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The Unified Neutral Theory of Biodiversity and Biogeography
01 Jan 2001-
TL;DR: A study of the issue indicates that it is not a serious problem for neutral theory, and there is sometimes a difference between some of the simulation-based results of Hubbell and the analytical results of Volkov et al. (2003).
Abstract: study of the issue indicates that it is not a serious problem for neutral theory, for reasons we discuss below. First, a bit of background. Hubbell (2001) derived the analytical expression for the stochastic mean and variance of the abundance of a single arbitrary species in a neutral community undergoing immigration from a metacommunity source area. However, his approach did not lend itself to an analytical solution for the distribution of relative species abundance (RSA) in a multispecies community for community sizes larger than a handful of individuals. As a result, all of Hubbell's RSA distributions for local communities were based on simulations. This problem was solved by Volkov et al. (2003), who derived an analytical expression for the RSA distribution in local communities of arbitrary size. However, as Chisholm and Burgman noted, there is sometimes a difference between some of the simulation-based results of Hubbell and the analytical results of Volkov et al. (2003). Chisholm and Burgman computed Volkov's equation and resimulated Hubbell's results for the four cases
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TL;DR: This work has developed a quantitative theory for how metabolic rate varies with body size and temperature, and predicts how metabolic theory predicts how this rate controls ecological processes at all levels of organization from individuals to the biosphere.
Abstract: Metabolism provides a basis for using first principles of physics, chemistry, and biology to link the biology of individual organisms to the ecology of populations, communities, and ecosystems. Metabolic rate, the rate at which organisms take up, transform, and expend energy and materials, is the most fundamental biological rate. We have developed a quantitative theory for how metabolic rate varies with body size and temperature. Metabolic theory predicts how metabolic rate, by setting the rates of resource uptake from the environment and resource allocation to survival, growth, and reproduction, controls ecological processes at all levels of organization from individuals to the biosphere. Examples include: (1) life history attributes, including devel- opment rate, mortality rate, age at maturity, life span, and population growth rate; (2) population interactions, including carrying capacity, rates of competition and predation, and patterns of species diversity; and (3) ecosystem processes, including rates of biomass production and respiration and patterns of trophic dynamics. Data compiled from the ecological literature strongly support the theoretical predictions. Even- tually, metabolic theory may provide a conceptual foundation for much of ecology, just as genetic theory provides a foundation for much of evolutionary biology.
6,017 citations
University of Texas at Austin1, University of California, Davis2, University of Montpellier3, Florida State University4, University of Chicago5, Washington University in St. Louis6, University of California, Berkeley7, University of Florida8, University of British Columbia9, University of York10, PSL Research University11, McGill University12
TL;DR: This framework is used to discuss why the metacommunity concept is useful in modifying existing ecological thinking and illustrate this with a number of both theoretical and empirical examples.
Abstract: The metacommunity concept is an important way to think about linkages between different spatial scales in ecology. Here we review current understanding about this concept. We first investigate issues related to its definition as a set of local communities that are linked by dispersal of multiple potentially interacting species. We then identify four paradigms for metacommunities: the patch-dynamic view, the species-sorting view, the mass effects view and the neutral view, that each emphasizes different processes of potential importance in metacommunities. These have somewhat distinct intellectual histories and we discuss elements related to their potential future synthesis. We then use this framework to discuss why the concept is useful in modifying existing ecological thinking and illustrate this with a number of both theoretical and empirical examples. As ecologists strive to understand increasingly complex mechanisms and strive to work across multiple scales of spatio-temporal organization, concepts like the metacommunity can provide important insights that frequently contrast with those that would be obtained with more conventional approaches based on local communities alone.
4,266 citations
Cites background from "The Unified Neutral Theory of Biodi..."
...recognized, however, that other ecological processes involving species interactions occur at other scales (Wiens 1989; Levin 1992; Holt 1993; Maurer 1999; Hubbell 2001 )....
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... Hubbell (2001) has explored the model in situations where speciation acts to counteract the extinction process and points out that even slow speciation rates can lead to very high sustained levels of diversity in such metacommunities....
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...In the absence of any such differences among species, the behaviour of metacommunities can be different (Caswell 1976; Bell 2000; Hubbell 2001 )....
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...Neutral perspective A perspective in which all species are similar in their competitive ability, movement and fitness ( Hubbell 2001 )....
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...Levins 1969; Hastings 1980; Hubbell 2001; Mouquet & Loreau 2002) where patches can be viewed either as microsites or localities holding individuals or populations....
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TL;DR: A common pattern of phylogenetic conservatism in ecological character is recognized and the challenges of using phylogenies of partial lineages are highlighted and phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes are reviewed.
Abstract: ▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community ...
3,615 citations
Brown University1, Stanford University2, University of New Mexico3, University of Connecticut4, University of Southern California5, University of California, Merced6, University of Washington7, National Science Foundation8, Los Alamos National Laboratory9, Rutgers University10, Columbia University11, University of Bergen12, Portland State University13, University of Kansas14
TL;DR: Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity, but recent studies also dispute the idea that 'everything is everywhere'.
Abstract: We review the biogeography of microorganisms in light of the biogeography of macroorganisms A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity However, recent studies also dispute the idea that 'everything is everywhere' We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world
2,456 citations
TL;DR: Automatic Barcode Gap Discovery is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.
Abstract: Within uncharacterized groups, DNA barcodes, short DNA sequences that are present in a wide range of species, can be used to assign organisms into species. We propose an automatic procedure that sorts the sequences into hypothetical species based on the barcode gap, which can be observed whenever the divergence among organisms belonging to the same species is smaller than divergence among organisms from different species. We use a range of prior intraspecific divergence to infer from the data a model-based one-sided confidence limit for intraspecific divergence. The method, called Automatic Barcode Gap Discovery (ABGD), then detects the barcode gap as the first significant gap beyond this limit and uses it to partition the data. Inference of the limit and gap detection are then recursively applied to previously obtained groups to get finer partitions until there is no further partitioning. Using six published data sets of metazoans, we show that ABGD is computationally efficient and performs well for standard prior maximum intraspecific divergences (a few per cent of divergence for the five data sets), except for one data set where less than three sequences per species were sampled. We further explore the theoretical limitations of ABGD through simulation of explicit speciation and population genetics scenarios. Our results emphasize in particular the sensitivity of the method to the presence of recent speciation events, via (unrealistically) high rates of speciation or large numbers of species. In conclusion, ABGD is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.
2,336 citations
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TL;DR: This paper considers deductive and subsequently inductive questions relating to a sample of genes from a selectively neutral locus, and the test of the hypothesis that the alleles being sampled are indeed selectively neutral will be considered.
2,176 citations
TL;DR: In this paper, the authors take up a point inerely mentioned in 1948 that not only is the distribution lognormal, but the constants or parameters seem to be restricted in a peculiar way.
Abstract: In an earlier paper (Preston 1948) we found that, in a sufficiently large aggregation of individuals of many species, the individuals often tended to be distributed among the species according to a lognormal law. We plotted as abscissa equal increments in the logarithms of the number of individuals representing a species, and as ordinate the number of species falling into each of these increments. We found it convenient to use as such increments the "octave," that is the interval in which representation doubled, so that our abscissae became simply a scale of "octaves," but this choice of unit is arbitrary. Whatever logarithmic unit is used, the graph tended to take the form of a normal or Gaussian curve, so that the distribution was "lognormal." \Ve called this the "Species Curve." In the present paper we take up a point inerely mentioned in 1948 that not only is the distribution lognormal, but the constants or parameters seem to be restricted in a peculiar way. They are not fixed, but they are interlocked. The nature of this restriction and interlocking is the main theme of the present paper. In the earlier paper we graduated the experimental results with curves of the form
1,543 citations
TL;DR: Overall, however, communities in which different processes operated showed surprisingly similar patterns, which suggests that the form of community‐level patterns cannot in general be used to distinguish among mechanisms maintaining diversity there.
Abstract: Mechanisms proposed to explain the maintenance of species diversity within ecological communities of sessile organisms include niche differentiation mediated by competitive trade-offs, frequency dependence resulting from species-specific pests, re- cruitment limitation due to local dispersal, and a speciation- extinction dynamic equilibrium mediated by stochasticity (drift). While each of these processes, and more, have been shown to act in particular communities, much remains to be learned about their relative importance in shaping community-level patterns. We used a spatially-explicit, individual-based model to assess the effects of each of these processes on species richness, relative abundance, and spatial patterns such as the species-area curve. Our model com- munities had an order-of-magnitude more individuals than any previous such study, and we also developed a finite-size scaling analysis to infer the large-scale properties of these systems in order to establish the generality of our conclusions across system sizes. As expected, each mechanism can promote diversity. We found some qualitative differences in community patterns across com- munities in which different combinations of these mechanisms operate. Species-area curves follow a power law with short-range dispersal and a logarithmic law with global dispersal. Relative- abundance distributions are more even for systems with compet- itive differences and trade-offs than for those in which all species are competitively equivalent, and they are most even when fre- quency dependence (even if weak) is present. Overall, however, communities in which different processes operated showed sur- prisingly similar patterns, which suggests that the form of com- munity-level patterns cannot in general be used to distinguish among mechanisms maintaining diversity there. Nevertheless, pa- rameterization of models such as these from field data on the
547 citations