NicheA: creating virtual species and ecological niches in multivariate environmental scenarios

Robust methods by which to generate virtual species are needed urgently in the emerging field of distributional ecology to evaluate performance of techniques for modeling ecological niches and species distributions and to generate new questions in biogeography. Virtual species provide the opportunity to test hypotheses and methods based on known and unbiased distributions. We present Niche Analyst (NicheA), a toolkit developed to generate virtual species following the Hutchinsonian approach of an n‐multidimensional space occupied by the species. Ecological niche models are generated, analyzed, and visualized in an environmental space, and then projected to the geographic space in the form of continuous or binary species distribution models. NicheA is implemented in a stable and user‐friendly Java platform. The software, online manual, and user support are freely available at < http://nichea.sourceforge.net >.     

The effect of positional error on fine scale species distribution models increases for specialist species

Species occurrences inherently include positional error. Such error can be problematic for species distribution models (SDMs), especially those based on fine-resolution environmental data. It has been suggested that there could be a link between the influence of positional error and the width of the species ecological niche. Although positional errors in species occurrence data may imply serious limitations, especially for modelling species with narrow ecological niche, it has never been thoroughly explored. We used a virtual species approach to assess the effects of the positional error on fine-scale SDMs for species with environmental niches of different widths. We simulated three virtual species with varying niche breadth, from specialist to generalist. The true distribution of these virtual species was then altered by introducing different levels of positional error (from 5 to 500 m). We built generalized linear models and MaxEnt models using the distribution of the three virtual species (unaltered and altered) and a combination of environmental data at 5 m resolution. The models’ performance and niche overlap were compared to assess the effect of positional error with varying niche breadth in the geographical and environmental space. The positional error negatively impacted performance and niche overlap metrics. The amplitude of the influence of positional error depended on the species niche, with models for specialist species being more affected than those for generalist species. The positional error had the same effect on both modelling techniques. Finally, increasing sample size did not mitigate the negative influence of positional error. We showed that fine-scale SDMs are considerably affected by positional error, even when such error is low. Therefore, where new surveys are undertaken, we recommend paying attention to data collection techniques to minimize the positional error in occurrence data and thus to avoid its negative effect on SDMs, especially when studying specialist species.     

A comparison of methods for mapping species ranges and species richness

Aim  Maps of species richness are the basis for applied research and conservation planning as well as for theoretical research investigating patterns of richness and the processes shaping these patterns. The method used to create a richness map could influence the results of such studies, but differences between these methods have been insufficiently evaluated. We investigate how different methods of mapping species ranges can influence patterns of richness, at three spatial resolutions.
Location  California, USA.
Methods  We created richness maps by overlaying individual species range maps for terrestrial amphibians and reptiles. The methods we used to create ranges included: point-to-grid maps, obtained by overlaying point observations of species occurrences with a grid and determining presence or absence for each cell; expert-drawn maps; and maps obtained through species distribution modelling. We also used a hybrid method that incorporated data from all three methods. We assessed the correlation and similarity of the spatial patterns of richness maps created with each of these four methods at three different resolutions.
Results  Richness maps created with different methods were more correlated at lower spatial resolutions than at higher resolutions. At all resolutions, point-to-grid richness maps estimated the lowest species richness and those derived from species distribution models the highest. Expert-drawn maps and hybrid maps showed intermediate levels of richness but had different spatial patterns of species richness from those derived with the other methods.
Main conclusions  Even in relatively well-studied areas such as California, different data sources can lead to rather dissimilar maps of species richness. Evaluating the strengths and weaknesses of different methods for creating a richness map can provide guidance for selecting the approach that is most appropriate for a given application and region.     

virtualspecies,an R package to generate virtual species distributions

virtualspecies is a freely available package for R designed to generate virtual species distributions, a procedure increasingly used in ecology to improve species distribution models. This package combines the existing methodological approaches with the objective of generating virtual species distributions with increased ecological realism. The package includes 1) generating the probability of occurrence of a virtual species from a spatial set of environmental conditions (i.e. environmental suitability), with two different approaches; 2) converting the environmental suitability into presence–absence with a probabilistic approach; 3) introducing dispersal limitations in the realised virtual species distributions and 4) sampling occurrences with different biases in the sampling procedure. The package was designed to be extremely flexible, to allow users to simulate their own defined species–environment relationships, as well as to provide a fine control over every simulation parameter. The package also includes a function to generate random virtual species distributions. We provide a simple example in this paper showing how increasing ecological realism of the virtual species impacts the predictive performance of species distribution models. We expect that this new package will be valuable to researchers willing to test techniques and protocols of species distribution models as well as various biogeographical hypotheses.     

Interplay between ferritin metabolism, reactive oxygen species and nitric oxide

 The biological relevance of each of the three inorganic species – iron, oxygen, and nitric oxide (NO) – is crucial. Moreover, their metabolic pathways cross each other and thus create a complex network of connections responsible for the regulation of many essential biological processes. The iron storage protein ferritin, one of the main regulators of iron homeostasis, influences oxygen and NO metabolism. Here, examples are given of the biological interactions of the ferritin molecule (ferritin iron and ferritin shell) with reactive oxygen species (ROS) and NO. The focus is the regulation of ferritin expression by ROS and NO. From these data, ferritin emerges as an important cytoprotective component of the cellular response to ROS and NO. Also, by its ability to alter the amount of intracellular "free" iron, ferritin may affect the metabolism of ROS and NO. It is proposed that this putative activity of ferritin may constitute a missing link in the regulatory loop between iron, ROS, and NO. Received: 2 January 1997 / Accepted: 9 June 1997     

Validation of a model-based virtual trials method for tight glycemic control in intensive care

Background  

In-silico virtual patients and trials offer significant advantages in cost, time and safety for designing effective tight glycemic control (TGC) protocols. However, no such method has fully validated the independence of virtual patients (or resulting clinical trial predictions) from the data used to create them. This study uses matched cohorts from a TGC clinical trial to validate virtual patients and in-silico virtual trial models and methods.     

Detecting the role of individual species for overyielding in experimental grassland communities composed of potentially dominant species

Several studies have shown that the contribution of individual species to the positive relationship between species richness and community biomass production cannot be easily predicted from species monocultures. Here, we used a biodiversity experiment with a pool of nine potentially dominant grassland species to relate the species richness–productivity relationship to responses in density, size and aboveground allocation patterns of individual species. Aboveground community biomass increased strongly with the transition from monocultures to two-species mixtures but only slightly with the transition from two- to nine-species mixtures. Tripartite partitioning showed that the strong increase shown by the former was due to trait-independent complementarity effects, while the slight increase shown by the latter was due to dominance effects. Trait-dependent complementarity effects depended on species composition. Relative yield total (RYT) was greater than 1 (RYT > 1) in mixtures but did not increase with species richness, which is consistent with the constant complementarity effect. The relative yield (RY) of only one species, Arrhenatherum elatius, continually increased with species richness, while those of the other species studied decreased with species richness or varied among different species compositions within richness levels. High observed/expected RYs (RYo/RYe > 1) of individual species were mainly due to increased module densities, whereas low observed/expected RYs (RYo/RYe < 1) were due to more pronounced decreases in module density (species with stoloniferous or creeping growth) or module size (species with clearly-defined plant individuals). The trade-off between module density and size, typical for plant populations under the law of constant final yield, was compensated among species. The positive trait-independent complementarity effect could be explained by an increase in community module density, which reached a maximum at low species richness. In contrast, the increasing dominance effect was attributable to the species-specific ability, in particular that of A. elatius, to increase module size, while intrinsic growth limitations led to a suppression of the remaining species in many mixtures. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Assessment of instream structures for habitat improvement for two critically endangered fish species

The number of fish habitat improvement schemes has greatly increased in response to the widespread degradation of aquatic ecosystems. However, many of these enhancement projects often fail to create expected habitat conditions, because they are rarely planned and executed with inputs from the species’ habitat requirements throughout their life histories, and it is frequently assumed that the implementation of a specific instream structure for habitat improvement will always benefit all species present. Using a 2D hydraulic model, the present study evaluates the potential habitat improvement for two critically endangered fish species—the Southwestern arched-mouth nase Iberochondrostoma almacai and the Arade chub Squalius aradensis—resulting from simulating the introduction of different instream structures (islands, lateral bays, and deflectors) in a modified Mediterranean river reach. The introduction of islands in the river channel was found to be the best improvement measure for YOY and juvenile nase and chub, as shown by increases in the mean annual Weighted Usable Area (WUA) of more than 100 and 50%, respectively, compared to the present conditions. On the other hand, the simulation with current deflectors proved to be the worst scenario, particularly for nase, with mean annual WUA decreasing by 3.6, 17.8 and 22.7% for YOY, juveniles and adults, respectively. The findings of this study point to the need to account for different species life-history stages when modelling the implementation of instream structures for habitat improvement and also provide a sound basis for future conservation-related studies conducted in Mediterranean rivers that harbour other threatened “sister” species.     

基于投入产出分析的北京市虚拟水核算

城市化进程的加快与工农业的迅速发展使城市水消耗量日趋增加。水资源短缺不仅会造成居民生活质量下降,还会制约社会经济的可持续发展。从贸易和消费的角度核算虚拟水可为研究城市水资源管理提供新的视角。通过投入产出分析了构建了城市系统虚拟水核算模型,利用虚拟水直接和完全用水系数、虚拟水消费量等指标分析城市虚拟水消耗和虚拟水进出口特征。以北京市为例,利用2012年北京市投入产出表和部门的水资源消耗数据核算不同部门的用水系数、最终消费虚拟水量、虚拟水进出口贸易量及部门间虚拟水流转量。结果表明:北京市为虚拟水净进口城市,净进口虚拟水量6.77×10~9m~3,相当于北京市虚拟水用水总量(8.25×10~9m~3)的82%,农业和制造业为主要虚拟水进口部门;北京市虚拟水出口结构存在不合理之处,经济投入产出表中各部门出口总额占最终消费的79.9%,但出口产品消耗的虚拟水占了最终消费隐含虚拟水的85.04%,其中农产品消耗6.7%虚拟水但经济收益仅占1%,说明北京市出口以较大的虚拟水消耗量换取了较少的经济收益,需要减少虚拟水含量较大但经济价值不高的产品出口(如农产品);识别出的主要虚拟水流出-流入关系部门包括农业-制造业,农业-服务业和制造业-建筑业等部门的关联关系,可成为减少间接水消耗的关键路径。     

Distribution of alien animal species richness in the Czech Republic

Biogeographical barriers formed by natural forces over billions of years have been substantially disrupted by human activity, particularly in recent centuries. In response to these anthropogenic changes, global homogenization of biota is observed at an ever‐increasing rate, causing environmental and economic losses as well as emerging health risks. Identifying factors underlying alien species richness is essential for prevention of future introductions and subsequent spread. In this study, we examined the effects of environmental and human‐related factors on distribution of alien animal species richness in the Czech Republic (Central Europe). We compiled a set of maps showing the level of invasion of six categories of alien animal species in each of 628 grid cells (ca. 12.0 × 11.1 km) covering the Czech Republic. Relationships between alien species richness and 12 variables characterizing climatic conditions, topography, land cover, and human population size were calculated using the generalized least squares method. Species richness of all alien species, of invertebrates, and of terrestrial species showed the strongest positive relationship with mean annual temperature, while the number of black and grey (proposed prominent invaders) and aquatic species was most closely related to the presence of large rivers. Alien vertebrates showed a strong negative relationship with annual precipitation. The highest alien animal species richness was found in and near large population centers and in agricultural landscapes in warm and dry lowlands. The gateways for alien aquatic species are rather large rivers over sport fishing and aquaculture import. Compiled maps create a powerful visual communication tool, useful in development of programs to prevent future introductions.     

Effects of plant species on nutrient cycling

Plant species create positive feedbacks to patterns of nutrient cycling in natural ecosystems. For example, in nutrient-poor ecosystems, plants grow slowly, use nutrients efficiently and produce poor-quality litter that decomposes slowly and deters herbivores. /n contrast, plant species from nutrient-rich ecosystems grow rapidly, produce readily degradable litter and sustain high rates of herbivory, further enhancing rates of nutrient cycling. Plants may also create positive feedbacks to nutrient cycling because of species' differences in carbon deposition and competition with microbes for nutrients in the rhizosphere. New research is showing that species' effects can be as or more important than abiotic factors, such as climate, in controlling ecosystem fertility.     

Characterizing complex mixed-species bird flocks using an objective method for determining species participation

We developed sampling methods to characterize the participation of bird species in foraging flocks led by the Eastern Tufted Titmouse (Baeolophus bicolor) in North-central Florida during winter, because standard field methods, developed primarily for permanent resident Neotropical flocks, were intractable in our system. During January–February 2004 and November 2004–March 2005, we observed 55 mixed-species flocks, recorded 40 potential flocking species [mean of 12.4 species (SD = 3.8; range 3–20), 26.3 individuals (SD = 12.2; range 8–60), and 3.1 titmice (SD = 1.4; range 1–7), per flock]. Twenty-six species were observed frequently enough (>10% of observations) to be included in analyses. We paired 60-min flock observations with 10-min point counts conducted in locations used by flocks, but after flocks had moved more than 100 m away. This method yielded a measure of flocking propensity: the ratio of the number of individuals observed in the flock versus during the point count for each species. We used regression tree (RT) analysis to classify species into groupings according to their levels of flock participation, and to investigate relationships between flocking propensity and various environmental and social factors that we measured. Our analysis identified three clear species groups; “Nuclear/Regular Associate” (12 spp.; high/moderate), “Occasional Associate” (four spp.; moderate/low), and “Non-joiner/Accidental” (ten spp.; low/no flocking propensity). Groupings were similar to schemes produced via more time-intensive field methods. In order to contextualize grouping categories, we conducted a review of flocking group definitions and relevant autecological information (e.g., interspecific sociality) about our study species. We found this method to be useful for geographically extensive sampling of species’ participation in mixed-species flocks, despite high inter-flock variability in species composition and limited labor.     

Spatial and temporal changes in species composition of submersed aquatic vegetation reveal effects of river restoration

We examined temporal changes in spatial patterns of submersed aquatic vegetation (SAV) in response to the restoration of geomorphic habitat in Navigation Pool 8 of the Upper Mississippi River from 1998 to 2016. The frequency of occurrence and species composition of SAV at sampling sites were spatially interpolated for each year to create annual maps. Linear models were fitted to temporal changes in SAV within each map pixel. The frequency of occurrence of SAV (across all species) increased over time in much of the impounded region of the pool, including areas near restored islands. However, impounded areas maintained a relatively consistent species composition over time, with species known to be tolerant of higher flow velocities (>0.10 m/second) and wind fetch distances (>1,000 m) (e.g. Vallisneria americana) being most abundant. In contrast, areas protected by newly constructed islands transitioned from V. americana to species found in other protected backwater habitats and known to be intolerant of high flow velocities and wind fetch distances (e.g. Ceratophyllum demersum). The results suggest that previously reported improvements in water clarity may have improved growing conditions for all SAV species, especially in the lower impounded portion of the pool, while island restoration created more backwater‐like habitats and facilitated changes in species composition. Assessing changes in SAV occurrence alone offers only a partial view of local‐scale river restoration (e.g. island building), while analyses of species composition are likely to be more indicative of the types of changes (i.e. reduced flow velocity and wind fetch) associated with restoring geomorphic habitat.     

Relevance of crustacean carapace wettability for fouling

Carapace wettability and density of fouling organisms (bacteria, diatoms, protozoa, fungi, macro-organisms) were investigated for 45 crustacean species (Hoplocarida, Decapoda) from 15 families in the Gulf of Thailand. The results show that crustaceans can create and maintain characteristic carapace wettabilities. About 21 species (47%) possess highly wettable carapaces with contact angles below 20°. Contact angles between 20° and 40° were recorded for four species (2%), angles between 40° and 60° for eight species (4%) and from 60° to 70° for 11 (24%) species. One species, Alpheus euphrosyne (Alpheidae, Decapoda), exhibited an extremely low surface wettability (contact angle: 91°). Densities of colonisers and contact angles did not correlate. Very low wettability by water ( > 90°) may only contribute little to fouling reduction in A. euphrosyne which showed the most hydrophobic carapace surface and was colonised by the lowest numbers of bacteria among all species and no other colonisers at all. We conclude that surface wettability is of little relevance for antifouling defence in crustaceans.     

Crustose coralline algal species host distinct bacterial assemblages on their surfaces

Crustose coralline algae (CCA) are important components of many marine ecosystems. They aid in reef accretion and stabilization, create habitat for other organisms, contribute to carbon sequestration and are important settlement substrata for a number of marine invertebrates. Despite their ecological importance, little is known about the bacterial communities associated with CCA or whether differences in bacterial assemblages may have ecological implications. This study examined the bacterial communities on four different species of CCA collected in Belize using bacterial tag-encoded FLX amplicon pyrosequencing of the V1–V3 region of the 16S rDNA. CCA were dominated by Alphaproteobacteria, Gammaproteobacteria and Actinomycetes. At the operational taxonomic unit (OTU) level, each CCA species had a unique bacterial community that was significantly different from all other CCA species. Hydrolithon boergesenii and Titanoderma prototypum, CCA species that facilitate larval settlement in multiple corals, had higher abundances of OTUs related to bacteria that inhibit the growth and/or biofilm formation of coral pathogens. Fewer coral larvae settle on the surfaces of Paragoniolithon solubile and Porolithon pachydermum. These CCA species had higher abundances of OTUs related to known coral pathogens and cyanobacteria. Coral larvae may be able to use the observed differences in bacterial community composition on CCA species to assess the suitability of these substrata for settlement and selectively settle on CCA species that contain beneficial bacteria.     

The westernmost tarsier: A new genus and species from the Miocene of Pakistan

As the closest living sister group of anthropoids, tarsiers (Family Tarsiidae) are an important group in primate evolution. However, their fossil record is poor: only four species have been described, two from the Eocene of China and two from the Miocene of Thailand. All are from outside the range of the living species, which occur only on islands off Southeast Asia. Here, we describe a new fossil tarsier from Pakistan, a significant range extension. This record consists of two lower molars, an upper molar, and a lower premolar found in the Miocene Manchar Formation (∼18–16 Ma [millions of years ago]) of Sindh Province, southern Pakistan. The Pakistani tarsier is morphologically distinct from all living and fossil tarsiers, but most similar to the middle Miocene Thai species Tarsius thailandicus. Though living tarsiers have traditionally been classified in a single genus, a recent revision proposed a division into three genera, which is strongly supported by molecular data. The Pakistani species is not referable to any of these genera, and we create for it and T. thailandicus a new tarsiid genus. This discovery broadens our understanding of the geographic range and morphological diversity of Miocene tarsiers and helps to put the living tarsiers into their evolutionary context.     

Functional roles of an engineer species for coastal benthic invertebrates and demersal fish

Through their tissues or activities, engineer species create, modify, or maintain habitats and alter the distribution and abundance of many plants and animals. This study investigates key ecological functions performed by an engineer species that colonizes coastal ecosystems. The gregarious tubiculous amphipod Haploops nirae is used as a biological model. According to previous studies, the habitat engineered by H. nirae (i.e., Haploops habitat) could provide food and natural shelter for several benthic species such as benthic diatoms belonging to the gender Navicula, the micrograzer Geitodoris planata, or the bivalve Polititapes virgineus. Using data from scientific surveys conducted in two bays, this study explored whether (1) the Haploops sandy‐mud community modifies invertebrate and ichthyologic community structure (diversity and biomass); (2) H. nirae creates a preferential feeding ground; and (3) this habitat serves as a refuge for juvenile fish. Available Benthic Energy Coefficients, coupled with more traditional diversity indices, indicated higher energy available in Haploops habitat than in two nearby habitats (i.e., Sternaspis scutata and Amphiura filiformis/Owenia fusiformis habitats). The use of isotopic functional indices (IFIs) indicated (1) a higher functional richness in the Haploops habitat, related to greater diversity in food sources and longer food chains; and (2) a higher functional divergence, associated with greater consumption of a secondary food source. At the invertebrate‐prey level, IFIs indicated little specialization and little trophic redundancy in the engineered habitat, as expected for homogenous habitats. Our results partly support empirical knowledge about engineered versus nonengineered habitats and also add new perspectives on habitat use by fish and invertebrate species. Our analyses validated the refuge‐area hypothesis for a few fish species. Although unique benthic prey assemblages are associated with Haploops habitat, the hypothesis that it is a preferential feeding area was not verified. However, specialist feeding behavior was observed for predators, which calls for further investigation.     

The effect of species models on estimates of within-lineage variation in integration

Species may be modeled as comprised of individuals, populations or a virtual code. A virtual code can be understood as general potential that appears as actualization within specific environmental, both internal and external, contexts. These general potentials form a capacity to network that allows potentials to be expressed and offers robustness through its interconnections. In the present work, the degree of within-lineage variation in integration was not strongly model-dependent. However, the relationships among model-dependent estimates of such variation and within-lineage phyletic variation were not equal. The strongest relationship was between within-lineage variation in integration, when species were modeled as a virtual code, and within-lineage phyletic variation. The second strongest, and only other statistically significant relationship, was between variation in integration when species were modeled as a virtual code and as a collection of populations. The last result argues for a strong ontogenetic and micro-environmental effect on the expression of features in an individual. If species were a virtual code they would evolve by incorporation of all attributes, ontogenetic, environmental and genetic into that code until it becomes unstable and bifurcates. Species as a virtual code, an approach that explicitly incorporates developmental change into evolution, is a non-material representation of species as a complex information system, incorporating, if we refer to mathematical analysis, both the real and the imaginary. If one wished to stress the material, this study could be seen as empirical documentation of species as information systems.     

Disentangling scale dependencies in species environmental niches and distributions

Understanding species’ responses to environmental conditions, and how these ­species–environment associations shape spatial distributions, are longstanding goals in ecology and biogeography. However, an essential component of species–environment relationships – the spatial unit, or grain, at which they operate – remains unresolved. We identify three components of scale‐dependence in analyses of species–environment associations: 1) response grain, the grain at which species respond most strongly to their environment; 2) environment spatial structure, the pattern of spatial autocorrelation intrinsic to an environmental factor; and 3) analysis grain, the grain at which analyses are conducted and ecological inferences are made. We introduce a novel conceptual framework that defines these scale components in the context of analyzing species–environment relationships, and provide theoretical examples of their interactions for species with various ecological attributes. We then use a virtual species approach to investigate the impacts of each component on common methods of measuring and predicting species–environment relationships. We find that environment spatial structure has a substantial impact on the ability of even simple, univariate species distribution models (SDMs) to recover known species–­environment associations at coarse analysis grains. For simulated environments with ‘fine’ and ‘intermediate’ spatial structure, model explanatory power, and the frequency with which simple SDMs correctly estimated a virtual species’ response to the simulated environment, dramatically declined as analysis grain increased. Informed by these results, we use a scaling analysis to identify maximum analysis grains for individual environmental factors, and a scale optimization procedure to determine the grain of maximum predictive accuracy. Implementing these analysis grain thresholds and model performance standards in an example east African study system yields more accurate distribution predictions, compared to SDMs independently constructed at arbitrary analysis grains. Finally, we integrate our conceptual framework with virtual and empirical results to provide practical recommendations for researchers asking common questions about species–environment relationships.