A novel approach to understanding bird communities using informed diversity estimates at local and regional scales in northern California and southern Oregon

Assessment and preservation of biodiversity has been a central theme of conservation biology since the discipline's inception. However, when diversity estimates are based purely on measures of presence–absence, or even abundance, they do not directly assess in what way focal habitats support the life history needs of individual species making up biological communities. Here, we move beyond naïve measures of occurrence and introduce the concept of “informed diversity” indices which scale estimates of avian species richness and community assemblage by two critical phases of their life cycle: breeding and molt. We tested the validity of the “informed diversity” concept using bird capture data from multiple locations in northern California and southern Oregon to examine patterns of species richness among breeding, molting, and naïve (based solely on occurrence) bird communities at the landscape and local scales using linear regression, community similarity indices, and a Detrended Correspondence Analysis (DCA). At the landscape scale, we found a striking pattern of increased species richness for breeding, molting, and naïve bird communities further inland and at higher elevations throughout the study area. At the local scale, we found that some sites with species‐rich naïve communities were in fact species‐poor when informed by breeding status, indicating that naïve richness may mask more biologically meaningful patterns of diversity. We suggest that land managers use informed diversity estimates instead of naïve measures of diversity to identify ecologically valuable wildlife habitat.     

Species richness peaks for intermediate levels of biomass in a fractal succession with quasi-neutral interactions

The mechanisms that promote species richness, including net community interactions, are considered central to the investigation of the consequences of biodiversity loss for ecosystem functioning. Recently, some empirical studies at large spatiotemporal scales suggest that increasing species richness within natural communities results in a finer division of biomass among species rather than an increase in total biomass. In parallel, the most common pattern observed in nature is the peaked relationship between diversity and productivity estimated as total biomass. Thus, the aim of our study is to provide model predictions for the diversity–biomass relationship with various levels of net species interactions within communities: negative, neutral, quasi-neutral and positive. Using a scaling relationship between the number of species and total community biomass, we propose a new self-similar process of biomass partitioning during a community assembly process. At each step of the succession, K more species appear that are A times less abundant on average giving K=A^d; the parameter d being a fractal dimension related to the nature of interactions among coexisting species. Our results, compared to those from meta-analyses about empirical diversity–productivity relationships, illustrate that quasi-neutral interactions among coexisting species lead to the most commonly observed pattern: an 'envelope' where diversity peaks at intermediate values of total biomass, i.e. that the area below the hump-backed line (considered as the upper boundary) is filled with data points.     

Disintegration of the ecological community

In this essay, I argue that the seemingly indestructible concept of the community as a local, interacting assemblage of species has hindered progress toward understanding species richness at local to regional scales. I suggest that the distributions of species within a region reveal more about the processes that generate diversity patterns than does the co-occurrence of species at any given point. The local community is an epiphenomenon that has relatively little explanatory power in ecology and evolutionary biology. Local coexistence cannot provide insight into the ecogeographic distributions of species within a region, from which local assemblages of species derive, nor can local communities be used to test hypotheses concerning the origin, maintenance, and regulation of species richness, either locally or regionally. Ecologists are moving toward a community concept based on interactions between populations over a continuum of spatial and temporal scales within entire regions, including the population and evolutionary processes that produce new species.     

Genetic diversity and invasibility: a test using a model system with a novel experimental design

Biological invasion is one aspect of ecosystem function that may be controlled by the biological diversity of the invaded community, and there have been a number of recent studies that investigated relationships between diversity and invasibility. Most experimental studies report that higher species or functional group diversity increases resistance to invasion, but the role of genetic diversity is unknown. We used a model organism, Arabidopsis thaliana (Brassicaceae), to investigate relationships between genotypic richness and community invasibility by creating communities with 1, 2, 4, and 8 genotypes of A. thaliana at constant low (417 plants m⁻²) and high (834 plants m⁻²) densities, that once established, were invaded with a congener, Arabidopsis suecica. To reduce the potential effects of methodological confounding related to “sampling effects,”“variance reduction effects,” or confounding of abundance with diversity, we (1) created random communities from a relatively large pool of functionally and phenotypically similar genotypes, (2) evaluated individual and community traits across richness treatments, and (3) analyzed similarity of communities within treatments (for “quasi- replication”) and between adjacent treatments (for “nestedness”). Genotypic richness had no effect on A. suecica demography (emergence, survivorship), size (biomass, rosette area), or reproductive potential (rates of bolting and fruiting or number and size of bolts). In contrast, the density of A. thaliana genotypes had strong effects on the size and reproductive potential of A. suecica, which suggests that characteristics of the recipient community other than genotypic richness (e.g. light) form the most important determinant of community invasibility. Individual- and community-level traits of community members (cover, biomass, survivorship) did not differ among richness treatments, and within- and between-treatment similarity was reduced (relative to other recent experiments) but not eliminated. We evaluate our results vis-a-vis recent analyses of diversity-invasibility experiments, and provide directions for future investigations of genetic diversity.     

Local richness-species pool ratio: A consequence of the species-area relationship

A constant ratio between species richness estimated at the local and regional scale is interpreted as a proof of quasi-neutral unsaturated communities. Based on Zobel’s model of plant community (Zobel,Folia Geobot. 36: 3–8, 2001) we tested the methodology of the species-pool concept by comparing the saturated and unsaturated communities generated by spatially-explicit mechanistic simulations with known assembly rules. Tests show that local-regional species plots can be applied to distinguish saturated vs. unsaturated communities, however, the outcome of tests, i.e. the relationship between local and regional richness depends on the size of the areas compared. Independently from the mechanisms controlling diversity, trivial saturation will appear if one of the scales is either too small or too broad because species-area curves are bound at these extreme scales. Similarly, trivial unsaturaton will appear if the two scales compared are close to each other. The application of species-area curves is useful because they help to find scales for non-trivial relationships. Field tests reporting quasi-neutrality and unsaturated plant communities were performed at the intermediate scales of the corresponding species-area curves, and they were estimated from heterogeneous samples. Therefore, this field evidence might be biased by scaling artefacts. We propose to reanalyze the field evidence with solid scaling conventions and to restrict the concept of quasi-neutrality to subordinated functional groups based on the following hypotheses: (1) neutrality will appear within subordinated guilds as a consequence of the hierarchical structure of plant communities; (2) the lower a guild in the hierarchy the higher neutrality of within-layer processes detected; (3) quasi-neutrality found at the community level is not a proof of community-level neutrality but it is due to the higher number of subordinated species in the samples.     

Integration of local and regional species-area relationships from space-time species accumulation

A long-standing observation in community ecology is that the scaling of species richness, as exemplified by species-area curves, differs on local and regional scales. This decoupling of scales may be largely due to sampling processes (the increasing constraint imposed by sampling fewer individuals at fine scales), as distinct from ecological processes, such as environmental heterogeneity, that operate across scales. Removal of the sampling constraint from fine-scale richness estimates should yield species-area curves that behave like those of the regions in which they are embedded, but an effective method for this removal has not been available. We suggest an approach that incorporates the manner in which small areas accumulate species over time as a way to remove the signature of sampling processes from fine-scale species-area curves. We report for three species-rich grasslands from two continents how local plant species richness is distributed through time at multiple, nested spatial scales, and we ask whether sampling-corrected curves reflect the spatial scaling of richness of each larger floristic province. Our analysis suggests that fine-scale values of richness are highly constrained by sampling processes, but once these constraints are removed, the spatial scaling of species richness is consistent from the scale of individuals to that of an entire province.     

Community Turnover of Wood-Inhabiting Fungi across Hierarchical Spatial Scales

For efficient use of conservation resources it is important to determine how species diversity changes across spatial scales. In many poorly known species groups little is known about at which spatial scales the conservation efforts should be focused. Here we examined how the community turnover of wood-inhabiting fungi is realised at three hierarchical levels, and how much of community variation is explained by variation in resource composition and spatial proximity. The hierarchical study design consisted of management type (fixed factor), forest site (random factor, nested within management type) and study plots (randomly placed plots within each study site). To examine how species richness varied across the three hierarchical scales, randomized species accumulation curves and additive partitioning of species richness were applied. To analyse variation in wood-inhabiting species and dead wood composition at each scale, linear and Permanova modelling approaches were used. Wood-inhabiting fungal communities were dominated by rare and infrequent species. The similarity of fungal communities was higher within sites and within management categories than among sites or between the two management categories, and it decreased with increasing distance among the sampling plots and with decreasing similarity of dead wood resources. However, only a small part of community variation could be explained by these factors. The species present in managed forests were in a large extent a subset of those species present in natural forests. Our results suggest that in particular the protection of rare species requires a large total area. As managed forests have only little additional value complementing the diversity of natural forests, the conservation of natural forests is the key to ecologically effective conservation. As the dissimilarity of fungal communities increases with distance, the conserved natural forest sites should be broadly distributed in space, yet the individual conserved areas should be large enough to ensure local persistence.     

Experimental evidence that soil heterogeneity enhances plant diversity during community assembly

Aims Environmental heterogeneity is a primary mechanism explaining species coexistence and extant patterns of diversity. Despite strong theoretical support and ample observational evidence, few experimental studies in plant communities have been able to demonstrate a causal link between environmental heterogeneity and plant diversity. This lack of experimental evidence suggests that either fine-scale heterogeneity has weak effects on plant diversity or previous experiments have been unable to effectively manipulate heterogeneity. Here, we utilize a unique soil manipulation to test whether fine-scale soil heterogeneity will increase plant richness through species sorting among experimental patch types.Methods This experiment was conducted in the tallgrass prairie region of south-central Kansas, USA. We utilized the inherent variation found in the vertical soil profile, which varied in both biotic and abiotic characteristics, and redistributed these strata into either homogeneous or heterogeneous spatial arrangements in 2.4×2.4 m plots. After the soil manipulation, 34 native prairie species were sown into all plots. We conducted annual censuses at peak biomass to quantify species composition and plant density by species within the experimental communities.Important findings After 2 years, species richness was significantly higher in heterogeneous relative to homogeneous plots and this pattern was independent of total plant density. In the heterogeneous plots, 13 species had higher establishment in a specific patch type representing one of the three soil strata. Conversely, no species had greater establishment in the mixed stratum, which comprised the homogeneous plots, relative to the heterogeneous strata. These species sorting patterns suggest that fine-scale heterogeneity creates opportunities for plant establishment due to niche differences, which translates into increased plant diversity at the plot scale. Species richness was more strongly related to plant density among patches comprising homogenous plots—where fine-scale heterogeneity was minimized, but weak in heterogeneous plots. This pattern is consistent with the idea that richness–density relationships dominate when neutral processes are important but are weak when niche processes operate. Unlike many previous attempts, our results provide clear, experimental evidence that fine-scale soil heterogeneity increases species richness through species sorting during community assembly.     

How specialised must natural enemies be to facilitate coexistence among plants?

The Janzen‐Connell hypothesis proposes that plant interactions with host‐specific antagonists can impair the fitness of locally abundant species and thereby facilitate coexistence. However, insects and pathogens that associate with multiple hosts may mediate exclusion rather than coexistence. We employ a simulation model to examine the effect of enemy host breadth on plant species richness and defence community structure, and to assess expected diversity maintenance in example systems. Only models in which plant enemy similarity declines rapidly with defence similarity support greater species richness than models of neutral drift. In contrast, a wide range of enemy host breadths result in spatial dispersion of defence traits, at both landscape and local scales, indicating that enemy‐mediated competition may increase defence‐trait diversity without enhancing species richness. Nevertheless, insect and pathogen host associations in Panama and Papua New Guinea demonstrate a potential to enhance plant species richness and defence‐trait diversity comparable to strictly specialised enemies.     

Experimental demonstration that plant diversity reduces invasibility – evidence of a biological mechanism or a consequence of sampling effect?

Several recent studies have claimed to present experimental evidence from synthesised plant communities in which diversity was varied as a treatment that diversity reduces community invasibility by other plant species. This type of result contrasts from that of many observational studies which find diversity and invasibility to be positively correlated in nature, but some recent literature has claimed that these observational studies are confounded by extrinsic covarying factors while experimental studies are not. In this article I evaluate each of eight experiments from six recent publications in which the effect of varying plant diversity on the success of invasive species was investigated. In each case that invasibility was identified by the authors as being adversely affected by plant species richness, the result can be explained by factors that covaried with diversity in the experiment, most notably as a consequence of “sampling effect” (in which the most competitive species or species combination in the total species pool has a greater probability of occurring as species richness is increased), or through the incorrect use of statistical techniques. It is proposed that the apparent discrepancy between the results of many observational and experimental studies at least in grasslands is because: (1) in observational studies competitive dominant species are often associated with the most productive plots, and these dominants both reduce diversity through competitive exclusion of subordinates and competitively suppress invasive species; and (2) in recent experimental studies “sampling effect” results in the most competitive species (and therefore those most likely to suppress the invader) occurring with greater frequency as diversity is increased. Both observational and experimental studies therefore point to the role of competitive dominants in reducing invasibility, and in both situations species richness of the plant community need not be invoked as an explanation for the results.     

Both facilitation and limiting similarity shape the species coexistence in dry alkali grasslands

Facilitation is an important driver of community assembly, and often overwhelms the effect of competition in stressed habitats. Thus, net effect of biotic interactions is often positive in stressed grasslands, where dominant species and litter can protect the subordinate species. Besides facilitation, niche partitioning can also support species coexistence leading to limiting similarity between subordinate species. Our aim was to provide a detailed analysis of fine-scale biotic interactions in stressed alkali grasslands. We supposed, that there are positive relationships between the main biomass fractions and species richness. We expected the expansion of trait ranges and the increase of trait dissimilarity with increasing biomass scores (total litter, green biomass of dominant species) and species richness. We studied the relationships between main biomass fractions, species richness, functional diversity and functional trait indices (ranges, weighted means and Rao indices). We used fine-scale biomass sampling in nine stands of dry alkali grasslands dominated by Festuca pseudovina. The detected relationships were always positive between the main biomass fractions (green biomass of dominant species, total litter and green biomass of subordinate species) and species richness. We found that the green biomass of dominant species and total litter increased ranges and dissimilarity of functional traits. Our results suggest that in dry alkali grasslands facilitation is crucial in shaping vegetation composition. The green biomass of dominant species and total litter increased the biomass production of subordinate species leading to overyielding. We found that mechanisms of facilitation and limiting similarity were jointly shaping the species coexistence in stressed grasslands, such as alkali grasslands.     

The stability–diversity relationship in stream macroinvertebrates: influences of sampling effects and habitat complexity

1. Theory predicts that the stability of a community should increase with diversity. However, despite increasing interest in the topic, most studies have focused on aggregate community properties (e.g. biomass, productivity) in small‐scale experiments, while studies using observational field data on realistic scales to examine the relationship between diversity and compositional stability are surprisingly rare. 2. We examined the diversity–stability relationship of stream invertebrate communities based on a 4‐year data set from boreal headwater streams, using among‐year similarity in community composition (Bray–Curtis coefficient) as our measure of compositional stability. We related stability to species richness and key environmental factors that may affect the diversity–stability relationship (stream size, habitat complexity, productivity and flow variability) using simple and partial regressions. 3. In simple regressions, compositional stability was positively related to species richness, stream size, productivity and habitat complexity, but only species richness and habitat complexity were significantly related to stability in partial regressions. There was, however, a strong relationship between species richness and abundance. When abundance was controlled for through re‐sampling, stability was unrelated to species richness, indicating that sampling effects were the predominant mechanism producing the positive stability–diversity relationship. By contrast, the relationship between stability and habitat complexity (macrophyte cover) became even stronger when the influence of community abundance was controlled for. Habitat complexity is thus a key factor enhancing community stability in headwater streams.     

Plant diversity,biogeography and environment in Iberia: Patterns and possible causal factors

Abstract. We associated patterns of plant diversity with possible causal factors by considering 93 local regions in the Iberian Peninsula and Balearic Islands with respect to biogeography, environmental favourability, and environmental heterogeneity, and their relationship with measured species diversity at four different scales: mean local species richness standardized at a grain of 100 m², total species richness in a community type within a region (regional community richness), mean compositional similarity, and mosaic diversity. Local regions in biogeographic transition zones to the North African and Atlantic floras had higher regional community richness and greater mosaic diversity than did non‐transitional regions, whereas no differences existed in mean local species richness or mean compositional similarity. Mean local species richness was positively related to environmental favourability as measured by actual evapotranspiration, but negatively related to total precipitation and temporal heterogeneity in precipitation. Mean local species richness was greatest in annual grassland and dwarf shrubland communities, and on calcareous bedrock types. Regional community richness was similarly related to actual evapotranspiration and total precipitation, but in addition was positively related to spatial heterogeneity in topography and soil water holding capacity. Mean compositional similarity decreased with increasing spatial heterogeneity and temperature seasonality. Mosaic diversity, a measure of complexity, increased with increasing local and regional richness. We hypothesize that these relationships can be explained by four ecological and evolutionary classes of causal factors: numbers of individuals, intermediate environments, limits to adaptation, and niche variation. These factors operate at various scales and manifest themselves in various ways. For example, at the site level, apparently processes that increase the number of individuals increase mean local species richness, but at the level of the entire region no such effects were found.     

In and out: Effects of shoot- vs. rooted-presence sampling methods on plant diversity measures in mountain grasslands

Plant diversity measures (e.g., alpha- and beta-diversity) provide the basis for a number of ecological indication and monitoring methods. These measures are based on species counts in sampling units (plots or quadrats). However, there are two alternative conventions for defining a vascular plant species as “present” in a plot, i.e. “shoot presence” (a species is recorded if the vertical projection of any above-ground part falls within the plot) and “rooted presence” (a species is recorded only when an individual is rooted inside the plot). Very few studies addressed the effects of the two sampling conventions on species richness and diversity indices. We sampled mountain dry grasslands in Italy across different plot sizes and vegetation types to assess how large is the difference in alpha- and beta-diversity values and in sample-based rarefaction curves between the two methods. We found that the difference is greatly dependent on plot size, being more relevant, both in absolute and percentage values, at smaller grain; it is also dependent on habitat type, being larger in shallow-soil communities, as they have a sparser vegetation structure and host life-form types with a larger lateral spread. At fine spatial scales (<1 m²) the difference is large enough to bias statistical inference, and we conclude that at such scales one should not attempt to compare plant diversity indices if they were not obtained with the same sampling convention.     

Species accumulation curves and their applications in parasite ecology

Species accumulation curves (SACs) chart the increase in recovery of new species as a function of some measure of sampling effort. Studies of parasite diversity can benefit from the application of SACs, both as empirical tools to guide sampling efforts and predict richness, and because their properties are informative about community patterns and the structure of parasite diversity. SACs can be used to infer interactivity in parasite infracommunities, to partition species richness into contributions from different spatial scales and different levels of the host hierarchy (individuals, populations and communities) or to identify modes of community assembly (niche versus dispersal). A historical tendency to treat individual hosts as statistically equivalent replicates (quadrats) seemingly satisfies the sample-based subgroup of SACs but care is required in this because of the inequality of hosts as sampling units. Knowledge of the true distribution of parasite richness over multiple host-derived and spatial scales is far from complete but SACs can improve the understanding of diversity patterns in parasite assemblages.     

Functional diversity (FD), species richness and community composition

Functional diversity is an important component of biodiversity, yet in comparison to taxonomic diversity, methods of quantifying functional diversity are less well developed. Here, we propose a means for quantifying functional diversity that may be particularly useful for determining how functional diversity is related to ecosystem functioning. This measure of functional diversity “FD” is defined as the total branch length of a functional dendrogram. Various characteristics of FD make it preferable to other measures of functional diversity, such as the number of functional groups in a community. Simulating species' trait values illustrates how the relative importance of richness and composition for FD depends on the effective dimensionality of the trait space in which species separate. Fewer dimensions increase the importance of community composition and functional redundancy. More dimensions increase the importance of species richness and decreases functional redundancy. Clumping of species in trait space increases the relative importance of community composition. Five natural communities show remarkably similar relationships between FD and species richness.     

荒漠植被植物种多样性对空间尺度的依赖

物种多样性与空间尺度的关系是植物生态学的一个研究热点。传统植物生态学研究认为种面积曲线方程中 Z值是个近似常数 ,但近期对森林和草原群落的研究表明 Z是随尺度变化的。在荒漠带选择了 10个样地 ,每个样地包括 1m2 到 1km2 的 6个空间尺度样方 ,研究荒漠地区物种多样性与空间尺度的关系。结果表明 :荒漠植被物种多样性随空间尺度的增大空间依赖性减弱 ,Z也是随尺度变化的。对荒漠植被种面积曲线 Z的研究结果支持了 Z随尺度变化的结论 ,但 Z是随尺度增加而减小 ,斜率 z值从 0 .37降至 0 .0 35 ,与草原和森林群落 Z值随尺度增加而增加的结论是相反的。     

Spatial constraints masking community assembly rules: A simulation study

The effect of competition on species coexistence is usually strongly modified by other factors especially in non-equilibrium systems of sessile organisms with limited availability of propagules. As a consequence, competition-based assembly rules (even if their existence seems to be unambiguously detected) would result in incomplete understanding of the coexistence of species in plant communities. J. Bastow Wilson suggested measuring variance deficit in the number of co-occurring species as a means to detect niche limitation in a community. The method provides a relatively simple and quick “snap-shot” analysis of a community. However, it has been questioned whether niche limitation is the only factor which might account for variance deficit. The paper presents a spatially explicit simulation experiment in which artificial communities are produced by pre-defined rules for competitive interactions. Then we examine whether these rules can be detected by a proposed method for pattern analysis. Two limiting cases are simulated: (A) all the species share the same niche, and (B) all the species have different niches. The difference between these cases in the variance of species numbers is examined. Using the simulation results, some basic spatial constraints upon species assembly are emphasized. It is argued that the assumptions of Wilson’s approach confine its applicability to species-saturated equilibrium communities. The study of assembly rules in dynamically changing, spatially structured communities requires the consideration of a set of coenological characteristics and the use of careful spatio-temporal scaling to detect their patterns. The use of spatially explicit individual-based models to study the mechanisms and constraints limiting species coexistence at different scales is suggested.     

Increased community compositional dissimilarity alleviates species loss following nutrient enrichment at large spatial scales

Aims Anthropogenic activities have drastically increased nutrient availability, resulting in declines in species richness in many plant communities. However, most previous studies have explored only species-loss patterns and mechanisms over small sampling areas, so their results might overestimate species loss at larger spatial scales. The aim of this research was to explore species diversity change patterns and species-loss rates at multiple scales in alpine meadow communities following nutrient enrichment. Specifically, we asked two closely related questions: (i) do changes in species diversity and species-loss patterns differ among spatial scales? and (ii) how does community compositional dissimilarity and species turnover change among spatial scale?     

Measuring the synanthropy of species and communities to monitor the effects of urbanization on biodiversity

Urbanization is considered as one of the most important land-use and land-cover (LULC) changes with multiple pervasive effects on biodiversity. However, the quantitative assessment of biodiversity responses to urbanization remains challenging because some species can be directly and negatively affected by the spread of human settlements, while others can benefit from this LULC change. Moreover, although species sensitivity to urban settlements (their “synanthropy”) can either correspond to the spatial segregation of individuals within urban habitats or to their positive temporal trends in these habitats, these two facets are hardly distinguished explicitly. Here, we confronted the fine-scale spatial distribution of all the buildings in France with the spatial distribution and population trends of the 119 most common French breeding birds monitored in 2124 plots from 2001 to 2012. We developed and tested two indicators of “synanthropy”. The first indicator (S1) differentiates species along a continuous gradient from urban “avoiders” (low S1) to urban “dwellers” (high S1). The second indicator measures the beneficial or detrimental effect of building densities on the temporal trends of the populations. It allows the segregation among urban “losers” having lower temporal trends with increasing buildings (low S2) from urban “winners” (high S2) having more positive trends in more urbanized areas. We then tested the relationships between S1 and S2 with a set of species and life history traits. Finally, we transposed these species indicators to communities using community weighted means to test the link between the synanthropy of communities with bird species richness, and the spatial, temporal and spatio-temporal trends of the synanthropy of bird communities. We found that 43% of the species were “urban dwellers”, and 18% “urban winners”. Both urban dwellers and winners were species widely distributed and locally abundant. Urban dwellers were mainly ground feeders but did not nest on the ground. At the community level, high species richness was associated with medium-values of community synanthropy, following the intermediate-disturbance hypothesis. We found that the average value of community synanthropy and their trend were not randomly distributed in space. These two indicators of synanthropy can be used in different taxonomic groups and areas to assess the proportion of synanthropic species within communities, to monitor their temporal trends and their spatial distribution and represent a straightforward complement to the synthetic indicators of human footprint on biodiversity.