Distance decay of community dynamics in rocky intertidal sessile assemblages evaluated by transition matrix models

It is well known that the similarity in species composition between two communities decays with the geographic distance that separates them. It is thus likely that the similarity in the dynamics of two communities also decays with distance, because the distance–decay relationship is fundamental in nature. However, the distance–decay relationships of community dynamics have not yet been revealed. We used transition matrix models to evaluate distance–decay relationships of seasonal community dynamics (from spring to summer) in rocky intertidal sessile assemblages along the Pacific coast of Japan between 31°N and 43°N. We evaluated the distance–decay relationships of whole-community dynamics and of three dynamics-related components—recruitment, disturbance, and species interaction (competition and facilitation)—for communities separated by distances ranging from several meters to thousands of kilometers. The similarity of the recruitment dynamics among communities declined rapidly with distance within the fine spatial scale, but only moderately within larger scales. The similarity of the disturbance dynamics was independent of distance, and the similarity of species interaction declined slightly with increasing distance. The similarity of whole-community dynamics declined rapidly with distance at a fine spatial scale and moderately at larger scales. The fact that the distance–decay relationship of whole-community dynamics was similar to that of recruitment may suggest that recruitment processes are the most important determinant of spatial variability of community dynamics at our study sites during the study period.     

Biogeographical patterns of blood parasite lineage diversity in avian hosts from southern Melanesian islands

Aim (1) To describe the species–area relationships among communities of Plasmodium and Haemoproteus parasites in different island populations of the same host genus (Aves: Zosterops). (2) To compare distance–decay relationships (turnover) between parasite communities and those with potential avian and dipteran hosts, which differ with respect to their movement and potential to disperse parasite species over large distances. Location Two archipelagos in the south‐west Pacific, Vanuatu and New Caledonia (c. 250 km west of Vanuatu) and its Loyalty Islands, with samples collected from a total of 16 islands of varying sizes (328–16,648 km²). Methods We characterized parasite diversity and distribution via polymerase chain reaction (PCR) from avian (Zosterops) blood samples. Bayesian methods were used to reconstruct the parasite phylogeny. In accordance with recent molecular evidence, we treat distinct mitochondrial DNA lineages as equivalent to species in this study. Path analysis and parasite lineage accumulation curves were used to assess the confounding effect of inadequate sampling on the estimation of parasite richness. Species–area and species–distance relationships were assessed using linear regression: distance–decay relationships were assessed using Mantel tests. Results Birds and mosquito species and Plasmodium lineages exhibited significant species–area relationships. However, Plasmodium lineages showed the weakest ‘species–area’ relationship; no relationship was found for Haemoproteus lineages. Avian species richness influenced parasite lineage richness more than mosquito species richness did. Within individual avian host species, the species–area relationship of parasites showed differing patterns. Path analysis indicated that sampling effort was unlikely to have a confounding effect on parasite richness. Distance from mainland (isolation effect) showed no effect on parasite richness. Community similarity decayed significantly with distance for avifauna, mosquito fauna and Plasmodium lineages but not for Haemoproteus lineages. Main conclusions Plasmodium lineages and mosquito species fit the power‐law model with steeper slopes than found for the avian hosts. The lack of species–distance relationship in parasites suggests that other factors, such as the competence of specific vectors and habitat features, may be more important than distance. The decay in similarity with distance suggests that the sampled Plasmodium lineages and their potential hosts were not randomly distributed, but rather exhibited spatially predictable patterns. We discuss these results in the context of the effects that parasite generality may have on distribution patterns.     

Current measures for distance decay in similarity of species composition are influenced by study extent and grain size

Aim The relationship between geographic distance and similarity in species composition is regularly used as a measure of species turnover and beta diversity. Distance–decay analyses are applied, cited and compared despite the variable extent, and different grain sizes of records (e.g. plots, islands, states) are regularly used within such analyses. Currently, differences among distance–decay relationships that cover different grain sizes and extents are attributed to ecological processes that are suspected to operate differently over varying extents and grain sizes. We assess whether the implicit assumption that the distance–decay relation is independent of grain size and study extent is valid, or whether sampling design could be the underlying cause for observed differences. Location An artificial one‐dimensional ‘landscape’. Methods The distance–decay relationship was quantified in simulated communities. Grain and study extent were varied systematically. In each sampled data set the linear relation of Simpson and Sørensen similarity to geographic distance (on both log‐transformed and original scales) between 100 even‐sized equidistant plots was assessed using linear regression and generalized linear regression with a log‐link function. Regressions were applied either including or removing zero similarities from the data. Results Both the slope (measuring turnover) and the goodness of fit measure r² (quantifying the influence of space on species composition) of the distance–decay relationship were strongly influenced by grain and study extent. Approaches that are able to cope with zero similarity values of large distance comparisons were less dependent on grain and extent. Main conclusions Reported differences between landscapes detected by current distance–decay measures cannot be explicitly traced back to ecological scale‐specific processes. Instead, they can largely be attributed to sampling design and are highly sensitive to grain size and study extent. More appropriate approaches for the study of distance–decay and the understanding of scale‐specific processes are required.     

Parasite body size and interspecific variation in levels of aggregation among nematodes

The aggregation of parasites among individual hosts is one of the best documented features of parasite populations; we still do not know, however, why certain parasite species are more highly aggregated than other, related species. Here we search for a general explanation of interspecific variation in aggregation levels, based on the relationship between parasite body size and fecundity, transmission success, and intensity-dependent population regulation. We test the prediction that larger-bodied parasite species are more weakly aggregated than smaller-bodied related species, in a comparative analysis across parasitic nematode species. Across species, the variance-to-mean abundance ratio correlated negatively and significantly with nematode body sizes, as predicted. All other tests, however, including the more robust analyses controlling for phylogenetic influences, failed to support this result. This is mainly because the variance in infection levels is almost completely explained by mean parasite abundance. For this reason, it may prove difficult to identify a general biological explanation for interspecific variability in aggregation levels among parasites.     

Not everything is everywhere: the distance decay of similarity in a marine host–parasite system

Aim We test the similarity–distance decay hypothesis on a marine host–parasite system, inferring the relationships from abundance data gathered at the lowest scale of parasite community organization (i.e. that of the individual host). Location Twenty‐two seasonal samples of the bogue Boops boops (Teleostei: Sparidae) were collected at seven localities along a coastal positional gradient from the northern North‐East Atlantic to the northern Mediterranean coast of Spain. Methods We used our own, taxonomically consistent, data on parasite communities. The variations in parasite composition and structure with geographical and regional distance were examined at two spatial scales, namely local parasite faunas and component communities, using both presence–absence (neighbour joining distance) and abundance (Mahalanobis distance) data. The influence of geographical and regional distance on faunal/community divergence was assessed through the permutation of distance matrices. Results Our results revealed that: (1) geographical and regional distances do not affect the species composition in the system under study at the higher scales; (2) geographical distance between localities contributes significantly to the decay of similarity estimated from parasite abundance at the lowest scale (i.e. the individual host); (3) the structured spatial patterns are consistent in time but not across seasons; and (4) a restricted clade of species (the ‘core’ species of the bogue parasite fauna) contributes substantially to the observed patterns of both community homogenization and differentiation owing to the strong relationship between local abundance and regional distribution of species. Main conclusions The main factors that tend to homogenize the composition of parasite communities of bogue at higher regional scales are related to the dispersal of parasite colonizers across host populations, which we denote as horizontal neighbourhood colonization. In contrast, the spatial structure detectable in quantitative comparisons only, is related to a vertical neighbourhood colonization associated with larval dispersal on a local level. The stronger decline with distance in the spatial synchrony of the assemblages of the ‘core’ species indicates a close‐echoing environmental synchrony that declines with distance. Our results emphasize the importance of the parasite supracommunity (i.e. parasites that exploit all hosts in the ecosystem) to the decay of similarity with distance.     

The influence of dispersal on macroecological patterns of Lesser Antillean birds

Aim Dispersal is often assumed to be a major force in shaping macroecological patterns, but this is rarely tested. Here I describe macroecological patterns for two groups of Lesser Antillean birds and then use population genetic data to assess if differences in dispersal ability could be responsible for the groups’ contrasting patterns. Importantly, the population genetic data are derived independently from any data used to generate the macroecological patterns. Location The Lesser Antilles, Caribbean. Methods I used data from the literature to construct species–area curves and evaluate the decline in species compositional similarity with geographic distance (hereafter distance–decay) for two sets of bird communities in the Lesser Antilles, those found in rain forest and those in dry forest. I then used mitochondrial DNA sequences from island populations to assess the dispersal ability of rain forest and dry forest species. Results Rain forest species show steeper species–area curves and greater distance–decay in community similarity than dry forest species, patterns that could be explained by rain forest species having more limited dispersal ability. Both conventional analyses of M, the number of migrants per generation between populations, and alternative analyses of D_A, the genetic distance between populations, suggest that rain forest species disperse between islands less frequently than dry forest species. Main conclusions Differences in dispersal ability are a plausible explanation for the contrasting macroecological patterns of rain forest and dry forest species. Additionally, historical factors, such as the taxon cycle and Pleistocene climate fluctuations, may have played a role in shaping the distribution patterns of Lesser Antillean birds.     

Spatial scaling of mountain pine beetle infestations

1. The relationship between occupancy and spatial contagion during the spread of eruptive and invasive species demands greater study, as it could lead to improved prediction of ecosystem damage. 2. We applied a recently developed model that links occupancy and its fractal dimension to model the spatial distribution of mountain pine beetle infestations in British Columbia, Canada. We showed that the distribution of infestation was scale-invariant in at least 24 out of 37 years (mostly in epidemic years), and presented some degree of scale-invariance in the rest. There was a general logarithmic relationship between fractal dimension and infestation occupancy. Based on the scale-invariance assumption, we further assessed the interrelationships for several landscape metrics, such as correlation length, maximum cluster size, total edge length and total number of clusters. 3. The scale-invariance assumption allows fitting the above metrics, and provides a framework to establish the scaling relationship between occupancy and spatial contagion. 4. We concluded that scale-invariance dominates the spread of mountain pine beetle. In this context, spatial aggregation can be predicted from occupancy, hence occupancy is the only variable one needs to know in order to predict the spatial distributions of populations. This supports the hypothesis that fractal dispersal kernels may be abundant among outbreaks of pests and invasive species.     

Community robustness and limiting similarity in periodic environments

Temporal environmental variation has long been considered as one of the potential factors that could promote species coexistence. A question of particular interest is how the ecology of fluctuating environments relates to that of equilibrium systems. Equilibrium theory says that the more similar two species are in their modes of regulation, the less robust their coexistence will be; that is, the volume of external parameters for which all populations persist shrinks with increasing similarity. In this study, we will attempt to generalize these results to temporally varying situations and establish the precise mathematical relationship between the two. Our treatment considers unstructured populations in continuous time with periodic attractors of fixed period length, where the periodic behavior is due to external forcing. Within these conditions, our treatment is general. We provide a coherent theoretical framework for defining measures of species similarity and niche. Our main conclusion is that all factors that function to regulate population growth may be considered as separate regulating factors for each moment of time. In particular, a single resource becomes a resource continuum, along which species may segregate in the same manner as along classical resource continua. Therefore, we provide a mathematical underpinning for considering fluctuation-mediated coexistence as temporal niche segregation.     

A statistical theory for sampling species abundances

The pattern of species abundances is central to ecology. But direct measurements of species abundances at ecologically relevant scales are typically unfeasible. This limitation has motivated a long-standing interest in the relationship between the abundance distribution in a large, regional community and the distribution observed in a small sample from the community. Here, we develop a statistical sampling theory to describe how observed patterns of species abundances are influenced by the spatial distributions of populations. For a wide range of regional-scale abundance distributions we derive exact expressions for the sampled abundance distributions, as a function of sample size and the degree of conspecific spatial aggregation. We show that if populations are randomly distributed in space then the sampled and regional-scale species-abundance distribution typically have the same functional form: sampling can be expressed by a simple scaling relationship. In the case of aggregated spatial distributions, however, the shape of a sampled species-abundance distribution diverges from the regional-scale distribution. Conspecific aggregation results in sampled distributions that are skewed towards both rare and common species. We discuss our findings in light of recent results from neutral community theory, and in the context of estimating biodiversity.     

Environment, dispersal and patterns of species similarity

Aim The aim of this paper is to evaluate the combined effects of geographical distance and environmental distance on patterns of species similarity (similarity in species composition between sites), and to identify factors affecting the rate of decay in species similarity with each type of distance. Location Israel. Methods Data on species composition of land snails and land birds were recorded in 27 sites of 1 × 1 km scattered across a rainfall gradient in Israel. Matrices of similarity in species composition between all pairs of sites were computed and analysed with respect to corresponding matrices of geographical distance and rainfall distance (defined as the difference in mean annual rainfall between sites, and used as a measure of environmental distance). Mantel tests were applied to determine the correlation between species similarity and each type of distance. Factors affecting the decay in species similarity were investigated by comparing different subsets of the data using randomization tests. Results Both rainfall distance and geographical distance had negative effects on species similarity. The effect of rainfall distance was statistically significant even after controlling for differences in geographical distance, and vice versa. The per‐unit effect of rainfall distance on species similarity decreased with increasing geographical distance, indicating that the two types of distances interacted in determining the similarity in species composition. Snails showed a higher rate of decay in species similarity with geographical distance than birds, and large snails showed a higher rate of decay than small snails, which are better passive dispersers. The per‐unit effects of both rainfall distance and geographical distance on species similarity were higher in the desert region than in the Mediterranean region. Analyses focusing on a grain size of 10 × 10 m showed a lower similarity in species composition and a lower rate of decay in species similarity with rainfall distance than analyses carried out at a grain size of 1 × 1 km. Main conclusions Patterns of similarity in species composition are influenced by the combined effects of environmental variation, the position of the area along environmental gradients, the dispersal properties of the component species, and the scale (both spatial extent and grain size) at which the patterns are examined.     

Aggregation and species coexistence in fleas parasitic on small mammals

The aggregation model of coexistence states that species coexistence is facilitated if interspecific aggregation is reduced relative to intraspecific aggregation. We investigated the relationship between intraspecific and interspecific aggregation in 17 component communities (the flea assemblage of a host population) of fleas parasitic on small mammals and hypothesized that interspecific interactions should be reduced relative to intraspecific interactions, facilitating species coexistence. We predicted that the reduction of the level of interspecific aggregation in relation to the level of intraspecific aggregation would be positively correlated with total flea abundance and species richness of flea assemblages. We also expected that the higher degree of facilitation of flea coexistence would be affected by host parameters such as body mass, basal metabolic rate (BMR) and depth and complexity of burrows. Results of this study supported the aggregation model of coexistence and demonstrated that, in general, a) conspecific fleas were aggregated across their hosts; b) flea assemblages were not dominated by negative interspecific interactions; and c) the level of interspecific aggregation in flea assemblages was reduced in relation to the level of intraspecific aggregation. Intraspecific aggregation tended to be correlated positively to body mass, burrow complexity and mass-independent BMR of a host. Positive interspecific associations of fleas tended to occur more frequently in species-rich flea assemblages and/or in larger hosts possessing deep complex burrows. Intraspecific aggregation increased relative to interspecific aggregation when species richness of flea infracommunities (the flea assemblage of a host individual) and component communities increased. We conclude that the pattern of flea coexistence is related both to the structure of flea communities and affinities of host species.     

Loss of animal seed dispersal increases extinction risk in a tropical tree species due to pervasive negative density dependence across life stages

Overhunting in tropical forests reduces populations of vertebrate seed dispersers. If reduced seed dispersal has a negative impact on tree population viability, overhunting could lead to altered forest structure and dynamics, including decreased biodiversity. However, empirical data showing decreased animal-dispersed tree abundance in overhunted forests contradict demographic models which predict minimal sensitivity of tree population growth rate to early life stages. One resolution to this discrepancy is that seed dispersal determines spatial aggregation, which could have demographic consequences for all life stages. We tested the impact of dispersal loss on population viability of a tropical tree species, Miliusa horsfieldii, currently dispersed by an intact community of large mammals in a Thai forest. We evaluated the effect of spatial aggregation for all tree life stages, from seeds to adult trees, and constructed simulation models to compare population viability with and without animal-mediated seed dispersal. In simulated populations, disperser loss increased spatial aggregation by fourfold, leading to increased negative density dependence across the life cycle and a 10-fold increase in the probability of extinction. Given that the majority of tree species in tropical forests are animal-dispersed, overhunting will potentially result in forests that are fundamentally different from those existing now.     

The wealth of species: ecological communities, complex systems and the legacy of Frank Preston

General statistical patterns in community ecology have attracted considerable recent debate. Difficulties in discriminating among mathematical models and the ecological mechanisms underlying them are likely related to a phenomenon first described by Frank Preston. He noted that the frequency distribution of abundances among species was uncannily similar to the Boltzmann distribution of kinetic energies among gas molecules and the Pareto distribution of incomes among wage earners. We provide additional examples to show that four different 'distributions of wealth' (species abundance distributions, species–area and species–time relations, and distance decay of compositional similarity) are not unique to ecology, but have analogues in other physical, geological, economic and cultural systems. Because these appear to be general statistical patterns characteristic of many complex dynamical systems they are likely not generated by uniquely ecological mechanistic processes.     

A General Unified Framework to Assess the Sampling Variance of Heritability Estimates Using Pedigree or Marker-Based Relationships

Heritability is a population parameter of importance in evolution, plant and animal breeding, and human medical genetics. It can be estimated using pedigree designs and, more recently, using relationships estimated from markers. We derive the sampling variance of the estimate of heritability for a wide range of experimental designs, assuming that estimation is by maximum likelihood and that the resemblance between relatives is solely due to additive genetic variation. We show that well-known results for balanced designs are special cases of a more general unified framework. For pedigree designs, the sampling variance is inversely proportional to the variance of relationship in the pedigree and it is proportional to 1/N, whereas for population samples it is approximately proportional to 1/N², where N is the sample size. Variation in relatedness is a key parameter in the quantification of the sampling variance of heritability. Consequently, the sampling variance is high for populations with large recent effective population size (e.g., humans) because this causes low variation in relationship. However, even using human population samples, low sampling variance is possible with high N.     

Distance decay relationships in foliar fungal endophytes are driven by rare taxa

Foliar fungal endophytes represent a diverse and species‐rich plant microbiome. Their biogeography provides essential clues to their cryptic relationship with hosts and the environment in which they disperse. We present species composition, diversity, and dispersal patterns of endophytic fungi associated with needles of Pinus taeda trees across regional scales in the absence of strong environmental gradients as well as within individual trees. An empirical designation of rare and abundant taxa enlightens us on the structure of endophyte communities. We report multiple distance‐decay patterns consistent with effects of dispersal limitation, largely driven by community changes in rare taxa, those taxonomic units that made up less than 0.31% of reads per sample on average. Distance‐decay rates and community structure also depended on specific classes of fungi and were predominantly influenced by rare members of Dothideomycetes. Communities separated by urban areas also revealed stronger effects of distance on community similarity, confirming that host density and diversity plays an important role in symbiont biogeography, which may ultimately lead to a mosaic of functional diversity as well as rare species diversity across landscapes.     

Habitat selection and the value of information in heterogenous landscapes

Despite the wide usage of the term information in evolutionary ecology, there is no general treatise between fitness (i.e. density‐dependent population growth) and selection of the environment sensu lato. Here we 1) initiate the building of a quantitative framework with which to examine the relationship between information use in spatially heterogeneous landscapes and density‐dependent population growth, and 2) illustrate its utility by applying the framework to an existing model of breeding habitat selection. We begin by linking information, as a process of narrowing choice, to population growth/fitness. Second, we define a measure of a population's penalty of ignorance based on the Kullback–Leibler index that combines the contributions of resource selection (i.e. biased use of breeding sites) and density‐dependent depletion. Third, we quantify the extent to which environmental heterogeneity (i.e. mean and variance within a landscape) constrains sustainable population growth of unbiased agents. We call this the heterogeneity‐based fitness deficit, and combine this with population simulations to quantify the independent contribution of information‐use strategies to the total population growth rate. We further capitalize on this example to highlight the interactive effects of information between ecological scales when fear affects individual fitness through phenotypic plasticity. Informed breeding habitat selection moderates the demographic cost of fear commensurate with density‐dependent information use. Thus, future work should attempt to differentiate between phenotypic plasticity (i.e. acute fear) and demographic responses (i.e. chronic changes in population size). We conclude with a broader discussion of information in alternative contexts, and explore some evolutionary considerations for information use. We note how competition among individuals may constrain the information state among individuals, and the implications of this constraint under environmental change.     

Density and assemblage influence the nature of the species richness–productivity relationship in Australian dry sclerophyll forest species

The relationship between species richness and productivity is important from both a basic, theoretical perspective and also because it has important ramifications for applied ecology including ecosystem restoration and the design of carbon offset plantings. While a more species‐rich community is often believed to be more productive than a species‐poor community, findings from observational and experimental studies differ and our understanding of the relationship comes largely from grasslands. Consequently, we aimed to determine for the first time the nature of the species richness–productivity relationship in a southern‐hemisphere dry sclerophyll ecosystem. We investigated the impact of species richness on productivity, plant density and mean plant biomass at three sowing densities in three species assemblages. Eucalyptus globulus, Acacia mearnsii and Allocasuarina verticillata were each grown as monocultures and included in every subsequent level of species richness, forming three distinct species assemblages. Communities were grown in a glasshouse pot experiment for four months, then harvested and above‐ground biomass measured. We found no general species richness–productivity relationship in the communities studied. There were no overall increases in productivity as species richness increased and in fact in most cases the productivity of communities with 4 and 8 species was lower than monocultures of the dominants. Importantly, density influenced the way richness affected productivity and this effect was dependent upon assemblage, indicating that species identity is a key determinant of productivity. These results demonstrate important ecological principles in a previously untested system. A key outcome of this experiment is that density alters the relationship between species richness and initial productivity in assemblages of Australian dry sclerophyll species.     

No biogeographical pattern for a root‐associated fungal species complex

Aim The biogeography of microbes is poorly understood and there is an open debate regarding if and how microbial biodiversity is structured. At the beginning of the 20th century, Baas Becking laid the foundations for the biogeography of microbes by stating that ‘Everything is everywhere, but the environment selects’ (the EisE hypothesis). This hypothesis remained dogma for almost a century. However, the recognition that microbial ‘species’ are often assemblages of reproductively isolated lineages challenged the EisE hypothesis, leading to the now common assumption that microbial communities possess cryptic biogeographic structures. We tested the presence of a cryptic biogeographical structure for a well‐characterized fungal species complex (the Phialocephala fortinii s.l.–Acephala applanata species complex, PAC) using precise molecular species resolution. In addition, we analysed factors that could govern PAC community assembling. Locations Forty‐four study sites in temperate and boreal forests across the Northern Hemisphere were included. Methods (1) The distance–decay relationship among PAC communities was calculated and a resampling procedure was applied to analyse the effect of sampling intensity and geographic distances among PAC communities. (2) Factors shaping PAC communities (e.g. climatic factors and tree species composition) were studied. (3) We tested PAC communities for random composition. Results We found that the similarity of species assemblages did not decrease with increasing geographical distance. Moreover, species diversity did not increase by expanding the area sampled. Instead, species diversity increased by increasing the sampling effort. Community composition correlated neither with tree species composition nor climate, and no association among species was observed. Main conclusions We could not discover any cryptic biogeographic structure even after applying refined species assignment but we demonstrate the importance of sampling effort for understanding the biogeography of microorganisms. Moreover, we show that primarily stochastic effects are responsible for the species composition of PAC communities.     

Metazoan parasites of freshwater cyprinid fish ( Leuciscus cephalus): testing biogeographical hypotheses of species diversity

The diversity and similarity of parasite communities is a result of many determinants widely considered in parasite ecology. In this study, the metazoan parasite communities of 15 chub populations (Leuciscus cephalus) were sampled across a wide geographical range. Three hypotheses of biogeographical gradients in species diversity were tested: (1) latitudinal gradient, (2) a 'favourable centre' versus 'local oasis' model, and (3) decay of similarity with distance. We found that the localities in marginal zones of chub distribution showed lower parasite species richness and diversity. A latitudinal gradient, with increasing abundance of larvae of Diplostomum species, was observed. There was a general trend for a negative relationship between relative prevalence or abundance and the distance from the locality with maximum prevalence or abundance for the majority of parasite species. However, statistical support for a 'favourable centre' model was found only for total abundance of Monogenea and for larvae of Diplostomum species. The phylogenetic relatedness of host populations inferred an important role when the 'favourable centre' model was tested. Testing of the hypothesis of 'decay of similarity with geographical distance' showed that phylogenetic distance was more important as a determinant of similarity in parasite communities than geographical distance between host populations.