Does plant species co-occurrence influence soil mite diversity?

Few studies have considered whether plant taxa can be used as predictors of belowground faunal diversity in natural ecosystems. We examined soil mite (Acari) diversity beneath six grass species at the Konza Prairie Biological Station, Kansas, USA. We tested the hypotheses that soil mite species richness, abundance, and taxonomic diversity are greater (1) beneath grasses in dicultures (different species) compared to monocultures (same species), (2) beneath grasses of higher resource quality (lower C:N) compared to lower resource quality, and (3) beneath heterogeneous mixes of grasses (C3 and C4 grasses growing together) compared to homogeneous mixes (C3 or C4 grasses) using natural occurrences of plant species as treatments. This study is the first to examine the interaction between above- and belowground diversity in a natural setting with species-level resolution of a hyper-diverse taxon. Our results indicate that grasses in diculture supported a more species and phylogenetically rich soil mite fauna than was observed for monocultures and that this relationship was significant at depth but not in the upper soil horizon. We noted that mite species richness was not linearly related to grass species richness, which suggests that simple extrapolations of soil faunal diversity based on plant species inventories may underestimate the richness of associated soil mite communities. The distribution of mite size classes in dicultures was considerably different than those for monocultures. There was no difference in soil mite richness between grass combinations of differing resource quality, or resource heterogeneity.     

Modeling mammal response to fire based on species’ traits

Fire has shaped ecological communities worldwide for millennia, but impacts of fire on individual species are often poorly understood. We performed a meta-analysis to predict which traits, habitat, or study variables and fire characteristics affect how mammal species respond to fire. We modeled effect sizes of measures of population abundance or occupancy as a function of various combinations of these traits and variables with phylogenetic least squares regression. Nine of 115 modeled species (7.83%) returned statistically significant effect sizes, suggesting most mammals are resilient to fire. The top-ranked model predicted a negative impact of fire on species with lower reproductive rates, regardless of fire type (estimate = –0.68), a positive impact of burrowing in prescribed fires (estimate = 1.46) but not wildfires, and a positive impact of average fire return interval for wildfires (estimate = 0.93) but not prescribed fires. If a species’ International Union for Conservation of Nature Red List assessment includes fire as a known or possible threat, the species was predicted to respond negatively to wildfire relative to prescribed fire (estimate = –2.84). These findings provide evidence of experts’ abilities to predict whether fire is a threat to a mammal species and the ability of managers to meet the needs of fire-threatened species through prescribed fire. Where empirical data are lacking, our methods provide a basis for predicting mammal responses to fire and thus can guide conservation actions or interventions in species or communities.     

Highly dynamic fission–fusion species can exhibit leadership when traveling

Leadership by specific individuals is thought to enhance the fitness of followers by allowing them to take advantage of the knowledge or skills of key individuals. In general, consistent leadership is expected to occur primarily in stable groups of related individuals where the benefits enhance the inclusive fitness of a leader. Societies with less stability in group composition (i.e., fission–fusion groups) are less likely to feature unshared decision making. However, in situations where frequent interactions among individuals occur (e.g., small population size and small range of movement) and/or the complexity of the environment requires substantial experience and knowledge, consistent leadership might be expected. We tested if a highly dynamic fission–fusion population of bottlenose dolphins (Tursiops truncatus), inhabiting a complex environment, exhibited leadership when traveling. A small number of specific individuals led group travel more often than expected by chance, and were more likely to initiate successful direction changes of groups than following individuals. The number of leaders in a group remained relatively constant across a wide range of group sizes and was not affected by the number of potential leaders (i.e., those that had led previously) present in the group. Together, these results suggest that leadership can occur in species with high rates of group fission and fusion. Therefore, the loss of key individuals could have disproportionate effects on population dynamics.     

Are ecological groups of species optimal for forest dynamics modelling?

The huge diversity of tree species in tropical rain-forests makes the modelling of its dynamics a difficult task. One-way to deal with it is to define species groups. A classical approach for building species groups consists in grouping species with nearby characteristics, using cluster analysis. A group of species is then characterized by the same list of attributes as a single species, and it is incorporated in the model of forest dynamics in the same way as a single species. In this paper, a new approach for building species group is proposed. It relies on the discrepancy between model predictions when all species are considered separately, and model predictions when species groups are used. An aggregation error that quantifies the bias in model predictions that results from species grouping is thus defined. We then define the optimal species grouping as the one that minimizes the aggregation error. Using data from a tropical rain-forest in French Guiana and a toy model of forest dynamics, this new method for species grouping is confronted to the classical method based on cluster analysis of the species characteristics, and to a combined method based on a cluster analysis that uses the aggregation error as a dissimilarity between species. The optimal species grouping is quite different from the classical species grouping. The ecological interpretation of the optimal groups is difficult, as there is no direct linkage between the species characteristics and the way that they are grouped. The combined approach yields species groups that are closed to the optimal ones, with much less computations. The optimal species groups are thus specific to the model of forest dynamics and lack the generality of those of the classical method, that in turn are not optimal.     

Does the self-similar species distribution model lead to unrealistic predictions?

J. Harte et al. demonstrated that the power law form of the species-area relationship may be derived from a bisected, self-similar landscape and a community-level probability rule. Harte's self-similarity model has been widely applied in modeling species distributions. However, R. D. Maddux showed that this self-similarity model generates biologically unrealistic predictions. We resolve the Harte-Maddux debate by demonstrating that the problems identified by Maddux result from an assumption that the probability of occurrence of a species at one scale is independent of its probability of occurrence at the next. We refer to this as a "non-heritage assumption." By altering this assumption to one in which each species in the community has an occupancy status that is partially inherited across scales (a scale-heritage assumption), the predictions of the self-similarity model are neither mathematically inconsistent nor biologically unrealistic. Harte's self-similarity model remains an important framework for modeling species distributions. Our results illustrate the importance of considering patterns of species co-occurrence, and the way in which species occupancy patterns change with scale, when modeling species distributions.     

Consumer resource matching in urbanizing landscapes: are synanthropic species over-matching?

Population responses of synanthropic species to urbanization may be explained by the resource-matching rule, which postulates that individuals should distribute themselves according to resource availability. According to the resource-matching rule, urban habitats will contain greater densities if they provide better resources than rural habitats. However, because resource availability is density dependent, individuals in urban areas would ultimately achieve fitness levels comparable to, but no better than, individuals in less urban areas. Some ecologists suggest that synanthropic birds may not conform to the resource-matching rule and may instead overmatch (i.e., overexploit) in urban habitats, ultimately leading to lower fitness despite greater resource levels. Using the Northern Cardinal (Cardinalis cardinalis) as a focal species, we evaluated if Cardinal populations in urban and rural habitats were consistent with predictions of consumer resource matching. During 2003-2006 we documented population density, adult body condition, apparent survival, and annual reproductive productivity of Cardinals in riparian forest stands within urban (n = 8 stands) and rural (n = 6 stands) landscapes in Ohio, USA. Density of Cardinals in urban forests was four times that found in more rural forests. Mark-resight data from 147 males and 125 females over four years indicated that apparent survival rates were similar between urban and rural landscapes (phi = 0.64, SE = 0.039 for males and phi = 0.57, SE = 0.04 for females). Similarly, body condition indices of 168 males, 142 females, and 118 nestlings did not differ significantly between landscapes. Annual reproductive productivity (mean number of fledglings per pair over breeding season) of 294 pairs was comparable for urban (2.4 +/- 0.18 [mean +/- SE] and rural (2.1 +/- 0.18) young birds. Thus, contrary to recent suggestions, we find that high densities of certain synanthropic species in urban landscapes are consistent with expectations of consumer resource matching.     

Does local competition increase the coexistence of species in intransitive networks?

Competitive intransitivity, a situation in which species' competitive ranks cannot be listed in a strict hierarchy, promotes species coexistence through "enemy's enemy indirect facilitation." Theory suggests that intransitivity-mediated coexistence is enhanced when competitive interactions occur at local spatial scales, although this hypothesis has not been thoroughly tested. Here, we use a lattice model to investigate the effect of local vs. global competition on intransitivity-mediated coexistence across a range of species richness values and levels of intransitivity. Our simulations show that local competition can enhance intransitivity-mediated coexistence in the short-term, yet hinder it in the long-term, when compared to global competition. This occurs because local competition slows species disaggregation, allowing weaker competitors to persist longer in the shifting spatial refuges of intransitive networks, enhancing short-term coexistence. Conversely, our simulations show that, in the long-term, local competition traps disaggregated species in unfavorable areas of the competitive arena, where they are excluded by superior competitors. As a result, in the long-term, global intransitive competition allows a greater number of species to coexist than local intransitive competition.     

Can spatial isolation help predict dispersal-limited sites for native species restoration?

When the distribution of species is limited by propagule supply, new populations may be initiated by seed addition, but identifying suitable sites for efficiently targeted seed addition remains a major challenge for restoration. In addition to the biotic or abiotic variables typically used in species distribution models, spatial isolation from conspecifics could help predict the suitability of unoccupied sites. Site suitability might be expected to increase with spatial isolation after other factors are accounted for, since isolation increases the chance that a site is unoccupied only because of propagule limitation. For two native annual forbs in Californian grasslands, we combined experimental seeding and niche modeling to ask whether suitability of unoccupied sites could be predicted by spatial variables (either distances from, or densities of, conspecific populations), either by themselves or in combination with niche models. We also asked whether experimental tests of these predictions held up not only in the short term (one year), but also in the longer term (three years). For Lasthenia californica, seed additions were only successful relatively near existing populations. For Lupinus nanus, seeding success was low and was positively related to the number of conspecifics within 1 km. For both species, a few previously unoccupied sites remained occupied three years after seeding, but this subset was not predictable based on either spatial or niche variables. Seed addition alone may be a limited means of native forb restoration if suitable unoccupied sites are either rare or unpredictable, or if they tend to be close to where the species already occurs.     

Can entropy maximization use functional traits to explain species abundances? A comprehensive evaluation

Entropy maximization (EM) is a method that can link functional traits and community composition by predicting relative abundances of each species in a community using limited trait information. We developed a complementary suite of tests to examine the strengths and limitations of EM and the community-aggregated traits (CATs; i.e., weighted averages) on which it depends that can be applied to virtually any plant community data set. We show that suites of CATs can be used to differentiate communities and that EM can address the classic problem of characterizing ecological niches by quantifying constraints (CATs) on complex trait relationships in local communities. EM outperformed null models and comparable regression models in communities with different levels of dominance, diversity, and trait similarity. EM predicted well the abundance of the dominant species that drive community-level traits; it typically identified rarer species as such, although it struggled to predict the abundances of the rarest species in some cases. Predictions were sensitive to choice of traits, were substantially improved by using informative priors based on null models, and were robust to variation in trait measurement due to intraspecific variability or measurement error. We demonstrate how similarity in species' traits confounds predictions and provide guidelines for applying EM.     

Is spread of invasive species regulated? Using ecological theory to interpret statistical analysis

We investigate a recent proposal that invasive species display patterns of spatial "spread regulation" analogous to density-dependent regulation of population abundances. While invasive species do offer valuable tests of ecological theories about spatial spread, we argue that the statistical approach used in the study is not useful, and that the proposed definition of "spread regulation" is likely to be confusing. While concepts of negative feedbacks in spatial spread may be reasonable, the proposed definition of "spread regulation" encompasses accelerating, constant, or decelerating spread. There is no compelling biological or practical reason to adopt such a definition. Moreover, we show that the statistical patterns (from time series of ratios of newly to recently invaded sites) proposed as evidence of spread regulation are predictable from basic diffusion models or other common models of constant spread with some stochasticity in dynamics and/or observations. Because such a wide range of processes would generate the observed patterns, no clear biological conclusions emerge from the proposed approach to spread analysis. When regarded in the context of the impacts and management of invasive species, the proposed regulation concept has the potential to create costly misunderstandings.     

Optimization of capture–recapture monitoring of elusive species illustrated with a threatened grasshopper

Information on population sizes and trends of threatened species is essential for their conservation, but obtaining reliable estimates can be challenging. We devised a method to improve the precision of estimates of population size obtained from capture–recapture studies for species with low capture and recapture probabilities and short seasonal activity, illustrated with population data of an elusive grasshopper (Prionotropis rhodanica). We used data from 5 capture–recapture studies to identify methodological and environmental factors affecting capture and recapture probabilities and estimates of population size. In a simulation, we used the population size and capture and recapture probability estimates obtained from the field studies to identify the minimum number of sampling occasions needed to obtain unbiased and robust estimates of population size. Based on these results we optimized the capture–recapture design, implemented it in 2 additional studies, and compared their precision with those of the nonoptimized studies. Additionally, we simulated scenarios based on thresholds of population size in criteria C and D of the International Union for Conservation of Nature (IUCN) Red List to investigate whether estimates of population size for elusive species can reliably inform red-list assessments. Identifying parameters that affect capture and recapture probabilities (for the grasshopper time since emergence of first adults) and optimizing field protocols based on this information reduced study effort (−6% to −27% sampling occasions) and provided more precise estimates of population size (reduced coefficient of variation) compared with nonoptimized studies. Estimates of population size from the scenarios based on the IUCN thresholds were mostly unbiased and robust (only the combination of very small populations and little study effort produced unreliable estimates), suggesting capture–recapture can be considered reliable for informing red-list assessments. Although capture–recapture remains difficult and costly for elusive species, our optimization procedure can help determine efficient protocols to increase data quality and minimize monitoring effort.     

Does including physiology improve species distribution model predictions of responses to recent climate change?

Thermal constraints on development are often invoked to predict insect distributions. These constraints tend to be characterized in species distribution models (SDMs) by calculating development time based on a constant lower development temperature (LDT). Here, we assessed whether species-specific estimates of LDT based on laboratory experiments can improve the ability of SDMs to predict the distribution shifts of six U.K. butterflies in response to recent climate warming. We find that species-specific and constant (5 degrees C) LDT degree-day models perform similarly at predicting distributions during the period of 1970-1982. However, when the models for the 1970-1982 period are projected to predict distributions in 1995-1999 and 2000-2004, species-specific LDT degree-day models modestly outperform constant LDT degree-day models. Our results suggest that, while including species-specific physiology in correlative models may enhance predictions of species' distribution responses to climate change, more detailed models may be needed to adequately account for interspecific physiological differences.     

Do predators control prey species abundance? An experimental test with brown treesnakes on Guam

The effect of predators on the abundance of prey species is a topic of ongoing debate in ecology; the effect of snake predators on their prey has been less debated, as there exists a general consensus that snakes do not negatively influence the abundance of their prey. However, this viewpoint has not been adequately tested. We quantified the effect of brown treesnake (Boiga irregularis) predation on the abundance and size of lizards on Guam by contrasting lizards in two 1-ha treatment plots of secondary forest from which snakes had been removed and excluded vs. two 1-ha control plots in which snakes were monitored but not removed or excluded. We removed resident snakes from the treatment plots with snake traps and hand capture, and snake immigration into these plots was precluded by electrified snake barriers. Lizards were sampled in all plots quarterly for a year following snake elimination in the treatment plots. Following the completion of this experiment, we used total removal sampling to census lizards on a 100-m2 subsample of each plot. Results of systematic lizard population monitoring before and after snake removal suggest that the abundance of the skink, Carlia ailanpalai, increased substantially and the abundance of two species of gekkonids, Lepidodactylus lugubris and Hemidactylus frenatus, also increased on snake-free plots. No treatment effect was observed for the skink Emoia caeruleocauda. Mean snout-vent length of all lizard species only increased following snake removal in the treatment plots. The general increase in prey density and mean size was unexpected in light of the literature consensus that snakes do not control the abundance of their prey species. Our findings show that, at least where alternate predators are lacking, snakes may indeed affect prey populations.     

Are sea snakes pertinent bio-indicators for coral reefs? a comparison between species and sites

Classical sampling methods often miss important components of coral reef biodiversity, notably organisms that remain sheltered within the coral matrix. Recent studies using sea kraits (sea snakes) as bio-indicators suggest that the guild of predators represented by anguilliform fish (Congridae, Muraenidae, Ophichthidae, henceforth “eels” for simplicity) were far more abundant and diverse than previously suspected. In the current study, eel diversity (similarity and species richness indices) estimated via sea snake sampling (SSS) was compared among six areas of one of the main oceanic biodiversity hotspot of the Pacific Ocean (southwest lagoon of New Caledonia). Based on the eel diversity in the snakes’ diet, the results obtained in six areas, in two snake species, and using different estimates (ANOSIM, Shannon index…) were consistent, suggesting that SSS provided robust information. Analyses also suggested subtle, albeit significant, differences in the eel assemblages among islets. Such spatial differences are discussed in light of local management practices. As SSS is easy to use, cost-effective, and provides the best picture of eel assemblages to date, it can be employed to monitor the eel assemblages in addition to the snakes themselves in many areas of the Indo-Pacific Ocean, thereby providing an index of the top predator biodiversity of many coral reefs.     

Is Syllis gracilis (Polychaeta: Syllidae) a species complex? An allozyme perspective

The genetic relationships between morphologically indistinguishable marine and brackish populations of Syllis gracilis Grube, 1840 (Polychaeta: Syllidae) were studied by means of allozyme electrophoresis. Samples of S. gracilis from marine coastal and brackish-water habitats were examined for variation at 13 presumptive loci. In addition, a sample of the closely related species S. prolifera (Krohn, 1852) was analysed. Five loci were multiallelic in at least one population of S. gracilis and eight loci in S. prolifera. Low to moderate levels of within-population genetic variability were found, with average expected heterozygosity values ranging from H = 0.068 (±0.043 SE) to 0.187 (±0.069 SE) in the populations of S. gracilis; higher values were found in S. prolifera (H = 0.325 ± 0.076). The presence of various private alleles indicated a marked genetic divergence among populations of S. gracilis, with Nei's genetic distances ranging from D = 0.000 to 0.833 and a highly significant F _ST value. Furthermore, evidence for strong genetic heterogeneity between two sympatric marine populations was found. UPGMA cluster analysis and multidimensional scaling pointed out a clear genetic divergence between brackish and marine populations. At least two genetically divergent entities occurred in marine and brackish habitats. This could be due to local adaptation of individuals coming from marine populations to brackish habitats, but more presumably to the occurrence of a species complex within S. gracilis. Received: 6 June 1999 / Accepted: 7 February 2000     

When is a male not a male? Sex recognition and choice in two sex-changing species

For dioecious species, choosing a mate of the same sex can have reproductive costs. For sex-changing animals, however, a lack of sex recognition may not carry a reproductive cost, as pairs that were initially same-sex can become opposite-sex pairs as one partner changes sex. The strength of sex discrimination in sex changers, then, should depend on the duration of mating associations and whether the time of sex change is influenced by social situation (“flexible” sex change). We studied two species of marine snails that change sex from male to female, one with flexible sex change and long-term or permanent mating associations (Crepidula fornicata) and one with short-term pairings and relatively fixed time of sex change (Crepidula convexa), to determine whether either species exhibits sex recognition and whether members of C. convexa show stronger sex discrimination. In laboratory experiments, small males, the choosing animals, were placed with either a male or a female conspecific (no-choice experiments) or given a choice of a male or female (choice experiments). We controlled for shell length in all experiments, as relative size may influence sex change or choice. Males of both species paired more often with females than males, but, as predicted, males of C. convexa showed stronger discrimination: When given a choice, no C. convexa male paired with another male. In contrast, some C. fornicata males always chose other males even when given the choice of a female. These results suggest that sex recognition can be adaptive even for sex changers but demonstrate that the level of sex recognition will depend on other aspects of reproductive behavior.     

Growth rates, seed size, and physiology: do small-seeded species really grow faster?

Relative growth rate (RGR) is currently the most commonly used method for measuring and comparing species' intrinsic growth potential. Comparative studies have, for example, revealed that small-seeded species have higher RGR, leading to the common belief that small-seeded species possess physiological adaptations for rapid growth that would allow them to outgrow large-seeded species, given sufficient time. We show that, because RGR declines as individual plants grow, it is heavily biased by initial size and does not measure the size-corrected growth potential that determines the outcome of competition in the long-term. We develop a daily growth model that includes a simple mechanistic representation of aboveground and belowground growth and its dependency on plant size and environmental factors. Intrinsic growth potential is encapsulated by the size-independent growth coefficient, G. We parameterized the model using repeated-harvest data from 1724 plants of nine species growing in contrasting nutrient and temperature regimes. Using information-theoretic criteria, we found evidence for interspecific differences in only three of nine model parameters: G, aboveground allocation, and frost damage. With other parameters shared between species, the model accurately reproduced above- and belowground biomass trajectories for all nine species in each set of environmental conditions. In contrast to conventional wisdom, the relationship between G and seed size was positive, despite a strong negative correlation between seed size and average RGR, meaning that large-seeded rather than small-seeded species have higher size-corrected growth potential. Further, we found a significant positive correlation between G and frost damage that, according to simulations, causes rank reversals in final biomass under daily temperature changes of +/- 5 degrees C. We recommend the wider use of this new kind of plant growth analysis as a better way of understanding underlying differences in species' physiology; but we recognize that RGR is still a useful metric if considering the potential rate of population increase in empty habitats.     

Nonparametric estimation of Shannon’s index of diversity when there are unseen species in sample

A biological community usually has a large number of species with relatively small abundances. When a random sample of individuals is selected and each individual is classified according to species identity, some rare species may not be discovered. This paper is concerned with the estimation of Shannons index of diversity when the number of species and the species abundances are unknown. The traditional estimator that ignores the missing species underestimates when there is a non-negligible number of unseen species. We provide a different approach based on unequal probability sampling theory because species have different probabilities of being discovered in the sample. No parametric forms are assumed for the species abundances. The proposed estimation procedure combines the Horvitz–Thompson (1952) adjustment for missing species and the concept of sample coverage, which is used to properly estimate the relative abundances of species discovered in the sample. Simulation results show that the proposed estimator works well under various abundance models even when a relatively large fraction of the species is missing. Three real data sets, two from biology and the other one from numismatics, are given for illustration.     

Pyrite-driven reactive oxygen species formation in simulated lung fluid: implications for coal workers’ pneumoconiosis

The origin of coal worker's pneumoconiosis (CWP) has been long debated. A recent epidemiological study shows a correlation between what is essentially the concentration of pyrite within coal and the prevalence of CWP in miners. Hydrogen peroxide and hydroxyl radical, both reactive oxygen species (ROS), form as byproducts of pyrite oxidative dissolution in air-saturated water. Motivated by the possible importance of ROS in the pathogenesis of CWP, we conducted an experimental study to evaluate if ROS form as byproducts in the oxidative dissolution of pyrite in simulated lung fluid (SLF) under biologically applicable conditions and to determine the persistence of pyrite in SLF. While the rate of pyrite oxidative dissolution in SLF is suppressed by 51% when compared to that in air-saturated water, the initial amount of hydrogen peroxide formed as a byproduct in SLF is nearly doubled. Hydroxyl radical is also formed in the experiments with SLF, but at lower concentrations than in the experiments with water. The formation of these ROS indicates that the reaction mechanism for pyrite oxidative dissolution in SLF is no different from that in water. The elevated hydrogen peroxide concentration in SLF suggests that the decomposition, via the Fenton mechanism to hydroxyl radical or with Fe(III) to form water and molecular oxygen, is initially inhibited by the presence of SLF components. On the basis of the oxidative dissolution rate of pyrite measured in this paper, it is calculated that a respirable two micron pyrite particle will take over 3?years to dissolve completely.