Implications of recurrent disturbance for genetic diversity

Exploring interactions between ecological disturbance, species’ abundances and community composition provides critical insights for ecological dynamics. While disturbance is also potentially an important driver of landscape genetic patterns, the mechanisms by which these patterns may arise by selective and neutral processes are not well‐understood. We used simulation to evaluate the relative importance of disturbance regime components, and their interaction with demographic and dispersal processes, on the distribution of genetic diversity across landscapes. We investigated genetic impacts of variation in key components of disturbance regimes and spatial patterns that are likely to respond to climate change and land management, including disturbance size, frequency, and severity. The influence of disturbance was mediated by dispersal distance and, to a limited extent, by birth rate. Nevertheless, all three disturbance regime components strongly influenced spatial and temporal patterns of genetic diversity within subpopulations, and were associated with changes in genetic structure. Furthermore, disturbance‐induced changes in temporal population dynamics and the spatial distribution of populations across the landscape resulted in disrupted isolation by distance patterns among populations. Our results show that forecast changes in disturbance regimes have the potential to cause major changes to the distribution of genetic diversity within and among populations. We highlight likely scenarios under which future changes to disturbance size, severity, or frequency will have the strongest impacts on population genetic patterns. In addition, our results have implications for the inference of biological processes from genetic data, because the effects of dispersal on genetic patterns were strongly mediated by disturbance regimes.     

Dispersal,niche, and isolation processes jointly explain species turnover patterns of nonvolant small mammals in a large mountainous region of China

Understanding the mechanisms that govern the spatial patterns of species turnover (beta diversity) has been one of the fundamental issues in biogeography. Species turnover is generally recognized as strong in mountainous regions, but the way in which different processes (dispersal, niche, and isolation) have shaped the spatial turnover patterns in mountainous regions remains largely unexplored. Here, we explore the directional and elevational patterns of species turnover for nonvolant small mammals in the Hengduan Mountains of southwest China and distinguish the relative roles of geographic distance, environmental distance, and geographic isolation on the patterns. The spatial turnover was assessed using the halving distance (km), which was the geographic distance that halved the similarity (Jaccard similarity) from its initial value. The halving distance was calculated for the linear, logarithmic, and exponential regression models between Jaccard similarity and geographic distance. We found that the east–west turnover is generally faster than the south–north turnover for high‐latitudinal regions in the Hengduan Mountains and that this pattern corresponds to the geographic structure of the major mountain ranges and rivers that mainly extend in a south–north direction. There is an increasing trend of turnover toward the higher‐elevation zones. Most of the variation in the Jaccard similarity could be explained by the pure effect of geographic distance and the joint effects of geographic distance, environmental distance, and average elevation difference. Our study indicates that dispersal, niche, and isolation processes are all important determinants of the spatial turnover patterns of nonvolant small mammals in the Hengduan Mountains. The spatial configuration of the landscape and geographic isolation can strongly influence the rate of species turnover in mountainous regions at multiple spatial scales.     

Stochastically driven adult–recruit associations of tree species on Barro Colorado Island

The spatial placement of recruits around adult conspecifics represents the accumulated outcome of several pattern-forming processes and mechanisms such as primary and secondary seed dispersal, habitat associations or Janzen–Connell effects. Studying the adult–recruit relationship should therefore allow the derivation of specific hypotheses on the processes shaping population and community dynamics. We analysed adult–recruit associations for 65 tree species taken from six censuses of the 50 ha neotropical forest plot on Barro Colorado Island (BCI), Panama. We used point pattern analysis to test, at a range of neighbourhood scales, for spatial independence between recruits and adults, to assess the strength and type of departure from independence, and its relationship with species properties. Positive associations expected to prevail due to dispersal limitation occurred only in 16% of all cases; instead a majority of species showed spatial independence (≈73%). Independence described the placement of recruits around conspecific adults in good approximation, although we found weak and noisy signals of species properties related to seed dispersal. We hypothesize that spatial mechanisms with strong stochastic components such as animal seed dispersal overpower the pattern-forming effects of dispersal limitation, density dependence and habitat association, or that some of the pattern-forming processes cancel out each other.     

Decomposing the process of species accumulation into area dependent and time dependent parts

In 1960, Preston predicted that the process of species accumulation in time (species–time relationship, STR) should be similar to the species–area relationship (SAR) and follow a power function with a slope of about 0.26. Here these two conjectures are tested using data of the spatiotemporal species accumulation in a local community of beech forest Hymenoptera. A power function species–area–time model of the form S = S₀ A^z t gave better fits to observed species numbers than a simple power function SAR model, and was able to predict similar species turnover rates (about 9% per year) to those inferred by other methods. The STR was well fitted by a power function, although due the limited time span (8 years) a logarithmic STR pattern cannot be ruled out. STR slopes ranged between 0.01 and 0.23 and were lower than predicted by Preston. Temporal species turnover appeared to be negatively correlated to species densities and positively correlated to species body weights. Ecological guild and taxon membership did not significantly influence temporal species turnover.     

A Multi-Clade Test Supports the Intermediate Dispersal Model of Biogeography

Background

Biogeography models typically focus on explaining patterns through island properties, such as size, complexity, age, and isolation. Such models explain variation in the richness of island biotas. Properties of the organisms themselves, such as their size, age, and dispersal abilities, in turn may explain which organisms come to occupy, and diversify across island archipelagos. Here, we restate and test the intermediate dispersal model (IDM) predicting peak diversity in clades of relatively intermediate dispersers.

Methodology

We test the model through a review of terrestrial and freshwater organisms in the western Indian Ocean examining the correlation among species richness and three potential explanatory variables: dispersal ability quantified as the number of estimated dispersal events, average body size for animals, and clade age.

Conclusions

Our study supports the IDM with dispersal ability being the best predictor of regional diversity among the explored variables. We find a weaker relationship between diversity and clade age, but not body size. Principally, we find that richness strongly and positively correlates with dispersal ability in poor to good dispersers while a prior study found a strong decrease in richness with increased dispersal ability among excellent dispersers. Both studies therefore support the intermediate dispersal model, especially when considered together. We note that many additional variables not here considered are at play. For example, some taxa may lose dispersal ability subsequent to island colonization and some poor dispersers have reached high diversity through within island radiations. Nevertheless, our findings highlight the fundamental importance of dispersal ability in explaining patterns of biodiversity generation across islands.     

The Impact of the Species–Area Relationship on Estimates of Paleodiversity

Estimates of paleodiversity patterns through time have relied on datasets that lump taxonomic occurrences from geographic areas of varying size per interval of time. In essence, such estimates assume that the species–area effect, whereby more species are recorded from larger geographic areas, is negligible for fossil data. We tested this assumption by using the newly developed Miocene Mammal Mapping Project database of western North American fossil mammals and its associated analysis tools to empirically determine the geographic area that contributed to species diversity counts in successive temporal bins. The results indicate that a species–area effect markedly influences counts of fossil species, just as variable spatial sampling influences diversity counts on the modern landscape. Removing this bias suggests some traditionally recognized peaks in paleodiversity are just artifacts of the species–area effect while others stand out as meriting further attention. This discovery means that there is great potential for refining existing time-series estimates of paleodiversity, and for using species–area relationships to more reliably understand the magnitude and timing of such biotically important events as extinction, lineage diversification, and long-term trends in ecological structure.     

Strong but opposing β-diversity–stability relationships in coral reef fish communities

The ‘diversity–stability hypothesis’, in which higher species diversity within biological communities buffers the risk of ecological collapse, is now generally accepted. However, empirical evidence for a relationship between β-diversity (spatial turnover in community structure) and temporal stability in community structure remains equivocal, despite important implications for theoretical ecology and conservation biology. Here, we report strong β-diversity–stability relationships across a broad sample of fish taxa on Australia''s Great Barrier Reef. These relationships were robust to random sampling error and spatial and environmental factors, such as latitude, reef size and isolation. While β-diversity was positively associated with temporal stability at the community level, the relationship was negative for some taxa, for example surgeonfishes (Acanthuridae), one of the most abundant reef fish families. This demonstrates that the β-diversity–stability relationship should not be indiscriminately assumed for all taxa, but that a species’ risk of extirpation in response to disturbance is likely to be taxon specific and trait based. By combining predictions of spatial and temporal turnover across the study area with observations in marine-protected areas, we conclude that protection alone does not necessarily confer temporal stability and that taxon-specific considerations will improve the outcome of conservation efforts.     

Selection,drift and community interactions shape microbial biogeographic patterns in the Pacific Ocean

Despite accumulating data on microbial biogeographic patterns in terrestrial and aquatic environments, we still lack a comprehensive understanding of how these patterns establish, in particular in ocean basins. Here we show the relative significance of the ecological mechanisms selection, dispersal and drift for shaping the composition of microbial communities in the Pacific Ocean over a transect of 12,400 km between subantarctic and subarctic regions. In the epipelagic, homogeneous selection contributes 50–60% and drift least to the three mechanism for the assembly of prokaryotic communities whereas in the upper mesopelagic, drift is relatively most important for the particle-associated subcommunities. Temperature is important for the relative significance of homogeneous selection and dispersal limitation for community assembly. The relative significance of both mechanisms was inverted with increasing temperature difference along the transect. For eukaryotes >8 µm, homogeneous selection is also the most important mechanisms at two epipelagic depths whereas at all other depths drift is predominant. As species interactions are essential for structuring microbial communities we further analyzed co-occurrence-based community metrics to assess biogeographic patterns over the transect. These interaction-adjusted indices explained much better variations in microbial community composition as a function of abiotic and biotic variables than compositional or phylogenetic distance measures like Bray–Curtis or UniFrac. Our analyses are important to better understand assembly processes of microbial communities in the upper layers of the largest ocean and how they adapt to effectively perform in global biogeochemical processes. Similar principles presumably act upon microbial community assembly in other ocean basins.Subject terms: Microbial ecology, Microbiology     

The insular herpetofauna of Mexico: Composition,conservation, and biogeographic patterns

We compile a Mexican insular herpetofaunal checklist to estimate endemism, conservation status, island threats, net taxonomic turnover among six biogeographic provinces belonging to the Nearctic and Neotropical regions, and the relationships between island area and mainland distance versus species richness. We compile a checklist of insular herpetofaunal through performing a literature and collection review. We define the conservation status according to conservation Mexican law, the Red List of International Union for Conservation of Nature, and Environmental Vulnerability Scores. We determine threat percentages on islands according to the 11 major classes of threats to biodiversity. We estimate the net taxonomic turnover with beta diversity analysis between the Nearctic and Neotropical provinces. The Mexican insular herpetofauna is composed of 18 amphibian species, 204 species with 101 subspecies of reptiles, and 263 taxa in total. Endemism levels are 11.76% in amphibians, 53.57% in reptiles, and 27.91% being insular endemic taxa. Two conservation status systems classify the species at high extinction risk, while the remaining system suggests less concern. However, all systems indicate species lacking assessment. Human activities and exotic alien species are present on 60% of 131 islands. The taxonomic turnover value is high (0.89), with a clear herpetofaunal differentiation between the two biogeographic regions. The species–area and species–mainland distance relationships are positive. Insular herpetofauna faces a high percentage of threats, with the Neotropical provinces more heavily impacted. It is urgent to explore the remaining islands (3,079 islands) and better incorporate insular populations and species in ecological, evolutionary, and systematic studies. In the face of the biodiversity crisis, islands will play a leading role as a model to apply restoration and conservation strategies.     

Effects of spatial distance and woody plant cover on beta diversity point to dispersal limitation as a driver of community assembly during postfire succession in a Mediterranean shrubland

Beta diversity, and its components of turnover and nestedness, reflects the processes governing community assembly, such as dispersal limitation or biotic interactions, but it is unclear how they operate at the local scale and how their role changes along postfire succession. Here, we analyzed the patterns of beta diversity and its components in a herbaceous plant community after fire, and in relation to dispersal ability, in Central Spain. We calculated multiple‐site beta diversity (β_SOR) and its components of turnover (β_SIM) and nestedness (β_SNE) of all herbaceous plants, or grouped by dispersal syndrome (autochory, anemochory, and zoochory), during the first 3 years after wildfire. We evaluated the relationship between pairwise beta diversity (β_sor), and its components (β_sim, β_sne), and spatial distance or differences in woody plant cover, a proxy of biotic interactions. We found high multiple‐site beta diversity dominated by the turnover component. Community dissimilarity increased with spatial distance, driven mostly by the turnover component. Species with less dispersal ability (i.e., autochory) showed a stronger spatial pattern of dissimilarity. Biotic interactions with woody plants contributed less to community dissimilarity, which tended to occur through the nestedness component. These results suggest that dispersal limitation prevails over biotic interactions with woody plants as a driver of local community assembly, even for species with high dispersal ability. These results contribute to our understanding of postfire community assembly and vegetation dynamics.     

Large frugivores matter more on an island: Insights from island‐mainland comparison of plant–frugivore communities

Endozoochory, a mutualistic interaction between plants and frugivores, is one of the key processes responsible for maintenance of tropical biodiversity. Islands, which have a smaller subset of plants and frugivores when compared with mainland communities, offer an interesting setting to understand the organization of plant–frugivore communities vis‐a‐vis the mainland sites. We examined the relative influence of functional traits and phylogenetic relationships on the plant–seed disperser interactions on an island and a mainland site. The island site allowed us to investigate the organization of the plant–seed disperser community in the natural absence of key frugivore groups (bulbuls and barbets) of Asian tropics. The endemic Narcondam Hornbill was the most abundant frugivore on the island and played a central role in the community. Species strength of frugivores (a measure of relevance of frugivores for plants) was positively associated with their abundance. Among plants, figs had the highest species strength and played a central role in the community. Island‐mainland comparison revealed that the island plant–seed disperser community was more asymmetric, connected, and nested as compared to the mainland community. Neither phylogenetic relationships nor functional traits (after controlling for phylogenetic relationships) were able to explain the patterns of interactions between plants and frugivores on the island or the mainland pointing toward the diffused nature of plant–frugivore interactions. The diffused nature is a likely consequence of plasticity in foraging behavior and trait convergence that contribute to governing the interactions between plants and frugivores. This is one of the few studies to compare the plant–seed disperser communities between a tropical island and mainland and demonstrates key role played by a point‐endemic frugivore in seed dispersal on island.     

Common spatial patterns of trees in various tropical forests: Small trees are associated with increased diversity at small spatial scales

Tropical forests are notable for their high species diversity, even on small spatial scales, and right‐skewed species and size abundance distributions. The role of individual species as drivers of the spatial organization of diversity in these forests has been explained by several hypotheses and processes, for example, stochastic dilution, negative density dependence, or gap dynamics. These processes leave a signature in spatial distribution of small trees, particularly in the vicinity of large trees, likely having stronger effects on their neighbors. We are exploring species diversity patterns within the framework of various diversity‐generating hypotheses using individual species–area relationships. We used the data from three tropical forest plots (Wanang—Papua New Guinea, Barro Colorado Island—Panama, and Sinharaja—Sri Lanka) and included also the saplings (DBH ≥ 1 cm). Resulting cross‐size patterns of species richness and evenness reflect the dynamics of saplings affected by the distribution of large trees. When all individuals with DBH ≥1 cm are included, ~50% of all tree species from the 25‐ or 50‐ha plot can be found within 35 m radius of an individual tree. For all trees, 72%–78% of species were identified as species richness accumulators, having more species present in their surroundings than expected by null models. This pattern was driven by small trees as the analysis of DBH >10 cm trees showed much lower proportion of accumulators, 14%–65% of species identified as richness repellers and had low richness of surrounding small trees. Only 11%–26% of species had lower species evenness than was expected by null models. High proportions of species richness accumulators were probably due to gap dynamics and support Janzen–Connell hypothesis driven by competition or top‐down control by pathogens and herbivores. Observed species diversity patterns show the importance of including small tree size classes in analyses of the spatial organization of diversity.     

Bayesian island biogeography in a continental setting: the Rand Flora case

We here explore the use of a Bayesian approach to island biogeography for disentangling the evolutionary origins of a continental-scale floristic pattern, the enigmatic ‘Rand Flora’. The existence of disjunct distributions across many plant lineages between Macaronesia–northwest Africa, Horn of Africa–southern Arabia and east–south Africa has long intrigued botanists, but only now can we start analysing it within a statistical framework.Phylogenetic and distributional data from 13 plant lineages exhibiting this disjunct distribution were analysed to estimate area carrying capacities and historical rates of biotic exchange between areas. The results indicate that there has been little exchange between southern Africa and the northern African region, and that this exchange occurred via east Africa. Northwest Africa–Macaronesia shows the smallest carrying capacity but highest dispersal rate with other regions, suggesting that its flora was built up by immigration of lineages, probably from the Mediterranean region and western Asia. In contrast, southern Africa shows the highest carrying capacity and lowest dispersal rate, suggesting a flora formed by in situ diversification.We discuss further improvements of the method for addressing more complex hypotheses, such as asymmetric dispersal between regions or repeated cyclical events.     

Phenotypic evolution of dispersal-enhancing traits in insular voles

Evolutionary theory predicts that in metapopulations subject to rapid extinction–recolonization dynamics, natural selection should favour evolution of traits that enhance dispersal and recolonization ability. Metapopulations of field voles (Microtus agrestis) on islands in the Stockholm archipelago, Sweden, are characterized by frequent local extinction and recolonization of subpopulations. Here, we show that voles on the islands were larger and had longer feet than expected for their body size, compared with voles from the mainland; that body size and size-specific foot length increased with increasing geographical isolation and distance from mainland; and that the differences in body size and size-specific foot length were genetically based. These findings provide rare evidence for relatively recent (less than 1000 years) and rapid (corresponding to 100–250 darwins) evolution of traits facilitating dispersal and recolonization in island metapopulations.     

Beyond the continuum: a multi-dimensional phase space for neutral–niche community assembly

Neutral and niche processes are generally considered to interact in natural communities along a continuum, exhibiting community patterns bounded by pure neutral and pure niche processes. The continuum concept uses niche separation, an attribute of the community, to test the hypothesis that communities are bounded by pure niche or pure neutral conditions. It does not accommodate interactions via feedback between processes and the environment. By contrast, we introduce the Community Assembly Phase Space (CAPS), a multi-dimensional space that uses community processes (such as dispersal and niche selection) to define the limiting neutral and niche conditions and to test the continuum hypothesis. We compare the outputs of modelled communities in a heterogeneous landscape, assembled by pure neutral, pure niche and composite processes. Differences in patterns under different combinations of processes in CAPS reveal hidden complexity in neutral–niche community dynamics. The neutral–niche continuum only holds for strong dispersal limitation and niche separation. For weaker dispersal limitation and niche separation, neutral and niche processes amplify each other via feedback with the environment. This generates patterns that lie well beyond those predicted by a continuum. Inferences drawn from patterns about community assembly processes can therefore be misguided when based on the continuum perspective. CAPS also demonstrates the complementary information value of different patterns for inferring community processes and captures the complexity of community assembly. It provides a general tool for studying the processes structuring communities and can be applied to address a range of questions in community and metacommunity ecology.     

Including tree spatial extension in the evaluation of neighborhood competition effects in Bornean rain forest

Classical tree neighborhood models use size variables acting at point distances. In a new approach here, trees were spatially extended as a function of their crown sizes, represented impressionistically as points within crown areas. Extension was accompanied by plasticity in the form of crown removal or relocation under the overlap of taller trees. Root systems were supposedly extended in a similar manner. For the 38 most abundant species in the focal size class (10–<100 cm stem girth) in two 4‐ha plots at Danum (Sabah), for periods P₁ (1986–1996) and P₂ (1996–2007), stem growth rate and tree survival were individually regressed against stem size, and neighborhood conspecific (CON) and heterospecific (HET) basal areas within incremented steps in radius. Model parameters were critically assessed, and statistical robustness in the modeling was set by randomization testing. Classical and extended models differed importantly in their outcomes. Crown extension weakened the relationship of CON effect on growth versus plot species’ abundance, showing that models without plasticity overestimated negative density dependence. A significant negative trend of difference in CON effects on growth (P₂−P₁) versus CON or HET effect on survival in P₁ was strongest with crown extension. Model outcomes did not then support an explanation of CON and HET effects being due to (asymmetric) competition for light alone. An alternative hypothesis is that changes in CON effects on small trees, largely incurred by a drought phase (relaxing light limitation) in P₂, and following the more shaded (suppressing) conditions in P₁, were likely due to species‐specific (symmetric) root competition and mycorrhizal processes. The very high variation in neighborhood composition and abundances led to a strong “neighborhood stochasticity” and hence to largely idiosyncratic species’ responses. A need to much better understand the roles of rooting structure and processes at the individual tree level was highlighted.     

Size-Class Effect Contributes to Tree Species Assembly through Influencing Dispersal in Tropical Forests

We have investigated the processes of community assembly using size classes of trees. Specifically our work examined (1) whether point process models incorporating an effect of size-class produce more realistic summary outcomes than do models without this effect; (2) which of three selected models incorporating, respectively environmental effects, dispersal and the joint-effect of both of these, is most useful in explaining species-area relationships (SARs) and point dispersion patterns. For this evaluation we used tree species data from the 50-ha forest dynamics plot in Barro Colorado Island, Panama and the comparable 20 ha plot at Bubeng, Southwest China. Our results demonstrated that incorporating an size-class effect dramatically improved the SAR estimation at both the plots when the dispersal only model was used. The joint effect model produced similar improvement but only for the 50-ha plot in Panama. The point patterns results were not improved by incorporation of size-class effects using any of the three models. Our results indicate that dispersal is likely to be a key process determining both SARs and point patterns. The environment-only model and joint-effects model were effective at the species level and the community level, respectively. We conclude that it is critical to use multiple summary characteristics when modelling spatial patterns at the species and community levels if a comprehensive understanding of the ecological processes that shape species’ distributions is sought; without this results may have inherent biases. By influencing dispersal, the effect of size-class contributes to species assembly and enhances our understanding of species coexistence.     

Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system

How diversity is structured has been a central goal of microbial ecology. In freshwater ecosystems, selection has been found to be the main driver shaping bacterial communities. However, its relative importance compared with other processes (dispersal, drift, diversification) may depend on spatial heterogeneity and the dispersal rates within a metacommunity. Still, a decrease in the role of selection is expected with increasing dispersal homogenization. Here, we investigate the main ecological processes modulating bacterial assembly in contrasting scenarios of environmental heterogeneity. We carried out a spatiotemporal survey in the floodplain system of the Paraná River. The bacterioplankton metacommunity was studied using both statistical inferences based on phylogenetic and taxa turnover as well as co-occurrence networks. We found that selection was the main process determining community assembly even at both extremes of environmental heterogeneity and homogeneity, challenging the general view that the strength of selection is weakened due to dispersal homogenization. The ecological processes acting on the community also determined the connectedness of bacterial networks associations. Heterogeneous selection promoted more interconnected networks increasing β-diversity. Finally, spatiotemporal heterogeneity was an important factor determining the number and identity of the most highly connected taxa in the system. Integrating all these empirical evidences, we propose a new conceptual model that elucidates how the environmental heterogeneity determines the action of the ecological processes shaping the bacterial metacommunity.Subject terms: Community ecology, Microbial ecology     

Effects of branching spatial structure and life history on the asymptotic growth rate of a population

The dendritic structure of a river network creates directional dispersal and a hierarchical arrangement of habitats. These two features have important consequences for the ecological dynamics of species living within the network. We apply matrix population models to a stage-structured population in a network of habitat patches connected in a dendritic arrangement. By considering a range of life histories and dispersal patterns, both constant in time and seasonal, we illustrate how spatial structure, directional dispersal, survival, and reproduction interact to determine population growth rate and distribution. We investigate the sensitivity of the asymptotic growth rate to the demographic parameters of the model, the system size, and the connections between the patches. Although some general patterns emerge, we find that a species’ modes of reproduction and dispersal are quite important in its response to changes in its life history parameters or in the spatial structure. The framework we use here can be customized to incorporate a wide range of demographic and dispersal scenarios.