Estimating fish swimming metrics and metabolic rates with accelerometers: the influence of sampling frequency

Accelerometry is growing in popularity for remotely measuring fish swimming metrics, but appropriate sampling frequencies for accurately measuring these metrics are not well studied. This research examined the influence of sampling frequency (1–25 Hz) with tri‐axial accelerometer biologgers on estimates of overall dynamic body acceleration (ODBA), tail‐beat frequency, swimming speed and metabolic rate of bonefish Albula vulpes in a swim‐tunnel respirometer and free‐swimming in a wetland mesocosm. In the swim tunnel, sampling frequencies of ≥ 5 Hz were sufficient to establish strong relationships between ODBA, swimming speed and metabolic rate. However, in free‐swimming bonefish, estimates of metabolic rate were more variable below 10 Hz. Sampling frequencies should be at least twice the maximum tail‐beat frequency to estimate this metric effectively, which is generally higher than those required to estimate ODBA, swimming speed and metabolic rate. While optimal sampling frequency probably varies among species due to tail‐beat frequency and swimming style, this study provides a reference point with a medium body‐sized sub‐carangiform teleost fish, enabling researchers to measure these metrics effectively and maximize study duration.     

landscapemetrics: an open‐source R tool to calculate landscape metrics

Quantifying landscape characteristics and linking them to ecological processes is one of the central goals of landscape ecology. Landscape metrics are a widely used tool for the analysis of patch‐based, discrete land‐cover classes. Existing software to calculate landscape metrics has several constraints, such as being limited to a single platform, not being open‐source or involving a complicated integration into large workflows. We present landscapemetrics, an open‐source R package that overcomes many constraints of existing landscape metric software. The package includes an extensive collection of commonly used landscape metrics in a tidy workflow. To facilitate the integration into large workflows, landscapemetrics is based on a well‐established spatial framework in R. This allows pre‐processing of land‐cover maps or further statistical analysis without importing and exporting the data from and to different software environments. Additionally, the package provides many utility functions to visualize, extract, and sample landscape metrics. Lastly, we provide building‐blocks to motivate the development and integration of new metrics in the future. We demonstrate the usage and advantages of landscapemetrics by analysing the influence of different sampling schemes on the estimation of landscape metrics. In so doing, we demonstrate the many advantages of the package, especially its easy integration into large workflows. These new developments should help with the integration of landscape analysis in ecological research, given that ecologists are increasingly using R for the statistical analysis, modelling and visualization of spatial data.     

A guide to phylogenetic metrics for conservation,community ecology and macroecology

The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub‐disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub‐disciplines hampers potential meta‐analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo‐diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo‐diversity metrics based on their mathematical form within these three dimensions and identify ‘anchor’ representatives: for α‐diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.     

Comparative anatomy of internal incubational sacs in cupuladriid bryozoans and the evolution of brooding in free‐living cheilostomes

Numerous gross morphological attributes are shared among unrelated free‐living bryozoans revealing convergent evolution associated with functional demands of living on soft sediments. Here, we show that the reproductive structures across free‐living groups evolved convergently. The most prominent convergent traits are the collective reduction of external brood chambers (ovicells) and the acquisition of internal brooding. Anatomical studies of four species from the cheilostome genera Cupuladria and Discoporella (Cupuladriidae) show that these species incubate their embryos in internal brooding sacs located in the coelom of the maternal nonpolymorphic autozooids. This sac consists of a main chamber and a narrow neck communicating to the vestibulum. The distal wall of the vestibulum possesses a cuticular thickening, which may further isolate the brood cavity. The presence of this character in all four species strongly supports grouping Cupuladria and Discoporella in one taxon. Further evidence suggests that the Cupuladriidae may be nested within the Calloporidae. Based on the structure of brooding organs, two scenarios are proposed to explain the evolution of the internal brooding in cupuladriids. The evolution of brood chambers and their origin in other free‐living cheilostomes is discussed. Unlike the vast majority of Neocheilostomina, almost all free‐living cheilostomes possess nonprominent chambers for embryonic incubation, either endozooidal and immersed ovicells or internal brooding sacs, supporting the idea that internal embryonic incubation is derived. We speculate that prominent skeletal brood chambers are disadvantageous to a free‐living mode of life that demands easy movement through sediment in instable sea‐floor settings. J. Morphol., 2009. © 2009 Wiley‐Liss, Inc.     

Novel summary metrics for insular biotic assemblages based on taxonomy and phylogeny: Biogeographical,palaeogeographical and possible conservational applications

Using the land‐bound vertebrates on the marine islands as model organisms, two metrics are presented that permit quantitative and succinct synopses of the ‘evolutionary maturity’ of the hosted faunal assemblages. In turn, these reflect the geo‐physical settings and geological developments of the substrates. The assemblage lineage‐taxonomy spectrum (ALTS) is based on the constituent lineages’ taxonomic distinctiveness and diversity. Individual lineages within assemblages can in most cases be assigned to one of six categories, LT1?LT6: LT1 is a non‐endemic taxon, whereas LT6 comprises multiple endemic genera from a family that arose elsewhere. If required, the scheme can be expanded: LT9 is an endemic order. The data can then be combined to provide an assemblage spectrum, for example, 00:08:38:30:08:15[ 13 ]. Here, the first six values denote the number of lineages assigned to each category expressed as percentages of the overall total, with the sum of the processed lineages listed as the seventh (in brackets and bold). The ALTS metric highlights efficiently the key features of a marine island's biological assemblage. Notably, the contrast between spectra for suites on geologically and geo‐physically varied island types can be striking, for instance the squamate suite on the young, proximate orogenic margin island of Taiwan is coded 78:16:05:00:00:00[ 37 ] whereas the one on the distantly located, Late Eocene composite terrane island of New Caledonia is 00:11:00:11:33:44[ 9 ]. To overcome the subjectivity that is inherent in assigning supraspecific ranks, an alternative assemblage lineage‐age spectrum (ALAS) is also introduced that makes use of the binary logarithm values of the colonization times of the island lineages (0–2, 2–4, … , 32–64, >64 Ma). It is represented using a seven‐plus‐two‐number code, for instance Madagascar's squamates are 00:06:00:00:19:62:12[ 19 ( 16 )]; most colonizations took place in the Palaeogene (66–23 Ma); there are 19 lineages, but only 16 are presently age‐dated. In addition to marine‐island biogeography studies, the ALTS–ALAS spectrum approach is potentially useful for encapsulating biotas in other sorts of insular setting (e.g. lakes, mountain tops), and for evaluating palaeogeographical models. Furthermore, it may help emphasize the conservation value of an island's faunal assemblage.     

Does habitat fragmentation cause stress in the agile antechinus? A haematological approach

Although the vertebrate stress response is essential for survival, frequent or prolonged stress responses can result in chronic physiological stress, which is associated with a suite of conditions that can impair survivorship and reproductive output. Anthropogenic habitat fragmentation and degradation are potential stressors of free-living vertebrates, and in theory could result in chronic stress. To address this issue, we compared haematological indicators of stress and condition in agile antechinus (Antechinus agilis) populations in 30 forest fragments and 30 undisturbed, continuous forest sites (pseudofragments) in south-eastern Australia over 2 years. In peripheral blood, the total leucocyte count was lower and the neutrophil/lymphocyte ratio and percentage of eosinophils in the total leucocyte population was higher in fragment than pseudofragment populations, indicating that fragment populations were probably experiencing higher levels of stress hormone-mediated and/or parasite infection-related chronic physiological stress. The total erythrocyte count and haematocrit were higher and mean erythrocyte haemoglobin content was lower in fragment than pseudofragment populations. This suggests that fragment populations showed possible signs of regenerative anaemia, a syndrome associated with elevated hypothalamus–pituitary–adrenal axis mediated stress. However, mean erythrocyte volume was also lower in fragments, and red blood cell distribution width did not differ between the study populations, findings which were not consistent with this diagnosis. Whole blood and mean cell haemoglobin concentrations were similar in fragment and pseudofragment populations. We suggest that where anthropogenic activity results in habitat fragmentation and degradation, chronic stress could contribute to a decline in agile antechinus populations. The broader implication is that chronic stress could be both symptomatic of, and contributing to, decline of some vertebrate populations in anthropogenically fragmented and degraded habitats.     

Performance of pairwise shape dissimilarity morphometrics on nonmammalian taxa (Insecta: Neuroptera: Mantispidae)

Morphometric dissimilarity metrics aim to quantify the variation between compared specimens such that inferences about their relatedness and alpha taxonomy can be made. Recently, the technique has developed metrics that purport to quantify shape dissimilarity between specimens—employing the use of least squares regression analysis. These metrics have been well applied by studies in the hominin fossil record with an arguably unsubstantiated backing for the technique. Originally postulated was the log₁₀ se_m metric which subsequently led to the standard error test of the null hypothesis metric. Following this, the standard deviation of logged ratios (S_LR) metric arose as a pairwise dissimilarity metric that constrains the regression to a zero‐intercept, that is, a significant development in the robustness of the technique. This metric was tested on extant primates in order to evaluate its effectiveness alongside the two other metrics. It was shown to be the most reliable for comparisons between specimens of primates, but was unable to discriminate between heterospecific and conspecific comparisons. Arguably, an alternative model organism with which to compare the technique is lacking. This study considers shape dissimilarity metrics with respect to a group of nonmammalian organisms (mantidflies) and tests the metrics against three lines of evidence (morphology, CO1‐DNA, and geographic distribution) that can delimit the species‐level taxonomy for the group. It is shown that the metrics are unable to discriminate between pairwise comparisons of closely related species, resulting in biologically erroneous groupings, and contradicting the groupings derived from morphological, CO1‐DNA, and distributional comparisons. It is thus asserted that the technique is unsuitable for use in alpha taxonomy as an additional line of evidence in mantidflies. It is further supposed that morphometrics in general should be employed with caution in studies of evolutionary history as phylogeny is not the only information contained within morphometric data. J. Morphol. 276:1482–1494, 2015. © 2015 Wiley Periodicals, Inc.     

Detection of ecological change using multiple organism groups: metrics and uncertainty

A number of biological approaches are commonly used to assess the ecological integrity of stream ecosystems. Recently, it is becoming increasingly common to use multiple organism groups in bioassessment. Advocates of the multiple organism approach argue that the use of different organism groups should strengthen inference-based models and ultimately result in lower assessment error, while opponents argue that organism groups often respond similarly to stress implying a high degree of redundancy. Using fish, macroinvertebrate, macrophyte and benthic diatom data, site-specific parameters (e.g., water chemistry and substratum) and catchment variables from European mountain (n = 77) and lowland (n = 85) streams we evaluated the discriminatory power and uncertainty associated with the use of a number of biological metrics commonly used in stream assessment. The primary environmental gradient for both streams types was land use and nutrient enrichment. Secondary and tertiary gradients were related to habitat quality or alterations in hydromorphology. Benthic diatom and macroinvertebrate metrics showed high discriminatory power (R² values often >0.50) and low error (<30%) with the primary (nutrient) gradient, while both fish and macrophyte metrics performed relatively poorly. Conversely, both fish and macrophyte metrics showed higher response (high coefficients of determination) than either benthic diatom or macroinvertebrate metrics to the second (e.g., alteration in habitat/hydromorphology) gradient. However, the discriminatory power and error associated with individual metrics varied markedly, indicating that caution should be exercised when selecting the ‘best’ organism group or metric to monitor stress.     

Range‐constrained co‐occurrence simulation reveals little niche partitioning among rock‐dwelling Montenegrina land snails (Gastropoda: Clausiliidae)

Aim

Taxon co‐occurrence analysis is commonly used in ecology, but it has not been applied to range‐wide distribution data of partly allopatric taxa because existing methods cannot differentiate between distribution‐related effects and taxon interactions. Our first aim was to develop a taxon co‐occurrence analysis method that is also capable of taking into account the effect of species ranges and can handle faunistic records from museum databases or biodiversity inventories. Our second aim was to test the independence of taxon co‐occurrences of rock‐dwelling gastropods at different taxonomic levels, with a special focus on the Clausiliidae subfamily Alopiinae, and in particular the genus Montenegrina.

Location

Balkan Peninsula in south‐eastern Europe (46N–36N, 13.5E–28E).

Methods

We introduced a taxon‐specific metric that characterizes the occurrence probability at a given location. This probability was calculated as a distance‐weighted mean of the taxon's presence and absence records at all sites. We applied corrections to account for the biases introduced by varying sampling intensity in our dataset. Then we used probabilistic null‐models to simulate taxon distributions under the null hypothesis of no taxon interactions and calculated pairwise and cumulated co‐occurrences. Independence of taxon occurrences was tested by comparing observed co‐occurrences to simulated values.

Results

We observed significantly fewer co‐occurrences among species and intra‐generic lineages of Montenegrina than expected under the assumption of no taxon interaction.

Main conclusions

Fewer than expected co‐occurrences among species and intra‐generic clades indicate that species divergence preceded niche partitioning. This suggests a primary role of non‐adaptive processes in the speciation of rock‐dwelling gastropods. The method can account for the effects of distributional constraints in range‐wide datasets, making it suitable for testing ecological, biogeographical, or evolutionary hypotheses where interactions of partly allopatric taxa are in question.     

Meta-analysis reveals impacts of disturbance on reptile and amphibian body condition

Ecosystem disturbance is increasing in extent, severity and frequency across the globe. To date, research has largely focussed on the impacts of disturbance on animal population size, extinction risk and species richness. However, individual responses, such as changes in body condition, can act as more sensitive metrics and may provide early warning signs of reduced fitness and population declines. We conducted the first global systematic review and meta-analysis investigating the impacts of ecosystem disturbance on reptile and amphibian body condition. We collated 384 effect sizes representing 137 species from 133 studies. We tested how disturbance type, species traits, biome and taxon moderate the impacts of disturbance on body condition. We found an overall negative effect of disturbance on herpetofauna body condition (Hedges' g = −0.37, 95% CI: −0.57, −0.18). Disturbance type was an influential predictor of body condition response and all disturbance types had a negative mean effect. Drought, invasive species and agriculture had the largest effects. The impact of disturbance varied in strength and direction across biomes, with the largest negative effects found within Mediterranean and temperate biomes. In contrast, taxon, body size, habitat specialisation and conservation status were not influential predictors of disturbance effects. Our findings reveal the widespread effects of disturbance on herpetofauna body condition and highlight the potential role of individual-level response metrics in enhancing wildlife monitoring. The use of individual response metrics alongside population and community metrics would deepen our understanding of disturbance impacts by revealing both early impacts and chronic effects within affected populations. This could enable early and more informed conservation management.     

Variability in stream macroinvertebrates at multiple spatial scales

1. We intensively sampled 16 western Oregon streams to characterize: (1) the variability in macroinvertebrate assemblages at seven spatial scales; and (2) the change in taxon richness with increasing sampling effort. An analysis of variance (ANOVA) model calculated spatial variance components for taxon richness, total density, percent individuals of Ephemeroptera, Plecoptera and Trichoptera (EPT), percent dominance and Shannon diversity.
2. At the landscape level, ecoregion and among‐streams components dominated variance for most metrics, accounting for 43–72% of total variance. However, ecoregion accounted for very little variance in total density and 36% of the variance was attributable to differences between streams. For other metrics, variance components were more evenly divided between stream and ecoregion effects.
3. Within streams, approximately 70% of variance was associated with unstructured local spatial variation and not associated with habitat type or transect position. The remaining variance was typically split about evenly between habitat and transect. Sample position within a transect (left, centre or right) accounted for virtually none of the variance for any metric.
4. New taxa per stream increased rapidly with sampling effort with the first four to eight Surber samples (500–1000 individuals counted), then increased more gradually. After counting more than 50 samples, new taxa continued to be added in stream reaches that were 80 times as long as their mean wetted width. Thus taxon richness was highly dependent on sampling effort, and comparisons between sites or streams must be normalized for sampling effort.
5. Characterization of spatial variance structure is fundamental to designing sampling programmes where spatial comparisons range from local to regional scales. Differences in metric responses across spatial scales demonstrate the importance of designing sampling strategies and analyses capable of discerning differences at the scale of interest.     

Response of three lotic assemblages to riparian and catchment‐scale land use: implications for designing catchment monitoring programmes

1. Although many studies have focussed on the effects of catchment land use on lotic systems, the importance of broad (catchment) and fine (segment/reach) scale effects on stream assemblages remain poorly understood. 2. Nine biological metrics for macrophytes (498 sites), benthic macroinvertebrates (491) and fish (478) of lowland and mountain streams in four ecoregions of France and Germany were related to catchment and riparian buffer land use using partial Redundancy Analysis and Boosted Regression Trees (BRTs). 3. Lotic fauna was better correlated (mean max., r = 0.450) than flora (r = 0.277) to both scales of land use: the strongest correlations were noted for mountain streams. BRTs revealed strong non‐linear relationships between mountain assemblage metrics and land use. Correlations increased with increasing buffer lengths, suggesting the importance of near‐stream land use on biotic assemblages. 4. Several metrics changed markedly between 10–20% (mountain ecoregions) and 40–45% (lowland) of arable land use, irrespective of the buffer size. At mountain sites with >10% catchment arable land use, metric values differed between sites with <30% and sites with >30% forest in the near‐stream riparian area. 5. These findings support the role of riparian land use in catchment management; however, differences between mountain and lowland ecoregions support the need for ecoregion‐specific management.     

Ecological niche modeling re‐examined: A case study with the Darwin's fox

Many previous studies have attempted to assess ecological niche modeling performance using receiver operating characteristic (ROC) approaches, even though diverse problems with this metric have been pointed out in the literature. We explored different evaluation metrics based on independent testing data using the Darwin's Fox (Lycalopex fulvipes) as a detailed case in point. Six ecological niche models (ENMs; generalized linear models, boosted regression trees, Maxent, GARP, multivariable kernel density estimation, and NicheA) were explored and tested using six evaluation metrics (partial ROC, Akaike information criterion, omission rate, cumulative binomial probability), including two novel metrics to quantify model extrapolation versus interpolation (E‐space index I) and extent of extrapolation versus Jaccard similarity (E‐space index II). Different ENMs showed diverse and mixed performance, depending on the evaluation metric used. Because ENMs performed differently according to the evaluation metric employed, model selection should be based on the data available, assumptions necessary, and the particular research question. The typical ROC AUC evaluation approach should be discontinued when only presence data are available, and evaluations in environmental dimensions should be adopted as part of the toolkit of ENM researchers. Our results suggest that selecting Maxent ENM based solely on previous reports of its performance is a questionable practice. Instead, model comparisons, including diverse algorithms and parameterizations, should be the sine qua non for every study using ecological niche modeling. ENM evaluations should be developed using metrics that assess desired model characteristics instead of single measurement of fit between model and data. The metrics proposed herein that assess model performance in environmental space (i.e., E‐space indices I and II) may complement current methods for ENM evaluation.     

Macroinvertebrate assemblage response to highway crossings in forested wetlands: implications for biological assessment

Despite the mandate of the Clean Water Act to protectthe physical, chemical, and biological integrity ofthe USA's wetlands, the use of biota to assess wetlandcondition has not been well explored. During June,1996, we evaluated the response of macroinvertebrateassemblages to fill-culvert highway crossings in twobottomland forested wetlands in North Carolina. Ourobjective was to apply biological assessment methodsand metrics that have been effectively used in streamsto explore their applicability in forested wetlands.We found significant changes in several metrics as afunction of distance from the highway crossings. Arealand numerical taxon richness increased within at least40 m of highway when compared to control locations.Percent dominant taxon values were lowest within 10 mof the highway. Percent herbivores also increasedsignificantly within at least 40 m of the highway,reflecting the lower % crown closure and associatedshift in primary production from trees to herbaceousmacrophytes and algae. The North Carolina BioticIndex, a metric of tolerance, did not reflectassemblage changes near the highway. Ordination andpermutation tests revealed that assemblage compositionwas significantly different from controls at 10 and 40 mdistances from the highway crossings. In particular,algal grazers such as the mayflies Caenissp.and Callibaetissp. responded positively and thedamselflies Ischnuraspp. and the fingernailclams Sphaeriumspp. responded negatively to thecrossings. Favorable algal and herbaceous detritalresources, greater patchiness and habitat complexity,and overall high tolerance to natural stressorsprobably contributed to the increase in taxon richnessnear the highway. However, significant deviation fromcontrol locations indicated the highway was a sourceof perturbation. Our findings illustrate the potentialutility of macroinvertebrate assemblages for wetlandassessment, but suggest the importance of defining thereference condition as well as the need fordevelopment of metrics for specific classes ofwetlands.     

Euclidean sections of protein conformation space and their implications in dimensionality reduction

Dimensionality reduction is widely used in searching for the intrinsic reaction coordinates for protein conformational changes. We find the dimensionality?reduction methods using the pairwise root?mean?square deviation (RMSD) as the local distance metric face a challenge. We use Isomap as an example to illustrate the problem. We believe that there is an implied assumption for the dimensionality‐reduction approaches that aim to preserve the geometric relations between the objects: both the original space and the reduced space have the same kind of geometry, such as Euclidean geometry vs. Euclidean geometry or spherical geometry vs. spherical geometry. When the protein free energy landscape is mapped onto a 2D plane or 3D space, the reduced space is Euclidean, thus the original space should also be Euclidean. For a protein with N atoms, its conformation space is a subset of the 3N‐dimensional Euclidean space R^3N. We formally define the protein conformation space as the quotient space of R^3N by the equivalence relation of rigid motions. Whether the quotient space is Euclidean or not depends on how it is parameterized. When the pairwise RMSD is employed as the local distance metric, implicit representations are used for the protein conformation space, leading to no direct correspondence to a Euclidean set. We have demonstrated that an explicit Euclidean‐based representation of protein conformation space and the local distance metric associated to it improve the quality of dimensionality reduction in the tetra‐peptide and β‐hairpin systems. Proteins 2014; 82:2585–2596. © 2014 Wiley Periodicals, Inc.     

Global phylogeography of pelagic Polynucleobacter bacteria: Restricted geographic distribution of subgroups,isolation by distance and influence of climate

The free‐living planktonic freshwater bacterium Polynucleobacter necessarius subspecies asymbioticus (> 99% 16S rRNA similarity) represents a taxon with a cosmopolitan distribution and apparently ubiquitous occurrence in lentic freshwater habitats. We tested for intra‐taxon biogeographic patterns by combining cultivation‐independent and cultivation methods. A culture collection of 204 strains isolated from globally distributed freshwater habitats (Arctic to Antarctica) was investigated for phylogeographic patterns based on sequences of two markers, the 16S–23S internal transcribed spacers and the glutamine synthetase gene (glnA). Genetic distance between isolates showed significant geographic distance‐decay patterns for both markers, suggesting that an isolation‐by‐distance mechanism influences the global phylogeography. Furthermore, a couple of subgroups showed restricted geographic distributions. Strains of one subgroup were exclusively obtained from tropical sites on four continents (pantropical subgroup). Cultivation‐independent methods were used to confirm the restricted geographic distributions of two subgroups. The pantropical taxon could be detected in 63% of investigated tropical habitats but not in any of 121 European freshwater samples. Physiological tests indicated that almost all strains of the pantropical subgroup failed to grow at temperatures of 4°C, while strains affiliated with other subgroups showed good growth at this temperature. This suggests that thermal adaptation is involved in phylogeographic structuring of the global Polynucleobacter population.     

The frugivory network properties of a simplified ecosystem: Birds and plants in a Neotropical periurban park

Frugivory networks exhibit a set of properties characterized by a number of network theory‐derived metrics. Their structures often form deterministic patterns that can be explained by the functional roles of interacting species. Although we know lots about how these networks are organized when ecosystems are in a complete, functional condition, we know much less about how incomplete and simplified networks (such as those found in urban and periurban parks) are organized, which features are maintained, which ones are not, and why. In this paper, we examine the properties of a network between frugivorous birds and plants in a small Neotropical periurban park. We found a frugivory network composed of 29 species of birds and 23 of plants. The main roles in this network are played by four species of generalist birds (three resident, one migratory: Myiozetetes similis, Turdus grayi, Chlorospingus flavopectus, and Dumetella carolinensis) and three species of plants (one exotic, two early successional: Phoenix canariensis, Phoradendron sp., and Witheringia stramoniifolia). When compared to reference data from other locations in the Neotropics, species richness is low, one important network‐level metric is maintained (modularity) whereas another one is not (nestedness). Nestedness, a metric associated with network specialists, is a feature this network lacks. Species‐level metrics such as degree, species strength, and module roles, are not maintained. Our work supports modularity as the most pervasive network‐level metric of altered habitats. From a successional point of view, our results suggest that properties revealed by species‐level indices may be developed at a later time, lagging the acquisition of structural elements.     

Temporal response of stream benthic macroinvertebrate communities to the synergistic effects of anthropogenic acidification and natural drought events

1. We evaluated whether the surprisingly weak biological recovery associated with declines in acid deposition were related to drought‐induced re‐acidification of streams. We used test site analysis (TSA) to characterise temporal changes (1995–2003) in the degree and nature of impairments to stream benthic macroinvertebrate (BMI) communities influenced by acid deposition and drought. 2. The BMI communities in four historically impacted test streams were compared with communities in 30 minimally impacted reference streams. Six multivariate (e.g. ordination axes scores) and four traditional (e.g. % Diptera) summary metrics were used to describe BMI communities. Using all metrics simultaneously (i.e. Mahalanobis or generalised distance), the TSA provided a single probability that a test community was impaired. If a test community was significantly impaired, a further analysis was done to identify the metric(s) important in distinguishing the test community from reference condition. 3. Results of the TSAs indicated that the generalised distances between test communities and the reference condition were inversely related to stream water pH (n = 36). The TSAs also indicated ordination metrics based on BMI abundance were important in distinguishing significantly impaired communities from reference conditions. Temporal trends indicated that there has been short‐term recovery of these BMI communities, but that overall improvements have been hampered by acid or metal toxicity associated with drought‐induced re‐acidification of the streams. 4. Our use of a variety of summary metrics to obtain a single statistical test of significance within the context of the reference‐condition approach provided a simple and unambiguous framework for evaluating the biological condition of test sites.     

Phylogenetic community structure metrics and null models: a review with new methods and software

Competitive exclusion and habitat filtering influence community assembly, but ecologists and evolutionary biologists have not reached consensus on how to quantify patterns that would reveal the action of these processes. Currently, at least 22 α‐diversity and 10 β‐diversity metrics of community phylogenetic structure can be combined with nine null models (eight for β‐diversity metrics), providing 278 potentially distinct approaches to test for phylogenetic clustering and overdispersion. Selecting the appropriate approach for a study is daunting. First, we describe similarities among metrics and null models across variance in phylogeny size and shape, species abundance, and species richness. Second, we develop spatially explicit, individual‐based simulations of neutral, competitive exclusion, or habitat filtering community assembly, and quantify the performance (type I and II error rates) of all 278 metric and null model combinations against each assembly process. Many α‐diversity metrics and null models are at least functionally equivalent, reducing the number of truly unique metrics to 12 and the number of unique metric + null model combinations to 72. An even smaller subset of metric and null model combinations showed robust statistical performance. For α‐diversity metrics, phylogenetic diversity and mean nearest taxon distance were best able to detect habitat filtering, while mean pairwise phylogenetic distance‐based metrics were best able to detect competitive exclusion. Overall, β‐diversity metrics tended to have greater power to detect habitat filtering and competitive exclusion than α‐diversity metrics, but had higher type 1 error in some cases. Across both α‐ and β‐diversity metrics, null model selection affected type I error rates more than metric selection. A null model that maintained species richness, and approximately maintained species occurrence frequency and abundance across sites, exhibited low type I and II error rates. This regional null model simulates neutral dispersal of individuals into local communities by sampling from a regional species pool. We introduce a flexible new R package, metricTester, to facilitate robust analyses of method performance.     

Relationship of fish and macroinvertebrate communities in the mid-Atlantic uplands: Implications for integrated assessments

Indices developed for stream bioassessment are typically based on either fish or macroinvertebrate assemblages. These indices consist of metrics which subsume attributes of various species into aggregate measures reflecting community-level ecological responses to disturbance. However, little is known about the relationship between fish and macroinvertebrate metrics, or about how ecological health assessments are affected by assemblage-specific responses to disturbance. We used principal component analysis (PCA) and regression analysis of existing fish (n = 371) and macroinvertebrate (n = 442) stream bioassessment data from a multi-source dataset to determine broad scale, within-assemblage metric patterns, and to examine the intercorrelation of fish and macroinvertebrate metrics (n = 246) and their response to watershed area and land use/land cover gradients. Fish and macroinvertebrate metrics expressed as principal components (PCs) accounted for 72.4 and 85.4% of dataset variance, respectively, with PC-metric patterns reflecting aspects of stream impairment including water and habitat quality. Model components predicting fish metric response differed among fish PCs, with watershed area and macroinvertebrate metric response strongly correlated with the first fish PC, and remaining fish PC models consisting of watershed area, land use, and macroinvertebrate PCs. Correlation between fish and macroinvertebrate PCs, and models relating fish and macroinvertebrate PCs generally explained less variation (13–27%) than metric response models of fish (25–34%) and macroinvertebrates (8–38%) to watershed area and land use/land cover variables. Best-response models integrating fish and macroinvertebrate PCs, watershed area, and land use/land cover variables accounted for the greatest variation in fish PCs (32–50%) across sites. Because fish and macroinvertebrate metrics provide different information on ecological condition, integrated use of information from multiple groups may be appropriate when developing monitoring programs.