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Tonin R, Wilhelmi S, Gültas M, Gerdol R, Paun O, Trucchi E, Schmitt AO, Wellstein C. Ice holes microrefugia harbor genetically and functionally distinct populations of Vaccinium vitis-idaea (Ericaceae). Sci Rep 2023; 13:13055. [PMID: 37567871 PMCID: PMC10421893 DOI: 10.1038/s41598-023-39772-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
In the mountain terrain, ice holes are little depressions between rock boulders that are characterized by the exit of cold air able to cool down the rock surface even in summer. This cold air creates cold microrefugia in warmer surroundings that preserve plant species probably over thousands of years under extra-zonal climatic conditions. We hypothesized that ice hole populations of the model species Vaccinium vitis-idaea (Ericaceae) show genetic differentiation from nearby zonal subalpine populations, and high functional trait distinctiveness, in agreement with genetic patterns. We genotyped almost 30,000 single nucleotide polymorphisms using restriction site-associated DNA sequencing and measured eight functional traits indicative of individual performance and ecological strategies. Genetic results showed high differentiation among the six populations suggesting isolation. On siliceous bedrock, ice hole individuals exhibited higher levels of admixture than those from subalpine populations which could have experienced more bottlenecks during demographic fluctuations related to glacial cycles. Ice hole and subalpine calcareous populations clearly separated from siliceous populations, indicating a possible effect of bedrock in shaping genetic patterns. Trait analysis reflected the bedrock effect on populations' differentiation. The significant correlation between trait and genetic distances suggests the genetic contribution in shaping intraspecific functional differentiation. In conclusion, extra-zonal populations reveal a prominent genetic and phenotypic differentiation determined by history and ecological contingency. Therefore, microrefugia populations can contribute to the overall variability of the species and lead to intraspecific-driven responses to upcoming environmental changes.
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Affiliation(s)
- Rita Tonin
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100, Bozen, Italy
| | - Selina Wilhelmi
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, 37075, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), 37075, Göttingen, Germany
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, 37077, Göttingen, Germany
| | - Mehmet Gültas
- Center for Integrated Breeding Research (CiBreed), 37075, Göttingen, Germany
- Faculty of Agriculture, South Westphalia University of Applied Sciences, 59494, Soest, Germany
| | - Renato Gerdol
- Department of Environmental and Prevention Sciences, University of Ferrara, 44121, Ferrara, Italy
| | - Ovidiu Paun
- Department for Botany and Biodiversity Research, University of Vienna, 1030, Vienna, Austria
| | - Emiliano Trucchi
- Department of Life and Environmental Science, Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, 37075, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), 37075, Göttingen, Germany
| | - Camilla Wellstein
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100, Bozen, Italy.
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2
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Felkel S, Tremetsberger K, Moser D, Dohm JC, Himmelbauer H, Winkler M. Genome-environment associations along elevation gradients in two snowbed species of the North-Eastern Calcareous Alps. BMC PLANT BIOLOGY 2023; 23:203. [PMID: 37076814 PMCID: PMC10114330 DOI: 10.1186/s12870-023-04187-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Anthropogenic climate change leads to increasing temperatures and altered precipitation and snowmelt patterns, especially in alpine ecosystems. To understand species' responses to climate change, assessment of genetic structure and diversity is crucial as the basis for the evaluation of migration patterns, genetic adaptation potential as well as the identification of adaptive alleles. RESULTS We studied genetic structure, diversity and genome-environment associations of two snowbed species endemic to the Eastern Alps with a large elevational range, Achillea clusiana Tausch and Campanula pulla L. Genotyping-by-sequencing was employed to assemble loci de novo, call variants and perform population genetic analyses. Populations of either species were distinguishable by mountain, and to some extent by elevation. We found evidence for gene flow between elevations. Results of genome-environment associations suggested similar selective pressures acting on both species, emanating mainly from precipitation and exposition rather than temperature. CONCLUSIONS Given their genetic structure and amount of gene flow among populations the two study species are suitable to serve as a model for genetic monitoring of climate change adaptation along an elevation gradient. Consequences of climate change will predominantly manifest via changes in precipitation and, thus, duration of snow cover in the snowbeds and indirectly via shrub encroachment accompanied by increasing shading of snowbeds at lower range margins. Assembling genomes of the study species and studying larger sample sizes and time series will be necessary to functionally characterize and validate the herein identified genomic loci putatively involved in adaptive processes.
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Affiliation(s)
- Sabine Felkel
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, 1190, Austria
| | - Karin Tremetsberger
- Institute of Botany, Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences, Vienna, Vienna, 1180, Austria
| | - Dietmar Moser
- Biodiversity Dynamics and Conservation Group, Department of Botany and Biodiversity Research, University of Vienna, Vienna, 1030, Austria
| | - Juliane C Dohm
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, 1190, Austria
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, 1190, Austria
| | - Manuela Winkler
- GLORIA Coordination, Institute for Interdisciplinary Mountain Research, Austrian Academy of Sciences, Vienna, 1190, Austria.
- GLORIA Coordination, Institute of Botany, Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences, Vienna, Vienna, 1190, Austria.
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3
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Carnicero P, Wessely J, Moser D, Font X, Dullinger S, Schönswetter P. Postglacial range expansion of high-elevation plants is restricted by dispersal ability and habitat specialization. JOURNAL OF BIOGEOGRAPHY 2022; 49:1739-1752. [PMID: 36245965 PMCID: PMC9541807 DOI: 10.1111/jbi.14390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 06/16/2023]
Abstract
AIM Species' ecological traits influence their spatial genetic patterns. Bedrock preference strongly shapes the phylogeography of alpine plants, but its interactions with other ecological traits have rarely been disentangled. Here, we explore whether dispersal ability and degree of habitat specialization account for divergent postglacial expansion patterns of high-elevation plants in spite of similar bedrock preference. LOCATION The Pyrenees, southwestern Europe. TAXON Cirsium glabrum (Asteraceae), Salix pyrenaica (Salicaceae) and Silene borderei (Caryophyllaceae). METHODS Phylogenetic, genetic structure and demographic modelling analyses based on restriction-site-associated DNA sequencing (RADseq) data from a range-wide populational sampling were conducted. Occurrence data and environmental variables were used to construct species distribution models, which were projected under current and Last Glacial Maximum conditions, and were combined with RADseq data to reconstruct the postglacial history of the study species. The degree of habitat specialization of each species was estimated based on the plant communities within which they occur, and their climatic niche breadth. RESULTS Salix pyrenaica, which occupies a broad range of habitats, shows a high level of range filling, a blurred genetic structure and an admixture cline between the two main genetic groups, congruent with rapid postglacial expansion. The microsite specialists C. glabrum and S. borderei exhibit a strong genetic structure and low levels of range filling, indicative of slow postglacial expansion. The good disperser C. glabrum shows higher levels of admixture between genetic groups and weaker population differentiation than the poor disperser S. borderei. MAIN CONCLUSIONS Factors other than bedrock preference have a strong impact on the postglacial range dynamics of high-elevation species. Habitat specialization plays an important role, allowing species occupying a broad range of habitats to more rapidly expand their ranges after environmental change. The effect of dispersal ability is lower than expected for the study species.
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Affiliation(s)
- Pau Carnicero
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
| | - Johannes Wessely
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Dietmar Moser
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Xavier Font
- Department of Evolutionary Biology, Ecology and Environmental SciencesUniversity of BarcelonaBarcelonaSpain
| | - Stefan Dullinger
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
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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: 10] [Impact Index Per Article: 5.0] [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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Malanson GP, Pansing ER, Testolin R, Abdulhak S, Bergamini A, Ćušterevska R, Marcenò C, Kuzmanović N, Milanović Đ, Ruprecht E, Šibík J, Vassilev K, Willner W, Jiménez‐Alfaro B. Explanation of beta diversity in European alpine grasslands changes with scale. Ecosphere 2022. [DOI: 10.1002/ecs2.4066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- George P. Malanson
- Department of Geographical & Sustainability Sciences University of Iowa Iowa City Iowa USA
| | - Elizabeth R. Pansing
- Department of Geographical & Sustainability Sciences University of Iowa Iowa City Iowa USA
| | - Riccardo Testolin
- Department of Environmental Biology Sapienza University of Rome Rome Italy
- Department of Biological, Geological and Environmental Sciences Alma Mater Studiorum University of Bologna Bologna Italy
| | | | - Ariel Bergamini
- WSL Swiss Federal Research Institute Birmensdorf Switzerland
| | - Renata Ćušterevska
- Institute of Biology, Faculty of Natural Sciences and Mathematics University of Ss. Cyril and Methodius Skopje North Macedonia
| | - Corrado Marcenò
- Department of Botany and Zoology Masaryk University Brno Czechia
| | - Nevena Kuzmanović
- Faculty of Biology Institute of Botany and Botanical Garden Jevremovac, University of Belgrade Belgrade Serbia
| | - Đorđije Milanović
- Faculty of Forestry University of Banja Luka Banja Luka Bosnia and Herzegovina
| | - Eszter Ruprecht
- Hungarian Department of Biology and Ecology Babeș‐Bolyai University Cluj‐Napoca Romania
| | - Jozef Šibík
- Plant Science and Biodiversity Center Slovak Academy of Sciences, Institute of Botany Bratislava Slovakia
| | - Kiril Vassilev
- Department of Plant and Fungal Diversity and Resources Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Science Sofia Bulgaria
| | - Wolfgang Willner
- Department of Botany and Biodiversity Research University of Vienna Vienna Austria
| | - Borja Jiménez‐Alfaro
- Research Unit of Biodiversity Research (CSIC/UO/PA) University of Oviedo Mieres Spain
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6
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Cytogenetic, Morphometric, and Ecological Characterization of Festuca indigesta Boiss. in the Southeast of Spain. PLANTS 2022; 11:plants11050693. [PMID: 35270163 PMCID: PMC8912771 DOI: 10.3390/plants11050693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/15/2022] [Accepted: 03/01/2022] [Indexed: 11/21/2022]
Abstract
Festuca indigesta subsp. indigesta (Poaceae) is endemic to the southeast of Spain, and until recently, it was considered that its range of distribution was restricted to the siliceous core of Sierra Nevada. However, it has been recently extended in the territory to others calcareous mountains. This study investigates the cytogenetic variability throughout the geographic range of this taxon, the possible edaphic preferences of each cytotype, and the morphological variation of cytotypes. Genome sizes and ploidy levels were estimated using flow cytometry and chromosome count. Soil samples were collected to test the nature of the substrate, i.e., pH, and calcium and magnesium contents. Finally, morphological characters were measured in herbarium specimens. This study provides the first genome size data for the species. Hidden cytogenetic diversity was detected in the taxon, comprising hexaploid (2n = 6x = 42), octoploid (2n = 8x = 56) and dodecaploid (2n = 12x = 84) individuals. No relationship between substrate nature and cytotype was observed. Morphological differences were detected for the size of floral parts and stomata among cytotypes, but these were blurred if the entire morphological variation range was considered. Our results suggest that each mountain range could act as a reservoir of morphologically cryptic genetic diversity regarding this taxon.
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7
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Borokini IT, Klingler KB, Peacock MM. Life in the desert: The impact of geographic and environmental gradients on genetic diversity and population structure of Ivesia webberi. Ecol Evol 2021; 11:17537-17556. [PMID: 34938528 PMCID: PMC8668734 DOI: 10.1002/ece3.8389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/25/2021] [Accepted: 11/05/2021] [Indexed: 11/11/2022] Open
Abstract
For range-restricted species with disjunct populations, it is critical to characterize population genetic structure, gene flow, and factors that influence functional connectivity among populations in order to design effective conservation programs. In this study, we genotyped 314 individuals from 16 extant populations of Ivesia webberi, a United States federally threatened Great Basin Desert using six microsatellite loci. We assessed the effects of Euclidean distance, landscape features, and ecological dissimilarity on the pairwise genetic distance of the sampled populations, while also testing for a potential relationship between I. webberi genetic diversity and diversity in the vegetative communities. The results show low levels of genetic diversity overall (H e = 0.200-0.441; H o = 0.192-0.605) and high genetic differentiation among populations. Genetic diversity was structured along a geographic gradient, congruent with patterns of isolation by distance. Populations near the species' range core have relatively high genetic diversity, supporting in part a central-marginal pattern, while also showing some evidence for a metapopulation dynamic. Peripheral populations have lower genetic diversity, significantly higher genetic distances, and higher relatedness. Genotype cluster admixture results suggest a complex dispersal pattern among populations with dispersal direction and distance varying on the landscape. Pairwise genetic distance strongly correlates with elevation, actual evapotranspiration, and summer seasonal precipitation, indicating a role for isolation by environment, which the observed phenological mismatches among the populations also support. The significant correlation between pairwise genetic distance and floristic dissimilarity in the germinated soil seed bank suggests that annual regeneration in the plant communities contribute to the maintenance of genetic diversity in I. webberi.
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Affiliation(s)
- Israel T. Borokini
- Ecology, Evolution and Conservation Biology Graduate ProgramDepartment of BiologyUniversity of Nevada, RenoRenoNevadaUSA
- University and Jepson HerbariaDepartment of Integrative BiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Kelly B. Klingler
- Department of Environmental ConservationUniversity of MassachusettsAmherstMassachusettsUSA
| | - Mary M. Peacock
- Ecology, Evolution and Conservation Biology Graduate ProgramDepartment of BiologyUniversity of Nevada, RenoRenoNevadaUSA
- Department of BiologyUniversity of Nevada, RenoRenoNevadaUSA
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8
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López-Delgado J, Meirmans PG. History or demography? Determining the drivers of genetic variation in North American plants. Mol Ecol 2021; 31:1951-1962. [PMID: 34662483 PMCID: PMC9543403 DOI: 10.1111/mec.16230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/22/2022]
Abstract
Understanding the impact of historical and demographic processes on genetic variation is essential for devising conservation strategies and predicting responses to climate change. Recolonization after Pleistocene glaciations is expected to leave distinct genetic signatures, characterised by lower genetic diversity in previously glaciated regions. Populations’ positions within species ranges also shape genetic variation, following the central‐marginal paradigm dictating that peripheral populations are depauperate, sparse and isolated. However, the general applicability of these patterns and relative importance of historical and demographic factors remains unknown. Here, we analysed the distribution of genetic variation in 91 native species of North American plants by coupling microsatellite data and species distribution modelling. We tested the contributions of historical climatic shifts and the central‐marginal hypothesis on genetic diversity and structure on the whole data set and across subsets based on taxonomic groups and growth forms. Decreased diversity was found with increased distance from potential glacial refugia, coinciding with the expected make‐up of postglacially colonised localities. At the range periphery, lower genetic diversity, higher inbreeding levels and genetic differentiation were reported, following the assumptions of the central‐marginal hypothesis. History and demography were found to have approximately equal importance in shaping genetic variation.
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Affiliation(s)
- Julia López-Delgado
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.,Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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9
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Wötzel S, Andrello M, Albani MC, Koch MA, Coupland G, Gugerli F. Arabis alpina: A perennial model plant for ecological genomics and life-history evolution. Mol Ecol Resour 2021; 22:468-486. [PMID: 34415668 PMCID: PMC9293087 DOI: 10.1111/1755-0998.13490] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/28/2021] [Accepted: 08/16/2021] [Indexed: 01/03/2023]
Abstract
Many model organisms were chosen and achieved prominence because of an advantageous combination of their life‐history characteristics, genetic properties and also practical considerations. Discoveries made in Arabidopsis thaliana, the most renowned noncrop plant model species, have markedly stimulated studies in other species with different biology. Within the family Brassicaceae, the arctic–alpine Arabis alpina has become a model complementary to Arabidopsis thaliana to study the evolution of life‐history traits, such as perenniality, and ecological genomics in harsh environments. In this review, we provide an overview of the properties that facilitated the rapid emergence of A. alpina as a plant model. We summarize the evolutionary history of A. alpina, including genomic aspects, the diversification of its mating system and demographic properties, and we discuss recent progress in the molecular dissection of developmental traits that are related to its perennial life history and environmental adaptation. From this published knowledge, we derive open questions that might inspire future research in A. alpina, other Brassicaceae species or more distantly related plant families.
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Affiliation(s)
- Stefan Wötzel
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt and Senckenberg Biodiversity and Climate Research Centre, Frankfurt (Main), Germany
| | - Marco Andrello
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment, National Research Council, CNR-IAS, Rome, Italy
| | - Maria C Albani
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Marcus A Koch
- Biodiversity and Plant Systematics, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - George Coupland
- Department of Plant Development Biology, MPI for Plant Breeding Research, Cologne, Germany
| | - Felix Gugerli
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
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10
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Larsson DJ, Pan D, Schneeweiss GM. Addressing alpine plant phylogeography using integrative distributional, demographic and coalescent modeling. ALPINE BOTANY 2021; 132:5-19. [PMID: 35368907 PMCID: PMC8933363 DOI: 10.1007/s00035-021-00263-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 07/05/2021] [Indexed: 06/14/2023]
Abstract
Phylogeographic studies of alpine plants have evolved considerably in the last two decades from ad hoc interpretations of genetic data to statistical model-based approaches. In this review we outline the developments in alpine plant phylogeography focusing on the recent approach of integrative distributional, demographic and coalescent (iDDC) modeling. By integrating distributional data with spatially explicit demographic modeling and subsequent coalescent simulations, the history of alpine species can be inferred and long-standing hypotheses, such as species-specific responses to climate change or survival on nunataks during the last glacial maximum, can be efficiently tested as exemplified by available case studies. We also discuss future prospects and improvements of iDDC.
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Affiliation(s)
- Dennis J. Larsson
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Da Pan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Gerald M. Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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11
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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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12
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Cheikh Albassatneh M, Escudero M, Monnet A, Arroyo J, Bacchetta G, Bagnoli F, Dimopoulos P, Hampe A, Leriche A, Médail F, Nikolic T, Ponger L, Vendramin GG, Fady B. Spatial patterns of genus‐level phylogenetic endemism in the tree flora of Mediterranean Europe. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Marwan Cheikh Albassatneh
- Institut de Systématique, Evolution, Biodiversité (ISYEB) Muséum national d’Histoire naturelle (MNHN), CNRS, Sorbonne Université, EPHE, Université des Antilles Paris France
- Aix Marseille Université, Avignon Université, CNRS, IRD IMBE Aix‐en‐Provence France
- Institute of Ecology and Environmental Sciences Sorbonne University Paris France
| | - Marcial Escudero
- Department of Plant Biology and Ecology University of Seville Seville Spain
| | - Anne‐Christine Monnet
- Institut de Systématique, Evolution, Biodiversité (ISYEB) Muséum national d’Histoire naturelle (MNHN), CNRS, Sorbonne Université, EPHE, Université des Antilles Paris France
- Aix Marseille Université, Avignon Université, CNRS, IRD IMBE Aix‐en‐Provence France
| | - Juan Arroyo
- Department of Plant Biology and Ecology University of Seville Seville Spain
| | - Gianluigi Bacchetta
- Department of Life and Environmental Sciences University of Cagliari Cagliari Italy
| | | | | | - Arndt Hampe
- BIOGECO INRAE, Bordeaux University Cestas France
| | - Agathe Leriche
- Aix Marseille Université, Avignon Université, CNRS, IRD IMBE Aix‐en‐Provence France
| | - Frédéric Médail
- Aix Marseille Université, Avignon Université, CNRS, IRD IMBE Aix‐en‐Provence France
| | - Toni Nikolic
- Department of Botany Faculty of Science University of Zagreb Zagreb Croatia
| | - Loïc Ponger
- Structure et Instabilité des Génomes "Muséum National d'Histoire Naturelle" (MNHN), CNRS Paris France
| | | | - Bruno Fady
- Ecology of Mediterranean Forests (URFM) INRAE Avignon France
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13
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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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14
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Dufresnes C, Rodrigues N, Savary R. Slow and steady wins the race: contrasted phylogeographic signatures in two Alpine amphibians. Integr Zool 2021; 17:181-190. [PMID: 33433936 DOI: 10.1111/1749-4877.12518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A deeper phylogeographic structure is expected for slow-dispersing habitat specialists compared to widespread adaptable species, especially in topographically complex regions. We tested this classic assumption by comparing the genomic (RAD-sequencing) phylogeographies of two amphibians inhabiting the Swiss Alps: the mobile, cosmopolitan common frog (Rana temporaria) against the stationary, mountain endemic Alpine salamander (Salamandra atra). Our results ran opposite of predictions: the frog displayed significantly higher genetic divergences and lower within-population variation compared to the salamander. This implies a prominent role for their distinctive glacial histories in shaping intraspecific diversity and structure: diversification and recolonization from several circum-Alpine micro-refugia for the frog versus a single refugium for the salamander, potentially combined with better population connectivity and stability. These striking differences emphasize the great variability of phylogeographic responses to the Quaternary glaciations, hence the complexity to predict general patterns of genetic diversity at the regional scale, and the forces that underlie them.
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Affiliation(s)
- Christophe Dufresnes
- LASER, College of Biology and Environment, Nanjing Forestry University, Nanjing, China
| | - Nicolas Rodrigues
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - Romain Savary
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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15
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Kurata S, Sakaguchi S, Hirota SK, Kurashima O, Suyama Y, Nishida S, Ito M. Refugia within refugium of Geranium yesoense (Geraniaceae) in Japan were driven by recolonization into the southern interglacial refugium. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Recent studies have found that geographical fragmentation and recurrent colonization result in complex genetic structures in refugial areas. This phenomenon, known as ‘refugia within refugium’, has been identified from many geographical locations. In Japan, the high-elevation mountains of central Honshu provided an interglacial refugium for alpine plants. Here we focused on the Geranium yesoense complex, which exhibits increased morphological variation in the refugial area, to determine whether this variation was shaped by recurrent colonization, range fragmentation or phenotypic changes independent of population history. We analysed single nucleotide polymorphism data and chloroplast genome sequences. Diversification in the G. yesoense species complex occurred in the mid-Pleistocene. The varieties are distinct entities and suggest the presence of a genetic cluster with highly disjunct distributions, occurring both in northern Japan and in southern refugial areas in central Honshu. Demographic analysis suggests that a single ancestral variety (var. nipponicum) evolved in the alpine region of central Honshu, and that subsequent migration from one of the two diverged northern varieties (var. pseudopratense) led to secondary contact with var. nipponicum during the last glacial period. Recolonization into refugial populations in central Honshu and hybridization between diverged populations have resulted in complex genetic structures among refugial populations.
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Affiliation(s)
- Seikan Kurata
- Laboratory of Plant Evolution and Biodiversity, Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, Japan
| | - Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, Aza-yomogida, Naruko Onsen, Osaki City, Miyagi, Japan
| | - Osamu Kurashima
- National Museum of Nature and Science, Ueno-koen, Taito-ku, Tokyo, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, Aza-yomogida, Naruko Onsen, Osaki City, Miyagi, Japan
| | - Sachiko Nishida
- Nagoya University Museum, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Motomi Ito
- Laboratory of Plant Evolution and Biodiversity, Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, Japan
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16
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Nistelberger HM, Tapper S, Coates DJ, McArthur SL, Byrne M. As old as the hills: Pliocene palaeogeographical processes influence patterns of genetic structure in the widespread, common shrub Banksia sessilis. Ecol Evol 2021; 11:1069-1082. [PMID: 33520187 PMCID: PMC7820165 DOI: 10.1002/ece3.7127] [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: 03/13/2020] [Revised: 11/04/2020] [Accepted: 11/25/2020] [Indexed: 11/12/2022] Open
Abstract
The impact of Quaternary glaciation on the development of phylogeographic structure in plant species is well documented. In unglaciated landscapes, phylogeographic patterns tend to reflect processes relating to persistence and stochasticity, yet other factors, associated with the palaeogeographical history of the landscape, including geomorphological events, can also have a significant influence. The unglaciated landscape of south-western Western Australia is an ideal location to observe these ancient drivers of lineage diversification, with tectonic activity associated with the Darling Fault in the late Pliocene attributed to patterns of deep phylogeographic divergence in a widespread tree from this region. Interestingly, other species within this region have not shown this pattern and this palaeogeographical boundary therefore presents an opportunity to examine age and historical distribution of plant species endemic to this region. In this study, we assess patterns of genetic diversity and structure across 28 populations of the widespread shrub Banksia sessilis using three cpDNA markers and nine nuclear microsatellite markers. Sixteen cpDNA haplotypes were identified, comprising two major chloroplast DNA lineages that are estimated to have diverged in the Pliocene, approximately 3.3 million years ago. This timing coincides with major geomorphological processes in the landscape, including the separation of the Darling Plateau from the adjacent Swan Coastal Plain, as well as eustatic changes on the Swan Coastal Plain that are likely to have resulted in the physical isolation of historical plant lineages. Chloroplast lineages were broadly aligned with populations associated with older lateritic soils of the Darling Plateau and Geraldton sandplains or the younger sandy soils associated with the Swan Coastal Plain and Southern Coastline. This structural pattern of lateritic versus non-lateritic division was not observed in the nuclear microsatellite data that identified three genetic clades that roughly corresponded to populations in the North, South, and Central portions of the distributions.
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Affiliation(s)
- Heidi Maria Nistelberger
- Department of Biodiversity, Conservation and AttractionsBiodiversity and Conservation ScienceBentleyWAAustralia
| | - Sarah‐Louise Tapper
- Department of Biodiversity, Conservation and AttractionsBiodiversity and Conservation ScienceBentleyWAAustralia
| | - David J. Coates
- Department of Biodiversity, Conservation and AttractionsBiodiversity and Conservation ScienceBentleyWAAustralia
| | - Shelley L. McArthur
- Department of Biodiversity, Conservation and AttractionsBiodiversity and Conservation ScienceBentleyWAAustralia
| | - Margaret Byrne
- Department of Biodiversity, Conservation and AttractionsBiodiversity and Conservation ScienceBentleyWAAustralia
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17
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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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18
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Comparative studies on population genetic structure of two closely related selfing and outcrossing Zingiber species in Hainan Island. Sci Rep 2019; 9:17997. [PMID: 31784623 PMCID: PMC6884562 DOI: 10.1038/s41598-019-54526-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 11/15/2019] [Indexed: 02/04/2023] Open
Abstract
How mating system impacts the genetic diversity of plants has long fascinated and puzzled evolutionary biologists. Numerous studies have shown that self-fertilising plants have less genetic diversity at both the population and species levels than outcrossers. However, the phylogenetic relationships between species and correlated ecological traits have not been accounted for in these previous studies. Here, we conduct a comparative population genetic study of two closely related selfing and outcrossing Zingiber species, with sympatric distribution in Hainan Island, and obtain a result contrary to previous studies. The results indicate that selfing Z. corallinum can maintain high genetic diversity through differentiation intensified by local adaptation in populations across the species’ range. In contrast, outcrossing Z. nudicarpum preserves high genetic diversity through gene exchange by frequent export of pollen within or among populations. Contrary to expectations, the major portion of genetic variation of outcrossing Z. nudicarpum may exist among populations, depending on the dispersal ability of pollen and seed. Our results also reveal that the main factor affecting population structure of selfing Z. corallinum is mountain ranges, followed by a moist climate, while that of outcrossing Z. nudicarpum is likely moisture, but not mountain ranges, due to gene flow via pollen.
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19
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Sullivan J, Smith ML, Espíndola A, Ruffley M, Rankin A, Tank D, Carstens B. Integrating life history traits into predictive phylogeography. Mol Ecol 2019; 28:2062-2073. [DOI: 10.1111/mec.15029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/04/2019] [Accepted: 01/16/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Jack Sullivan
- Department of Biological Sciences University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - Megan L. Smith
- Department of Ecology, Evolution and Organismal Biology The Ohio State University Columbus Ohio
| | - Anahí Espíndola
- Department of Biological Sciences University of Idaho Moscow Idaho
- Department of Entomology University of Maryland College Park Maryland
| | - Megan Ruffley
- Department of Biological Sciences University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - Andrew Rankin
- Department of Biological Sciences University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - David Tank
- Department of Biological Sciences University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies University of Idaho Moscow Idaho
| | - Bryan Carstens
- Department of Ecology, Evolution and Organismal Biology The Ohio State University Columbus Ohio
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20
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21
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Hanson JO, Fuller RA, Rhodes JR. Conventional methods for enhancing connectivity in conservation planning do not always maintain gene flow. J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13315] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jeffrey O. Hanson
- School of Biological SciencesThe University of Queensland Brisbane Queensland Australia
| | - Richard A. Fuller
- School of Biological SciencesThe University of Queensland Brisbane Queensland Australia
| | - Jonathan R. Rhodes
- School of Earth and Environmental SciencesThe University of Queensland Brisbane Queensland Australia
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22
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Gao N, Guan T, Zhou J, Cai W, Zhang X, Li H, Jiang L, Zheng Y. Vegetation patterns and causal factors in different reaches of an endorheic basin in arid China. ECOSCIENCE 2019. [DOI: 10.1080/11956860.2018.1522147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Nannan Gao
- Key Laboratory of Resource Plants, West China Subalpine Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianyu Guan
- Key Laboratory of Resource Plants, West China Subalpine Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jihua Zhou
- Key Laboratory of Resource Plants, West China Subalpine Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wentao Cai
- Key Laboratory of Resource Plants, West China Subalpine Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolong Zhang
- Key Laboratory of Resource Plants, West China Subalpine Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Heyi Li
- Key Laboratory of Resource Plants, West China Subalpine Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lianhe Jiang
- Key Laboratory of Resource Plants, West China Subalpine Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuanrun Zheng
- Key Laboratory of Resource Plants, West China Subalpine Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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23
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Salmerón-Sánchez E, Fuertes-Aguilar J, Španiel S, Pérez-García FJ, Merlo E, Garrido-Becerra JA, Mota J. Plant evolution in alkaline magnesium-rich soils: A phylogenetic study of the Mediterranean genus Hormathophylla (Cruciferae: Alysseae) based on nuclear and plastid sequences. PLoS One 2018; 13:e0208307. [PMID: 30576314 PMCID: PMC6303028 DOI: 10.1371/journal.pone.0208307] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/15/2018] [Indexed: 11/18/2022] Open
Abstract
Habitats with alkaline edaphic substrates are often associated with plant speciation and diversification. The tribe Alysseae, in the family Brassicaceae, epitomizes this evolutionary trend. In this lineage, some genera, like Hormathophylla, can serve as a good case for testing the evolutionary framework. This genus is centered in the western Mediterranean. It grows on different substrates, but mostly on alkaline soils. It has been suggested that diversification in many lineages of the tribe Alysseae and in the genus Hormathophylla is linked to a tolerance for high levels of Mg+2 in xeric environments. In this study, we investigated the controversial phylogenetic placement of Hormathophylla in the tribe, the generic limits and the evolutionary relationships between the species using ribosomal and plastid DNA sequences. We also examined the putative association between the evolution of different ploidy levels, trichome morphology and the type of substrates. Our analyses demonstrated the monophyly of the genus Hormathophylla including all previously described species. Nuclear sequences revealed two lineages that differ in basic chromosome numbers (x = 7 and x = 8 or derived 11, 15) and in their trichome morphology. Contrasting results with plastid genes indicates more complex relationships between these two lineages involving recent hybridization processes. We also found an association between chloroplast haplotypes and substrate, especially in populations growing on dolomites. Finally, our dated phylogeny demonstrates that the origin of the genus took place in the mid-Miocene, during the establishment of temporal land bridges between the Tethys and Paratethys seas, with a later diversification during the upper Pliocene.
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Affiliation(s)
- Esteban Salmerón-Sánchez
- Departamento de Biología y Geología, CEI.MAR and CECOUAL, Universidad de Almería, Almería, Spain
- Departamento de Botánica, Unidad de Conservación Vegetal, Universidad de Granada, Granada, Spain
| | | | - Stanislav Španiel
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | | | - Encarna Merlo
- Departamento de Biología y Geología, CEI.MAR and CECOUAL, Universidad de Almería, Almería, Spain
| | | | - Juan Mota
- Departamento de Biología y Geología, CEI.MAR and CECOUAL, Universidad de Almería, Almería, Spain
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24
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Ley AC, Nissen J, Wölk A, Röser M. Glacial refugia and speciation in a group of wind-pollinated and -dispersed, endemic Alpine species of Helictotrichon (Poaceae). PLoS One 2018; 13:e0205354. [PMID: 30321199 PMCID: PMC6188759 DOI: 10.1371/journal.pone.0205354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 09/24/2018] [Indexed: 11/30/2022] Open
Abstract
In the Alps phylogeographic studies indicate for small insect-pollinated herbs that climatic fluctuations caused significant population migrations and fragmentations into glacial refugia at the periphery of the Alps. Here we investigate whether this holds also for wind-pollinated and -dispersed species. We therefore analysed the phylogeographic pattern (nuclear and chloroplast dataset) of a clade of the four species of the Helictotrichon parlatorei species group (Poaceae) endemic to the Alps. In contrast to earlier findings for small insect-pollinated herbs no clear barriers to gene flow could be detected in this species group. Instead a few haplotypes are widespread across the entire Alpine region. While the complete absence of a phylogeographic structure in the plastid dataset hints towards very efficient long distance seed dispersal, the moderate phylogeographic structure in the nuclear dataset indicates at least some spatial restriction to pollen dispersal. Rare haplotypes cluster solely in the Western and Southern central Alps and thereby suggest this to be the area of origin for the H. parlatorei species group from where expansion occurred following the presence of calcareous bedrock into the Eastern Alps. We thus conclude that the inclusion of taxa with complementary life-history traits is vital in understanding the glacial history of the Alpine flora.
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Affiliation(s)
- Alexandra C. Ley
- Institute of Geobotany and Botanical Garden, University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail: (ACL); (MR)
| | - Jana Nissen
- Institute of Geobotany and Botanical Garden, University Halle-Wittenberg, Halle (Saale), Germany
| | - Alexandra Wölk
- Institute of Geobotany and Botanical Garden, University Halle-Wittenberg, Halle (Saale), Germany
| | - Martin Röser
- Institute of Geobotany and Botanical Garden, University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail: (ACL); (MR)
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25
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Urbaniak J, Kwiatkowski P, Pawlikowski P. Phylogeography of Swertia perennis in Europe based on cpDNA markers. PeerJ 2018; 6:e5512. [PMID: 30245925 PMCID: PMC6147141 DOI: 10.7717/peerj.5512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/03/2018] [Indexed: 11/20/2022] Open
Abstract
Background Swertia perennis(Gentianaceae) is a perennial diploid and clonal plant species that is discontinuously distributed in peat bogs in the mountains of Europe, Asia and North America as well as in the lowlands of Europe. The current geographical dispersion of S. perennis is probably the result of quaternary climatic changes that have played an important role in determining the distribution of Swertia and other plant and animal species. Methods In this study we used molecular techniques and combined data from chloroplast DNA markers (trnLF region and trnH-psbA spacer) to elucidate the phylogeography of S. perennis in Europe. Plants were collected from 28 populations in different locations in the lowlands and mountainous areas of Europe (e.g., the Carpathians, Sudetes, Bohemian Forest and Alps). cDNA was analysed to detect the genetic relationship between specimens from different locations. Results A total of 20 haplotypes were identified across the dataset. They were characterised by a high level of genetic variability but showed a lack of phylogeographical structure. This pattern may be the result of repeated recolonization and expansion from several areas. Such genetic differentiation may also be attributed to the relatively long-term isolation of S. perennis in Pleistocene refugia in Europe, which resulted in independent separation of different cpDNA phylogenetic lineages and variation in the nucleotide composition of cpDNA. Discussion The lack of strong phylogeographical structure makes it impossible to indicate the centre of haplotype diversity; however, refugia located in the Carpathians, Sudetes or Alps are the most probable sites where S. perennis existed in Europe. This lack of structure may also indicate a high level of gene flow in times when the landscape and fen systems were not fragmented in numerous geographically-isolated populations. This makes it difficult to speculate about the relationships between Asiatic and European plant populations and the origin and distribution of this species in Europe. Today, it seems to be restricted due to the occurrence of plants which clearly reflects the genetic variability from the ancient period.
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Affiliation(s)
- Jacek Urbaniak
- Department of Botany and Plant Ecology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Paweł Kwiatkowski
- Department of Botany and Nature Protection, University of Silesia in Katowice, Katowice, Poland
| | - Paweł Pawlikowski
- Department of Plant Ecology and Environmental Conservation, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
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26
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Blanco-Pastor JL, Fernández-Mazuecos M, Coello AJ, Pastor J, Vargas P. Topography explains the distribution of genetic diversity in one of the most fragile European hotspots. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12836] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- José Luis Blanco-Pastor
- Real Jardín Botánico de Madrid (RJB-CSIC); Madrid Spain
- INRA; Centre Nouvelle-Aquitaine-Poitiers, UR4 (URP3F); Lusignan France
| | | | - Alberto J. Coello
- Real Jardín Botánico de Madrid (RJB-CSIC); Madrid Spain
- Universidad Rey Juan Carlos; Madrid Spain
| | - Julia Pastor
- Real Jardín Botánico de Madrid (RJB-CSIC); Madrid Spain
| | - Pablo Vargas
- Real Jardín Botánico de Madrid (RJB-CSIC); Madrid Spain
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27
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Folk RA, Visger CJ, Soltis PS, Soltis DE, Guralnick RP. Geographic Range Dynamics Drove Ancient Hybridization in a Lineage of Angiosperms. Am Nat 2018; 192:171-187. [DOI: 10.1086/698120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Subsampling reveals that unbalanced sampling affects STRUCTURE results in a multi-species dataset. Heredity (Edinb) 2018; 122:276-287. [PMID: 30026534 DOI: 10.1038/s41437-018-0124-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 11/08/2022] Open
Abstract
Studying the genetic population structure of species can reveal important insights into several key evolutionary, historical, demographic, and anthropogenic processes. One of the most important statistical tools for inferring genetic clusters is the program STRUCTURE. Recently, several papers have pointed out that STRUCTURE may show a bias when the sampling design is unbalanced, resulting in spurious joining of underrepresented populations and spurious separation of overrepresented populations. Suggestions to overcome this bias include subsampling and changing the ancestry model, but the performance of these two methods has not yet been tested on actual data. Here, I use a data set of 12 high-alpine plant species to test whether unbalanced sampling affects the STRUCTURE inference of population differentiation between the European Alps and the Carpathians. For four of the 12 species, subsampling of the Alpine populations-to match the sample size between the Alps and the Carpathians-resulted in a drastically different clustering than the full data set. On the other hand, STRUCTURE results with the alternative ancestry model were indistinguishable from the results with the default model. Based on these results, the subsampling strategy seems a more viable approach to overcome the bias than the alternative ancestry model. However, subsampling is only possible when there is an a priori expectation of what constitute the main clusters. Though these results do not mean that the use of STRUCTURE should be discarded, it does indicate that users of the software should be cautious about the interpretation of the results when sampling is unbalanced.
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Gentili R, Abeli T, Parolo G, Ciappetta S, Montagnani C, Müller JV, Rossi G, Citterio S. Genetic structure of Leucojum aestivum L. in the Po Valley (N-Italy) drives conservation management actions. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1057-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Mosca E, Di Pierro EA, Budde KB, Neale DB, González-Martínez SC. Environmental effects on fine-scale spatial genetic structure in four Alpine keystone forest tree species. Mol Ecol 2018; 27:647-658. [PMID: 29274175 DOI: 10.1111/mec.14469] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 11/15/2017] [Accepted: 11/22/2017] [Indexed: 12/22/2022]
Abstract
Genetic responses to environmental changes take place at different spatial scales. While the effect of environment on the distribution of species' genetic diversity at large geographical scales has been the focus of several recent studies, its potential effects on genetic structure at local scales are understudied. Environmental effects on fine-scale spatial genetic structure (FSGS) were investigated in four Alpine conifer species (five to eight populations per species) from the eastern Italian Alps. Significant FSGS was found for 11 of 25 populations. Interestingly, we found no significant differences in FSGS across species but great variation among populations within species, highlighting the importance of local environmental factors. Interannual variability in spring temperature had a small but significant effect on FSGS of Larix decidua, probably related to species-specific life history traits. For Abies alba, Picea abies and Pinus cembra, linear models identified spring precipitation as a potentially relevant climate factor associated with differences in FSGS across populations; however, models had low explanatory power and were strongly influenced by a P. cembra outlier population from a very dry site. Overall, the direction of the identified effects is according to expectations, with drier and more variable environments increasing FSGS. Underlying mechanisms may include climate-related changes in the variance of reproductive success and/or environmental selection of specific families. This study provides new insights on potential changes in local genetic structure of four Alpine conifers in the face of environmental changes, suggesting that new climates, through altering FSGS, may also have relevant impacts on plant microevolution.
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Affiliation(s)
- Elena Mosca
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige, Italy.,Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy
| | - Erica A Di Pierro
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige, Italy
| | | | - David B Neale
- Department of Plant Sciences, University of California at Davis, Davis, CA, USA
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31
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Environmental and geographic variables are effective surrogates for genetic variation in conservation planning. Proc Natl Acad Sci U S A 2017; 114:12755-12760. [PMID: 29087942 DOI: 10.1073/pnas.1711009114] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Protected areas buffer species from anthropogenic threats and provide places for the processes that generate and maintain biodiversity to continue. However, genetic variation, the raw material for evolution, is difficult to capture in conservation planning, not least because genetic data require considerable resources to obtain and analyze. Here we show that freely available environmental and geographic distance variables can be highly effective surrogates in conservation planning for representing adaptive and neutral intraspecific genetic variation. We obtained occurrence and genetic data from the IntraBioDiv project for 27 plant species collected over the European Alps using a gridded sampling scheme. For each species, we identified loci that were potentially under selection using outlier loci methods, and mapped their main gradients of adaptive and neutral genetic variation across the grid cells. We then used the cells as planning units to prioritize protected area acquisitions. First, we verified that the spatial patterns of environmental and geographic variation were correlated, respectively, with adaptive and neutral genetic variation. Second, we showed that these surrogates can predict the proportion of genetic variation secured in randomly generated solutions. Finally, we discovered that solutions based only on surrogate information secured substantial amounts of adaptive and neutral genetic variation. Our work paves the way for widespread integration of surrogates for genetic variation into conservation planning.
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32
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Genetic differentiation and diversity of two sympatric subspecies of Castilleja affinis; a comparison between the endangered serpentine endemic (spp. neglecta) and its widespread congener (ssp. affinis). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1009-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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33
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Hanson JO, Rhodes JR, Possingham HP, Fuller RA. raptr: Representative and adequate prioritization toolkit in R. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12862] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jeffrey O. Hanson
- School of Biological Sciences University of Queensland Brisbane Qld. Australia
| | - Jonathan R. Rhodes
- School of Earth and Environmental Sciences University of Queensland Brisbane Qld. Australia
| | - Hugh P. Possingham
- School of Biological Sciences University of Queensland Brisbane Qld. Australia
- The Nature Conservancy South Brisbane Qld. Australia
| | - Richard A. Fuller
- School of Biological Sciences University of Queensland Brisbane Qld. Australia
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Dillenberger MS, Kadereit JW. Simultaneous speciation in the European high mountain flowering plant genus Facchinia (Minuartia s.l., Caryophyllaceae) revealed by genotyping-by-sequencing. Mol Phylogenet Evol 2017; 112:23-35. [PMID: 28433621 DOI: 10.1016/j.ympev.2017.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/12/2017] [Accepted: 04/17/2017] [Indexed: 11/18/2022]
Abstract
Understanding the relative importance of different mechanisms of speciation in a given lineage requires fully resolved interspecific relationships. Using Facchinia, a genus of seven species centred in the European Alps, we explore whether the polytomy found by Sanger sequencing analyses of standard nuclear (ITS) and plastid markers (trnQ-rps16) is a hard or soft polytomy by substantially increasing the amount of DNA sequence data, generated by genotyping-by-sequencing. In comparison to 142 phylogenetically informative sites in the Sanger sequences the GBS sequences yielded 3363 phylogenetically informative sites after exclusion of apparently oversaturated SNPs. Maximum parsimony, maximum likelihood, NeighborNet, SVDquartets and Astral-II analyses all resulted in phylogenetic trees (and networks) in which interspecific relationships were largely unresolved. After excluding incomplete lineage sorting, hybridisation and oversaturation of characters as possible causes for lack of phylogenetic resolution, we conclude that the polytomy obtained most likely represents a hard polytomy. We hypothesize that diversification of Facchinia is best interpreted as the result of multiple simultaneous vicariance in response to climatic changes during the Early Quaternary.
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Affiliation(s)
- Markus S Dillenberger
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
| | - Joachim W Kadereit
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
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35
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Selkoe KA, Gaggiotti OE, Treml EA, Wren JLK, Donovan MK, Toonen RJ. The DNA of coral reef biodiversity: predicting and protecting genetic diversity of reef assemblages. Proc Biol Sci 2017; 283:rspb.2016.0354. [PMID: 27122569 PMCID: PMC4855387 DOI: 10.1098/rspb.2016.0354] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/06/2016] [Indexed: 12/02/2022] Open
Abstract
Conservation of ecological communities requires deepening our understanding of genetic diversity patterns and drivers at community-wide scales. Here, we use seascape genetic analysis of a diversity metric, allelic richness (AR), for 47 reef species sampled across 13 Hawaiian Islands to empirically demonstrate that large reefs high in coral cover harbour the greatest genetic diversity on average. We found that a species's life history (e.g. depth range and herbivory) mediates response of genetic diversity to seascape drivers in logical ways. Furthermore, a metric of combined multi-species AR showed strong coupling to species richness and habitat area, quality and stability that few species showed individually. We hypothesize that macro-ecological forces and species interactions, by mediating species turnover and occupancy (and thus a site's mean effective population size), influence the aggregate genetic diversity of a site, potentially allowing it to behave as an apparent emergent trait that is shaped by the dominant seascape drivers. The results highlight inherent feedbacks between ecology and genetics, raise concern that genetic resilience of entire reef communities is compromised by factors that reduce coral cover or available habitat, including thermal stress, and provide a foundation for new strategies for monitoring and preserving biodiversity of entire reef ecosystems.
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Affiliation(s)
- Kimberly A Selkoe
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, HI 97644, USA National Center for Ecological Analysis and Synthesis, 735 State Street, Santa Barbara, CA 93101, USA
| | - Oscar E Gaggiotti
- School of Biology, Scottish Oceans Institute, University of St Andrews, St Andrews, Fife KY16 8LB, UK
| | - Eric A Treml
- School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Johanna L K Wren
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Mary K Donovan
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | | | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, HI 97644, USA
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36
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Kolář F, Dušková E, Sklenář P. Niche shifts and range expansions along cordilleras drove diversification in a high-elevation endemic plant genus in the tropical Andes. Mol Ecol 2016; 25:4593-610. [PMID: 27482945 DOI: 10.1111/mec.13788] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 07/18/2016] [Accepted: 07/22/2016] [Indexed: 12/25/2022]
Abstract
The tropical Andes represent one of the world's biodiversity hot spots, but the evolutionary drivers generating their striking species diversity still remain poorly understood. In the treeless high-elevation Andean environments, Pleistocene glacial oscillations and niche differentiation are frequently hypothesized diversification mechanisms; however, sufficiently densely sampled population genetic data supporting this are still lacking. Here, we reconstruct the evolutionary history of Loricaria (Asteraceae), a plant genus endemic to the Andean treeless alpine zone, based on comprehensive population-level sampling of 289 individuals from 67 populations across the entire distribution ranges of its northern Andean species. Partly incongruent AFLP and plastid DNA markers reveal that the distinct genetic structure was shaped by a complex interplay of biogeography (spread along and across the cordilleras), history (Pleistocene glacial oscillations) and local ecological conditions. While plastid variation documents an early split or colonization of the northern Andes by at least two lineages, one of which further diversified, a major split in the AFLP data correlate with altitudinal ecological differentiation. This suggests that niche shifts may be important drivers of Andean diversification not only in forest-alpine transitions, but also within the treeless alpine zone itself. The patterns of genetic differentiation at the intraspecific level reject the hypothesized separation in spatially isolated cordilleras and instead suggest extensive gene flow among populations from distinct mountain chains. Our study highlights that leveraging highly variable markers against extensive population-level sampling is a promising approach to address mechanisms of rapid species diversifications.
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Affiliation(s)
- Filip Kolář
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, Oslo, NO-0318, Norway. .,Department of Botany, Faculty of Science, Charles University in Prague, Prague, CZ-128 01, Czech Republic. .,Institute of Botany, The Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic.
| | - Eva Dušková
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, CZ-128 01, Czech Republic
| | - Petr Sklenář
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, CZ-128 01, Czech Republic
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37
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Kolář F, Fuxová G, Záveská E, Nagano AJ, Hyklová L, Lučanová M, Kudoh H, Marhold K. Northern glacial refugia and altitudinal niche divergence shape genome-wide differentiation in the emerging plant modelArabidopsis arenosa. Mol Ecol 2016; 25:3929-49. [DOI: 10.1111/mec.13721] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 05/25/2016] [Accepted: 06/01/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Filip Kolář
- Natural History Museum; University of Oslo; PO Box 1172 Blindern Oslo NO-0318 Norway
- Department of Botany; Faculty of Science; Charles University in Prague; Prague CZ-128 01 Czech Republic
- Institute of Botany; The Czech Academy of Sciences; Průhonice CZ-252 43 Czech Republic
| | - Gabriela Fuxová
- Department of Botany; Faculty of Science; Charles University in Prague; Prague CZ-128 01 Czech Republic
| | - Eliška Záveská
- Institute of Botany; University of Innsbruck; Innsbruck AT-6020 Austria
| | - Atsushi J. Nagano
- Center for Ecological Research; Kyoto University; Kyoto JP-520-2113 Japan
- Faculty of Agriculture; Ryukoku University; Shiga JP-612-8577 Japan
- JST PRESTO; Saitama JP-332-0012 Japan
| | - Lucie Hyklová
- Department of Botany; Faculty of Science; Charles University in Prague; Prague CZ-128 01 Czech Republic
| | - Magdalena Lučanová
- Department of Botany; Faculty of Science; Charles University in Prague; Prague CZ-128 01 Czech Republic
- Institute of Botany; The Czech Academy of Sciences; Průhonice CZ-252 43 Czech Republic
| | - Hiroshi Kudoh
- Center for Ecological Research; Kyoto University; Kyoto JP-520-2113 Japan
| | - Karol Marhold
- Department of Botany; Faculty of Science; Charles University in Prague; Prague CZ-128 01 Czech Republic
- Institute of Botany; Slovak Academy of Sciences; Bratislava SK-845 23 Slovak Republic
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38
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Papadopoulou A, Knowles LL. Toward a paradigm shift in comparative phylogeography driven by trait-based hypotheses. Proc Natl Acad Sci U S A 2016; 113:8018-24. [PMID: 27432974 PMCID: PMC4961141 DOI: 10.1073/pnas.1601069113] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
For three decades, comparative phylogeography has conceptually and methodologically relied on the concordance criterion for providing insights into the historical/biogeographic processes driving population genetic structure and divergence. Here we discuss how this emphasis, and the corresponding lack of methods for extracting information about biotic/intrinsic contributions to patterns of genetic variation, may bias our general understanding of the factors driving genetic structure. Specifically, this emphasis has promoted a tendency to attribute discordant phylogeographic patterns to the idiosyncracies of history, as well as an adherence to generic null expectations of concordance with reduced predictive power. We advocate that it is time for a paradigm shift in comparative phylogeography, especially given the limited utility of the concordance criterion as genomic data provide ever-increasing levels of resolution. Instead of adhering to the concordance-discordance dichotomy, comparative phylogeography needs to emphasize the contribution of taxon-specific traits that will determine whether concordance is a meaningful criterion for evaluating hypotheses or may predict discordant phylogeographic structure. Through reference to some case studies we illustrate how refined hypotheses based on taxon-specific traits can provide improved predictive frameworks to forecast species responses to climatic change or biogeographic barriers while gaining unique insights about the taxa themselves and their interactions with their environment. We outline a potential avenue toward a synthetic comparative phylogeographic paradigm that includes addressing some important conceptual and methodological challenges related to study design and application of model-based approaches for evaluating support of trait-based hypotheses under the proposed paradigm.
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Affiliation(s)
- Anna Papadopoulou
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109; Department of Integrative Ecology, Estación Biológica de Doñana, Consejo Superior de Investigaciones Cientificas, 41092 Seville, Spain
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109;
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39
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Günther T, Lampei C, Barilar I, Schmid KJ. Genomic and phenotypic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian Alps. Mol Ecol 2016; 25:3574-92. [PMID: 27220345 DOI: 10.1111/mec.13705] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 04/19/2016] [Accepted: 05/02/2016] [Indexed: 12/25/2022]
Abstract
Altitudinal gradients in mountain regions are short-range clines of different environmental parameters such as temperature or radiation. We investigated genomic and phenotypic signatures of adaptation to such gradients in five Arabidopsis thaliana populations from the North Italian Alps that originated from 580 to 2350 m altitude by resequencing pools of 19-29 individuals from each population. The sample includes two pairs of low- and high-altitude populations from two different valleys. High-altitude populations showed a lower nucleotide diversity and negative Tajima's D values and were more closely related to each other than to low-altitude populations from the same valley. Despite their close geographic proximity, demographic analysis revealed that low- and high-altitude populations split between 260 000 and 15 000 years before present. Single nucleotide polymorphisms whose allele frequencies were highly differentiated between low- and high-altitude populations identified genomic regions of up to 50 kb length where patterns of genetic diversity are consistent with signatures of local selective sweeps. These regions harbour multiple genes involved in stress response. Variation among populations in two putative adaptive phenotypic traits, frost tolerance and response to light/UV stress was not correlated with altitude. Taken together, the spatial distribution of genetic diversity reflects a potentially adaptive differentiation between low- and high-altitude populations, whereas the phenotypic differentiation in the two traits investigated does not. It may resemble an interaction between adaptation to the local microhabitat and demographic history influenced by historical glaciation cycles, recent seed dispersal and genetic drift in local populations.
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Affiliation(s)
- Torsten Günther
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany.,Department of Evolutionary Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Christian Lampei
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Ivan Barilar
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Karl J Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
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40
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Van Nuland ME, Wooliver RC, Pfennigwerth AA, Read QD, Ware IM, Mueller L, Fordyce JA, Schweitzer JA, Bailey JK. Plant–soil feedbacks: connecting ecosystem ecology and evolution. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12690] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael E. Van Nuland
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
| | - Rachel C. Wooliver
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
| | - Alix A. Pfennigwerth
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
| | - Quentin D. Read
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
| | - Ian M. Ware
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
| | - Liam Mueller
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
| | - James A. Fordyce
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
| | - Jennifer A. Schweitzer
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
| | - Joseph K. Bailey
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
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41
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Wasowicz P, Pauwels M, Pasierbinski A, Przedpelska-Wasowicz EM, Babst-Kostecka AA, Saumitou-Laprade P, Rostanski A. Phylogeography of Arabidopsis halleri (Brassicaceae) in mountain regions of Central Europe inferred from cpDNA variation and ecological niche modelling. PeerJ 2016; 4:e1645. [PMID: 26835186 PMCID: PMC4734066 DOI: 10.7717/peerj.1645] [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: 07/22/2015] [Accepted: 01/11/2016] [Indexed: 11/20/2022] Open
Abstract
The present study aimed to investigate phylogeographical patterns present within A. halleri in Central Europe. 1,281 accessions sampled from 52 populations within the investigated area were used in the study of genetic variation based on chloroplast DNA. Over 500 high-quality species occurrence records were used in ecological niche modelling experiments. We evidenced the presence of a clear phylogeographic structure within A. halleri in Central Europe. Our results showed that two genetically different groups of populations are present in western and eastern part of the Carpathians. The hypothesis of the existence of a glacial refugium in the Western Carpathians adn the Bohemian Forest cannot be rejected from our data. It seems, however, that the evidence collected during the present study is not conclusive. The area of Sudetes was colonised after LGM probably by migrants from the Bohemian Forest.
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Affiliation(s)
- Pawel Wasowicz
- Icelandic Institute of Natural History, Iceland
- Faculty of Biology and Environmental Protection, Department of Botany and Nature Protection, University of Silesia, Katowice, Poland
| | - Maxime Pauwels
- Unité Evo-Eco-Paléo (EEP)—UMR 8198, Université de Lille—Sciences et Technologies, CNRS, Villeneuve d’Ascq, France
| | - Andrzej Pasierbinski
- Faculty of Biology and Environmental Protection, Department of Botany and Nature Protection, University of Silesia, Katowice, Poland
| | | | | | - Pierre Saumitou-Laprade
- Unité Evo-Eco-Paléo (EEP)—UMR 8198, Université des Sciences et Technologies de Lille (Lille I), Villeneuve d’Ascq, France
| | - Adam Rostanski
- Faculty of Biology and Environmental Protection, Department of Botany and Nature Protection, University of Silesia, Katowice, Poland
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42
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Tedder A, Carleial S, Gołębiewska M, Kappel C, Shimizu KK, Stift M. Evolution of the Selfing Syndrome in Arabis alpina (Brassicaceae). PLoS One 2015; 10:e0126618. [PMID: 26039362 PMCID: PMC4454584 DOI: 10.1371/journal.pone.0126618] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 04/04/2015] [Indexed: 12/03/2022] Open
Abstract
Introduction The transition from cross-fertilisation (outcrossing) to self-fertilisation (selfing) frequently coincides with changes towards a floral morphology that optimises self-pollination, the selfing syndrome. Population genetic studies have reported the existence of both outcrossing and selfing populations in Arabis alpina (Brassicaceae), which is an emerging model species for studying the molecular basis of perenniality and local adaptation. It is unknown whether its selfing populations have evolved a selfing syndrome. Methods Using macro-photography, microscopy and automated cell counting, we compared floral syndromes (size, herkogamy, pollen and ovule numbers) between three outcrossing populations from the Apuan Alps and three selfing populations from the Western and Central Alps (Maritime Alps and Dolomites). In addition, we genotyped the plants for 12 microsatellite loci to confirm previous measures of diversity and inbreeding coefficients based on allozymes, and performed Bayesian clustering. Results and Discussion Plants from the three selfing populations had markedly smaller flowers, less herkogamy and lower pollen production than plants from the three outcrossing populations, whereas pistil length and ovule number have remained constant. Compared to allozymes, microsatellite variation was higher, but revealed similar patterns of low diversity and high Fis in selfing populations. Bayesian clustering revealed two clusters. The first cluster contained the three outcrossing populations from the Apuan Alps, the second contained the three selfing populations from the Maritime Alps and Dolomites. Conclusion We conclude that in comparison to three outcrossing populations, three populations with high selfing rates are characterised by a flower morphology that is closer to the selfing syndrome. The presence of outcrossing and selfing floral syndromes within a single species will facilitate unravelling the genetic basis of the selfing syndrome, and addressing which selective forces drive its evolution.
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Affiliation(s)
- Andrew Tedder
- Institute of Evolutionary Biology and Environmental studies, University of Zurich, Zurich, Switzerland
| | - Samuel Carleial
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martyna Gołębiewska
- Institute of Evolutionary Biology and Environmental studies, University of Zurich, Zurich, Switzerland
| | - Christian Kappel
- Institut für Biochemie und Biologie, Universität Potsdam, Potsdam-Golm, Germany
| | - Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental studies, University of Zurich, Zurich, Switzerland
- * E-mail: (KKS); (MS)
| | - Marc Stift
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
- * E-mail: (KKS); (MS)
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43
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Rodríguez A, Börner M, Pabijan M, Gehara M, Haddad CFB, Vences M. Genetic divergence in tropical anurans: deeper phylogeographic structure in forest specialists and in topographically complex regions. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9774-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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44
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Kolář F, Píšová S, Záveská E, Fér T, Weiser M, Ehrendorfer F, Suda J. The origin of unique diversity in deglaciated areas: traces of Pleistocene processes in north-European endemics from theGalium pusillumpolyploid complex (Rubiaceae). Mol Ecol 2015; 24:1311-34. [DOI: 10.1111/mec.13110] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Filip Kolář
- National Centre for Biosystematics, Natural History Museum; University of Oslo; Oslo NO-0318 Norway
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 Prague CZ-128 01 Czech Republic
- Institute of Botany; The Czech Academy of Sciences; Průhonice 1 CZ-252 43 Czech Republic
| | - Soňa Píšová
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 Prague CZ-128 01 Czech Republic
- Institute of Botany; The Czech Academy of Sciences; Průhonice 1 CZ-252 43 Czech Republic
| | - Eliška Záveská
- Institute of Botany; University of Innsbruck; Sternwartestraße 15 Innsbruck A-6020 Austria
| | - Tomáš Fér
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 Prague CZ-128 01 Czech Republic
| | - Martin Weiser
- 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; The Czech Academy of Sciences; Průhonice 1 CZ-252 43 Czech Republic
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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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Kolář F, Lučanová M, Záveská E, Fuxová G, Mandáková T, Španiel S, Senko D, Svitok M, Kolník M, Gudžinskas Z, Marhold K. Ecological segregation does not drive the intricate parapatric distribution of diploid and tetraploid cytotypes of theArabidopsis arenosagroup (Brassicaceae). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12479] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Filip Kolář
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 CZ-128 01 Prague Czech Republic
- Institute of Botany; Academy of Sciences of the Czech Republic; Zámek 1 CZ-252 43 Průhonice Czech Republic
| | - Magdalena Lučanová
- Institute of Botany; Academy of Sciences of the Czech Republic; Zámek 1 CZ-252 43 Průhonice Czech Republic
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 CZ-128 01 Prague Czech Republic
| | - Eliška Záveská
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 CZ-128 01 Prague Czech Republic
| | - Gabriela Fuxová
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 CZ-128 01 Prague Czech Republic
| | - Terezie Mandáková
- Plant Cytogenomics Research Group; Central European Institute of Technology (CEITEC); Masaryk University; Kamenice 5 CZ-62500 Brno Czech Republic
| | - Stanislav Španiel
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 CZ-128 01 Prague Czech Republic
| | - Dušan Senko
- Institute of Botany; Slovak Academy of Sciences; Dúbravská cesta 9 SK-845 23 Bratislava Slovak Republic
| | - Marek Svitok
- Department of Biology and General Ecology; Faculty of Ecology and Environmental Sciences; Technical University in Zvolen; T. G. Masaryka 24 SK-960 53 Zvolen Slovak Republic
- Eawag Swiss Federal Institute of Aquatic Science and Technology; Department of Aquatic Ecology, Centre of Ecology; Evolution and Biogeochemistry; Seestrasse 79 CH-6047 Kastanienbaum Switzerland
| | - Martin Kolník
- Tematínska 4 SK-91501 Nové Mesto nad Váhom Slovak Republic
| | - Zigmantas Gudžinskas
- Nature Research Centre; Institute of Botany; Laboratory of Flora and Geobotany; Žaliųjų Ežerų Str. 49 LT-08406 Vilnius Lithuania
| | - Karol Marhold
- Department of Botany; Faculty of Science; Charles University in Prague; Benátská 2 CZ-128 01 Prague Czech Republic
- Institute of Botany; Slovak Academy of Sciences; Dúbravská cesta 9 SK-845 23 Bratislava Slovak Republic
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Espíndola A, Carstens BC, Alvarez N. Comparative phylogeography of mutualists and the effect of the host on the genetic structure of its partners. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12393] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Anahí Espíndola
- Department of Ecology and Evolution; University of Lausanne; Biophore Building 1015 Lausanne Switzerland
- Department of Biological Sciences; University of Idaho; Life Sciences South 252, 875 Perimeter Drive Moscow ID 83844-3051 USA
| | - Bryan C. Carstens
- Department of Evolution; Ecology and Organismal Biology; 300 Aronoff Laboratory; The Ohio State University; 318 West 12th Avenue Columbus OH 43210 USA
| | - Nadir Alvarez
- Department of Ecology and Evolution; University of Lausanne; Biophore Building 1015 Lausanne Switzerland
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Buehler D, Holderegger R, Brodbeck S, Schnyder E, Gugerli F. Validation of outlier loci through replication in independent data sets: a test on Arabis alpina. Ecol Evol 2014; 4:4296-306. [PMID: 25540691 PMCID: PMC4267868 DOI: 10.1002/ece3.1300] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 09/11/2014] [Accepted: 10/01/2014] [Indexed: 12/25/2022] Open
Abstract
Outlier detection and environmental association analysis are common methods to search for loci or genomic regions exhibiting signals of adaptation to environmental factors. However, a validation of outlier loci and corresponding allele distribution models through functional molecular biology or transplant/common garden experiments is rarely carried out. Here, we employ another method for validation, namely testing outlier loci in specifically designed, independent data sets. Previously, an outlier locus associated with three different habitat types had been detected in Arabis alpina. For the independent validation data set, we sampled 30 populations occurring in these three habitat types across five biogeographic regions of the Swiss Alps. The allele distribution model found in the original study could not be validated in the independent test data set: The outlier locus was no longer indicative of habitat-mediated selection. We propose several potential causes of this failure of validation, of which unaccounted genetic structure and technical issues in the original data set used to detect the outlier locus were most probable. Thus, our study shows that validating outlier loci and allele distribution models in independent data sets is a helpful tool in ecological genomics which, in the case of positive validation, adds confidence to outlier loci and their association with environmental factors or, in the case of failure of validation, helps to explain inconsistencies.
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Affiliation(s)
- Dominique Buehler
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland ; Department of Environmental Systems Science, ETH Zürich Universitätsstrasse 16, CH-8092, Zürich, Switzerland
| | - Rolf Holderegger
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland ; Department of Environmental Systems Science, ETH Zürich Universitätsstrasse 16, CH-8092, Zürich, Switzerland
| | - Sabine Brodbeck
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Elvira Schnyder
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
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Lega M, Fior S, Li M, Leonardi S, Varotto C. Genetic Drift Linked to Heterogeneous Landscape and Ecological Specialization Drives Diversification in the Alpine Endemic Columbine Aquilegia thalictrifolia. J Hered 2014; 105:542-554. [PMID: 24864044 DOI: 10.1093/jhered/esu028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 02/10/2014] [Indexed: 11/13/2022] Open
Abstract
The European Alpine system is an extensive mountain range, whose heterogeneous landscape together with Quaternary climatic oscillations significantly affected organismal diversity and distribution in Europe. The model genus Aquilegia represents a textbook example of a rapid and recent radiation through the Northern hemisphere, with the majority of the European taxa occuring in the Alpine system. However, the processes governing genetic differentiation of the genus in this complex geographic area are still widely unexplored. In this work, we used 9 microsatellite loci to study the genetic structure and diversity of 11 populations of Aquilegia thalictrifolia Schott & Kotschy, an alpine taxon characterized by a marked ecological specificity. We found that, despite the endemic and fragmented distribution, A. thalictrifolia has overall high levels of heterozygosity, which is consistent to the substantial inbreeding depression that characterizes the genus. Strong spatial genetic structuring of populations suggests a historical prevalence of genetic drift over gene flow, with natural barriers and ecological niche hindering migration. An analytical comparison of fixation and population differentiation indexes allowed us to infer hypotheses of the postglacial history and more recent demographic events that have influenced the genetics of the species. Overall, our results indicate allopatry as a major force of differentiation in the European scenario, likely to underlie the development of taxonomic boundaries in a broader geographic context. This adds to previous notions on the primary evolutionary forces shaping the Aquilegia radiation in Europe.
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Affiliation(s)
- Margherita Lega
- From the Department of Biodiversity and Molecular Ecology, Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy (Lega, Fior, Li, and Varotto); the Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland (Fior), and the Dipartimento di Bioscienze, Università di Parma, Parma, Italy (Leonardi)
| | - Simone Fior
- From the Department of Biodiversity and Molecular Ecology, Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy (Lega, Fior, Li, and Varotto); the Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland (Fior), and the Dipartimento di Bioscienze, Università di Parma, Parma, Italy (Leonardi)
| | - Mingai Li
- From the Department of Biodiversity and Molecular Ecology, Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy (Lega, Fior, Li, and Varotto); the Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland (Fior), and the Dipartimento di Bioscienze, Università di Parma, Parma, Italy (Leonardi)
| | - Stefano Leonardi
- From the Department of Biodiversity and Molecular Ecology, Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy (Lega, Fior, Li, and Varotto); the Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland (Fior), and the Dipartimento di Bioscienze, Università di Parma, Parma, Italy (Leonardi)
| | - Claudio Varotto
- From the Department of Biodiversity and Molecular Ecology, Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy (Lega, Fior, Li, and Varotto); the Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland (Fior), and the Dipartimento di Bioscienze, Università di Parma, Parma, Italy (Leonardi).
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Christensen S, Heimes C, Agerbirk N, Kuzina V, Olsen CE, Hauser TP. Different Geographical Distributions of Two Chemotypes of Barbarea vulgaris that Differ in Resistance to Insects and a Pathogen. J Chem Ecol 2014; 40:491-501. [DOI: 10.1007/s10886-014-0430-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/16/2014] [Accepted: 04/07/2014] [Indexed: 11/28/2022]
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