. ingens complex. In addition, we find that an intermediate morphotype within the N. ingens complex is the product of historical hybridization of N. riversi and N. ingens in the San Joaquin basin during glaciation. This study highlights the importance of considering ecological preferences in how species respond to climate fluctuations and provides an explanation for discordances that are often observed in comparative phylogeographical studies.
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Affiliation(s)
- Yi-Ming Weng
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - David H Kavanaugh
- Department of Entomology, California Academy of Sciences, San Francisco, CA, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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9
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Common Patterns and Diverging Trajectories in Primary Succession of Plants in Eastern Alpine Glacier Forelands. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12050191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This paper deals with the vegetation development in four glacier forelands, aligned along a distance of 250 km from West to East in the siliceous Eastern Central Alps. The study employs a chronosequence approach, which assumes a temporal sequence in vegetation development by spatially different sites regarding time since deglaciation. The chronosequences cover the area between Little Ice Age (LIA) maximum glacier extent around 1850, and the current glacier terminus. Despite some shortcomings, chronosequences allow the identification of general patterns of primary succession of plants as a function of site age and local environmental conditions, e.g., changes in species richness, ground cover, plant functional traits, and community structure. While there is no shortage of chronosequence studies in glacier forelands of the Alps, a straightforward comparison aimed at the deduction of general successional trajectories is tricky, due to different procedures of vegetation sampling and data analyses. The comparative examination by a standardized sampling and analyzing protocol of four glacier forelands in the Eastern Central Alps presented here proves the existence of several common patterns in primary succession, but also diverging successional trajectories from West to East. While the pioneer stage in all glacier forelands is similar both floristically and structurally, from the early successional stage onwards, differences increase, leading to different phases in the late successional stage, which is shrub dominated throughout in the westernmost study site, herb–grass–dwarfshrub dominated throughout in the easternmost study site, and divided into an earlier herb–grass–dwarfshrub phase and a later shrub phase in the two study sites in between.
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10
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Pan D, Hülber K, Willner W, Schneeweiss GM. An explicit test of Pleistocene survival in peripheral versus nunatak refugia in two high mountain plant species. Mol Ecol 2019; 29:172-183. [PMID: 31765501 PMCID: PMC7003806 DOI: 10.1111/mec.15316] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 01/15/2023]
Abstract
Pleistocene climate fluctuations had profound influence on the biogeographical history of many biota. As large areas in high mountain ranges were covered by glaciers, biota were forced either to peripheral refugia (and possibly beyond to lowland refugia) or to interior refugia (nunataks). However, nunatak survival remains controversial as it relies solely on correlative genetic evidence. Here, we test hypotheses of glacial survival using two high alpine plant species (the insect‐pollinated Pedicularis asplenifolia and wind‐pollinated Carex fuliginosa) in the European Alps. Employing the iDDC (integrative Distributional, Demographic and Coalescent) approach, which couples species distribution modelling, spatial and temporal demographic simulation and Approximate Bayesian Computation, we explicitly test three hypotheses of glacial survival: (a) peripheral survival only, (b) nunatak survival only and (c) peripheral plus nunatak survival. In P. asplenifolia the peripheral plus nunatak survival hypothesis was supported by Bayes factors (BF> 100), whereas in C. fuliginosa the peripheral survival only hypothesis, although best supported, could not be unambiguously distinguished from the peripheral plus nunatak survival hypothesis (BF = 5.58). These results are consistent with current habitat preferences (P. asplenifolia extends to higher elevations) and the potential for genetic swamping (i.e., replacement of local genotypes via hybridization with immigrating genotypes [expected to be higher in the wind‐pollinated C. fuliginosa]). Although the persistence of plants on nunataks during glacial periods has been debated and studied over decades, this is one of the first studies to explicitly test the hypothesis instead of solely using correlative evidence.
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Affiliation(s)
- Da Pan
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Karl Hülber
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Wolfgang Willner
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Gerald M Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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Schönswetter P, Schneeweiss GM. Is the incidence of survival in interior Pleistocene refugia (nunataks) underestimated? Phylogeography of the high mountain plant Androsace alpina (Primulaceae) in the European Alps revisited. Ecol Evol 2019; 9:4078-4086. [PMID: 31015989 PMCID: PMC6468090 DOI: 10.1002/ece3.5037] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/11/2019] [Accepted: 02/18/2019] [Indexed: 01/17/2023] Open
Abstract
Temperate mountain ranges such as the European Alps have been strongly affected by the Pleistocene glaciations. Glacial advances forced biota into refugia, which were situated either at the periphery of mountain ranges or in their interior. Whereas in the Alps peripheral refugia have been repeatedly and congruently identified, support for the latter scenario, termed "nunatak hypothesis," is still limited and no general pattern is recognizable yet. Here, we test the hypothesis of nunatak survival for species growing in the high alpine to subnival zones on siliceous substrate using the cushion plant Androsace alpina (Primulaceae), endemic to the European Alps, as our model species. To this end, we analyzed AFLP and plastid DNA sequence data obtained from a dense and range-wide sampling. Both AFLPs and plastid sequence data identified the southwestern-most population as the most divergent one. AFLP data did not allow for discrimination of interior and peripheral populations, but rather identified two to three longitudinally separated major gene pools. In contrast, in the eastern half of the Alps several plastid haplotypes of regional or local distribution in interior ranges-the Alpine periphery mostly harbored a widespread haplotype-were indicative for the presence of interior refugia. Together with evidence from other Alpine plant species, this study shows that in the eastern Alps silicicolous species of open habitats in the alpine and subnival zone survived, also or exclusively so, in interior refugia. As the corresponding genetic structure may be lost in mostly nuclear-derived, rapidly homogenizing marker systems such as AFLPs or RAD sequencing tags, markers not prone to homogenization, as is the case for plastid sequences (Sanger-sequenced or extracted from an NGS data set) will continue to be important for detecting older, biogeographically relevant patterns.
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12
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Zhang YZ, Zhu RW, Zhong DL, Zhang JQ. Nunataks or massif de refuge? A phylogeographic study of Rhodiola crenulata (Crassulaceae) on the world's highest sky islands. BMC Evol Biol 2018; 18:154. [PMID: 30326836 PMCID: PMC6192188 DOI: 10.1186/s12862-018-1270-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 10/01/2018] [Indexed: 11/21/2022] Open
Abstract
Background Quaternary climatic oscillations had tremendous effects on the current distribution of species. Here, we aim to elucidate the glacial history of Rhodiola crenulata, a perennial herb almost exclusively restricted to rock crevices on mountain peaks, and to test whether the nunatak or massif de refuge hypotheses could explain its distribution pattern. Results Six haplotypes and six ribotypes were detected in the cpDNA data set and the ITS data set, respectively. The divergence of R. crenulata and its closest relatives was dated have occurred ca. 0.65 Mya, during the Naynayxungla glaciation on the QTP. Mismatch distribution analysis suggested that the species experienced a range expansion around 0.31 Mya. Populations with high genetic and haplotype diversity were found on the QTP platform as well in the Hengduan Mountains. The ecological niche modeling results showed that there were suitable habitats on both the QTP platform and in the Hengduan Mountains during the LGM. Conclusion Our results support a scenario that both nunataks and the massif de refuge hypotheses could explain the distribution of R. crenulata. We also confirmed that Quaternary climatic oscillations could promote plant speciation in some circumstances. This study adds to a growing body of evidence suggesting that the QTP plant lineages exhibited diverse reactions to the Quaternary climatic oscillations. Electronic supplementary material The online version of this article (10.1186/s12862-018-1270-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuan-Zhen Zhang
- College of Life Sciences, Shaanxi Normal University, No. 620, West Chang'an Avenue, Chang'an District, Xi'an, 710119, China
| | - Ruo-Wei Zhu
- College of Life Sciences, Shaanxi Normal University, No. 620, West Chang'an Avenue, Chang'an District, Xi'an, 710119, China
| | - Da-Lv Zhong
- College of Life Sciences, Shaanxi Normal University, No. 620, West Chang'an Avenue, Chang'an District, Xi'an, 710119, China
| | - Jian-Qiang Zhang
- College of Life Sciences, Shaanxi Normal University, No. 620, West Chang'an Avenue, Chang'an District, Xi'an, 710119, China.
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Koch MA, Michling F, Walther A, Huang XC, Tewes L, Müller C. Early-Mid Pleistocene genetic differentiation and range expansions as exemplified by invasive Eurasian Bunias orientalis (Brassicaceae) indicates the Caucasus as key region. Sci Rep 2017; 7:16764. [PMID: 29196646 PMCID: PMC5711908 DOI: 10.1038/s41598-017-17085-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/22/2017] [Indexed: 11/12/2022] Open
Abstract
Turkish Warty cabbage, Bunias orientalis L. (Brassicaceae) is a perennial herb known for its 250 years of invasion history into Europe and worldwide temperate regions. Putative centers of origin were debated to be located in Turkey, the Caucasus or Eastern Europe. Based on the genetic variation from the nuclear and plastid genomes, we identified two major gene pools in the Caucasian-Irano-Turanian region and close to the Northern Caucasus, respectively. These gene pools are old and started to diverge and expand approximately 930 kya in the Caucasus. Pleistocene glaciation and deglaciation cycles favoured later expansion of a European gene pool 230 kya, which was effectively separated from the Caucasian-Irano-Turanian gene pool. Although the European gene pool is genetically less diverse, it has largely served as source for colonization of Western and Northern Europe in modern times with rare observations of genetic contributions from the Caucasian-Irano-Turanian gene pool such as in North-East America. This study largely utilized herbarium material to take advantage of a biodiversity treasure trove providing biological material and also giving access to detailed collection information.
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Affiliation(s)
- Marcus A Koch
- Heidelberg University, Centre for Organismal Studies, Heidelberg, 69120, Germany.
| | - Florian Michling
- Heidelberg University, Centre for Organismal Studies, Heidelberg, 69120, Germany
| | - Andrea Walther
- Heidelberg University, Centre for Organismal Studies, Heidelberg, 69120, Germany
| | - Xiao-Chen Huang
- Heidelberg University, Centre for Organismal Studies, Heidelberg, 69120, Germany
| | - Lisa Tewes
- Bielefeld University, Chemical Ecology, Bielefeld, 33615, Germany
| | - Caroline Müller
- Bielefeld University, Chemical Ecology, Bielefeld, 33615, Germany
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Weng YM, Yang MM, Yeh WB. A comparative phylogeographic study reveals discordant evolutionary histories of alpine ground beetles (Coleoptera, Carabidae). Ecol Evol 2016; 6:2061-73. [PMID: 27066226 PMCID: PMC4768753 DOI: 10.1002/ece3.2006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 01/03/2016] [Accepted: 01/18/2016] [Indexed: 11/10/2022] Open
Abstract
Taiwan, an island with three major mountain ranges, provides an ideal topography to study mountain-island effect on organisms that would be diversified in the isolation areas. Glaciations, however, might drive these organisms to lower elevations, causing gene flow among previously isolated populations. Two hypotheses have been proposed to depict the possible refugia for alpine organisms during glaciations. Nunatak hypothesis suggests that alpine species might have stayed in situ in high mountain areas during glaciations. Massif de refuge, on the other hand, proposes that alpine species might have migrated to lower ice-free areas. By sampling five sympatric carabid species of Nebria and Leistus, and using two mitochondrial genes and two nuclear genes, we evaluated the mountain-island effect on alpine carabids and tested the two proposed hypotheses with comparative phylogeographic method. Results from the phylogenetic relationships, network analysis, lineage calibration, and genetic structure indicate that the deep divergence among populations in all L. smetanai, N. formosana, and N. niitakana was subjected to long-term isolation, a phenomenon in agreement with the nunatak hypothesis. However, genetic admixture among populations of N. uenoiana and some populations of L. nokoensis complex suggests that gene flow occurred during glaciations, as a massif de refuge depicts. The speciation event in N. niitakana is estimated to have occurred before 1.89 million years ago (Mya), while differentiation among isolated populations in N. niitakana, N. formosana, L. smetanai, and L. nokoensis complex might have taken place during 0.65-1.65 Mya. While each of the alpine carabids arriving in Taiwan during different glaciation events acquired its evolutionary history, all of them had confronted the existing mountain ranges.
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Affiliation(s)
- Yi-Ming Weng
- Department of Entomology National Chung Hsing University 250 Kuo-Kuang Rd South District Taichung Taiwan 40227
| | - Man-Miao Yang
- Department of Entomology National Chung Hsing University 250 Kuo-Kuang Rd South District Taichung Taiwan 40227
| | - Wen-Bin Yeh
- Department of Entomology National Chung Hsing University 250 Kuo-Kuang Rd South District Taichung Taiwan 40227
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Vargas-Rodriguez YL, Platt WJ, Urbatsch LE, Foltz DW. Large scale patterns of genetic variation and differentiation in sugar maple from tropical Central America to temperate North America. BMC Evol Biol 2015; 15:257. [PMID: 26586372 PMCID: PMC4653954 DOI: 10.1186/s12862-015-0518-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 10/22/2015] [Indexed: 12/02/2022] Open
Abstract
Background Geological events in the latter Cenozoic have influenced the distribution, abundance and genetic structure of tree populations in temperate and tropical North America. The biogeographical history of temperate vegetation that spans large ranges of latitude is complex, involving multiple latitudinal shifts that might have occurred via different migration routes. We determined the regional structuring of genetic variation of sugar maple (Acer saccharum subsp. saccharum) and its only subspecies in tropical America (Acer saccharum subsp. skutchii) using nuclear and chloroplast data. The studied populations span a geographic range from Maine, USA (46°N), to El Progreso, Guatemala (15°N). We examined genetic subdivisions, explored the locations of ancestral haplotypes, analyzed genetic data to explore the presence of a single or multiple glacial refugia, and tested whether genetic lineages are temporally consistent with a Pleistocene or older divergence. Results Nuclear and chloroplast data indicated that populations in midwestern USA and western Mexico were highly differentiated from populations in the rest of the sites. The time of the most recent common ancestor of the western Mexico haplotype lineage was dated to the Pliocene (5.9 Ma, 95 % HPD: 4.3–7.3 Ma). Splits during the Pleistocene separated the rest of the phylogroups. The most frequent and widespread haplotype occurred in half of the sites (Guatemala, eastern Mexico, southeastern USA, and Ohio). Our data also suggested that multiple Pleistocene refugia (tropics-southeastern USA, midwestern, and northeastern USA), but not western Mexico (Jalisco), contributed to post-glacial northward expansion of ranges. Current southern Mexican and Guatemalan populations have reduced population sizes, genetic bottlenecks and tend toward homozygosity, as indicated using nuclear and chloroplast markers. Conclusions The divergence of western Mexican populations from the rest of the sugar maples likely resulted from orographic and volcanic barriers to gene flow. Past connectivity among populations in the southeastern USA and eastern Mexico and Guatemala possible occurred through gene flow during the Pleistocene. The time to the most common ancestor values revealed that populations from the Midwest and Northeast USA represented different haplotype lineages, indicating major divergence of haplotypes lineages before the Last Glacial Maximum and suggesting the existence of multiple glacial refugia. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0518-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yalma L Vargas-Rodriguez
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA.
| | - William J Platt
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA.
| | - Lowell E Urbatsch
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA.
| | - David W Foltz
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA.
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Pachschwöll C, Escobar García P, Winkler M, Schneeweiss GM, Schönswetter P. Polyploidisation and geographic differentiation drive diversification in a European High Mountain Plant Group (Doronicum clusii Aggregate, Asteraceae). PLoS One 2015; 10:e0118197. [PMID: 25749621 PMCID: PMC4352020 DOI: 10.1371/journal.pone.0118197] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/08/2015] [Indexed: 11/19/2022] Open
Abstract
Range shifts (especially during the Pleistocene), polyploidisation and hybridization are major factors affecting high-mountain biodiversity. A good system to study their role in the European high mountains is the Doronicum clusii aggregate (Asteraceae), whose four taxa (D. clusii s.s., D. stiriacum, D. glaciale subsp. glaciale and D. glaciale subsp. calcareum) are differentiated geographically, ecologically (basiphilous versus silicicolous) and/or via their ploidy levels (diploid versus tetraploid). Here, we use DNA sequences (three plastid and one nuclear spacer) and AFLP fingerprinting data generated for 58 populations to infer phylogenetic relationships, origin of polyploids-whose ploidy level was confirmed by chromosomally calibrated DNA ploidy level estimates-and phylogeographic history. Taxonomic conclusions were informed, among others, by a Gaussian clustering method for species delimitation using dominant multilocus data. Based on molecular data we identified three lineages: (i) silicicolous diploid D. clusii s.s. in the Alps, (ii) silicicolous tetraploid D. stiriacum in the eastern Alps (outside the range of D. clusii s.s.) and the Carpathians and (iii) the basiphilous diploids D. glaciale subsp. glaciale (eastern Alps) and D. glaciale subsp. calcareum (northeastern Alps); each taxon was identified as distinct by the Gaussian clustering, but the separation of D. glaciale subsp. calcareum and D. glaciale subsp. glaciale was not stable, supporting their taxonomic treatment as subspecies. Carpathian and Alpine populations of D. stiriacum were genetically differentiated suggesting phases of vicariance, probably during the Pleistocene. The origin (autopolyploid versus allopolyploid) of D. stiriacum remained unclear. Doronicum glaciale subsp. calcareum was genetically and morphologically weakly separated from D. glaciale subsp. glaciale but exhibited significantly higher genetic diversity and rarity. This suggests that the more widespread D. glaciale subsp. glaciale originated from D. glaciale subsp. calcareum, which is restricted to a prominent Pleistocene refugium previously identified in other alpine plant species.
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Affiliation(s)
- Clemens Pachschwöll
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Pedro Escobar García
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
- Department of Botany, Natural History Museum, Burgring 7, A-1010 Vienna, Austria
| | - Manuela Winkler
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
- GLORIA co-ordination, University of Natural Resources and Life Sciences Vienna, Center for Global Change and Sustainability & Austrian Academy of Sciences, Institute for Interdisciplinary Mountain Research, Silbergasse 30, A-1190 Vienna, Austria
| | - Gerald M. Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
- * E-mail:
| | - Peter Schönswetter
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, A-6020 Innsbruck, Austria
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17
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Potential warm-stage microrefugia for alpine plants: Feedback between geomorphological and biological processes. ECOLOGICAL COMPLEXITY 2015. [DOI: 10.1016/j.ecocom.2014.11.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Maura M, Salvi D, Bologna MA, Nascetti G, Canestrelli D. Northern richness and cryptic refugia: phylogeography of the Italian smooth newtLissotriton vulgaris meridionalis. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12360] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michela Maura
- Dipartimento di Scienze; Università degli studi Roma Tre; Viale G. Marconi 446 00146 Rome Italy
| | - Daniele Salvi
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO; Universidade do Porto; Campus Agrário de Vairão 4485-661 Vairão Portugal
| | - Marco A. Bologna
- Dipartimento di Scienze; Università degli studi Roma Tre; Viale G. Marconi 446 00146 Rome Italy
| | - Giuseppe Nascetti
- Dipartimento di Scienze Ecologiche e Biologiche; Università della Tuscia; Viale dell'Università s.n.c. I-01100 Viterbo Italy
| | - Daniele Canestrelli
- Dipartimento di Scienze Ecologiche e Biologiche; Università della Tuscia; Viale dell'Università s.n.c. I-01100 Viterbo Italy
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Kolář F, Lučanová M, Vít P, Urfus T, Chrtek J, Fér T, Ehrendorfer F, Suda J. Diversity and endemism in deglaciated areas: ploidy, relative genome size and niche differentiation in the Galium pusillum complex (Rubiaceae) in Northern and Central Europe. ANNALS OF BOTANY 2013; 111:1095-1108. [PMID: 23589633 PMCID: PMC3662515 DOI: 10.1093/aob/mct074] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Accepted: 02/11/2013] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Plants endemic to areas covered by ice sheets during the last glaciation represent paradigmatic examples of rapid speciation in changing environments, yet very few systems outside the harsh arctic zone have been comprehensively investigated so far. The Galium pusillum aggregate (Rubiaceae) is a challenging species complex that exhibits a marked differentiation in boreal parts of Northern Europe. As a first step towards understanding its evolutionary history in deglaciated regions, this study assesses cytological variation and ecological preferences of the northern endemics and compares the results with corresponding data for species occurring in neighbouring unglaciated parts of Central and Western Europe. METHODS DNA flow cytometry was used together with confirmatory chromosome counts to determine ploidy levels and relative genome sizes in 1158 individuals from 181 populations. A formalized analysis of habitat preferences was applied to explore niche differentiation among species and ploidy levels. KEY RESULTS The G. pusillum complex evolved at diploid and tetraploid levels in Northern Europe, in contrast to the high-polyploid evolution of most other northern endemics. A high level of eco-geographic segregation was observed between different species (particularly along gradients of soil pH and competition) which is unusual for plants in deglaciated areas and most probably contributes to maintaining species integrity. Relative monoploid DNA contents of the species from previously glaciated regions were significantly lower than those of their counterparts from mostly unglaciated Central Europe, suggesting independent evolutionary histories. CONCLUSIONS The aggregate of G. pusillum in Northern Europe represents an exceptional case with a geographically vicariant and ecologically distinct diploid/tetraploid species endemic to formerly glaciated areas. The high level of interspecific differentiation substantially widens our perception of the evolutionary dynamics and speciation rates in the dramatically changing environments of Northern Europe.
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Affiliation(s)
- Filip Kolář
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01 Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice 1, CZ-252 43 Czech Republic
| | - Magdalena Lučanová
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01 Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice 1, CZ-252 43 Czech Republic
| | - Petr Vít
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01 Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice 1, CZ-252 43 Czech Republic
| | - Tomáš Urfus
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01 Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice 1, CZ-252 43 Czech Republic
| | - Jindřich Chrtek
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01 Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice 1, CZ-252 43 Czech Republic
| | - Tomáš Fér
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01 Czech Republic
| | - Friedrich Ehrendorfer
- Department of Systematic and Evolutionary Botany, Faculty Centre for Biodiversity, University of Vienna, Rennweg 14, Vienna, A-1030 Austria
| | - Jan Suda
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01 Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice 1, CZ-252 43 Czech Republic
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Wachter GA, Arthofer W, Dejaco T, Rinnhofer LJ, Steiner FM, Schlick-Steiner BC. Pleistocene survival on central Alpine nunataks: genetic evidence from the jumping bristletail Machilis pallida. Mol Ecol 2012; 21:4983-95. [PMID: 22994297 DOI: 10.1111/j.1365-294x.2012.05758.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 06/23/2012] [Accepted: 07/05/2012] [Indexed: 11/30/2022]
Abstract
Mechanisms of survival during the Pleistocene glaciation periods have been studied for more than a century. Until now, molecular studies that confirmed animal survival on Alpine nunataks, that is, ice-free summits surrounded by glaciers, were restricted to peripheral areas. Here, we search for molecular signatures of inner-Alpine survival of the narrow endemic and putatively parthenogenetic Alpine jumping bristletail Machilis pallida combining mitochondrial and AFLP data from its three known populations. The mitochondrial data indicate survival on both peripheral and central nunataks, the latter suggesting that refugia in the centre of the Alpine main ridge were more widespread than previously recognized. Incongruences between mitochondrial and AFLP patterns suggest a complex evolutionary history of the species and may be explained via parallel fixation of parthenogenesis of different origins during the last glacial maximum. We suggest that the inferred parthenogenesis may have been essential for central nunatak survival, but may pose a serious threat for M. pallida in consideration of the present climatic changes.
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Affiliation(s)
- Gregor A Wachter
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria.
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21
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Canestrelli D, Salvi D, Maura M, Bologna MA, Nascetti G. One species, three Pleistocene evolutionary histories: phylogeography of the Italian crested newt, Triturus carnifex. PLoS One 2012; 7:e41754. [PMID: 22848590 PMCID: PMC3406094 DOI: 10.1371/journal.pone.0041754] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 06/25/2012] [Indexed: 11/19/2022] Open
Abstract
Phylogeographic patterns of temperate species from the Mediterranean peninsulas have been investigated intensively. Nevertheless, as more phylogeographies become available, either unique patterns or new lines of concordance continue to emerge, providing new insights on the evolution of regional biotas. Here, we investigated the phylogeography and evolutionary history of the Italian crested newt, Triturus carnifex, through phylogenetic, molecular dating and population structure analyses of two mitochondrial gene fragments (ND2 and ND4; overall 1273 bp). We found three main mtDNA lineages having parapatric distribution and estimated divergence times between Late Pliocene and Early Pleistocene. One lineage (S) was widespread south of the northern Apennine chain and was further geographically structured into five sublineages, likely of Middle Pleistocene origin. The second lineage (C) was widespread throughout the Padano-Venetian plain and did not show a clear phylogeographic structure. The third lineage (N) was observed in only two populations located on western Croatia/Slovenia. Results of analysis of molecular variance suggested that partitioning populations according to the geographic distribution of these lineages and sublineages explains 76% of the observed genetic variation. The phylogeographic structure observed within T. carnifex and divergence time estimates among its lineages, suggest that responses to Pleistocene environmental changes in this single species have been as diverse as those found previously among several codistributed temperate species combined. Consistent with the landscape heterogeneity, physiographic features, and palaeogeographical evolution of its distribution range, these responses encompass multiple refugia along the Apennine chain, lowland refugia in large peri-coastal plains, and a 'cryptic' northern refugium.
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Affiliation(s)
- Daniele Canestrelli
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viterbo, Italy.
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22
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Dang XD, Kelleher CT, Howard-Williams E, Meade CV. Rapid identification of chloroplast haplotypes using High Resolution Melting analysis. Mol Ecol Resour 2012; 12:894-908. [PMID: 22783911 DOI: 10.1111/j.1755-0998.2012.03164.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have evaluated High Resolution Melting (HRM) analysis as a method for one-step haplotype identification in phylogeographic analysis. Using two adjoined internal amplicons (c. 360 and 390 bp) at the chloroplast rps16 intron (c. 750 bp) we applied HRM to identify haplotypes in 21 populations of two European arctic-alpine herb species Arenaria ciliata and Arenaria norvegica (Caryophyllaceae). From 446 accessions studied, 20 composite rps16 haplotypes were identified by the melting-curve protocol, 18 of which could be identified uniquely. In a comparative sensitivity analysis with in silico PCR-RFLP, only seven of these 20 haplotypes could be identified uniquely. Observed in vitro experimental HRM profiles were corroborated by in silico HRM analysis generated on uMelt(SM) . In silico mutation analysis carried out on a 360 bp wild-type rps16I amplicon determined that the expected rate of missed single-nucleotide polymorphisms (SNP) detection in vitro was similar to existing evaluations of HRM sensitivity, with transversion SNPs being more likely to go undetected compared to transition SNPs. In vitro HRM successfully discriminated between all amplicon templates differing by two or more base changes (352 cases) and between 11 pairs of amplicons where the only difference was a single transition or transversion SNP. Only one pairwise comparison yielded no discernable HRM curve difference between haplotypes, and these samples differed by one transversion (C/G) SNP. HRM analysis represents an untapped resource in phylogeographic analysis, and with appropriate primer design any polymorphic locus is potentially amenable to this single-reaction method for haplotype identification.
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Affiliation(s)
- Xiao-Dong Dang
- Molecular Ecology Laboratory, Department of Biology, National University of Ireland Maynooth, Co. Kildare, Ireland
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Escobar García P, Winkler M, Flatscher R, Sonnleitner M, Krejčíková J, Suda J, Hülber K, Schneeweiss GM, Schönswetter P. Extensive range persistence in peripheral and interior refugia characterizes Pleistocene range dynamics in a widespread Alpine plant species (Senecio carniolicus, Asteraceae). Mol Ecol 2012; 21:1255-70. [PMID: 22276934 PMCID: PMC3306793 DOI: 10.1111/j.1365-294x.2012.05456.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Recent evidence suggests that survival of arctic-alpine organisms in peripheral or interior glacial refugia are not mutually exclusive and may both be involved in shaping an organism’s Pleistocene history, yet potentially at different time levels. Here, we test this hypothesis in a high-mountain plant (diploid lineage of Senecio carniolicus, Asteraceae) from the Eastern European Alps, in which patterns of morphological variation and current habitat requirements suggest survival in both types of refugia. To this end, we used AFLPs, nuclear and plastid DNA sequences and analysed them, among others, within a graph theoretic framework and using novel Bayesian methods of phylogeographic inference. On the basis of patterns of genetic diversity, occurrence of rare markers, distribution of distinct genetic lineages and patterns of range connectivity both interior refugia in the formerly strongly glaciated central Alps and peripheral refugia along the southern margin of the Alps were identified. The presence of refugia congruently inferred by markers resolving at different time levels suggests that these refugia acted as such throughout several glacial cycles. The high degree of range persistence together with gradual range expansion, which contrasts with the extent of range shifts implied for other Alpine species, is likely responsible for incipient lineage differentiation evident from the genetic data. Replacing a simplistic peripheral vs. interior refugia dualism by more complex models involving both types of refugia and considering different time levels will help identifying common phylogeographic patterns with respect to, for instance, location of refugia and colonization routes and elucidating their underlying genetic and/or ecological causes.
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Affiliation(s)
- Pedro Escobar García
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, Vienna, Austria
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Bisconti R, Canestrelli D, Colangelo P, Nascetti G. Multiple lines of evidence for demographic and range expansion of a temperate species (Hyla sarda) during the last glaciation. Mol Ecol 2011; 20:5313-27. [PMID: 22097966 DOI: 10.1111/j.1365-294x.2011.05363.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Many temperate species experienced demographic and range contractions in response to climatic changes during Pleistocene glaciations. In this study, we investigate the evolutionary history of the Tyrrhenian tree frog Hyla sarda, a species inhabiting the Corsica-Sardinia island system (Western Mediterranean basin). We used sequence analysis of two mitochondrial (overall 1229 bp) and three nuclear (overall 1692 bp) gene fragments to assess the phylogeography and demographic history of this species, and species distribution modelling (SDM) to predict its range variation over time. Phylogeographic, historical demographic and SDM analyses consistently indicate that H. sarda does not conform to the scenario generally expected for temperate species but rather underwent demographic and range expansion mostly during the last glacial phase. Palaeogeographic data and SDM analyses suggest that such expansion was driven by the glaciation-induced increase in lowland areas during marine regression. This unusual scenario suggests that at least some temperate species may not have suffered the adverse effects of glacial climate on their population size and range extent, owing to the mitigating effects of other glaciations-induced palaeoenvironmental changes. We discuss previous clues for the occurrence of such a scenario in other species and some possible challenges with its identification. Early phylogeographic literature suggested that responses to the Pleistocene glacial-interglacial cycles were expected to vary among species and regions. Our results point out that such variation may have been greater than previously thought.
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Affiliation(s)
- Roberta Bisconti
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Largo dell'Università snc, I-01100 Viterbo, Italy
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