Species phylogenetic relatedness, priority effects, and ecosystem functioning

Species immigration history can structure ecological communities through priority effects, which are often mediated by competition. As competition tends to be stronger between species with more similar niches, we hypothesize that species phylogenetic relatedness, under niche conservatism, may be a reasonable surrogate of niche similarity between species, and thus influence the strength of priority effects. We tested this hypothesis using a laboratory microcosm experiment in which we established bacterial species pools with different levels of phylogenetic relatedness and manipulated the immigration history of species from each pool into microcosms. Our results showed that strong priority effects, and hence multiple community states, only emerged for the species pool with the greatest phylogenetic relatedness. Community assembly also resulted in a significant positive relationship between bacterial phylogenetic diversity and ecosystem functions. Interestingly, these results emerged despite a lack of phylogenetic conservatism for most of the bacterial functional traits considered. Our results highlight the utility of phylogenetic information for understanding the structure and functioning of ecological communities, even when phylogenetically conserved functional traits are not identified or measured.     

Life history traits predict relative abundance in an assemblage of forest caterpillars

Species in a given trophic level occur in vastly unequal abundance, a pattern commonly documented but poorly explained for most taxa. Theoretical predictions of species density such as those arising from the metabolic theory of ecology hold well at large spatial and temporal scales but are not supported in many communities sampled at a relatively small scale. At these scales ecological factors may be more important than the inherent limits to energy use set by allometric scaling of mass. These factors include the amount of resources available, and the ability of individuals to convert these resources successfully into population growth. While previous studies have demonstrated the limits of macroecological theory in explaining local abundance, few studies have tested alternative generalized mechanisms determining abundance at the community scale. Using an assemblage of forest moth species found co-occurring as caterpillars on a single host plant species, we tested whether species abundance on that plant could be explained by mass allometry, intrinsic population growth, diet breadth, or some combination of these traits. We parameterized life history traits of the caterpillars in association with the host plant in both field and laboratory settings, so that the population growth estimate was specific to the plant on which abundance was measured. Using a generalized least-squares regression method incorporating phylogenetic relatedness, we found no relationship between abundance and mass but found that abundance was best explained by both intrinsic population growth rate and diet breadth. Species population growth potential was most affected by survivorship and larval development time on the host plant. Metabolic constraints may determine upper limits to local abundance levels for species, but local community abundance is strongly predicted by the potential for population increase and the resources available to that species in the environment.     

The problem and promise of scale dependency in community phylogenetics

The problem of scale dependency is widespread in investigations of ecological communities. Null model investigations of community assembly exemplify the challenges involved because they typically include subjectively defined "regional species pools." The burgeoning field of community phylogenetics appears poised to face similar challenges. Our objective is to quantify the scope of the problem of scale dependency by comparing the phylogenetic structure of assemblages across contrasting geographic and taxonomic scales. We conduct phylogenetic analyses on communities within three tropical forests, and perform a sensitivity analysis with respect to two scaleable inputs: taxonomy and species pool size. We show that (1) estimates of phylogenetic overdispersion within local assemblages depend strongly on the taxonomic makeup of the local assemblage and (2) comparing the phylogenetic structure of a local assemblage to a species pool drawn from increasingly larger geographic scales results in an increased signal of phylogenetic clustering. We argue that, rather than posing a problem, "scale sensitivities" are likely to reveal general patterns of diversity that could help identify critical scales at which local or regional influences gain primacy for the structuring of communities. In this way, community phylogenetics promises to fill an important gap in community ecology and biogeography research.     

Effects of Growth Form and Functional Traits on Response of Woody Plants to Clearing and Fragmentation of Subtropical Rainforest

The conservation implications of large‐scale rainforest clearing and fragmentation on the persistence of functional and taxonomic diversity remain poorly understood. If traits represent adaptive strategies of plant species to particular circumstances, the expectation is that the effect of forest clearing and fragmentation will be affected by species functional traits, particularly those related to dispersal. We used species occurrence data for woody plants in 46 rainforest patches across 75,000 ha largely cleared of forest by the early 1900s to determine the combined effects of area reduction, fragmentation, and patch size on the taxonomic structure and functional diversity of subtropical rainforest. We compiled species trait values for leaf area, seed dry mass, wood density, and maximum height and calculated species niche breadths. Taxonomic structure, trait values (means, ranges), and the functional diversity of assemblages of climbing and free‐standing plants in remnant patches were quantified. Larger rainforest patches had higher species richness. Species in smaller patches were taxonomically less related than species in larger patches. Free‐standing plants had a high percentage of frugivore dispersed seeds; climbers had a high proportion of small wind‐dispersed seeds. Connections between the patchy spatial distribution of free‐standing species, larger seed sizes, and dispersal syndrome were weak. Assemblages of free‐standing plants in patches showed more taxonomic and spatial structuring than climbing plants. Smaller isolated patches retained relatively high functional diversity and similar taxonomic structure to larger tracts of forest despite lower species richness. The response of woody plants to clearing and fragmentation of subtropical rainforest differed between climbers and slow‐growing mature‐phase forest trees but not between climbers and pioneer trees. Quantifying taxonomic structure and functional diversity provides an improved basis for conservation planning and management by elucidating the effects of forest‐area reduction and fragmentation. Efectos de la Forma de Crecimiento y Atributos Funcionales en la Respuesta de Plantas Leñosas al Desmonte y Fragmentación de Bosque Lluvioso Subtropical     

Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism

The tendency for more closely related species to share similar traits and ecological strategies can be explained by their longer shared evolutionary histories and represents phylogenetic conservatism. How strongly species traits co-vary with phylogeny can significantly impact how we analyze cross-species data and can influence our interpretation of assembly rules in the rapidly expanding field of community phylogenetics. Phylogenetic conservatism is typically quantified by analyzing the distribution of species values on the phylogenetic tree that connects them. Many phylogenetic approaches, however, assume a completely sampled phylogeny: while we have good estimates of deeper phylogenetic relationships for many species-rich groups, such as birds and flowering plants, we often lack information on more recent interspecific relationships (i.e., within a genus). A common solution has been to represent these relationships as polytomies on trees using taxonomy as a guide. Here we show that such trees can dramatically inflate estimates of phylogenetic conservatism quantified using S. P. Blomberg et al.'s K statistic. Using simulations, we show that even randomly generated traits can appear to be phylogenetically conserved on poorly resolved trees. We provide a simple rarefaction-based solution that can reliably retrieve unbiased estimates of K, and we illustrate our method using data on first flowering times from Thoreau's woods (Concord, Massachusetts, USA).     

Seasonal polydomy and unicoloniality in a polygynous population of the red wood ant Formica truncorum

Ant colonies may have a single or several reproductive queens (monogyny and polygyny, respectively). In polygynous colonies, colony reproduction may occur by budding, forming multinest, polydomous colonies. In most cases, budding leads to strong genetic structuring within populations, and positive relatedness among nestmates. However, in a few cases, polydomous populations may be unicolonial, with no structuring and intra-nest relatedness approaching zero. We investigated the spatial organisation and genetic structure of a polygynous, polydomous population of Formica truncorum in Finland. F. truncorum shifts nest sites between hibernation and the reproductive season, which raises the following question: are colonies maintained as genetic entities throughout the seasons, or is the population unicolonial throughout the season? Using nest-specific marking and five microsatellite loci, we found a high degree of mixing between individuals of the population, and no evidence for a biologically significant genetic structuring. The nestmate relatedness was also indistinguishable from zero. Taken together, the results show that the population is unicolonial. In addition, we found that the population has undergone a recent bottleneck, suggesting that the entire population may have been founded by a very limited number of females. The precise causes for unicoloniality in this species remain open, but we discuss the potential influence of intra-specific competition, disintegration of recognition cues and the particular hibernation habits of this species.     

Trends over time in tree and seedling phylogenetic diversity indicate regional differences in forest biodiversity change

Changing climate conditions may impact the short-term ability of forest tree species to regenerate in many locations. In the longer term, tree species may be unable to persist in some locations while they become established in new places. Over both time frames, forest tree biodiversity may change in unexpected ways. Using repeated inventory measurements five years apart from more than 7000 forested plots in the eastern United States, we tested three hypotheses: phylogenetic diversity is substantially different from species richness as a measure of biodiversity; forest communities have undergone recent changes in phylogenetic diversity that differ by size class, region, and seed dispersal strategy; and these patterns are consistent with expected early effects of climate change. Specifically, the magnitude of diversity change across broad regions should be greater among seedlings than in trees, should be associated with latitude and elevation, and should be greater among species with high dispersal capacity. Our analyses demonstrated that phylogenetic diversity and species richness are decoupled at small and medium scales and are imperfectly associated at large scales. This suggests that it is appropriate to apply indicators of biodiversity change based on phylogenetic diversity, which account for evolutionary relationships among species and may better represent community functional diversity. Our results also detected broadscale patterns of forest biodiversity change that are consistent with expected early effects of climate change. First, the statistically significant increase over time in seedling diversity in the South suggests that conditions there have become more favorable for the reproduction and dispersal of a wider variety of species, whereas the significant decrease in northern seedling diversity indicates that northern conditions have become less favorable. Second, we found weak correlations between seedling diversity change and latitude in both zones, with stronger relationships apparent in some ecoregions. Finally, we detected broadscale seedling diversity increases among species with longer-distance dispersal capacity, even in the northern zone, where overall seedling diversity declined. The statistical power and geographic extent of such analyses will increase as data become available over larger areas and as plot measurements are repeated at regular intervals over a longer period of time.     

Spatial location dominates over host plant genotype in structuring an herbivore community

Recent work has shown a potential role for both host plant genotype and spatial context in structuring insect communities. In this study, we use three separate data sets on herbivorous insects on oak (Quercus robur) to estimate the relative effects of host plant genotype (G), location (E), and the G x E interaction on herbivore community structure: a common garden experiment replicated at the landscape scale (approximately 5 km2); two common gardens separated at the regional scale (approximately 10 000 km2); and survey data on wild trees in various spatial settings. Our experiments and survey reveal that, at the landscape scale, the insect community is strongly affected by the spatial setting, with 32% of the variation in species richness explained by spatial connectivity. In contrast, G and G x E play minor roles in structuring the insect community. Results remained similar when extending the spatial scale of the study from the more local (landscape) level to the regional level. We conclude that in our study system, spatial processes play a major role in structuring these insect communities at both the landscape and regional scales, whereas host plant genotype seems of secondary importance.     

Vulnerability and Resilience of Tropical Forest Species to Land‐Use Change

Abstract: We provide a cross‐taxon and historical analysis of what makes tropical forest species vulnerable to extinction. Several traits have been important for species survival in the recent and distant geological past, including seed dormancy and vegetative growth in plants, small body size in mammals, and vagility in insects. For major past catastrophes, such as the five mass extinction events, large range size and vagility or dispersal were key to species survival. Traits that make some species more vulnerable to extinction are consistent across time scales. Terrestrial organisms, particularly animals, are more extinction prone than marine organisms. Plants that persist through dramatic changes often reproduce vegetatively and possess mechanisms of die back. Synergistic interactions between current anthropogenic threats, such as logging, fire, hunting, pests and diseases, and climate change are frequent. Rising temperatures threaten all organisms, perhaps particularly tropical organisms adapted to small temperature ranges and isolated by distance from suitable future climates. Mutualist species and trophic specialists may also be more threatened because of such range‐shift gaps. Phylogenetically specialized groups may be collectively more prone to extinction than generalists. Characterization of tropical forest species’ vulnerability to anthropogenic change is constrained by complex interactions among threats and by both taxonomic and ecological impediments, including gross undersampling of biotas and poor understanding of the spatial patterns of taxa at all scales.     

Phylogeny, niches, and relative abundance in natural communities

Community structure refers to the number of species in a community and the pattern of distribution of individuals among those species. We use a novel way of representing community structure to show that abundance within closely related pairs of co-occurring tree species in a highly diverse Mexican forest is more equitable than is abundance within more distantly related pairs. This observation is at odds with the fundamental assumption of neutral models of community structure, i.e., that species are interchangeable. The observed patterns suggest niche apportionment, in which interaction is focused pairwise between congeners but falls away from the phylogenetic structure above the genus level. Thus niche processes may significantly affect community structure through regulating relative abundance in a substantial proportion of species, which in turn potentially enhances community stability. One such mechanism of stable coexistence has already been shown to be active in this forest.     

A tree and climate assessment tool for modelling ecosystem response to climate change

Understanding how vulnerable forest ecosystems are to climate change is a key requirement if sustainable forest management is to be achieved. Modelling the response of species in their regeneration niche to phenological and biophysical processes that are directly influenced by climate is one method for achieving this understanding. A model was developed to investigate species resilience and vulnerability to climate change within its fundamental-regeneration niche. The utility of the developed model, tree and climate assessment (TACA), was tested within the interior Douglas-fir ecosystem in south-central British Columbia. TACA modelled the current potential tree species composition of the ecosystem with high accuracy and modelled significant responses amongst tree species to climate change. The response of individual species suggests that the studied ecosystem could transition to a new ecosystem over the next 100 years. TACA showed that it can be an effective tool for identifying species resilience and vulnerability to changes in climate within the most sensitive stage of development, the regeneration phase. The TACA model was able to identify the degree of change in phenological and biophysical variables that control tree establishment, growth and persistence. The response to changes in one or more of these variables resulted in changes in the climatic suitability of the ecosystem for species and enabled a measure of vulnerability to be quantified. TACA could be useful to forest managers as a decision support tool for adaptation actions and by researchers interested in modelling stand dynamics under climate change.     

Allometric scaling predicts preferences for burned patches in a guild of East African grazers

The high herbivore diversity in savanna systems has been attributed to the inherent spatial and temporal heterogeneity related to the quantity and quality of food resources. Allometric scaling predicts that smaller-bodied grazers rely on higher quality forage than larger-bodied grazers. We replicated burns at varying scales in an East African savanna and measured visitation by an entire guild of larger grazers ranging in size from hare to elephant. We found a strong negative relationship between burn preference and body mass with foregut fermenters preferring burns to a greater degree than hindgut fermenters. Burns with higher quality forage were preferred more than burns with lower quality forage by small-bodied grazers, while the opposite was true for large-bodied grazers. Our results represent some of the first experimental evidence demonstrating the importance of body size in predicting how large herbivores respond to fire-induced changes in plant quality and quantity.     

Effect of scale on trait predictors of species responses to agriculture

Species persistence in human‐altered landscapes can depend on factors operating at multiple spatial scales. To understand anthropogenic impacts on biodiversity, it is useful to examine relationships between species traits and their responses to land‐use change. A key knowledge gap concerns whether these relationships vary depending on the scale of response under consideration. We examined how local‐ and large‐scale habitat variables influence the occupancy dynamics of a bird community in cloud forest zones in the Colombian Chocó‐Andes. Using data collected across a continuum of forest and agriculture, we examined which traits best predict species responses to local variation in farmland and which traits best predict species responses to isolation from contiguous forest. Global range size was a strong predictor of species responses to agriculture at both scales; widespread species were less likely to decline as local habitat cover decreased and as distance from forest increased. Habitat specialization was a strong predictor of species responses only at the local scale. Open‐habitat species were particularly likely to increase as pasture increased, but they were relatively insensitive to variation in distance to forest. Foraging plasticity and flocking behavior were strong predictors of species responses to distance from forest, but not their responses to local habitat. Species with lower plasticity in foraging behaviors and obligate flock‐following species were more likely to decline as distance from contiguous forest increased. For species exhibiting these latter traits, persistence in tropical landscapes may depend on the protection of larger contiguous blocks of forest, rather than the integration of smaller‐scale woodland areas within farmland. Species listed as threatened or near threatened on the International Union for Conservation of Nature Red List were also more likely to decline in response to both local habitat quality and isolation from forest relative to least‐concern species, underlining the importance of contiguous forests for threatened taxa.     

Spatial predictions of phylogenetic diversity in conservation decision making

Considering genetic relatedness among species has long been argued as an important step toward measuring biological diversity more accurately, rather than relying solely on species richness. Some researchers have correlated measures of phylogenetic diversity and species richness across a series of sites and suggest that values of phylogenetic diversity do not differ enough from those of species richness to justify their inclusion in conservation planning. We compared predictions of species richness and 10 measures of phylogenetic diversity by creating distribution models for 168 individual species of a species-rich plant family, the Cape Proteaceae. When we used average amounts of land set aside for conservation to compare areas selected on the basis of species richness with areas selected on the basis of phylogenetic diversity, correlations between species richness and different measures of phylogenetic diversity varied considerably. Correlations between species richness and measures that were based on the length of phylogenetic tree branches and tree shape were weaker than those that were based on tree shape alone. Elevation explained up to 31% of the segregation of species rich versus phylogenetically rich areas. Given these results, the increased availability of molecular data, and the known ecological effect of phylogenetically rich communities, consideration of phylogenetic diversity in conservation decision making may be feasible and informative.     

Scaling range sizes to threats for robust predictions of risks to biodiversity

Assessments of risk to biodiversity often rely on spatial distributions of species and ecosystems. Range‐size metrics used extensively in these assessments, such as area of occupancy (AOO), are sensitive to measurement scale, prompting proposals to measure them at finer scales or at different scales based on the shape of the distribution or ecological characteristics of the biota. Despite its dominant role in red‐list assessments for decades, appropriate spatial scales of AOO for predicting risks of species’ extinction or ecosystem collapse remain untested and contentious. There are no quantitative evaluations of the scale‐sensitivity of AOO as a predictor of risks, the relationship between optimal AOO scale and threat scale, or the effect of grid uncertainty. We used stochastic simulation models to explore risks to ecosystems and species with clustered, dispersed, and linear distribution patterns subject to regimes of threat events with different frequency and spatial extent. Area of occupancy was an accurate predictor of risk (0.81<|r|<0.98) and performed optimally when measured with grid cells 0.1–1.0 times the largest plausible area threatened by an event. Contrary to previous assertions, estimates of AOO at these relatively coarse scales were better predictors of risk than finer‐scale estimates of AOO (e.g., when measurement cells are <1% of the area of the largest threat). The optimal scale depended on the spatial scales of threats more than the shape or size of biotic distributions. Although we found appreciable potential for grid‐measurement errors, current IUCN guidelines for estimating AOO neutralize geometric uncertainty and incorporate effective scaling procedures for assessing risks posed by landscape‐scale threats to species and ecosystems.     

The probabilistic niche model reveals substantial variation in the niche structure of empirical food webs

The structure of food webs, complex networks of interspecies feeding interactions, plays a crucial role in ecosystem resilience and function, and understanding food web structure remains a central problem in ecology. Previous studies have shown that key features of empirical food webs can be reproduced by low-dimensional "niche" models. Here we examine the form and variability of food web niche structure by fitting a probabilistic niche model to 37 empirical food webs, a much larger number of food webs than used in previous studies. The model relaxes previous assumptions about parameter distributions and hierarchy and returns parameter estimates for each species in each web. The model significantly outperforms previous niche model variants and also performs well for several webs where a body-size-based niche model performs poorly, implying that traits other than body size are important in structuring these webs' niche space. Parameter estimates frequently violate previous models' assumptions: in 19 of 37 webs, parameter values are not significantly hierarchical, 32 of 37 webs have nonuniform niche value distributions, and 15 of 37 webs lack a correlation between niche width and niche position. Extending the model to a two-dimensional niche space yields networks with a mixture of one- and two-dimensional niches and provides a significantly better fit for webs with a large number of species and links. These results confirm that food webs are strongly niche-structured but reveal substantial variation in the form of the niche structuring, a result with fundamental implications for ecosystem resilience and function.     

Climatic niche divergence or conservatism? Environmental niches and range limits in ecologically similar damselflies

The factors that determine species' range limits are of central interest to biologists. One particularly interesting group comprises odonates (dragonflies and damselflies), which show large differences in secondary sexual traits and respond quickly to climatic factors, but often have minor interspecific niche differences, challenging models of niche-based species coexistence. We quantified the environmental niches at two geographic scales to understand the ecological causes of northern range limits and the coexistence of two congeneric damselflies (Calopteryx splendens and C. virgo). Using environmental niche modeling, we quantified niche divergence first across the whole geographic range in Fennoscandia, and second only in the sympatric part of this range. We found evidence for interspecific divergence along the environmental axes of temperature and precipitation across the northern range in Fennoscandia, suggesting that adaptation to colder and wetter climate might have allowed C. virgo to expand farther north than C. splendens. However, in the sympatric zone in southern Fennoscandia we found only negligible and nonsignificant niche differences. Minor niche differences in sympatry lead to frequent encounters and intense interspecific sexual interactions at the local scale of populations. Nevertheless, niche differences across Fennoscandia suggest that species differences in physiological tolerances limit range expansions northward, and that current and future climate could have large effects on the distributional ranges of these and ecologically similar insects.     

Leaf herbivory and decomposability in a Malaysian tropical rain forest

There is accumulating evidence that similar suites of plant traits may affect leaf palatability and leaf litter decomposability. However, the possible association between leaf herbivory and litter decomposition rates across species in species-diverse natural ecosystems such as tropical rain forests remains unexplored, despite its importance in estimating the herbivory effects on carbon and nutrient cycling of ecosystems. We found no strong association between leaf herbivory and litter decomposition rates across 40 tree species in a Malaysian tropical rain forest, even though the leaf and litter traits were tightly correlated. This is because the leaf and litter traits related to herbivory and decomposition rates in the field were inconsistent. Leaf toughness accounted for only a small part of the variation in the herbivory rate, whereas a number of litter traits (the leaf mass per area, lignin to nitrogen ratio, and condensed tannin concentration) accurately predicted the decomposition rate across species. These results suggest that herbivory rate across species may not be strongly related to single leaf traits, probably because plant-herbivore interactions in tropical rain forests are highly diverse; on the other hand, plant-decomposer interactions are less specific and can be governed by litter chemicals. We also investigated two factors, phylogeny and tree functional types, that could affect the relationship between herbivory and decomposition across species. Phylogenetic relatedness among the species did not affect the relationship between herbivory and decomposition. In contrast, when the plants were segregated according to their leaf emergence pattern, we found a significant positive relationship between herbivory and decomposition rates for continuous-leafing species. In these species, the condensed tannin to N ratios in leaves and litter were related to herbivory and decomposition rates, respectively. However, we did not observe a similar trend for synchronous-leafing species. These results suggest that the relationship between herbivory and decomposition may be more greatly affected by functional types than by phylogenetic relatedness among species. In conclusion, our results suggest that well-defended leaves are not necessarily less decomposable litter in a tropical rain forest community, implying that herbivory may not generate positive feedback for carbon and nutrient cycling in this type of ecosystem.     

Neighborhood and community interactions determine the spatial pattern of tropical tree seedling survival

Factors affecting survival and recruitment of 3531 individually mapped seedlings of Myristicaceae were examined over three years in a highly diverse neotropical rain forest, at spatial scales of 1-9 m and 25 ha. We found convincing evidence of a community compensatory trend (CCT) in seedling survival (i.e., more abundant species had higher seedling mortality at the 25-ha scale), which suggests that density-dependent mortality may contribute to the spatial dynamics of seedling recruitment. Unlike previous studies, we demonstrate that the CCT was not caused by differences in microhabitat preferences or life history strategy among the study species. In local neighborhood analyses, the spatial autocorrelation of seedling survival was important at small spatial scales (1-5 m) but decayed rapidly with increasing distance. Relative seedling height had the greatest effect on seedling survival. Conspecific seedling density had a more negative effect on survival than heterospecific seedling density and was stronger and extended farther in rare species than in common species. Taken together, the CCT and neighborhood analyses suggest that seedling mortality is coupled more strongly to the landscape-scale abundance of conspecific large trees in common species and the local density of conspecific seedlings in rare species. We conclude that negative density dependence could promote species coexistence in this rain forest community but that the scale dependence of interactions differs between rare and common species.