Body size and abundance of benthic animals in Mirror Lake, New Hampshire

1. There is a strong negative correlation between body mass and population density for 192 species from the zoobenthos of Mirror Lake, a small, oligotrophic lake. This correlation spans seven—nine orders of magnitude in body mass. 2. The slopes of both the regression and the upper bound on the distribution of data points are significantly shallower than -0.75, the slope that has been suggested to imply that metabolic constraints limit animal abundance. 3. The regressions for individual taxonomic groups (i.e. classes, phyla) do not conform closely to the overall regression line. 4. It is suggested that metabolic constraints on community structure need not be expressed by a slope of -0.75 for regressions (or upper bounds) on body mass—abundance functions.     

An approach to analyzing environmental drivers to shape spatial variations in body-size structure of biofilm-dwelling protozoa during an annual cycle in marine ecosystems

As an inherent trait, body-size structure has been used to summarize functional features of a community instead of taxonomic resolutions due to the high redundancy for bioassessment. In this study, the multivariate approaches were used to determine the environmental drivers to the spatial variation in body-size structure based on an annual dataset of biofilm-dwelling protozoa. Samples were monthly collected at four stations within a gradient of pollution in coastal waters of the Yellow Sea, northern China during a 1-year cycle. The second-stage (2STAGE) clustering and ordination analyses demonstrated that the annual patterns were significantly different among four sampling stations. Mantel analysis showed the spatial variations in body-size structures of the protozoa were significantly correlated with the water quality status along the pollution gradient. Best matching analysis revealed that the potential environmental drivers to shape the spatial difference in body-size structure may be pH, chemical oxygen demand (COD) and nutrients (e.g., soluble phosphates, ammonia and nitrates). It is suggested that the multivariate approaches used may determine the environmental drivers to shape the spatial variations in body-size structure of biofilm-dwelling protozoa in marine ecosystems.     

Beta diversity and taxonomic sufficiency: Do higher‐level taxa reflect heterogeneity in species composition?

Aim Virtually all studies exploring the use of taxonomic surrogates in assessing patterns of diversity have focused on clear shifts in the location of samples in multivariate space. The potential use of coarser levels of taxonomic resolution to detect patterns of variability in multivariate space, corresponding to β‐diversity in the case of presence/absence data, remains unexplored. Here we considered five ecological data sets of highly diverse marine molluscan assemblages to test the hypothesis that patterns in compositional heterogeneity would be maintained at coarser levels of taxonomic resolution. Location Italy, Norway, New Zealand and the Arctic. Methods We used multivariate dispersion based on the Jaccard resemblance measure of presence/absence data as a measure of β‐diversity to test the null hypothesis that patterns of heterogeneity in species composition for molluscs would be maintained at coarser levels of taxonomic resolution. Tests to compare β‐diversities among groups (based on distances to centroids and using 9999 permutations) were carried out separately for each of five data sets at the species level and then for each of genus, family, order and class levels. Results Differences in multivariate dispersion at the species level (heterogeneity in the identities of species) were maintained for genera and for families, but not at coarser levels of taxonomic resolution (order or class). These results were consistent across all data sets, despite differences in their spatial scale and extent, geographical location, environmental and habitat features (benthic soft sediments, rocky reefs or kelp holdfasts). Main conclusions These results suggest that either genera or families may be used as effective taxonomic surrogates to detect spatial differences in β‐diversity for molluscs. The use of surrogates can provide considerable sampling efficiencies for biodiversity assessments. We consider, however, that a degree of caution and more work is needed, as heterogeneity at the species level may not be reflected by taxonomic surrogates at smaller spatial scales.     

Exploring predictions of abundance from body mass using hierarchical comparative approaches

Understanding and predicting how and why abundance varies is one of the central questions in ecology. One of the few consistent predictors of variation in abundance between species has been body mass, but the nature of this relationship has been contentious. Here I explore the relationship between body mass and abundance in birds of North America, using hierarchical partitioning of variance and regressions at taxonomic levels above the species. These analyses show that much variation in abundance is found across space, while a moderate amount of variation is found at the species/genus and also at the family/order level. However, body size and trophic level primarily vary at the family/order level, suggesting that mechanisms based on body size and energy should primarily explain only this moderate-sized, taxonomically conserved component of variation in abundance. Body size does explain more than 50% of the variation at this level (and almost 75% when trophic level is also included). This tighter relationship makes clear that energetic equivalence (slope = -3/4) sets an upper limit but does not describe the relationship between body mass and average abundance for birds of North America. Finally, I suggest that this hierarchical, multivariate approach should be used more often in macroecology.     

青藏高原高寒草甸土壤环境对线虫功能多样性的影响

土壤线虫是地下食物网的重要组成部分, 在生态系统能量流动和物质循环中起着至关重要的作用。大量研究报道了肥力等土壤环境对土壤线虫物种多样性及各功能群多度的影响, 而我们对土壤线虫功能多样性如何响应土壤环境变化依然知之甚少。本研究以群落水平个体大小和个体大小多样性表征土壤线虫功能多样性。在青藏高原高寒草甸选择3个研究点, 调查和分析了不同生境(沟底平地、阴坡、阳坡和山顶)土壤线虫物种多样性、各功能群多度和功能多样性及其与土壤理化因子和植物多样性的关系。结果表明: (1)土壤线虫个体多度和物种多样性在阳坡最高, 随土壤pH值和土壤总磷增加而升高; 而基于个体大小的土壤线虫功能多样性主要受土壤养分影响, 随土壤总氮和有机质增加而增加, 随土壤总磷含量增加而减少; (2)食细菌和食真菌线虫多度在沟底最高, 植食与捕食杂食线虫多度在山顶最低; 除捕食杂食线虫外, 各功能群多度也主要随土壤磷增加而升高; 除食真菌线虫外, 各功能群多度随植物物种丰富度的增加而减少。本研究强调了土壤线虫物种和功能多样性受不同土壤环境因子的影响, 丰富了土壤线虫多样性研究的内容, 为理解高寒草甸土壤动物多样性形成、维持和变化提供了更广阔的 视角。     

Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot

Background

Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete) data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny.

Methodology/Principal Findings

Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history.

Conclusions/Significance

As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.     

Insights into discriminating water quality status using new biodiversity measures based on a trait hierarchy of body-size units

Biofilm-dwelling protozoa have successfully used as a feasible bioindicator for bioassessment of water quality status in marine ecosystems. Based on a dataset of biofilm-dwelling protozoa in coastal waters of the Yellow Sea, we demonstrated a spatial variation in body-size spectrum of protozoan communities along a gradient of increasing environmental pollution. Two biodiversity indices, as a new indicator of water quality, were proposed, first being body-size diversity (Δ′) logistically corresponded to taxonomic diversity index but with a trait hierarchy of body-size units based on Euclidean distance resemblance, and the second a modified body-size diversity index (Δ′_m) with a modified hierarchy based on the trait matrix. The values of both indices Δ′ and Δ′_m were found to be significantly correlated with the changes of environmental variables, especially the nutrients. Furthermore, the body-size diversity (Δ′_mrk) at body-size-rank-1 (“genus-level”) resolution might be used as a potential surrogate of those at “species-level” resolution. Thus, we suggest that the ecological parameters based on body-size spectrum may be used as potential bioindicator of water quality status, and that the body-size rank sufficiency might be an effective time-efficient protocol for monitoring programs by identifying taxa to “genus-level” body-size rank.     

Phylogenetic signal common to three data sets: Combining data which initially appear heterogeneous

This study makes use of three sources of data, morphology and two chloroplast DNA sequences,ndhF andrbcL, to resolve relationships in Gesneriaceae. Cladograms from each of the three data sets separately are not topologically congruent. Statistical indices suggest that each data set is congruent with thendhF data althoughrbcL and morphology are themselves incongruent. Consensus methods provide no resolution of taxonomic relationships when trees from the different data sets are combined. Combining data sets generally results in cladograms that are more fully resolved than each of the data sets analyzed separately and support for the clades increases based on higher decay index and bootstrap values. These results indicate that there is a phylogenetic signal common to each of the data sets, however, the noise (errors due to homoplasy, mis-scoring, etc.) unique to each data source masks this signal. In combining the data, the evidence for the common evolutionary history in each data set overcomes the noise and is apparent in the resulting trees.     

Small world patterns in food webs

The analysis of some species-rich, well-defined food webs shows that they display the so-called small world behavior shared by a number of disparate complex systems. The three systems analysed (Ythan estuary web, Silwood web and the Little Rock lake web) have different levels of taxonomic resolution, but all of them involve high clustering and short path lengths (near two degrees of separation) between species. Additionally, the distribution of connections P(k) which is skewed in all the webs analysed shows long tails indicative of power-law scaling. These features suggest that communities might be self-organized in a non-random fashion that might have important consequences in their resistance to perturbations (such as species removal). The consequences for ecological theory are outlined.     

Plant species richness–productivity relationships in a low-productive boreal region

Local species richness–productivity (SR–P) relationship is usually reported as unimodal if long productivity gradients are sampled. However, it tends to be monotonically increasing in low-productive environments due to the decreasing part of the SR–P curve being truncated. Previous work indicated that this can hold true for forest herb layers, because of an upper bound on productivity caused mainly by canopy shading. Here, we ask whether the same pattern exists in a region with an upper bound on productivity caused by a harsh climate. We sampled herbaceous vegetation of boreal forests and grasslands in a low-productive region of central Yakutia (NE Siberia) with dry and winter-cool continental climate. We collected data on species composition, herb-layer productivity (aboveground herbaceous biomass), soil chemistry and light availability. We applied regression models to discriminate between monotonically increasing, decreasing and unimodal responses of herb-layer species richness to measured variables and analysed trends in the species-pool size and beta diversity along the productivity gradient. Our expectation of the monotonically increasing SR–P relationship was confirmed for neither forest herb layers nor grasslands. In the forest herb layers, no relationship was detected. In grasslands, the relationship was unimodal with species richness decline starting at much lower productivity levels than in more productive temperate grasslands. Potential causes for this decline are either limitation of local species richness by the species pool, which contains few species adapted to more productive habitats, or competitive exclusion, which can become an important control of species richness under lower levels of productivity than is the case in temperate grasslands.     

A comparative analysis of fine versus coarse taxonomic resolution in benthic chironomid community analyses

The analysis of sedimentary chironomid assemblages is an approach that has been widely adopted for inferring past environmental conditions. However, there is an ongoing discussion in the literature about whether this approach could become more sensitive at detecting past environmental changes if paleolimnologists conducted finer taxonomic analyses of their specimens. To advance this discussion, we conducted comparative analyses of larval chironomid assemblages resolved to two levels of taxonomic resolution. For this exercise, we chose to use live assemblages (as opposed to sub-fossil assemblages) because fine taxonomic resolution of live assemblages is more easily obtained. Our specific aims were to (i) determine if finely resolved taxa comprising a coarsely resolved group have similar ecological niches, (ii) determine if different environmental predictors of community composition are identified when two different levels of taxonomic resolution are applied and (iii) evaluate whether the variance explained by environmental variables differs substantially between levels of taxonomic resolution. We found that there was substantial dispersion among finely resolved taxa belonging to a single coarse group, which suggests that the merging of these taxa results in the loss of ecological information, and therefore warrants higher taxonomic precision. However, the identification of significant environmental predictors and the proportion of variance explained by these did not differ greatly between our two levels of taxonomic resolution. Overall our results show that coarse-resolution analyses may be adequate for some applications, but if the aim is to infer subtle environmental changes (as is the case in most paleolimnological studies) we recommend the highest possible level of taxonomic resolution.     

Measuring beta‐diversity from taxonomic similarity

Question: The utility of beta (β‐) diversity measures that incorporate information about the degree of taxonomic (dis)similarity between species plots is becoming increasingly recognized. In this framework, the question for this study is: can we define an ecologically meaningful index of β‐diversity that, besides indicating simple species turnover, is able to account for taxonomic similarity amongst species in plots? Methods: First, the properties of existing measures of taxonomic similarity measures are briefly reviewed. Next, a new measure of plot‐to‐plot taxonomic similarity is presented that is based on the maximal common subgraph of two taxonomic trees. The proposed measure is computed from species presences and absences and include information about the degree of higher‐level taxonomic similarity between species plots. The performance of the proposed measure with respect to existing coefficients of taxonomic similarity and the coefficient of Jaccard is discussed using a small data set of heath plant communities. Finally, a method to quantify β‐diversity from taxonomic dissimilarities is discussed. Results: The proposed measure of taxonomic β‐diversity incorporates not only species richness, but also information about the degree of higher‐order taxonomic structure between species plots. In this view, it comes closer to a modern notion of biological diversity than more traditional measures of β‐di‐versity. From regression analysis between the new coefficient and existing measures of taxonomic similarity it is shown that there is an evident nonlinearity between the coefficients. This nonlinearity demonstrates that the new coefficient measures similarity in a conceptually different way from previous indices. Also, in good agreement with the findings of previous authors, the regression between the new index and the Jaccard coefficient of similarity shows that more than 80% of the variance of the former is explained by the community structure at the species level, while only the residual variance is explained by differences in the higher‐order taxonomic structure of the species plots. This means that a genuine taxonomic approach to the quantification of plot‐to‐plot similarity is only needed if we are interested in the residual system's variation that is related to the higher‐order taxonomic structure of a pair of species plots.     

Abundance and habitat segregation in Mediterranean grassland species: the importance of seed weight

Abstract. We analysed the relationship between seed traits (weight, shape and dispersal structures) and the abundance and habitat segregation of Mediterranean grassland species. To take into account possible correlations with other plant traits, the study also includes 5 vegetative traits (growth form, plant longevity, clonality, onset of flowering and plant size) of commonly accepted functional importance. Data were recorded for 85 species from dehesa grasslands in central Spain. Species abundance was measured in upper (dry and less productive, high stress) and lower (moist and more productive, low stress) slope zones in the same area. Habitat segregation was estimated using an index based on the relative frequencies of species in upper and lower slope zones. Multiple regression models were fitted using species, as well as phylogenetically independent contrasts, as data points. Annual small‐seeded species without specialised dispersal structures are over‐represented in dehesa grasslands. Abundance was negatively related to seed weight in upper slope zones. None of the recorded plant traits were related to abundance in the lower slope zones. Habitat segregation was mainly related to seed weight, but also to some vegetative traits. Annual, early flowering and small‐seeded species were relatively more abundant in the upper than the lower slope zones. This pattern is independent of phylogeny. Our results suggest that in dry Mediterranean grasslands, abundance of many species is determined by dispersal (production of numerous small seeds) rather than by competitive ability.     

Computational methods for defining the allowed conformational space of 16S rRNA based on chemical footprinting data.

Structural models for 16S ribosomal RNA have been proposed based on combinations of crosslinking, chemical protection, shape, and phylogenetic evidence. These models have been based for the most part on independent data sets and different sets of modeling assumptions. In order to evaluate such models meaningfully, methods are required to explicitly model the spatial certainty with which individual structural components are positioned by specific data sets. In this report, we use a constraint satisfaction algorithm to explicitly assess the location of the secondary structural elements of the 16S RNA, as well as the certainty with which these elements can be positioned. The algorithm initially assumes that these helical elements can occupy any position and orientation and then systematically eliminates those positions and orientations that do not satisfy formally parameterized interpretations of structural constraints. Using a conservative interpretation of the hydroxyl radical footprinting data, the positions of the ribosomal proteins as defined by neutron diffraction studies, and the secondary structure of 16S rRNA, the location of the RNA secondary structural elements can be defined with an average precision of 25 A (ranging from 12.8 to 56.3 A). The uncertainty in individual helix positions is both heterogeneous and dependent upon the number of constraints imposed on the helix. The topology of the resulting model is consistent with previous models based on independent approaches. The result of our computation is a conservative upper bound on the possible positions of the RNA secondary structural elements allowed by this data set, and provides a suitable starting point for refinement with other sources of data or different sets of modeling assumptions.     

Global species–energy relationship in forest plots: role of abundance,temperature and species climatic tolerances

Aim To evaluate the strength of evidence for hypotheses explaining the relationship between climate and species richness in forest plots. We focused on the effect of energy availability which has been hypothesized to influence species richness: (1) via the effect of productivity on the total number of individuals (the more individuals hypothesis, MIH); (2) through the effect of temperature on metabolic rate (metabolic theory of biodiversity, MTB); or (3) by imposing climatic limits on species distributions. Location Global. Methods We utilized a unique ‘Gentry‐style’ 370 forest plots data set comprising tree counts and individual stem measurements, covering tropical and temperate forests across all six forested continents. We analysed variation in plot species richness and species richness controlled for the number of individuals by using rarefaction. Ordinary least squares (OLS) regression and spatial regressions were used to explore the relative performance of different sets of environmental variables. Results Species richness patterns do not differ whether we use raw number of species or number of species controlled for number of individuals, indicating that number of individuals is not the proximate driver of species richness. Productivity‐related variables (actual evapotranspiration, net primary productivity, normalized difference vegetation index) perform relatively poorly as correlates of tree species richness. The best predictors of species richness consistently include the minimum temperature and precipitation values together with the annual means of these variables. Main conclusion Across the world's forests there is no evidence to support the MIH, and a very limited evidence for a prominent role of productivity as a driver of species richness patterns. The role of temperature is much more important, although this effect is more complex than originally assumed by the MTB. Variation in forest plot diversity appears to be mostly affected by variation in the minimum climatic values. This is consistent with the ‘climatic tolerance hypothesis’ that climatic extremes have acted as a strong constraint on species distribution and diversity.     

Test of the Optimal Body Size Model for Strepsirhines

We determined if data on strepsirhine body and home range sizes support an optimal body size (OBS) model of 100 g, as predicted from studies of energetics in terrestrial mammals. We also tested the following predictions of the OBS model: 1) relationships between body and home range sizes will change slope and sign above and below the OBS threshold of 100 g and 2) best-fit lines for OBS regression models (above and below the 100-g threshold) will intersect at ca. 100 g (range of 80–250 g). We collected data on body mass, home range size, and vertical ranging behavior for 37 strepsirhines from the literature. Linear regression analyses and phylogenetic independent contrasts methods revealed that body size is a significant determinant of both 2-dimensional (ha) and 3-dimensional (km³) home range sizes only in taxa weighing >100 g. There were consistent changes in the sign of the slopes above and below the OBS threshold. The intersections of the best-fit lines were within the OBS range for the body size to 3-dimensional home range comparisons. Thus, the data provide some support for the OBS model in strepsirhines. However, no regression model was statistically significant for the taxa below the OBS threshold, which may reflect small sample sizes. Also, no slope differed significantly between taxa above and below the OBS. Significant correlations between body and home range sizes for the complete data sets refute the √-shaped constraint space predicted via the OBS model.     

The effects of hybridization on growth allometry and craniofacial form in Sulawesi macaques

The present research investigates the effects of hybridization between Macaca maurus and M. tonkeana on adult male form and patterns of growth allometry. Comparisons of adult hybrid mean phenotypic values with the adult averages of the parental species indicate a condition of heterosis for cranial vault length and crown-rump length. Negative heterosis is indicated for body mass. Regression parameters describing growth allometry are generated for four craniofacial measurement variables and one body measurement using both least squares and reduced major axis regression. Comparisons of hybrid and parental regression slopes and intercepts using analysis of covariance and t-tests suggest that there is a hybrid pattern of growth allometry characterized by an increase in regression slope values coupled with lower intercept values compared to those of the parental species and the parental averages for most regression parameters. Multivariate analyses of the adult and ontogenetic morphometric data indicate significant differences across species taxa in form and shape during development and adulthood. Our finding of significant differences between hybrids and their parental taxa in growth allometry and craniofacial form and shape during development challenges the assumption often made regarding the reproductive and taxonomic significance of observed ontogenetic divergence between Neandertals and modern humans. We propose that anthropological primatology, with its goal of developing nonhuman primate models for investigating human evolution, can provide a biologically relevant means by which to empirically estimate the taxonomic significance of morphological and ontogenetic divergence observed in the hominid fossil record.     

Data sets,partitions, and characters: philosophies and procedures for analyzing multiple data sets

We compared four approaches for analyzing three data sets derived from staphylinoid beetles, a superfamily whose known species diversity is roughly comparable to that of vertebrates. One data set is derived from adult morphology and the two molecular data sets are from 12S ribosomal RNA and cytochrome b mitochondrial DNA. We found that taxonomic congruence following conditional data combination, herein called compatible evidence (CE), resolved more nodes compatible with an initial conservative hypothesis than did total evidence (TE), conditional data combination (CDC), or taxonomic congruence (TC). CE sets a base of nodes obtained by CDC analysis and then investigates what further agreement may arise in a universe where these nodes are accepted as given. We suggest that CE75-75 may be appropriate for future studies that aim to both generate a well-corroborated tree and investigate conflicts between data sets, partitions, and characters. CE75-75 is a 75% bootstrap consensus CDC tree followed by combinable-component consensus of a 75% bootstrap consensus of each homogeneous set of partitions having hierarchical structure.     

Vegetation structure in relation to micro-landform in an evergreen broad-leaved forest on Amami Ohshima Island,south-west Japan

The relationship between micro-landform and vegetation structure was studied in a plot that was established on a slope from the ridge to the valley bottom in an evergreen broad-leaved forest on Amami Ohshima Island, south-west Japan. Five micro-landform units recognized in the plot were grouped into the upper and lower slopes by their location in relation to the erosion front, and plant distributions and vegetation structure were compared between them. Although small trees with d.b.h. less than 10 cm occurred almost all over the plot, the occurrence of larger trees was limited mostly to the upper slope. Based on the spatial distribution pattern in the plot, woody species are classified into three groups: group A mostly or strictly confined to the upper slope; group B confined to the lower slope; and group C associated statistically with neither slope. A well-developed forest stand, whose dominant species wereCastanopsis sieboldii ssp.lutchuensis andSchima wallichii, was seen on the upper slope, whereas only a poorly developed stand was seen on the lower slope. The difference in stability of the land surface is likely to be the major cause of the observed differences in stand structure between the upper and lower slopes. It is suggested that the erosion front is important as a line demarcating different habitats within a slope from the ridge to the valley bottom.