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Yang J, Wang Z, Pan Y, Zheng Y. Woody plant functional traits and phylogenetic signals correlate with urbanization in remnant forest patches. Ecol Evol 2023; 13:e10366. [PMID: 37529580 PMCID: PMC10388403 DOI: 10.1002/ece3.10366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 07/05/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023] Open
Abstract
Exploring the alterations in functional traits of urban remnant vegetation offers a more comprehensive perspective on plant assembly within the context of urbanization. While plant functional traits are influenced by both environmental gradients and the evolutionary history of plant species, the specific mechanisms by which urbanization mediates the combination of functional traits and the evolutionary history of remnant vegetation remain unclear. To examine the relationship between functional traits and phylogenies of remnant vegetation and urbanization, we classified the woody plant species surveyed in 72 sample plots in nine remnant forest patches in Guiyang, China, into four groups (urban, rural, middle and general groups) according to their location under different levels of urbanization and measured nine functional traits of these species. The phylogenetic signals of each functional trait of the four species groups were then quantified based on Blomberg's K. Furthermore, we analysed the correlations between functional traits and species abundance using phylogenetic generalized least squares. The results showed that significant phylogenetic signals were detected in more functional traits of the urban group than other groups. Thirteen and three significant relationships between functional traits and species abundance were detected for tree and shrub species after removing phylogenies. Tall tree species were more abundant in the urban group, while the general group favoured the species with adaptable traits (low height and high leaf area and C/N). Overall, we demonstrate that urbanization drove shifts in plant functional traits in remnant forests after combining the phylogenetic patterns.
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Affiliation(s)
- Jingyi Yang
- College of ForestryGuizhou UniversityGuiyangChina
| | - Zijin Wang
- College of ForestryGuizhou UniversityGuiyangChina
| | - Ying Pan
- College of ForestryGuizhou UniversityGuiyangChina
| | - Yanjun Zheng
- College of ForestryGuizhou UniversityGuiyangChina
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2
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Herzog SA, Latvis M. Community‐level phylogenetic diversity does not differ between rare and common lineages across tallgrass prairies in the northern Great Plains. Ecol Evol 2022; 12:e9453. [PMID: 36340814 PMCID: PMC9627050 DOI: 10.1002/ece3.9453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 11/07/2022] Open
Abstract
Niche differentiation has served as one explanation for species coexistence, and phylogenetic relatedness provides a means to approximate how ecologically similar species are to each other. To explore the contribution of rare species to community phylogenetic diversity, we sampled 21 plant communities across the Prairie Coteau ecoregion, an area of high conservation concern. We used breakpoint analysis through the iterative addition of less abundant species to the phylogenetic tree for each community to assess the contribution of rare species to community phylogenetic diversity. We also quantify the phylogenetic signal of abundance using Blomberg's K statistic and calculated the phylogenetic similarity between rare and common species using a phylogenetic beta‐diversity metric (Dnn). To estimate the phylogenetic structuring of these prairie communities, we calculated two common metrics that capture evolutionary relatedness at different scales (MPD and MNTD). Additionally, we examine the correlation between Faith's PD, MPD, and MNTD and species richness. We found rare species do not generally contribute higher levels of phylogenetic diversity than common species. Eight communities had significant breakpoints, with only four communities having an increasing trend for the rarest species. The phylogenetic signal for abundance was low but significant in only four communities, and communities had lower phylogenetic diversity than expected from the regional species pool. Finally, the strength of the correlation between species richness and phylogenetic diversity was mixed. Our results indicate niche differentiation does not explain the persistence of rare species in tallgrass prairies, as they were more closely related than expected from random, suggesting high functional redundancy between rare and common species. This is promising for the long‐term resilience of this ecosystem, but only insofar as enough species remain in the system. With ongoing biodiversity loss, it is essential that we understand the role rare species play in their communities.
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Affiliation(s)
- Sarah A. Herzog
- Department of Natural Resource ManagementSouth Dakota State UniversityBrookingsSouth DakotaUSA,C.A. Taylor HerbariumSouth Dakota State UniversityBrookingsSouth DakotaUSA,Division of BiologyKansas State UniversityManhattanKansasUSA
| | - Maribeth Latvis
- Department of Natural Resource ManagementSouth Dakota State UniversityBrookingsSouth DakotaUSA,C.A. Taylor HerbariumSouth Dakota State UniversityBrookingsSouth DakotaUSA
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3
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Sfair JC, Lososová Z, Chytrý M, de Bello F. Functional rarity and evolutionary uniqueness of threatened species across different scales and habitats in a Central European flora. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Júlia C. Sfair
- Department of Botany, Faculty of Science University of South Bohemia České Budějovice Czech Republic
- Department of Biology Federal University of Ceará – UFC Fortaleza CE Brazil
| | - Zdeňka Lososová
- Department of Botany and Zoology, Faculty of Science Masaryk University Brno Czech Republic
| | - Milan Chytrý
- Department of Botany and Zoology, Faculty of Science Masaryk University Brno Czech Republic
| | - Francesco de Bello
- Department of Botany, Faculty of Science University of South Bohemia České Budějovice Czech Republic
- Centro de Investigaciones sobre Desertificación (CSIC‐UV‐GV) Valencia Spain
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4
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Phylogenetic and Functional Structure of Wood Communities among Different Disturbance Regimes in a Temperate Mountain Forest. FORESTS 2022. [DOI: 10.3390/f13060896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mechanisms responsible for biodiversity formation and maintenance are central themes in biodiversity conservation. However, the relationships between community assembly, phylogeny, and functional traits remain poorly understood, especially following disturbance. In this study, we examined forest community assembly mechanisms in different disturbance regimes across spatial scales and including tree life history classes, using phylogenetic and functional trait metrics. Across disturbance regimes, phylogenetic structure tended to be over-dispersed, while functional structure tended to be clustered. The over-dispersion of phylogenetic structure also increased from small to large diameter species. Moreover, the explanation of spatial distance for the turnover of phylogenetic and functional structure was increased, while environmental distance explained less structure as disturbance intensity decreased. Our findings suggest that niche theory largely explains forest community assembly in different disturbance regimes. Furthermore, environmental filtering plays a major role in moderate to high disturbance regimes, while competitive exclusion is more important in undisturbed and slightly disturbed ecosystems.
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Miranda Cebrián H, Font X, Roquet C, Pizarro Gavilán M, García MB. Assessing the vulnerability of habitats through plant rarity patterns in the Pyrenean range. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Héctor Miranda Cebrián
- Pyrenean Institute of Ecology (CSIC) Zaragoza Spain
- Escuela Internacional de Doctorado Universidad Rey Juan Carlos Madrid Spain
| | - Xavier Font
- Plant Biodiversity Resource Center, University of Barcelona Barcelona Spain
| | - Cristina Roquet
- Facultat de Biociències, Departament de Biologia Animal, Biologia Vegetal I Ecologia Universitat Autònoma de Barcelona Bellaterra Spain
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Marques V, Castagné P, Polanco A, Borrero-Pérez GH, Hocdé R, Guérin PÉ, Juhel JB, Velez L, Loiseau N, Letessier TB, Bessudo S, Valentini A, Dejean T, Mouillot D, Pellissier L, Villéger S. Use of environmental DNA in assessment of fish functional and phylogenetic diversity. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:1944-1956. [PMID: 34224158 DOI: 10.1111/cobi.13802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/19/2021] [Accepted: 05/03/2021] [Indexed: 06/13/2023]
Abstract
Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long-term remote video to assess species' phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hr of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than species on video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hr of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded.
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Affiliation(s)
- Virginie Marques
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valery Montpellier 3, Montpellier, France
| | - Paul Castagné
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Andréa Polanco
- Instituto de Investigaciones Marinas y Costeras-INVEMAR, Colombia, Museo de Historia Natural Marina de Colombia (MHNMC), Programa de Biodiversidad y Ecosistemas Marinos, Santa Marta, Colombia
| | - Giomar Helena Borrero-Pérez
- Instituto de Investigaciones Marinas y Costeras-INVEMAR, Colombia, Museo de Historia Natural Marina de Colombia (MHNMC), Programa de Biodiversidad y Ecosistemas Marinos, Santa Marta, Colombia
| | - Régis Hocdé
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Pierre-Édouard Guérin
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valery Montpellier 3, Montpellier, France
| | | | - Laure Velez
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Nicolas Loiseau
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | | | - Sandra Bessudo
- Fundación Malpelo y Otros Ecosistemas Marinos, Bogotá, Colombia
| | | | | | - David Mouillot
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Loïc Pellissier
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
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Yin D, Liu Y, Ye Q, Cadotte MW, He F. Trait hierarchies are stronger than trait dissimilarities in structuring spatial co-occurrence patterns of common tree species in a subtropical forest. Ecol Evol 2021; 11:7366-7377. [PMID: 34188819 PMCID: PMC8216963 DOI: 10.1002/ece3.7567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/16/2021] [Accepted: 03/23/2021] [Indexed: 11/11/2022] Open
Abstract
The dissimilarity and hierarchy of trait values that characterize niche and fitness differences, respectively, have been increasingly applied to infer mechanisms driving community assembly and to explain species co-occurrence patterns. Here, we predict that limiting similarity should result in the spatial segregation of functionally similar species, while functionally similar species will be more likely to co-occur either due to environmental filtering or due to competitive exclusion of inferior competitors (hereafter hierarchical competition).We used a fully mapped 50-ha subtropical forest plot in southern China to explore how pairwise spatial associations between saplings and between adult trees were influenced by trait dissimilarity and hierarchy in order to gain insight into assembly mechanisms. We assessed pairwise spatial associations using two summary statistics of spatial point patterns at different spatial scales and compared the effects of trait dissimilarity and trait hierarchy of different functional traits on the interspecific spatial associations. These comparisons allow us to disentangle the effects of limiting similarity, environmental filtering, and hierarchical competition on species co-occurrence.We found that trait dissimilarity was generally negatively related to interspecific spatial associations for both saplings and adult trees across spatial scales, meaning that species with similar trait values were more likely to co-occur and thus supporting environmental filtering or hierarchical competition. We further found that trait hierarchy outweighed trait dissimilarity in structuring pairwise spatial associations, suggesting that hierarchical competition played a more important role in structuring our forest community than environmental filtering across life stages.This study employed a novel method, by offering the integration of pairwise spatial association and trait dissimilarity as well as trait hierarchy, to disentangle the relative importance of multiple assembly mechanisms in structuring co-occurrence patterns, especially the mechanisms of environmental filtering and hierarchical competition, which lead to indistinguishable co-occurrence patterns. This study also reinforced the importance of trait hierarchy rather than trait dissimilarity in driving neighborhood competition.
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Affiliation(s)
- Deyi Yin
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied BotanySouth China Botanical Garden, Chinese Academy of SciencesGuangzhouChina
- Center for Plant Ecology, Core Botanical GardenChinese Academy of SciencesGuangzhouChina
- Department of Biological SciencesUniversity of Toronto‐ScarboroughTorontoOntarioCanada
| | - Yu Liu
- ECNU‐Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecology and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Qing Ye
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied BotanySouth China Botanical Garden, Chinese Academy of SciencesGuangzhouChina
- Center for Plant Ecology, Core Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Marc W. Cadotte
- Department of Biological SciencesUniversity of Toronto‐ScarboroughTorontoOntarioCanada
- Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - Fangliang He
- ECNU‐Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecology and Environmental SciencesEast China Normal UniversityShanghaiChina
- Department of Renewable ResourcesUniversity of AlbertaEdmontonAlbertaCanada
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8
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Ibanez T, Ainsworth A, Gross J, Price JP, Webb EL, Hart PJ. Rarity patterns of woody plant species are associated with life form and diversification rates in Pacific islands forests. AMERICAN JOURNAL OF BOTANY 2021; 108:946-957. [PMID: 34160827 PMCID: PMC9328433 DOI: 10.1002/ajb2.1687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 02/08/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Rarity is a complex and central concept in ecology and conservation biology. Yet, it is still poorly understood why some species are rare and others common. Here, we aimed to understand the drivers of species rarity patterns in woody plant communities. METHODS We analyzed the local abundance and landscape frequency of 121 woody plant species across 238 plots on American Samoa and Hawaiian islands. We first assessed whether taxonomy, life form (shrub, small tree, large tree), and dispersal syndrome (dispersed by animals or by other means) are associated with the rarity of species. We then analyzed phylogenetic patterns in plant rarity and tested whether rarity patterns are associated with species evolutionary distinctiveness and the number of species within genera and families. RESULTS Large trees were less abundant but more frequent than shrub species. Animal-dispersed species tended to be less abundant than species dispersed by other means, while species frequency was not associated with dispersal syndromes. Relative frequency in Hawai'i exhibited a more robust phylogenetic signal than did abundance. Both evolutionary distinctiveness and taxa species richness were significantly associated with the frequency of shrub species in Hawai'i. CONCLUSIONS Life form appears consistently associated with the rarity of species. High diversification rate is probably a key factor explaining landscape-scale rarity of native species on isolated archipelagos like Hawai'i. At the landscape scale, rarity appears to be inversely associated with evolutionary distinctiveness, but at the local scale, species abundance may be not associated with evolutionary distinctiveness.
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Affiliation(s)
- Thomas Ibanez
- Department of BiologyUniversity of Hawai'i at Hilo200 West Kawili StreetHiloHI96712USA
- Present address:
AMAPUniv MontpellierCIRADCNRSINRAEIRDMontpellierFrance
| | - Alison Ainsworth
- National Park Service, Inventory and Monitoring Program, Pacific Island NetworkP.O. Box 52Hawai'i Volcanoes National ParkHI96718USA
| | - Jacob Gross
- National Park Service, Inventory and Monitoring Program, Pacific Island NetworkP.O. Box 52Hawai'i Volcanoes National ParkHI96718USA
| | - Jonathan P. Price
- Department of Geography and Environmental StudiesUniversity of Hawai'i at Hilo200 West Kawili StreetHiloHI96712USA
| | - Edward L. Webb
- Department of Biological SciencesNational University of Singapore14 Science Drive 4117543Singapore
| | - Patrick J. Hart
- Department of BiologyUniversity of Hawai'i at Hilo200 West Kawili StreetHiloHI96712USA
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9
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Gheyret G, Guo Y, Fang J, Tang Z. Latitudinal and elevational patterns of phylogenetic structure in forest communities in China's mountains. SCIENCE CHINA. LIFE SCIENCES 2020; 63:1895-1904. [PMID: 32382981 DOI: 10.1007/s11427-019-1663-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/23/2020] [Indexed: 11/29/2022]
Abstract
The phylogenetic structure incorporates both ecological and evolutionary processes to explain assembly of a local community. The "phylogenetic niche conservatism" (PNC) hypothesis suggests that distributions of species along environmental gradients reflect both ancestral traits and ecological fitness of individual species The temperature is generally regarded to change in similar ways along both latitudinal and elevational gradients but with different historical contingence. Therefore, comparing the latitudinal and elevational patterns of phylogenetic structure of communities is of help to depict the effects of ecological and evolutionary processes in shaping the community assembly. In this study, we explored the latitudinal, elevational and climatic patterns of phylogenetic structure of 569 angiosperm tree communities from 38 mountains across China. We found a larger mean abundance-weighted net relatedness index (NRI) than the presence/absence-based NRI; and the NRI decreased when the species pool downscaled from the full pool to county-level pool. The mean family age and phylogenetic species evenness decreased with latitude, and increased with temperature of the coldest month and precipitation; whilst NRI increased with latitude, and decreased with mean temperature of the coldest month. In most mountains, NRI, mean family age and phylogenetic species evenness showed non-significant trends along the elevational gradient. Our results support the main predictions of PNC for the latitudinal gradient, i.e., species tend to be more phylogenetically related to each other and clades are younger in temperate environments, compared to those in tropical environments. We suggested that independent species pools and abundance should be incorporated in analysis to fully represent the phylogenetic structure of communities.
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Affiliation(s)
- Gheyur Gheyret
- Institute of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of Ministry of Education, Peking University, Beijing, 100871, China
| | - Yanpei Guo
- Institute of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of Ministry of Education, Peking University, Beijing, 100871, China
| | - Jingyun Fang
- Institute of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of Ministry of Education, Peking University, Beijing, 100871, China
| | - Zhiyao Tang
- Institute of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of Ministry of Education, Peking University, Beijing, 100871, China.
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10
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Mi X, Sun Z, Song Y, Liu X, Yang J, Wu J, Ci X, Li J, Lin L, Cao M, Ma K. Rare tree species have narrow environmental but not functional niches. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiangcheng Mi
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
| | - Zhenhua Sun
- Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of Sciences Kunming China
| | - Yunfeng Song
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
| | - Xiaojuan Liu
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
| | - Jie Yang
- Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of Sciences Kunming China
- Southeast Asia Biodiversity Research InstituteChinese Academy of Sciences Menglun China
| | - Junjie Wu
- Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of Sciences Kunming China
| | - Xiuqin Ci
- Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of Sciences Kunming China
| | - Jie Li
- Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of Sciences Kunming China
| | - Luxiang Lin
- Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of Sciences Kunming China
- Southeast Asia Biodiversity Research InstituteChinese Academy of Sciences Menglun China
| | - Min Cao
- Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of Sciences Kunming China
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
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11
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Moss C, Lukac M, Harris F, Outhwaite CL, Scheelbeek PFD, Green R, Berstein FM, Dangour AD. The effects of crop diversity and crop type on biological diversity in agricultural landscapes: a systematic review protocol. Wellcome Open Res 2020; 4:101. [PMID: 32509965 PMCID: PMC7241271 DOI: 10.12688/wellcomeopenres.15343.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2020] [Indexed: 11/30/2022] Open
Abstract
Agricultural intensification is a well-known driver of biodiversity loss. Crop diversity and its changes over space and time drive land use intensity and impact biodiversity of agricultural landscapes, while meeting the growing demand for human food and nutrition resources. Loss of biodiversity in agricultural landscapes reduces primary productivity and soil health and erodes a range of other ecosystem services. At present, while having partial understanding of many processes, we lack a general synthesis of our knowledge of the links between crop diversity and biodiversity. We will therefore conduct a systematic review by searching multiple agriculture, ecology and environmental science databases (e.g. Web of Science, Geobase, Agris, AGRICOLA, GreenFILE) to identify studies reporting the impacts of crop diversity and crop type on the biological diversity of fauna and flora in agricultural landscapes. Response variables will include metrics of species richness, abundance, assemblage, community composition and species rarity. Screening, data coding and data extraction will be carried out by one researcher and a subset will be independently carried out by a second researcher for quality control. Study quality and risk of bias will be assessed. Evidence will first be mapped to species/taxa then assessed for further narrative or statistical synthesis based on comparability of results and likely robustness. Gaps in the evidence base will also be identified with a view toward future research and policy directions for nutrition, food systems and ecology.
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Affiliation(s)
- Cami Moss
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.,Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Martin Lukac
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR, UK
| | - Francesca Harris
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.,Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Charlotte L Outhwaite
- Centre for Biodiversity and Environment Research, University College London, London, WC1E 6BT, UK
| | - Pauline F D Scheelbeek
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.,Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Rosemary Green
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.,Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Fernanda Morales Berstein
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Alan D Dangour
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.,Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
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12
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Haug I, Setaro S, Suárez JP. Species composition of arbuscular mycorrhizal communities changes with elevation in the Andes of South Ecuador. PLoS One 2019; 14:e0221091. [PMID: 31419262 PMCID: PMC6697372 DOI: 10.1371/journal.pone.0221091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 07/30/2019] [Indexed: 12/24/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are the most prominent mycobionts of plants in the tropics, yet little is known about their diversity, species compositions and factors driving AMF distribution patterns. To investigate whether elevation and associated vegetation type affect species composition, we sampled 646 mycorrhizal samples in locations between 1000 and 4000 m above sea level (masl) in the South of Ecuador. We estimated diversity, distribution and species compositions of AMF by cloning and Sanger sequencing the 18S rDNA (the section between AML1 and AML2) and subsequent derivation of fungal OTUs based on 99% sequence similarity. In addition, we analyzed the phylogenetic structure of the sites by computing the mean pairwise distance (MPD) and the mean nearest taxon difference (MNTD) for each elevation level. It revealed that AMF species compositions at 1000 and 2000 masl differ from 3000 and 4000 masl. Lower elevations (1000 and 2000 masl) were dominated by members of Glomeraceae, whereas Acaulosporaceae were more abundant in higher elevations (3000 and 4000 masl). Ordination of OTUs with respect to study sites revealed a correlation to elevation with a continuous turnover of species from lower to higher elevations. Most of the abundant OTUs are not endemic to South Ecuador. We also found a high proportion of rare OTUs at all elevations: 79-85% of OTUs occurred in less than 5% of the samples. Phylogenetic community analysis indicated clustering and evenness for most elevation levels indicating that both, stochastic processes and habitat filtering are driving factors of AMF community compositions.
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Affiliation(s)
- Ingeborg Haug
- Evolutionary Ecology of Plants, Eberhard-Karls-University, Tübingen, Germany
| | - Sabrina Setaro
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Juan Pablo Suárez
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
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13
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Kondratyeva A, Grandcolas P, Pavoine S. Reconciling the concepts and measures of diversity, rarity and originality in ecology and evolution. Biol Rev Camb Philos Soc 2019; 94:1317-1337. [PMID: 30861626 PMCID: PMC6850657 DOI: 10.1111/brv.12504] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 12/29/2022]
Abstract
The concept of biological diversity, or biodiversity, is at the core of evolutionary and ecological studies. Many indices of biodiversity have been developed in the last four decades, with species being one of the central units of these indices. However, evolutionary and ecological studies need a precise description of species' characteristics to best quantify inter-species diversity, as species are not equivalent and exchangeable. One of the first concepts characterizing species in biodiversity studies was abundance-based rarity. Abundance-based rarity was then complemented by trait- and phylo-based rarity, called species' trait-based and phylogenetic originalities, respectively. Originality, which is a property of an individual species, represents a species' contribution to the overall diversity of a reference set of species. Originality can also be defined as the rarity of a species' characteristics such as the state of a functional trait, which is often assumed to be represented by the position of the species on a phylogenetic tree. We review and compare various approaches for measuring originality, rarity and diversity and demonstrate that (i) even if attempts to bridge these concepts do exist, only a few ecological and evolutionary studies have tried to combine them all in the past two decades; (ii) phylo- and trait-based diversity indices can be written as a function of species rarity and originality measures in several ways; and (iii) there is a need for the joint use of these three types of indices to understand community assembly processes and species' roles in ecosystem functioning in order to protect biodiversity efficiently.
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Affiliation(s)
- Anna Kondratyeva
- Centre d'Ecologie et des Sciences de la Conservation (CESCO), Département Homme et Environnement, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, 57 Rue Cuvier, CP 135, 75005ParisFrance
- Institut Systématique Evolution Biodiversité (ISYEB), Département Origines et Evolution, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université EPHE, 57 Rue Cuvier, CP 50, 75005ParisFrance
| | - Philippe Grandcolas
- Institut Systématique Evolution Biodiversité (ISYEB), Département Origines et Evolution, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université EPHE, 57 Rue Cuvier, CP 50, 75005ParisFrance
| | - Sandrine Pavoine
- Centre d'Ecologie et des Sciences de la Conservation (CESCO), Département Homme et Environnement, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, 57 Rue Cuvier, CP 135, 75005ParisFrance
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14
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Moss C, Lukac M, Harris F, Outhwaite CL, Scheelbeek PF, Green R, Dangour AD. The effects of crop diversity and crop species on biological diversity in agricultural landscapes: a systematic review protocol. Wellcome Open Res 2019; 4:101. [DOI: 10.12688/wellcomeopenres.15343.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2019] [Indexed: 01/01/2023] Open
Abstract
Agricultural intensification is a well-known driver of biodiversity loss. Diversity of crop production over space and time reduces land use intensity and may mitigate impacts on biodiversity while contributing to growing demand for human food and nutrition resources. Crop species are also known to have independent impacts on biodiversity. To date, reviews synthesising our knowledge of crop species and crop diversity-biodiversity links are missing. We will therefore conduct a systematic review by searching multiple agriculture, ecology and environmental science databases (e.g. Web of Science, Geobase, Agris, AGRICOLA, GreenFILE) to identify studies reporting the impacts of crop diversity and crop species on the biological diversity of fauna, flora and microbes in agricultural landscapes. Outcomes will include metrics of species richness, abundance, assemblage, community composition and species rarity. Screening, data coding and data extraction will be carried out by one reviewer and a proportion will be independently conducted by a second reviewer. Study quality and risk of bias will be assessed. Evidence will first be mapped by species/taxa then assessed for further narrative or statistical synthesis based on comparability of results and likely robustness. Gaps in the evidence base will also be identified with a view toward future research and policy directions for nutrition, food systems and ecology.
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15
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Karpinets TV, Gopalakrishnan V, Wargo J, Futreal AP, Schadt CW, Zhang J. Linking Associations of Rare Low-Abundance Species to Their Environments by Association Networks. Front Microbiol 2018; 9:297. [PMID: 29563898 PMCID: PMC5850922 DOI: 10.3389/fmicb.2018.00297] [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: 10/20/2017] [Accepted: 02/08/2018] [Indexed: 01/07/2023] Open
Abstract
Studies of microbial communities by targeted sequencing of rRNA genes lead to recovering numerous rare low-abundance taxa with unknown biological roles. We propose to study associations of such rare organisms with their environments by a computational framework based on transformation of the data into qualitative variables. Namely, we analyze the sparse table of putative species or OTUs (operational taxonomic units) and samples generated in such studies, also known as an OTU table, by collecting statistics on co-occurrences of the species and on shared species richness across samples. Based on the statistics we built two association networks, of the rare putative species and of the samples respectively, using a known computational technique, Association networks (Anets) developed for analysis of qualitative data. Clusters of samples and clusters of OTUs are then integrated and combined with metadata of the study to produce a map of associated putative species in their environments. We tested and validated the framework on two types of microbiomes, of human body sites and that of the Populus tree root systems. We show that in both studies the associations of OTUs can separate samples according to environmental or physiological characteristics of the studied systems.
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Affiliation(s)
- Tatiana V Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Vancheswaran Gopalakrishnan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Dallas, TX, United States
| | - Jennifer Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Andrew P Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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Escobedo VM, Rios RS, Salgado-Luarte C, Stotz GC, Gianoli E. Disturbance by an endemic rodent in an arid shrubland is a habitat filter: effects on plant invasion and taxonomical, functional and phylogenetic community structure. ANNALS OF BOTANY 2017; 119:659-670. [PMID: 28087661 PMCID: PMC5571376 DOI: 10.1093/aob/mcw258] [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: 09/09/2016] [Accepted: 11/09/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND AND AIMS Disturbance often drives plant invasion and may modify community assembly. However, little is known about how these modifications of community patterns occur in terms of taxonomic, functional and phylogenetic structure. This study evaluated in an arid shrubland the influence of disturbance by an endemic rodent on community functional divergence and phylogenetic structure as well as on plant invasion. It was expected that disturbance would operate as a habitat filter favouring exotic species with short life cycles. METHODS Sixteen plots were sampled along a disturbance gradient caused by the endemic fossorial rodent Spalacopus cyanus , measuring community parameters and estimating functional divergence for life history traits (functional dispersion index) and the relative contribution to functional divergence of exotic and native species. The phylogenetic signal (Pagel's lambda) and phylogenetic community structure (mean phylogenetic distance and mean nearest taxon phylogenetic distance) were also estimated. The use of a continuous approach to the disturbance gradient allowed the identification of non-linear relationships between disturbance and community parameters. KEY RESULTS The relationship between disturbance and both species richness and abundance was positive for exotic species and negative for native species. Disturbance modified community composition, and exotic species were associated with more disturbed sites. Disturbance increased trait convergence, which resulted in phylogenetic clustering because traits showed a significant phylogenetic signal. The relative contribution of exotic species to functional divergence increased, while that of natives decreased, with disturbance. Exotic and native species were not phylogenetically distinct. CONCLUSIONS Disturbance by rodents in this arid shrubland constitutes a habitat filter over phylogeny-dependent life history traits, leading to phylogenetic clustering, and drives invasion by favouring species with short life cycles. Results can be explained by high phenotypic and phylogenetic resemblance between exotic and native species. The use of continuous gradients when studying the effects of disturbance on community assembly is advocated.
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Affiliation(s)
- Víctor M. Escobedo
- Departamento de Biología, Universidad de La Serena, Casilla 554 La Serena, Chile
| | - Rodrigo S. Rios
- Departamento de Biología, Universidad de La Serena, Casilla 554 La Serena, Chile
| | | | - Gisela C. Stotz
- Department of Biological Sciences, University of Alberta, Edmonton, Canada T6G 2E9
| | - Ernesto Gianoli
- Departamento de Biología, Universidad de La Serena, Casilla 554 La Serena, Chile
- Departamento de Botánica, Universidad de Concepción, Casilla 160-C Concepción, Chile
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Leitão RP, Zuanon J, Villéger S, Williams SE, Baraloto C, Fortunel C, Mendonça FP, Mouillot D. Rare species contribute disproportionately to the functional structure of species assemblages. Proc Biol Sci 2016; 283:rspb.2016.0084. [PMID: 27053754 DOI: 10.1098/rspb.2016.0084] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/11/2016] [Indexed: 11/12/2022] Open
Abstract
There is broad consensus that the diversity of functional traits within species assemblages drives several ecological processes. It is also widely recognized that rare species are the first to become extinct following human-induced disturbances. Surprisingly, however, the functional importance of rare species is still poorly understood, particularly in tropical species-rich assemblages where the majority of species are rare, and the rate of species extinction can be high. Here, we investigated the consequences of local and regional extinctions on the functional structure of species assemblages. We used three extensive datasets (stream fish from the Brazilian Amazon, rainforest trees from French Guiana, and birds from the Australian Wet Tropics) and built an integrative measure of species rarity versus commonness, combining local abundance, geographical range, and habitat breadth. Using different scenarios of species loss, we found a disproportionate impact of rare species extinction for the three groups, with significant reductions in levels of functional richness, specialization, and originality of assemblages, which may severely undermine the integrity of ecological processes. The whole breadth of functional abilities within species assemblages, which is disproportionately supported by rare species, is certainly critical in maintaining ecosystems particularly under the ongoing rapid environmental transitions.
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Affiliation(s)
- Rafael P Leitão
- PPG Biologia de Água Doce e Pesca Interior, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil Laboratoire Biodiversité Marine et ses Usages, MARBEC, Université de Montpellier, Montpellier, France
| | - Jansen Zuanon
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Sébastien Villéger
- Laboratoire Biodiversité Marine et ses Usages, MARBEC, Université de Montpellier, Montpellier, France
| | - Stephen E Williams
- Centre for Tropical Biodiversity and Climate Change, James Cook University, Townsville, Australia
| | - Christopher Baraloto
- INRA, UMR Ecologie des Forêts de Guyane, INRA, Kourou, French Guiana International Center for Tropical Botany, Department of Biol Sci, FIU, Miami, USA
| | - Claire Fortunel
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Fernando P Mendonça
- Instituto Federal de Educação, Ciência e Tecnologia, Presidente Figueiredo, Brazil
| | - David Mouillot
- Laboratoire Biodiversité Marine et ses Usages, MARBEC, Université de Montpellier, Montpellier, France Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
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18
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Jarzyna MA, Jetz W. Detecting the Multiple Facets of Biodiversity. Trends Ecol Evol 2016; 31:527-538. [DOI: 10.1016/j.tree.2016.04.002] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/17/2016] [Accepted: 04/11/2016] [Indexed: 11/28/2022]
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Villalobos S, Vamosi JC. Increasing land use drives changes in plant phylogenetic diversity and prevalence of specialists. PeerJ 2016; 4:e1740. [PMID: 26966669 PMCID: PMC4782714 DOI: 10.7717/peerj.1740] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/05/2016] [Indexed: 11/20/2022] Open
Abstract
Increased human land use has resulted in the increased homogenization of biodiversity between sites, yet we lack sufficient indicators to predict which species decline and the consequence of their potential loss on ecosystem services. We used comparative phylogenetic analysis to (1) characterize how increasing conversion of forest and grasslands to grazing pasturelands changes plant diversity and composition; (2) examine how changes in land use relate to declines in functional trait diversity; and (3) specifically investigate how these changes in plant composition affect the prevalence of zygomorphy and the possible consequences that these changes may have on pollinator functional groups. As predicted, we found that the conversion to grazing pasturelands negatively impacted species richness and phylogenetic composition. Clades with significantly more represented taxa in grasslands (GL) were genera with a high representation of agricultural weeds, while the composition was biased towards clades of subalpine herbaceous wildflowers in Mixed Forest (MF). Changes in community composition and structure had strong effects on the prevalence of zygomorphic species likely driven by nitrogen-fixing abilities of certain clades with zygomorphic flowers (e.g., Fabaceae). Land conversion can thus have unexpected impacts on trait distributions relevant for the functioning of the community in other capacities (e.g., cascading effects to other trophic levels (i.e., pollinators). Finally, the combination of traits represented by the current composition of species in GL and MF might enhance the diagnostic value of productivity and ecosystem processes in the most eroded ecosystems.
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Affiliation(s)
- Soraya Villalobos
- Department of Biological Sciences, University of Calgary , Calgary, Alberta , Canada
| | - Jana C Vamosi
- Department of Biological Sciences, University of Calgary , Calgary, Alberta , Canada
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20
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Ngo Ngwe MFS, Omokolo DN, Joly S. Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices. PLoS One 2015; 10:e0145364. [PMID: 26691919 PMCID: PMC4686806 DOI: 10.1371/journal.pone.0145364] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/01/2015] [Indexed: 11/25/2022] Open
Abstract
Yams (Dioscorea spp.) consist of approximately 600 species. Presently, these species are threatened by genetic erosion due to many factors such as pest attacks and farming practices. In parallel, complex taxonomic boundaries in this genus makes it more challenging to properly address the genetic diversity of yam and manage its germplasm. As a first step toward evaluating and preserving the genetic diversity yam species, we use a phylogenetic diversity (PD) approach that has the advantage to investigate phylogenetic relationships and test hypotheses of species monophyly while alleviating to the problem of ploidy variation within and among species. The Bayesian phylogenetic analysis of 62 accessions from 7 species from three regions of Cameroon showed that most Dioscorea sections were monophyletic, but species within sections were generally non-monophyletic. The wild species D. praehensilis and cultivated D. cayenensis were the species with the highest PD. At the opposite, D. esculenta has a low PD and future studies should focus on this species to properly address its conservation status. We also show that wild species show a stronger genetic structure than cultivated species, which potentially reflects the management of the yam germplasm by farmers. These findings show that phylogenetic diversity is a promising approach for an initial investigation of genetic diversity in a crop consisting of closely related species.
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Affiliation(s)
- Marie Florence Sandrine Ngo Ngwe
- Laboratory of Plant Physiology, Higher Teacher’s Training College, University of Yaoundé 1, P. O. Box 47, Yaounde, Cameroon
- Institute of Agricultural Research for Development-CEREFEN, BP 167, Meyomessala, Cameroon
- * E-mail:
| | - Denis Ndoumou Omokolo
- Laboratory of Plant Physiology, Higher Teacher’s Training College, University of Yaoundé 1, P. O. Box 47, Yaounde, Cameroon
| | - Simon Joly
- Institut de recherche en biologie végétale, Montreal Botanical Garden and Université de Montréal, 4101 Sherbrooke East, Montréal, QC, H1X 2B2, Canada
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21
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Coro G, Webb TJ, Appeltans W, Bailly N, Cattrijsse A, Pagano P. Classifying degrees of species commonness: North Sea fish as a case study. Ecol Modell 2015. [DOI: 10.1016/j.ecolmodel.2015.05.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Hol WHG, de Boer W, de Hollander M, Kuramae EE, Meisner A, van der Putten WH. Context dependency and saturating effects of loss of rare soil microbes on plant productivity. FRONTIERS IN PLANT SCIENCE 2015; 6:485. [PMID: 26175749 PMCID: PMC4485053 DOI: 10.3389/fpls.2015.00485] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 06/16/2015] [Indexed: 05/09/2023]
Abstract
Land use intensification is associated with loss of biodiversity and altered ecosystem functioning. Until now most studies on the relationship between biodiversity and ecosystem functioning focused on random loss of species, while loss of rare species that usually are the first to disappear received less attention. Here we test if the effect of rare microbial species loss on plant productivity depends on the origin of the microbial soil community. Soils were sampled from three land use types at two farms. Microbial communities with increasing loss of rare species were created by inoculating sterilized soils with serially diluted soil suspensions. After 8 months of incubation, the effects of the different soil communities on abiotic soil properties, soil processes, microbial community composition, and plant productivity was measured. Dilution treatments resulted in increasing species loss, which was in relation to abundance of bacteria in the original field soil, without affecting most of the other soil parameters and processes. Microbial species loss affected plant biomass positively, negatively or not at all, depending on soil origin, but not on land use history. Even within fields the effects of dilution on plant biomass varied between replicates, suggesting heterogeneity in microbial community composition. The effects of medium and severe species loss on plant biomass were similar, pointing toward a saturating effect of species loss. We conclude that changes in the composition of the soil microbial community, including rare species loss, can affect plant productivity, depending on the composition of the initial microbial community. Future work on the relation between function and species loss effects should address this variation by including multiple sampling origins.
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Affiliation(s)
- W. H. Gera Hol
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, WageningenNetherlands
- *Correspondence: W. H. Gera Hol, Department of Terrestrial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, P.O. Box 50, 6700 AB Wageningen, Netherlands,
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology, WageningenNetherlands
- Department of Soil Quality, Wageningen University, WageningenNetherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology, WageningenNetherlands
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, WageningenNetherlands
| | - Annelein Meisner
- Microbial Ecology Group, Department of Biology, Lund University, LundSweden
- Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, CopenhagenDenmark
- Department of Biology, University of Copenhagen, CopenhagenDenmark
| | - Wim H. van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, WageningenNetherlands
- Laboratory of Nematology, Wageningen University, WageningenNetherlands
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Liu J, Zhang X, Song F, Zhou S, Cadotte MW, Bradshaw CJA. Explaining maximum variation in productivity requires phylogenetic diversity and single functional traits. Ecology 2015; 96:176-83. [DOI: 10.1890/14-1034.1] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Jiajia Liu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433 People's Republic of China
| | - Xinxin Zhang
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000 People's Republic of China
| | - Feifan Song
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000 People's Republic of China
| | - Shurong Zhou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433 People's Republic of China
| | - Marc W. Cadotte
- Department of Biological Sciences, University of Toronto–Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4 Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Wilcocks Street, Toronto, Ontario M5S 3B2 Canada
| | - Corey J. A. Bradshaw
- The Environment Institute and School of Earth and Environmental Sciences, University of Adelaide, South Australia 5005 Australia
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Muscarella R, Uriarte M, Erickson DL, Swenson NG, Zimmerman JK, Kress WJ. A well-resolved phylogeny of the trees of Puerto Rico based on DNA barcode sequence data. PLoS One 2014; 9:e112843. [PMID: 25386879 PMCID: PMC4227909 DOI: 10.1371/journal.pone.0112843] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 10/17/2014] [Indexed: 11/23/2022] Open
Abstract
Background The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools. Methodology/principal findings We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny. Conclusions/significance With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii) provide insight into Caribbean biogeography, and (iii) aid in incorporating evolutionary history into conservation planning.
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Affiliation(s)
- Robert Muscarella
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York 10027, United States of America
| | - María Uriarte
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York 10027, United States of America
| | - David L Erickson
- Department of Botany, MRC-166, National Museum of Natural History Smithsonian Institution, P.O. Box 37012, Washington, D. C., 20013, United States of America
| | - Nathan G Swenson
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, United States of America
| | - Jess K Zimmerman
- Department of Environmental Science, University of Puerto Rico, San Juan, Puerto Rico 00925, United States of America
| | - W John Kress
- Department of Botany, MRC-166, National Museum of Natural History Smithsonian Institution, P.O. Box 37012, Washington, D. C., 20013, United States of America
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Karpinets TV, Park BH, Syed MH, Klotz MG, Uberbacher EC. Metabolic environments and genomic features associated with pathogenic and mutualistic interactions between bacteria and plants. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:664-677. [PMID: 24580106 DOI: 10.1094/mpmi-12-13-0368-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Genomic characteristics discriminating parasitic and mutualistic relationship of bacterial symbionts with plants are poorly understood. This study comparatively analyzed the genomes of 54 mutualists and pathogens to discover genomic markers associated with the different phenotypes. Using metabolic network models, we predict external environments associated with free-living and symbiotic lifestyles and quantify dependences of symbionts on the host in terms of the consumed metabolites. We show that specific differences between the phenotypes are pronounced at the levels of metabolic enzymes, especially carbohydrate active, and protein functions. Overall, biosynthetic functions are enriched and more diverse in plant mutualists whereas processes and functions involved in degradation and host invasion are enriched and more diverse in pathogens. A distinctive characteristic of plant pathogens is a putative novel secretion system with a circadian rhythm regulator. A specific marker of plant mutualists is the co-residence of genes encoding nitrogenase and ribulose bisphosphate carboxylase/oxygenase (RuBisCO). We predict that RuBisCO is likely used in a putative metabolic pathway to supplement carbon obtained heterotrophically with low-cost assimilation of carbon from CO2. We validate results of the comparative analysis by predicting correct phenotype, pathogenic or mutualistic, for 20 symbionts in an independent set of 30 pathogens, mutualists, and commensals.
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26
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Santorelli S, Magnusson W, Ferreira E, Caramaschi E, Zuanon J, Amadio S. Phylogenetic community structure: temporal variation in fish assemblage. Ecol Evol 2014; 4:2146-53. [PMID: 25360256 PMCID: PMC4201429 DOI: 10.1002/ece3.1026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 02/07/2014] [Accepted: 02/18/2014] [Indexed: 11/26/2022] Open
Abstract
Hypotheses about phylogenetic relationships among species allow inferences about the mechanisms that affect species coexistence. Nevertheless, most studies assume that phylogenetic patterns identified are stable over time. We used data on monthly samples of fish from a single lake over 10 years to show that the structure in phylogenetic assemblages varies over time and conclusions depend heavily on the time scale investigated. The data set was organized in guild structures and temporal scales (grouped at three temporal scales). Phylogenetic distance was measured as the mean pairwise distances (MPD) and as mean nearest-neighbor distance (MNTD). Both distances were based on counts of nodes. We compared the observed values of MPD and MNTD with values that were generated randomly using null model independent swap. A serial runs test was used to assess the temporal independence of indices over time. The phylogenetic pattern in the whole assemblage and the functional groups varied widely over time. Conclusions about phylogenetic clustering or dispersion depended on the temporal scales. Conclusions about the frequency with which biotic processes and environmental filters affect the local assembly do not depend only on taxonomic grouping and spatial scales. While these analyzes allow the assertion that all proposed patterns apply to the fish assemblages in the floodplain, the assessment of the relative importance of these processes, and how they vary depending on the temporal scale and functional group studied, cannot be determined with the effort commonly used. It appears that, at least in the system that we studied, the assemblages are forming and breaking continuously, resulting in various phylogeny-related structures that makes summarizing difficult.
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Affiliation(s)
- Sergio Santorelli
- Programa de Pós graduação em Biologia de Água Doce e Pesca Interior, Instituto Nacional de Pesquisas da AmazôniaManaus, Brazil
- Centro de Estudos Integrados da Biodiversidade AmazônicaManaus, Brazil
| | - William Magnusson
- Centro de Estudos Integrados da Biodiversidade AmazônicaManaus, Brazil
- Coordenação de Pesquisas em Biodiversidade, Instituto Nacional de Pesquisas da AmazôniaManaus, Brazil
| | - Efrem Ferreira
- Coordenação de Pesquisas em Biodiversidade, Instituto Nacional de Pesquisas da AmazôniaManaus, Brazil
| | - Erica Caramaschi
- Programa de Pós graduação em Ecologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Jansen Zuanon
- Coordenação de Pesquisas em Biodiversidade, Instituto Nacional de Pesquisas da AmazôniaManaus, Brazil
| | - Sidnéia Amadio
- Coordenação de Pesquisas em Biodiversidade, Instituto Nacional de Pesquisas da AmazôniaManaus, Brazil
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Huang JX, Zhang J, Shen Y, Lian JY, Cao HL, Ye WH, Wu LF, Bin Y. Different relationships between temporal phylogenetic turnover and phylogenetic similarity and in two forests were detected by a new null model. PLoS One 2014; 9:e95703. [PMID: 24748022 PMCID: PMC3991709 DOI: 10.1371/journal.pone.0095703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/30/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Ecologists have been monitoring community dynamics with the purpose of understanding the rates and causes of community change. However, there is a lack of monitoring of community dynamics from the perspective of phylogeny. METHODS/PRINCIPLE FINDINGS We attempted to understand temporal phylogenetic turnover in a 50 ha tropical forest (Barro Colorado Island, BCI) and a 20 ha subtropical forest (Dinghushan in southern China, DHS). To obtain temporal phylogenetic turnover under random conditions, two null models were used. The first shuffled names of species that are widely used in community phylogenetic analyses. The second simulated demographic processes with careful consideration on the variation in dispersal ability among species and the variations in mortality both among species and among size classes. With the two models, we tested the relationships between temporal phylogenetic turnover and phylogenetic similarity at different spatial scales in the two forests. Results were more consistent with previous findings using the second null model suggesting that the second null model is more appropriate for our purposes. With the second null model, a significantly positive relationship was detected between phylogenetic turnover and phylogenetic similarity in BCI at a 10 m×10 m scale, potentially indicating phylogenetic density dependence. This relationship in DHS was significantly negative at three of five spatial scales. This could indicate abiotic filtering processes for community assembly. Using variation partitioning, we found phylogenetic similarity contributed to variation in temporal phylogenetic turnover in the DHS plot but not in BCI plot. CONCLUSIONS/SIGNIFICANCE The mechanisms for community assembly in BCI and DHS vary from phylogenetic perspective. Only the second null model detected this difference indicating the importance of choosing a proper null model.
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Affiliation(s)
- Jian-Xiong Huang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Yong Shen
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ju-yu Lian
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hong-lin Cao
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Wan-hui Ye
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Lin-fang Wu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yue Bin
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Faith DP. Biodiversity and evolutionary history: useful extensions of the PD phylogenetic diversity assessment framework. Ann N Y Acad Sci 2013; 1289:69-89. [PMID: 23773093 DOI: 10.1111/nyas.12186] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Evolutionary biology is a core discipline in biodiversity science. Evolutionary history or phylogeny provides one natural measure of biodiversity through the popular phylogenetic diversity (PD) measure. The evolutionary model underlying PD means that it can be interpreted as quantifying the relative feature diversity of sets of species. Quantifying feature diversity measures possible future uses and benefits or option values. Interpretation of PD as counting-up features is the basis for an emerging broad family of PD calculations, of use to both biodiversity researchers and decision makers. Many of these calculations extend conventional species-level indices to the features level. Useful PD calculations include PD complementarity and endemism, Hill and Valley numbers incorporating abundance, and PD dissimilarities. A flexible analysis framework is provided by expected PD calculations, applied to either probabilities of extinction or presence-absence. Practical extensions include phylogenetic risk analysis and measures of distinctiveness and endemism. These support the integration of phylogenetic diversity into biodiversity conservation and monitoring programs.
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Yang J, Swenson NG, Cao M, Chuyong GB, Ewango CEN, Howe R, Kenfack D, Thomas D, Wolf A, Lin L. A phylogenetic perspective on the individual species-area relationship in temperate and tropical tree communities. PLoS One 2013; 8:e63192. [PMID: 23650553 PMCID: PMC3641141 DOI: 10.1371/journal.pone.0063192] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 04/02/2013] [Indexed: 11/25/2022] Open
Abstract
Ecologists have historically used species-area relationships (SARs) as a tool to understand the spatial distribution of species. Recent work has extended SARs to focus on individual-level distributions to generate individual species area relationships (ISARs). The ISAR approach quantifies whether individuals of a species tend have more or less species richness surrounding them than expected by chance. By identifying richness 'accumulators' and 'repellers', respectively, the ISAR approach has been used to infer the relative importance of abiotic and biotic interactions and neutrality. A clear limitation of the SAR and ISAR approaches is that all species are treated as evolutionarily independent and that a large amount of work has now shown that local tree neighborhoods exhibit non-random phylogenetic structure given the species richness. Here, we use nine tropical and temperate forest dynamics plots to ask: (i) do ISARs change predictably across latitude?; (ii) is the phylogenetic diversity in the neighborhood of species accumulators and repellers higher or lower than that expected given the observed species richness?; and (iii) do species accumulators, repellers distributed non-randomly on the community phylogenetic tree? The results indicate no clear trend in ISARs from the temperate zone to the tropics and that the phylogenetic diversity surrounding the individuals of species is generally only non-random on very local scales. Interestingly the distribution of species accumulators and repellers was non-random on the community phylogenies suggesting the presence of phylogenetic signal in the ISAR across latitude.
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Affiliation(s)
- Jie Yang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Nathan G. Swenson
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Min Cao
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - George B. Chuyong
- Department of Botany and Plant Physiology, University of Buea, Buea, Cameroon
| | - Corneille E. N. Ewango
- Centre de Formation et de Recherche en Conservation Forestière (CEFRECOF) Epulu, Ituri Forest, Reserve de Faune a Okapis, Democratic Republic of Congo
| | - Robert Howe
- Department of Natural and Applied Science, University of Wisconsin – Green Bay, Green Bay, Wisconsin, United States of America
| | - David Kenfack
- Smithsonian Global Earth Observatory Network, Smithsonian Institution, Washington, D.C., United States of America
| | - Duncan Thomas
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Amy Wolf
- Department of Natural and Applied Science, University of Wisconsin – Green Bay, Green Bay, Wisconsin, United States of America
| | - Luxiang Lin
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
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Marmeisse R, Nehls U, Öpik M, Selosse MA, Pringle A. Bridging mycorrhizal genomics, metagenomics and forest ecology. THE NEW PHYTOLOGIST 2013; 198:343-346. [PMID: 23510186 DOI: 10.1111/nph.12205] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- Roland Marmeisse
- Ecologie Microbienne, CNRS-Université Lyon 1, Villeurbanne, France
| | - Uwe Nehls
- Department of Ecology, University of Bremen, Bremen, Germany
| | - Maarja Öpik
- Department of Botany, University of Tartu, Tartu, Estonia
| | - Marc-André Selosse
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-Université Montpellier II, Muséum National d'Histoire Naturelle (Paris), Montpellier, France
| | - Anne Pringle
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA, USA
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31
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Winter M, Devictor V, Schweiger O. Phylogenetic diversity and nature conservation: where are we? Trends Ecol Evol 2012; 28:199-204. [PMID: 23218499 DOI: 10.1016/j.tree.2012.10.015] [Citation(s) in RCA: 241] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 10/25/2012] [Accepted: 10/26/2012] [Indexed: 01/04/2023]
Abstract
To date, there is little evidence that phylogenetic diversity has contributed to nature conservation. Here, we discuss the scientific justification of using phylogenetic diversity in conservation and the reasons for its neglect. We show that, apart from valuing the rarity and richness aspect, commonly quoted justifications based on the usage of phylogenetic diversity as a proxy for functional diversity or evolutionary potential are still based on uncertainties. We discuss how a missing guideline through the variety of phylogenetic diversity metrics and their relevance for conservation might be responsible for the hesitation to include phylogenetic diversity in conservation practice. We outline research routes that can help to ease uncertainties and bridge gaps between research and conservation with respect to phylogenetic diversity.
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Affiliation(s)
- Marten Winter
- Helmholtz Centre for Environmental Research - UFZ, Department of Community Ecology, Theodor-Lieser Str. 4, 06120 Halle (Saale), Germany.
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Affiliation(s)
- Kevin J Gaston
- Environment and Sustainability Institute, University of Exeter, Penryn TR10 9EZ, UK.
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