1
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Jang YT, Brännström Å, Pontarp M. The interactive effects of environmental gradient and dispersal shape spatial phylogenetic patterns. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1037980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
IntroductionThe emergence and maintenance of biodiversity include interacting environmental conditions, organismal adaptation to such conditions, and dispersal. To understand and quantify such ecological, evolutionary, and spatial processes, observation and interpretation of phylogenetic relatedness across space (e.g., phylogenetic beta diversity) is arguably a way forward as such patterns contain signals from all the processes listed above. However, it remains challenging to extract information about complex eco-evolutionary and spatial processes from phylogenetic patterns.MethodsWe link environmental gradients and organismal dispersal with phylogenetic beta diversity using a trait-based and eco-evolutionary model of diversification along environmental gradients. The combined effect of the environment and dispersal leads to distinct phylogenetic patterns between subsets of species and across geographical distances.Results and discussionSteep environmental gradients combined with low dispersal lead to asymmetric phylogenies, a high phylogenetic beta diversity, and the phylogenetic diversity between communities increases linearly along the environmental gradient. High dispersal combined with a less steep environmental gradient leads to symmetric phylogenies, low phylogenetic beta diversity, and the phylogenetic diversity between communities along the gradient increases in a sigmoidal form. By disentangling the eco-evolutionary mechanisms that link such interacting environment and dispersal effects and community phylogenetic patterns, our results improve understanding of biodiversity in general and help interpretation of observed phylogenetic beta diversity.
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2
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Guillén‐Escribà C, Schneider FD, Schmid B, Tedder A, Morsdorf F, Furrer R, Hueni A, Niklaus PA, Schaepman ME. Remotely sensed between-individual functional trait variation in a temperate forest. Ecol Evol 2021; 11:10834-10867. [PMID: 34429885 PMCID: PMC8366889 DOI: 10.1002/ece3.7758] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 11/09/2022] Open
Abstract
Trait-based ecology holds the promise to explain how plant communities work, for example, how functional diversity may support community productivity. However, so far it has been difficult to combine field-based approaches assessing traits at the level of plant individuals with limited spatial coverage and approaches using remote sensing (RS) with complete spatial coverage but assessing traits at the level of vegetation pixels rather than individuals. By delineating all individual-tree crowns within a temperate forest site and then assigning RS-derived trait measures to these trees, we combine the two approaches, allowing us to use general linear models to estimate the influence of taxonomic or environmental variation on between- and within-species variation across contiguous space.We used airborne imaging spectroscopy and laser scanning to collect individual-tree RS data from a mixed conifer-angiosperm forest on a mountain slope extending over 5.5 ha and covering large environmental gradients in elevation as well as light and soil conditions. We derived three biochemical (leaf chlorophyll, carotenoids, and water content) and three architectural traits (plant area index, foliage-height diversity, and canopy height), which had previously been used to characterize plant function, from the RS data. We then quantified the contributions of taxonomic and environmental variation and their interaction to trait variation and partitioned the remaining within-species trait variation into smaller-scale spatial and residual variation. We also investigated the correlation between functional trait and phylogenetic distances at the between-species level. The forest consisted of 13 tree species of which eight occurred in sufficient abundance for quantitative analysis.On average, taxonomic variation between species accounted for more than 15% of trait variation in biochemical traits but only around 5% (still highly significant) in architectural traits. Biochemical trait distances among species also showed a stronger correlation with phylogenetic distances than did architectural trait distances. Light and soil conditions together with elevation explained slightly more variation than taxonomy across all traits, but in particular increased plant area index (light) and reduced canopy height (elevation). Except for foliage-height diversity, all traits were affected by significant interactions between taxonomic and environmental variation, the different responses of the eight species to the within-site environmental gradients potentially contributing to the coexistence of the eight abundant species.We conclude that with high-resolution RS data it is possible to delineate individual-tree crowns within a forest and thus assess functional traits derived from RS data at individual level. With this precondition fulfilled, it is then possible to apply tools commonly used in field-based trait ecology to partition trait variation among individuals into taxonomic and potentially even genetic variation, environmental variation, and interactions between the two. The method proposed here presents a promising way of assessing individual-based trait information with complete spatial coverage and thus allowing analysis of functional diversity at different scales. This information can help to better understand processes shaping community structure, productivity, and stability of forests.
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Affiliation(s)
- Carla Guillén‐Escribà
- Remote Sensing LaboratoriesDepartment of GeographyUniversity of ZürichZürichSwitzerland
- Present address:
WeesenSwitzerland
| | - Fabian D. Schneider
- Remote Sensing LaboratoriesDepartment of GeographyUniversity of ZürichZürichSwitzerland
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | - Bernhard Schmid
- Remote Sensing LaboratoriesDepartment of GeographyUniversity of ZürichZürichSwitzerland
| | - Andrew Tedder
- School of Chemistry and BiosciencesFaculty of Life SciencesUniversity of BradfordBradfordUK
| | - Felix Morsdorf
- Remote Sensing LaboratoriesDepartment of GeographyUniversity of ZürichZürichSwitzerland
| | - Reinhard Furrer
- Department of MathematicsUniversity of ZürichZürichSwitzerland
- Department of Computational ScienceUniversity of ZürichZürichSwitzerland
| | - Andreas Hueni
- Remote Sensing LaboratoriesDepartment of GeographyUniversity of ZürichZürichSwitzerland
| | - Pascal A. Niklaus
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichZürichSwitzerland
| | - Michael E. Schaepman
- Remote Sensing LaboratoriesDepartment of GeographyUniversity of ZürichZürichSwitzerland
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3
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Staab M, Liu X, Assmann T, Bruelheide H, Buscot F, Durka W, Erfmeier A, Klein A, Ma K, Michalski S, Wubet T, Schmid B, Schuldt A. Tree phylogenetic diversity structures multitrophic communities. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13722] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michael Staab
- Nature Conservation and Landscape Ecology University of Freiburg Freiburg Germany
- Freiburg Institute of Advanced Studies (FRIAS) University of Freiburg Freiburg Germany
- Ecological Networks Technical University Darmstadt Darmstadt Germany
| | - Xiaojuan Liu
- State Key Laboratory of Environmental Change and Vegetation Institute of Botany Chinese Academy of Sciences Beijing China
| | - Thorsten Assmann
- Institute of Ecology Leuphana University Lüneburg Lüneburg Germany
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden Martin Luther University Halle‐Wittenberg Halle (Saale) Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Soil Ecology Helmholtz Centre for Environmental Research – UFZ Halle (Saale) Germany
| | - Walter Durka
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Community Ecology Helmholtz Centre for Environmental Research – UFZ Halle (Saale) Germany
| | - Alexandra Erfmeier
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Institute for Ecosystem Research Kiel University Kiel Germany
| | | | - Keping Ma
- State Key Laboratory of Environmental Change and Vegetation Institute of Botany Chinese Academy of Sciences Beijing China
| | - Stefan Michalski
- Department of Community Ecology Helmholtz Centre for Environmental Research – UFZ Halle (Saale) Germany
| | - Tesfaye Wubet
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Community Ecology Helmholtz Centre for Environmental Research – UFZ Halle (Saale) Germany
| | - Bernhard Schmid
- Department of Geography University of Zurich Zurich Switzerland
- Institute of Ecology Peking University Beijing China
| | - Andreas Schuldt
- Forest Nature ConservationGeorg‐August‐University Göttingen Göttingen Germany
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4
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Kaplan I, Bokulich NA, Caporaso JG, Enders LS, Ghanem W, Ingerslew KS. Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? Evol Appl 2020; 13:1984-1999. [PMID: 32908599 PMCID: PMC7463318 DOI: 10.1111/eva.12956] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/06/2020] [Accepted: 03/12/2020] [Indexed: 12/17/2022] Open
Abstract
Agriculture has long employed phylogenetic rules whereby farmers are encouraged to rotate taxonomically unrelated plants in shared soil. Although this forms a central tenet of sustainable agriculture, strangely, this on-farm "rule of thumb" has never been rigorously tested in a scientific framework. To experimentally evaluate the relationship between phylogenetic distance and crop performance, we used a plant-soil feedback approach whereby 35 crops and weeds varying in their relatedness to tomato (Solanum lycopersicum) were tested in a two-year field experiment. We used community profiling of the bacteria and fungi to determine the extent to which soil microbes contribute to phenotypic differences in crop growth. Overall, tomato yield was ca. 15% lower in soil previously cultivated with tomato; yet, past the species level there was no effect of phylogenetic distance on crop performance. Soil microbial communities, on the other hand, were compositionally more similar between close plant relatives. Random forest regression predicted log10 phylogenetic distance to tomato with moderate accuracy (R 2 = .52), primarily driven by bacteria in the genus Sphingobium. These data indicate that, beyond avoiding conspecifics, evolutionary history contributes little to understanding plant-soil feedbacks in agricultural fields; however, microbial legacies can be predicted by species identity and relatedness.
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Affiliation(s)
- Ian Kaplan
- Department of EntomologyPurdue UniversityWest LafayetteINUSA
| | - Nicholas A. Bokulich
- Center for Applied Microbiome ScienceThe Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffAZUSA
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffAZUSA
| | - J. Gregory Caporaso
- Center for Applied Microbiome ScienceThe Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffAZUSA
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffAZUSA
| | | | - Wadih Ghanem
- Department of EntomologyPurdue UniversityWest LafayetteINUSA
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5
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Brun P, Zimmermann NE, Graham CH, Lavergne S, Pellissier L, Münkemüller T, Thuiller W. The productivity-biodiversity relationship varies across diversity dimensions. Nat Commun 2019; 10:5691. [PMID: 31831803 PMCID: PMC6908676 DOI: 10.1038/s41467-019-13678-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 11/21/2019] [Indexed: 11/09/2022] Open
Abstract
Understanding the processes that drive the dramatic changes in biodiversity along the productivity gradient remains a major challenge. Insight from simple, bivariate relationships so far has been limited. We combined >11,000 community plots in the French Alps with a molecular phylogeny and trait information for >1200 plant species to simultaneously investigate the relationships between all major biodiversity dimensions and satellite-sensed productivity. Using an approach that tests for differential effects of species dominance, species similarity and the interplay between phylogeny and traits, we demonstrate that unimodal productivity-biodiversity relationships only dominate for taxonomic diversity. In forests, trait and phylogenetic diversity typically increase with productivity, while in grasslands, relationships shift from unimodal to declining with greater land-use intensity. High productivity may increase trait/phylogenetic diversity in ecosystems with few external constraints (forests) by promoting complementary strategies, but under external constraints (managed grasslands) successful strategies are similar and thus the best competitors may be selected.
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Affiliation(s)
- Philipp Brun
- Swiss Federal Research Institute (WSL), 8903, Birmensdorf, Switzerland.
| | | | | | - Sébastien Lavergne
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Écologie Alpine, F- 38000, Grenoble, France
| | - Loïc Pellissier
- Swiss Federal Research Institute (WSL), 8903, Birmensdorf, Switzerland.,Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, 8092, Zürich, Switzerland
| | - Tamara Münkemüller
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Écologie Alpine, F- 38000, Grenoble, France
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Écologie Alpine, F- 38000, Grenoble, France
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6
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Vogel A, Ebeling A, Gleixner G, Roscher C, Scheu S, Ciobanu M, Koller-France E, Lange M, Lochner A, Meyer ST, Oelmann Y, Wilcke W, Schmid B, Eisenhauer N. A new experimental approach to test why biodiversity effects strengthen as ecosystems age. ADV ECOL RES 2019. [DOI: 10.1016/bs.aecr.2019.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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7
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Lost in trait space: species-poor communities are inflexible in properties that drive ecosystem functioning. ADV ECOL RES 2019. [DOI: 10.1016/bs.aecr.2019.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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8
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Schmid MW, Heichinger C, Coman Schmid D, Guthörl D, Gagliardini V, Bruggmann R, Aluri S, Aquino C, Schmid B, Turnbull LA, Grossniklaus U. Contribution of epigenetic variation to adaptation in Arabidopsis. Nat Commun 2018; 9:4446. [PMID: 30361538 PMCID: PMC6202389 DOI: 10.1038/s41467-018-06932-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 10/05/2018] [Indexed: 12/20/2022] Open
Abstract
In plants, transgenerational inheritance of some epialleles has been demonstrated but it remains controversial whether epigenetic variation is subject to selection and contributes to adaptation. Simulating selection in a rapidly changing environment, we compare phenotypic traits and epigenetic variation between Arabidopsis thaliana populations grown for five generations under selection and their genetically nearly identical ancestors. Selected populations of two distinct genotypes show significant differences in flowering time and plant architecture, which are maintained for at least 2–3 generations in the absence of selection. While we cannot detect consistent genetic changes, we observe a reduction of epigenetic diversity and changes in the methylation state of about 50,000 cytosines, some of which are associated with phenotypic changes. Thus, we propose that epigenetic variation is subject to selection and can contribute to rapid adaptive responses, although the extent to which epigenetics plays a role in adaptation is still unclear. Whether plant epigenetic variation is subject to selection and contributes to adaptation is under debate. Here, the authors compare DNA methylation and phenotypes of Arabidopsis lines subject to simulated selection and their nearly isogenic ancestors and provide evidence that epigenetic variation contributes to adaptive responses.
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Affiliation(s)
- Marc W Schmid
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,Service and Support for Science IT, University of Zurich, Stampfenbachstrasse 73, 8006, Zurich, Switzerland.,MWSchmid GmbH, Möhrlistrasse 25, 8006, Zurich, Switzerland
| | - Christian Heichinger
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,L. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Diana Coman Schmid
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,Scientific IT Services, ETH Zurich, Weinbergstrasse 11, 8092, Zurich, Switzerland
| | - Daniela Guthörl
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Hochschulstrasse 6, 3012, Bern, Switzerland
| | - Sirisha Aluri
- Functional Genomics Center Zurich, ETH and University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Catharine Aquino
- Functional Genomics Center Zurich, ETH and University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Bernhard Schmid
- Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Lindsay A Turnbull
- Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland. .,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich and University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.
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9
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Kuczynski L, Grenouillet G. Community disassembly under global change: Evidence in favor of the stress-dominance hypothesis. GLOBAL CHANGE BIOLOGY 2018; 24:4417-4427. [PMID: 29788536 DOI: 10.1111/gcb.14320] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 05/02/2018] [Accepted: 05/10/2018] [Indexed: 06/08/2023]
Abstract
Ecological theory suggests that communities are not random combinations of species but rather the results of community assembly processes filtering and sorting species that are able to coexist together. To date, such processes (i.e., assembly rules) have been inferred from observed spatial patterns of biodiversity combined with null model approaches, but relatively few attempts have been made to assess how these processes may be changing through time. Specifically, in the context of the ongoing biodiversity crisis and global change, understanding how processes shaping communities may be changing and identifying the potential drivers underlying these changes become increasingly critical. Here, we used time series of 460 French freshwater fish communities and assessed both functional and phylogenetic diversity patterns to determine the relative importance of two key assembly rules (i.e., habitat filtering and limiting similarity) in shaping these communities over the last two decades. We aimed to (a) describe the temporal changes in both functional and phylogenetic diversity patterns, (b) determine to what extent temporal changes in processes inferred through the use of standardized diversity indices were congruent, and (c) test the relationships between the dynamics of assembly rules and both climatic and biotic drivers. Our results revealed that habitat filtering, although already largely predominant over limiting similarity, became more widespread over time. We also highlighted that phylogenetic and trait-based approaches offered complementary information about temporal changes in assembly rules. Finally, we found that increased environmental harshness over the study period (especially higher seasonality of temperature) led to an increase in habitat filtering and that biological invasions increased functional redundancy within communities. Overall, these findings underlie the need to develop temporal perspectives in community assembly studies, as understanding ongoing temporal changes could provide a better vision about the way communities could respond to future global changes.
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Affiliation(s)
- Lucie Kuczynski
- UMR Laboratoire Evolution et Diversité Biologique, IRD 253, CNRS 5174, UPS, ENFA, Toulouse, France
| | - Gaël Grenouillet
- UMR Laboratoire Evolution et Diversité Biologique, IRD 253, CNRS 5174, UPS, ENFA, Toulouse, France
- Institut Universitaire de France, Paris, France
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10
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Kempel A, Rindisbacher A, Fischer M, Allan E. Plant soil feedback strength in relation to large-scale plant rarity and phylogenetic relatedness. Ecology 2018; 99:597-606. [DOI: 10.1002/ecy.2145] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Anne Kempel
- Institute of Plant Sciences; Altenbergrain 21 3013 Bern Switzerland
| | | | - Markus Fischer
- Institute of Plant Sciences; Altenbergrain 21 3013 Bern Switzerland
| | - Eric Allan
- Institute of Plant Sciences; Altenbergrain 21 3013 Bern Switzerland
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11
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Weisser WW, Roscher C, Meyer ST, Ebeling A, Luo G, Allan E, Beßler H, Barnard RL, Buchmann N, Buscot F, Engels C, Fischer C, Fischer M, Gessler A, Gleixner G, Halle S, Hildebrandt A, Hillebrand H, de Kroon H, Lange M, Leimer S, Le Roux X, Milcu A, Mommer L, Niklaus PA, Oelmann Y, Proulx R, Roy J, Scherber C, Scherer-Lorenzen M, Scheu S, Tscharntke T, Wachendorf M, Wagg C, Weigelt A, Wilcke W, Wirth C, Schulze ED, Schmid B, Eisenhauer N. Biodiversity effects on ecosystem functioning in a 15-year grassland experiment: Patterns, mechanisms, and open questions. Basic Appl Ecol 2017. [DOI: 10.1016/j.baae.2017.06.002] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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12
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Ulrich W, Lens L, Tobias JA, Habel JC. Contrasting Patterns of Species Richness and Functional Diversity in Bird Communities of East African Cloud Forest Fragments. PLoS One 2016; 11:e0163338. [PMID: 27855174 PMCID: PMC5113869 DOI: 10.1371/journal.pone.0163338] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/06/2016] [Indexed: 11/18/2022] Open
Abstract
Rapid fragmentation and degradation of large undisturbed habitats constitute major threats to biodiversity. Several studies have shown that populations in small and highly isolated habitat patches are prone to strong environmental and demographic stochasticity and increased risk of extinction. Based on community assembly theory, we predict recent rapid forest fragmentation to cause a decline in species and functional guild richness of forest birds combined with a high species turnover among habitat patches, and well defined dominance structures, if competition is the major driver of community assembly. To test these predictions, we analysed species co-occurrence, nestedness, and competitive strength to infer effects of interspecific competition, habitat structure, and species' traits on the assembly of bird species communities from 12 cloud forest fragments in southern Kenya. Our results do not point to a single ecological driver of variation in species composition. Interspecific competition does not appear to be a major driver of species segregation in small forest patches, while its relative importance appears to be higher in larger ones, which may be indicative for a generic shift from competition-dominated to colonisation-driven community structure with decreasing fragment size. Functional trait diversity was independent of fragment size after controlling for species richness. As fragmentation effects vary among feeding guilds and habitat generalists, in particular, tend to decline in low quality forest patches, we plead for taking species ecology fully into account when predicting tropical community responses to habitat change.
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Affiliation(s)
- Werner Ulrich
- Nicolaus Copernicus University in Toruń, Chair of Ecology and Biogeography, Pl-87-100 Toruń, Poland
- * E-mail:
| | - Luc Lens
- Ghent University, Department of Biology, Terrestrial Ecology Unit, B-9000 Ghent, Belgium
| | - Joseph A. Tobias
- Department of Life Sciences, Imperial College London, Silwood Park, Buckhurst Road, Ascot, Berkshire, SL5 7PY, United Kingdom
| | - Jan C. Habel
- Technische Universität München, Department of Ecology and Ecosystem Management, Terrestrial Ecology Research Group, D-85354 Freising, Germany
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13
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Villa Martín P, Hidalgo J, Rubio de Casas R, Muñoz MA. Eco-evolutionary Model of Rapid Phenotypic Diversification in Species-Rich Communities. PLoS Comput Biol 2016; 12:e1005139. [PMID: 27736874 PMCID: PMC5063285 DOI: 10.1371/journal.pcbi.1005139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/09/2016] [Indexed: 12/30/2022] Open
Abstract
Evolutionary and ecosystem dynamics are often treated as different processes –operating at separate timescales– even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field experiment has explicitly shown that communities of competing plant species can experience very fast phenotypic diversification, and that this gives rise to enhanced complementarity in resource exploitation and to enlarged ecosystem-level productivity. Here, we build on progress made in recent years in the integration of eco-evolutionary dynamics, and present a computational approach aimed at describing these empirical findings in detail. In particular we model a community of organisms of different but similar species evolving in time through mechanisms of birth, competition, sexual reproduction, descent with modification, and death. Based on simple rules, this model provides a rationalization for the emergence of rapid phenotypic diversification in species-rich communities. Furthermore, it also leads to non-trivial predictions about long-term phenotypic change and ecological interactions. Our results illustrate that the presence of highly specialized, non-competing species leads to very stable communities and reveals that phenotypically equivalent species occupying the same niche may emerge and coexist for very long times. Thus, the framework presented here provides a simple approach –complementing existing theories, but specifically devised to account for the specificities of the recent empirical findings for plant communities– to explain the collective emergence of diversification at a community level, and paves the way to further scrutinize the intimate entanglement of ecological and evolutionary processes, especially in species-rich communities. Population ecology and evolutionary biology have been traditionally studied as separate disciplines, even if feedbacks between community and evolutionary processes are known to exist, having been empirically characterized in recent years in different types of communities (from microbes to plants and vertebrates), and theoretically analyzed with novel and powerful mathematical tools. Recent long-term field experiments with plants have proven that rapid co-evolution and diversification of species traits results in an overall enhancement of the ecosystem productivity, with important consequences for agriculture and conservation. Here, we propose a relatively simple computational eco-evolutionary model specifically devised to describe rapid phenotypic diversification in this type of species-rich communities. Our model captures the main phenomenology observed experimentally, and it also makes non-trivial predictions for long term phenotypic change and ecological interactions, such as the stable coexistence of highly specialized species or the possible emergence of phenotypically equivalent species occupying the same niche. Finally, the model is easily generalizable to analyze different eco-evolutionary problems within a relatively simple and unified computational framework.
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Affiliation(s)
- Paula Villa Martín
- Departamento de Electromagnetismo y Física de la Materia and Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Granada, Spain
| | - Jorge Hidalgo
- Departamento de Electromagnetismo y Física de la Materia and Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Granada, Spain
- Dipartimento di Fisica ’G.Galilei’ and CNISM, INFN, Università di Padova, Padova, Italy
| | - Rafael Rubio de Casas
- Estación Experimental de Zonas Áridas, EEZA-CSIC, Almería, Spain
- UMR 5175 Centre d’Ecologie Fonctionnelle et Evolutive (CNRS), Montpellier, France
- Departamento de Ecología, Universidad de Granada, Granada, Spain
| | - Miguel A. Muñoz
- Departamento de Electromagnetismo y Física de la Materia and Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Granada, Spain
- * E-mail:
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14
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Khalil MI, Gibson DJ, Baer SG. Phylogenetic diversity reveals hidden patterns related to population source and species pools during restoration. J Appl Ecol 2016. [DOI: 10.1111/1365-2664.12743] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mohammed I. Khalil
- Department of Plant Biology and Center for Ecology Southern Illinois University, Carbondale 1263 Lincoln Drive Carbondale IL 62901 USA
| | - David J. Gibson
- Department of Plant Biology and Center for Ecology Southern Illinois University, Carbondale 1263 Lincoln Drive Carbondale IL 62901 USA
| | - Sara G. Baer
- Department of Plant Biology and Center for Ecology Southern Illinois University, Carbondale 1263 Lincoln Drive Carbondale IL 62901 USA
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15
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Lopez B, Burgio K, Carlucci M, Palmquist K, Parada A, Weinberger V, Hurlbert A. A new framework for inferring community assembly processes using phylogenetic information, relevant traits and environmental gradients. ONE ECOSYSTEM 2016. [DOI: 10.3897/oneeco.1.e9501] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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16
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Valladares F, Bastias CC, Godoy O, Granda E, Escudero A. Species coexistence in a changing world. FRONTIERS IN PLANT SCIENCE 2015; 6:866. [PMID: 26528323 PMCID: PMC4604266 DOI: 10.3389/fpls.2015.00866] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/30/2015] [Indexed: 05/26/2023]
Abstract
The consequences of global change for the maintenance of species diversity will depend on the sum of each species responses to the environment and on the interactions among them. A wide ecological literature supports that these species-specific responses can arise from factors related to life strategies, evolutionary history and intraspecific variation, and also from environmental variation in space and time. In the light of recent advances from coexistence theory combined with mechanistic explanations of diversity maintenance, we discuss how global change drivers can influence species coexistence. We revise the importance of both competition and facilitation for understanding coexistence in different ecosystems, address the influence of phylogenetic relatedness, functional traits, phenotypic plasticity and intraspecific variability, and discuss lessons learnt from invasion ecology. While most previous studies have focused their efforts on disentangling the mechanisms that maintain the biological diversity in species-rich ecosystems such as tropical forests, grasslands and coral reefs, we argue that much can be learnt from pauci-specific communities where functional variability within each species, together with demographic and stochastic processes becomes key to understand species interactions and eventually community responses to global change.
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Affiliation(s)
- Fernando Valladares
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Ciencias, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - Cristina C. Bastias
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Oscar Godoy
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Elena Granda
- Laboratoire Ecologie Systématique et Evolution, Université Paris Sud/Centre National de la Recherche Scientifique/AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Adrián Escudero
- Departamento de Ciencias, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
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Li SP, Cadotte MW, Meiners SJ, Hua ZS, Jiang L, Shu WS. Species colonisation, not competitive exclusion, drives community overdispersion over long-term succession. Ecol Lett 2015; 18:964-73. [PMID: 26189648 DOI: 10.1111/ele.12476] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 06/02/2015] [Accepted: 06/15/2015] [Indexed: 11/28/2022]
Abstract
Ecological communities often transition from phylogenetic and functional clustering to overdispersion over succession as judged by space-for-time substitution studies. Such a pattern has been generally attributed to the increase in competitive exclusion of closely related species with similar traits through time, although colonisation and extinction have rarely been examined. Using 44 years of uninterrupted old-field succession in New Jersey, USA, we confirmed that phylogenetic and functional clustering decreased as succession unfolded, but the transition was largely driven by colonisation. Early colonists were closely related and functionally similar to residents, while later colonists became less similar to the species present. Extirpated species were generally more distantly related to residents than by chance, or exhibited random phylogenetic/functional patterns, and their relatedness to residents was not associated with time. These results provide direct evidence that the colonisation of distant relatives, rather than extinction of close relatives, drives phylogenetic and functional overdispersion over succession.
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Affiliation(s)
- Shao-Peng Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, 510275, China.,Biological Sciences, University of Toronto-Scarborough & Ecology and Evolutionary Biology, University of Toronto, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada.,School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA, 30332, USA
| | - Marc W Cadotte
- Biological Sciences, University of Toronto-Scarborough & Ecology and Evolutionary Biology, University of Toronto, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Scott J Meiners
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL, 61920, USA
| | - Zheng-Shuang Hua
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, 510275, China
| | - Lin Jiang
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA, 30332, USA
| | - Wen-Sheng Shu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, 510275, China
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18
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Biodiversity enhances ecosystem multifunctionality across trophic levels and habitats. Nat Commun 2015; 6:6936. [PMID: 25907115 PMCID: PMC4423209 DOI: 10.1038/ncomms7936] [Citation(s) in RCA: 282] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/17/2015] [Indexed: 12/05/2022] Open
Abstract
The importance of biodiversity for the integrated functioning of ecosystems remains unclear because most evidence comes from analyses of biodiversity's effect on individual functions. Here we show that the effects of biodiversity on ecosystem function become more important as more functions are considered. We present the first systematic investigation of biodiversity's effect on ecosystem multifunctionality across multiple taxa, trophic levels and habitats using a comprehensive database of 94 manipulations of species richness. We show that species-rich communities maintained multiple functions at higher levels than depauperate ones. These effects were stronger for herbivore biodiversity than for plant biodiversity, and were remarkably consistent across aquatic and terrestrial habitats. Despite observed tradeoffs, the overall effect of biodiversity on multifunctionality grew stronger as more functions were considered. These results indicate that prior research has underestimated the importance of biodiversity for ecosystem functioning by focusing on individual functions and taxonomic groups. The influence of biodiversity on multiple ecosystem processes is not well understood. Analysing 94 biodiversity-ecosystem functioning experiments, Lefcheck et al. find that increased species richness maintains more ecological functions, across multiple taxa, trophic levels and habitats.
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19
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Different assembly processes drive shifts in species and functional composition in experimental grasslands varying in sown diversity and community history. PLoS One 2014; 9:e101928. [PMID: 25029105 PMCID: PMC4100744 DOI: 10.1371/journal.pone.0101928] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 06/13/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The prevalence of different biotic processes (limiting similarity, weaker competitor exclusion) and historical contingency due to priority effects are in the focus of ongoing discussions about community assembly and non-random functional trait distributions. METHODOLOGY/PRINCIPAL FINDINGS We experimentally manipulated assembly history in a grassland biodiversity experiment (Jena Experiment) by applying two factorially crossed split-plot treatments to all communities: (i) duration of weeding (never weeded since sowing or cessation of weeding after 3 or 6 years); (ii) seed addition (control vs. seed addition 4 years after sowing). Spontaneous colonization of new species in the control treatment without seed addition increased realized species richness and functional richness (FRic), indicating continuously denser packing of niches. Seed addition resulted in forced colonization and increased realized species richness, FRic, functional evenness (FEve) and functional divergence (FDiv), i.e. higher abundances of species with extreme trait values. Furthermore, the colonization of new species led to a decline in FEve through time, suggesting that weaker competitors were reduced in abundance or excluded. Communities with higher initial species richness or with longer time since cessation of weeding were more restricted in the entry of new species and showed smaller increases in FRic after seed addition than other communities. The two assembly-history treatments caused a divergence of species compositions within communities originally established with the same species. Communities originally established with different species converged in species richness and functional trait composition over time, but remained more distinct in species composition. CONCLUSIONS/SIGNIFICANCE Contrasting biotic processes (limiting similarity, weaker competitor exclusion) increase functional convergence between communities initially established with different species. Historical contingency with regard to realized species compositions could not be eradicated by cessation of weeding or forced colonization and was still detectable 5 years after application of these treatments, providing evidence for the role of priority effects in community assembly.
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Ulrich W, Piwczyński M, Zaplata MK, Winter S, Schaaf W, Fischer A. Small-scale spatial variability in phylogenetic community structure during early plant succession depends on soil properties. Oecologia 2014; 175:985-95. [PMID: 24810325 PMCID: PMC4059990 DOI: 10.1007/s00442-014-2954-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 04/16/2014] [Indexed: 12/03/2022]
Abstract
During early plant succession, the phylogenetic structure of a community changes in response to important environmental filters and emerging species interactions. We traced the development of temperate-zone plant communities during the first 7 years of primary succession on catchment soils to explore patterns of initial species assembly. We found pronounced small-scale differences in the phylogenetic composition of neighbouring plant assemblages and a large-scale trend towards phylogenetic evenness. This small-scale variability appears to be mediated by soil properties, particularly carbonate content. Therefore, abiotic environmental conditions might counteract or even supersede the effects of interspecific competition among closely related species, which are usually predicted to exhibit patterns of phylogenetic evenness. We conclude that theories on phylogenetic community composition need to incorporate effects of small-scale variability of environmental factors.
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Affiliation(s)
- Werner Ulrich
- Chair of Ecology and Biogeography, Nicolaus Copernicus University in Torun, Lwowska 1, 87-100, Toruń, Poland,
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Molina-Venegas R, Roquet C. Directional biases in phylogenetic structure quantification: a Mediterranean case study. ECOGRAPHY 2014; 37:572-580. [PMID: 25076812 PMCID: PMC4112217 DOI: 10.1111/j.1600-0587.2013.00442.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Recent years have seen an increasing effort to incorporate phylogenetic hypotheses to the study of community assembly processes. The incorporation of such evolutionary information has been eased by the emergence of specialized software for the automatic estimation of partially resolved supertrees based on published phylogenies. Despite this growing interest in the use of phylogenies in ecological research, very few studies have attempted to quantify the potential biases related to the use of partially resolved phylogenies and to branch length accuracy, and no work has examined how tree shape may affect inference of community phylogenetic metrics. In this study, using a large plant community and elevational dataset, we tested the influence of phylogenetic resolution and branch length information on the quantification of phylogenetic structure; and also explored the impact of tree shape (stemminess) on the loss of accuracy in phylogenetic structure quantification due to phylogenetic resolution. For this purpose, we used 9 sets of phylogenetic hypotheses of varying resolution and branch lengths to calculate three indices of phylogenetic structure: the mean phylogenetic distance (NRI), the mean nearest taxon distance (NTI) and phylogenetic diversity (stdPD) metrics. The NRI metric was the less sensitive to phylogenetic resolution, stdPD showed an intermediate sensitivity, and NTI was the most sensitive one; NRI was also less sensitive to branch length accuracy than NTI and stdPD, the degree of sensitivity being strongly dependent on the dating method and the sample size. Directional biases were generally towards type II errors. Interestingly, we detected that tree shape influenced the accuracy loss derived from the lack of phylogenetic resolution, particularly for NRI and stdPD. We conclude that well-resolved molecular phylogenies with accurate branch length information are needed to identify the underlying phylogenetic structure of communities, and also that sensitivity of phylogenetic structure measures to low phylogenetic resolution can strongly differ depending on phylogenetic tree shape.
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Affiliation(s)
- Rafael Molina-Venegas
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Apartado 1095, E-41080 Sevilla, Spain
| | - Cristina Roquet
- Laboratoire d’Écologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, Grenoble 1, BP 53, 38041 Grenoble Cedex 9, France
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22
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Godoy O, Kraft NJB, Levine JM. Phylogenetic relatedness and the determinants of competitive outcomes. Ecol Lett 2014; 17:836-44. [DOI: 10.1111/ele.12289] [Citation(s) in RCA: 246] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/11/2014] [Accepted: 04/02/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Oscar Godoy
- Department of Ecology; Evolution & Marine Biology; University of California; Santa Barbara CA 93106 USA
| | - Nathan J. B. Kraft
- Department of Biology; University of Maryland; College Park MD 20742 USA
| | - Jonathan M. Levine
- Department of Ecology; Evolution & Marine Biology; University of California; Santa Barbara CA 93106 USA
- Institute of Integrative Biology; ETH Zurich; Universitaetstrasse 16; Zurich 8092 Switzerland
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23
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Valiente-Banuet A, Verdú M. Plant Facilitation and Phylogenetics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135855] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The relationship between facilitation and evolutionary ecology is poorly understood. We review five issues elucidating how the phylogenetic relatedness of species provides insight into the role of facilitation in community assembly: (a) Are the facilitative interactions more common between species that differ in a regeneration niche? (b) Are facilitative interactions more common between distantly related species? (c) Do communities governed by facilitation (rather than competition) have higher phylogenetic diversity? (d) As facilitated juvenile plants mature, do they compete with their nurses more often if they are closely related to them? (e) How does the phylogenetic signature in a community reveal ecological processes, such as succession, regeneration dynamics, indirect interactions, and coextinction cascades? The evolutionary history of lineages explains the regeneration niche of species, which ultimately determines the facilitation-competition balance and therefore community assembly and dynamics. We apply this framework to the conservation of biodiversity and propose future research avenues.
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Affiliation(s)
- Alfonso Valiente-Banuet
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología,
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Federal District 04510, Mexico
| | - Miguel Verdú
- Centro de Investigaciones sobre Desertificación (Consejo Superior Investigaciones Científicas-Universidad de Valencia-Generalitat Valenciana), 46113 Valencia, Spain
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Milcu A, Allan E, Roscher C, Jenkins T, Meyer ST, Flynn D, Bessler H, Buscot F, Engels C, Gubsch M, König S, Lipowsky A, Loranger J, Renker C, Scherber C, Schmid B, Thébault E, Wubet T, Weisser WW, Scheu S, Eisenhauer N. Functionally and phylogenetically diverse plant communities key to soil biota. Ecology 2013; 94:1878-85. [DOI: 10.1890/12-1936.1] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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