151
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Hipp AL, Larkin DJ, Barak RS, Bowles ML, Cadotte MW, Jacobi SK, Lonsdorf E, Scharenbroch BC, Williams E, Weiher E. Phylogeny in the service of ecological restoration. AMERICAN JOURNAL OF BOTANY 2015; 102:647-648. [PMID: 26022478 DOI: 10.3732/ajb.1500119] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
| | | | - Rebecca S Barak
- Chicago Botanic Garden, Glencoe, Illinois 60222 USA Plant Biology and Conservation, Northwestern University, Evanston, Illinois 60208 USA
| | | | - Marc W Cadotte
- Department of Biological Sciences, University of Toronto-Scarborough, Toronto ON M1C 1A4 Canada
| | | | | | - Bryant C Scharenbroch
- The Morton Arboretum, Lisle, Illinois 60532 USA College of Natural Resources, University of Wisconsin Stevens Point, Stevens Point, Wisconsin 54481 USA
| | | | - Evan Weiher
- Department of Biology, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702 USA
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152
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Münkemüller T, Gallien L. VirtualCom: a simulation model for eco‐evolutionary community assembly and invasion. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12364] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Laure Gallien
- University of Grenoble Alpes LECA F‐38000 Grenoble France
- CNRS LECA F‐38000 Grenoble France
- Landscape Dynamics Swiss Federal Research Institute WSL CH‐8903 Birmensdorf Switzerland
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153
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Cadotte MW. Phylogenetic diversity–ecosystem function relationships are insensitive to phylogenetic edge lengths. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12429] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marc W. Cadotte
- Department of Biological Sciences University of Toronto Scarborough 1265 Military TrailScarborough ON Canada
- Department of Ecology and Evolutionary Biology University of Toronto 25 Willcocks Street, Toronto Scarborough ON Canada
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154
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Paquette A, Joly S, Messier C. Explaining forest productivity using tree functional traits and phylogenetic information: two sides of the same coin over evolutionary scale? Ecol Evol 2015; 5:1774-83. [PMID: 26140194 PMCID: PMC4485959 DOI: 10.1002/ece3.1456] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 02/22/2015] [Indexed: 12/03/2022] Open
Abstract
Given evidences that diverse ecosystems provide more services than depauperate ones, much attention has now turned toward finding meaningful and operational diversity indices. We ask two questions: (1) Does phylogenetic diversity contain additional information not explained by functional traits? And (2) What are the strength and nature of the correlation between phylogeny and functional traits according to the evolutionary scale considered? We used data from permanent forest plots of northeastern Canada for which these links have been demonstrated and important functional traits identified. We show that the nature of the relationship between traits and phylogeny varies dramatically among traits, but also according to the evolutionary distance considered. The demonstration that different characters show phylogenetic autocorrelation at different evolutionary depths suggests that phylogenetic content of traits may be too crude to determine whether phylogenies contain relevant information. However, our study provides support for the use of phylogenies to assess ecosystem functioning when key functional traits are unavailable. We also highlight a potentially important contribution of phylogenetics for conservation and the study of the impact of biodiversity loss on ecosystem functioning and the provision of services, given the accumulating evidence that mechanisms promoting diversity effects shift over time to involve different traits.
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Affiliation(s)
- Alain Paquette
- Center for Forest Research, Université du Québec à Montréal P.O. Box 8888, Centre-ville Station, Montréal, QC, H3C 3P8, Canada
| | - Simon Joly
- Institut de recherche en biologie végétale, Jardin botanique de Montréal and Université de Montréal 4101 Sherbrooke East, Montréal, QC, H1X 2B2, Canada
| | - Christian Messier
- Center for Forest Research, Université du Québec à Montréal P.O. Box 8888, Centre-ville Station, Montréal, QC, H3C 3P8, Canada ; Institut des Sciences de la Forêt tempérée, Université du Québec en Outaouais 58 Rue Principale, Ripon, QC, JOV 1V0, Canada
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155
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Gerhold P, Cahill JF, Winter M, Bartish IV, Prinzing A. Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better). Funct Ecol 2015. [DOI: 10.1111/1365-2435.12425] [Citation(s) in RCA: 332] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Pille Gerhold
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Lai 40 51005 Tartu Estonia
| | - James F. Cahill
- Department of Biological Sciences University of Alberta Edmonton AB T6G 2E9 Canada
| | - Marten Winter
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Deutscher Platz 5e 04103 Leipzig Germany
| | - Igor V. Bartish
- Department of Genetic Ecology Institute of Botany Academy of Sciences CZ‐25243 Pruhonice 1 Czech Republic
| | - Andreas Prinzing
- Research Unit “Ecosystèmes Biodiversité, Evolution” («UMR 6553») Centre National de la Recherche Scientifique University Rennes 1 Campus Beaulieu, Bâtiment 14 A 35042 Rennes France
- Alterra, Wageningen UR (University & Research Centre) PO Box 47 NL‐6700 AA Wageningen The Netherlands
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156
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Thuiller W, Maiorano L, Mazel F, Guilhaumon F, Ficetola GF, Lavergne S, Renaud J, Roquet C, Mouillot D. Conserving the functional and phylogenetic trees of life of European tetrapods. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140005. [PMID: 25561666 PMCID: PMC4290419 DOI: 10.1098/rstb.2014.0005] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Protected areas (PAs) are pivotal tools for biodiversity conservation on the Earth. Europe has had an extensive protection system since Natura 2000 areas were created in parallel with traditional parks and reserves. However, the extent to which this system covers not only taxonomic diversity but also other biodiversity facets, such as evolutionary history and functional diversity, has never been evaluated. Using high-resolution distribution data of all European tetrapods together with dated molecular phylogenies and detailed trait information, we first tested whether the existing European protection system effectively covers all species and in particular, those with the highest evolutionary or functional distinctiveness. We then tested the ability of PAs to protect the entire tetrapod phylogenetic and functional trees of life by mapping species' target achievements along the internal branches of these two trees. We found that the current system is adequately representative in terms of the evolutionary history of amphibians while it fails for the rest. However, the most functionally distinct species were better represented than they would be under random conservation efforts. These results imply better protection of the tetrapod functional tree of life, which could help to ensure long-term functioning of the ecosystem, potentially at the expense of conserving evolutionary history.
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Affiliation(s)
- Wilfried Thuiller
- LECA, Université Grenoble Alpes, Grenoble 38000, France LECA, CNRS, Grenoble 38000, France
| | - Luigi Maiorano
- Dipartimento di Biologia e Biotecnologie 'Charles Darwin', Università di Roma 'La Sapienza', Roma 00185, Italy
| | - Florent Mazel
- LECA, Université Grenoble Alpes, Grenoble 38000, France LECA, CNRS, Grenoble 38000, France
| | - François Guilhaumon
- Laboratoire ECOSYM, UMR 5119 CNRS-UM2-IRD-IFREMER, Place Eugène Bataillon cc 93, Montpellier 34095, France
| | | | - Sébastien Lavergne
- LECA, Université Grenoble Alpes, Grenoble 38000, France LECA, CNRS, Grenoble 38000, France
| | - Julien Renaud
- LECA, Université Grenoble Alpes, Grenoble 38000, France LECA, CNRS, Grenoble 38000, France
| | - Cristina Roquet
- LECA, Université Grenoble Alpes, Grenoble 38000, France LECA, CNRS, Grenoble 38000, France
| | - David Mouillot
- Laboratoire ECOSYM, UMR 5119 CNRS-UM2-IRD-IFREMER, Place Eugène Bataillon cc 93, Montpellier 34095, France
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157
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Tropical Refuges with Exceptionally High Phylogenetic Diversity Reveal Contrasting Phylogenetic Structures. ACTA ACUST UNITED AC 2015. [DOI: 10.1155/2015/758019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Loss of phylogenetic diversity (PD) has gained increasing attention in conservation biology. However, PD is not equally distributed in a phylogeny and can be better assessed when species relatedness (phylogenetic structure: PS) is also considered. Here, we investigate PD and PS in two refuges of biodiversity in northeastern Brazil: the Bahia Costal Forest (BCF) in the Atlantic Forest domain and Chapada Diamantina (CD) in the Caatinga domain. We used geographic data of 205 species at two spatial scales and a chronogram of Apocynaceae based on matK sequences to estimate PD and PS. Our results show an exceptionally high PD in both refuges, overdispersed in BCF and clustered in CD, although this difference is less evident or absent for recent relationships, especially at a smaller spatial scale. Overall, PS suggests long-term competitive exclusion under climatic stability, currently balanced by habitat filtering, in BCF, and biome conservatism and limited dispersal leading to in situ diversification and high density of microendemics in CD. The phylogenetically clustered flora in CD, also threatened by climate changes, are naturally more vulnerable than BCF. Therefore, while in situ conservation may ensure protection of biodiversity in BCF, emergency ex situ conservation is strongly recommended in CD.
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158
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Chen H, Shao KT, Kishino H. Phylogenetic skew: an index of community diversity. Mol Ecol 2015; 24:759-70. [PMID: 25580733 DOI: 10.1111/mec.13064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/18/2014] [Accepted: 12/30/2014] [Indexed: 11/28/2022]
Abstract
The distribution of divergence times between member species of a community reflects the pattern of species composition. In this study, we contrast the species composition of a community against the meta-community, which we define as the species composition of a set of target communities. We regard the collection of species that comprise a community as a sample from the set of member species of the meta-community, and interpret the pattern of the community species composition in terms of the type of species sampled from the meta-community. A newly defined effective species sampling proportion explains the amount of the difference between the divergence time distributions of the community and that of the meta-community, assuming random sampling. We propose a new index of phylogenetic skew (PS), as the ratio of the maximum-likelihood estimate of the effective species sampling proportion to the observed sampling proportion. A PS value of 1 is interpreted as random sampling. If the value is >1, the sampling is suspected to be phylogenetically skewed. If it is <1, systematic thinning of species is likely. Unlike other indices, the PS does not depend on species richness as long as the community has more than a few members of a species. Because it is possible to compare partially observed communities, the index may be effectively used in exploratory analysis to detect candidate communities with unique species compositions from a large number of communities.
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Affiliation(s)
- Hungyen Chen
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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159
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Mehrabi Z, Tuck SL. Relatedness is a poor predictor of negative plant-soil feedbacks. THE NEW PHYTOLOGIST 2015; 205:1071-1075. [PMID: 25557183 PMCID: PMC4303931 DOI: 10.1111/nph.13238] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 11/18/2014] [Indexed: 05/29/2023]
Abstract
Understanding the mechanisms underlying negative plant-soil feedbacks remains a critical challenge in plant ecology. If closely related species are more similar, then phylogeny could be used as a predictor for plant species interactions, simplifying our understanding of how plant-soil feedbacks structure plant communities, underlie invasive species dynamics, or reduce agricultural productivity. Here, we test the utility of phylogeny for predicting plant-soil feedbacks by undertaking a hierarchical Bayesian meta-analysis on all available pairwise plant-soil feedback experiments conducted over the last two decades, including 133 plant species in 329 pairwise interactions. We found that the sign and magnitude of plant-soil feedback effects were not explained by the phylogenetic distance separating interacting species. This result was consistent across different life forms, life cycles, provenances, and phylogenetic scales. Our analysis shows that, contrary to widespread assumption, relatedness is a poor predictor of plant-soil feedback effects.
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Affiliation(s)
- Zia Mehrabi
- Long Term Ecology Laboratory, Department of Zoology, University of Oxford, OxfordOX1 3PS, UK
| | - Sean L Tuck
- Department of Plant Sciences, University of OxfordSouth Parks Road, Oxford, OX1 3RB, UK
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160
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Comparing the conservatism of ecological interactions in plant–pollinator and plant–herbivore networks. POPUL ECOL 2015. [DOI: 10.1007/s10144-014-0473-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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161
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Chalmandrier L, Münkemüller T, Lavergne S, Thuiller W. Effects of species' similarity and dominance on the functional and phylogenetic structure of a plant meta‐community. Ecology 2015; 96:143-53. [DOI: 10.1890/13-2153.1] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- L. Chalmandrier
- Université Grenoble Alpes, Laboratoire d'Écologie Alpine (LECA), F-38000 Grenoble, France
- CNRS, Laboratoire d'Écologie Alpine (LECA), F-38000 Grenoble, France
| | - T. Münkemüller
- Université Grenoble Alpes, Laboratoire d'Écologie Alpine (LECA), F-38000 Grenoble, France
- CNRS, Laboratoire d'Écologie Alpine (LECA), F-38000 Grenoble, France
| | - S. Lavergne
- Université Grenoble Alpes, Laboratoire d'Écologie Alpine (LECA), F-38000 Grenoble, France
- CNRS, Laboratoire d'Écologie Alpine (LECA), F-38000 Grenoble, France
| | - W. Thuiller
- Université Grenoble Alpes, Laboratoire d'Écologie Alpine (LECA), F-38000 Grenoble, France
- CNRS, Laboratoire d'Écologie Alpine (LECA), F-38000 Grenoble, France
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162
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163
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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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164
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165
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Chalmandrier L, Münkemüller T, Devictor V, Lavergne S, Thuiller W. Decomposing changes in phylogenetic and functional diversity over space and time. Methods Ecol Evol 2014; 6:109-118. [PMID: 25685310 DOI: 10.1111/2041-210x.12297] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The α, β, γ diversity decomposition methodology is commonly used to investigate changes in diversity over space or time but rarely conjointly. However, with the ever-increasing availability of large-scale biodiversity monitoring data, there is a need for a sound methodology capable of simultaneously accounting for spatial and temporal changes in diversity.Using the properties of Chao's index, we adapted Rao's framework of diversity decomposition between orthogonal dimensions to a multiplicative α, β, γ decomposition of functional or phylogenetic diversity over space and time, thereby combining their respective properties. We also developed guidelines for interpreting both temporal and spatial β-diversities and their interaction.We characterised the range of β-diversity estimates and their relationship to the nested decomposition of diversity. Using simulations, we empirically demonstrated that temporal and spatial β-diversities are independent from each other and from α and γ-diversities when the study design is balanced, but not otherwise. Furthermore, we showed that the interaction term between the temporal and the spatial β-diversities lacked such properties.We illustrated our methodology with a case study of the spatio-temporal dynamics of functional diversity in bird assemblages in four regions of France. Based on these data, our method makes it possible to discriminate between regions experiencing different diversity changes in time. Our methodology may therefore be valuable for comparing diversity changes over space and time using large-scale datasets of repeated surveys.
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Affiliation(s)
- Loïc Chalmandrier
- Univ. Grenoble Alpes, LECA, F-38000 Grenoble, France ; CNRS, LECA, F-38000 Grenoble, France
| | - Tamara Münkemüller
- Univ. Grenoble Alpes, LECA, F-38000 Grenoble, France ; CNRS, LECA, F-38000 Grenoble, France
| | - Vincent Devictor
- Institut des Sciences de l'Évolution de Montpellier, UMR CNRS 5554, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - Sébastien Lavergne
- Univ. Grenoble Alpes, LECA, F-38000 Grenoble, France ; CNRS, LECA, F-38000 Grenoble, France
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, LECA, F-38000 Grenoble, France ; CNRS, LECA, F-38000 Grenoble, France
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166
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Rohr RP, Bascompte J. Components of Phylogenetic Signal in Antagonistic and Mutualistic Networks. Am Nat 2014; 184:556-64. [DOI: 10.1086/678234] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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167
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Nuismer SL, Harmon LJ. Predicting rates of interspecific interaction from phylogenetic trees. Ecol Lett 2014; 18:17-27. [DOI: 10.1111/ele.12384] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/10/2014] [Accepted: 09/17/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Scott L. Nuismer
- Department of Biological Sciences; Institute for Bioinformatics and Evolutionary Studies (IBEST); University of Idaho; Moscow ID USA
| | - Luke J. Harmon
- Department of Biological Sciences; Institute for Bioinformatics and Evolutionary Studies (IBEST); University of Idaho; Moscow ID USA
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168
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Peralta G, Frost CM, Didham RK, Varsani A, Tylianakis JM. Phylogenetic diversity and co-evolutionary signals among trophic levels change across a habitat edge. J Anim Ecol 2014; 84:364-72. [DOI: 10.1111/1365-2656.12296] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 09/19/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Guadalupe Peralta
- School of Biological Sciences; University of Canterbury; Private bag 4800 Christchurch 8140 New Zealand
| | - Carol M. Frost
- School of Biological Sciences; University of Canterbury; Private bag 4800 Christchurch 8140 New Zealand
| | - Raphael K. Didham
- School of Animal Biology; University of Western Australia; 35 Stirling Highway Crawley WA 6009 Australia
- CSIRO Ecosystem Sciences; Centre for Environment and Life Sciences; Underwood Ave Floreat WA 6014 Australia
| | - Arvind Varsani
- School of Biological Sciences; University of Canterbury; Private bag 4800 Christchurch 8140 New Zealand
- Biomolecular Interaction Centre; University of Canterbury; Private Bag 4800 Christchurch 8140 New Zealand
- Electron Microscope Unit; University of Cape Town; Rondebosch Cape Town 7701 South Africa
- Department of Plant Pathology and Emerging Pathogens Institute; University of Florida; PO Box 110680 Gainesville FL 32611-0680 USA
| | - Jason M. Tylianakis
- School of Biological Sciences; University of Canterbury; Private bag 4800 Christchurch 8140 New Zealand
- Department of Life Sciences; Imperial College London; Silwood Park Campus; Buckhurst Road Ascot Berkshire SL5 7PY UK
- Allan Wilson Centre for Molecular Ecology and Evolution; University of Canterbury; Private Bag 4800 Christchurch 8140 New Zealand
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169
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Schweizer M, Ayé R, Kashkarov R, Roth T. Conservation action based on threatened species capture taxonomic and phylogenetic richness in breeding and wintering populations of Central Asian birds. PLoS One 2014; 9:e110511. [PMID: 25337861 PMCID: PMC4206344 DOI: 10.1371/journal.pone.0110511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/15/2014] [Indexed: 11/18/2022] Open
Abstract
Although phylogenetic diversity has been suggested to be relevant from a conservation point of view, its role is still limited in applied nature conservation. Recently, the practice of investing conservation resources based on threatened species was identified as a reason for the slow integration of phylogenetic diversity in nature conservation planning. One of the main arguments is based on the observation that threatened species are not evenly distributed over the phylogenetic tree. However this argument seems to dismiss the fact that conservation action is a spatially explicit process, and even if threatened species are not evenly distributed over the phylogenetic tree, the occurrence of threatened species could still indicate areas with above average phylogenetic diversity and consequently could protect phylogenetic diversity. Here we aim to study the selection of important bird areas in Central Asia, which were nominated largely based on the presence of threatened bird species. We show that although threatened species occurring in Central Asia do not capture phylogenetically more distinct species than expected by chance, the current spatially explicit conservation approach of selecting important bird areas covers above average taxonomic and phylogenetic diversity of breeding and wintering birds. We conclude that the spatially explicit processes of conservation actions need to be considered in the current discussion of whether new prioritization methods are needed to complement conservation action based on threatened species.
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Affiliation(s)
- Manuel Schweizer
- Naturhistorisches Museum der Burgergemeinde Bern, Bern, Switzerland
| | - Raffael Ayé
- SVS/BirdLife Switzerland, Zurich, Switzerland
| | - Roman Kashkarov
- National University of Uzbekistan, Tashkent, Uzbekistan
- Uzbekistan Society for the Protection of Birds, Tashkent, Uzbekistan
| | - Tobias Roth
- University of Basel, Zoological Institute, Basel, Switzerland
- Hintermann & Weber AG, Reinach, Switzerland
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170
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Carroll SP, Jørgensen PS, Kinnison MT, Bergstrom CT, Denison RF, Gluckman P, Smith TB, Strauss SY, Tabashnik BE. Applying evolutionary biology to address global challenges. Science 2014; 346:1245993. [PMID: 25213376 PMCID: PMC4245030 DOI: 10.1126/science.1245993] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens, and pests that evolve too quickly and the second, from the inability of many valued species to adapt quickly enough. Applied evolutionary biology provides a suite of strategies to address these global challenges that threaten human health, food security, and biodiversity. This Review highlights both progress and gaps in genetic, developmental, and environmental manipulations across the life sciences that either target the rate and direction of evolution or reduce the mismatch between organisms and human-altered environments. Increased development and application of these underused tools will be vital in meeting current and future targets for sustainable development.
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Affiliation(s)
- Scott P Carroll
- Department of Entomology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA. Institute for Contemporary Evolution, Davis, CA 95616, USA.
| | - Peter Søgaard Jørgensen
- Center for Macroecology, Evolution and Climate, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark. Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Michael T Kinnison
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - Carl T Bergstrom
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - R Ford Denison
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55108, USA
| | - Peter Gluckman
- Centre for Human Evolution, Adaptation and Disease, Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Thomas B Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA. Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, 619 Charles E. Young Drive East, Los Angeles, 90095-1496, CA
| | - Sharon Y Strauss
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, One Shields Avenue, CA 95616, USA
| | - Bruce E Tabashnik
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA
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171
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Scorched mussels (BIVALVIA: MYTILIDAE: BRACHIDONTINAE) from the temperate coasts of South America: phylogenetic relationships, trans-Pacific connections and the footprints of Quaternary glaciations. Mol Phylogenet Evol 2014; 82 Pt A:60-74. [PMID: 25451805 DOI: 10.1016/j.ympev.2014.10.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 08/26/2014] [Accepted: 10/03/2014] [Indexed: 11/22/2022]
Abstract
This study addresses aspects of the phylogeny and phylogeography of scorched mussels (BIVALVIA: MYTILIDAE: BRACHIDONTINAE) from southern South America (Argentina and Chile), as well as their ecophylogenetic implications. Relationships were inferred from sequences of two nuclear (28S and 18S) and one mitochondrial (COI) genes, using Bayesian and maximum likelihood analyses. Our results indicate that the monophyletic BRACHIDONTINAE include three well supported clades: [i] Brachidontes Swainson (=Hormomya Mörch), [ii] Ischadium Jukes-Browne+Geukensia van de Poel, and [iii] Austromytilus Laseron+Mytilisepta Habe (usually considered a member of the SEPTIFERINAE)+Perumytilus Olsson. Species of clade [iii] are distributed along the temperate coasts of the Pacific Ocean. Available evidence supports divergence between Austromytilus (Australia) and Perumytilus (South American) following the breakup of Australian, Antarctic and South American shelves. Four brachidontins occur in southern South America: Brachidontes rodriguezii (d'Orbigny), B. granulatus (Hanley), and two genetically distinct clades of Perumytilus. The latter are confined to the Chile-Peru (North Clade) and Magellanic (South Clade) Biogeographic Provinces, respectively warm- and cold-temperate. The South Clade is the only brachidontin restricted to cold-temperate waters. Biogeographic considerations and the fossil record prompted the hypothesis that the South Clade originated from the North Clade by incipient peripatric differentiation, followed by isolation during the Quaternary glaciations, genetic differentiation in the non-glaciated coasts of eastern Patagonia, back-expansion over southern Chile following post-LGM de-glaciation, and development of a secondary contact zone between the two clades in south-central Chile. Evidence of upper Pleistocene expansion of the South Clade parallels similar results on other organisms that have colonized coastal ecosystems from eastern Patagonia since the LGM, apparently occupying free ecological space. We emphasize that the assembly of communities cannot be explained solely in terms of environmental drivers, as history also matters.
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172
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Morlon H, Kefi S, Martinez ND. Effects of trophic similarity on community composition. Ecol Lett 2014; 17:1495-506. [DOI: 10.1111/ele.12356] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 06/02/2014] [Accepted: 08/19/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Hélène Morlon
- Institut de Biologie; Ecole Normale Supérieure; UMR CNRS 8197, 46 rue d'Ulm Paris 75005 France
- Centre de Mathématiques Appliquées; Ecole Polytechnique; UMR CNRS 7641, Route de Saclay Palaiseau Cedex 91128 France
| | - Sonia Kefi
- Institut des Sciences de l'Evolution; Université de Montpellier II; CNRS, IRD, CC 065; Place Eugène Bataillon; 34095 Montpellier Cedex 05 France
| | - Neo D. Martinez
- Department of Ecology and Evolutionary; University of Arizona; Tucson AZ 85721 USA
- Pacific Ecoinformatics and Computational Ecology Lab; Berkeley CA 94703 USA
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173
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Munoz F, Ramesh BR, Couteron P. How do habitat filtering and niche conservatism affect community composition at different taxonomic resolutions? Ecology 2014; 95:2179-91. [PMID: 25230469 DOI: 10.1890/13-0064.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Understanding how local species assembly depends on the regional biogeographic and environmental context is a challenging task in community ecology. In spatially implicit neutral models, a single immigration parameter, I(k), represents the flux of immigrants from a regional pool that compete with local offspring for establishment in communities. This flux counterbalances the effect of local stochastic extinctions to maintain local species diversity. If some species within the regional pool are not adapted to the local environment (habitat filtering), the migrant flux is reduced beyond that of the neutral model, such that habitat filtering influences the value of I(k) in non-neutral situations. Here, we propose a novel model in which immigrants from the regional pool are filtered according to their habitat preferences and the local environment, while taxa potentially retain habitat preferences from their ancestors (niche conservatism). Using both analytical reasoning and simulations, we demonstrate that I(k) is expected to be constant when estimated based on the community composition at several taxonomic levels, not only under neutral assumptions, but also when habitat filtering occurs, unless there is substantial niche conservatism. In the latter case, I(k) is expected to decrease when estimated based on the composition at species to genus and family levels, thus allowing a signature of niche conservatism to be detected by simply comparing I(k) estimates across taxonomic levels. We applied this approach to three rain forest data sets from South India and Central America and found no significant signature of niche conservatism when I(k) was compared across taxonomic levels, except at the family level in South India. We further observed more limited immigration in South Indian forests, supporting the hypothesis of a greater impact of habitat filtering and heterogeneity there than in Central America. Our results highlight the relevance of studying variations of I(k) in space and across taxonomic levels to test hypotheses about the ecological and evolutionary drivers of biodiversity patterns.
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174
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Abstract
Bacteria are omnipotent and they can be found everywhere. The study of bacterial pathogens has been happening from olden days to prevent epidemics, food spoilage, losses in agricultural production, and loss of lives. Modern techniques in DNA based species identification are considered. So, there is a need to acquire simple and quick identification technique. Hence, this review article covers the efficacy of DNA barcoding of bacteria. Routine DNA barcoding involves the production of PCR amplicons from particular regions to sequence them and these sequence data are used to identify or “barcode” that organism to make a distinction from other species.
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175
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Roquet C, Lavergne S, Thuiller W. One tree to link them all: a phylogenetic dataset for the European tetrapoda. PLOS CURRENTS 2014; 6:ecurrents.tol.5102670fff8aa5c918e78f5592790e48. [PMID: 25685620 PMCID: PMC4322008 DOI: 10.1371/currents.tol.5102670fff8aa5c918e78f5592790e48] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Since the ever-increasing availability of phylogenetic informative data, the last decade has seen an upsurge of ecological studies incorporating information on evolutionary relationships among species. However, detailed species-level phylogenies are still lacking for many large groups and regions, which are necessary for comprehensive large-scale eco-phylogenetic analyses. Here, we provide a dataset of 100 dated phylogenetic trees for all European tetrapods based on a mixture of supermatrix and supertree approaches. Phylogenetic inference was performed separately for each of the main Tetrapoda groups of Europe except mammals (i.e. amphibians, birds, squamates and turtles) by means of maximum likelihood (ML) analyses of supermatrix applying a tree constraint at the family (amphibians and squamates) or order (birds and turtles) levels based on consensus knowledge. For each group, we inferred 100 ML trees to be able to provide a phylogenetic dataset that accounts for phylogenetic uncertainty, and assessed node support with bootstrap analyses. Each tree was dated using penalized-likelihood and fossil calibration. The trees obtained were well-supported by existing knowledge and previous phylogenetic studies. For mammals, we modified the most complete supertree dataset available on the literature to include a recent update of the Carnivora clade. As a final step, we merged the phylogenetic trees of all groups to obtain a set of 100 phylogenetic trees for all European Tetrapoda species for which data was available (91%). We provide this phylogenetic dataset (100 chronograms) for the purpose of comparative analyses, macro-ecological or community ecology studies aiming to incorporate phylogenetic information while accounting for phylogenetic uncertainty.
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Affiliation(s)
- Cristina Roquet
- Evolution, Modeling and Analysis of Biodiversity, CNRS LECA, Université Joseph Fourier, Grenoble, France
| | - Sébastien Lavergne
- Evolution, Modeling and Analysis of Biodiversity, CNRS LECA, Université Joseph Fourier, Grenoble, France
| | - Wilfried Thuiller
- Evolution, Modeling and Analysis of Biodiversity, CNRS LECA, Université Joseph Fourier, Grenoble, France
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176
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Mazel F, Guilhaumon F, Mouquet N, Devictor V, Gravel D, Renaud J, Cianciaruso MV, Loyola RD, Diniz-Filho JAF, Mouillot D, Thuiller W. Multifaceted diversity-area relationships reveal global hotspots of mammalian species, trait and lineage diversity. GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2014; 23:836-847. [PMID: 25071413 PMCID: PMC4110700 DOI: 10.1111/geb.12158] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
AIM To define biome-scale hotspots of phylogenetic and functional mammalian biodiversity (PD and FD, respectively) and compare them to 'classical' hotspots based on species richness (SR) only. LOCATION Global. METHODS SR, PD & FD were computed for 782 terrestrial ecoregions using distribution ranges of 4616 mammalian species. We used a set of comprehensive diversity indices unified by a recent framework that incorporates the species relative coverage in each ecoregion. We build large-scale multifaceted diversity-area relationships to rank ecoregions according to their levels of biodiversity while accounting for the effect of area on each diversity facet. Finally we defined hotspots as the top-ranked ecoregions. RESULTS While ignoring species relative coverage led to a relative good congruence between biome top ranked SR, PD and FD hotspots, ecoregions harboring a rich and abundantly represented evolutionary history and functional diversity did not match with top ranked ecoregions defined by species richness. More importantly PD and FD hotspots showed important spatial mismatches. We also found that FD and PD generally reached their maximum values faster than species richness as a function of area. MAIN CONCLUSIONS The fact that PD/FD reach faster their maximal value than SR may suggest that the two former facets might be less vulnerable to habitat loss than the latter. While this point is expected, it is the first time that it is quantified at global scale and should have important consequences in conservation. Incorporating species relative coverage into the delineation of multifaceted hotspots of diversity lead to weak congruence between SR, PD and FD hotspots. This means that maximizing species number may fail at preserving those nodes (in the phylogenetic or functional tree) that are relatively abundant in the ecoregion. As a consequence it may be of prime importance to adopt a multifaceted biodiversity perspective to inform conservation strategies at global scale.
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Affiliation(s)
| | | | - Nicolas Mouquet
- Institut des Sciences de l'Evolution, UMR 5554, CNRS, Université Montpellier 2, Montpellier, France;
| | - Vincent Devictor
- Institut des Sciences de l'Evolution, Université Montpellier2, France;
| | - Dominique Gravel
- Université du Québec à Rimouski, Département de biologie, Chimie et Géographie, Québec, Canada;
| | | | | | - Rafael Dias Loyola
- Departamento de Ecologia, ICB, Universidade federal de Goiàs, Goiâna, Brasil;
| | | | - David Mouillot
- Laboratoire ECOSYM Université Montpellier 2, France; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld 4811, Australia ;
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177
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Egorov E, Prati D, Durka W, Michalski S, Fischer M, Schmitt B, Blaser S, Brändle M. Does land-use intensification decrease plant phylogenetic diversity in local grasslands? PLoS One 2014; 9:e103252. [PMID: 25061934 PMCID: PMC4111588 DOI: 10.1371/journal.pone.0103252] [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: 01/09/2014] [Accepted: 06/28/2014] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic diversity (PD) has been successfully used as a complement to classical measures of biological diversity such as species richness or functional diversity. By considering the phylogenetic history of species, PD broadly summarizes the trait space within a community. This covers amongst others complex physiological or biochemical traits that are often not considered in estimates of functional diversity, but may be important for the understanding of community assembly and the relationship between diversity and ecosystem functions. In this study we analyzed the relationship between PD of plant communities and land-use intensification in 150 local grassland plots in three regions in Germany. Specifically we asked whether PD decreases with land-use intensification and if so, whether the relationship is robust across different regions. Overall, we found that species richness decreased along land-use gradients the results however differed for common and rare species assemblages. PD only weakly decreased with increasing land-use intensity. The strength of the relationship thereby varied among regions and PD metrics used. From our results we suggest that there is no general relationship between PD and land-use intensification probably due to lack of phylogenetic conservatism in land-use sensitive traits. Nevertheless, we suggest that depending on specific regional idiosyncrasies the consideration of PD as a complement to other measures of diversity can be useful.
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Affiliation(s)
- Eugen Egorov
- Department of Ecology, Faculty of Biology, Philipps Universität, Marburg, Germany
- * E-mail:
| | - Daniel Prati
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Walter Durka
- Department Community Ecology, Helmholtz Centre for Environmental Research, Halle, Germany
| | - Stefan Michalski
- Department Community Ecology, Helmholtz Centre for Environmental Research, Halle, Germany
| | - Markus Fischer
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Barbara Schmitt
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Stefan Blaser
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Martin Brändle
- Department of Ecology, Faculty of Biology, Philipps Universität, Marburg, Germany
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178
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Hope AG, Ho SYW, Malaney JL, Cook JA, Talbot SL. ACCOUNTING FOR RATE VARIATION AMONG LINEAGES IN COMPARATIVE DEMOGRAPHIC ANALYSES. Evolution 2014; 68:2689-700. [DOI: 10.1111/evo.12469] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 05/22/2014] [Indexed: 01/16/2023]
Affiliation(s)
- Andrew G. Hope
- U.S. Geological Survey; Alaska Science Center; 4210 University Drive Anchorage Alaska 99508
| | - Simon Y. W. Ho
- School of Biological Sciences; Edgeworth David Building A11; The University of Sydney; Sydney New South Wales 2006 Australia
| | - Jason L. Malaney
- Department of Natural Resources and Environmental Science; University of Nevada-Reno; Reno Nevada 89557
| | - Joseph A. Cook
- Department of Biology; University of New Mexico; Museum of Southwestern Biology MSC03 2020; Albuquerque New Mexico 87131
| | - Sandra L. Talbot
- U.S. Geological Survey; Alaska Science Center; 4210 University Drive Anchorage Alaska 99508
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179
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Manel S, Couvreur TLP, Munoz F, Couteron P, Hardy OJ, Sonké B. Characterizing the phylogenetic tree community structure of a protected tropical rain forest area in Cameroon. PLoS One 2014; 9:e98920. [PMID: 24936786 PMCID: PMC4061019 DOI: 10.1371/journal.pone.0098920] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 05/09/2014] [Indexed: 11/18/2022] Open
Abstract
Tropical rain forests, the richest terrestrial ecosystems in biodiversity on Earth are highly threatened by global changes. This paper aims to infer the mechanisms governing species tree assemblages by characterizing the phylogenetic structure of a tropical rain forest in a protected area of the Congo Basin, the Dja Faunal Reserve (Cameroon). We re-analyzed a dataset of 11538 individuals belonging to 372 taxa found along nine transects spanning five habitat types. We generated a dated phylogenetic tree including all sampled taxa to partition the phylogenetic diversity of the nine transects into alpha and beta components at the level of the transects and of the habitat types. The variation in phylogenetic composition among transects did not deviate from a random pattern at the scale of the Dja Faunal Reserve, probably due to a common history and weak environmental variation across the park. This lack of phylogenetic structure combined with an isolation-by-distance pattern of taxonomic diversity suggests that neutral dispersal limitation is a major driver of community assembly in the Dja. To assess any lack of sensitivity to the variation in habitat types, we restricted the analyses of transects to the terra firme primary forest and found results consistent with those of the whole dataset at the level of the transects. Additionally to previous analyses, we detected a weak but significant phylogenetic turnover among habitat types, suggesting that species sort in varying environments, even though it is not predominating on the overall phylogenetic structure. Finer analyses of clades indicated a signal of clustering for species from the Annonaceae family, while species from the Apocynaceae family indicated overdispersion. These results can contribute to the conservation of the park by improving our understanding of the processes dictating community assembly in these hyperdiverse but threatened regions of the world.
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Affiliation(s)
- Stéphanie Manel
- Aix Marseille Université, IRD, LPED UMR 151, Marseille, France
- Centre de coopération internationale en recherche agronomique pour le développement, UMR AMAP, Montpellier, France
- * E-mail:
| | - Thomas L. P. Couvreur
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- Département des Sciences Biologiques, Laboratoire de Botanique Systématique et d’Ecologie, Université de Yaoundé I, Ecole Normale Supérieure, Yaoundé, Cameroon
| | | | - Pierre Couteron
- Institut de Recherche Pour le Développement, UMR AMAP, Montpellier, France
| | - Olivier J. Hardy
- Université Libre de Bruxelles, Faculté des Sciences, Evolutionary Biology and Ecology Brussels, Belgium
| | - Bonaventure Sonké
- Département des Sciences Biologiques, Laboratoire de Botanique Systématique et d’Ecologie, Université de Yaoundé I, Ecole Normale Supérieure, Yaoundé, Cameroon
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180
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Münkemüller T, Gallien L, Lavergne S, Renaud J, Roquet C, Abdulhak S, Dullinger S, Garraud L, Guisan A, Lenoir J, Svenning JC, Van Es J, Vittoz P, Willner W, Wohlgemuth T, Zimmermann NE, Thuiller W. Scale decisions can reverse conclusions on community assembly processes. GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2014; 23:620-632. [PMID: 24791149 PMCID: PMC4001086 DOI: 10.1111/geb.12137] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
AIM Phylogenetic diversity patterns are increasingly being used to better understand the role of ecological and evolutionary processes in community assembly. Here, we quantify how these patterns are influenced by scale choices in terms of spatial and environmental extent and organismic scales. LOCATION European Alps. METHODS We applied 42 sampling strategies differing in their combination of focal scales. For each resulting sub-dataset, we estimated the phylogenetic diversity of the species pools, phylogenetic α-diversities of local communities, and statistics commonly used together with null models in order to infer non-random diversity patterns (i.e. phylogenetic clustering versus over-dispersion). Finally, we studied the effects of scale choices on these measures using regression analyses. RESULTS Scale choices were decisive for revealing signals in diversity patterns. Notably, changes in focal scales sometimes reversed a pattern of over-dispersion into clustering. Organismic scale had a stronger effect than spatial and environmental extent. However, we did not find general rules for the direction of change from over-dispersion to clustering with changing scales. Importantly, these scale issues had only a weak influence when focusing on regional diversity patterns that change along abiotic gradients. MAIN CONCLUSIONS Our results call for caution when combining phylogenetic data with distributional data to study how and why communities differ from random expectations of phylogenetic relatedness. These analyses seem to be robust when the focus is on relating community diversity patterns to variation in habitat conditions, such as abiotic gradients. However, if the focus is on identifying relevant assembly rules for local communities, the uncertainty arising from a certain scale choice can be immense. In the latter case, it becomes necessary to test whether emerging patterns are robust to alternative scale choices.
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Affiliation(s)
- Tamara Münkemüller
- Laboratoire d’Ecologie Alpine, UMR CNRS 5553, University Joseph Fourier, Grenoble 1, BP 53, 38041 Grenoble Cedex 9, France
| | - Laure Gallien
- Laboratoire d’Ecologie Alpine, UMR CNRS 5553, University Joseph Fourier, Grenoble 1, BP 53, 38041 Grenoble Cedex 9, France
| | - Sébastien Lavergne
- Laboratoire d’Ecologie Alpine, UMR CNRS 5553, University Joseph Fourier, Grenoble 1, BP 53, 38041 Grenoble Cedex 9, France
| | - Julien Renaud
- Laboratoire d’Ecologie Alpine, UMR CNRS 5553, University Joseph Fourier, Grenoble 1, BP 53, 38041 Grenoble Cedex 9, France
| | - Cristina Roquet
- Laboratoire d’Ecologie Alpine, UMR CNRS 5553, University Joseph Fourier, Grenoble 1, BP 53, 38041 Grenoble Cedex 9, France
| | - Sylvain Abdulhak
- Domaine de Charance, Conservatoire Botanique National Alpin, Gap, 05000, France
| | - Stefan Dullinger
- Department of Conservation Biology, Vegetation- and Landscape Ecology, Faculty Centre of Biodiversity, Rennweg 14, 1030 Vienna
| | - Luc Garraud
- Domaine de Charance, Conservatoire Botanique National Alpin, Gap, 05000, France
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Institute of Earth Sciences, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jonathan Lenoir
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, FRE 3498 CNRS), Plant Biodiversity Lab, Jules Verne University of Picardie, 1 Rue des Louvels, FR-80037 Amiens Cedex 1, France
| | - Jens-Christian Svenning
- Ecoinformatics and Biodiversity Group, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
| | - Jérémie Van Es
- Domaine de Charance, Conservatoire Botanique National Alpin, Gap, 05000, France
| | - Pascal Vittoz
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Institute of Earth Sciences, University of Lausanne, 1015 Lausanne, Switzerland
| | - Wolfgang Willner
- Vienna Institute for Nature Conservation and Analyses, Giessergasse 6/7, 1090 Vienna, Austria
| | - Thomas Wohlgemuth
- Landscape Dynamics, Swiss Federal Research Institute WSL, CH-8903 Birmensdorf, Switzerland
| | - Niklaus E. Zimmermann
- Landscape Dynamics, Swiss Federal Research Institute WSL, CH-8903 Birmensdorf, Switzerland
| | - Wilfried Thuiller
- Laboratoire d’Ecologie Alpine, UMR CNRS 5553, University Joseph Fourier, Grenoble 1, BP 53, 38041 Grenoble Cedex 9, France
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181
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Gouveia SF, Villalobos F, Dobrovolski R, Beltrão-Mendes R, Ferrari SF. Forest structure drives global diversity of primates. J Anim Ecol 2014; 83:1523-30. [PMID: 24773500 DOI: 10.1111/1365-2656.12241] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 04/22/2014] [Indexed: 11/28/2022]
Abstract
Geographic gradients in the species richness of non-human primates have traditionally been attributed to the variation in forest productivity (related to precipitation levels), although an all-inclusive, global-scale analysis has never been conducted. We perform a more comprehensive test on the role of precipitation and biomass production and propose an alternative hypothesis - the variation in vertical structure of forest habitats as measured by forest canopy height - in determining primate species richness on a global scale. Considering the potential causal relationships among precipitation, productivity and forest structure, we arranged these variables within a path framework to assess their direct and indirect associations with the pattern of primate species richness using structural equation modelling. The analysis also accounted for the influence of spatial autocorrelation in the relationships and assessed possible historical differences among biogeographical regions. The path coefficients indicate that forest canopy height (used as a proxy for vertical forest structure) is a better predictor of primate species richness than either precipitation or productivity on both global and continental scales. The only exception was Asia, where precipitation prevailed, albeit independently from productivity or forest structure. The influence of spatially structured processes varied markedly among biogeographical regions. Our results challenge the traditional rainfall-based viewpoint in favour of forest distribution and structure as primary drivers of primate species richness, which aggregate potential effects from both climatic factors and habitat complexity. These findings may support predictions of the impact of forest removal on primate species richness.
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Affiliation(s)
- Sidney F Gouveia
- Department of Ecology, Federal University of Sergipe, São Cristóvão, SE, Brazil
| | | | | | - Raone Beltrão-Mendes
- Graduate Program in Biological Sciences (Zoology), Federal University of Paraíba, João Pessoa, PB, Brazil
| | - Stephen F Ferrari
- Department of Ecology, Federal University of Sergipe, São Cristóvão, SE, Brazil
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182
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Genung MA, Schweitzer JA, Bailey JK. Evolutionary history determines how plant productivity responds to phylogenetic diversity and species richness. PeerJ 2014; 2:e288. [PMID: 24688865 PMCID: PMC3961147 DOI: 10.7717/peerj.288] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 02/04/2014] [Indexed: 12/02/2022] Open
Abstract
The relationship between biodiversity and ecosystem function has received a great deal of attention in ecological research and recent results, from re-analyses, suggest that ecosystem function improves with increases in phylogenetic diversity. However, many of these results have been generalized across a range of different species and clades, and plants with different evolutionary histories could display different relationships between biodiversity and ecosystem function. To experimentally test this hypothesis, we manipulated species richness and phylogenetic diversity using 26 species from two subgenera of the genus Eucalyptus (subgenus Eucalyptus and subgenus Symphyomyrtus). We found that plant biomass (a measurement of ecosystem function) sometimes, but not always, responded to increases in species richness and phylogenetic diversity. Specifically, Symphyomyrtus plants showed a positive response while no comparable effect was observed for Eucalyptus plants, showing that responses to biodiversity can vary across different phylogenetic groups. Our results show that the impacts of evolutionary history may complicate the relationship between the diversity of plant communities and plant biomass.
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Affiliation(s)
- Mark A Genung
- Department of Ecology and Evolutionary Biology, University of Tennessee-Knoxville , Knoxville, TN , USA
| | - Jennifer A Schweitzer
- Department of Ecology and Evolutionary Biology, University of Tennessee-Knoxville , Knoxville, TN , USA
| | - Joseph K Bailey
- Department of Ecology and Evolutionary Biology, University of Tennessee-Knoxville , Knoxville, TN , USA
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183
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Mikryukov VS, Vorobeichik EL, Mikhailova IN. Variation of the epiphytic lichen diversity in a gradient of atmospheric pollution: do taxonomic, genetic, and functional distances between species add any information? DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2014; 454:22-5. [PMID: 24659281 DOI: 10.1134/s0012496614010025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Indexed: 11/22/2022]
Affiliation(s)
- V S Mikryukov
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, ul. 8 Marta 202, Yekaterinburg, 620144, Russia
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184
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Kelly S, Grenyer R, Scotland RW. Phylogenetic trees do not reliably predict feature diversity. DIVERS DISTRIB 2014. [DOI: 10.1111/ddi.12188] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Steven Kelly
- Department of Plant Sciences; University of Oxford; South Parks Road Oxford OX1 3RB UK
| | - Richard Grenyer
- School of Geography and the Environment; University of Oxford; South Parks Road Oxford OX1 3QY UK
| | - Robert W. Scotland
- Department of Plant Sciences; University of Oxford; South Parks Road Oxford OX1 3RB UK
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185
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Zupan L, Cabeza M, Maiorano L, Roquet C, Devictor V, Lavergne S, Mouillot D, Mouquet N, Renaud J, Thuiller W. Spatial mismatch of phylogenetic diversity across three vertebrate groups and protected areas in Europe. DIVERS DISTRIB 2014; 20:674-685. [PMID: 24791146 DOI: 10.1111/ddi.12186] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
AIM We investigate patterns of phylogenetic diversity in relation to species diversity for European birds, mammals and amphibians, to evaluate their congruence and highlight areas of particular evolutionary history. We estimate the extent to which the European network of protected areas (PAs) network retains interesting evolutionary history areas for the three groups separately and simultaneously. LOCATION Europe. METHODS Phylogenetic (QEPD) and species diversity (SD) were estimated using the Rao's quadratic entropy at 10' resolution. We determined the regional relationship between QEPD and SD for each taxa with a spatial regression model and used the tails of the residuals (QERES) distribution to identify areas of higher and lower QEPD than predicted. Spatial congruence of biodiversity between groups was assessed with Pearson's correlation. A simple classification scheme allowed building a convergence map where a convergent pixel equalled to a QERES value of the same sign for the 3 groups. This convergence map was overlaid to the current PAs network to estimate the level of protection in convergent pixels and compared it to a null expectation built on 1000 randomization of PAs over the landscape. RESULTS QERES patterns across vertebrates show a strong spatial mismatch highlighting different evolutionary histories. Convergent areas represent only 2.7% of the Western Palearctic, with only 8.4% of these areas being covered by the current PAs network while a random distribution would retain 10.4% of them. QERES are unequally represented within PAs: areas with higher QEPD than predicted are better covered than expected, while low QEPD areas are undersampled. MAIN CONCLUSIONS Patterns of diversity strongly diverge between groups of vertebrates in Europe. Although Europe has the world's most extensive PAs network, evolutionary history of terrestrial vertebrates is unequally protected. The challenge is now to reconcile effective conservation planning with a contemporary view of biodiversity integrating multiple facets.
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Affiliation(s)
- Laure Zupan
- Laboratoire d'Écologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble Cedex 9, France
| | - Mar Cabeza
- Metapopulation Research Group, Department of Biosciences, P.O. Box 65, 00014 University of Helsinki, Finland
| | - Luigi Maiorano
- Department of Biology and Biotechnologies "Charles Darwin", University of Rome "La Sapienza", viale dell'Università 32, 00185 Roma, Italia
| | - Cristina Roquet
- Laboratoire d'Écologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble Cedex 9, France
| | - Vincent Devictor
- Institut des Sciences de l'Evolution, UMR 5554, CNRS, Université Montpellier 2, CC 065, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - Sébastien Lavergne
- Laboratoire d'Écologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble Cedex 9, France
| | - David Mouillot
- Laboratoire ECOSYM UMR 5119, Université Montpellier 2, 34095 Montpellier Cedex 5, France
| | - Nicolas Mouquet
- Institut des Sciences de l'Evolution, UMR 5554, CNRS, Université Montpellier 2, CC 065, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - Julien Renaud
- Laboratoire d'Écologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble Cedex 9, France
| | - Wilfried Thuiller
- Laboratoire d'Écologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble Cedex 9, France
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186
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Cooke SJ, Killen SS, Metcalfe JD, McKenzie DJ, Mouillot D, Jørgensen C, Peck MA. Conservation physiology across scales: insights from the marine realm. CONSERVATION PHYSIOLOGY 2014; 2:cou024. [PMID: 27293645 PMCID: PMC4732490 DOI: 10.1093/conphys/cou024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/11/2014] [Accepted: 05/19/2014] [Indexed: 05/21/2023]
Abstract
As the field of conservation physiology develops and becomes increasingly integrated with ecology and conservation science, the fundamental concept of scale is being recognized as important, particularly for ensuring that physiological knowledge is contextualized in a manner most relevant to policy makers, conservation practitioners and stakeholders. Failure to consider the importance of scale in conservation physiology-both the challenges and the opportunities that it creates-will impede the ability of this discipline to generate the scientific understanding needed to contribute to meaningful conservation outcomes. Here, we have focused on five aspects of scale: biological, spatial, temporal, allometric and phylogenetic. We also considered the scale of policy and policy application relevant to those five types of scale as well as the merits of upscaling and downscaling to explore and address conservation problems. Although relevant to all systems (e.g. freshwater, terrestrial) we have used examples from the marine realm, with a particular emphasis on fishes, given the fact that there is existing discourse regarding scale and its relevance for marine conservation and management. Our synthesis revealed that all five aspects of scale are relevant to conservation physiology, with many aspects inherently linked. It is apparent that there are both opportunities and challenges afforded by working across scales but, to understand mechanisms underlying conservation problems, it is essential to consider scale of all sorts and to work across scales to the greatest extent possible. Moreover, given that the scales in biological processes will often not match policy and management scales, conservation physiology needs to show how it is relevant to aspects at different policy/management scales, change the scales at which policy/management intervention is applied or be prepared to be ignored.
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Affiliation(s)
- Steven J. Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental Science, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6
- Corresponding author: Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental Science, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6. Tel: +1 613 867 6711.
| | - Shaun S. Killen
- Institute of Biodiversity, Animal Health, and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - Julian D. Metcalfe
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft Laboratory, Suffolk NR33 0HT, UK
| | - David J. McKenzie
- Equipe Diversité et Ecologie des Poissons, UMR5119 Ecologie des Systèmes Marins Côtiers, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - David Mouillot
- Equipe Diversité et Ecologie des Poissons, UMR5119 Ecologie des Systèmes Marins Côtiers, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | | | - Myron A. Peck
- Institute of Hydrobiology and Fisheries Science, University of Hamburg, Olbersweg 24, D-22767 Hamburg, Germany
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187
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Vannette RL, Fukami T, Wootton T. Historical contingency in species interactions: towards niche-based predictions. Ecol Lett 2014; 17:115-24. [PMID: 24341984 PMCID: PMC4344821 DOI: 10.1111/ele.12204] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 08/19/2013] [Accepted: 10/01/2013] [Indexed: 12/29/2022]
Abstract
The way species affect one another in ecological communities often depends on the order of species arrival. The magnitude of such historical contingency, known as priority effects, varies across species and environments, but this variation has proven difficult to predict, presenting a major challenge in understanding species interactions and consequences for community structure and function. Here, we argue that improved predictions can be achieved by decomposing species' niches into three components: overlap, impact and requirement. Based on classic theories of community assembly, three hypotheses that emphasise related, but distinct influences of the niche components are proposed: priority effects are stronger among species with higher resource use overlap; species that impact the environment to a greater extent exert stronger priority effects; and species whose growth rate is more sensitive to changes in the environment experience stronger priority effects. Using nectar-inhabiting microorganisms as a model system, we present evidence that these hypotheses complement the conventional hypothesis that focuses on the role of environmental harshness, and show that niches can be twice as predictive when separated into components. Taken together, our hypotheses provide a basis for developing a general framework within which the magnitude of historical contingency in species interactions can be predicted.
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Affiliation(s)
- Rachel L Vannette
- Department of Biology, Stanford UniversityStanford, California, 94305-5020, USA
| | - Tadashi Fukami
- Department of Biology, Stanford UniversityStanford, California, 94305-5020, USA
| | - Tim Wootton
- Department of Biology, Stanford UniversityStanford, California, 94305-5020, USA
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188
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Scriber JM. Climate-Driven Reshuffling of Species and Genes: Potential Conservation Roles for Species Translocations and Recombinant Hybrid Genotypes. INSECTS 2013; 5:1-61. [PMID: 26462579 PMCID: PMC4592632 DOI: 10.3390/insects5010001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/04/2013] [Accepted: 12/06/2013] [Indexed: 01/11/2023]
Abstract
Comprising 50%-75% of the world's fauna, insects are a prominent part of biodiversity in communities and ecosystems globally. Biodiversity across all levels of biological classifications is fundamentally based on genetic diversity. However, the integration of genomics and phylogenetics into conservation management may not be as rapid as climate change. The genetics of hybrid introgression as a source of novel variation for ecological divergence and evolutionary speciation (and resilience) may generate adaptive potential and diversity fast enough to respond to locally-altered environmental conditions. Major plant and herbivore hybrid zones with associated communities deserve conservation consideration. This review addresses functional genetics across multi-trophic-level interactions including "invasive species" in various ecosystems as they may become disrupted in different ways by rapid climate change. "Invasive genes" (into new species and populations) need to be recognized for their positive creative potential and addressed in conservation programs. "Genetic rescue" via hybrid translocations may provide needed adaptive flexibility for rapid adaptation to environmental change. While concerns persist for some conservationists, this review emphasizes the positive aspects of hybrids and hybridization. Specific implications of natural genetic introgression are addressed with a few examples from butterflies, including transgressive phenotypes and climate-driven homoploid recombinant hybrid speciation. Some specific examples illustrate these points using the swallowtail butterflies (Papilionidae) with their long-term historical data base (phylogeographical diversity changes) and recent (3-decade) climate-driven temporal and genetic divergence in recombinant homoploid hybrids and relatively recent hybrid speciation of Papilio appalachiensis in North America. Climate-induced "reshuffling" (recombinations) of species composition, genotypes, and genomes may become increasingly ecologically and evolutionarily predictable, but future conservation management programs are more likely to remain constrained by human behavior than by lack of academic knowledge.
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Affiliation(s)
- Jon Mark Scriber
- Department of Entomology, Michigan State University, East Lansing, Michigan, MI 48824, USA.
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
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189
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Pellissier L, Rohr RP, Ndiribe C, Pradervand JN, Salamin N, Guisan A, Wisz M. Combining food web and species distribution models for improved community projections. Ecol Evol 2013; 3:4572-83. [PMID: 24340196 PMCID: PMC3856755 DOI: 10.1002/ece3.843] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 09/03/2013] [Accepted: 09/09/2013] [Indexed: 11/22/2022] Open
Abstract
The ability to model biodiversity patterns is of prime importance in this era of severe environmental crisis. Species assemblage along environmental gradients is subject to the interplay of biotic interactions in complement to abiotic filtering and stochastic forces. Accounting for complex biotic interactions for a wide array of species remains so far challenging. Here, we propose using food web models that can infer the potential interaction links between species as a constraint in species distribution models. Using a plant-herbivore (butterfly) interaction dataset, we demonstrate that this combined approach is able to improve species distribution and community forecasts. The trophic interaction network between butterfly larvae and host plant was phylogenetically structured and driven by host plant nitrogen content allowing forecasting the food web model to unknown interactions links. This combined approach is very useful in rendering models of more generalist species that have multiple potential interaction links, where gap in the literature may occur. Our combined approach points toward a promising direction for modeling the spatial variation in entire species interaction networks.
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Affiliation(s)
- Loïc Pellissier
- Department of Bioscience, The Arctic Research Centre, Aarhus UniversityNy Munkegade 114, DK-8000, Aarhus, Denmark
| | - Rudolf P Rohr
- Integrative Ecology Group, Estación Biológica de Doñana (EBD – CSIC)Calle Américo Vespucio s/n, Sevilla, 41092, Spain
| | - Charlotte Ndiribe
- Department of Ecology and Evolution, University of LausanneBâtiment Biophore, Lausanne, CH-1015, Switzerland
| | - Jean-Nicolas Pradervand
- Department of Ecology and Evolution, University of LausanneBâtiment Biophore, Lausanne, CH-1015, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, University of LausanneBâtiment Biophore, Lausanne, CH-1015, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of LausanneBâtiment Biophore, Lausanne, CH-1015, Switzerland
| | - Mary Wisz
- Department of Bioscience, The Arctic Research Centre, Aarhus UniversityNy Munkegade 114, DK-8000, Aarhus, Denmark
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190
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Castagneyrol B, Jactel H, Vacher C, Brockerhoff EG, Koricheva J. Effects of plant phylogenetic diversity on herbivory depend on herbivore specialization. J Appl Ecol 2013. [DOI: 10.1111/1365-2664.12175] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bastien Castagneyrol
- INRA; UMR 1202 BIOGECO; F-33610 Cestas France
- Univ. Bordeaux; BIOGECO; UMR 1202; F-33400 Talence France
- School of Biological Sciences; Royal Holloway University of London; Egham Surrey TW20 0EX UK
| | - Hervé Jactel
- INRA; UMR 1202 BIOGECO; F-33610 Cestas France
- Univ. Bordeaux; BIOGECO; UMR 1202; F-33400 Talence France
| | - Corinne Vacher
- INRA; UMR 1202 BIOGECO; F-33610 Cestas France
- Univ. Bordeaux; BIOGECO; UMR 1202; F-33400 Talence France
| | | | - Julia Koricheva
- School of Biological Sciences; Royal Holloway University of London; Egham Surrey TW20 0EX UK
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191
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Joly S, Davies TJ, Archambault A, Bruneau A, Derry A, Kembel SW, Peres-Neto P, Vamosi J, Wheeler TA. Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead. Mol Ecol Resour 2013; 14:221-32. [DOI: 10.1111/1755-0998.12173] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 09/03/2013] [Accepted: 09/16/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Simon Joly
- Institut de recherche en biologie végétale; Département de sciences biologiques; Université de Montréal; 4101 Sherbrooke East Montréal Quebec, Canada H1X 2B2
- Montreal Botanical Garden; 4101 Sherbrooke East Montréal Quebec, Canada H1X 2B2
| | - T. Jonathan Davies
- Biology Department; McGill University; 1205 Dr Penfield Montréal Quebec, Canada H3A 1B1
| | - Annie Archambault
- Québec Centre for Biodiversity Science; 1205 Dr Penfield Montréal Quebec, Canada H3A 1B1
| | - Anne Bruneau
- Institut de recherche en biologie végétale; Département de sciences biologiques; Université de Montréal; 4101 Sherbrooke East Montréal Quebec, Canada H1X 2B2
| | - Alison Derry
- Département des sciences biologiques; Université du Québec à Montréal; 141 Avenue du Président-Kennedy Montréal Quebec, Canada H2X 1Y4
| | - Steven W. Kembel
- Département des sciences biologiques; Université du Québec à Montréal; 141 Avenue du Président-Kennedy Montréal Quebec, Canada H2X 1Y4
| | - Pedro Peres-Neto
- Département des sciences biologiques; Université du Québec à Montréal; 141 Avenue du Président-Kennedy Montréal Quebec, Canada H2X 1Y4
| | - Jana Vamosi
- Department of Biological Sciences; University of Calgary; 2500 University Drive NW Calgary Alberta, Canada T2N 1N4
| | - Terry A. Wheeler
- Department of Natural Resources Sciences; McGill University; Macdonald Campus Ste. Anne de Bellevue Quebec, Canada H9X 3V9
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192
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Livingston G, Jha S, Vega A, Gilbert L. Conservation value and permeability of neotropical oil palm landscapes for orchid bees. PLoS One 2013; 8:e78523. [PMID: 24147137 PMCID: PMC3798381 DOI: 10.1371/journal.pone.0078523] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/20/2013] [Indexed: 11/22/2022] Open
Abstract
The proliferation of oil palm plantations has led to dramatic changes in tropical landscapes across the globe. However, relatively little is known about the effects of oil palm expansion on biodiversity, especially in key ecosystem-service providing organisms like pollinators. Rapid land use change is exacerbated by limited knowledge of the mechanisms causing biodiversity decline in the tropics, particularly those involving landscape features. We examined these mechanisms by undertaking a survey of orchid bees, a well-known group of Neotropical pollinators, across forest and oil palm plantations in Costa Rica. We used chemical baits to survey the community in four regions: continuous forest sites, oil palm sites immediately adjacent to forest, oil palm sites 2 km from forest, and oil palm sites greater than 5 km from forest. We found that although orchid bees are present in all environments, orchid bee communities diverged across the gradient, and community richness, abundance, and similarity to forest declined as distance from forest increased. In addition, mean phylogenetic distance of the orchid bee community declined and was more clustered in oil palm. Community traits also differed with individuals in oil palm having shorter average tongue length and larger average geographic range size than those in the forest. Our results indicate two key features about Neotropical landscapes that contain oil palm: 1) oil palm is selectively permeable to orchid bees and 2) orchid bee communities in oil palm have distinct phylogenetic and trait structure compared to communities in forest. These results suggest that conservation and management efforts in oil palm-cultivating regions should focus on landscape features.
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Affiliation(s)
- George Livingston
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Shalene Jha
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| | | | - Lawrence Gilbert
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
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193
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Venail PA, Alexandrou MA, Oakley TH, Cardinale BJ. Shared ancestry influences community stability by altering competitive interactions: evidence from a laboratory microcosm experiment using freshwater green algae. Proc Biol Sci 2013; 280:20131548. [PMID: 23945692 PMCID: PMC3757983 DOI: 10.1098/rspb.2013.1548] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 07/17/2013] [Indexed: 11/12/2022] Open
Abstract
The impact of biodiversity on the stability of ecological communities has been debated among biologists for more than a century. Recently summarized empirical evidence suggests that biodiversity tends to enhance the temporal stability of community-level properties such as biomass; however, the underlying mechanisms driving this relationship remain poorly understood. Here, we report the results of a microcosm study in which we used simplified systems of freshwater microalgae to explore how the phylogenetic relatedness of species influences the temporal stability of community biomass by altering the nature of their competitive interactions. We show that combinations of two species that are more evolutionarily divergent tend to have lower temporal stability of biomass. In part, this is due to negative 'selection effects' in which bicultures composed of distantly related species are more likely to contain strong competitors that achieve low biomass. In addition, bicultures of distantly related species had on average weaker competitive interactions, which reduced compensatory dynamics and decreased the stability of community biomass. Our results demonstrate that evolutionary history plays a key role in controlling the mechanisms, which give rise to diversity-stability relationships. As such, patterns of shared ancestry may help us predict the ecosystem-level consequences of biodiversity loss.
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Affiliation(s)
- Patrick A Venail
- School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI 48109-1041, USA.
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194
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Diniz-Filho JAF, Loyola RD, Raia P, Mooers AO, Bini LM. Darwinian shortfalls in biodiversity conservation. Trends Ecol Evol 2013; 28:689-95. [PMID: 24091208 DOI: 10.1016/j.tree.2013.09.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 08/30/2013] [Accepted: 09/03/2013] [Indexed: 11/25/2022]
Abstract
If we were to describe all the species on Earth and determine their distributions, we would solve the popularly termed 'Linnean' and 'Wallacean' shortfalls in biodiversity conservation. Even so, we would still be hindered by a 'Darwinian shortfall', that is, the lack of relevant phylogenetic information for most organisms. Overall, there are too few comprehensive phylogenies, large uncertainties in the estimation of divergence times, and, most critically, unknown evolutionary models linking phylogenies to relevant ecological traits and life history variation. Here, we discuss these issues and offer suggestions for further research to support evolutionary-based conservation planning.
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195
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Hidasi-Neto J, Loyola RD, Cianciaruso MV. Conservation actions based on red lists do not capture the functional and phylogenetic diversity of birds in Brazil. PLoS One 2013; 8:e73431. [PMID: 24039939 PMCID: PMC3767746 DOI: 10.1371/journal.pone.0073431] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 07/19/2013] [Indexed: 11/19/2022] Open
Abstract
Red Lists of threatened species play a critical role in conservation science and practice. However, policy-making based on Red Lists ignores ecological and evolutionary consequences of losing biodiversity because these lists focus on species alone. To decide if relying on Red Lists alone can help to conserve communities' functional (FD) and phylogenetic (PD) diversity, it is useful to evaluate whether Red List categories represent species with diverse ecological traits and evolutionary histories. Additionally, local scale analyses using regional Red Lists should represent more realistic pools of co-occurring species and thereby better capture eventual losses of FD and PD. Here, we used 21 life-history traits and a phylogeny for all Brazilian birds to determine whether species assigned under the IUCN global Red List, the Brazilian national, and regional Red Lists capture more FD and PD than expected by chance. We also built local Red Lists and analysed if they capture more FD and PD at the local scale. Further, we investigated whether individual threat categories have species with greater FD and PD than expected by chance. At any given scale, threat categories did not capture greater FD or PD than expected by chance. Indeed, mostly categories captured equal or less FD or PD than expected by chance. These findings would not have great consequences if Red Lists were not often considered as a major decision support tool for policy-making. Our results challenge the practice of investing conservation resources based only on species Red Lists because, from an ecological and evolutionary point of view, this would be the same as protecting similar or random sets of species. Thus, new prioritization methods, such as the EDGE of Existence initiative, should be developed and applied to conserve species' ecological traits and evolutionary histories at different spatial scales.
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Affiliation(s)
- José Hidasi-Neto
- Programa de Pós-Graduação em Ecologia e Evolução, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Rafael Dias Loyola
- Departamento de Ecologia, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
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196
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Gravel D, Poisot T, Albouy C, Velez L, Mouillot D. Inferring food web structure from predator-prey body size relationships. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12103] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dominique Gravel
- Département de biologie, chimie et géographie; Université du Québec à Rimouski; 300 Allée des Ursulines G5L 3A1 Québec Canada
- Québec Centre for Biodiversity Science
| | - Timothée Poisot
- Département de biologie, chimie et géographie; Université du Québec à Rimouski; 300 Allée des Ursulines G5L 3A1 Québec Canada
- Québec Centre for Biodiversity Science
| | - Camille Albouy
- UMR CNRS-UM2-IRD-IFREMER 5119 ECOSYM; Université Montpellier 2, CC 093 34095 Montpellier Cedex5 France
- Laboratoire Ecosystèmes Marins Exploités UMR 212; IRD, IFREMER, UMII, UMI; avenue Jean Monnet BP171 34203 Sete Cedex France
| | - Laure Velez
- UMR CNRS-UM2-IRD-IFREMER 5119 ECOSYM; Université Montpellier 2, CC 093 34095 Montpellier Cedex5 France
| | - David Mouillot
- UMR CNRS-UM2-IRD-IFREMER 5119 ECOSYM; Université Montpellier 2, CC 093 34095 Montpellier Cedex5 France
- ARC Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
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197
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Chalmandrier L, Müunkemüller T, Gallien L, de Bello F, Mazel F, Lavergne S, Thuiller W. A family of null models to distinguish between environmental filtering and biotic interactions in functional diversity patterns. JOURNAL OF VEGETATION SCIENCE : OFFICIAL ORGAN OF THE INTERNATIONAL ASSOCIATION FOR VEGETATION SCIENCE 2013; 24:853-864. [PMID: 24791143 PMCID: PMC4003529 DOI: 10.1111/jvs.12031] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
QUESTIONS Traditional null models used to reveal assembly processes from functional diversity patterns are not tailored for comparing different spatial and evolutionary scales. In this study, we present and explore a family of null models that can help disentangling assembly processes at their appropriate scales and thereby elucidate the ecological drivers of community assembly. LOCATION French Alps. METHODS Our approach gradually constrains null models by: (1) filtering out species not able to survive in the regional conditions in order to reduce the spatial scale, and (2) shuffling species only within lineages of different ages to reduce the evolutionary scale of the analysis. We first tested and validated this approach using simulated communities. We then applied it to study the functional diversity patterns of the leaf-height-seed strategy of plant communities in the French Alps. RESULTS Using simulations, we found that reducing the spatial scale correctly detected a signature of competition (functional divergence) even when environmental filtering produced an overlaying signal of functional convergence. However, constraining the evolutionary scale did not change the identified functional diversity patterns. In the case study of alpine plant communities, investigating scale effects revealed that environmental filtering had a strong influence at larger spatial and evolutionary scales and that neutral processes were more important at smaller scales. In contrast to the simulation study results, decreasing the evolutionary scale tended to increase patterns of functional divergence. CONCLUSION We argue that the traditional null model approach can only identify a single main process at a time and suggest to rather use a family of null models to disentangle intertwined assembly processes acting across spatial and evolutionary scales.
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Affiliation(s)
- L Chalmandrier
- : Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, BP 53, Grenoble Cedex 9, 38041, France
| | - T Müunkemüller
- ( ): Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, BP 53, Grenoble Cedex 9, 38041, France
| | - L Gallien
- ( ): Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, BP 53, Grenoble Cedex 9, 38041, France
| | - F de Bello
- ( ): Institute of Botany, Academy of Sciences of the Czech Republic, Třeboň, CZ-379 82, Czech Republic
| | - F Mazel
- ( ): Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, BP 53, Grenoble Cedex 9, 38041, France
| | - S Lavergne
- ( ): Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, BP 53, Grenoble Cedex 9, 38041, France
| | - W Thuiller
- ( ): Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, BP 53, Grenoble Cedex 9, 38041, France
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198
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Cadotte M, Albert CH, Walker SC. The ecology of differences: assessing community assembly with trait and evolutionary distances. Ecol Lett 2013; 16:1234-44. [DOI: 10.1111/ele.12161] [Citation(s) in RCA: 206] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 04/10/2013] [Accepted: 06/26/2013] [Indexed: 10/26/2022]
Affiliation(s)
- Marc Cadotte
- Department of Biological Sciences; University of Toronto - Scarborough; 1265 Military trail Toronto ON Canada M1C 1A4
- Department of Ecology and Evolutionary Biology; University of Toronto; 25 Wilcocks St. Toronto ON M5S 3B2 Canada
| | - Cecile H. Albert
- Laboratoire d'Ecologie Alpine; UMR CNRS 5553, CNRS; Universite Joseph Fourier; BP 53 38041 Grenoble Cedex 9 France
- Department of Biology; McGill University; 1205 Dr. Penfield Avenue Montreal QC Canada H3A 1B1
| | - Steve C. Walker
- Departement de Sciences Biologiques; Universite de Montreal; C.P. 6128, Succursale Centre-ville Montreal QC Canada H3C 3J7
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199
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Meynard CN, Lavergne S, Boulangeat I, Garraud L, Van Es J, Mouquet N, Thuiller W. Disentangling the drivers of metacommunity structure across spatial scales. JOURNAL OF BIOGEOGRAPHY 2013; 40:1560-1571. [PMID: 24790288 PMCID: PMC4000944 DOI: 10.1111/jbi.12116] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
AIM Metacommunity theories attribute different relative degrees of importance to dispersal, environmental filtering, biotic interactions and stochastic processes in community assembly, but the role of spatial scale remains uncertain. Here we used two complementary statistical tools to test: (1) whether or not the patterns of community structure and environmental influences are consistent across resolutions; and (2) whether and how the joint use of two fundamentally different statistical approaches provides a complementary interpretation of results. LOCATION Grassland plants in the French Alps. METHODS We used two approaches across five spatial resolutions (ranging from 1 km × 1 km to 30 km × 30 km): variance partitioning, and analysis of metacommunity structure on the site-by-species incidence matrices. Both methods allow the testing of expected patterns resulting from environmental filtering, but variance partitioning allows the role of dispersal and environmental gradients to be studied, while analysis of the site-by-species metacommunity structure informs an understanding of how environmental filtering occurs and whether or not patterns differ from chance expectation. We also used spatial regressions on species richness to identify relevant environmental factors at each scale and to link results from the two approaches. RESULTS Major environmental drivers of richness included growing degree-days, temperature, moisture and spatial or temporal heterogeneity. Variance partitioning pointed to an increase in the role of dispersal at coarser resolutions, while metacommunity structure analysis pointed to environmental filtering having an important role at all resolutions through a Clementsian assembly process (i.e. groups of species having similar range boundaries and co-occurring in similar environments). MAIN CONCLUSIONS The combination of methods used here allows a better understanding of the forces structuring ecological communities than either one of them used separately. A key aspect in this complementarity is that variance partitioning can detect effects of dispersal whereas metacommunity structure analysis cannot. Moreover, the latter can distinguish between different forms of environmental filtering (e.g. individualistic versus group species responses to environmental gradients).
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Affiliation(s)
- Christine N. Meynard
- INRA, UMR CBGP (INRA / IRD / Cirad / Montpellier SupAgro), Campus International de Baillarguet, CS 30016, F-34988, Montferrier-sur-Lez cedex, France
| | - Sébastien Lavergne
- Laboratoire d’Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourrier, Grenoble I, 38041, Grenoble, Cedex 9, France
| | - Isabelle Boulangeat
- Laboratoire d’Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourrier, Grenoble I, 38041, Grenoble, Cedex 9, France
| | - Luc Garraud
- Conservatoire Botanique National Alpin, Domaine de Charance, 05000, Gap, France
| | - Jérémie Van Es
- Conservatoire Botanique National Alpin, Domaine de Charance, 05000, Gap, France
| | - Nicolas Mouquet
- Institut des Sciences de l’Evolution, UMR 5554-CNRS, Université de Montpellier II, Place Eugene Bataillon, 34095, Montpellier Cedex 05, France
| | - Wilfried Thuiller
- Laboratoire d’Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourrier, Grenoble I, 38041, Grenoble, Cedex 9, France
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200
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Bennett JA, Lamb EG, Hall JC, Cardinal-McTeague WM, Cahill JF. Increased competition does not lead to increased phylogenetic overdispersion in a native grassland. Ecol Lett 2013; 16:1168-76. [DOI: 10.1111/ele.12153] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/03/2013] [Accepted: 06/13/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Jonathan A. Bennett
- Department of Biological Sciences; University of Alberta; Edmonton; AB; T6G 2E9; Canada
| | - Eric G. Lamb
- Department of Plant Sciences; University of Saskatchewan; Saskatoon; SK; S7N 5A8; Canada
| | - Jocelyn C. Hall
- Department of Biological Sciences; University of Alberta; Edmonton; AB; T6G 2E9; Canada
| | | | - James F. Cahill
- Department of Biological Sciences; University of Alberta; Edmonton; AB; T6G 2E9; Canada
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