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Li H, Zhou H, Yang S, Dai X. Stochastic and Deterministic Assembly Processes in Seamount Microbial Communities. Appl Environ Microbiol 2023; 89:e0070123. [PMID: 37404136 PMCID: PMC10370332 DOI: 10.1128/aem.00701-23] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/07/2023] [Indexed: 07/06/2023] Open
Abstract
Seamounts are ubiquitous in the ocean. However, little is known about how seamount habitat features influence the local microbial community. In this study, the microbial populations of sediment cores from sampling depths of 0.1 to 35 cm from 10 seamount summit sites with a water depth of 1,850 to 3,827 m across the South China Sea (SCS) Basin were analyzed. Compared with nonseamount ecosystems, isolated seamounts function as oases for microbiomes, with average moderate to high levels of microbial abundance, richness, and diversity, and they harbor distinct microbial communities. The distinct characteristics of different seamounts provide a high level of habitat heterogeneity, resulting in the wide range of microbial community diversity observed across all seamounts. Using dormant thermospores as tracers to study the effect of dispersal by ocean currents, the observed distance-decay biogeography across different seamounts shaped simultaneously by the seamounts' naturally occurring heterogeneous habitat and the limitation of ocean current dispersal was found. We also established a framework that links initial community assembly with successional dynamics in seamounts. Seamounts provide resource-rich and dynamic environments, which leads to a dominance of stochasticity during initial community establishment in surface sediments. However, a progressive increase in deterministic environmental selection, correlated with resource depletion in subsurface sediments, leads to the selective growth of rare species of surface sediment communities in shaping the subsurface community. Overall, the study indicates that seamounts are a previously ignored oasis in the deep sea. This study also provides a case study for understanding the microbial ecology in globally widespread seamounts. IMPORTANCE Although there are approximately 25 million seamounts in the ocean, surprisingly little is known about seamount microbial ecology. We provide evidence that seamounts are island-like habitats harboring microbial communities distinct from those of nonseamount habitats, and they exhibit a distance-decay pattern. Environmental selection and dispersal limitation simultaneously shape the observed biogeography. Coupling empirical data with a null mode revealed a shift in the type and strength, which controls microbial community assembly and succession from the seamount surface to the subsurface sediments as follows: (i) community assembly is initially primarily driven by stochastic processes such as dispersal limitation, and (ii) changes in the subsurface environment progressively increase the importance of environmental selection. This case study contributes to the mechanistic understanding essential for a predictive microbial ecology of seamounts.
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Affiliation(s)
- Haizhou Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Shanghai, China
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Huaiyang Zhou
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Shanshan Yang
- College of Marine Science and Technology, China University of Geosciences, Wuhan, Hubei, China
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institutes of Microbiology, Chinese Academy of Sciences, Beijing, China
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2
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Shi P, Lu Z, Zhou M, Wang N, Wu Y. Niche Suitability Evaluation and Path Selection for the High-Quality Development of Cities in the Yellow River Basin. Int J Environ Res Public Health 2023; 20:3727. [PMID: 36834420 PMCID: PMC9959046 DOI: 10.3390/ijerph20043727] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/17/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
The urban development in the Yellow River basin (YRB) varies widely. Therefore, it is necessary to choose a development path that fits the characteristics of each city to achieve high-quality development. The purpose of this paper is to address the problem of how to choose a characteristic path for high-quality development and clarify its suitability for YRB cities. Firstly, based on data from 50 YRB cities from 2011 to 2020, the suitability evaluation was carried out from the perspective of an ecological niche, followed by the measurement of sub-dimensional niche breadth and overlap. The results confirmed the great diversity of development between cities and the intense competition for resources. Then, based on the classification approach using the k-means method, this study proposes a method for selecting a suitable path for high-quality development. It classifies the suitable paths into 3 major types with 7 minor types and recommends policies for the suitable paths for YRB cities. The systematic thinking and specific path selection method for the high-quality development of YRB cities is not only of practical significance for implementing city classification strategies but also provides a reference for the sustainable development of basin cities in other countries.
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Affiliation(s)
| | - Zhaohan Lu
- Research Center of Energy Economics, School of Business Administration, Henan Polytechnic University, Jiaozuo 454003, China
| | | | | | - Yuping Wu
- Research Center of Energy Economics, School of Business Administration, Henan Polytechnic University, Jiaozuo 454003, China
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3
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Brandl SJ, Lefcheck JS, Bates AE, Rasher DB, Norin T. Can metabolic traits explain animal community assembly and functioning? Biol Rev Camb Philos Soc 2023; 98:1-18. [PMID: 36054431 DOI: 10.1111/brv.12892] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 01/12/2023]
Abstract
All animals on Earth compete for free energy, which is acquired, assimilated, and ultimately allocated to growth and reproduction. Competition is strongest within communities of sympatric, ecologically similar animals of roughly equal size (i.e. horizontal communities), which are often the focus of traditional community ecology. The replacement of taxonomic identities with functional traits has improved our ability to decipher the ecological dynamics that govern the assembly and functioning of animal communities. Yet, the use of low-resolution and taxonomically idiosyncratic traits in animals may have hampered progress to date. An animal's metabolic rate (MR) determines the costs of basic organismal processes and activities, thus linking major aspects of the multifaceted constructs of ecological niches (where, when, and how energy is obtained) and ecological fitness (how much energy is accumulated and passed on to future generations). We review evidence from organismal physiology to large-scale analyses across the tree of life to propose that MR gives rise to a group of meaningful functional traits - resting metabolic rate (RMR), maximum metabolic rate (MMR), and aerobic scope (AS) - that may permit an improved quantification of the energetic basis of species coexistence and, ultimately, the assembly and functioning of animal communities. Specifically, metabolic traits integrate across a variety of typical trait proxies for energy acquisition and allocation in animals (e.g. body size, diet, mobility, life history, habitat use), to yield a smaller suite of continuous quantities that: (1) can be precisely measured for individuals in a standardized fashion; and (2) apply to all animals regardless of their body plan, habitat, or taxonomic affiliation. While integrating metabolic traits into animal community ecology is neither a panacea to disentangling the nuanced effects of biological differences on animal community structure and functioning, nor without challenges, a small number of studies across different taxa suggest that MR may serve as a useful proxy for the energetic basis of competition in animals. Thus, the application of MR traits for animal communities can lead to a more general understanding of community assembly and functioning, enhance our ability to trace eco-evolutionary dynamics from genotypes to phenotypes (and vice versa), and help predict the responses of animal communities to environmental change. While trait-based ecology has improved our knowledge of animal communities to date, a more explicit energetic lens via the integration of metabolic traits may further strengthen the existing framework.
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Affiliation(s)
- Simon J Brandl
- Department of Marine Science, The University of Texas at Austin, Marine Science Institute, Port Aransas, TX, 78373, USA
| | - Jonathan S Lefcheck
- Tennenbaum Marine Observatories Network and MarineGEO Program, Smithsonian Environmental Research Center, Edgewater, MD, 21037, USA
| | - Amanda E Bates
- Biology Department, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8P 5C2, Canada
| | - Douglas B Rasher
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Tommy Norin
- DTU Aqua: National Institute of Aquatic Resources, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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Abstract
In a paper entitled The paradox of the plankton, Hutchinson asked 'how it is possible for a number of species to coexist in a relatively isotropic or unstructured environment all competing for the same sorts of materials' (Hutchinson 1961 Am. Nat. 95, 137-145 (doi:10.1086/282171)). Particularly relevant for phytoplankton, this paradox was based on two implicit, and perhaps naive, postulates, i.e. (i) that all plankton species have similar requirements and (ii) that the marine environment is relatively homogeneous in space and time. A number of hypotheses, based on purely theoretical or experimental studies, have been proposed to solve this conundrum, ranging from spatio-temporal environmental heterogeneity to biotic chaotic variability. Here, we characterize the ecological niche of 117 plankton species belonging to three different taxonomic groups and show that all species have a niche sufficiently distinct to ensure coexistence in a structured marine environment. We also provide evidence that pelagic habitats are, unsurprisingly, more diverse in space and time than Hutchinson imagined, the marine environment being neither unstructured nor stable in space and time. We, therefore, conclude that the niche theory, and its corollary the principle of competitive exclusion, apply as much for the plankton as for other forms of life, be they terrestrial or marine.
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Affiliation(s)
- Loïck Kléparski
- Laboratoire d'Océanologie et de Géosciences, University Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187 - LOG, Wimereux F-62930, France.,Marine Biological Association, Citadel Hill, Plymouth PL1 2PB, UK
| | - Grégory Beaugrand
- Laboratoire d'Océanologie et de Géosciences, University Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187 - LOG, Wimereux F-62930, France
| | - Richard R Kirby
- The Secchi Disk Foundation, Kiln Cottage, Gnaton, Yealmpton PL8 2HU, UK.,Ronin Institute, Montclair, NJ 07043, USA
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Müller C, Junker RR. Chemical phenotype as important and dynamic niche dimension of plants. New Phytol 2022; 234:1168-1174. [PMID: 35297052 DOI: 10.1111/nph.18075] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 10/29/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Niche theory considering the traits of species and individuals provides a powerful tool to integrate ecology and evolution of species. In plant ecology, morphological and physiological traits are commonly considered as niche dimensions, whereas phytochemical traits are mostly neglected in this context despite their pivotal functions in plant responses to their environment and in mediating interactions. The diversity of plant phytochemicals can thus mediate three key processes: niche choice, conformance and construction. Here, we integrate frameworks from niche theory with chemical ecology and argue that plants use their individual-specific diversity in phytochemicals (chemodiversity) for different niche realization processes. Our concept has important implications for ecosystem processes and stability and increases the predictive ability of chemical ecology.
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Affiliation(s)
- Caroline Müller
- Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Robert R Junker
- Evolutionary Ecology of Plants, Department of Biology, University of Marburg, 35043, Marburg, Germany
- Department of Environment and Biodiversity, University of Salzburg, 5020, Salzburg, Austria
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Abstract
Theoretical models are useful to investigate the drivers of community dynamics. In the simplest case of neutral models, the events of death, birth and immigration of individuals are assumed to only depend on their abundance-thus, all types share the same parameters. The community level expectations arising from these simple models and their agreement to empirical data have been discussed extensively, often suggesting that in nature, rates might indeed be neutral or their differences might not be important. However, how robust are these model predictions to type-specific rates? Also, what are the consequences at the level of types? Here, we address these questions moving from simple neutral communities to heterogeneous communities. For this, we build a model where types are differently adapted to the environment. We compute the equilibrium distribution of the abundances. Then, we look into the occurrence-abundance pattern often reported in microbial communities. We observe that large immigration and biodiversity-common in microbial systems-lead to such patterns, regardless of whether the rates are neutral or non-neutral. We conclude by discussing the implications to interpret and test empirical data.
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Affiliation(s)
| | - Michael Sieber
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Arne Traulsen
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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Nielsen SMB, Bilde T, Toft S. Macronutrient niches and field limitation in a woodland assemblage of harvestmen. J Anim Ecol 2021; 91:593-603. [PMID: 34894154 DOI: 10.1111/1365-2656.13649] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/06/2021] [Indexed: 12/01/2022]
Abstract
Description of animals' trophic niches helps us understand interactions between species in biological communities that are not easily observed. Analyses of macronutrient niches, that is, the range of macronutrient (protein:lipid:carbohydrate) ratios selected by generalist feeders, may be a useful alternative approach to inter-species comparisons of diets, especially within taxonomic assemblages of predators where species with similar nutritional requirements are likely to accept similar types of prey. Here we analysed the macronutritional niches of a woodland assemblage of seven harvestman species, all supposed to be predators with omnivorous tendencies. Five species (Mitopus morio, Leiobunum gracile, Oligolophus tridens, O. hanseni and Paroligolophus agrestis) were native and two species (Opilio canestrinii and Dicranopalpus ramosus) were recent invaders into the community. We compare the fundamental (FMN) and realized (RMN) macronutritional niche positions of the species using a 'double-test procedure', which provides information on whether the species were food limited in their natural habitat, and whether they were limited by specific macronutrients. All seven species were food limited and six species were non-protein limited in the field; of these, four species were carbohydrate limited, and in one species females were lipid limited and males were carbohydrate limited. These findings add to the notion that predators are mainly non-protein limited in the field. The FMN positions of the assemblage fell within 46%-50% protein, 29%-38% lipid and 16%-22% carbohydrate. The amount of carbohydrate in the self-selected diet combined with carbohydrate limitation confirms that the species are zoophytophagous. Two morphological clusters of species (large long-legged vs. small short-legged species) differed not only in microhabitat (upper vs. lower forest strata) but also in macronutrient selection, where large long-legged species selected higher proportion of carbohydrate than small short-legged species. Thus, morphologically similar species occupy the same habitat stratum and have similar macronutritional niches. We discuss the hypothesis that the invasive O. canestrinii might have an impact on native species as it allegedly had in urban environments previously. Two basic assumptions about interspecific resource competition were fulfilled, that is, high overlap of nutritional requirements and limitation by food and macronutrients.
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Affiliation(s)
| | - Trine Bilde
- Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Søren Toft
- Department of Biology, Aarhus University, Aarhus C, Denmark
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Zhu WT, Xie FL, Li T, He NJ, Zhang KR, Zhang QF, Dang HS. [Species-habitat association of a deciduous broadleaved forest in the subtropical and tempe-rate transition zone]. Ying Yong Sheng Tai Xue Bao 2021; 32:2755-2762. [PMID: 34664448 DOI: 10.13287/j.1001-9332.202108.009] [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] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The species-habitat association analysis facilitates a better understanding of species coexis-tence and community assembly. Here, all trees in a 25-hm2 broadleaved deciduous forest plot in the Qinling Mountains of North-central China were classified into three life stages (i.e., seedling, sapling, and adult). The Torus-translation test was used to examine the species-habitat association. The results showed that the association of species with habitats varied across different species. Most species were significantly associated with high slopes, 95.7% of which showed negative association. 89.5% and 90.9% of tree species were negatively associated with low slopes and ridges, respectively. Most species had positive association with high valley, with only one negative association (0.03%). There were 80, 44 and 23 significant associations with habitats at seedling, sapling and adult stages, respectively, indicating that a greater dependence of seedlings on habitat. 38 species at seedling stage and 25 species at the sapling stage were associated with at least one habitat type, while only 17 species at the adult stage were significantly associated. The effects of habitat on species varied across life stages, showing a weaker species-habitat association at the later stage. Due to the specific environmental demands, most species showed different habitat preferences across life stages.
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Affiliation(s)
- Wen-Ting Zhu
- College of Science, Tibet University, Lhasa 850000, China.,Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng-Lin Xie
- College of Science, Tibet University, Lhasa 850000, China.,Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Li
- Foping National Nature Reserve Administration, Foping 723400, Shaanxi, China
| | - Nian-Jun He
- Foping National Nature Reserve Administration, Foping 723400, Shaanxi, China
| | - Ke-Rong Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Quan-Fa Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Hai-Shan Dang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
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Furness EN, Garwood RJ, Mannion PD, Sutton MD. Productivity, niche availability, species richness, and extinction risk: Untangling relationships using individual-based simulations. Ecol Evol 2021; 11:8923-8940. [PMID: 34257936 PMCID: PMC8258231 DOI: 10.1002/ece3.7730] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/11/2021] [Indexed: 11/18/2022] Open
Abstract
It has often been suggested that the productivity of an ecosystem affects the number of species that it can support. Despite decades of study, the nature, extent, and underlying mechanisms of this relationship are unclear. One suggested mechanism is the "more individuals" hypothesis (MIH). This proposes that productivity controls the number of individuals in the ecosystem, and that more individuals can be divided into a greater number of species before their population size is sufficiently small for each to be at substantial risk of extinction. Here, we test this hypothesis using REvoSim: an individual-based eco-evolutionary system that simulates the evolution and speciation of populations over geological time, allowing phenomena occurring over timescales that cannot be easily observed in the real world to be evaluated. The individual-based nature of this system allows us to remove assumptions about the nature of speciation and extinction that previous models have had to make. Many of the predictions of the MIH are supported in our simulations: Rare species are more likely to undergo extinction than common species, and species richness scales with productivity. However, we also find support for relationships that contradict the predictions of the strict MIH: species population size scales with productivity, and species extinction risk is better predicted by relative than absolute species population size, apparently due to increased competition when total community abundance is higher. Furthermore, we show that the scaling of species richness with productivity depends upon the ability of species to partition niche space. Consequently, we suggest that the MIH is applicable only to ecosystems in which niche partitioning has not been halted by species saturation. Some hypotheses regarding patterns of biodiversity implicitly or explicitly overlook niche theory in favor of neutral explanations, as has historically been the case with the MIH. Our simulations demonstrate that niche theory exerts a control on the applicability of the MIH and thus needs to be accounted for in macroecology.
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Affiliation(s)
- Euan N. Furness
- Department of Earth Sciences and EngineeringImperial College LondonLondonUK
- Grantham InstituteImperial College LondonLondonUK
| | - Russell J. Garwood
- Department of Earth and Environmental SciencesUniversity of ManchesterManchesterUK
- Earth Sciences DepartmentNatural History MuseumLondonUK
| | | | - Mark D. Sutton
- Department of Earth Sciences and EngineeringImperial College LondonLondonUK
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Cardoso TDS, de Andreazzi CS, Maldonado Junior A, Gentile R. Functional traits shape small mammal-helminth network: patterns and processes in species interactions. Parasitology 2021; 148:947-955. [PMID: 33879271 PMCID: PMC8193565 DOI: 10.1017/s0031182021000640] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/08/2021] [Accepted: 04/14/2021] [Indexed: 01/01/2023]
Abstract
Understanding the role of species traits in mediating ecological interactions and shaping community structure is a key question in ecology. In this sense, parasite population parameters allow us to estimate the functional importance of traits in shaping the strength of interactions among hosts and parasites in a network. The aim of this study was to survey and analyse the small mammal-helminth network in a forest reserve of the Brazilian Atlantic Forest in order to understand (i) how functional traits (type of parasite life cycle, site of infection in their host, host and parasite body length, host diet, host locomotor habit and host activity period) and abundance influence host–parasite interactions, (ii) whether these traits explain species roles, and (iii) if this relationship is consistent across different parasite population parameters (presence and absence, mean abundance and prevalence). Networks were modular and their structural patterns did not vary among the population parameters. Functional traits and abundance shaped the interactions observed between parasites and hosts. Host species abundance, host diet and locomotor habit affected their centrality and/or vulnerability to parasites. For helminths, infection niche was the main trait determining their central roles in the networks.
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Affiliation(s)
- Thiago dos Santos Cardoso
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brasil
- Programa Fiocruz de Fomento à Inovação – INOVA FIOCRUZ, Fundação Oswaldo Cruz, Av. Brasil 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brasil
| | - Cecilia Siliansky de Andreazzi
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brasil
| | - Arnaldo Maldonado Junior
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brasil
| | - Rosana Gentile
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brasil
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11
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Yin G, Xia Y. Corrigendum: Assessing the Hybrid Effects of Neutral and Niche Processes on Gut Microbiome Influenced by HIV Infection. Front Microbiol 2021; 12:710865. [PMID: 34177878 PMCID: PMC8220203 DOI: 10.3389/fmicb.2021.710865] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2019.01467.].
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Affiliation(s)
- Guanshu Yin
- The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yao Xia
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
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Abstract
AbstractFifty years ago, Robert MacArthur showed that stable equilibria optimize quadratic functions of the population sizes in several important ecological models. Here, we generalize this finding to a broader class of systems within the framework of contemporary niche theory and precisely state the conditions under which an optimization principle (not necessarily quadratic) can be obtained. We show that conducting the optimization in the space of environmental states instead of population sizes leads to a universal and transparent physical interpretation of the objective function. Specifically, the equilibrium state minimizes the perturbation of the environment induced by the presence of the competing species, subject to the constraint that no species has a positive net growth rate. We use this "minimum environmental perturbation principle" to make new predictions for evolution and community assembly, where the minimum perturbation increases monotonically under invasion by new species. We also describe a simple experimental setting where the conditions of validity for this optimization principle have been empirically tested.
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Liu W, Graham EB, Zhong L, Zhang J, Li S, Lin X, Feng Y. Long-Term Stochasticity Combines With Short-Term Variability in Assembly Processes to Underlie Rice Paddy Sustainability. Front Microbiol 2020; 11:873. [PMID: 32499764 PMCID: PMC7243440 DOI: 10.3389/fmicb.2020.00873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 02/15/2020] [Accepted: 04/14/2020] [Indexed: 12/04/2022] Open
Abstract
Revealing temporal patterns of community assembly processes is important for understanding how microorganisms underlie the sustainability of agroecosystem. The ancient terraced rice paddies at Longji provide an ideal platform to study temporal dynamics of agroecosystem sustainability due to their chronosequential records of soil physicochemistry and well-archived microbial information along 630-year rice cultivation. We used statistical null models to evaluate microbial assembly processes along the soil chronosequences of Longji rice paddies through time. Stochastic and deterministic assembly processes jointly governed microbial community composition within successional eras (less than 250 years), and within-era determinism was mainly driven by soil fertility and redox conditions alone or in combination. Conversely, across successional eras (i.e., over 300 years), stochasticity linearly increased with increasing duration between eras and was eventually predominant for the whole 630 years. We suggest that the impact of stochasticity vs. determinism on assembly is timescale-dependent, and we propose that the importance of stochastic assembly of microbial community at longer timescales is due to the gradual changes in soil properties under long-term rice cultivation, which in turn contribute to the sustainability of paddy ecosystem by maintaining a diverse community of microorganisms with multi-functional traits. In total, our results indicate that knowledge on the timescales at which assembly processes govern microbial community composition is key to understanding the ecological mechanisms generating agroecosystem sustainability.
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Affiliation(s)
- Wenjing Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- The College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Emily B. Graham
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Linghao Zhong
- Department of Chemistry, Pennsylvania State University, Mont Alto, PA, United States
| | - Jianwei Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Shijie Li
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Thakur MP, Phillips HRP, Brose U, De Vries FT, Lavelle P, Loreau M, Mathieu J, Mulder C, Van der Putten WH, Rillig MC, Wardle DA, Bach EM, Bartz MLC, Bennett JM, Briones MJI, Brown G, Decaëns T, Eisenhauer N, Ferlian O, Guerra CA, König‐Ries B, Orgiazzi A, Ramirez KS, Russell DJ, Rutgers M, Wall DH, Cameron EK. Towards an integrative understanding of soil biodiversity. Biol Rev Camb Philos Soc 2020; 95:350-364. [PMID: 31729831 PMCID: PMC7078968 DOI: 10.1111/brv.12567] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [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] [Received: 01/08/2019] [Revised: 10/07/2019] [Accepted: 10/11/2019] [Indexed: 12/25/2022]
Abstract
Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species-energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity.
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Affiliation(s)
- Madhav P. Thakur
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenGelderland, The Netherlands
- German Centre for Integrative Biodiversity Research (iDiv), Halle‐Jena‐LeipzigLeipzigSaxony, Germany
- Institute of Biology, Leipzig UniversityLeipzigSaxony, Germany
| | - Helen R. P. Phillips
- German Centre for Integrative Biodiversity Research (iDiv), Halle‐Jena‐LeipzigLeipzigSaxony, Germany
| | - Ulrich Brose
- German Centre for Integrative Biodiversity Research (iDiv), Halle‐Jena‐LeipzigLeipzigSaxony, Germany
- Institute of Biodiversity, Friedrich Schiller University JenaJenaThuringia, Germany
| | - Franciska T. De Vries
- School of Earth and Environmental Sciences, The University of ManchesterManchesterNorth West England, UK
| | | | - Michel Loreau
- Centre for Biodiversity Theory and Modelling, Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier UniversityMoulisOccitanie, France
| | - Jerome Mathieu
- Sorbonne Université, CNRS, UPECParisÎle-de-France, France
| | - Christian Mulder
- Department BiologicalGeological and Environmental Sciences, University of CataniaCataniaSicily, Italy
| | - Wim H. Van der Putten
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenGelderland, The Netherlands
- Laboratory of NematologyWageningen UniversityWageningenGelderland, The Netherlands
| | - Matthias C. Rillig
- Freie Universität Berlin, Institute of BiologyBerlinGermany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB)BerlinGermany
| | - David A. Wardle
- Asian School for the Environment, Nanyang Technological UniversitySingaporeSingapore
| | - Elizabeth M. Bach
- Department of Biology and School of Global Environmental SustainabilityColorado State UniversityFort CollinsCOUSA
| | - Marie L. C. Bartz
- Center of Functional Ecology, Department of Life SciencesUniversity of CoimbraCoimbraCentro, Portugal
- Universidade Positivo, Rua Professor Pedro Viriato Parigot de SouzaCuritiba Paraná, Brazil
| | - Joanne M. Bennett
- German Centre for Integrative Biodiversity Research (iDiv), Halle‐Jena‐LeipzigLeipzigSaxony, Germany
- Institute of Biology, Martin Luther University Halle‐WittenbergHalle (Saale)Saxony-Anhalt, Germany
| | - Maria J. I. Briones
- Departamento de Ecología y Biología AnimalUniversidad de VigoVigoGalicien, Spain
| | | | - Thibaud Decaëns
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE UMR 5175, CNRS–Université de Montpellier–Université Paul‐Valéry Montpellier–EPHE)MontpellierOccitanie, France
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv), Halle‐Jena‐LeipzigLeipzigSaxony, Germany
- Institute of Biology, Leipzig UniversityLeipzigSaxony, Germany
| | - Olga Ferlian
- German Centre for Integrative Biodiversity Research (iDiv), Halle‐Jena‐LeipzigLeipzigSaxony, Germany
- Institute of Biology, Leipzig UniversityLeipzigSaxony, Germany
| | - Carlos António Guerra
- German Centre for Integrative Biodiversity Research (iDiv), Halle‐Jena‐LeipzigLeipzigSaxony, Germany
- Institute of Biology, Martin Luther University Halle‐WittenbergHalle (Saale)Saxony-Anhalt, Germany
| | - Birgitta König‐Ries
- German Centre for Integrative Biodiversity Research (iDiv), Halle‐Jena‐LeipzigLeipzigSaxony, Germany
- Institute of Computer Science, Friedrich Schiller University JenaJenaThuringia, Germany
| | - Alberto Orgiazzi
- European Commission, Joint Research Centre (JRC), Sustainable Resources DirectorateIspraVareseItaly
| | - Kelly S. Ramirez
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenGelderland, The Netherlands
| | - David J. Russell
- Senckenberg Museum of Natural History GörlitzGoerlitzSaxony, Germany
| | - Michiel Rutgers
- National Institute for Public Health and the EnvironmentBilthovenUtrecht, The Netherlands
| | - Diana H. Wall
- Department of Biology and School of Global Environmental SustainabilityColorado State UniversityFort CollinsCOUSA
| | - Erin K. Cameron
- Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinki, Uusimaa, Finland
- Department of Environmental ScienceSaint Mary's UniversityHalifaxNova ScotiaCanada
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15
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Vasl A, Schindler BY, Kadas GJ, Blaustein L. Fine-scale substrate heterogeneity in green roof plant communities: The constraint of size. Ecol Evol 2019; 9:11557-11568. [PMID: 31695868 PMCID: PMC6822028 DOI: 10.1002/ece3.5517] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 06/13/2018] [Revised: 11/10/2018] [Accepted: 03/25/2019] [Indexed: 11/09/2022] Open
Abstract
Heterogeneity-diversity relationship (HDR) is commonly shown to be positive in accordance with classic niche processes. However, recent soil-based studies have often found neutral and even negative HDRs. Some of the suggested reasons for this discrepancy include the lack of resemblance between manipulated substrate and natural settings, the treated areas not being large enough to contain species' root span, and finally limited-sized plots may not sustain focal species' populations over time. Vegetated green roofs are a growing phenomenon in many cities that could be an ideal testing ground for this problem. Recent studies have focused on the ability of these roofs to sustain stable and diverse plant communities and substrate heterogeneity that would increase niches on the roof has been proposed as a method to attain this goal. We constructed an experimental design using green roof experimental modules (4 m2) where we manipulated mineral and organic substrate component heterogeneity in different subplots (0.25 m2) within the experimental module while maintaining the total sum of mineral and organic components. A local annual plant community was seeded in the modules and monitored over three growing seasons. We found that plant diversity and biomass were not affected by experimentally created substrate heterogeneity. In addition, we found that different treatments, as well as specific subplot substrates, had an effect on plant community assemblages during the first year but not during the second and third years. Substrate heterogeneity levels were mostly unchanged over time. The inability to retain plant community composition over the years despite the maintenance of substrate differences supports the hypothesis that maintenance of diversity is constrained at these spatial scales by unfavorable dispersal and increased stochastic events as opposed to predictions of classic niche processes.
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Affiliation(s)
- Amiel Vasl
- Kadas Green Roofs Ecology Research CenterInstitute of Evolution and Department of Evolutionary and Environmental BiologyFaculty of Natural SciencesUniversity of HaifaHaifaIsrael
| | - Bracha Y. Schindler
- Kadas Green Roofs Ecology Research CenterInstitute of Evolution and Department of Evolutionary and Environmental BiologyFaculty of Natural SciencesUniversity of HaifaHaifaIsrael
| | - Gyongyver J. Kadas
- Kadas Green Roofs Ecology Research CenterInstitute of Evolution and Department of Evolutionary and Environmental BiologyFaculty of Natural SciencesUniversity of HaifaHaifaIsrael
- Environmental Research GroupSustainability Research InstituteUniversity of East LondonLondonUK
| | - Leon Blaustein
- Kadas Green Roofs Ecology Research CenterInstitute of Evolution and Department of Evolutionary and Environmental BiologyFaculty of Natural SciencesUniversity of HaifaHaifaIsrael
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16
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Oliveira-Junior JMB, Juen L. Structuring of Dragonfly Communities (Insecta: Odonata) in Eastern Amazon: Effects of Environmental and Spatial Factors in Preserved and Altered Streams. Insects 2019; 10:E322. [PMID: 31569784 DOI: 10.3390/insects10100322] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/26/2019] [Accepted: 08/29/2019] [Indexed: 11/18/2022]
Abstract
The evaluation of the effects of environmental factors on natural communities has been one of the principal approaches in ecology; although, over the past decade, increasing importance has been given to spatial factors. In this context, we evaluated the relative importance of environmental and spatial factors for the structuring of the local odonate communities in preserved and altered streams. Adult Odonata were sampled in 98 streams in eastern Amazonia, Brazil. The physical features of each stream were evaluated and spatial variables were generated. Only environmental factors accounted for the variation in the Odonata community. The same pattern was observed in the suborder Zygoptera. For Anisoptera, environmental factors alone affect the variation in the community, considering all the environments together, and the altered areas on their own. As the two Odonata suborders presented distinct responses to environmental factors, this partitioning may contribute to an improvement in the precision of studies in biomonitoring. We thus suggest that studies would have a greater explanatory potential if additional variables are included, related to biotic interactions (e.g., competition). This will require further investigation on a finer scale of environmental variation to determine how the Odonata fauna of Amazonian streams behaves under this analytical perspective.
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17
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Zhang CJ, Pan J, Duan CH, Wang YM, Liu Y, Sun J, Zhou HC, Song X, Li M. Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes. mSystems 2019; 4:e00442-19. [PMID: 31506265 DOI: 10.1128/mSystems.00442-19] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves. Mangroves, as a blue carbon reservoir, provide an environment for a variety of microorganisms. Mangroves lie in special locations connecting coastal and estuarine areas and experience fluctuating conditions, which are expected to intensify with climate change, creating a need to better understand the relative roles of stochastic and deterministic processes in shaping microbial community assembly. Here, a study of microbial communities inhabiting mangrove sediments across southeastern China, spanning mangroves in six nature reserves, was conducted. We performed high-throughput DNA sequencing of these samples and compared them with data of 1,370 sediment samples collected from the Earth Microbiome Project (EMP) to compare the microbial diversity of mangroves with that of other biomes. Our results showed that prokaryotic alpha diversity in mangroves was significantly higher than that in other biomes and that microbial beta diversity generally clustered according to biome types. The core operational taxonomic units (OTUs) in mangroves were mostly assigned to Gammaproteobacteria, Deltaproteobacteria, Chloroflexi, and Euryarchaeota. The majority of beta nearest-taxon index values were higher than 2, indicating that community assembly in mangroves was better explained through a deterministic process than through a stochastic process. Mean annual precipitation (MAP) and total organic carbon (TOC) were main deterministic factors explaining variation in the microbial community. This study fills a gap in addressing the unique microbial diversity of mangrove ecosystems and their microbial community assembly mechanisms. IMPORTANCE Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves.
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18
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Yin G, Xia Y. Assessing the Hybrid Effects of Neutral and Niche Processes on Gut Microbiome Influenced by HIV Infection. Front Microbiol 2019; 10:1467. [PMID: 31354638 PMCID: PMC6639661 DOI: 10.3389/fmicb.2019.01467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 03/25/2019] [Accepted: 06/11/2019] [Indexed: 11/13/2022] Open
Abstract
That both stochastic neutral and deterministic niche forces are in effect in shaping the community assembly and diversity maintenance is becoming an increasingly important consensus. However, assessing the effects of disease on the balance between the two forces in the human microbiome has not been explored to the best of our knowledge. In this article, we applied a hybrid model to address this issue by analyzing the potential effect of HIV infection on the human gut microbiome and adopted a further step of multimodality testing to improve the interpretation of their model. Our study revealed that although niche process is the dominant force in shaping human gut microbial communities, niche process- and neutral process-driven taxa could coexist in the same microbiome, confirming the notion of their joint responsibility. However, we failed to detect the effect of HIV infection in changing the balance. This suggests that the rule governing community assembly and diversity maintenance may be changed by the disturbance from HIV infection-caused dysbiosis. Although we admit that the general question of disease effect on community assembly and diversity maintenance may still be an open question, our study presents the first piece of evidence to reject the significant influence of diseases.
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Affiliation(s)
- Guanshu Yin
- The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yao Xia
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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19
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Stover HJ, Henry HAL. Interactions between soil heterogeneity and freezing: Implications for grassland plant diversity and relative species abundances. Glob Chang Biol 2019; 25:2275-2284. [PMID: 30963661 DOI: 10.1111/gcb.14645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 10/02/2018] [Revised: 02/11/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Plant stress resulting from soil freezing is expected to increase in northern temperate regions over the next century due to reductions in snow cover caused by climate change. Within plant communities, soil spatial heterogeneity can potentially buffer the effects of plant freezing stress by increasing the availability of soil microsites that function as microrefugia. Moreover, increased species richness resulting from soil heterogeneity can increase the likelihood of stress-tolerant species being present in a community. We used a field experiment to examine interactions between soil heterogeneity and increased freezing intensity (achieved via snow removal) on plant abundance and diversity in a grassland. Patches of topsoil were mixed with either sand or woodchips to create heterogeneous and homogeneous treatments, and plant community responses to snow removal were assessed over three growing seasons. Soil heterogeneity interacted significantly with snow removal, but it either buffered or exacerbated the snow removal response depending on the specific substrate (sand vs. woodchips) and plant functional group. In turn, snow removal influenced plant responses to soil heterogeneity; for example, adventive forb cover responded to increased heterogeneity under ambient snow cover, but this effect diminished with snow removal. Our results reveal that soil heterogeneity can play an important role in determining plant responses to changes in soil freezing stress resulting from global climate change. While the deliberate creation of soil microsites in ecological restoration projects as a land management practice could increase the frequency of microrefugia that mitigate plant community responses to increased freezing stress, the design of these microsites must be optimized, given that soil heterogeneity also has the potential to exacerbate freezing stress responses.
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Affiliation(s)
- Holly J Stover
- Department of Biology, Western University, London, Ontario, Canada
| | - Hugh A L Henry
- Department of Biology, Western University, London, Ontario, Canada
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20
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Leray M, Alldredge AL, Yang JY, Meyer CP, Holbrook SJ, Schmitt RJ, Knowlton N, Brooks AJ. Dietary partitioning promotes the coexistence of planktivorous species on coral reefs. Mol Ecol 2019; 28:2694-2710. [PMID: 30933383 PMCID: PMC6852152 DOI: 10.1111/mec.15090] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 10/01/2018] [Revised: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 11/29/2022]
Abstract
Theories involving niche diversification to explain high levels of tropical diversity propose that species are more likely to co‐occur if they partition at least one dimension of their ecological niche space. Yet, numerous species appear to have widely overlapping niches based upon broad categorizations of resource use or functional traits. In particular, the extent to which food partitioning contributes to species coexistence in hyperdiverse tropical ecosystems remains unresolved. Here, we use a molecular approach to investigate inter‐ and intraspecific dietary partitioning between two species of damselfish (Dascyllus flavicaudus, Chromis viridis) that commonly co‐occur in branching corals. Species‐level identification of their diverse zooplankton prey revealed significant differences in diet composition between species despite their seemingly similar feeding strategies. Dascyllus exhibited a more diverse diet than Chromis, whereas Chromis tended to select larger prey items. A large calanoid copepod, Labidocera sp., found in low density and higher in the water column during the day, explained more than 19% of the variation in dietary composition between Dascyllus and Chromis. Dascyllus did not significantly shift its diet in the presence of Chromis, which suggests intrinsic differences in feeding behaviour. Finally, prey composition significantly shifted during the ontogeny of both fish species. Our findings show that levels of dietary specialization among coral reef associated species have likely been underestimated, and they underscore the importance of characterizing trophic webs in tropical ecosystems at higher levels of taxonomic resolution. They also suggest that niche redundancy may not be as common as previously thought.
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Affiliation(s)
- Matthieu Leray
- Smithsonian Tropical Research Institute, Smithsonian Institution, Panama City, Balboa, Ancon, Panama
| | - Alice L Alldredge
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California
| | - Joy Y Yang
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christopher P Meyer
- National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia
| | - Sally J Holbrook
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California.,Coastal Research Center, Marine Science Institute, University of California Santa Barbara, Santa Barbara, California
| | - Russell J Schmitt
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California.,Coastal Research Center, Marine Science Institute, University of California Santa Barbara, Santa Barbara, California
| | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia
| | - Andrew J Brooks
- Coastal Research Center, Marine Science Institute, University of California Santa Barbara, Santa Barbara, California
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21
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Levi T, Barfield M, Barrantes S, Sullivan C, Holt RD, Terborgh J. Tropical forests can maintain hyperdiversity because of enemies. Proc Natl Acad Sci U S A 2019; 116:581-6. [PMID: 30584100 DOI: 10.1073/pnas.1813211116] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Explaining the maintenance of tropical forest diversity under the countervailing forces of drift and competition poses a major challenge to ecological theory. Janzen-Connell effects, in which host-specific natural enemies restrict the recruitment of juveniles near conspecific adults, provide a potential mechanism. Janzen-Connell is strongly supported empirically, but existing theory does not address the stable coexistence of hundreds of species. Here we use high-performance computing and analytical models to demonstrate that tropical forest diversity can be maintained nearly indefinitely in a prolonged state of transient dynamics due to distance-responsive natural enemies. Further, we show that Janzen-Connell effects lead to community regulation of diversity by imposing a diversity-dependent cost to commonness and benefit to rarity. The resulting species-area and rank-abundance relationships are consistent with empirical results. Diversity maintenance over long time spans does not require dispersal from an external metacommunity, speciation, or resource niche partitioning, only a small zone around conspecific adults in which saplings fail to recruit. We conclude that the Janzen-Connell mechanism can explain the maintenance of tropical tree diversity while not precluding the operation of other niche-based mechanisms such as resource partitioning.
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22
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Li W, Yuan Y, Xia Y, Sun Y, Miao Y, Ma S. A Cross-Scale Neutral Theory Approach to the Influence of Obesity on Community Assembly of Human Gut Microbiome. Front Microbiol 2018; 9:2320. [PMID: 30420838 PMCID: PMC6215851 DOI: 10.3389/fmicb.2018.02320] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 05/31/2018] [Accepted: 09/11/2018] [Indexed: 12/23/2022] Open
Abstract
Background: The implications of gut microbiome to obesity have been extensively investigated in recent years although the exact mechanism is still unclear. The question whether or not obesity influences gut microbiome assembly has not been addressed. The question is significant because it is fundamental for investigating the diversity maintenance and stability of gut microbiome, and the latter should hold a key for understanding the etiological implications of gut microbiome to obesity. Methods: In this study, we adopt a dual neutral theory modeling strategy to address this question from both species and community perspectives, with both discrete and continuous neutral theory models. The first neutral theory model we apply is Hubbell's neutral theory of biodiversity that has been extensively tested in macro-ecology of plants and animals, and the second we apply is Sloan's neutral theory model that was developed particularly for microbial communities based on metagenomic sequencing data. Both the neutral models are complementary to each other and integrated together offering a comprehensive approach to more accurately revealing the possible influence of obesity on gut microbiome assembly. This is not only because the focus of both neutral theory models is different (community vs. species), but also because they adopted two different modeling strategies (discrete vs. continuous). Results: We test both the neutral theory models with datasets from Turnbaugh et al. (2009). Our tests showed that the species abundance distributions of more than ½ species (59-69%) in gut microbiome satisfied the prediction of Sloan's neutral theory, although at the community level, the number of communities satisfied the Hubbell's neutral theory was negligible (2 out of 278). Conclusion: The apparently contradictory findings above suggest that both stochastic neutral effects and deterministic environmental (host) factors play important roles in shaping the assembly and diversity of gut microbiome. Furthermore, obesity may just be one of the host factors, but its influence may not be strong enough to tip the balance between stochastic and deterministic forces that shape the community assembly. Finally, the apparent contradiction from both the neutral theories should not be surprising given that there are still near 30-40% species that do not obey the neutral law.
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Affiliation(s)
- Wendy Li
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yali Yuan
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- College of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Yao Xia
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yang Sun
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, China
| | - Yinglei Miao
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, China
| | - Sam Ma
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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Huang Q, Wang Y, Xia Y, Li L, Luo J, Xia S, Sun Y, Miao Y, Wang K, Chen Y. Testing the neutral theory of biodiversity with the microbiome dataset from cystic fibrosis patients. Medicine (Baltimore) 2018; 97:e12248. [PMID: 30212959 PMCID: PMC6156045 DOI: 10.1097/md.0000000000012248] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Cystic fibrosis (CF) is a hereditary disease that is characterized by defective mucociliary clearance, airway obstruction, chronic infection, and persistent inflammation. Cystic fibrosis pulmonary exacerbation (CFPE) majorly causes the morbidity of CF patients. Although CF has been demonstrated to change the composition of lung microbial community, previous studies have not made efforts to study the differences in the mechanism of assembly and diversity maintenance of lung microbial community in CF patients. In this study, we applied the neutral theory of biodiversity to comparatively investigate the assembly and diversity maintenance of the lung microbial community before and after the antibiotic treatment by reanalyzing the dataset from Fodor et al's study. We found that no one sample in the lung microbial communities of the sputum samples of Exacerbation group, nor those of End-of-treatment group satisfied the predictions of neutral model, suggesting that the neutral-process does not dominate in CF patients before and after antibiotic treatments. By comparing the biodiversity parameter between Exacerbation and End-of-treatment group, we found that the former had the significantly higher biodiversity, but the change in diversity parameter is slight and the P value is close to.05 (P value = .41). Therefore, our second finding is that although CFPE may increase the biodiversity of lung microbial community, the change is not essential.
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Affiliation(s)
- Qi Huang
- Department of Gastroenterology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Gastroenterology, Guangdong Gastrointestinal Disease Research Center, Nanfang Hospital, Southern Medical University, Guangzhou
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming
| | - Yaqiang Wang
- Institute of Mathematics and Information Science, Baoji University of Arts and Sciences, Baoji, Shaanxi
| | - Yao Xia
- Computational Biology and Medical Ecology Lab, State Key Lab of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
| | - Lianwei Li
- Computational Biology and Medical Ecology Lab, State Key Lab of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
| | - Juan Luo
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming
| | - Shuxian Xia
- Department of Gastroenterology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Gastroenterology, Guangdong Gastrointestinal Disease Research Center, Nanfang Hospital, Southern Medical University, Guangzhou
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming
| | - Yang Sun
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming
| | - Yinglei Miao
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming
| | - Kunhua Wang
- Department of General Surgery, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of digestive disease, Kunming, China
| | - Ye Chen
- Department of Gastroenterology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Gastroenterology, Guangdong Gastrointestinal Disease Research Center, Nanfang Hospital, Southern Medical University, Guangzhou
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24
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Yuan Z, Wei B, Chen Y, Jia H, Wei Q, Ye Y. How do similarities in spatial distributions and interspecific associations affect the coexistence of Quercus species in the Baotianman National Nature Reserve, Henan, China. Ecol Evol 2018; 8:2580-2593. [PMID: 29531678 PMCID: PMC5838042 DOI: 10.1002/ece3.3863] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 12/08/2016] [Revised: 12/09/2017] [Accepted: 01/02/2018] [Indexed: 11/07/2022] Open
Abstract
Congeneric species often have similar ecological characteristics and use similar resources. These similarities may make it easier for them to co-occur in a similar habitat but may also lead to strong competitions that limit their coexistence. Hence, how do similarities in congeneric species affect their coexistence exactly? This study mainly used spatial point pattern analysis in two 1 hm2 plots in the Baotianman National Nature Reserve, Henan, China, to compare the similarities in spatial distributions and interspecific associations of Quercus species. Results revealed that Quercus species were all aggregated under the complete spatial randomness null model, and aggregations were weaker under the heterogeneous Poisson process null model in each plot. The interspecific associations of Quercus species to non-Quercus species were very similar in Plot 1. However, they can be either positive or negative in different plots between the co-occurring Quercus species. The spatial distributions of congeneric species, interspecific associations with non-Quercus species, neighborhood richness around species, and species diversity were all different between the two plots. We found that congeneric species did have some similarities, and the closely related congeneric species can positive or negative associate with each other in different plots. The co-occurring congeneric species may have different survival strategies in different habitats. On the one hand, competition among congenerics may lead to differentiation in resource utilization. On the other hand, their similar interspecific associations can strengthen their competitive ability and promote local exclusion to noncongeneric species to obtain more living space. Our results provide new knowledge for us to better understand the coexistence mechanisms of species.
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Affiliation(s)
| | - Boliang Wei
- College of Life SciencesZhejiang UniversityHangzhouZhejiangChina
| | - Yun Chen
- Henan Agricultural UniversityZhengzhouHenanChina
| | - Hongru Jia
- Educational Administration DepartmentHenan College of Finance and TaxationZhengzhouHenanChina
| | | | - Yongzhong Ye
- Henan Agricultural UniversityZhengzhouHenanChina
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25
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Doherty TS, Driscoll DA. Competition in the Historical Niche: A Response to Scheele et al. Trends Ecol Evol 2017; 33:147-148. [PMID: 29274664 DOI: 10.1016/j.tree.2017.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/01/2017] [Indexed: 11/24/2022]
Affiliation(s)
- Tim S Doherty
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology (Burwood Campus), Geelong, Australia.
| | - Don A Driscoll
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology (Burwood Campus), Geelong, Australia
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26
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Ord TJ, Emblen J, Hagman M, Shofner R, Unruh S. Manipulation of habitat isolation and area implicates deterministic factors and limited neutrality in community assembly. Ecol Evol 2017; 7:5845-5860. [PMID: 28811885 PMCID: PMC5552957 DOI: 10.1002/ece3.3126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 04/04/2017] [Revised: 05/03/2017] [Accepted: 05/08/2017] [Indexed: 11/12/2022] Open
Abstract
Theory predicts deterministic and stochastic factors will contribute to community assembly in different ways: Environmental filters should regulate those species that establish in a particular area resulting in the ecological requirements of species being the primary driver of species distributions, while chance and dispersal limitation should dictate the likelihood of species reaching certain areas with the ecology of species being largely neutral. These factors are specifically relevant for understanding how the area and isolation of different habitats or islands interact to affect community composition. Our review of the literature found few experimental studies have examined the interactive effect of habitat area and isolation on community assembly, and the results of those experiments have been mixed. We manipulated the area and isolation of rock “islands” created de novo in a grassland matrix to experimentally test how deterministic and stochastic factors shape colonizing animal communities. Over 64 weeks, the experiment revealed the primacy of deterministic factors in community assembly, with habitat islands of the same size exhibiting remarkable consistency in community composition and diversity, irrespective of isolation. Nevertheless, tangible differences still existed in abundance inequality among taxa: Large, near islands had consistently higher numbers of common taxa compared to all other island types. Dispersal limitation is often assumed to be negligible at small spatial scales, but our data shows this not to be the case. Furthermore, the dispersal limitation of a subset of species has potentially complex flow‐on effects for dictating the type of deterministic factors affecting other colonizing species.
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Affiliation(s)
- Terry J Ord
- Evolution and Ecology Research Centre and the School of Biological Earth and Environmental Sciences University of New South Wales Kensington NSW Australia
| | - Jack Emblen
- Evolution and Ecology Research Centre and the School of Biological Earth and Environmental Sciences University of New South Wales Kensington NSW Australia
| | - Mattias Hagman
- Evolution and Ecology Research Centre and the School of Biological Earth and Environmental Sciences University of New South Wales Kensington NSW Australia
| | - Ryan Shofner
- Evolution and Ecology Research Centre and the School of Biological Earth and Environmental Sciences University of New South Wales Kensington NSW Australia
| | - Sara Unruh
- Evolution and Ecology Research Centre and the School of Biological Earth and Environmental Sciences University of New South Wales Kensington NSW Australia
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27
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Gallien L, Zimmermann NE, Levine JM, Adler PB. The effects of intransitive competition on coexistence. Ecol Lett 2017; 20:791-800. [PMID: 28547799 DOI: 10.1111/ele.12775] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [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: 10/12/2016] [Revised: 11/23/2016] [Accepted: 03/31/2017] [Indexed: 11/29/2022]
Abstract
Coexistence theory has been developed with an almost exclusive focus on interactions between two species, often ignoring more complex and indirect interactions, such as intransitive loops, that can emerge in competition networks. In fact, intransitive competition has typically been studied in isolation from other pairwise stabilising processes, and thus little is known about how intransitivity interacts with more traditional drivers of species coexistence such as niche partitioning. To integrate intransitivity into traditional coexistence theory, we developed a metric of growth rate when rare, Δri¯, to identify and quantify the impact of intransitive competition against a backdrop of pairwise stabilising niche differences. Using this index with simulations of community dynamics, we demonstrate that intransitive loops can both stabilise or destabilise species coexistence, but the strength and importance of intransitive interactions are significantly affected by the length and the topology of these loops. We conclude by showing how Δri¯ can be used to evaluate effects of intransitivity in empirical studies. Our results emphasise the need to integrate complex mechanisms emerging from diverse interactions into our understanding of species coexistence.
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Affiliation(s)
- Laure Gallien
- Swiss Federal Research Institute WSL, Birmensdorf, 8903, Switzerland.,Deparment of Botany & Zoology, Centre for Invasion Biology, Stellenbosch University, Matieland, 7602, South Africa
| | | | - Jonathan M Levine
- Institute of Integrative Biology, ETH Zurich, Zurich, 8092, Switzerland
| | - Peter B Adler
- Department of Wildland Resources and the Ecology Center, Utah State University, Logan, UT, 84322, USA
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28
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Sánchez-Hernández J, Gabler HM, Amundsen PA. Prey diversity as a driver of resource partitioning between river-dwelling fish species. Ecol Evol 2017; 7:2058-2068. [PMID: 28405272 PMCID: PMC5383502 DOI: 10.1002/ece3.2793] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [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: 06/30/2016] [Revised: 12/28/2016] [Accepted: 01/14/2017] [Indexed: 11/11/2022] Open
Abstract
Although food resource partitioning among sympatric species has often been explored in riverine systems, the potential influence of prey diversity on resource partitioning is little known. Using empirical data, we modeled food resource partitioning (assessed as dietary overlap) of coexisting juvenile Atlantic salmon (Salmo salar) and alpine bullhead (Cottus poecilopus). Explanatory variables incorporated into the model were fish abundance, benthic prey diversity and abundance, and several dietary metrics to give a total of seventeen potential explanatory variables. First, a forward stepwise procedure based on the Akaike information criterion was used to select explanatory variables with significant effects on food resource partitioning. Then, linear mixed‐effect models were constructed using the selected explanatory variables and with sampling site as a random factor. Food resource partitioning between salmon and bullhead increased significantly with increasing prey diversity, and the variation in food resource partitioning was best described by the model that included prey diversity as the only explanatory variable. This study provides empirical support for the notion that prey diversity is a key driver of resource partitioning among competing species.
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Affiliation(s)
- Javier Sánchez-Hernández
- Department of Arctic and Marine Biology Faculty of Biosciences Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway; Department of Zoology, Genetics and Physical Anthropology Faculty of Biology University of Santiago de Compostela Santiago de Compostela Spain
| | - Heidi-Marie Gabler
- Department of Arctic and Marine Biology Faculty of Biosciences Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway
| | - Per-Arne Amundsen
- Department of Arctic and Marine Biology Faculty of Biosciences Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway
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29
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Colautti RI, Alexander JM, Dlugosch KM, Keller SR, Sultan SE. Invasions and extinctions through the looking glass of evolutionary ecology. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160031. [PMID: 27920376 PMCID: PMC5182427 DOI: 10.1098/rstb.2016.0031] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [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] [Accepted: 08/30/2016] [Indexed: 11/12/2022] Open
Abstract
Invasive and endangered species reflect opposite ends of a spectrum of ecological success, yet they experience many similar eco-evolutionary challenges including demographic bottlenecks, hybridization and novel environments. Despite these similarities, important differences exist. Demographic bottlenecks are more transient in invasive species, which (i) maintains ecologically relevant genetic variation, (ii) reduces mutation load, and (iii) increases the efficiency of natural selection relative to genetic drift. Endangered species are less likely to benefit from admixture, which offsets mutation load but also reduces fitness when populations are locally adapted. Invading species generally experience more benign environments with fewer natural enemies, which increases fitness directly and also indirectly by masking inbreeding depression. Adaptive phenotypic plasticity can maintain fitness in novel environments but is more likely to evolve in invasive species encountering variable habitats and to be compromised by demographic factors in endangered species. Placed in an eco-evolutionary context, these differences affect the breadth of the ecological niche, which arises as an emergent property of antagonistic selection and genetic constraints. Comparative studies of invasions and extinctions that apply an eco-evolutionary perspective could provide new insights into the environmental and genetic basis of ecological success in novel environments and improve efforts to preserve global biodiversity.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.
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Affiliation(s)
- Robert I Colautti
- Department of Biology, Queen's University, 116 Barrie Street, Kingston, Ontario, Canada K7L 3N6
| | - Jake M Alexander
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Universitätsstrasse 16, 8092 Zürich, Switzerland
| | - Katrina M Dlugosch
- Department of Ecology and Evolutionary Biology, University of Arizona, PO Box 210088, Tucson, AZ 85721, USA
| | - Stephen R Keller
- Department of Plant Biology, University of Vermont, 111 Jeffords Hall, Burlington, VT 05405, USA
| | - Sonia E Sultan
- Department of Biology, Wesleyan University, 237 Church Street, Middletown, CT 06459, USA
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30
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Rohr RP, Saavedra S, Peralta G, Frost CM, Bersier LF, Bascompte J, Tylianakis JM. Persist or Produce: A Community Trade-Off Tuned by Species Evenness. Am Nat 2016; 188:411-22. [PMID: 27622875 DOI: 10.1086/688046] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Understanding the effects of biodiversity on community persistence and productivity is key to managing both natural and production systems. Because rare species face greater danger of extinction, species evenness, a measure of how similar abundances are across species in a community, is seen as a key component of biodiversity. However, previous studies have failed to find a consistent association of species evenness with species survival and biomass production. Here we provide a theoretical framework for the relationship among these three elements. We demonstrate that the lack of consistent outcomes is not an idiosyncratic artifact of different studies but can be unified under one common framework. Applying a niche theory approach, we confirm that under demographic stochasticity evenness is a general indicator of the risk of future species extinctions in a community, in accordance with the majority of empirical studies. In contrast, evenness cannot be used as a direct indicator of the level of biomass production in a community. When a single species dominates, as expressed by the constraints imposed by the population dynamics, biomass production depends on the niche position of the dominating species and can increase or decrease with evenness. We demonstrate that high species evenness and an intermediate level of biomass production is the configuration that maximizes the average species survival probability in response to demographic stochasticity.
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31
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Dini-Andreote F, Stegen JC, van Elsas JD, Salles JF. Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. Proc Natl Acad Sci U S A 2015; 112:E1326-32. [PMID: 25733885 PMCID: PMC4371938 DOI: 10.1073/pnas.1414261112] [Citation(s) in RCA: 631] [Impact Index Per Article: 70.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ecological succession and the balance between stochastic and deterministic processes are two major themes within microbial ecology, but these conceptual domains have mostly developed independent of each other. Here we provide a framework that integrates shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. Synthesizing previous work, we devised a conceptual model that links ecosystem development to alternative hypotheses related to shifts in ecological assembly processes. Conceptual model hypotheses were tested by coupling spatiotemporal data on soil bacterial communities with environmental conditions in a salt marsh chronosequence spanning 105 years of succession. Analyses within successional stages showed community composition to be initially governed by stochasticity, but as succession proceeded, there was a progressive increase in deterministic selection correlated with increasing sodium concentration. Analyses of community turnover among successional stages--which provide a larger spatiotemporal scale relative to within stage analyses--revealed that changes in the concentration of soil organic matter were the main predictor of the type and relative influence of determinism. Taken together, these results suggest scale-dependency in the mechanisms underlying selection. To better understand mechanisms governing these patterns, we developed an ecological simulation model that revealed how changes in selective environments cause shifts in the stochastic/deterministic balance. Finally, we propose an extended--and experimentally testable--conceptual model integrating ecological assembly processes with primary and secondary succession. This framework provides a priori hypotheses for future experiments, thereby facilitating a systematic approach to understand assembly and succession in microbial communities across ecosystems.
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Affiliation(s)
- Francisco Dini-Andreote
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG Groningen, The Netherlands; and
| | - James C Stegen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG Groningen, The Netherlands; and
| | - Joana Falcão Salles
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG Groningen, The Netherlands; and
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32
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Abstract
Host immunity is a major driver of pathogen evolution and thus a major determinant of pathogen diversity. Explanations for pathogen diversity traditionally assume simple interactions between pathogens and the immune system, a view encapsulated by the susceptible-infected-recovered (SIR) model. However, there is growing evidence that the complexity of many host-pathogen interactions is dynamically important. This revised perspective requires broadening the definition of a pathogen's immunological phenotype, or what can be thought of as its immunological niche. After reviewing evidence that interactions between pathogens and host immunity drive much of pathogen evolution, I introduce the concept of a pathogen's immunological phenotype. Models that depart from the SIR paradigm demonstrate the utility of this perspective and show that it is particularly useful in understanding vaccine-induced evolution. This paper highlights questions in immunology, evolution, and ecology that must be answered to advance theories of pathogen diversity.
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Affiliation(s)
- Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois
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33
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Abstract
An ongoing debate in ecology concerns the impacts of ecological drift and selection on community assembly. Here, we show that there is a transition in diverse ecological communities between a selection-dominated regime (the niche phase) and a drift-dominated regime (the neutral phase). Simulations and analytic arguments show that the niche phase is favored in communities with large population sizes and relatively constant environments, whereas the neutral phase is favored in communities with small population sizes and fluctuating environments. Our results demonstrate how apparently neutral populations may arise even in communities inhabited by species with varying traits.
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Affiliation(s)
| | - Pankaj Mehta
- Department of Physics, Boston University, Boston, MA 02215
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34
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Fraterrigo JM, Wagner S, Warren RJ. Local-scale biotic interactions embedded in macroscale climate drivers suggest Eltonian noise hypothesis distribution patterns for an invasive grass. Ecol Lett 2014; 17:1447-54. [PMID: 25199542 DOI: 10.1111/ele.12352] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [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: 04/09/2014] [Revised: 05/13/2014] [Accepted: 07/28/2014] [Indexed: 11/27/2022]
Abstract
A hierarchical view of niche relations reconciles the scale-dependent effects of abiotic and biotic processes on species distribution patterns and underlies most current approaches to distribution modeling. A key prediction of this framework is that the effects of biotic interactions will be averaged out at macroscales - an idea termed the Eltonian noise hypothesis (ENH). We test this prediction by quantifying regional variation in local abiotic and biotic niche relations and assess the role of macroclimate in structuring biotic interactions, using a non-native invasive grass, Microstegium vimineum, in its introduced range. Consistent with hierarchical niche relations and the ENH, macroclimate structures local biotic interactions, while local abiotic relations are regionally conserved. Biotic interactions suppress M. vimineum in drier climates but have little effect in wetter climates. A similar approach could be used to identify the macroclimatic conditions under which biotic interactions affect the accuracy of local predictions of species distributions.
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Affiliation(s)
- Jennifer M Fraterrigo
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL, 61801, USA
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35
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Mendes LW, Kuramae EE, Navarrete AA, van Veen JA, Tsai SM. Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J 2014; 8:1577-87. [PMID: 24553468 PMCID: PMC4817605 DOI: 10.1038/ismej.2014.17] [Citation(s) in RCA: 332] [Impact Index Per Article: 33.2] [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: 10/23/2013] [Revised: 01/10/2014] [Accepted: 01/14/2014] [Indexed: 11/08/2022]
Abstract
This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors.
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Affiliation(s)
- Lucas W Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Piracicaba, Brazil
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, The Netherlands
| | - Acácio A Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Piracicaba, Brazil
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, The Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Piracicaba, Brazil
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36
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Matthews TJ, Whittaker RJ. Neutral theory and the species abundance distribution: recent developments and prospects for unifying niche and neutral perspectives. Ecol Evol 2014; 4:2263-77. [PMID: 25360266 PMCID: PMC4201439 DOI: 10.1002/ece3.1092] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [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: 01/13/2014] [Revised: 04/04/2014] [Accepted: 04/07/2014] [Indexed: 11/14/2022] Open
Abstract
Published in 2001, The Unified Neutral Theory of Biodiversity and Biogeography (UNTB) emphasizes the importance of stochastic processes in ecological community structure, and has challenged the traditional niche-based view of ecology. While neutral models have since been applied to a broad range of ecological and macroecological phenomena, the majority of research relating to neutral theory has focused exclusively on the species abundance distribution (SAD). Here, we synthesize the large body of work on neutral theory in the context of the species abundance distribution, with a particular focus on integrating ideas from neutral theory with traditional niche theory. First, we summarize the basic tenets of neutral theory; both in general and in the context of SADs. Second, we explore the issues associated with neutral theory and the SAD, such as complications with fitting and model comparison, the underlying assumptions of neutral models, and the difficultly of linking pattern to process. Third, we highlight the advances in understanding of SADs that have resulted from neutral theory and models. Finally, we focus consideration on recent developments aimed at unifying neutral- and niche-based approaches to ecology, with a particular emphasis on what this means for SAD theory, embracing, for instance, ideas of emergent neutrality and stochastic niche theory. We put forward the argument that the prospect of the unification of niche and neutral perspectives represents one of the most promising future avenues of neutral theory research.
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Affiliation(s)
- Thomas J Matthews
- Conservation Biogeography and Macroecology Programme, School of Geography and the Environment, University of Oxford South Parks Road, Oxford, OX1 3QY, UK ; Azorean Biodiversity Group (ABG CITA-A) and Portuguese Platform for Enhancing Ecological Research and Sustainability (PEERS), Departamento de Ciências Agrárias, University of the Azores Rua Capitão João d'Ávila, Pico da Urze, 9700-042, Angra do Heroísmo, Portugal
| | - Robert J Whittaker
- Conservation Biogeography and Macroecology Programme, School of Geography and the Environment, University of Oxford South Parks Road, Oxford, OX1 3QY, UK ; Center for Macroecology, Evolution and Climate, Department of Biology, University of Copenhagen Universitetsparken 15, DK-2100, Copenhagen Ø, Denmark
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Edeline E, Lacroix G, Delire C, Poulet N, Legendre S. Ecological emergence of thermal clines in body size. Glob Chang Biol 2013; 19:3062-3068. [PMID: 23780903 DOI: 10.1111/gcb.12299] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [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: 03/07/2013] [Accepted: 06/10/2013] [Indexed: 06/02/2023]
Abstract
The unprecedented rate of global warming requires a better understanding of how ecosystems will respond. Organisms often have smaller body sizes under warmer climates (Bergmann's rule and the temperature-size rule), and body size is a major determinant of life histories, demography, population size, nutrient turnover rate, and food-web structure. Therefore, by altering body sizes in whole communities, current warming can potentially disrupt ecosystem function and services. However, the underlying drivers of warming-induced body downsizing remain far from clear. Here, we show that thermal clines in body size are predicted from universal laws of ecology and metabolism, so that size-dependent selection from competition (both intra and interspecific) and predation favors smaller individuals under warmer conditions. We validate this prediction using 4.1 × 10(6) individual body size measurements from French river fish spanning 29 years and 52 species. Our results suggest that warming-induced body downsizing is an emergent property of size-structured food webs, and highlight the need to consider trophic interactions when predicting biosphere reorganizations under global warming.
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Affiliation(s)
- Eric Edeline
- Université Pierre et Marie Curie - Paris 6, UMR 7618 BIOEMCO, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris Cedex 05, France
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38
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Abstract
Nonhierarchical competition between species has been proposed as a potential mechanism for biodiversity maintenance, but theoretical and empirical research has thus far concentrated on systems composed of relatively few species. Here we develop a theory of biodiversity based on a network representation of competition for systems with large numbers of competitors. All species pairs are connected by an arrow from the inferior to the superior. Using game theory, we show how the equilibrium density of all species can be derived from the structure of the network. We show that when species are limited by multiple factors, the coexistence of a large number of species is the most probable outcome and that habitat heterogeneity interacts with network structure to favor diversity.
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Affiliation(s)
- Stefano Allesina
- Department of Ecology and Evolution, Computation Institute, University of Chicago, Chicago, IL 60637, USA.
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39
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Chisholm RA, Pacala SW. Niche and neutral models predict asymptotically equivalent species abundance distributions in high-diversity ecological communities. Proc Natl Acad Sci U S A 2010; 107:15821-5. [PMID: 20733073 PMCID: PMC2936647 DOI: 10.1073/pnas.1009387107] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A fundamental challenge in ecology is to understand the mechanisms that govern patterns of relative species abundance. Previous numerical simulations have suggested that complex niche-structured models produce species abundance distributions (SADs) that are qualitatively similar to those of very simple neutral models that ignore differences between species. However, in the absence of an analytical treatment of niche models, one cannot tell whether the two classes of model produce the same patterns via similar or different mechanisms. We present an analytical proof that, in the limit as diversity becomes large, a strong niche model give rises to exactly the same asymptotic form of SAD as the neutral model, and we verify the analytical predictions for a Panamanian tropical forest data set. Our results strongly suggest that neutral processes drive patterns of relative species abundance in high-diversity ecological communities, even when strong niche structure exists. However, neutral theory cannot explain what generates high diversity in the first place, and it may not be valid in low-diversity communities. Our results also confirm that neutral theory cannot be used to infer an absence of niche structure or to explain ecosystem function.
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Affiliation(s)
- Ryan A. Chisholm
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | - Stephen W. Pacala
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
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Yamamoto N, Yokoyama J, Kawata M. Relative resource abundance explains butterfly biodiversity in island communities. Proc Natl Acad Sci U S A 2007; 104:10524-9. [PMID: 17553963 PMCID: PMC1888573 DOI: 10.1073/pnas.0701583104] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Indexed: 11/18/2022] Open
Abstract
Ecologists have long been intrigued by the factors that control the pattern of biodiversity, i.e., the distribution and abundance of species. Previous studies have demonstrated that coexisting species partition their resources and/or that the compositional similarity between communities is determined by environmental factors, lending support to the niche-assembly model. However, no attempt has been made to test whether the relative amount of resources that reflects relative niche space controls relative species abundance in communities. Here, we demonstrate that the relative abundance of butterfly species in island communities is significantly related to the relative biomasses of their host plants but not to the geographic distance between communities. In the studied communities, the biomass of particular host plant species positively affected the abundance of the butterfly species that used them, and consequently, influenced the relative abundance of the butterfly communities. This indicated that the niche space of butterflies (i.e., the amount of resources) strongly influences butterfly biodiversity patterns. We present this field evidence of the niche-apportionment model that propose that the relative amount of niche space explains the pattern of the relative abundance of the species in communities.
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Affiliation(s)
- Naoaki Yamamoto
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku Sendai 980-8578, Japan
| | - Jun Yokoyama
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku Sendai 980-8578, Japan
| | - Masakado Kawata
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku Sendai 980-8578, Japan
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Choler P, Erschbamer B, Tribsch A, Gielly L, Taberlet P. Genetic introgression as a potential to widen a species' niche: insights from alpine Carex curvula. Proc Natl Acad Sci U S A 2004; 101:171-6. [PMID: 14691249 PMCID: PMC314157 DOI: 10.1073/pnas.2237235100] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2002] [Indexed: 11/18/2022] Open
Abstract
Understanding what causes the decreasing abundance of species at the margins of their distributions along environmental gradients has drawn considerable interest, especially because of the recent need to predict shifts in species distribution patterns in response to climatic changes. Here, we address the ecological range limit problem by focusing on the sedge, Carex curvula, a dominant plant of high-elevation grasslands in Europe, for which two ecologically differentiated but crosscompatible taxa have been described in the Alps. Our study heuristically combines an extensive phytoecological survey of alpine plant communities to set the niche attributes of each taxon and a population genetic study to assess the multilocus genotypes of 177 individuals sampled in typical and marginal habitats. We found that ecological variation strongly correlates with genetic differentiation. Our data strongly suggest that ecologically marginal populations of each taxon are mainly composed of individuals with genotypes resulting from introgressive hybridization. Conversely, no hybrids were found in typical habitats, even though the two taxa were close enough to crossbreed. Thus, our results indicate that genotype integrity is maintained in optimal habitats, whereas introgressed individuals are favored in marginal habitats. We conclude that gene flow between closely related taxa might be an important, although underestimated, mechanism shaping species distribution along gradients.
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Affiliation(s)
- P Choler
- Laboratoire d'Ecologie Alpine Unité Mixte de Recherche 5553 UJF-Centre National de la Recherche Scientifique and Station Alpine du Lautaret, University Joseph Fourier, BP 53-38041 Grenoble Cedex 9, France
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Abstract
Very precise data on the dynamics of a competitive system of two species of Drosophila have been obtained. By a curvilinear regression approach, analytical models of competition have been fitted. By statistical and biological criteria of simplicity, reality, generality, and accuracy, the best of these models has been chosen. This model represents an extension of the Lotka-Volterra model of competition; it adds a fourth parameter that controls the degree of nonlinearity in intraspecific growth regulation. It represents a similar extension of the logistic model of population growth.
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