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Twist BA, Mazel F, Zaklan Duff S, Lemay MA, Pearce CM, Martone PT. Kelp and sea urchin settlement mediated by biotic interactions with benthic coralline algal species. J Phycol 2024; 60:363-379. [PMID: 38147464 DOI: 10.1111/jpy.13420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 12/28/2023]
Abstract
Species interactions can influence key ecological processes that support community assembly and composition. For example, coralline algae encompass extensive diversity and may play a major role in regime shifts from kelp forests to urchin-dominated barrens through their role in inducing invertebrate larval metamorphosis and influencing kelp spore settlement. In a series of laboratory experiments, we tested the hypothesis that different coralline communities facilitate the maintenance of either ecosystem state by either promoting or inhibiting early recruitment of kelps or urchins. Coralline algae significantly increased red urchin metamorphosis compared with a control, while they had varying effects on kelp settlement. Urchin metamorphosis and density of juvenile canopy kelps did not differ significantly across coralline species abundant in both kelp forests and urchin barrens, suggesting that recruitment of urchin and canopy kelps does not depend on specific corallines. Non-calcified fleshy red algal crusts promoted the highest mean urchin metamorphosis percentage and showed some of the lowest canopy kelp settlement. In contrast, settlement of one subcanopy kelp species was reduced on crustose corallines, but elevated on articulated corallines, suggesting that articulated corallines, typically absent in urchin barrens, may need to recover before this subcanopy kelp could return. Coralline species differed in surface bacterial microbiome composition; however, urchin metamorphosis was not significantly different when microbiomes were removed with antibiotics. Our results clarify the role played by coralline algal species in kelp forest community assembly and could have important implications for kelp forest recovery.
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Affiliation(s)
- Brenton A Twist
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Hakai Institute, Vancouver, British Columbia, Canada
| | - Florent Mazel
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Stefanie Zaklan Duff
- Department of Fisheries and Aquaculture, Vancouver Island University, Nanaimo, British Columbia, Canada
| | | | - Christopher M Pearce
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Patrick T Martone
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Hakai Institute, Vancouver, British Columbia, Canada
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2
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Mazel F, Guisan A, Parfrey LW. Transmission mode and dispersal traits correlate with host specificity in mammalian gut microbes. Mol Ecol 2024; 33:e16862. [PMID: 36786039 DOI: 10.1111/mec.16862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/24/2022] [Accepted: 01/09/2023] [Indexed: 02/15/2023]
Abstract
Different host species associate with distinct gut microbes in mammals, a pattern sometimes referred to as phylosymbiosis. However, the processes shaping this host specificity are not well understood. One model proposes that barriers to microbial transmission promote specificity by limiting microbial dispersal between hosts. This model predicts that specificity levels measured across microbes is correlated to transmission mode (vertical vs. horizontal) and individual dispersal traits. Here, we leverage two large publicly available gut microbiota data sets (1490 samples from 195 host species) to test this prediction. We found that host specificity varies widely across bacteria (i.e., there are generalist and specialist bacteria) and depends on transmission mode and dispersal ability. Horizontally-like transmitted bacteria equipped with traits that facilitate switches between host (e.g., tolerance to oxygen) were found to be less specific (more generalist) than microbes without those traits, for example, vertically-like inherited bacteria that are intolerant to oxygen. Altogether, our findings are compatible with a model in which limited microbial dispersal abilities foster host specificity.
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Affiliation(s)
- Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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3
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Mazel F, Pitteloud C, Guisan A, Pellissier L. Contrasted host specificity of gut and endosymbiont bacterial communities in alpine grasshoppers and crickets. ISME Commun 2024; 4:ycad013. [PMID: 38374896 PMCID: PMC10875604 DOI: 10.1093/ismeco/ycad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 02/21/2024]
Abstract
Bacteria colonize the body of macroorganisms to form associations ranging from parasitic to mutualistic. Endosymbiont and gut symbiont communities are distinct microbiomes whose compositions are influenced by host ecology and evolution. Although the composition of horizontally acquired symbiont communities can correlate to host species identity (i.e. harbor host specificity) and host phylogeny (i.e. harbor phylosymbiosis), we hypothesize that the microbiota structure of vertically inherited symbionts (e.g. endosymbionts like Wolbachia) is more strongly associated with the host species identity and phylogeny than horizontally acquired symbionts (e.g. most gut symbionts). Here, using 16S metabarcoding on 336 guts from 24 orthopteran species (grasshoppers and crickets) in the Alps, we observed that microbiota correlated to host species identity, i.e. hosts from the same species had more similar microbiota than hosts from different species. This effect was ~5 times stronger for endosymbionts than for putative gut symbionts. Although elevation correlated with microbiome composition, we did not detect phylosymbiosis for endosymbionts and putative gut symbionts: closely related host species did not harbor more similar microbiota than distantly related species. Our findings indicate that gut microbiota of studied orthopteran species is more correlated to host identity and habitat than to the host phylogeny. The higher host specificity in endosymbionts corroborates the idea that-everything else being equal-vertically transmitted microbes harbor stronger host specificity signal, but the absence of phylosymbiosis suggests that host specificity changes quickly on evolutionary time scales.
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Affiliation(s)
- Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Camille Pitteloud
- Département de la mobilité, du territoire et de l'environnement, Service des forêts, de la nature et du paysage, Sion 1950, Switzerland
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf 8903, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne 1015, Switzerland
| | - Loïc Pellissier
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf 8903, Switzerland
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4
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Mazel F, Knowles SCL, Videvall E, Sweeny AR. Evolutionary patterns and processes in animal microbiomes. J Evol Biol 2023; 36:1653-1658. [PMID: 38117572 DOI: 10.1111/jeb.14248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2023] [Indexed: 12/22/2023]
Affiliation(s)
- Florent Mazel
- Department of Ecology and Evolution and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Elin Videvall
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Amy R Sweeny
- School of Biosciences, University of Sheffield, Sheffield, UK
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Sarton-Lohéac G, Nunes da Silva CG, Mazel F, Baud G, de Bakker V, Das S, El Chazli Y, Ellegaard K, Garcia-Garcera M, Glover N, Liberti J, Nacif Marçal L, Prasad A, Somerville V, Bonilla-Rosso G, Engel P. Deep Divergence and Genomic Diversification of Gut Symbionts of Neotropical Stingless Bees. mBio 2023; 14:e0353822. [PMID: 36939321 PMCID: PMC10128065 DOI: 10.1128/mbio.03538-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Social bees harbor conserved gut microbiotas that may have been acquired in a common ancestor of social bees and subsequently codiversified with their hosts. However, most of this knowledge is based on studies on the gut microbiotas of honey bees and bumblebees. Much less is known about the gut microbiotas of the third and most diverse group of social bees, the stingless bees. Specifically, the absence of genomic data from their microbiotas presents an important knowledge gap in understanding the evolution and functional diversity of the social bee microbiota. Here, we combined community profiling with culturing and genome sequencing of gut bacteria from six neotropical stingless bee species from Brazil. Phylogenomic analyses show that most stingless bee gut isolates form deep-branching sister clades of core members of the honey bee and bumblebee gut microbiota with conserved functional capabilities, confirming the common ancestry and ecology of their microbiota. However, our bacterial phylogenies were not congruent with those of the host, indicating that the evolution of the social bee gut microbiota was not driven by strict codiversification but included host switches and independent symbiont gain and losses. Finally, as reported for the honey bee and bumblebee microbiotas, we found substantial genomic divergence among strains of stingless bee gut bacteria, suggesting adaptation to different host species and glycan niches. Our study offers first insights into the genomic diversity of the stingless bee microbiota and highlights the need for broader samplings to understand the evolution of the social bee gut microbiota. IMPORTANCE Stingless bees are the most diverse group of the corbiculate bees and represent important pollinator species throughout the tropics and subtropics. They harbor specialized microbial communities in their gut that are related to those found in honey bees and bumblebees and that are likely important for bee health. Few bacteria have been cultured from the gut of stingless bees, which has prevented characterization of their genomic diversity and functional potential. Here, we established cultures of major members of the gut microbiotas of six stingless bee species and sequenced their genomes. We found that most stingless bee isolates belong to novel bacterial species distantly related to those found in honey bees and bumblebees and encoding similar functional capabilities. Our study offers a new perspective on the evolution of the social bee gut microbiota and presents a basis for characterizing the symbiotic relationships between gut bacteria and stingless bees.
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Affiliation(s)
- Garance Sarton-Lohéac
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Gilles Baud
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vincent de Bakker
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sudip Das
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Yassine El Chazli
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Kirsten Ellegaard
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Natasha Glover
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joanito Liberti
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Lorena Nacif Marçal
- Department of Morphology, Instituto de Ciências Biológicas, Federal University of Amazonas, Manaus, Brazil
| | - Aiswarya Prasad
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Germán Bonilla-Rosso
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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6
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Roy J, Mazel F, Dumack K, Bonkowski M, Rillig MC. Hierarchical phylogenetic community assembly of soil protists in a temperate agricultural field. Environ Microbiol 2022; 24:5498-5508. [PMID: 35837871 DOI: 10.1111/1462-2920.16134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/27/2022] [Accepted: 07/09/2022] [Indexed: 11/27/2022]
Abstract
Protists are abundant, diverse and perform essential functions in soils. Protistan community structure and its change across time or space are traditionally studied at the species-level but the relative importance of the processes shaping these patterns depends on the taxon phylogenetic resolution. Using 18S rDNA amplicon data of the Cercozoa, a group of dominant soil protists, from an agricultural field in western Germany, we observed a turnover of relatively closely related taxa (from sequence variants to genus-level clades) across soil depth; while across soil habitats (rhizosphere, bulk soil, drilosphere) we observed turnover of relatively distantly related taxa, confirming Paracercomonadidae as a rhizosphere-associated clade. We extended our approach to show that closely related Cercozoa encounter divergent AM fungi across soil depth and that distantly related Cercozoa encounter closely related AM fungi across soil compartments. This study suggests that soil Cercozoa community assembly at the field-scale is driven by niche-based processes shaped by evolutionary legacy of adaptation to conditions primarily related to soil compartment, followed by soil layer, giving a deeper understanding on the selection pressures that shaped their evolution.
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Affiliation(s)
- Julien Roy
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Kennet Dumack
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Michael Bonkowski
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Matthias C Rillig
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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7
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Mazel F, Malard L, Niculita-Hirzel H, Yashiro E, Mod HK, Mitchell EAD, Singer D, Buri A, Pinto E, Guex N, Lara E, Guisan A. Soil protist function varies with elevation in the Swiss Alps. Environ Microbiol 2021; 24:1689-1702. [PMID: 34347350 PMCID: PMC9290697 DOI: 10.1111/1462-2920.15686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/06/2021] [Accepted: 07/25/2021] [Indexed: 11/29/2022]
Abstract
Protists are abundant and play key trophic functions in soil. Documenting how their trophic contributions vary across large environmental gradients is essential to understand and predict how biogeochemical cycles will be impacted by global changes. Here, using amplicon sequencing of environmental DNA in open habitat soil from 161 locations spanning 2600 m of elevation in the Swiss Alps (from 400 to 3000 m), we found that, over the whole study area, soils are dominated by consumers, followed by parasites and phototrophs. In contrast, the proportion of these groups in local communities shows large variations in relation to elevation. While there is, on average, three times more consumers than parasites at low elevation (400–1000 m), this ratio increases to 12 at high elevation (2000–3000 m). This suggests that the decrease in protist host biomass and diversity toward mountains tops impact protist functional composition. Furthermore, the taxonomic composition of protists that infect animals was related to elevation while that of protists that infect plants or of protist consumers was related to soil pH. This study provides a first step to document and understand how soil protist functions vary along the elevational gradient.
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Affiliation(s)
- Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Lucie Malard
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Hélène Niculita-Hirzel
- Department of Occupational Health and Environment, Center for Primary Care and Public Health (Unisanté), University of Lausanne, Epalinges, CH-1066, Switzerland
| | - Erika Yashiro
- Center for Microbial Communities, Section of Biotechnology, Aalborg University, Aalborg, Denmark
| | - Heidi K Mod
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, CH-2000, Switzerland.,Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, Neuchâtel, CH-2000, Switzerland
| | - David Singer
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, CH-2000, Switzerland.,UMR CNRS 6112 LPG-BIAF, Université d'Angers, Angers Cedex 1, France
| | - Aline Buri
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Eric Pinto
- Terrabiom Association, Dörflistrasse 32, Oberrieden, Zürich, 8942, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
| | - Enrique Lara
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, Madrid, 28014, Spain
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland.,Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, 1015, Switzerland
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Davis KM, Mazel F, Parfrey LW. The microbiota of intertidal macroalgae Fucus distichus is site-specific and resistant to change following transplant. Environ Microbiol 2021; 23:2617-2631. [PMID: 33817918 DOI: 10.1111/1462-2920.15496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 01/04/2023]
Abstract
It is unclear how host-associated microbial communities will be affected by future environmental change. Characterizing how microbiota differ across sites with varying environmental conditions and assessing the stability of the microbiota in response to abiotic variation are critical steps towards predicting outcomes of environmental change. Intertidal organisms are valuable study systems because they experience extreme variation in environmental conditions on tractable timescales such as tide cycles and across small spatial gradients in the intertidal zone. Here we show a widespread intertidal macroalgae, Fucus distichus, hosts site-specific microbiota over small (meters to kilometres) spatial scales. We demonstrate stability of site-specific microbial associations by manipulating the host environment and microbial species pool with common garden and reciprocal transplant experiments. We hypothesized that F. distichus microbiota would readily shift to reflect the contemporary environment due to selective filtering by abiotic conditions and/or colonization by microbes from the new environment or nearby hosts. Instead, F. distichus microbiota was stable for days after transplantation in both the laboratory and field. Our findings expand the current understanding of microbiota dynamics on an intertidal foundation species. These results may also point to adaptations for withstanding short-term environmental variation, in hosts and/or microbes, facilitating stable host-microbial associations.
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Affiliation(s)
- Katherine M Davis
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Hakai Institute, PO Box 309, Heriot Bay, BC, V0P 1H0, Canada
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Abstract
We live in an increasingly data-driven world, where high-throughput sequencing and mass spectrometry platforms are transforming biology into an information science. This has shifted major challenges in biological research from data generation and processing to interpretation and knowledge translation. However, postsecondary training in bioinformatics, or more generally data science for life scientists, lags behind current demand. In particular, development of accessible, undergraduate data science curricula has the potential to improve research and learning outcomes as well as better prepare students in the life sciences to thrive in public and private sector careers. Here, we describe the Experiential Data science for Undergraduate Cross-Disciplinary Education (EDUCE) initiative, which aims to progressively build data science competency across several years of integrated practice. Through EDUCE, students complete data science modules integrated into required and elective courses augmented with coordinated cocurricular activities. The EDUCE initiative draws on a community of practice consisting of teaching assistants (TAs), postdocs, instructors, and research faculty from multiple disciplines to overcome several reported barriers to data science for life scientists, including instructor capacity, student prior knowledge, and relevance to discipline-specific problems. Preliminary survey results indicate that even a single module improves student self-reported interest and/or experience in bioinformatics and computer science. Thus, EDUCE provides a flexible and extensible active learning framework for integration of data science curriculum into undergraduate courses and programs across the life sciences.
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Affiliation(s)
- Kimberly A Dill-McFarland
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephan G König
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE, University of British Columbia, Vancouver, British Columbia, Canada
| | - Florent Mazel
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany and Biodiversity Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - David C Oliver
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lisa M McEwen
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE, University of British Columbia, Vancouver, British Columbia, Canada
- School of Health Information Science, Faculty of Human and Social Development, University of Victoria, Victoria, British Columbia, Canada
| | - Kris Y Hong
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE, University of British Columbia, Vancouver, British Columbia, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
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11
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Roy J, Mazel F, Sosa-Hernández MA, Dueñas JF, Hempel S, Zinger L, Rillig MC. The relative importance of ecological drivers of arbuscular mycorrhizal fungal distribution varies with taxon phylogenetic resolution. New Phytol 2019; 224:936-948. [PMID: 31355954 DOI: 10.1111/nph.16080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
The phylogenetic depth at which arbuscular mycorrhizal (AM) fungi harbor a coherent ecological niche is unknown, which has consequences for operational taxonomic unit (OTU) delineation from sequence data and the study of their biogeography. We tested how changes in AM fungi community composition across habitats (beta diversity) vary with OTU phylogenetic resolution. We inferred exact sequence variants (ESVs) to resolve phylotypes at resolutions finer than provided by traditional sequence clustering and analyzed beta diversity profiles up to order-level sequence clusters. At the ESV level, we detected the environmental predictors revealed with traditional OTUs or at higher genetic distances. However, the correlation between environmental predictors and community turnover steeply increased at a genetic distance of c. 0.03 substitutions per site. Furthermore, we observed a turnover of either closely or distantly related taxa (respectively at or above 0.03 substitutions per site) along different environmental gradients. This study suggests that different axes of AM fungal ecological niche are conserved at different phylogenetic depths. Delineating AM fungal phylotypes using DNA sequences should screen different phylogenetic resolutions to better elucidate the factors that shape communities and predict the fate of AM symbioses in a changing environment.
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Affiliation(s)
- Julien Roy
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Florent Mazel
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Moisés A Sosa-Hernández
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Juan F Dueñas
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Stefan Hempel
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Lucie Zinger
- Ecole Normale Supérieure, CNRS, Inserm, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), PSL Research University, F-75005, Paris, France
| | - Matthias C Rillig
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
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Cantalapiedra JL, Aze T, Cadotte MW, Dalla Riva GV, Huang D, Mazel F, Pennell MW, Ríos M, Mooers AØ. Conserving evolutionary history does not result in greater diversity over geological time scales. Proc Biol Sci 2019; 286:20182896. [PMID: 31161910 PMCID: PMC6571466 DOI: 10.1098/rspb.2018.2896] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Alternative prioritization strategies have been proposed to safeguard biodiversity over macroevolutionary time scales. The first prioritizes the most distantly related species—maximizing phylogenetic diversity (PD)—in the hopes of capturing at least some lineages that will successfully diversify into the future. The second prioritizes lineages that are currently speciating, in the hopes that successful lineages will continue to generate species into the future. These contrasting schemes also map onto contrasting predictions about the role of slow diversifiers in the production of biodiversity over palaeontological time scales. We consider the performance of the two schemes across 10 dated species-level palaeo-phylogenetic trees ranging from Foraminifera to dinosaurs. We find that prioritizing PD for conservation generally led to fewer subsequent lineages, while prioritizing diversifiers led to modestly more subsequent diversity, compared with random sets of lineages. Importantly for conservation, the tree shape when decisions are made cannot predict which scheme will be most successful. These patterns are inconsistent with the notion that long-lived lineages are the source of new species. While there may be sound reasons for prioritizing PD for conservation, long-term species production might not be one of them.
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Affiliation(s)
- J L Cantalapiedra
- 1 Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung , Invalidenstraße 43, Berlin 10115 , Germany.,2 Departamento de Ciencias de la Vida, Universidad de Alcalá , 28805 Alcalá de Henares, Madrid , Spain
| | - T Aze
- 3 School of Earth and Environment, The University of Leeds , Leeds LS2 9JT , UK
| | - M W Cadotte
- 4 Department of Biological Sciences, University of Toronto-Scarborough , 1265 Military Trail, Toronto, Ontario , Canada M1C 1A4.,5 Department of Ecology and Evolutionary Biology, University of Toronto , 25 Wilcocks Street, Toronto, Ontario , Canada M5S 3B2
| | - G V Dalla Riva
- 6 Department of Statistics, University of British Columbia , 4200-6270 University Boulevard, Vancouver, BC , Canada V6T 1Z4.,9 School of Mathematics and Statistics, University of Canterbury , Private Bag 4800, Christchurch 8140 , New Zealand
| | - D Huang
- 10 Department of Biological Sciences and Tropical Marine Science Institute, National University of Singapore , 16 Science Drive 4 , Singapore 117558 , Singapore
| | - F Mazel
- 7 Department of Botany, University of British Columbia , 4200-6270 University Boulevard, Vancouver, BC , Canada V6T 1Z4.,11 Department of Biological Sciences, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia , Canada V5A 1S6
| | - M W Pennell
- 8 Department of Zoology, University of British Columbia , 4200-6270 University Boulevard, Vancouver, BC , Canada V6T 1Z4
| | - M Ríos
- 12 Departamento de Paleobiología, Museo Nacional de Ciencias Naturales (CSIC) , José Gutiérrez Abascal 2, 28006 Madrid , Spain
| | - A Ø Mooers
- 11 Department of Biological Sciences, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia , Canada V5A 1S6
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13
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Tucker CM, Aze T, Cadotte MW, Cantalapiedra JL, Chisholm C, Díaz S, Grenyer R, Huang D, Mazel F, Pearse WD, Pennell MW, Winter M, Mooers AO. Assessing the utility of conserving evolutionary history. Biol Rev Camb Philos Soc 2019; 94:1740-1760. [PMID: 31149769 PMCID: PMC6852562 DOI: 10.1111/brv.12526] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 05/02/2019] [Accepted: 05/08/2019] [Indexed: 01/05/2023]
Abstract
It is often claimed that conserving evolutionary history is more efficient than species‐based approaches for capturing the attributes of biodiversity that benefit people. This claim underpins academic analyses and recommendations about the distribution and prioritization of species and areas for conservation, but evolutionary history is rarely considered in practical conservation activities. One impediment to implementation is that arguments related to the human‐centric benefits of evolutionary history are often vague and the underlying mechanisms poorly explored. Herein we identify the arguments linking the prioritization of evolutionary history with benefits to people, and for each we explicate the purported mechanism, and evaluate its theoretical and empirical support. We find that, even after 25 years of academic research, the strength of evidence linking evolutionary history to human benefits is still fragile. Most – but not all – arguments rely on the assumption that evolutionary history is a useful surrogate for phenotypic diversity. This surrogacy relationship in turn underlies additional arguments, particularly that, by capturing more phenotypic diversity, evolutionary history will preserve greater ecosystem functioning, capture more of the natural variety that humans prefer, and allow the maintenance of future benefits to humans. A surrogate relationship between evolutionary history and phenotypic diversity appears reasonable given theoretical and empirical results, but the strength of this relationship varies greatly. To the extent that evolutionary history captures unmeasured phenotypic diversity, maximizing the representation of evolutionary history should capture variation in species characteristics that are otherwise unknown, supporting some of the existing arguments. However, there is great variation in the strength and availability of evidence for benefits associated with protecting phenotypic diversity. There are many studies finding positive biodiversity–ecosystem functioning relationships, but little work exists on the maintenance of future benefits or the degree to which humans prefer sets of species with high phenotypic diversity or evolutionary history. Although several arguments link the protection of evolutionary history directly with the reduction of extinction rates, and with the production of relatively greater future biodiversity via increased adaptation or diversification, there are few direct tests. Several of these putative benefits have mismatches between the relevant spatial scales for conservation actions and the spatial scales at which benefits to humans are realized. It will be important for future work to fill in some of these gaps through direct tests of the arguments we define here.
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Affiliation(s)
- Caroline M Tucker
- Department of Biology, University of North Carolina at Chapel Hill, Coker Hall, CB #3280 120 South Road, Chapel Hill, NC 27599-3280, U.S.A.,Centre d'Écologie Fonctionnelle et Évolutive (UMR 5175), CNRS, 34090 Montpellier, France
| | - Tracy Aze
- School of Earth and Environment, Maths/Earth and Environment Building, University of Leeds, Leeds, LS2 9JT, U.K
| | - Marc W Cadotte
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Juan L Cantalapiedra
- Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung, Invalidenstraße 43, 10115, Berlin, Germany.,Departamento de Ciencias de la Vida, Universidad de Alcalá, 28805, Alcalá de Henares, Madrid, Spain
| | - Chelsea Chisholm
- Department of Ecology and Evolution, Quartier UNIL-Sorge Batiment Biophore CH-1015 Lausanne, Switzerland
| | - Sandra Díaz
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas and Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Casilla de Correo 495, 5000, Córdoba, Argentina
| | - Richard Grenyer
- School of Geography and the Environment, South Parks Road, University of Oxford, Oxford, OX1 3QY, U.K
| | - Danwei Huang
- Department of Biological Sciences and Tropical Marine Science Institute, National University of Singapore, 16 Science Drive 4, 117558, Singapore
| | - Florent Mazel
- Department of Biological Sciences, 8888 University Drive, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,Department of Botany, 2329 West Mall, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Biodiversity Research Centre, 2212 Main Mall, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - William D Pearse
- Department of Biology & Ecology Center, 5205 Old Main Hill, Utah State University, Logan, UT, 84322, U.S.A
| | - Matthew W Pennell
- Biodiversity Research Centre, 2212 Main Mall, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Zoology, South Parks Road, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Marten Winter
- German Centre for Integrative Biodiversity Research (iDiv), Deutscher Platz 5E, 04103 Leipzig, Germany
| | - Arne O Mooers
- Department of Biological Sciences, 8888 University Drive, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
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14
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Abstract
At high altitude, the reduced availability of thermal energy and oxygen poses major challenges to organisms. Different species or populations have evolved similar solutions to these challenges, such as blood flow regulation in animals (Bouverot, 1985). Previous studies investigating such convergent adaptations have primarily looked at changes in host genomes (e.g., see Scheinfeldt & Tishkoff, 2010), but have rarely considered the potential role of the gut microbiome in mediating host adaptation. As gut microbes can indirectly regulate host blood pressure (Pluznick, 2014) and energy intake efficiency, it has been hypothesized that they could help maintain normal energy production and/or optimize nutritional assimilation in high-altitude hypoxic environments (e.g., Li & Zhao, 2015). However, it has been hard to (a) show that there is a direct effect of altitude on the gut microbiota, because of the many potential confounding effects of altitude (e.g., diet is correlated to altitude, as well as to the microbiome) and to (b) understand the mechanisms by which the microbiota could mediate host hypoxic and thermoregulatory stresses. In this issue of Molecular Ecology, Suzuki, Martins, and Nachman (2018) show that, independently of diet, taxonomic composition and functions of mouse gut microbiota converge in independent high-altitude environments and propose the intriguing hypothesis that some of these functional convergences might be beneficial to their host.
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Affiliation(s)
- Florent Mazel
- Biodiversity Research Centre, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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15
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Mazel F, Pennell MW, Cadotte MW, Diaz S, Riva GVD, Grenyer R, Leprieur F, Mooers AO, Mouillot D, Tucker CM, Pearse WD. Reply to: "Global conservation of phylogenetic diversity captures more than just functional diversity". Nat Commun 2019; 10:858. [PMID: 30787308 PMCID: PMC6382820 DOI: 10.1038/s41467-019-08603-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/18/2019] [Indexed: 11/18/2022] Open
Affiliation(s)
- Florent Mazel
- Department of Biological Sciences, Simon Fraser University, Burnaby, V5A 1S6, BC, Canada.
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Matthew W Pennell
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Marc W Cadotte
- Biological Sciences, University of Toronto-Scarborough, Scarborough, M1C, 1A4, Canada
- Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, ON, Canada
| | - Sandra Diaz
- Instituto Multidisciplinario de Biología Vegetal, CONICET and FECFyN, Universidad Nacional de Córdoba, Casilla de Correo 495, 5000, Córdoba, Argentina
| | | | - Richard Grenyer
- School of Geography and the Environment, University of Oxford, Oxford, OX1 3QY, UK
| | - Fabien Leprieur
- Marine Biodiversity, Exploitation, and Conservation (MARBEC), UMR 9190, Université de Montpellier, Montpellier, 34095, France
| | - Arne O Mooers
- Department of Biological Sciences, Simon Fraser University, Burnaby, V5A 1S6, BC, Canada
| | - David Mouillot
- Marine Biodiversity, Exploitation, and Conservation (MARBEC), UMR 9190, Université de Montpellier, Montpellier, 34095, France
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, QLD, Australia
| | - Caroline M Tucker
- Department of Biology, University of North Carolina-Chapel Hill, Chapel Hill, 27599-3280, NC, USA
| | - William D Pearse
- Ecology Center and Department of Biology, Utah State University, Logan, 84322, UT, USA
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16
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Mazel F, Pennell MW, Cadotte MW, Diaz S, Riva GVD, Grenyer R, Leprieur F, Mooers AO, Mouillot D, Tucker CM, Pearse WD. Author Correction: Prioritizing phylogenetic diversity captures functional diversity unreliably. Nat Commun 2019; 10:974. [PMID: 30796209 PMCID: PMC6385199 DOI: 10.1038/s41467-019-08612-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Florent Mazel
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada. .,Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. .,Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Matthew W Pennell
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Marc W Cadotte
- Biological Sciences, University of Toronto-Scarborough, Scarborough, M1C 1A4, Canada.,Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Sandra Diaz
- Instituto Multidisciplinario de Biología Vegetal, CONICET and FECFyN - Universidad Nacional de Córdoba, Casilla de Correo 495, 5000, Córdoba, Argentina
| | | | - Richard Grenyer
- School of Geography and the Environment, University of Oxford, Oxford, OX1 3QY, UK
| | - Fabien Leprieur
- Marine Biodiversity, Exploitation, and Conservation (MARBEC), UMR 9190, Université de Montpellier, Montpellier, 34095, France
| | - Arne O Mooers
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - David Mouillot
- Marine Biodiversity, Exploitation, and Conservation (MARBEC), UMR 9190, Université de Montpellier, Montpellier, 34095, France.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Caroline M Tucker
- Department of Biology, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599-3280, USA
| | - William D Pearse
- Ecology Center and Department of Biology, Utah State University, Logan, UT, 84322, USA
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17
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Abstract
The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attempt to census the bulk of Earth's bacterial and archaeal ("prokaryotic") clades and to estimate their overall global richness, we analyzed over 1.7 billion 16S ribosomal RNA amplicon sequences in the V4 hypervariable region obtained from 492 studies worldwide, covering a multitude of environments and using multiple alternative primers. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs, 16S-V4 gene clusters at 97% similarity), a commonly used measure of microbial richness. Using several statistical approaches, we estimate that there exist globally about 0.8–1.6 million prokaryotic OTUs, of which we recovered somewhere between 47%–96%, representing >99.98% of prokaryotic cells. Consistent with this conclusion, our data set independently "recaptured" 91%–93% of 16S sequences from multiple previous global surveys, including PCR-independent metagenomic surveys. The distribution of relative OTU abundances is consistent with a log-normal model commonly observed in larger organisms; the total number of OTUs predicted by this model is also consistent with our global richness estimates. By combining our estimates with the ratio of full-length versus partial-length (V4) sequence diversity in the SILVA sequence database, we further estimate that there exist about 2.2–4.3 million full-length OTUs worldwide. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar richness estimates as for the global data set, suggesting that most OTUs are globally distributed. Qualitatively similar results are also obtained for other 16S similarity thresholds (90%, 95%, and 99%). Our estimates constrain the extent of a poorly quantified rare microbial biosphere and refute recent predictions that there exist trillions of prokaryotic OTUs. A massive survey of Earth's Bacteria and Archaea reveals that their diversity is orders of magnitude lower than previously thought. The study also indicates that extinctions played an important role in prokaryotic evolution. The global diversity of Bacteria and Archaea ("prokaryotes"), the most ancient and most widespread forms of life on Earth, is subject to high uncertainty. Here, to estimate the global diversity of prokaryotes, we analyzed a large number of 16S ribosomal RNA gene sequences, found in all prokaryotes and commonly used to catalogue prokaryotic diversity. Sequences were obtained from a multitude of environments across thousands of geographic locations worldwide. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs), i.e., 16S gene clusters sharing 97% similarity, roughly corresponding to prokaryotic species. Using several statistical approaches and through comparison with existing databases and previous independent surveys, we estimate that there exist globally between 0.8 and 1.6 million prokaryotic OTUs. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar estimates as for the global data set, suggesting that most OTUs are not restricted to a single continent but are instead globally distributed. Our estimates constrain the extent of a commonly hypothesized but poorly quantified rare prokaryotic biosphere and refute recent predictions that there exists trillions of prokaryotic OTUs. Our findings also indicate that, contrary to common speculation, extinctions may strongly influence global prokaryotic diversity.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, Eugene, Oregon, United States of America
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- * E-mail:
| | - Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
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18
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Mazel F, Davis KM, Loudon A, Kwong WK, Groussin M, Parfrey LW. Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life? mSystems 2018; 3:e00097-18. [PMID: 30417109 PMCID: PMC6208643 DOI: 10.1128/msystems.00097-18] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 12/13/2022] Open
Abstract
Host-associated microbiota composition can be conserved over evolutionary time scales. Indeed, closely related species often host similar microbiota; i.e., the composition of their microbiota harbors a phylogenetic signal, a pattern sometimes referred to as "phylosymbiosis." Elucidating the origins of this pattern is important to better understand microbiota ecology and evolution. However, this is hampered by our lack of theoretical expectations and a comprehensive overview of phylosymbiosis prevalence in nature. Here, we use simulations to provide a simple expectation for when we should expect this pattern to occur and then review the literature to document the prevalence and strength of phylosymbiosis across the host tree of life. We demonstrate that phylosymbiosis can readily emerge from a simple ecological filtering process, whereby a given host trait (e.g., gut pH) that varies with host phylogeny (i.e., harbors a phylogenetic signal) filters preadapted microbes. We found marked differences between methods used to detect phylosymbiosis, so we proposed a series of practical recommendations based on using multiple best-performing approaches. Importantly, we found that, while the prevalence of phylosymbiosis is mixed in nature, it appears to be stronger for microbiotas living in internal host compartments (e.g., the gut) than those living in external compartments (e.g., the rhizosphere). We show that phylosymbiosis can theoretically emerge without any intimate, long-term coevolutionary mechanisms and that most phylosymbiosis patterns observed in nature are compatible with a simple ecological process. Deviations from baseline ecological expectations might be used to further explore more complex hypotheses, such as codiversification. IMPORTANCE Phylosymbiosis is a pattern defined as the tendency of closely related species to host microbiota whose compositions resemble each other more than host species drawn at random from the same tree. Understanding the mechanisms behind phylosymbiosis is important because it can shed light on rules governing the assembly of host-associated microbiotas and, potentially, their coevolutionary dynamics with hosts. For example, is phylosymbiosis a result of coevolution, or can it be generated by simple ecological filtering processes? Beyond qualitative theoretical models, quantitative theoretical expectations can provide new insights. For example, deviations from a simple baseline of ecological filtering may be used to test more-complex hypotheses (e.g., coevolution). Here, we use simulations to provide evidence that simple host-related ecological filtering can readily generate phylosymbiosis, and we contrast these predictions with real-world data. We find that while phylosymbiosis is widespread in nature, phylosymbiosis patterns are compatible with a simple ecological model in the majority of taxa. Internal compartments of hosts, such as the animal gut, often display stronger phylosymbiosis than expected from a purely ecological filtering process, suggesting that other mechanisms are also involved.
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Affiliation(s)
- Florent Mazel
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Katherine M. Davis
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Loudon
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Waldan K. Kwong
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mathieu Groussin
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Laura Wegener Parfrey
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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19
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Ohlmann M, Mazel F, Chalmandrier L, Bec S, Coissac E, Gielly L, Pansu J, Schilling V, Taberlet P, Zinger L, Chave J, Thuiller W. Mapping the imprint of biotic interactions on β-diversity. Ecol Lett 2018; 21:1660-1669. [DOI: 10.1111/ele.13143] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/01/2018] [Accepted: 07/25/2018] [Indexed: 01/23/2023]
Affiliation(s)
- Marc Ohlmann
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
| | - Florent Mazel
- Department of Botany and Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Loïc Chalmandrier
- Landscape Ecology; Institute of Terrestrial Ecosystems; ETH Zürich; Zürich Switzerland
- Swiss Federal Research Institute WSL; 8903 Birmensdorf Switzerland
| | - Stéphane Bec
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
| | - Eric Coissac
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
| | - Ludovic Gielly
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
| | - Johan Pansu
- Princeton University; 110 Morrison Hall Princeton NJ 08544 USA
| | - Vincent Schilling
- Université Toulouse 3 Paul Sabatier; CNRS; IRD; UMR 5174 Evolution et Diversité Biologique (EDB); F-31062 Toulouse France
| | - Pierre Taberlet
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
| | - Lucie Zinger
- Ecole Normale Supérieure; PSL Research University; CNRS; Inserm; Institut de Biologie de l'Ecole Normale Supérieure (IBENS); F-75005 Paris France
| | - Jérome Chave
- Université Toulouse 3 Paul Sabatier; CNRS; IRD; UMR 5174 Evolution et Diversité Biologique (EDB); F-31062 Toulouse France
| | - Wilfried Thuiller
- University Grenoble Alpes; CNRS; Univ. Savoie Mont Blanc; CNRS; LECA; Laboratoire d’Écologie Alpine F-38000 Grenoble France
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20
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Mazel F, Pennell MW, Cadotte MW, Diaz S, Dalla Riva GV, Grenyer R, Leprieur F, Mooers AO, Mouillot D, Tucker CM, Pearse WD. Prioritizing phylogenetic diversity captures functional diversity unreliably. Nat Commun 2018; 9:2888. [PMID: 30038259 PMCID: PMC6056549 DOI: 10.1038/s41467-018-05126-3] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/14/2018] [Indexed: 12/05/2022] Open
Abstract
In the face of the biodiversity crisis, it is argued that we should prioritize species in order to capture high functional diversity (FD). Because species traits often reflect shared evolutionary history, many researchers have assumed that maximizing phylogenetic diversity (PD) should indirectly capture FD, a hypothesis that we name the “phylogenetic gambit”. Here, we empirically test this gambit using data on ecologically relevant traits from >15,000 vertebrate species. Specifically, we estimate a measure of surrogacy of PD for FD. We find that maximizing PD results in an average gain of 18% of FD relative to random choice. However, this average gain obscures the fact that in over one-third of the comparisons, maximum PD sets contain less FD than randomly chosen sets of species. These results suggest that, while maximizing PD protection can help to protect FD, it represents a risky conservation strategy. An ongoing conservation question is if we can maintain functional diversity by optimizing for preservation of phylogenetic diversity. Here, Mazel et al. show that functional diversity increases with phylogenetic diversity in some clades but not others, and thus could be a risky conservation strategy.
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Affiliation(s)
- Florent Mazel
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada. .,Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. .,Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Matthew W Pennell
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Marc W Cadotte
- Biological Sciences, University of Toronto-Scarborough, Scarborough, M1C 1A4, Canada.,Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Sandra Diaz
- Instituto Multidisciplinario de Biología Vegetal, CONICET and FECFyN - Universidad Nacional de Córdoba, Casilla de Correo 495, 5000, Córdoba, Argentina
| | | | - Richard Grenyer
- School of Geography and the Environment, University of Oxford, Oxford, OX1 3QY, UK
| | - Fabien Leprieur
- Marine Biodiversity, Exploitation, and Conservation (MARBEC), UMR 9190, Université de Montpellier, Montpellier, 34095, France
| | - Arne O Mooers
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - David Mouillot
- Marine Biodiversity, Exploitation, and Conservation (MARBEC), UMR 9190, Université de Montpellier, Montpellier, 34095, France.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Caroline M Tucker
- Department of Biology, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599-3280, USA
| | - William D Pearse
- Ecology Center and Department of Biology, Utah State University, Logan, UT, 84322, USA
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21
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Mazel F, Mooers AO, Riva GVD, Pennell MW. Conserving Phylogenetic Diversity Can Be a Poor Strategy for Conserving Functional Diversity. Syst Biol 2018; 66:1019-1027. [PMID: 28595366 DOI: 10.1093/sysbio/syx054] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/24/2017] [Indexed: 11/14/2022] Open
Abstract
For decades, academic biologists have advocated for making conservation decisions in light of evolutionary history. Specifically, they suggest that policy makers should prioritize conserving phylogenetically diverse assemblages. The most prominent argument is that conserving phylogenetic diversity (PD) will also conserve diversity in traits and features (functional diversity [FD]), which may be valuable for a number of reasons. The claim that PD-maximized ("maxPD") sets of taxa will also have high FD is often taken at face value and in cases where researchers have actually tested it, they have done so by measuring the phylogenetic signal in ecologically important functional traits. The rationale is that if traits closely mirror phylogeny, then saving the maxPD set of taxa will tend to maximize FD and if traits do not have phylogenetic structure, then saving the maxPD set of taxa will be no better at capturing FD than criteria that ignore PD. Here, we suggest that measuring the phylogenetic signal in traits is uninformative for evaluating the effectiveness of using PD in conservation. We evolve traits under several different models and, for the first time, directly compare the FD of a set of taxa that maximize PD to the FD of a random set of the same size. Under many common models of trait evolution and tree shapes, conserving the maxPD set of taxa will conserve more FD than conserving a random set of the same size. However, this result cannot be generalized to other classes of models. We find that under biologically plausible scenarios, using PD to select species can actually lead to less FD compared with a random set. Critically, this can occur even when there is phylogenetic signal in the traits. Predicting exactly when we expect using PD to be a good strategy for conserving FD is challenging, as it depends on complex interactions between tree shape and the assumptions of the evolutionary model. Nonetheless, if our goal is to maintain trait diversity, the fact that conserving taxa based on PD will not reliably conserve at least as much FD as choosing randomly raises serious concerns about the general utility of PD in conservation.
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Affiliation(s)
- Florent Mazel
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby BC V5A 1S6, Canada
| | - Arne O Mooers
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby BC V5A 1S6, Canada
| | - Giulio Valentino Dalla Riva
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Matthew W Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver BC V6T 1Z4, Canada
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22
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Groussin M, Mazel F. Évolution des microbiotes intestinaux de mammifères et ses conséquences sur la santé humaine. Med Sci (Paris) 2017; 33:1038-1042. [DOI: 10.1051/medsci/20173312007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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23
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Mazel F, Wüest RO, Gueguen M, Renaud J, Ficetola GF, Lavergne S, Thuiller W. The Geography of Ecological Niche Evolution in Mammals. Curr Biol 2017; 27:1369-1374. [PMID: 28457870 DOI: 10.1016/j.cub.2017.03.046] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/02/2017] [Accepted: 03/21/2017] [Indexed: 11/19/2022]
Abstract
Convergent adaptive evolution of species' ecological niches-i.e., the appearance of similar niches in independent lineages-is the result of natural selection acting on niche-related species traits ("traits" hereafter) and contrasts with neutral evolution [1-4]. Although trait convergences are recognized as being of importance at the species scale, we still know little about the impact of species convergence on the overall trait and niche structure of entire biotas at large spatial scales [5]. Here, we map the convergent evolution of four traits (diet, body mass, activity cycle, and foraging strata) for mammal species and assemblages (defined at 200 × 200 km resolution) at a global scale. Using data on the geographic distributions, traits, and phylogenetic relationships of species and by comparing observed patterns of trait β-diversity to evolutionary neutral expectations, we show that trait convergence is not restricted to particular lineages but scales up to entire assemblages (i.e., whole species communities). We find region-wide biota convergence in traits between regions with similar climates, particularly between Australia and other continents. Pairs of assemblages that show trait divergence often involves Arctic regions where rapid evolutionary changes occurred in response to extreme climatic constraints. By integrating both macroecological and macroevolutionary approaches into a single framework, our study quantifies the crucial role of evolutionary processes such as natural selection in the spatial distribution and structure of large-scale species assemblages.
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Affiliation(s)
- Florent Mazel
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine (LECA), 38000 Grenoble, France.
| | - Rafael O Wüest
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine (LECA), 38000 Grenoble, France; Swiss Federal Research Institute WSL, Landscape Dynamics, 8903 Birmensdorf, Switzerland
| | - Maya Gueguen
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine (LECA), 38000 Grenoble, France
| | - Julien Renaud
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine (LECA), 38000 Grenoble, France
| | - Gentile Francesco Ficetola
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine (LECA), 38000 Grenoble, France; Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Sébastien Lavergne
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine (LECA), 38000 Grenoble, France
| | - Wilfried Thuiller
- Université Grenoble Alpes, CNRS, Laboratoire d'Écologie Alpine (LECA), 38000 Grenoble, France
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24
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Groussin M, Mazel F, Sanders JG, Smillie CS, Lavergne S, Thuiller W, Alm EJ. Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Nat Commun 2017; 8:14319. [PMID: 28230052 PMCID: PMC5331214 DOI: 10.1038/ncomms14319] [Citation(s) in RCA: 244] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/08/2016] [Indexed: 12/28/2022] Open
Abstract
Whether mammal–microbiome interactions are persistent and specific over evolutionary time is controversial. Here we show that host phylogeny and major dietary shifts have affected the distribution of different gut bacterial lineages and did so on vastly different bacterial phylogenetic resolutions. Diet mostly influences the acquisition of ancient and large microbial lineages. Conversely, correlation with host phylogeny is mostly seen among more recently diverged bacterial lineages, consistent with processes operating at similar timescales to host evolution. Considering microbiomes at appropriate phylogenetic scales allows us to model their evolution along the mammalian tree and to infer ancient diets from the predicted microbiomes of mammalian ancestors. Phylogenetic analyses support co-speciation as having a significant role in the evolution of mammalian gut microbiome compositions. Highly co-speciating bacterial genera are also associated with immune diseases in humans, laying a path for future studies that probe these co-speciating bacteria for signs of co-evolution. Both host diet and phylogeny have been argued to shape mammalian microbiome communities. Here, the authors show that diet predicts the presence of ancient bacterial lineages in the microbiome, but that co-speciation between more recent bacterial lineages and their hosts may drive associations between microbiome composition and phylogeny.
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Affiliation(s)
- Mathieu Groussin
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Florent Mazel
- Laboratoire d Ecologie Alpine, CNRS, University of Grenoble Alpes, FR-38041, Grenoble Cedex 9, France
| | - Jon G Sanders
- Organismic and Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, Massachusetts 02138, USA
| | - Chris S Smillie
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,The Broad Institute of MIT and Harvard, 415 Main Street Cambridge, Massachusetts 02142, USA
| | - Sébastien Lavergne
- Laboratoire d Ecologie Alpine, CNRS, University of Grenoble Alpes, FR-38041, Grenoble Cedex 9, France
| | - Wilfried Thuiller
- Laboratoire d Ecologie Alpine, CNRS, University of Grenoble Alpes, FR-38041, Grenoble Cedex 9, France
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,The Broad Institute of MIT and Harvard, 415 Main Street Cambridge, Massachusetts 02142, USA
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25
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Mazel F, Davies TJ, Gallien L, Renaud J, Groussin M, Münkemüller T, Thuiller W. Influence of tree shape and evolutionary time-scale on phylogenetic diversity metrics. Ecography 2016; 39:913-920. [PMID: 27713599 PMCID: PMC5049687 DOI: 10.1111/ecog.01694] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
During the last decades, describing, analysing and understanding the phylogenetic structure of species assemblages has been a central theme in both community ecology and macro-ecology. Among the wide variety of phylogenetic structure metrics, three have been predominant in the literature: Faith's phylogenetic diversity (PDFaith), which represents the sum of the branch lengths of the phylogenetic tree linking all species of a particular assemblage, the mean pairwise distance between all species in an assemblage (MPD) and the pairwise distance between the closest relatives in an assemblage (MNTD). Comparisons between studies using one or several of these metrics are difficult because there has been no comprehensive evaluation of the phylogenetic properties each metric captures. In particular it is unknown how PDFaith relates to MDP and MNTD. Consequently, it is possible that apparently opposing patterns in different studies might simply reflect differences in metric properties. Here, we aim to fill this gap by comparing these metrics using simulations and empirical data. We first used simulation experiments to test the influence of community structure and size on the mismatch between metrics whilst varying the shape and size of the phylogenetic tree of the species pool. Second we investigated the mismatch between metrics for two empirical datasets (gut microbes and global carnivoran assemblages). We show that MNTD and PDFaith provide similar information on phylogenetic structure, and respond similarly to variation in species richness and assemblage structure. However, MPD demonstrate a very different behaviour, and is highly sensitive to deep branching structure. We suggest that by combining complementary metrics that are sensitive to processes operating at different phylogenetic depths (i.e. MPD and MNTD or PDFaith) we can obtain a better understanding of assemblage structure.
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Affiliation(s)
- F Mazel
- Univ. Grenoble Alpes, Laboratoire d'Écologie Alpine (LECA), F-38000 Grenoble, France. CNRS, Laboratoire d'Écologie Alpine (LECA), F-38000 Grenoble, France;
| | - T J Davies
- Department of Biology, McGill University, 1205, Avenue Docteur Penfield, Montreal, Quebec, Canada. African Centre for DNA Barcoding, University of Johannesburg, APK Campus, PO Box 524, Auckland Park 2006, Johannesburg, South Africa;
| | - L Gallien
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland;
| | - J Renaud
- Univ. Grenoble Alpes, Laboratoire d'Écologie Alpine (LECA), F-38000 Grenoble, France. CNRS, Laboratoire d'Écologie Alpine (LECA), F-38000 Grenoble, France;
| | - M Groussin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America;
| | - T Münkemüller
- Univ. Grenoble & CNRS Alpes, Laboratoire d'Écologie Alpine (LECA), F-38000 Grenoble, France;
| | - W Thuiller
- Univ. 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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26
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Abstract
Phylogenetic Generalized Least Square (PGLS) is the tool of choice among phylogenetic comparative methods to measure the correlation between species features such as morphological and life-history traits or niche characteristics. In its usual form, it assumes that the residual variation follows a homogenous model of evolution across the branches of the phylogenetic tree. Since a homogenous model of evolution is unlikely to be realistic in nature, we explored the robustness of the phylogenetic regression when this assumption is violated. We did so by simulating a set of traits under various heterogeneous models of evolution, and evaluating the statistical performance (type I error [the percentage of tests based on samples that incorrectly rejected a true null hypothesis] and power [the percentage of tests that correctly rejected a false null hypothesis]) of classical phylogenetic regression. We found that PGLS has good power but unacceptable type I error rates. This finding is important since this method has been increasingly used in comparative analyses over the last decade. To address this issue, we propose a simple solution based on transforming the underlying variance-covariance matrix to adjust for model heterogeneity within PGLS. We suggest that heterogeneous rates of evolution might be particularly prevalent in large phylogenetic trees, while most current approaches assume a homogenous rate of evolution. Our analysis demonstrates that overlooking rate heterogeneity can result in inflated type I errors, thus misleading comparative analyses. We show that it is possible to correct for this bias even when the underlying model of evolution is not known a priori.
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27
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Tucker CM, Cadotte MW, Carvalho SB, Davies TJ, Ferrier S, Fritz SA, Grenyer R, Helmus MR, Jin LS, Mooers AO, Pavoine S, Purschke O, Redding DW, Rosauer DF, Winter M, Mazel F. A guide to phylogenetic metrics for conservation, community ecology and macroecology. Biol Rev Camb Philos Soc 2016; 92:698-715. [PMID: 26785932 PMCID: PMC5096690 DOI: 10.1111/brv.12252] [Citation(s) in RCA: 275] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 12/01/2015] [Accepted: 12/14/2015] [Indexed: 01/02/2023]
Abstract
The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub‐disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub‐disciplines hampers potential meta‐analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo‐diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo‐diversity metrics based on their mathematical form within these three dimensions and identify ‘anchor’ representatives: for α‐diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.
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Affiliation(s)
- Caroline M Tucker
- Department of Ecology and Evolutionary Biology, University of Colorado, Box 334, Boulder, CO, 80309-0334, U.S.A
| | - Marc W Cadotte
- Biological Sciences, University of Toronto-Scarborough, Scarborough, M1C 1A4, Canada.,Stake Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong, Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, PR China
| | - Silvia B Carvalho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, 4485-661, Vairão, Portugal
| | - T Jonathan Davies
- Department of Biology, McGill University, Montréal, H3A 1B1, Canada.,African Centre for DNA Barcoding, University of Johannesburg, PO Box 524, Johannesburg, 2006, South Africa
| | - Simon Ferrier
- CSIRO Ecosystem Sciences, Climate Adaptation Flagship, GPO BOX 1600, Canberra, 2601, Australia
| | - Susanne A Fritz
- Biodiversity & Climate Research Centre (BiK-F) and Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt am Main, Germany.,Institute of Ecology, Evolution and Diversity, Goethe University, 60438, Frankfurt, Germany
| | - Rich Grenyer
- School of Geography and the Environment, University of Oxford, Oxford, OX1 3QY, U.K
| | - Matthew R Helmus
- Department of Ecological Sciences - Animal Ecology, Vrije Universiteit, Amsterdam, Netherlands.,Center for Biodiversity, Department of Biology, Temple University, Suite 502, Philadelphia, PA, 19122, U.S.A
| | - Lanna S Jin
- Ecology & Evolutionary Biology, University of Toronto, Room 3055, Toronto, M5S 3B2, Canada
| | - Arne O Mooers
- Department of Biology, Simon Fraser University, Burnaby, V5A 1S6, Canada
| | - Sandrine Pavoine
- Centre of Ecology and Conservation Sciences (UMR 7204 CESCO), Museum National d'Histoire Naturelle, Paris, France.,Department of Zoology, University of Oxford, Oxford, OX1 3QY, UK
| | - Oliver Purschke
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, DE-04103, Leipzig, Germany.,Geobotany and Botanical Garden, Institute of Biology, Martin Luther University, Halle-Wittenberg, DE-06108, Halle (Saale), Germany.,Department of Computer Science, Martin-Luther-University, Halle-Wittenberg, DE-06120, Halle (Saale), Germany
| | - David W Redding
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, U.K
| | - Dan F Rosauer
- Research School of Biology, Australian National University, Acton, 2601, Australia
| | - Marten Winter
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, DE-04103, Leipzig, Germany
| | - Florent Mazel
- Laboratoire d'Ecologie Alpine (LECA), CNRS - Université Grenoble Alpes (UMR 5553), BP 53, 38041, Grenoble Cedex 9, France
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28
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Abstract
In analogy to the species-area relationship (SAR), one of the few laws in ecology, the phylogenetic diversity-area relationship (PDAR) describes the tendency of phylogenetic diversity (PD) to increase with area. Although investigating PDAR has the potential to unravel the underlying processes shaping assemblages across spatial scales and to predict PD loss through habitat reduction, it has been little investigated so far. Focusing on PD has noticeable advantages compared to species richness (SR), since PD also gives insights on processes such as speciation/extinction, assembly rules and ecosystem functioning. Here we investigate the universality and pervasiveness of the PDAR at continental scale using terrestrial mammals as study case. We define the relative robustness of PD (compared to SR) to habitat loss as the area between the standardized PDAR and standardized SAR (i.e., standardized by the diversity of the largest spatial window) divided by the area under the standardized SAR only. This metric quantifies the relative increase of PD robustness compared to SR robustness. We show that PD robustness is higher than SR robustness but that it varies among continents. We further use a null model approach to disentangle the relative effect of phylogenetic tree shape and nonrandom spatial distribution of evolutionary history on the PDAR. We find that, for most spatial scales and for all continents except Eurasia, PDARs are not different from expected by a model using only the observed SAR and the shape of the phylogenetic tree at continental scale. Interestingly, we detect a strong phylogenetic structure of the Eurasian PDAR that can be predicted by a model that specifically account for a finer biogeographical delineation of this continent. In conclusion, the relative robustness of PD to habitat loss compared to species richness is determined by the phylogenetic tree shape but also depends on the spatial structure of PD.
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Affiliation(s)
- Florent Mazel
- Univ. Grenoble Alpes, Laboratoire d’Écologie Alpine (LECA), F-38000 Grenoble, France; CNRS, Laboratoire d’Écologie Alpine (LECA), F-38000 Grenoble, France
| | - Julien Renaud
- Univ. Grenoble Alpes, Laboratoire d’Écologie Alpine (LECA), F-38000 Grenoble, France; CNRS, Laboratoire d’Écologie Alpine (LECA), F-38000 Grenoble, France;
| | | | - David Mouillot
- MARBEC Université de Montpellier, Montpellier, France; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld 4811, Australia;
| | - Dominique Gravel
- Université du Québec á Rimouski, Département de biologie, Chimie et Géographie, Québec, Canada;
| | - Wilfried Thuiller
- Univ. 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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29
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Gallien L, Mazel F, Lavergne S, Renaud J, Douzet R, Thuiller W. Contrasting the effects of environment, dispersal and biotic interactions to explain the distribution of invasive plants in alpine communities. Biol Invasions 2015; 17:1407-1423. [PMID: 26290653 PMCID: PMC4538782 DOI: 10.1007/s10530-014-0803-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite considerable efforts devoted to investigate the community assembly processes driving plant invasions, few general conclusions have been drawn so far. Three main processes, generally acting as successive filters, are thought to be of prime importance. The invader has to disperse (1st filter) into a suitable environment (2nd filter) and succeed in establishing in recipient communities through competitive interactions (3rd filter) using two strategies: competition avoidance by the use of different resources (resource opportunity), or competitive exclusion of native species. Surprisingly, despite the general consensus on the importance of investigating these three processes and their interplay, they are usually studied independently. Here we aim to analyse these three filters together, by including them all: abiotic environment, dispersal and biotic interactions, into models of invasive species distributions. We first propose a suite of indices (based on species functional dissimilarities) supposed to reflect the two competitive strategies (resource opportunity and competition exclusion). Then, we use a set of generalised linear models to explain the distribution of seven herbaceous invaders in natural communities (using a large vegetation database for the French Alps containing 5,000 community-plots). Finally, we measure the relative importance of competitive interaction indices, identify the type of coexistence mechanism involved and how this varies along environmental gradients. Adding competition indices significantly improved model's performance, but neither resource opportunity nor competitive exclusion were common strategies among the seven species. Overall, we show that combining environmental, dispersal and biotic information to model invasions has excellent potential for improving our understanding of invader success.
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Affiliation(s)
- Laure Gallien
- Univ. Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France ; CNRS, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France ; Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Florent Mazel
- Univ. Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France ; CNRS, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Sébastien Lavergne
- Univ. Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France ; CNRS, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Julien Renaud
- Univ. Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France ; CNRS, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Rolland Douzet
- Station Alpine Joseph Fourier, CNRS, Univ. Grenoble, F-38000 Grenoble, France
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France ; CNRS, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
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30
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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. Glob Ecol Biogeogr 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] [What about the content of this article? (0)] [Affiliation(s)] [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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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. J Veg Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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