Neutral Theory (neutral + theory)

Distribution by Scientific Domains
Distribution within Life Sciences


Selected Abstracts


Neutral theory: a historical perspective

JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 6 2007
E. G. LEIGH JR
Abstract To resolve a panselectionist paradox, the population geneticist Kimura invented a neutral theory, where each gene is equally likely to enter the next generation whatever its allelic type. To learn what could be explained without invoking Darwinian adaptive divergence, Hubbell devised a similar neutral theory for forest ecology, assuming each tree is equally likely to reproduce whatever its species. In both theories, some predictions worked; neither theory proved universally true. Simple assumptions allow neutral theorists to treat many subjects still immune to more realistic theory. Ecologists exploit far fewer of these possibilities than population geneticists, focussing instead on species abundance distributions, where their predictions work best, but most closely match non-neutral predictions. Neutral theory cannot explain adaptive divergence or ecosystem function, which ecologists must understand. By addressing new topics and predicting changes in time, however, ecological neutral theory can provide probing null hypotheses and stimulate more realistic theory. [source]


The implicit assumption of symmetry and the species abundance distribution

ECOLOGY LETTERS, Issue 2 2008
David Alonso
Abstract Species abundance distributions (SADs) have played a historical role in the development of community ecology. They summarize information about the number and the relative abundance of the species encountered in a sample from a given community. For years ecologists have developed theory to characterize species abundance patterns, and the study of these patterns has received special attention in recent years. In particular, ecologists have developed statistical sampling theories to predict the SAD expected in a sample taken from a region. Here, we emphasize an important limitation of all current sampling theories: they ignore species identity. We present an alternative formulation of statistical sampling theory that incorporates species asymmetries in sampling and dynamics, and relate, in a general way, the community-level SAD to the distribution of population abundances of the species integrating the community. We illustrate the theory on a stochastic community model that can accommodate species asymmetry. Finally, we discuss the potentially important role of species asymmetries in shaping recently observed multi-humped SADs and in comparisons of the relative success of niche and neutral theories at predicting SADs. [source]


Sampling Hubbell's neutral theory of biodiversity

ECOLOGY LETTERS, Issue 10 2004
David Alonso
Abstract In the context of neutral theories of community ecology, a novel genealogy-based framework has recently furnished an analytic extension of Ewens' sampling multivariate abundance distribution, which also applies to a random sample from a local community. Here, instead of taking a multivariate approach, we further develop the sampling theory of Hubbell's neutral spatially implicit theory and derive simple abundance distributions for a random sample both from a local community and a metacommunity. Our result is given in terms of the average number of species with a given abundance in any randomly extracted sample. Contrary to what has been widely assumed, a random sample from a metacommunity is not fully described by the Fisher log-series, but by a new distribution. This new sample distribution matches the log-series expectation at high biodiversity values (, > 1) but clearly departs from it for species-poor metacommunities (, < 1). Our theoretical framework should be helpful in the better assessment of diversity and testing of the neutral theory by using abundance data. [source]


Parasites and the neutral theory of biodiversity

ECOGRAPHY, Issue 1 2004
Robert Poulin
First page of article [source]


Linking dispersal, immigration and scale in the neutral theory of biodiversity

ECOLOGY LETTERS, Issue 12 2009
Ryan A. Chisholm
Abstract In the classic spatially implicit formulation of Hubbell's neutral theory of biodiversity a local community receives immigrants from a metacommunity operating on a relatively slow timescale, and dispersal into the local community is governed by an immigration parameter m. A current problem with neutral theory is that m lacks a clear biological interpretation. Here, we derive analytical expressions that relate the immigration parameter m to the geometry of the plot defining the local community and the parameters of a dispersal kernel. Our results facilitate more rigorous and extensive tests of the neutral theory: we conduct a test of neutral theory by comparing estimates of m derived from fits to empirical species abundance distributions to those derived from dispersal kernels and find acceptable correspondence; and we generate a new prediction of neutral theory by investigating how the shapes of species abundance distributions change theoretically as the spatial scale of observation changes. We also discuss how our main analytical results can be used to assess the error in the mean-field approximations associated with spatially implicit formulations of neutral theory. Ecology Letters (2009) 12: 1385,1393 [source]


The maximum entropy formalism and the idiosyncratic theory of biodiversity

ECOLOGY LETTERS, Issue 11 2007
Salvador Pueyo
Abstract Why does the neutral theory, which is based on unrealistic assumptions, predict diversity patterns so accurately? Answering questions like this requires a radical change in the way we tackle them. The large number of degrees of freedom of ecosystems pose a fundamental obstacle to mechanistic modelling. However, there are tools of statistical physics, such as the maximum entropy formalism (MaxEnt), that allow transcending particular models to simultaneously work with immense families of models with different rules and parameters, sharing only well-established features. We applied MaxEnt allowing species to be ecologically idiosyncratic, instead of constraining them to be equivalent as the neutral theory does. The answer we found is that neutral models are just a subset of the majority of plausible models that lead to the same patterns. Small variations in these patterns naturally lead to the main classical species abundance distributions, which are thus unified in a single framework. [source]


Neutral community dynamics, the mid-domain effect and spatial patterns in species richness

ECOLOGY LETTERS, Issue 8 2005
Thiago F. L. V. B. Rangel
Abstract The mid-domain effect (MDE) aims to explain spatial patterns in species richness invoking only stochasticity and geometrical constraints. In this paper, we used simulations to show that its main qualitative prediction, a hump-shaped pattern in species richness, converges to the expectation of a spatially bounded neutral model when communities are linked by short-distance migration. As these two models can be linked under specific situations, neutral theory may provide a mechanistic population level basis for MDE. This link also allows establishing in which situations MDE patterns are more likely to be found. Also, in this situation, MDE models could be used as a first approximation to understand the role of both stochastic (ecological drift and migration) and deterministic (adaptation to environmental conditions) processes driving the spatial structure of species richness. [source]


Sampling Hubbell's neutral theory of biodiversity

ECOLOGY LETTERS, Issue 10 2004
David Alonso
Abstract In the context of neutral theories of community ecology, a novel genealogy-based framework has recently furnished an analytic extension of Ewens' sampling multivariate abundance distribution, which also applies to a random sample from a local community. Here, instead of taking a multivariate approach, we further develop the sampling theory of Hubbell's neutral spatially implicit theory and derive simple abundance distributions for a random sample both from a local community and a metacommunity. Our result is given in terms of the average number of species with a given abundance in any randomly extracted sample. Contrary to what has been widely assumed, a random sample from a metacommunity is not fully described by the Fisher log-series, but by a new distribution. This new sample distribution matches the log-series expectation at high biodiversity values (, > 1) but clearly departs from it for species-poor metacommunities (, < 1). Our theoretical framework should be helpful in the better assessment of diversity and testing of the neutral theory by using abundance data. [source]


A novel genealogical approach to neutral biodiversity theory

ECOLOGY LETTERS, Issue 3 2004
Rampal S. Etienne
Abstract Current neutral theory in community ecology views local biodiversity as a result of the interplay between speciation, extinction and immigration. Simulations and a mean-field approximation have been used to study this neutral theory. As simulations have limitations of convergence and the mean-field approximation ignores dependencies between species' abundances when applied to species-abundance data, there is still no final conclusion whether the neutral theory or the traditional lognormal model describes community structure best. We present a novel analytical framework, based on the genealogy of individuals in the local community, to overcome the problems of previous approaches, and show, using Bayesian statistics, that the lognormal model provides a slightly better fit to the species-abundance distribution of a much-discussed tropical tree community. A key feature of our approach is that it shows the tight link between genetic and species diversity, which creates important perspectives to future integration of evolutionary and community ecological theory. [source]


The structure of a local population of phytopathogenic Pseudomonas brassicacearum from agricultural soil indicates development under purifying selection pressure

ENVIRONMENTAL MICROBIOLOGY, Issue 3 2001
Johannes Sikorski
Among the isolates of a bacterial community from a soil sample taken from an agricultural plot in northern Germany, a population consisting of 119 strains was obtained that was identified by 16S rDNA sequencing and genomic fingerprinting as belonging to the recently described species Pseudomonas brassicacearum. Analysis of the population structure by allozyme electrophoresis (11 loci) and random amplified polymorphic DNA,polymerase chain reaction (RAPD,PCR; four primers) showed higher resolution with the latter method. Both methods indicated the presence of three lineages, one of which dominated strongly. Stochastic tests derived from the neutral theory of evolution (including Slatkin's exact test, Watterson's homozygosity test and the Tajima test) indicated that the population had developed under strong purifying selection pressure. The presence of strains clearly divergent from the majority of the population can be explained by in situ evolution or by influx of strains as a result of migration or both. Phytopathogenicity of a P. brassicacearum strain determined with tomato plants reached the level obtained with the type strain of the known pathogen Pseudomonas corrugata. The results show that a selective sweep was identified in a local population. Previously, a local selective sweep had not been seen in several populations of different bacterial species from a variety of environmental habitats. [source]


Drivers of lowland rain forest community assembly, species diversity and forest structure on islands in the tropical South Pacific

JOURNAL OF ECOLOGY, Issue 1 2010
Gunnar Keppel
Summary 1.,Testing the comparative strength and influence of age and area of islands, proximity of source propagules and disturbances on community assembly, species diversity and vegetation structure has proved difficult at large scales. The little-studied rain forests in the Tropical South Pacific (TSP) provide a unique study area to investigate determinants of community dynamics, with islands varying in age, isolation, area and cyclone frequency. We tested the effects of biogeographical factors and cyclone frequency on the species composition, species diversity and forest structure of old-growth rain forest using 1-ha inventory plots on 12 islands between New Guinea and the Solomon Islands. 2.,As predicted by the General Dynamic Model of Oceanic Island Biogeography, the biogeographical variables of archipelago age and island area are the most important factors affecting species richness and diversity, with older and larger islands having higher richness and diversity. There is no significant effect of cyclone frequency on species diversity. 3.,The theory that diversity drives endemism is not supported in this system as endemism is not correlated with species diversity. Instead, age and isolation of an island best explain patterns of endemism, with the latter suggesting dispersal limitations between archipelagos. 4.,Proximity to source area influences species composition of lowland tropical rain forests in the TSP, which is also supported by a strong correlation between geographic distance and floristic similarity. Vector-fitting onto non-metric multidimensional scaling suggests that archipelago age and cyclone frequency may, in addition to proximity to source area, influence species composition. This implies that a species' tolerance to cyclones affects its abundance at different cyclone frequencies. 5.,Synthesis. Both biogeographical variables (island area and isolation) and cyclone frequency appear to affect community assembly in lowland rain forests in the TSP. While species are hence not ecologically equivalent, interspecific ecological differences do not seem to affect the overall patterns of species diversity, which are mostly determined by biogeographical variables, as predicted by the neutral theory. [source]


Neutral theory: a historical perspective

JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 6 2007
E. G. LEIGH JR
Abstract To resolve a panselectionist paradox, the population geneticist Kimura invented a neutral theory, where each gene is equally likely to enter the next generation whatever its allelic type. To learn what could be explained without invoking Darwinian adaptive divergence, Hubbell devised a similar neutral theory for forest ecology, assuming each tree is equally likely to reproduce whatever its species. In both theories, some predictions worked; neither theory proved universally true. Simple assumptions allow neutral theorists to treat many subjects still immune to more realistic theory. Ecologists exploit far fewer of these possibilities than population geneticists, focussing instead on species abundance distributions, where their predictions work best, but most closely match non-neutral predictions. Neutral theory cannot explain adaptive divergence or ecosystem function, which ecologists must understand. By addressing new topics and predicting changes in time, however, ecological neutral theory can provide probing null hypotheses and stimulate more realistic theory. [source]


Comparative genomics and the study of evolution by natural selection

MOLECULAR ECOLOGY, Issue 21 2008
HANS ELLEGREN
Abstract Genomics profoundly affects most areas of biology, including ecology and evolutionary biology. By examining genome sequences from multiple species, comparative genomics offers new insight into genome evolution and the way natural selection moulds DNA sequence evolution. Functional divergence, as manifested in the accumulation of nonsynonymous substitutions in protein-coding genes, differs among lineages in a manner seemingly related to population size. For example, the ratio of nonsynonymous to synonymous substitution (dN/dS) is higher in apes than in rodents, compatible with Ohta's nearly neutral theory of molecular evolution, which suggests that the fixation of slightly deleterious mutations contributes to protein evolution at an extent negatively correlated with effective population size. While this supports the idea that functional evolution is not necessarily adaptive, comparative genomics is uncovering a role for positive Darwinian selection in 10,40% of all genes in different lineages, estimates that are likely to increase when the addition of more genomes gives increased power. Again, population size seems to matter also in this context, with a higher proportion of fixed amino acid changes representing advantageous mutations in large populations. Genes that are particularly prone to be driven by positive selection include those involved with reproduction, immune response, sensory perception and apoptosis. Genetic innovations are also frequently obtained by the gain or loss of complete gene sequences. Moreover, it is increasingly realized, from comparative genomics, that purifying selection conserves much more than just the protein-coding part of the genome, and this points at an important role for regulatory elements in trait evolution. Finally, genome sequencing using outbred or multiple individuals has provided a wealth of polymorphism data that gives information on population history, demography and marker evolution. [source]


Applications of selective neutrality tests to molecular ecology

MOLECULAR ECOLOGY, Issue 8 2002
Michael J. Ford
Abstract This paper reviews how statistical tests of neutrality have been used to address questions in molecular ecology are reviewed. The work consists of four major parts: a brief review of the current status of the neutral theory; a review of several particularly interesting examples of how statistical tests of neutrality have led to insight into ecological problems; a brief discussion of the pitfalls of assuming a strictly neutral model if it is false; and a discussion of some of the opportunities and problems that molecular ecologists face when using neutrality tests to study natural selection. [source]


Mechanisms in macroecology: AWOL or purloined letter?

OIKOS, Issue 4 2010
Towards a pragmatic view of mechanism
Ecologists often believe the discovery of mechanism to be the central goal of scientific research. While many macroecologists have inherited this view, to date they have been much more efficient at producing patterns than identifying their underlying processes. We discuss several possible attitudes for macroecologists to adopt in this context while also arguing that in fact macroecology already has many mechanisms that are ignored. We briefly describe six of these: central limit theorem, fractals, random sampling and placement, neutral theory (and descendents), concordance of forces, and maximum entropy. We explore why these mechanisms are overlooked and discuss whether they should be. We conclude that macroecology needs to take a more pragmatic, less ideological approach to mechanism. We apply this viewpoint to the recent controversy over maximum entropy and suggest that maximum entropy needs to be viewed more pragmatically and less ideologically. [source]


A neutral-niche theory of nestedness in mutualistic networks

OIKOS, Issue 11 2008
Abhay Krishna
Recently, there has been a vigorous interest in community ecology about the structure of mutualistic networks and its importance for species persistence and coevolution. However, the mechanisms shaping mutualistic networks have been rarely explored. Here we extend for the first time the neutral theory of biodiversity to a multi trophic system. We focus on nestedness, a distinctive pattern of mutualistic community assembly showing two characteristics, namely, asymmetrical specialization (specialists interacting with generalists) and a generalist core (generalists interacting with generalists). We investigate the importance of relative species abundance (RSA) for the nested assembly of plant,animal mutualistic networks. Our results show that neutral mutualistic communities give rise to networks considerably more nested than real communities. RSA explains 60,70% of nested patterns in two real communities studied here, while 30,40% of nestedness is still unexplained. The nested pattern in real communities is better explained when we introduce interaction-specific species traits such as forbidden links and intensity of dependence (relative importance of fruits for the diet of a frugivore) in our analysis. The fact that neutral mutualistic communities exhibit a perfectly nested structure and do not show a random or compartmentalized structure, underlines the importance of RSA in the assembly of mutualistic networks. [source]


Genetic Heterogeneity of Icelanders

ANNALS OF HUMAN GENETICS, Issue 1 2003
E. Árnason
Summary Recently statements have been made about a special ,genetic homogeneity' of the Icelanders that are at variance with earlier work on blood groups and allozymes. To validate these claims an extensive reanalysis was undertaken of mtDNA variation by examining primary data from original sources on 26 European populations. The results show that Icelanders are among the most genetically heterogeneous Europeans by the mean number of nucleotide differences as well as by estimates of , parameters of the neutral theory. The distribution of pairwise differences in general has the same shape as European populations and shows no evidence of bottlenecks of numbers in Iceland. The allelic frequency distribution of Iceland is relatively even with a large number of haplotypes at polymorphic frequencies contrasting with other countries. This is a signature of admixture during the founding or history of Iceland. Assumptions of models used to simulate number of haplotypes at sampling saturation for comparing populations are violated to different degrees by various countries. Anomalies identified in data in previous reports on Icelandic mtDNA variation appear to be due to errors in publicly accessible databases. This study demonstrates the importance of basing analyses on primary data so that errors are not propagated. Claims about special genetic homogeneity of Icelanders are not supported by evidence. [source]


Speciation and the neutral theory of biodiversity

BIOESSAYS, Issue 7 2010
Modes of speciation affect patterns of biodiversity in neutral communities.
Abstract The neutral theory of biodiversity purports that patterns in the distribution and abundance of species do not depend on adaptive differences between species (i.e. niche differentiation) but solely on random fluctuations in population size ("ecological drift"), along with dispersal and speciation. In this framework, the ultimate driver of biodiversity is speciation. However, the original neutral theory made strongly simplifying assumptions about the mechanisms of speciation, which has led to some clearly unrealistic predictions. In response, several recent studies have combined neutral community models with more elaborate speciation models. These efforts have alleviated some of the problems of the earlier approaches, while confirming the general ability of neutral theory to predict empirical patterns of biodiversity. However, the models also show that the mode of speciation can have a strong impact on relative species abundances. Future work should compare these results to diversity patterns arising from non-neutral modes of speciation, such as adaptive radiations. [source]


Why Do Some Tropical Forests Have So Many Species of Trees?

BIOTROPICA, Issue 4 2004
Egbert Giles Leigh Jr.
ABSTRACT Understanding why there are so many kinds of tropical trees requires learning, not only how tree species coexist, but what factors drive tree speciation and what governs a tree clade's diversification rate. Many report that hybrid sterility evolves very slowly between separated tree populations. If so, tree species rarely originate by splitting of large populations. Instead, they begin with few trees. The few studies available suggest that reproductive isolation between plant populations usually results from selection driven by lowered fitness of hybrids: speciation is usually a response to a "niche opportunity." Using Hubbell's neutral theory of forest dynamics as a null hypothesis, we show that if new tree species begin as small populations, species that are now common must have spread more quickly than chance allows. Therefore, most tree species have some setting in which they can increase when rare. Trees face trade-offs in suitability for different microhabitats, different-sized clearings, different soils and climates, and resistance to different pests. These trade-offs underlie the mechanisms maintaining ,-diversity and species turnover. Disturbance and microhabitat specialization appear insufficient to maintain ,-diversity of tropical trees, although they may maintain tree diversity north of Mexico or in northern Europe. Many studies show that where trees grow readily, tree diversity is higher and temperature and rainfall are less seasonal. The few data available suggest that pest pressure is higher, maintaining higher tree diversity, where winter is absent. Tree a-diversity is also higher in regions with more tree species, which tend to be larger, free for a longer time from major shifts of climate, or in the tropics, where there are more opportunities for local coexistence. RESUMEN Comprender por qué hay tantos tipos de árboles tropicales, se requiere aprender no sólo cómo las especies de árboles coexisten, sino también, cuáles factores conducen a su especiación, y qué determina la velocidad de diversificación de un clado de árboles. Muchos reportan que la esterilidad hibrida evoluciona muy lentamente entre poblaciones separadas de árboles. De ser asi, las especies de árboles raramente se originarian por la separación de grandes poblaciones; más bien empezarian con pocos árboles. Los pocos estudios disponibles sugieren que el aislamiento reproductivo entre las poblaciones vegetales usualmente resulta de selección derivada del bajo éxito de los hibridos: la especiación general-mente responde a una "oportunidad de nicho". Usando la teoria neutral de Hubbell de dinámica de bosques como hipótesis nula, nosotros mostramos que si las nuevas especies de árboles comienzan como poblaciones pequeñas, especies que ahora son communes deberian haberse expandido más rápido que lo que el azar permite. Por lo tanto, la mayoria de las especies de árboles tendrian alguna condición donde sus poblaciones podrian crecer cunando son raras. Los árboles enfrentan compromises en su adecuación por diferentes microhábitats, claros de differentes tamanos, diferentes suelos y climas, y resistencia a differentes plagas. Esros compromises sirven de base para los mecanismos que mantienen la diversidad , y al reemplazo especial de especies. Los distrubios y la especialización de microhabitats parecen ser insuficiente para mantener la diversidad , de árboles tropicales, sin embargo elloss pueden mantener diversidad de árboles al norte de México o en Europa del norte. Muchos estudios muestran que en lugares donde los árboles cresen fácilmente, la diversidad de árboles es mayor donde la temperatura y la lluvia son menos estacionales. Los pocos estudios disponibles sugieren que la presión de las plagas es mayor, manteniendo asl la diversidad de árboles en lugares donde no hay invierno. La diversidad , de árboles también es más alta en regions con más especies de árboles, las culaes tienden a ser más largas, exentas por un largo periodo de tiempo de grandes cambios climáticos, oen los trópicos donde hay más oportunidades de coexistir localmente. [source]