Spatially structured intraspecific trait variation can foster biodiversity in disturbed,heterogeneous environments

Trait variation within populations is an important area of research for empirical and theoretical ecologists. While differences between individuals are doubtlessly ubiquitous, their role for species coexistence is much less clear and highly debated. Both unstructured (random) and structured (linked to space, time or inheritance) intraspecific trait variation (ITV) may modify species interactions with nontrivial consequences for emerging community compositions. In many ecosystems, these compositions are further driven by prevalent disturbance regimes. I therefore explored the effects of unstructured as well as spatially structured ITV under disturbances in a generic ecological model of competing sessile species. Using spatially explicit, individual‐based simulations, I studied how intraspecific variation in life history traits together with interspecific tradeoffs and disturbance regimes shape long‐term community composition. I found that 1) unstructured ITV does not affect species coexistence in the given context, 2) spatially structured ITV may considerably increase coexistence, but 3) spatially clumped disturbances reduce this effect of spatially structured ITV, especially if interspecific tradeoffs involve dispersal distance. The findings suggest that spatially structured ITV with individual trait responses to local habitat conditions differing among species may create or expand humps in disturbance–diversity relationships. Hence, if present, these forms of spatially structured ITV should be included in ecological models and will be important for reliably assessing community responses to environmental heterogeneity and change.     

The effect of population structure on the adaptive radiation of microbial populations evolving in spatially structured environments

Spatial structure is thought to be an important factor influencing the emergence and maintenance of genetic diversity. Previous studies have demonstrated that environmental heterogeneity, provided by spatial structure, leads to adaptive radiation of populations. In the present study, we investigate not only the impact of environmental heterogeneity on adaptive radiation, but also of population fragmentation and niche construction. Replicate populations founded by a single genotype of Escherichia coli were allowed to evolve for 900 generations by serial transfer in either a homogeneous environment, or a spatially structured environment that was either kept intact or destroyed with each daily transfer. Only populations evolving in the structured environment with intact population structure diversified: clones are significantly divergent in sugar catabolism, and show frequency-dependent fitness interactions indicative of stable coexistence. These findings demonstrate an important role for population fragmentation, a consequence of population structure in spatially structured environments, on the diversification of populations.     

The effects of archipelago spatial structure on island diversity and endemism: predictions from a spatially‐structured neutral model

Islands are particularly suited to testing hypotheses about the ecological and evolutionary mechanisms underpinning community assembly. Yet the complex spatial arrangements of real island systems have received little attention from both empirical studies and theoretical models. Here, we investigate the extent to which the spatial structure of archipelagos affects species diversity and endemism. We start by proposing a new spatially structured neutral model that explicitly considers archipelago structure, and then investigate its predictions under a diversity of scenarios. Our results suggest that considering the spatial structure of archipelagos is crucial to understanding their diversity and endemism, with structured island systems acting both as “museums” and “cradles” of biodiversity. These dynamics of diversification may change the traditionally expected pattern of decrease in species richness with distance from the mainland, even potentially leading to increasing patterns for taxa with high speciation rates in archipelagos off species‐poor continental areas. Our results also predict that, within spatially structured archipelagos, metapopulation dynamics and evolutionary processes can generate higher diversity on islands more centrally placed than at the periphery. We derive from our results a set of theoretical predictions, potentially testable with empirical data.     

Digest: Structuring interactions in Streptomyces*

For bacteria growing in colonies, spatial structure can allow maintenance of costly traits such as the production of antibiotics. Using spatially structured environments, Westhoff et al. examined the benefits of streptomycin production for the bacterium Streptomyces griseus in competition with a streptomycin-susceptible strain. Streptomyces griseus outcompeted susceptible competitors, but the benefit of its antibiotic decreased as competitor resistance to streptomycin increased. Spatial structure also increased the ability of S. griseus to invade susceptible competitor populations from low starting densities. These results demonstrate that spatially structured environments can both provide and amplify benefits of antibiotics to antibiotic-producing bacteria on a microbial scale.     

Limited Population Structure,Genetic Drift and Bottlenecks Characterise an Endangered Bird Species in a Dynamic,Fire-Prone Ecosystem

Fire is a major disturbance process in many ecosystems world-wide, resulting in spatially and temporally dynamic landscapes. For populations occupying such environments, fire-induced landscape change is likely to influence population processes, and genetic patterns and structure among populations. The Mallee Emu-wren Stipiturus mallee is an endangered passerine whose global distribution is confined to fire-prone, semi-arid mallee shrublands in south-eastern Australia. This species, with poor capacity for dispersal, has undergone a precipitous reduction in distribution and numbers in recent decades. We used genetic analyses of 11 length-variable, nuclear loci to examine population structure and processes within this species, across its global range. Populations of the Mallee Emu-wren exhibited a low to moderate level of genetic diversity, and evidence of bottlenecks and genetic drift. Bayesian clustering methods revealed weak genetic population structure across the species'' range. The direct effects of large fires, together with associated changes in the spatial and temporal patterns of suitable habitat, have the potential to cause population bottlenecks, serial local extinctions and subsequent recolonisation, all of which may interact to erode and homogenise genetic diversity in this species. Movement among temporally and spatially shifting habitat, appears to maintain long-term genetic connectivity. A plausible explanation for the observed genetic patterns is that, following extensive fires, recolonisation exceeds in-situ survival as the primary driver of population recovery in this species. These findings suggest that dynamic, fire-dominated landscapes can drive genetic homogenisation of populations of species with low-mobility and specialised habitat that otherwise would be expected to show strongly structured populations. Such effects must be considered when formulating management actions to conserve species in fire-prone systems.     

Plankton metacommunities in floodplain wetlands under contrasting hydrological conditions

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Shifts in Climate Foster Exceptional Opportunities for Species Radiation: The Case of South African Geraniums

Climate change is often assumed to be a major driver of biodiversity loss. However, it can also set the stage for novel diversification in lineages with the evolutionary ability to colonize new environments. Here we tested if the extraordinary evolutionary success of the genus Pelargonium was related to the ability of its species to capitalize on the climate niche variation produced by the historical changes in southern Africa. We evaluated the relationship between rates of climate niche evolution and diversification rates in the main Pelargonium lineages and disentangled the roles of deep and recent historical events in the modification of species niches. Pelargonium clades exhibiting higher ecological differentiation along summer precipitation (SPP) gradients also experienced higher diversification rates. Faster rates of niche differentiation in spatially structured variables, along with lower levels of niche overlap among closely related species, suggest recent modification in species niches (e.g. dispersal or range shift) and niche lability. We suggest that highly structured SPP gradients established during the aridification process within southern Africa, in concert with niche lability and low niche overlap, contributed to species divergence. These factors are likely to be responsible for the extensive diversification of other lineages in this diversity hot spot.     

Modelling tree diversity in a highly fragmented tropical montane landscape

Aim There is an urgent need for conservation in threatened tropical forest regions. We explain and predict the spatial variation of α (i.e. within plot) and β (i.e. between plot) tree diversity in a tropical montane landscape subjected to a high deforestation rate. A major aim is to demonstrate the potential of a method that combines data from multiple sources (field data, remote sensing imagery and GIS) to evaluate and monitor forest diversity on a broad scale over large unexplored areas. Location The study covered an area of c. 3500 km² in the Highlands of Chiapas, southern Mexico. Methods We identified all of the tree species within 204 field plots (1000 m² each) and measured different environmental, human disturbance‐related, and spatial variables using remote sensing and GIS data. To obtain a predictive model of α tree diversity (Fisher's alpha) based on selected explanatory variables, we used a generalized linear model with a gamma error distribution. Mantel tests of matrix correspondence were used to determine whether similarities in floristic composition were correlated with similarities in the explanatory variables. Finally, we used a method that combines α and β tree diversity to define priority areas for conservation. Results The model for α tree diversity explained 44% of the overall variability, of which most was mainly related to precipitation, temperature, NDVI, and canopy (all relationships were positive, and quadratic for temperature and NDVI). There were no spatially structured regional factors that were ignored. Similarity in tree composition was correlated positively with climate and NDVI. Main conclusions The results were used to: (1) identify and assign conservation priority of unexplored areas that have high tree diversity, and (2) demonstrate the importance of several vegetation formations in the region's biodiversity. The method we present can be particularly useful in assessing regional needs and in developing local conservation strategies in poorly surveyed (and often at risk) tropical areas worldwide, where accessibility is usually limited.     

The effect of cheats on siderophore diversity in Pseudomonas aeruginosa

Cooperation can be maintained if cooperative behaviours are preferentially directed towards other cooperative individuals. Tag‐based cooperation (greenbeards) – where cooperation benefits individuals with the same tag as the actor – is one way to achieve this. Tag‐based cooperation can be exploited by individuals who maintain the specific tag but do not cooperate, and selection to escape this exploitation can result in the evolution of tag diversity. We tested key predictions crucial for the evolution of cheat‐mediated tag diversity using the production of iron‐scavenging pyoverdine by the opportunistic pathogen, Pseduomonas aeruginosa as a model system. Using two strains that produce different pyoverdine types and their respective cheats, we show that cheats outcompete their homologous pyoverdine producer, but are outcompeted by the heterologous producer in well‐mixed environments. As a consequence, co‐inoculating two types of pyoverdine producer and one type of pyoverdine cheat resulted in the pyoverdine type whose cheat was not present having a large fitness advantage. Theory suggests that in such interactions, cheats can maintain tag diversity in spatially structured environments, but that tag‐based cooperation will be lost in well‐mixed populations, regardless of tag diversity. We saw that when all pyoverdine producers and cheats were co‐inoculated in well‐mixed environments, both types of pyoverdine producers were outcompeted, whereas spatial structure (agar plates and compost microcosms), rather than maintaining diversity, resulted in the domination of one pyoverdine producer. These results suggest cheats may play a more limited role in the evolution of pyoverdine diversity than predicted.     

Regional species pools control community saturation in lake phytoplankton

Recent research has highlighted that positive biodiversity–ecosystem functioning relationships hold for all groups of organisms, including microbes. Yet, we still lack understanding regarding the drivers of microbial diversity, in particular, whether diversity of microbial communities is a matter of local factors, or whether metacommunities are of similar importance to what is known from higher organisms. Here, we explore the driving forces behind spatial variability in lake phytoplankton diversity in Fennoscandia. While phytoplankton biovolume is best predicted by local phosphorus concentrations, phytoplankton diversity (measured as genus richness, G) only showed weak correlations with local concentrations of total phosphorus. By estimating spatial averages of total phosphorus concentrations on various scales from an independent, spatially representative lake survey, we found that close to 70 per cent of the variability in local phytoplankton diversity can be explained by regionally averaged phosphorus concentrations on a scale between 100 and 400 km. Thus, the data strongly indicate the existence of metacommunities on this scale. Furthermore, we show a strong dependency between lake productivity and spatial community turnover. Thus, regional productivity affects beta-diversity by controlling spatial community turnover, resulting in scale-dependent productivity-diversity relationships. As an illustration of the interaction between local and regional processes in shaping microbial diversity, our results offer both empirical support and a plausible mechanism for the existence of common scaling rules in both the macrobial and the microbial worlds. We argue that awareness of regional species pools in phytoplankton and other unicellular organisms may critically improve our understanding of ecosystems and their susceptibility to anthropogenic stressors.     

Peak and Persistent Excess of Genetic Diversity Following an Abrupt Migration Increase

Genetic diversity is essential for population survival and adaptation to changing environments. Demographic processes (e.g., bottleneck and expansion) and spatial structure (e.g., migration, number, and size of populations) are known to shape the patterns of the genetic diversity of populations. However, the impact of temporal changes in migration on genetic diversity has seldom been considered, although such events might be the norm. Indeed, during the millions of years of a species’ lifetime, repeated isolation and reconnection of populations occur. Geological and climatic events alternately isolate and reconnect habitats. We analytically document the dynamics of genetic diversity after an abrupt change in migration given the mutation rate and the number and sizes of the populations. We demonstrate that during transient dynamics, genetic diversity can reach unexpectedly high values that can be maintained over thousands of generations. We discuss the consequences of such processes for the evolution of species based on standing genetic variation and how they can affect the reconstruction of a population’s demographic and evolutionary history from genetic data. Our results also provide guidelines for the use of genetic data for the conservation of natural populations.     

Competitive interactions in Escherichia coli populations: the role of bacteriocins

Explaining the coexistence of competing species is a major challenge in community ecology. In bacterial systems, competition is often driven by the production of bacteriocins, which are narrow-spectrum proteinaceous toxins that serve to kill closely related species, providing the producer better access to limited resources. Bacteriocin producers have been shown to competitively exclude sensitive, nonproducing strains. However, the dynamics between bacteriocin producers, each lethal to its competitor, are largely unknown. In this study, we used in vitro, in vivo and in silico models to study competitive interactions between bacteriocin producers. Two Escherichia coli strains were generated, each carrying a DNA-degrading bacteriocin (colicins E2 and E7). Using reporter-gene assays, we showed that each DNase bacteriocin is not only lethal to its opponent but, at lower doses, can also induce the expression of its opponent''s toxin. In a well-mixed habitat, the E2 producer outcompeted its adversary; however, in structured environments (on plates or in mice colons), the two producers coexisted in a spatially ‘frozen'' pattern. Coexistence occurred when the producers were initiated with a clumped spatial distribution. This suggests that a ‘clump'' of each producer can block invasion of the other producer. Agent-based simulation of bacteriocin-mediated competition further showed that mutual exclusion in a structured environment is a relatively robust result. These models imply that colicin-mediated colicin induction enables producers to successfully compete and defend their niche against invaders. This suggests that localized interactions between producers of DNA-degrading toxins can lead to stable coexistence of heterogeneously distributed strains within the bacterial community and to the maintenance of diversity.     

Adaptive evolution in a spatially structured asexual population

We study the process of adaptation in a spatially structured asexual haploid population. The model assumes a local competition for replication, where each organism interacts only with its nearest neighbors. We observe that the substitution rate of beneficial mutations is smaller for a spatially structured population than that seen for populations without structure. The difference between structured and unstructured populations increases as the adaptive mutation rate increases. Furthermore, the substitution rate decreases as the number of neighbors for local competition is reduced. We have also studied the impact of structure on the distribution of adaptive mutations that fix during adaptation.     

Persistence of structured populations in random environments

Environmental fluctuations often have different impacts on individuals that differ in size, age, or spatial location. To understand how population structure, environmental fluctuations, and density-dependent interactions influence population dynamics, we provide a general theory for persistence for density-dependent matrix models in random environments. For populations with compensating density dependence, exhibiting “bounded” dynamics, and living in a stationary environment, we show that persistence is determined by the stochastic growth rate (alternatively, dominant Lyapunov exponent) when the population is rare. If this stochastic growth rate is negative, then the total population abundance goes to zero with probability one. If this stochastic growth rate is positive, there is a unique positive stationary distribution. Provided there are initially some individuals in the population, the population converges in distribution to this stationary distribution and the empirical measures almost surely converge to the distribution of the stationary distribution. For models with overcompensating density-dependence, weaker results are proven. Methods to estimate stochastic growth rates are presented. To illustrate the utility of these results, applications to unstructured, spatially structured, and stage-structured population models are given. For instance, we show that diffusively coupled sink populations can persist provided that within patch fitness is sufficiently variable in time but not strongly correlated across space.     

Deconstructing the dimensions of alpha diversity in squamate reptiles (Reptilia: Squamata) across the Americas

Aim

Our aim is to document the dimensions of current squamate reptile biodiversity in the Americas by integrating taxonomic, phylogenetic and functional data, and assessing how this may vary across phylogenetic scales. We also explore the potential underlying mechanisms that may be responsible for the observed geographical diversity patterns.

Location

The Americas.

Time period

Present.

Major taxa

Squamate reptiles.

Methods

We used published data on the distribution, phylogeny, and body size of squamate reptiles to document the current dimensions of their alpha diversity in the Americas. We overlapped species ranges to estimate taxonomic diversity (TD) and calculated phylogenetic diversity (PD) using mean pairwise phylogenetic distance (MPD), speciation rate (DivRate) and Faith's phylogenetic index (PD). We estimated functional diversity (FD) as trait dispersion in the multivariate space using body size and leg development data. We implemented a deconstructive macroecological approach to understand how spatial mismatches between the three facets of diversity vary across phylogenetic scales, and the potential eco-evolutionary mechanisms driving these patterns across space.

Results

We found a strong latitudinal gradient of TD with a large accumulation in tropical regions. PD and FD patterns were largely similar likely due to the high phylogenetic signal in the traits used, and higher values tended to be concentrated in harsh and/or heterogeneous environments. We found differences between major clades within Squamata that display contrasting geographical patterns. Several regions across the continent shared the same spatial mismatches between dimensions across clades, suggesting that similar eco-evolutionary processes are shaping these regional reptile assemblages. However, we also found evidence that non-mutually exclusive processes can operate differently across clades.

Main conclusions

The deconstructive approach implemented here is based on a solid macroecological framework. We can extend this to other taxonomic groups to establish whether there are particularities about how different eco-evolutionary mechanisms shape biodiversity facets in a spatially explicit context.     

The effect of spatial structure on adaptation in Escherichia coli

Populations of organisms are generally organized in a given spatial structure. However, the vast majority of population genetic studies are based on populations in which every individual competes globally. Here we use experimental evolution in Escherichia coli to directly test a recently made prediction that spatial structure slows down adaptation and that this cost increases with the mutation rate. This was studied by comparing populations of different mutation rates adapting to a liquid (unstructured) medium with populations that evolved in a Petri dish on solid (structured) medium. We find that mutators adapt faster to both environments and that adaptation is slower if there is spatial structure. We observed no significant difference in the cost of structure between mutator and wild-type populations, which suggests that clonal interference is intense in both genetic backgrounds.     

Effects of neutrality and productivity on mammal richness and evolutionary history in Australia

Explaining how heterogeneous spatial patterns of species diversity emerge is one of the most fascinating questions of biogeography. One of the great challenges is revealing the mechanistic effect of environmental variables on diversity. Correlative analyses indicate that productivity is associated with taxonomic, phylogenetic, and functional diversity of communities. Surprisingly, no unifying body of theory have been developed to understand the mechanism by which spatial variation of productivity affects the fundamental processes of biodiversity. Based on widely discussed verbal models in ecology about the effect of productivity on species diversity, we developed a spatially explicit neutral model that incorporates the effect of primary productivity on community size and confronted our model's predictions with observed patterns of species richness and evolutionary history of Australian terrestrial mammals. The imposed restrictions on community size create larger populations in areas of high productivity, which increases community turnover and local speciation, and reduces extinction. The effect of productivity on community size modeled in our study causes higher accumulation of species diversity in productive regions even in the absence of niche‐based processes. However, such a simple model is not capable of reproducing spatial patterns of mammal evolutionary history in Australia, implying that more complex evolutionary mechanisms are involved. Our study demonstrates that the overall patterns of species richness can be directly explained by changes in community sizes along productivity gradients, supporting a major role of processes associated with energetic constraints in shaping diversity patterns.     

Optimal sampling strategies for capture of genetic diversity differ between core and peripheral populations of <Emphasis Type="Italic">Picea sitchensis</Emphasis> (Bong.) Carr

In previous studies we reported that while core populations of Sitka spruce [Picea sitchensis (Bong.) Carr] have little within-population genetic structure, peripheral populations are strongly spatially structured at distances up to 500 m. Here we explore the implications of this difference in structure on ex situ gene conservation collections and estimates of genetic diversity from research collections. We test the effects of varying the number of individuals sampled and the total area they are sampled across on capture of neutral genetic variation in collections from core, continuous versus peripheral, disjunct populations. Bivariate response surface analysis of genetic marker data for eight sequence tagged site loci from core and peripheral populations suggest that a population sample from 150 trees covering at least 225 ha would be adequate for capturing 95% of the genetic diversity (as measured by allelic richness or expected heterozygosity) in core populations. However, a larger sample of 180 individuals from an area of at least 324 ha is needed in peripheral populations to capture the same proportion of standing variation because of stronger within-population spatial genetic structure. Standard population sampling protocols for estimating among and within-population genetic diversity would significantly underestimate the within-population allelic richness and expected heterozygosity of peripheral but not core populations, potentially leading to poor representation of genetic variation in peripheral populations as well as erroneous conclusions about their genetic impoverishment.     

Fitness benefits of low infectivity in a spatially structured population of bacteriophages

For a parasite evolving in a spatially structured environment, an evolutionarily advantageous strategy may be to reduce its transmission rate or infectivity. We demonstrate this empirically using bacteriophage (phage) from an evolution experiment where spatial structure was maintained over 550 phage generations on agar plates. We found that a single substitution in the major capsid protein led to slower adsorption of phage to host cells with no change in lysis time or burst size. Plaques formed by phage isolates containing this mutation were not only larger but also contained more phage per unit area. Using a spatially explicit, individual-based model, we showed that when there is a trade-off between adsorption and diffusion (i.e. less ‘sticky’ phage diffuse further), slow adsorption can maximize plaque size, plaque density and overall productivity. These findings suggest that less infective pathogens may have an advantage in spatially structured populations, even when well-mixed models predict that they will not.     

The Impact of Spatial Scales and Spatial Smoothing on the Outcome of Bayesian Spatial Model

Discretization of a geographical region is quite common in spatial analysis. There have been few studies into the impact of different geographical scales on the outcome of spatial models for different spatial patterns. This study aims to investigate the impact of spatial scales and spatial smoothing on the outcomes of modelling spatial point-based data. Given a spatial point-based dataset (such as occurrence of a disease), we study the geographical variation of residual disease risk using regular grid cells. The individual disease risk is modelled using a logistic model with the inclusion of spatially unstructured and/or spatially structured random effects. Three spatial smoothness priors for the spatially structured component are employed in modelling, namely an intrinsic Gaussian Markov random field, a second-order random walk on a lattice, and a Gaussian field with Matérn correlation function. We investigate how changes in grid cell size affect model outcomes under different spatial structures and different smoothness priors for the spatial component. A realistic example (the Humberside data) is analyzed and a simulation study is described. Bayesian computation is carried out using an integrated nested Laplace approximation. The results suggest that the performance and predictive capacity of the spatial models improve as the grid cell size decreases for certain spatial structures. It also appears that different spatial smoothness priors should be applied for different patterns of point data.