Support for the habitat amount hypothesis from a global synthesis of species density studies.

Decades of research suggest that species richness depends on spatial characteristics of habitat patches, especially their size and isolation. In contrast, the habitat amount hypothesis predicts that (1) species richness in plots of fixed size (species density) is more strongly and positively related to the amount of habitat around the plot than to patch size or isolation; (2) habitat amount better predicts species density than patch size and isolation combined, (3) there is no effect of habitat fragmentation per se on species density and (4) patch size and isolation effects do not become stronger with declining habitat amount. Data on eight taxonomic groups from 35 studies around the world support these predictions. Conserving species density requires minimising habitat loss, irrespective of the configuration of the patches in which that habitat is contained.

Sampling methods affect Nematode-Trapping Fungi biodiversity patterns across an elevational gradient.

BACKGROUND: Understanding the patterns of species richness across elevational gradients is a key concept for contemporary research in ecology and evolution, and critical to understanding large-scale trends in biodiversity, global change and conservation. However, patterns of elevational species richness between taxonomic groups, regions and latitudes are inconsistent, so that various, sometimes conflicting hypotheses exist. Several scholars have pointed out that research on elevational distribution patterns is often biased by the sampling design employed. To test this hypothesis, we analyzed species richness of Nematode-Trapping Fungi (NTF) across an elevation gradient at two mountainous sites in western Yunnan Province, P.R. China. We tested for potential differences in the results when using different sampling designs. RESULTS: A total of 3 genera, 17 species, 222 strains of NTF were isolated and identified from Gaoligongshan and Cangshan. Species accumulation curves for both sites and sampling modes had acceptable leveling, demonstrating sufficient sampling effort. At Gaoligongshan, the elevation distribution patterns of NTF were different under two sampling patterns. When reducing the analyzed altitude range in Gaoligongshan, the elevation distribution pattern of the NTF changed. A similar elevation distribution pattern was observed in Cangshan when testing the same altitude range. In general, when treating the same dataset using different sampling designs, the resulting distribution patterns of species richness and occurrence frequencies were clearly different. Moreover, after removal of the samples located within lower-altitude zones affected by anthropogenic interferences, the distribution pattern of NTF in the two sites tended to become uniform. CONCLUSION: The sampling design, and in particular the elevation interval between plots, has a significant effect on the assessment of species distribution in mountainous regions. Other factors such as human activities and the multi-dimensionality of biodiversity also contribute to result biases. It is recommended that sampling design is given careful consideration in future studies on the elevational gradients of species richness, using stratified approaches according to the most relevant factors.

Do constrained immigration rates and high ß diversity explain contrasting productivity-diversity patterns measured at different scales?

The relationship between productivity and diversity is controversial because of disparity between unimodal and monotonic patterns, especially when occurring simultaneously at different scales. We used stream-side artificial channels to investigate how the availability of a major resource (leaf litter) affected stream invertebrate abundance and diversity at leaf-pack and whole-channel scales. At the larger scale, invertebrate diversity increased monotonically with increasing litter resource density, whereas at the smaller scale the relationship was hump-shaped, in keeping with reports in the literature. This divergence at higher resource levels suggests that multiple mechanisms may be operating. Our results indicate that consistently high species turnover (ß diversity) caused the monotonic pattern because of a species-area or "sampling effect" in which new species accumulate with increasing number of samples. The hump-shaped pattern was due to constrained immigration because of a "dilution effect" in which a limited number of immigrants is spread out among the increasing number of available patches. We propose that the relationship between productivity or resource availability and α diversity is generally hump-shaped and the scale-dependent contrast in the relationship only arises where the species pool is large and ß diversity is high. Differences in ß diversity may, therefore, explain some of the contrasting patterns in the productivity-diversity relationship previously reported.We suggest that continuing immigration by rare taxa is important in sustaining species diversity when productivity is high. The hump-shaped pattern has implications for the impact of anthropogenic ecosystem enrichment on species diversity.

Deconstructing the relationships between phylogenetic diversity and ecology: a case study on ecosystem functioning.

Recent studies have supported a link between phylogenetic diversity and various ecological properties including ecosystem function. However, such studies typically assume that phylogenetic branches of equivalent length are more or less interchangeable. Here we suggest that there is a need to consider not only branch lengths but also their placement on the phylogeny. We demonstrate how two common indices of network centrality can be used to describe the evolutionary distinctiveness of network elements (nodes and branches) on a phylogeny. If phylogenetic diversity enhances ecosystem function via complementarity and the representation of functional diversity, we would predict a correlation between evolutionary distinctiveness of network elements and their contribution to ecosystem process. In contrast, if one or a few evolutionary innovations play key roles in ecosystem function, the relationship between evolutionary distinctiveness and functional contribution may be weak or absent. We illustrate how network elements associated with high functional contribution can be identified from regressions between phylogenetic diversity and productivity using a well-known empirical data set on plant productivity from the Cedar Creek Long-Term Ecological Research. We find no association between evolutionary distinctiveness and ecosystem functioning, but we are able to identify phylogenetic elements associated with species of known high functional contribution within the Fabaceae. Our perspective provides a useful guide in the search for ecological traits linking diversity and ecosystem function, and suggests a more nuanced consideration of phylogenetic diversity is required in the conservation and biodiversity-ecosystem-function literature.

Measuring partner choice in plant-pollinator networks: using null models to separate rewiring and fidelity from chance.

Recent studies of mutualistic networks show that interactions between partners change across years. Both biological mechanisms and chance could drive these patterns, but the relative importance of these factors has not been separated. We established a field experiment consisting of 102 monospecific plots of 17 native plant species, from which we collected 6713 specimens of 52 bee species over four years. We used these data and a null model to determine whether bee species' foraging choices varied more or less over time beyond the variation expected by chance. Thus we provide the first quantitative definition of rewiring and fidelity as these terms are used in the literature on interaction networks. All 52 bee species varied in plant partner choice across years, but for 27 species this variation was indistinguishable from random partner choice. Another 11 species showed rewiring, varying more across years than expected by chance, while 14 species showed fidelity, indicating that they both prefer certain plant species and are consistent in those preferences across years. Our study shows that rewiring and fidelity both exist in mutualist networks, but that once sampling effects have been accounted for, they are less common than has been reported in the ecological literature.

Invaded grassland communities have altered stability-maintenance mechanisms but equal stability compared to native communities.

Theory predicts that stability should increase with diversity via several mechanisms. We tested predictions in a 5-year experiment that compared low-diversity exotic to high-diversity native plant mixtures under two irrigation treatments. The study included both wet and dry years. Variation in biomass across years (CV) was 50% lower in mixtures than monocultures of both native and exotic species. Growth among species was more asynchronous and overyielding values were greater during and after a drought in native than exotic mixtures. Mean-variance slopes indicated strong portfolio effects in both community types, but the intercept was higher for exotics than for natives, suggesting that exotics were inherently more variable than native species. However, this failed to result in higher CV's in exotic communities because species that heavily dominated plots tended to have lower than expected variance. Results indicate that diversity-stability mechanisms are altered in invaded systems compared to native ones they replaced.

Does host plant richness explain diversity of ectomycorrhizal fungi? Re-evaluation of Gao et al. (2013) data sets reveals sampling effects.

The generally positive relationship between biodiversity of groups of directly or indirectly interacting organisms is one of the most important ecological concepts (Gaston, 2000 Nature, 405, 220-227; Scherber C, Eisenhauer N, Weisser WW et al., 2010 Nature, 468, 553-556). In a recent issue of Molecular Ecology, Gao C, Shi N-N, Liu Y-X et al. (2013: 22, 3403-3414) reported that the richness of plants and ectomycorrhizal fungi is positively correlated both at local and at global scales. Here, we challenge these findings by re-analysis of data and ascribe the reported results to sampling effect and poor data compilation.

Different mechanisms underlie similar species-area relationships in two tropical archipelagoes.

Despite much research in the field of island biogeography, mechanisms regulating insular diversity remain elusive. Here, we aim to explore mechanisms underlying plant species-area relationships in two tropical archipelagoes in the South China Sea. We found positive plant species-area relationships for both coral and continental archipelagoes. However, our results showed that different mechanisms contributed to similar plant species-area relationships between the two archipelagoes. For coral islands, soil nutrients and spatial distance among communities played major roles in shaping plant community structure and species diversity. By contrast, the direct effect of island area, and to a lesser extent, soil nutrients determined plant species richness on continental islands. Intriguingly, increasing soil nutrients availability (N, P, K) had opposite effects on plant diversity between the two archipelagoes. In summary, the habitat quality effect and dispersal limitation are important for regulating plant diversity on coral islands, whereas the passive sampling effect, and to a lesser extent, the habitat quality effect are important for regulating plant diversity on continental islands. More generally, our findings indicate that island plant species-area relationships are outcomes of the interplay of both niche and neutral processes, but the driving mechanisms behind these relationships depends on the type of islands.

Species diversity and interspecific information flow.

Interspecific information flow is known to affect individual fitness, population dynamics and community assembly, but there has been less study of how species diversity affects information flow and thereby ecosystem functioning and services. We address this question by first examining differences among species in the sensitivity, accuracy, transmissibility, detectability and value of the cues and signals they produce, and in how they receive, store and use information derived from heterospecifics. We then review how interspecific information flow occurs in communities, involving a diversity of species and sensory modes, and how this flow can affect ecosystem-level functions, such as decomposition, seed dispersal or algae removal on coral reefs. We highlight evidence that some keystone species are particularly critical as a source of information used by eavesdroppers, and so have a disproportionate effect on information flow. Such keystone species include community informants producing signals, particularly about predation risk, that influence other species' landscapes of fear, and aggregation initiators creating cues or signals about resources. We suggest that the presence of keystone species means that there will likely be a positive relationship in many communities between species diversity and information through a 'sampling effect', in which larger pools of species are more likely to include the keystone species by chance. We then consider whether the number and relative abundance of species, irrespective of the presence of keystone species, matter to interspecific information flow; on this issue, the theory is less developed, and the evidence scant and indirect. Higher diversity could increase the quantity or quality of information that is used by eavesdroppers because redundancy increases the reliability of information or because the species provide complementary information. Alternatively, there could be a lack of a relationship between species diversity and information if there is widespread information parasitism where users are not sources, or if information sourced from heterospecifics is of lower value than that gained personally or sourced from conspecifics. Recent research suggests that species diversity does have information-modulated community and ecosystem consequences, especially in birds, such as the diversity of species at feeders increasing resource exploitation, or the number of imitated species increasing responses to vocal mimics. A first step for future research includes comprehensive observations of information flow among different taxa and habitats. Then studies should investigate whether species diversity influences the cumulative quality or quantity of information at the community level, and consequently ecosystem-level processes. An applied objective is to conserve species in part for their value as sources of information for other species, including for humans.

The Impact of Sample Size and Population History on Observed Mutational Spectra: A Case Study in Human and Chimpanzee Populations.

Recent studies have highlighted variation in the mutational spectra among human populations as well as closely related hominoids-yet little remains known about the genetic and nongenetic factors driving these rate changes across the genome. Pinpointing the root causes of these differences is an important endeavor that requires careful comparative analyses of population-specific mutational landscapes at both broad and fine genomic scales. However, several factors can confound such analyses. Although previous studies have shown that technical artifacts, such as sequencing errors and batch effects, can contribute to observed mutational shifts, other potentially confounding parameters have received less attention thus far. Using population genetic simulations of human and chimpanzee populations as an illustrative example, we here show that the sample size required for robust inference of mutational spectra depends on the population-specific demographic history. As a consequence, the power to detect rate changes is high in certain hominoid populations while, for others, currently available sample sizes preclude analyses at fine genomic scales.

Resolving the SLOSS dilemma for biodiversity conservation: a research agenda.

The legacy of the 'SL > SS principle', that a single or a few large habitat patches (SL) conserve more species than several small patches (SS), is evident in decisions to protect large patches while down-weighting small ones. However, empirical support for this principle is lacking, and most studies find either no difference or the opposite pattern (SS > SL). To resolve this dilemma, we propose a research agenda by asking, 'are there consistent, empirically demonstrated conditions leading to SL > SS?' We first review and summarize 'single large or several small' (SLOSS) theory and predictions. We found that most predictions of SL > SS assume that between-patch variation in extinction rate dominates the outcome of the extinction-colonization dynamic. This is predicted to occur when populations in separate patches are largely independent of each other due to low between-patch movements, and when species differ in minimum patch size requirements, leading to strong nestedness in species composition along the patch size gradient. However, even when between-patch variation in extinction rate dominates the outcome of the extinction-colonization dynamic, theory can predict SS > SL. This occurs if extinctions are caused by antagonistic species interactions or disturbances, leading to spreading-of-risk of landscape-scale extinction across SS. SS > SL is also predicted when variation in colonization dominates the outcome of the extinction-colonization dynamic, due to higher immigration rates for SS than SL, and larger species pools in proximity to SS than SL. Theory that considers change in species composition among patches also predicts SS > SL because of higher beta diversity across SS than SL. This results mainly from greater environmental heterogeneity in SS due to greater variation in micro-habitats within and across SS habitat patches ('across-habitat heterogeneity'), and/or more heterogeneous successional trajectories across SS than SL. Based on our review of the relevant theory, we develop the 'SLOSS cube hypothesis', where the combination of three variables - between-patch movement, the role of spreading-of-risk in landscape-scale population persistence, and across-habitat heterogeneity - predict the SLOSS outcome. We use the SLOSS cube hypothesis and existing SLOSS empirical evidence, to predict SL > SS only when all of the following are true: low between-patch movement, low importance of spreading-of-risk for landscape-scale population persistence, and low across-habitat heterogeneity. Testing this prediction will be challenging, as it will require many studies of species groups and regions where these conditions hold. Each such study would compare gamma diversity across multiple landscapes varying in number and sizes of patches. If the prediction is not generally supported across such tests, then the mechanisms leading to SL > SS are extremely rare in nature and the SL > SS principle should be abandoned.

Species pool size alters species-area relationships during experimental community assembly.

The species pool concept has advanced our understanding for how biodiversity is coupled at local and regional scales. However, it remains unclear how species pool size, the number of species available to disperse to a site, influences community assembly across spatial scales. We provide one of the first studies that assesses diversity across scales after experimentally assembling grassland communities from species pools of different sizes. We show that species pool size causes scale-dependent effects on diversity in grasslands undergoing restoration by altering the shape of the species-area relationship (SAR). Specifically, larger species pools increased the slope of the SAR, but not the intercept, suggesting that dispersal from a larger pool causes species to be more spatially aggregated. This increased aggregation appears to be caused by sampling effects due to fewer individuals arriving per species, rather than stronger species sorting across variation in soil moisture. These scale-dependent effects suggest that studies evaluating species pools at a single, small scale may underestimate their effects, thereby contributing to uncertainty about the importance of regional processes for community assembly and their consequences for ecological restoration.

Mechanisms of Invasion Resistance of Aquatic Plant Communities.

Invasive plant species are among the major threats to freshwater biodiversity. Few experimental studies have investigated whether native plant diversity can provide biotic resistance to invaders in freshwater ecosystems. At small spatial scales, invasion resistance may increase with plant species richness due to a better use of available resources, leaving less available for a potential invader (Complementarity effect) and/or the greater probability to have a highly competitive (or productive) native species in the community (Selection effect). In submerged aquatic plant communities, we tested the following hypotheses: (1) invader establishment success is greatest in the absence of a native plant community; (2) lower in plant communities with greater native species richness, due to complementary and/or selection effects; and (3) invader establishment success would be lowest in rooted plant communities, based on the limiting similarity theory as the invader is a rooted submerged species. In a greenhouse experiment, we established mesocosms planted with 0 (bare sediment), 1, 2, and 4 submerged plant species native to NW Europe and subjected these to the South African invader Lagarosiphon major (Ridl.) Moss. We used two rooted (Myriophyllum spicatum L., Potamogeton perfoliatus L.) and two non-rooted native species (Ceratophyllum demersum L., Utricularia vulgaris L.) representing two distinct functional groups considering their nutrient acquisition strategy which follows from their growth form, with, respectively, the sediment and water column as their main nutrient source. We found that the presence of native vegetation overall decreased the establishment success of an alien aquatic plant species. The strength of this observed biotic resistance increased with increasing species richness of the native community. Mainly due to a selection effect, the native biomass of mixed communities overyielded, and this further lowered the establishment success of the invader in our experiment. The strongest biotic resistance was caused by the two native plant species that were of the same functional group, i.e., functionally most similar to the invader. These results support the prediction of Elton's biotic resistance hypothesis in aquatic ecosystems and indicate that both species richness and functional group identity can play an important role in decreasing establishment success of alien plant species.

Standardized experiments in mutant mice reveal behavioural similarity on 129S5 and C57BL/6J backgrounds.

Behavioural analysis of mice carrying engineered mutations is widely used to identify roles of specific genes in components of the mammalian behavioural repertoire. The reproducibility and robustness of phenotypic measures has become a concern that undermines the use of mouse genetic models for translational studies. Contributing factors include low individual study power, non-standardized behavioural testing, failure to address confounds and differences in genetic background of mutant mice. We have examined the importance of these factors using a statistically robust approach applied to behavioural data obtained from three mouse mutations on 129S5 and C57BL/6J backgrounds generated in a standardized battery of five behavioural assays. The largest confounding effect was sampling variation, which partially masked the genetic background effect. Our observations suggest that strong interaction of mutation with genetic background in mice in innate and learned behaviours is not necessarily to be expected. We found composite measures of innate and learned behaviour were similarly impacted by mutations across backgrounds. We determined that, for frequently used group sizes, a single retest of a significant result conforming to the commonly used P < 0.05 threshold results in a reproducibility of 60% between identical experiments. Reproducibility was reduced in the presence of strain differences. We also identified a P-value threshold that maximized reproducibility of mutant phenotypes across strains. This study illustrates the value of standardized approaches for quantitative assessment of behavioural phenotypes and highlights approaches that may improve the translational value of mouse behavioural studies.

Rarefaction and extrapolation of species richness using an area-based Fisher's logseries.

Fisher's logseries is widely used to characterize species abundance pattern, and some previous studies used it to predict species richness. However, this model, derived from the negative binomial model, degenerates at the zero-abundance point (i.e., its probability mass fully concentrates at zero abundance, leading to an odd situation that no species can occur in the studied sample). Moreover, it is not directly related to the sampling area size. In this sense, the original Fisher's alpha (correspondingly, species richness) is incomparable among ecological communities with varying area sizes. To overcome these limitations, we developed a novel area-based logseries model that can account for the compounding effect of the sampling area. The new model can be used to conduct area-based rarefaction and extrapolation of species richness, with the advantage of accurately predicting species richness in a large region that has an area size being hundreds or thousands of times larger than that of a locally observed sample, provided that data follow the proposed model. The power of our proposed model has been validated by extensive numerical simulations and empirically tested through tree species richness extrapolation and interpolation in Brazilian Atlantic forests. Our parametric model is data parsimonious as it is still applicable when only the information on species number, community size, or the numbers of singleton and doubleton species in the local sample is available. Notably, in comparison with the original Fisher's method, our area-based model can provide asymptotically unbiased variance estimation (therefore correct 95% confidence interval) for species richness. In conclusion, the proposed area-based Fisher's logseries model can be of broad applications with clear and proper statistical background. Particularly, it is very suitable for being applied to hyperdiverse ecological assemblages in which nonparametric richness estimators were found to greatly underestimate species richness.

The Polymerase Step Reaction (PSR) Method for Gene and Library Synthesis.

Current gene synthesis methods often incorporate a PCR-amplifying step in order to yield sufficient final product that is detectable and resolvable from multiple off-products. This amplification step can cause stochastic sampling effects that propagate errors during the synthesis and lower the variability when applied towards the construction of randomized libraries. We present the method for polymerase step reaction (PSR), a simple DNA polymerase-based gene synthesis reaction that assembles DNA oligonucleotides in a unidirectional fashion without the need for a PCR-type amplification (Lee et al., BioTechniques 59:163-166, 2015). The PSR method is simple and efficient with little off-product production, undetected stochastic sampling effects, and maximized variability when used to synthesize phage display libraries.

How plant diversity and legumes affect nitrogen dynamics in experimental grassland communities.

Positive relationships between species richness and ecosystem processes such as productivity or nitrogen cycling can be the result of a number of mechanisms. We examined how species richness, biomass, and legume presence, diversity, and abundance explained nitrogen dynamics in experimental grassland plots in northern Sweden. Nitrogen concentrations and δ15N values were measured in plants grown in 28 mixtures (58 plots) including 1, 2, 4, 8 or 12 local grassland species over four years. Values for δ15N declined over time for all three functional groups (grasses, legumes, and non-leguminous forbs), suggesting greater reliance on N fixed by legumes over time by all species. Above ground percent nitrogen (%N) also declined over time but root %N and total N did not. Path analysis of above ground data suggested that two main factors affected %N and the size of the N pool. First, higher plant diversity (species richness) increased total N through increased biomass in the plot. Although in the first two years of the experiment this was the result of a greater probability of inclusion of at least one legume, in the last two years diversity had a significant effect on biomass beyond this effect. Second, percent legumes planted in the plots had a strong effect on above ground %N and δ15N, but a much smaller effect on above ground biomass. In contrast, greater plant diversity affected N in roots both by increasing biomass and by decreasing %N (after controlling for effects mediated by root biomass and legume biomass). Increased legume biomass resulted in higher %N and lower δ15N for both non-legume forbs and grasses in the first year, but only for grasses in the third year. We conclude that a sampling effect (greater probability of including a legume) contributed towards greater biomass and total N in high-diversity communities early on in the experiment, but that over time this effect weakened and other positive effects of diversity became more important.

Resource availability dominates and alters the relationship between species diversity and ecosystem productivity in experimental plant communities.

Experimental evidence that plant species diversity has positive effects on biomass production appears to conflict with correlations of species diversity and standing biomass in natural communities. This may be due to the confounding effects of a third variable, resource availability, which has strong control over both diversity and productivity in natural systems and may conceal any positive effects of diversity on productivity. To test this hypothesis, I independently manipulated resource availability (soil fertility) and sown species diversity in a field experiment and measured their individual and interactive effects on productivity. Although fertility was a far stronger predictor of productivity than diversity, the effect of diversity on productivity significantly increased with fertility. Relative yield analyses indicated that plant mixtures of high fertility treatments significantly "overyielded," or were more productive than expected based on monoculture yields of component species. In contrast, plant mixtures of low fertility treatments had significantly lower-than-expected yields. The effect of diversity on productivity was also driven by sampling effects, where more species-rich mixtures were more likely to include particularly productive species. Unexpectedly, the strength of sampling effects was largely insensitive to fertility, although the particular species most responsible for sampling effects did change with fertility. These results suggest that positive effects of species diversity on ecosystem productivity in natural systems are likely to be masked by variation in environmental factors among habitats.

[Collection of mollusk intermediate hosts of Schistosoma at two sites in Lampsar (Senegal River valley): quantitative reproducibility]. / Collecte quantitative de mollusques hôtes intermédiaires de Schistosomes dans deux sites sur le Lampsar (Vallée du Fleuve Sénégal).

We studied the number of mollusks collected according to a specific protocol: 2 samplers prospecting in opposite directions for 1 min 30 s at 10 collection points regularly distributed on the site, for a total of 2 times 15 minutes. Because of the good reproducibility of the results of these collections, this method can be used for quantitative studies. A sampling effect was noted.