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Tietje M, Antonelli A, Forest F, Govaerts R, Smith SA, Sun M, Baker WJ, Eiserhardt WL. Global hotspots of plant phylogenetic diversity. THE NEW PHYTOLOGIST 2023; 240:1636-1646. [PMID: 37496281 DOI: 10.1111/nph.19151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/24/2023] [Indexed: 07/28/2023]
Abstract
Regions harbouring high unique phylogenetic diversity (PD) are priority targets for conservation. Here, we analyse the global distribution of plant PD, which remains poorly understood despite plants being the foundation of most terrestrial habitats and key to human livelihoods. Capitalising on a recently completed, comprehensive global checklist of vascular plants, we identify hotspots of unique plant PD and test three hypotheses: (1) PD is more evenly distributed than species diversity; (2) areas of highest PD (often called 'hotspots') do not maximise cumulative PD; and (3) many biomes are needed to maximise cumulative PD. Our results support all three hypotheses: more than twice as many regions are required to cover 50% of global plant PD compared to 50% of species; regions that maximise cumulative PD substantially differ from the regions with outstanding individual PD; and while (sub-)tropical moist forest regions dominate across PD hotspots, other forest types and open biomes are also essential. Safeguarding PD in the Anthropocene (including the protection of some comparatively species-poor areas) is a global, increasingly recognised responsibility. Having highlighted countries with outstanding unique plant PD, further analyses are now required to fully understand the global distribution of plant PD and associated conservation imperatives across spatial scales.
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Affiliation(s)
- Melanie Tietje
- Department of Biology, Aarhus University, Aarhus, 8000, Denmark
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, 413 19, Sweden
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | | | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Miao Sun
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, Hubei, 430070, China
| | | | - Wolf L Eiserhardt
- Department of Biology, Aarhus University, Aarhus, 8000, Denmark
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Aarhus Institute of Advanced Studies, Aarhus University, Aaarhus, 8000, Denmark
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2
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Skeels A, Boschman LM, McFadden IR, Joyce EM, Hagen O, Jiménez Robles O, Bach W, Boussange V, Keggin T, Jetz W, Pellissier L. Paleoenvironments shaped the exchange of terrestrial vertebrates across Wallace's Line. Science 2023; 381:86-92. [PMID: 37410831 DOI: 10.1126/science.adf7122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/01/2023] [Indexed: 07/08/2023]
Abstract
Faunal turnover in Indo-Australia across Wallace's Line is one of the most recognizable patterns in biogeography and has catalyzed debate about the role of evolutionary and geoclimatic history in biotic interchanges. Here, analysis of more than 20,000 vertebrate species with a model of geoclimate and biological diversification shows that broad precipitation tolerance and dispersal ability were key for exchange across the deep-time precipitation gradient spanning the region. Sundanian (Southeast Asian) lineages evolved in a climate similar to the humid "stepping stones" of Wallacea, facilitating colonization of the Sahulian (Australian) continental shelf. By contrast, Sahulian lineages predominantly evolved in drier conditions, hampering establishment in Sunda and shaping faunal distinctiveness. We demonstrate how the history of adaptation to past environmental conditions shapes asymmetrical colonization and global biogeographic structure.
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Affiliation(s)
- A Skeels
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
- Research School of Biology, Australian National University, Canberra 0200, Australia
| | - L M Boschman
- Department of Earth Sciences, Utrecht University, 3584 CB Utrecht, Netherlands
| | - I R McFadden
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, Netherlands
| | - E M Joyce
- Systematics, Biodiversity and Evolution of Plants, Ludwig Maximilian University of Munich, 80331 Munich, Germany
| | - O Hagen
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - O Jiménez Robles
- Research School of Biology, Australian National University, Canberra 0200, Australia
- Institute of Biology, École Normale Supérieure, 75005 Paris, France
| | - W Bach
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - V Boussange
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - T Keggin
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - W Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, CT 06520, USA
| | - L Pellissier
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
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3
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Ringelberg JJ, Koenen EJ, Sauter B, Aebli A, Rando JG, Iganci JR, de Queiroz LP, Murphy DJ, Gaudeul M, Bruneau A, Luckow M, Lewis GP, Miller JT, Simon MF, Jordão LS, Morales M, Bailey CD, Nageswara-Rao M, Nicholls JA, Loiseau O, Pennington RT, Dexter KG, Zimmermann NE, Hughes CE. Precipitation is the main axis of tropical plant phylogenetic turnover across space and time. SCIENCE ADVANCES 2023; 9:eade4954. [PMID: 36800419 PMCID: PMC10957106 DOI: 10.1126/sciadv.ade4954] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Early natural historians-Comte de Buffon, von Humboldt, and De Candolle-established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.
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Affiliation(s)
- Jens J. Ringelberg
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Benjamin Sauter
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Anahita Aebli
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Juliana G. Rando
- Programa de Pós Graduação em Ciências Ambientais, Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Rua Prof. José Seabra de Lemos, 316, Bairro Recanto dos Pássaros, 47808-021 Barreiras-BA, Brazil
| | - João R. Iganci
- Instituto de Biologia, Universidade Federal de Pelotas, Campus Universitário Capão do Leão, Travessa André Dreyfus s/n, 96010-900 Capão do Leão-RS, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, 91501-970 Porto Alegre-RS, Brazil
| | - Luciano P. de Queiroz
- Departamento Ciências Biológicas, Universidade Estadual de Feira de Santana, Avenida Transnordestina s/n, Novo Horizonte, 44036-900 Feira de Santana-BA, Brazil
| | - Daniel J. Murphy
- Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, Australia
- School of Biological, Earth and Environmental Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, France
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montreal, QC H1X 2B2, Canada
| | - Melissa Luckow
- School of Integrative Plant Science, Plant Biology Section, Cornell University, 215 Garden Avenue, Roberts Hall 260, Ithaca, NY 14853, USA
| | - Gwilym P. Lewis
- Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Joseph T. Miller
- Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Marcelo F. Simon
- Embrapa Recursos Genéticos e Biotecnologia, 70770-901 Brasília-DF, Brazil
| | - Lucas S. B. Jordão
- Programa de Pós-Graduação em Botânica, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, 22460-030 Rua Pacheco Leão-RJ, Brazil
| | - Matías Morales
- Instituto de Recursos Biológicos, CIRN-CNIA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1425FQB Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Agronomía y Ciencias Agroalimentarias, Universidad de Morón, B1708JPD Morón, Buenos Aires, Argentina
| | - C. Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, NM 88001, USA
| | - Madhugiri Nageswara-Rao
- United States Department of Agriculture - Agricultural Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Road, Miami, FL 33158, USA
| | - James A. Nicholls
- Australian National Insect Collection, CSIRO, Clunies Ross Street, Acton, ACT 2601, Australia
| | - Oriane Loiseau
- School of Geosciences, University of Edinburgh, Old College, South Bridge, Edinburgh EH8 9YL, UK
| | - R. Toby Pennington
- Department of Geography, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
- Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK
| | - Kyle G. Dexter
- School of Geosciences, University of Edinburgh, Old College, South Bridge, Edinburgh EH8 9YL, UK
- Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK
| | - Niklaus E. Zimmermann
- Department of Environmental System Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Colin E. Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
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4
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Velasco JA, Pinto-Ledezma JN. Mapping species diversification metrics in macroecology: Prospects and challenges. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.951271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The intersection of macroecology and macroevolution is one of today’s most active research in biology. In the last decade, we have witnessed a steady increment of macroecological studies that use metrics attempting to capture macroevolutionary processes to explain present-day biodiversity patterns. Evolutionary explanations of current species richness gradients are fundamental for understanding how diversity accumulates in a region. Although multiple hypotheses have been proposed to explain the patterns we observe in nature, it is well-known that the present-day diversity patterns result from speciation, extinction, colonization from nearby areas, or a combination of these macroevolutionary processes. Whether these metrics capture macroevolutionary processes across space is unknown. Some tip-rate metrics calculated directly from a phylogenetic tree (e.g., mean root distance -MRD-; mean diversification rate -mDR-) seem to return very similar geographical patterns regardless of how they are estimated (e.g., using branch lengths explicitly or not). Model-based tip-rate metrics —those estimated using macroevolutionary mixtures, e.g., the BAMM approach— seem to provide better net diversification estimates than only speciation rates. We argue that the lack of appropriate estimates of extinction and dispersal rates in phylogenetic trees may strongly limit our inferences about how species richness gradients have emerged at spatial and temporal scales. Here, we present a literature review about this topic and empirical comparisons between select taxa with several of these metrics. We implemented a simple null model approach to evaluate whether mapping of these metrics deviates from a random sampling process. We show that phylogenetic metrics by themselves are relatively poor at capturing speciation, extinction, and dispersal processes across geographical gradients. Furthermore, we provide evidence of how parametric biogeographic methods can improve our inference of past events and, therefore, our conclusions about the evolutionary processes driving biodiversity patterns. We recommend that further studies include several approaches simultaneously (e.g., spatial diversification modeling, parametric biogeographic methods, simulations) to disentangle the relative role of speciation, extinction, and dispersal in the generation and maintenance of species richness gradients at regional and global scales.
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5
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Dzekashu FF, Yusuf AA, Pirk CWW, Steffan‐Dewenter I, Lattorff HMG, Peters MK. Floral turnover and climate drive seasonal bee diversity along a tropical elevation gradient. Ecosphere 2022. [DOI: 10.1002/ecs2.3964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Fairo F. Dzekashu
- International Centre of Insect Physiology and Ecology (ICIPE) Nairobi Kenya
- Social Insects Research Group, Department of Zoology and Entomology University of Pretoria Pretoria South Africa
| | - Abdullahi A. Yusuf
- Social Insects Research Group, Department of Zoology and Entomology University of Pretoria Pretoria South Africa
| | - Christian W. W. Pirk
- Social Insects Research Group, Department of Zoology and Entomology University of Pretoria Pretoria South Africa
| | - Ingolf Steffan‐Dewenter
- Department of Animal Ecology and Tropical Biology, Biocenter University of Würzburg Würzburg Germany
| | | | - Marcell K. Peters
- Department of Animal Ecology and Tropical Biology, Biocenter University of Würzburg Würzburg Germany
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6
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Saito T, Hirano T, Ye B, Prozorova L, Shovon MS, Do TV, Kimura K, Surenkhorloo P, Kameda Y, Morii Y, Fukuda H, Chiba S. A comprehensive phylogeography of the widespread pond snail genus Radix revealed restricted colonization due to niche conservatism. Ecol Evol 2021; 11:18446-18459. [PMID: 35003683 PMCID: PMC8717273 DOI: 10.1002/ece3.8434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
To clarify the effect of niche conservatism on evolutionary history, we focused on freshwater snails, which have different ecological and phylogenetic properties from previously tested taxa. We conducted a phylogenetic analysis using 750 lymnaeid individuals from 357 sites of eleven Radix species. Then, we estimated the ancestral distribution using the geographic coordinates and colonization routes. In addition, a statistical test of the colonization distances in the latitudinal and longitudinal directions was performed. We also conducted ecological niche modeling for two widely distributed species using climatic data. Ancestral geographic reconstruction estimated the origin of the genus to be around the Indian subcontinental region and showed that latitudinal immigration distances were shorter than longitudinal immigration distances in the diversification process. Ecological niche models suggested that the current distribution was restricted by climate, with annual mean temperature and precipitation of the driest month as particularly strong factors. Niche conservatism to the climate can affect the diversification of freshwater snails.
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Affiliation(s)
- Takumi Saito
- Graduate School of Life ScienceTohoku UniversitySendaiJapan
- Department of BiologyFaculty of ScienceToho UniversityFunabashiJapan
| | - Takahiro Hirano
- Center for Northeast Asian StudiesTohoku UniversitySendaiJapan
| | - Bin Ye
- Graduate School of Life ScienceTohoku UniversitySendaiJapan
| | - Larisa Prozorova
- Federal Scientific Center of the East Asia Terrestrial BiodiversityFar Eastern BranchRussian Academy of SciencesVladivostokRussia
| | | | - Tu Van Do
- Institute of Ecology and Biological ResourcesVietnam Academy of Science and TechnologyHa NoiVietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and TechnologyHa NoiVietnam
| | - Kazuki Kimura
- Department of BiologyResearch Institute for Ulleung‐do and Dok‐do IslandsKyungpook National UniversityDaeguKorea
| | | | - Yuichi Kameda
- Center for Molecular Biodiversity ResearchNational Museum of Nature and ScienceTsukubaJapan
| | - Yuta Morii
- Laboratory of Animal EcologyDepartment of ZoologyGraduate School of ScienceKyoto UniversityKyotoJapan
- The Hakubi CenterKyoto UniversityKyotoJapan
| | - Hiroshi Fukuda
- Conservation of Aquatic BiodiversityFaculty of AgricultureOkayama UniversityOkayamaJapan
| | - Satoshi Chiba
- Center for Northeast Asian StudiesTohoku UniversitySendaiJapan
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7
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The contribution of environmental and dispersal filters on phylogenetic and taxonomic beta diversity patterns in Amazonian tree communities. Oecologia 2021; 196:1119-1137. [PMID: 34324078 PMCID: PMC8367926 DOI: 10.1007/s00442-021-04981-0] [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: 09/06/2020] [Accepted: 06/28/2021] [Indexed: 10/28/2022]
Abstract
Environmental and dispersal filters are key determinants of species distributions of Amazonian tree communities. However, a comprehensive analysis of the role of environmental and dispersal filters is needed to understand the ecological and evolutionary processes that drive phylogenetic and taxonomic turnover of Amazonian tree communities. We compare measures of taxonomic and phylogenetic beta diversity in 41 one-hectare plots to test the relative importance of climate, soils, geology, geomorphology, pure spatial variables and the spatial variation of environmental drivers of phylogenetic and taxonomic turnover in Ecuadorian Amazon tree communities. We found low phylogenetic and high taxonomic turnover with respect to environmental and dispersal filters. In addition, our results suggest that climate is a significantly better predictor of phylogenetic turnover and taxonomic turnover than geomorphology and soils at all spatial scales. The influence of climate as a predictor of phylogenetic turnover was stronger at broader spatial scales (50 km2) whereas geomorphology and soils appear to be better predictors of taxonomic turnover at mid (5 km2) and fine spatial scales (0.5 km2) but a weak predictor of phylogenetic turnover at broad spatial scales. We also found that the combined effect of geomorphology and soils was significantly higher for taxonomic turnover at all spatial scales but not for phylogenetic turnover at large spatial scales. Geographic distances as proxy of dispersal limitation was a better predictor of phylogenetic turnover at distances of 50 < 500 km. Our findings suggest that climatic variation at regional scales can better predict phylogenetic and taxonomic turnover than geomorphology and soils.
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8
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Phylogenetic and Functional Traits Verify the Combined Effect of Deterministic and Stochastic Processes in the Community Assembly of Temperate Forests along an Elevational Gradient. FORESTS 2021. [DOI: 10.3390/f12050591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Explaining community assembly mechanisms along elevational gradients dominated by deterministic processes or stochastic processes is a pressing challenge. Many studies suggest that phylogenetic and functional diversity are significant indicators of the process. In this study, we analyzed the structure and beta diversity of phylogenetic and functional traits along an elevational gradient and discussed the effects of environmental and spatial factors. We found that the phylogenetic and functional traits showed inconsistent changes, and their variations were closely related to the abiotic environment. The results suggested that the community assembly of woody plants was obviously affected by the combined effect of deterministic processes and the stochastic hypothesis (primarily by the latter). Phylogenetic and functional traits had a certain relationship but changed according to different rules. These results enhance our understanding of the assembly mechanism of forest communities by considering both phylogenetic and functional traits.
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9
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Melo WA, Vieira LD, Novaes E, Bacon CD, Collevatti RG. Selective Sweeps Lead to Evolutionary Success in an Amazonian Hyperdominant Palm. Front Genet 2020; 11:596662. [PMID: 33424928 PMCID: PMC7786001 DOI: 10.3389/fgene.2020.596662] [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: 08/20/2020] [Accepted: 11/18/2020] [Indexed: 01/21/2023] Open
Abstract
Despite the global importance of tropical ecosystems, few studies have identified how natural selection has shaped their megadiversity. Here, we test for the role of adaptation in the evolutionary success of the widespread, highly abundant Neotropical palm Mauritia flexuosa. We used a genome scan framework, sampling 16,262 single-nucleotide polymorphisms (SNPs) with target sequence capture in 264 individuals from 22 populations in rainforest and savanna ecosystems. We identified outlier loci as well as signal of adaptation using Bayesian correlations of allele frequency with environmental variables and detected both selective sweeps and genetic hitchhiking events. Functional annotation of SNPs with selection footprints identified loci affecting genes related to adaptation to environmental stress, plant development, and primary metabolic processes. The strong differences in climatic and soil variables between ecosystems matched the high differentiation and low admixture in population Bayesian clustering. Further, we found only small differences in allele frequency distribution in loci putatively under selection among widespread populations from different ecosystems, with fixation of a single allele in most populations. Taken together, our results indicate that adaptive selective sweeps related to environmental stress shaped the spatial pattern of genetic diversity in M. flexuosa, leading to high similarity in allele frequency among populations from different ecosystems.
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Affiliation(s)
- Warita A Melo
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Lucas D Vieira
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Evandro Novaes
- Departamento de Biologia, Universidade Federal de Lavras, Lavras, Brazil
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Rosane G Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
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10
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Saladin B, Pellissier L, Graham CH, Nobis MP, Salamin N, Zimmermann NE. Rapid climate change results in long-lasting spatial homogenization of phylogenetic diversity. Nat Commun 2020; 11:4663. [PMID: 32938914 PMCID: PMC7495423 DOI: 10.1038/s41467-020-18343-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/14/2020] [Indexed: 11/09/2022] Open
Abstract
Scientific understanding of biodiversity dynamics, resulting from past climate oscillations and projections of future changes in biodiversity, has advanced over the past decade. Little is known about how these responses, past or future, are spatially connected. Analyzing the spatial variability in biodiversity provides insight into how climate change affects the accumulation of diversity across space. Here, we evaluate the spatial variation of phylogenetic diversity of European seed plants among neighboring sites and assess the effects of past rapid climate changes during the Quaternary on these patterns. Our work shows a marked homogenization in phylogenetic diversity across Central and Northern Europe linked to high climate change velocity and large distances to refugia. Our results suggest that the future projected loss in evolutionary heritage may be even more dramatic, as homogenization in response to rapid climate change has occurred among sites across large landscapes, leaving a legacy that has lasted for millennia. How past climate change has affected biodiversity over large spatial scales remains underexplored. Here, the authors find marked homogenization in flowering plant phylogenetic diversity across Central and Northern Europe linked to rapid climate change and large distances to glacial refugia.
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Affiliation(s)
- Bianca Saladin
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland.
| | - Loïc Pellissier
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland.,Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, 8092, Zurich, Switzerland
| | | | - Michael P Nobis
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
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11
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Trethowan LA, Eiserhardt WL, Girmansyah D, Kintamani E, Utteridge TM, Brearley FQ. Floristics of forests across low nutrient soils in Sulawesi, Indonesia. Biotropica 2020. [DOI: 10.1111/btp.12838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Liam A. Trethowan
- Manchester Metropolitan University Manchester UK
- Royal Botanic Gardens Kew London UK
| | | | - Deden Girmansyah
- Herbarium Bogoriense Indonesian Institute of Sciences Cibinong Indonesia
| | - Endang Kintamani
- Herbarium Bogoriense Indonesian Institute of Sciences Cibinong Indonesia
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12
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Barrett CF, McKain MR, Sinn BT, Ge XJ, Zhang Y, Antonelli A, Bacon CD. Ancient Polyploidy and Genome Evolution in Palms. Genome Biol Evol 2019; 11:1501-1511. [PMID: 31028709 PMCID: PMC6535811 DOI: 10.1093/gbe/evz092] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2019] [Indexed: 12/23/2022] Open
Abstract
Mechanisms of genome evolution are fundamental to our understanding of adaptation and the generation and maintenance of biodiversity, yet genome dynamics are still poorly characterized in many clades. Strong correlations between variation in genomic attributes and species diversity across the plant tree of life suggest that polyploidy or other mechanisms of genome size change confer selective advantages due to the introduction of genomic novelty. Palms (order Arecales, family Arecaceae) are diverse, widespread, and dominant in tropical ecosystems, yet little is known about genome evolution in this ecologically and economically important clade. Here, we take a phylogenetic comparative approach to investigate palm genome dynamics using genomic and transcriptomic data in combination with a recent, densely sampled, phylogenetic tree. We find conclusive evidence of a paleopolyploid event shared by the ancestor of palms but not with the sister clade, Dasypogonales. We find evidence of incremental chromosome number change in the palms as opposed to one of recurrent polyploidy. We find strong phylogenetic signal in chromosome number, but no signal in genome size, and further no correlation between the two when correcting for phylogenetic relationships. Palms thus add to a growing number of diverse, ecologically successful clades with evidence of whole-genome duplication, sister to a species-poor clade with no evidence of such an event. Disentangling the causes of genome size variation in palms moves us closer to understanding the genomic conditions facilitating adaptive radiation and ecological dominance in an evolutionarily successful, emblematic tropical clade.
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Affiliation(s)
| | | | | | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Yuqu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Royal Botanical Gardens Kew, Richmond, United Kingdom
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
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Muscarella R, Bacon CD, Faurby S, Antonelli A, Kristiansen SM, Svenning JC, Balslev H. Soil fertility and flood regime are correlated with phylogenetic structure of Amazonian palm communities. ANNALS OF BOTANY 2019; 123:641-655. [PMID: 30395146 PMCID: PMC6417467 DOI: 10.1093/aob/mcy196] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/05/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Identifying the processes that generate and maintain biodiversity requires understanding of how evolutionary processes interact with abiotic conditions to structure communities. Edaphic gradients are strongly associated with floristic patterns but, compared with climatic gradients, have received relatively little attention. We asked (1) How does the phylogenetic composition of palm communities vary along edaphic gradients within major habitat types? and (2) To what extent are phylogenetic patterns determined by (a) habitat specialists, (b) small versus large palms, and (c) hyperdiverse genera? METHODS We paired data on palm community composition from 501 transects of 0.25 ha located in two main habitat types (non-inundated uplands and seasonally inundated floodplains) in western Amazonian rain forests with information on soil chemistry, climate, phylogeny and metrics of plant size. We focused on exchangeable base concentration (cmol+ kg-1) as a metric of soil fertility and a floristic index of inundation intensity. We used a null model approach to quantify the standard effect size of mean phylogenetic distance for each transect (a metric of phylogenetic community composition) and related this value to edaphic variables using generalized linear mixed models, including a term for spatial autocorrelation. KEY RESULTS Overall, we recorded 112 008 individuals belonging to 110 species. Palm communities in non-inundated upland transects (but not floodplain transects) were more phylogenetically clustered in areas of low soil fertility, measured as exchangeable base concentration. In contrast, floodplain transects with more severe flood regimes (as inferred from floristic structure) tended to be phylogenetically clustered. Nearly half of the species recorded (44 %) were upland specialists while 18 % were floodplain specialists. In both habitat types, phylogenetic clustering was largely due to the co-occurrence of small-sized habitat specialists belonging to two hyperdiverse genera (Bactris and Geonoma). CONCLUSIONS Edaphic conditions are associated with the phylogenetic community structure of palms across western Amazonia, and different factors (specifically, soil fertility and inundation intensity) appear to underlie diversity patterns in non-inundated upland versus floodplain habitats. By linking edaphic gradients with palm community phylogenetic structure, our study reinforces the need to integrate edaphic conditions in eco-evolutionary studies in order to better understand the processes that generate and maintain tropical forest diversity. Our results suggest a role for edaphic niche conservatism in the evolution and distribution of Amazonian palms, a finding with potential relevance for other clades.
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Affiliation(s)
- Robert Muscarella
- Department of Bioscience, Section for Ecoinformatics & Biodiversity, Aarhus University, Aarhus, Denmark
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Gothenburg Botanical Garden, Gothenburg, Sweden
| | | | - Jens-Christian Svenning
- Department of Bioscience, Section for Ecoinformatics & Biodiversity, Aarhus University, Aarhus, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Aarhus University, Aarhus, Denmark
| | - Henrik Balslev
- Department of Bioscience, Section for Ecoinformatics & Biodiversity, Aarhus University, Aarhus, Denmark
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Freitas CG, Bacon CD, Souza-Neto AC, Collevatti RG. Adjacency and Area Explain Species Bioregional Shifts in Neotropical Palms. FRONTIERS IN PLANT SCIENCE 2019; 10:55. [PMID: 30804955 PMCID: PMC6370682 DOI: 10.3389/fpls.2019.00055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 01/16/2019] [Indexed: 06/09/2023]
Abstract
Environmental and geographical variables are known drivers of community assembly, however their influence on phylogenetic structure and phylogenetic beta diversity of lineages within different bioregions is not well-understood. Using Neotropical palms as a model, we investigate how environmental and geographical variables affect the assembly of lineages into bioregions across an evolutionary time scale. We also determine lineage shifts between tropical (TRF) and non-tropical (non-TRF) forests. Our results identify that distance and area explain phylogenetic dissimilarity among bioregions. Lineages in smaller bioregions are a subset of larger bioregions and contribute significantly to the nestedness component of phylogenetic dissimilarity, here interpreted as evidence for a bioregional shift. We found a significant tendency of habitat shifts occurring preferentially between TRF and non-TRF bioregions (31 shifts) than from non-TRF to TRF (24) or from TRF to TRF (11) and non-TRF to non-TRF (9). Our results also present cases where low dissimilarity is found between TRF and non-TRF bioregions. Most bioregions showed phylogenetic clustering and larger bioregions tended to be more clustered than smaller ones, with a higher species turnover component of phylogenetic dissimilarity. However, phylogenetic structure did not differ between TRF and non-TRF bioregions and diversification rates were higher in only two lineages, Attaleinae and Bactridinae, which are widespread and overabundant in both TRF and non-TRF bioregions. Area and distance significantly affected Neotropical palm community assembly and contributed more than environmental variables. Despite palms being emblematic humid forest elements, we found multiple shifts from humid to dry bioregions, showing that palms are also important components of these environments.
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Affiliation(s)
- Cintia G. Freitas
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Christine D. Bacon
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Advaldo C. Souza-Neto
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Rosane G. Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
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15
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Saladin B, Thuiller W, Graham CH, Lavergne S, Maiorano L, Salamin N, Zimmermann NE. Environment and evolutionary history shape phylogenetic turnover in European tetrapods. Nat Commun 2019; 10:249. [PMID: 30651566 PMCID: PMC6335467 DOI: 10.1038/s41467-018-08232-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 12/21/2018] [Indexed: 11/09/2022] Open
Abstract
Phylogenetic turnover quantifies the evolutionary distance among species assemblages and is central to understanding the main drivers shaping biodiversity. It is affected both by geographic and environmental distance between sites. Therefore, analyzing phylogenetic turnover in environmental space requires removing the effect of geographic distance. Here, we apply a novel approach by deciphering phylogenetic turnover of European tetrapods in environmental space after removing geographic land distance effects. We demonstrate that phylogenetic turnover is strongly structured in environmental space, particularly in ectothermic tetrapods, and is well explained by macroecological characteristics such as niche size, species richness and relative phylogenetic diversity. In ectotherms, rather recent evolutionary processes were important in structuring phylogenetic turnover along environmental gradients. In contrast, early evolutionary processes had already shaped the current structure of phylogenetic turnover in endotherms. Our approach enables the disentangling of the idiosyncrasies of evolutionary processes such as the degree of niche conservatism and diversification rates in structuring biodiversity.
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Affiliation(s)
- Bianca Saladin
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland.
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Écologie Alpine, F-38000, Grenoble, France
| | | | - Sébastien Lavergne
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Écologie Alpine, F-38000, Grenoble, France
| | - Luigi Maiorano
- Dipartimento di Biologia e Biotechnologie 'Charles Darwin', Università di Roma 'La Sapienza', 00185, Roma, Italy
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland
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16
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Pashirzad M, Ejtehadi H, Vaezi J, Shefferson RP. Spatial scale-dependent phylogenetic signal in species distributions along geographic and elevation gradients in a mountainous rangeland. Ecol Evol 2018; 8:10364-10373. [PMID: 30464810 PMCID: PMC6238123 DOI: 10.1002/ece3.4293] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/01/2018] [Accepted: 05/16/2018] [Indexed: 11/09/2022] Open
Abstract
The mechanisms determining community phylogenetic structure range from local ecological mechanisms to broad biogeographical processes. How these community assembly processes determine phylogenetic structure and patterns in rangeland communities across multiple spatial scales is still poorly understood. We sought to determine whether the structure of herbaceous and shrub assemblages along local environmental gradients (elevation) and broad geography (latitude) exhibited phylogenetic signal at different spatial scales, across 2,500 ha of a mountainous rangeland. We analyzed species distribution and phylogenetic data at two spatial scales: the community level (1 m2 sample units obtained by stratified random sampling) and the habitat level (plant assemblages identified categorically based on environmental and geographical variables). We found significant phylogenetic signal in structure and pattern at both spatial scales, along local elevational, and latitudinal gradients. Moreover, beta diversity was affected by different environmental variables in herbaceous and shrub species distributions across different spatial scales. Our results highlight the relative importance of local ecological mechanisms, including niche-based deterministic processes (environmental filtering and species interactions) as well as those of biogeographical processes, such as stochastic dispersal limitation and habitat specialization in plant assemblages of mountainous rangeland.
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Affiliation(s)
- Maral Pashirzad
- Department of BiologyFaculty of SciencesFerdowsi University of MashhadMashhadIran
| | - Hamid Ejtehadi
- Department of BiologyFaculty of SciencesFerdowsi University of MashhadMashhadIran
| | - Jamil Vaezi
- Department of BiologyFaculty of SciencesFerdowsi University of MashhadMashhadIran
| | - Richard P. Shefferson
- Organization for Programs on Environmental Sciences, Faculty of Arts & SciencesUniversity of TokyoTokyoJapan
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17
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Chun JH, Lee CB. Disentangling the local-scale drivers of taxonomic, phylogenetic and functional diversity in woody plant assemblages along elevational gradients in South Korea. PLoS One 2017; 12:e0185763. [PMID: 28968448 PMCID: PMC5624625 DOI: 10.1371/journal.pone.0185763] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 09/19/2017] [Indexed: 11/19/2022] Open
Abstract
Recently, new alternative matrices of biodiversity such as phylogenetic and functional diversity as a complement to species diversity have provided new insights into the mechanisms of community assembly. In this study, we analyzed the phylogenetic signals of five functional traits and the relative contribution of environmental variables and distance matrices to the alpha and beta components of taxonomic, phylogenetic and functional diversity in woody plant assemblages along four local elevational transects on two different mountains. We observed low but significant phylogenetic signals of functional traits, which suggest that phylogenetic dispersion can provide a rough approximation of functional dispersion but not perfect correlations between phylogenetic and functional diversity. Taxonomic alpha diversity showed a monotonic decline with elevation, and climatic variables were the main drivers of this pattern along all studied transects. Furthermore, although the phylogenetic and functional alpha dispersions showed different elevational patterns including increase, decrease and no relationship, the underlying processes driving the patterns of both types of alpha dispersion could be explained by the gradients of climatic and habitat variables as well as biotic interactions such as competition. These results suggest that both alpha dispersion patterns may be significantly controlled by niche-based deterministic processes such as biotic interactions and environmental filtering in our study areas. Moreover, the beta diversity with geographical distances showed distance-decay relationships for all transects. Although the relative importance of the environmental and geographical distances for beta diversity varied across the three facets of diversity and the transects, we generally found that environmental distances were more important for the beta components of the three facets of diversity. However, we cannot discriminate the effects of both distances on the three facets of diversity. Therefore, our study suggests that niche-based deterministic processes, potentially combined with neutral processes such as dispersal limitation and demographic stochasticity, may influence patterns of woody plant assemblage turnover in our study areas.
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Affiliation(s)
- Jung-Hwa Chun
- Division of Forest Ecology, National Institute of Forest Science, Dongdaemungu, Seoul, Republic of Korea
| | - Chang-Bae Lee
- Global Resources Division, Korea Forestry Promotion Institute, Gangseogu, Seoul, Republic of Korea
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18
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Aldana AM, Carlucci MB, Fine PVA, Stevenson PR. Environmental filtering of eudicot lineages underlies phylogenetic clustering in tropical South American flooded forests. Oecologia 2016; 183:327-335. [PMID: 27665543 DOI: 10.1007/s00442-016-3734-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 09/12/2016] [Indexed: 11/30/2022]
Abstract
The phylogenetic community assembly approach has been used to elucidate the role of ecological and historical processes in shaping tropical tree communities. Recent studies have shown that stressful environments, such as seasonally dry, white-sand and flooded forests tend to be phylogenetically clustered, arguing for niche conservatism as the main driver for this pattern. Very few studies have attempted to identify the lineages that contribute to such assembly patterns. We aimed to improve our understanding of the assembly of flooded forest tree communities in Northern South America by asking the following questions: are seasonally flooded forests phylogenetically clustered? If so, which angiosperm lineages are over-represented in seasonally flooded forests? To assess our hypotheses, we investigated seasonally flooded and terra firme forests from the Magdalena, Orinoco and Amazon Basins, in Colombia. Our results show that, regardless of the river basin in which they are located, seasonally flooded forests of Northern South America tend to be phylogenetically clustered, which means that the more abundant taxa in these forests are more closely related to each other than expected by chance. Based on our alpha and beta phylodiversity analyses we interpret that eudicots are more likely to adapt to extreme environments such as seasonally flooded forests, which indicates the importance of environmental filtering in the assembly of the Neotropical flora.
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Affiliation(s)
- Ana M Aldana
- Departamento de Ciencias Biológicas, Universidad de los Andes, Carrera 1 No. 18A-10, Bogotá D.C., Colombia.
| | - Marcos B Carlucci
- Programa de Pós-Graduação em Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil.,CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, 70040-020, Brazil
| | - Paul V A Fine
- Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, CA, 94720, USA
| | - Pablo R Stevenson
- Departamento de Ciencias Biológicas, Universidad de los Andes, Carrera 1 No. 18A-10, Bogotá D.C., Colombia
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Chai Y, Yue M, Liu X, Guo Y, Wang M, Xu J, Zhang C, Chen Y, Zhang L, Zhang R. Patterns of taxonomic, phylogenetic diversity during a long-term succession of forest on the Loess Plateau, China: insights into assembly process. Sci Rep 2016; 6:27087. [PMID: 27272407 PMCID: PMC4897607 DOI: 10.1038/srep27087] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 05/09/2016] [Indexed: 11/09/2022] Open
Abstract
Quantifying the drivers underlying the distribution of biodiversity during succession is a critical issue in ecology and conservation, and also can provide insights into the mechanisms of community assembly. Ninety plots were established in the Loess Plateau region of northern Shaanxi in China. The taxonomic and phylogenetic (alpha and beta) diversity were quantified within six succession stages. Null models were used to test whether phylogenetic distance observed differed from random expectations. Taxonomic beta diversity did not show a regular pattern, while phylogenetic beta diversity decreased throughout succession. The shrub stage occurred as a transition from phylogenetic overdispersion to clustering either for NRI (Net Relatedness Index) or betaNRI. The betaNTI (Nearest Taxon Index) values for early stages were on average phylogenetically random, but for the betaNRI analyses, these stages were phylogenetically overdispersed. Assembly of woody plants differed from that of herbaceous plants during late community succession. We suggest that deterministic and stochastic processes respectively play a role in different aspects of community phylogenetic structure for early succession stage, and that community composition of late succession stage is governed by a deterministic process. In conclusion, the long-lasting evolutionary imprints on the present-day composition of communities arrayed along the succession gradient.
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Affiliation(s)
- Yongfu Chai
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Taibai north Rd.229, Xi'an City, Shaanxi Province, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Taibai north Rd.229, Xi'an City, Shaanxi Province, China
| | - Xiao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Taibai north Rd.229, Xi'an City, Shaanxi Province, China
| | - Yaoxin Guo
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Taibai north Rd.229, Xi'an City, Shaanxi Province, China
| | - Mao Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Taibai north Rd.229, Xi'an City, Shaanxi Province, China
| | - Jinshi Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Taibai north Rd.229, Xi'an City, Shaanxi Province, China
| | - Chenguang Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Taibai north Rd.229, Xi'an City, Shaanxi Province, China
| | - Yu Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Taibai north Rd.229, Xi'an City, Shaanxi Province, China
| | - Lixia Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Taibai north Rd.229, Xi'an City, Shaanxi Province, China
| | - Ruichang Zhang
- Plant Ecology Department, University of Tuebingen, Auf der Morgenstelle 3, 72076 Tuebingen, Germany
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20
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Matuszak S, Favre A, Schnitzler J, Muellner-Riehl AN. Key innovations and climatic niche divergence as drivers of diversification in subtropical Gentianinae in southeastern and eastern Asia. AMERICAN JOURNAL OF BOTANY 2016; 103:899-911. [PMID: 27208358 DOI: 10.3732/ajb.1500352] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 04/11/2016] [Indexed: 05/16/2023]
Abstract
PREMISE OF THE STUDY Geological and climatic changes associated with the uplift of the Qinghai-Tibet Plateau (QTP) have been suggested as drivers for biological diversification locally and in neighboring regions. To test this hypothesis, we investigated the niche evolution of Tripterospermum (Gentianaceae) and related Asian genera through time. METHODS We conducted Species Distribution Modeling using Maximum Entropy Modeling (MaxEnt). Furthermore, we performed stochastic character mapping and produced disparity-through-time plots, and examined putative key innovations using the binary state speciation and extinction approach (BISSE). KEY RESULTS Kuepferia and Sinogentiana prefer the coolest and driest habitat, having rather conserved niches. Despite a tendency for niche evolution, Crawfurdia and Metagentiana are probably restricted to a narrow distribution range because of their poor dispersal ability. In contrast, Tripterospermum has the broadest niche and occurs under the warmest and wettest conditions. A higher degree of niche evolution and a more efficient dispersal mechanism allowed this genus to diversify more and occupy a broader distribution range. CONCLUSIONS The QTP genera producing dry capsules, whether displaying niche conservatism (Kuepferia and Sinogentiana) or a tendency for niche evolution (Crawfurdia and Metagentiana), are less species-rich and have a more restricted distribution than Tripterospermum (stronger niche evolution and berry-like fruits). The evolution of berry-like fruits corresponds to increased speciation rates, and could therefore be viewed as a key innovation. In contrast to the majority of studies on plants occurring around the QTP, we find that speciation was probably mediated by niche breadth and dispersal ability rather than geophysical changes.
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Affiliation(s)
- Sabine Matuszak
- Leipzig University, Institute of Biology, Department of Molecular Evolution and Plant Systematics & Herbarium Lipsiense (LZ), Johannisallee 21-23, D-04103 Leipzig, Germany Goethe University, Institute for Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60439 Frankfurt/Main, Germany Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Adrien Favre
- Leipzig University, Institute of Biology, Department of Molecular Evolution and Plant Systematics & Herbarium Lipsiense (LZ), Johannisallee 21-23, D-04103 Leipzig, Germany
| | - Jan Schnitzler
- Leipzig University, Institute of Biology, Department of Molecular Evolution and Plant Systematics & Herbarium Lipsiense (LZ), Johannisallee 21-23, D-04103 Leipzig, Germany Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Alexandra N Muellner-Riehl
- Leipzig University, Institute of Biology, Department of Molecular Evolution and Plant Systematics & Herbarium Lipsiense (LZ), Johannisallee 21-23, D-04103 Leipzig, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
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Jezkova T, Jaeger JR, Oláh-Hemmings V, Jones KB, Lara-Resendiz RA, Mulcahy DG, Riddle BR. Range and niche shifts in response to past climate change in the desert horned lizard ( Phrynosoma platyrhinos). ECOGRAPHY 2016; 39:437-448. [PMID: 27231410 PMCID: PMC4876873 DOI: 10.1111/ecog.01464] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/26/2015] [Indexed: 06/05/2023]
Abstract
During climate change, species are often assumed to shift their geographic distributions (geographic ranges) in order to track environmental conditions - niches - to which they are adapted. Recent work, however, suggests that the niches do not always remain conserved during climate change but shift instead, allowing populations to persist in place or expand into new areas. We assessed the extent of range and niche shifts in response to the warming climate after the Last Glacial Maximum (LGM) in the desert horned lizard (Phrynosoma platyrhinos), a species occupying the western deserts of North America. We used a phylogeographic approach with mitochondrial DNA sequences to approximate the species range during the LGM by identifying populations that exhibit a genetic signal of population stability versus those that exhibit a signal of a recent (likely post-LGM) geographic expansion. We then compared the climatic niche that the species occupies today with the niche it occupied during the LGM using two models of simulated LGM climate. The genetic analyses indicated that P. platyrhinos persisted within the southern Mojave and Sonoran deserts throughout the latest glacial period and expanded from these deserts northwards, into the western and eastern Great Basin, after the LGM. The climatic niche comparisons revealed that P. platyrhinos expanded its climatic niche after the LGM towards novel, warmer and drier climates that allowed it to persist within the southern deserts. Simultaneously, the species shifted its climatic niche towards greater temperature and precipitation fluctuations after the LGM. We concluded that climatic changes at the end of the LGM promoted both range and niche shifts in this lizard. The mechanism that allowed the species to shift its niche remains unknown, but phenotypic plasticity likely contributes to the species ability to adjust to climate change.
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Affiliation(s)
- Tereza Jezkova
- School of Life Sciences, University of Nevada, Las Vegas, 4505 South Maryland Parkway, Las Vegas, Nevada, 89154-4004, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, P.O. Box 210088, Tucson, Arizona, 85721–0088, USA
| | - Jef R. Jaeger
- School of Life Sciences, University of Nevada, Las Vegas, 4505 South Maryland Parkway, Las Vegas, Nevada, 89154-4004, USA
| | - Viktória Oláh-Hemmings
- School of Life Sciences, University of Nevada, Las Vegas, 4505 South Maryland Parkway, Las Vegas, Nevada, 89154-4004, USA
| | - K. Bruce Jones
- Desert Research Institute, Division of Earth and Ecosystem Sciences, 755 East Flamingo Road, Las Vegas, Nevada, 89119, USA
| | - Rafael A. Lara-Resendiz
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, California, 95064, USA
| | - Daniel G. Mulcahy
- Smithsonian Institution, PO Box 37012, MRC 162, Washington, DC, 20013-7012, USA
| | - Brett R. Riddle
- School of Life Sciences, University of Nevada, Las Vegas, 4505 South Maryland Parkway, Las Vegas, Nevada, 89154-4004, USA
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Neutral Theory Overestimates Extinction Times in Nonhuman Primates. INT J PRIMATOL 2015. [DOI: 10.1007/s10764-015-9854-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Norman AJ, Spong G. Single nucleotide polymorphism-based dispersal estimates using noninvasive sampling. Ecol Evol 2015; 5:3056-65. [PMID: 26357536 PMCID: PMC4559049 DOI: 10.1002/ece3.1588] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 02/06/2023] Open
Abstract
Quantifying dispersal within wild populations is an important but challenging task. Here we present a method to estimate contemporary, individual-based dispersal distance from noninvasively collected samples using a specialized panel of 96 SNPs (single nucleotide polymorphisms). One main issue in conducting dispersal studies is the requirement for a high sampling resolution at a geographic scale appropriate for capturing the majority of dispersal events. In this study, fecal samples of brown bear (Ursus arctos) were collected by volunteer citizens, resulting in a high sampling resolution spanning over 45,000 km2 in Gävleborg and Dalarna counties in Sweden. SNP genotypes were obtained for unique individuals sampled (n = 433) and subsequently used to reconstruct pedigrees. A Mantel test for isolation by distance suggests that the sampling scale was appropriate for females but not for males, which are known to disperse long distances. Euclidean distance was estimated between mother and offspring pairs identified through the reconstructed pedigrees. The mean dispersal distance was 12.9 km (SE 3.2) and 33.8 km (SE 6.8) for females and males, respectively. These results were significantly different (Wilcoxon’s rank-sum test: P-value = 0.02) and are in agreement with the previously identified pattern of male-biased dispersal. Our results illustrate the potential of using a combination of noninvasively collected samples at high resolution and specialized SNPs for pedigree-based dispersal models.
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Affiliation(s)
- Anita J Norman
- Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences SE-901 83, Umeå, Sweden
| | - Göran Spong
- Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences SE-901 83, Umeå, Sweden
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Park DS, Potter D. Why close relatives make bad neighbours: phylogenetic conservatism in niche preferences and dispersal disproves Darwin's naturalization hypothesis in the thistle tribe. Mol Ecol 2015; 24:3181-93. [DOI: 10.1111/mec.13227] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Daniel S. Park
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA 02138 USA
| | - Daniel Potter
- Department of Plant Sciences; University of California; Davis CA 95616 USA
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Couvreur TLP, Kissling WD, Condamine FL, Svenning JC, Rowe NP, Baker WJ. Global diversification of a tropical plant growth form: environmental correlates and historical contingencies in climbing palms. Front Genet 2015; 5:452. [PMID: 25620977 DOI: 10.3389/fgene.2014.00452] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 12/10/2014] [Indexed: 01/15/2023] Open
Abstract
Tropical rain forests (TRF) are the most diverse terrestrial biome on Earth, but the diversification dynamics of their constituent growth forms remain largely unexplored. Climbing plants contribute significantly to species diversity and ecosystem processes in TRF. We investigate the broad-scale patterns and drivers of species richness as well as the diversification history of climbing and non-climbing palms (Arecaceae). We quantify to what extent macroecological diversity patterns are related to contemporary climate, forest canopy height, and paleoclimatic changes. We test whether diversification rates are higher for climbing than non-climbing palms and estimate the origin of the climbing habit. Climbers account for 22% of global palm species diversity, mostly concentrated in Southeast Asia. Global variation in climbing palm species richness can be partly explained by past and present-day climate and rain forest canopy height, but regional differences in residual species richness after accounting for current and past differences in environment suggest a strong role of historical contingencies in climbing palm diversification. Climbing palms show a higher net diversification rate than non-climbers. Diversification analyses of palms detected a diversification rate increase along the branches leading to the most species-rich clade of climbers. Ancestral character reconstructions revealed that the climbing habit originated between early Eocene and Miocene. These results imply that changes from non-climbing to climbing habits may have played an important role in palm diversification, resulting in the origin of one fifth of all palm species. We suggest that, in addition to current climate and paleoclimatic changes after the late Neogene, present-day diversity of climbing palms can be explained by morpho-anatomical innovations, the biogeographic history of Southeast Asia, and/or ecological opportunities due to the diversification of high-stature dipterocarps in Asian TRFs.
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Affiliation(s)
- Thomas L P Couvreur
- Institut de Recherche pour le Développement, UMR-DIADE, Montpellier France ; Laboratoire de Botanique Systématique et d'Ecologie, Département des Sciences Biologiques, Université de Yaoundé I - Ecole Normale Supérieure, Yaoundé Cameroon
| | - W Daniel Kissling
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam Netherlands
| | - Fabien L Condamine
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg Sweden
| | - Jens-Christian Svenning
- Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Aarhus Denmark
| | - Nick P Rowe
- University Montpellier 2, Montpellier France ; CNRS, UMR AMAP, Montpellier France
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Chi X, Tang Z, Fang J. Patterns of phylogenetic beta diversity in China's grasslands in relation to geographical and environmental distance. Basic Appl Ecol 2014. [DOI: 10.1016/j.baae.2014.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Couvreur TLP, Baker WJ. Tropical rain forest evolution: palms as a model group. BMC Biol 2013; 11:48. [PMID: 23587415 PMCID: PMC3627317 DOI: 10.1186/1741-7007-11-48] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/12/2013] [Indexed: 11/11/2022] Open
Affiliation(s)
- Thomas L P Couvreur
- Institut de Recherche pour le Développement (IRD), UMR DIADE, 911, avenue Agropolis, BP 64501, F-34394 Montpellier cedex 5, France.
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