Bio‐ORACLE: a global environmental dataset for marine species distribution modelling

Aim The oceans harbour a great diversity of organisms whose distribution and ecological preferences are often poorly understood. Species distribution modelling (SDM) could improve our knowledge and inform marine ecosystem management and conservation. Although marine environmental data are available from various sources, there are currently no user‐friendly, high‐resolution global datasets designed for SDM applications. This study aims to fill this gap by assembling a comprehensive, uniform, high‐resolution and readily usable package of global environmental rasters. Location Global, marine. Methods We compiled global coverage data, e.g. satellite‐based and in situ measured data, representing various aspects of the marine environment relevant for species distributions. Rasters were assembled at a resolution of 5 arcmin (c. 9.2 km) and a uniform landmask was applied. The utility of the dataset was evaluated by maximum entropy SDM of the invasive seaweed Codium fragile ssp. fragile. Results We present Bio‐ORACLE (ocean rasters for analysis of climate and environment), a global dataset consisting of 23 geophysical, biotic and climate rasters. This user‐friendly data package for marine species distribution modelling is available for download at http://www.bio‐oracle.ugent.be . The high predictive power of the distribution model of C. fragile ssp. fragile clearly illustrates the potential of the data package for SDM of shallow‐water marine organisms. Main conclusions The availability of this global environmental data package has the potential to stimulate marine SDM. The high predictive success of the presence‐only model of a notorious invasive seaweed shows that the information contained in Bio‐ORACLE can be informative about marine distributions and permits building highly accurate species distribution models.     

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

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

Biogeo: an R package for assessing and improving data quality of occurrence record datasets

Occurrence data from museum and herbarium collections are valuable for mapping biodiversity patterns in space and time. Unfortunately these collections datasets contain many errors and suffer from several data quality issues that can influence the quality of the products derived from them. It is up to the user to identify these errors and data quality issues when using these data. Despite the large number of potential users of these datasets there are few software tools dedicated to error detection and correction of collections datasets. The R package biogeo was developed for detecting and correcting errors and for assessing of data quality of collections datasets consisting of occurrence records. Features of the package include error detection, such as mismatches between the recorded country and the country where the record is plotted, records of terrestrial species that fall into the sea and outlier detection. A key feature of the package is the ability to identify likely alternative positions for points that represent obvious errors in the dataset and functions to explore records in geographical and environmental space in order to identify possible errors in the dataset. Functions are also available for converting coordinates that are in various text formats into degrees, minutes and seconds and then into decimal degrees.     

Phylogenetic position and composition of Zygiellinae and Caerostris,with new insight into orb‐web evolution and gigantism

Orb‐weaving spiders are good objects for evolutionary research, but phylogenetic relationships among and within orb‐weaving lineages are poorly understood. Here we present the first species‐level molecular phylogeny that includes the enigmatic orb weavers ‘Zygiellidae’ and Caerostris. Zygiellidae is interesting for the evolution of the sector web, and Caerostris is noteworthy for web gigantism and extraordinary silk biomechanics. We assembled a molecular data set using mitochondrial (COI, 16S) and nuclear (H3, 18S, 28S, ITS2) gene fragments for 112 orbicularian exemplars, focusing on taxa with diverse web architecture and size. We show that ‘Zygiellidae’ contains the Holarctic Zygiella genus group (Leviellus, Parazygiella, Stroemiellus, and Zygiella) and the Australasian Phonognatha and Deliochus. As this clade is placed with Araneidae in all analyses we treat it as a subfamily, Zygiellinae. Using the new phylogeny, we show that the sector web evolved eight times, and coevolved with the silk tube retreat, but that these features are not zygielline synapomorphies. Zygiellinae, Caerostris, and some other araneids form a basal grade of araneids that differ from ‘classical’ araneids in web‐building and preying behaviour. We also confirm that Caerostris represents the most striking case of spider‐web gigantism. © 2015 The Linnean Society of London     

ConR: An R package to assist large‐scale multispecies preliminary conservation assessments using distribution data

The Red List Categories and the accompanying five criteria developed by the International Union for Conservation of Nature (IUCN) provide an authoritative and comprehensive methodology to assess the conservation status of organisms. Red List criterion B, which principally uses distribution data, is the most widely used to assess conservation status, particularly of plant species. No software package has previously been available to perform large‐scale multispecies calculations of the three main criterion B parameters [extent of occurrence (EOO), area of occupancy (AOO) and an estimate of the number of locations] and provide preliminary conservation assessments using an automated batch process. We developed ConR, a dedicated R package, as a rapid and efficient tool to conduct large numbers of preliminary assessments, thereby facilitating complete Red List assessment. ConR (1) calculates key geographic range parameters (AOO and EOO) and estimates the number of locations sensu IUCN needed for an assessment under criterion B; (2) uses this information in a batch process to generate preliminary assessments of multiple species; (3) summarize the parameters and preliminary assessments in a spreadsheet; and (4) provides a visualization of the results by generating maps suitable for the submission of full assessments to the IUCN Red List. ConR can be used for any living organism for which reliable georeferenced distribution data are available. As distributional data for taxa become increasingly available via large open access datasets, ConR provides a novel, timely tool to guide and accelerate the work of the conservation and taxonomic communities by enabling practitioners to conduct preliminary assessments simultaneously for hundreds or even thousands of species in an efficient and time‐saving way.     

Kmasker plants – a tool for assessing complex sequence space in plant species

Many plant genomes display high levels of repetitive sequences. The assembly of these complex genomes using short high‐throughput sequence reads is still a challenging task. Underestimation or disregard of repeat complexity in these datasets can easily misguide downstream analysis. Detection of repetitive regions by k‐mer counting methods has proved to be reliable. Easy‐to‐use applications utilizing k‐mer counting are in high demand, especially in the domain of plants. We present Kmasker plants, a tool that uses k‐mer count information as an assistant throughout the analytical workflow of genome data that is provided as a command‐line and web‐based solution. Beside its core competence to screen and mask repetitive sequences, we have integrated features that enable comparative studies between different cultivars or closely related species and methods that estimate target specificity of guide RNAs for application of site‐directed mutagenesis using Cas9 endonuclease. In addition, we have set up a web service for Kmasker plants that maintains pre‐computed indices for 10 of the economically most important cultivated plants. Source code for Kmasker plants has been made publically available at https://github.com/tschmutzer/kmasker . The web service is accessible at https://kmasker.ipk-gatersleben.de .     

multimark: an R package for analysis of capture–recapture data consisting of multiple “noninvasive” marks

I describe an open‐source R package, multimark , for estimation of survival and abundance from capture–mark–recapture data consisting of multiple “noninvasive” marks. Noninvasive marks include natural pelt or skin patterns, scars, and genetic markers that enable individual identification in lieu of physical capture. multimark provides a means for combining and jointly analyzing encounter histories from multiple noninvasive sources that otherwise cannot be reliably matched (e.g., left‐ and right‐sided photographs of bilaterally asymmetrical individuals). The package is currently capable of fitting open population Cormack–Jolly–Seber (CJS) and closed population abundance models with up to two mark types using Bayesian Markov chain Monte Carlo (MCMC) methods. multimark can also be used for Bayesian analyses of conventional capture–recapture data consisting of a single‐mark type. Some package features include (1) general model specification using formulas already familiar to most R users, (2) ability to include temporal, behavioral, age, cohort, and individual heterogeneity effects in detection and survival probabilities, (3) improved MCMC algorithm that is computationally faster and more efficient than previously proposed methods, (4) Bayesian multimodel inference using reversible jump MCMC, and (5) data simulation capabilities for power analyses and assessing model performance. I demonstrate use of multimark using left‐ and right‐sided encounter histories for bobcats (Lynx rufus) collected from remote single‐camera stations in southern California. In this example, there is evidence of a behavioral effect (i.e., trap “happy” response) that is otherwise indiscernible using conventional single‐sided analyses. The package will be most useful to ecologists seeking stronger inferences by combining different sources of mark–recapture data that are difficult (or impossible) to reliably reconcile, particularly with the sparse datasets typical of rare or elusive species for which noninvasive sampling techniques are most commonly employed. Addressing deficiencies in currently available software, multimark also provides a user‐friendly interface for performing Bayesian multimodel inference using capture–recapture data consisting of a single conventional mark or multiple noninvasive marks.     

driftsel: an R package for detecting signals of natural selection in quantitative traits

Approaches and tools to differentiate between natural selection and genetic drift as causes of population differentiation are of frequent demand in evolutionary biology. Based on the approach of Ovaskainen et al. (2011), we have developed an R package (driftsel ) that can be used to differentiate between stabilizing selection, diversifying selection and random genetic drift as causes of population differentiation in quantitative traits when neutral marker and quantitative genetic data are available. Apart from illustrating the use of this method and the interpretation of results using simulated data, we apply the package on data from three‐spined sticklebacks (Gasterosteus aculeatus) to highlight its virtues. driftsel can also be used to perform usual quantitative genetic analyses in common‐garden study designs.     

Why to account for finite sites in population genetic studies and how to do this with Jaatha 2.0

With the advent of next‐generation sequencing technologies, large data sets of several thousand loci from multiple conspecific individuals are available. Such data sets should make it possible to obtain accurate estimates of population genetic parameters, even for complex models of population history. In the analyses of large data sets, it is difficult to consider finite‐sites mutation models (FSMs). Here, we use extensive simulations to demonstrate that the inclusion of FSMs is necessary to avoid severe biases in the estimation of the population mutation rate θ, population divergence times, and migration rates. We present a new version of Jaatha, an efficient composite‐likelihood method for estimating demographic parameters from population genetic data and evaluate the usefulness of Jaatha in two biological examples. For the first application, we infer the speciation process of two wild tomato species, Solanum chilense and Solanum peruvianum. In our second application example, we demonstrate that Jaatha is readily applicable to NGS data by analyzing genome‐wide data from two southern European populations of Arabidopsis thaliana. Jaatha is now freely available as an R package from the Comprehensive R Archive Network (CRAN).     

msap: a tool for the statistical analysis of methylation‐sensitive amplified polymorphism data

In this study msap, an R package which analyses methylation‐sensitive amplified polymorphism (MSAP or MS‐AFLP) data is presented. The program provides a deep analysis of epigenetic variation starting from a binary data matrix indicating the banding pattern between the isoesquizomeric endonucleases HpaII and MspI, with differential sensitivity to cytosine methylation. After comparing the restriction fragments, the program determines if each fragment is susceptible to methylation (representative of epigenetic variation) or if there is no evidence of methylation (representative of genetic variation). The package provides, in a user‐friendly command line interface, a pipeline of different analyses of the variation (genetic and epigenetic) among user‐defined groups of samples, as well as the classification of the methylation occurrences in those groups. Statistical testing provides support to the analyses. A comprehensive report of the analyses and several useful plots could help researchers to assess the epigenetic and genetic variation in their MSAP experiments. msap is downloadable from CRAN ( http://cran.r-project.org/ ) and its own webpage ( http://msap.r-forge.R-project.org/ ). The package is intended to be easy to use even for those people unfamiliar with the R command line environment. Advanced users may take advantage of the available source code to adapt msap to more complex analyses.     

Unlocking the potential of historical abundance datasets to study biomass change in flying insects

1. Trends in insect abundance are well established in some datasets, but far less is known about how abundance measures translate into biomass trends. Moths (Lepidoptera) provide particularly good opportunities to study trends and drivers of biomass change at large spatial and temporal scales, given the existence of long‐term abundance datasets. However, data on the body masses of moths are required for these analyses, but such data do not currently exist.
2. To address this data gap, we collected empirical data in 2018 on the forewing length and dry mass of field‐sampled moths, and used these to train and test a statistical model that predicts the body mass of moth species from their forewing lengths (with refined parameters for Crambidae, Erebidae, Geometridae and Noctuidae).
3. Modeled biomass was positively correlated, with high explanatory power, with measured biomass of moth species (R² = 0.886 ± 0.0006, across 10,000 bootstrapped replicates) and of mixed‐species samples of moths (R² = 0.873 ± 0.0003), showing that it is possible to predict biomass to an informative level of accuracy, and prediction error was smaller with larger sample sizes.
4. Our model allows biomass to be estimated for historical moth abundance datasets, and so our approach will create opportunities to investigate trends and drivers of insect biomass change over long timescales and broad geographic regions.

     

Contrasting Patch Residence Strategy in Two Species of Sit‐and‐Wait Foragers Under the Same Environment: A Constraint by Life History?

The present study explored the significance of life history constraints on patch residence strategy by using two congeneric web spider species living in the same habitat. Nephila maculata had a large body size but had a shorter developmental period compared with N. clavata, indicating that N. maculata should have a greater foraging efficiency to reach maturity and reproduce. Residence time at web‐sites in N. maculata was shorter than that in N. clavata, irrespective of the season. However, supplementation of food to N. maculata increased residence time, suggesting that it searches web‐sites with higher prey intake. Investment of web materials, an important trait influencing web relocation frequency, was not greater in N. maculata. In addition, microhabitat and prey size did not differ significantly after controlling for the effect of body size. Because N. maculata needs to attain a large body size in a shorter period of time, this species appears to take a risk of moving patches to seek high quality web‐sites.     

Variable littoral‐pelagic coupling as a food‐web response to seasonal changes in pelagic primary production

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Phylogenetic placement of the Tasmanian spider Acrobleps hygrophilus (Araneae, Anapidae) with comments on the evolution of the capture web in Araneoidea

This paper studies the family‐level phylogenetic placement of the conflicting Tasmanian spider genus Acrobleps using both morphological and behavioral data. We also provide a formal taxonomic revision of Acrobleps, including information on its web architecture and natural history, as well as detailed morphological information for A. hygrophilus, its only species. Acrobleps hygrophilus lacks the typical mysmenid features. Furthermore A. hygrophilus does have all typical and diagnostic characteristics of Anapidae, except for the labral spur. We also discuss two noteworthy morphological features of Acrobleps: the pore bearing depressions of the carapace and the granulated cuticle of the spinnerets. Variation in the latter feature might provide a useful phylogenetic character. Based on the results of cladistic analyses we propose the transfer of Acrobleps from the Mysmenidae to its original placement within the Anapidae. We also propose a new lineage, informally labeled as the “clawless female clade”, which includes synaphrids, cyatholipids and “symphytognathoids.” The secondary absence of the female palpal claw provides support for the “clawless female clade.” We discuss the evolution of the orb web within anapids and other symphytognathoids based on the results of our cladistic analyses. The identical bi‐dimensional webs of the anapid Elanapis and of symphytognathids have evolved independently. Finally, we comment on the implications of one of our analyses regarding araneoid web evolution. We conclude that the taxon sample included in the previous orbicularian data matrix (modified and used in this study) is adequate to test the phylogenetic placement of Acrobleps in Anapidae but insufficient to significantly assess web evolution within Araneoidea. © The Willi Hennig Society 2007.     

Molecular phylogenetics of slit‐faced bats (Chiroptera: Nycteridae) reveal deeply divergent African lineages

The bat family Nycteridae contains only the genus Nycteris, which comprises 13 currently recognized species from Africa and the Arabian Peninsula, one species from Madagascar, and two species restricted to Malaysia and Indonesia in South‐East Asia. We investigated genetic variation, clade membership, and phylogenetic relationships in Nycteridae with broad sampling across Africa for most clades. We sequenced mitochondrial cytochrome b (cytb) and four independent nuclear introns (2,166 bp) from 253 individuals. Although our samples did not include all recognized species, we recovered at least 16 deeply divergent monophyletic lineages using independent mitochondrial and multilocus nuclear datasets in both gene tree and species tree analyses. Mean pairwise uncorrected genetic distances among species‐ranked Nycteris clades (17% for cytb and 4% for concatenated introns) suggest high levels of phylogenetic diversity in Nycteridae. We found a large number of designated clades whose members are distributed wholly or partly in East Africa (10 of 16 clades), indicating that Nycteris diversity has been historically underestimated and raising the possibility that additional unsampled and/or undescribed Nycteris species occur in more poorly sampled Central and West Africa. Well‐resolved mitochondrial, concatenated nuclear, and species trees strongly supported African ancestry for SE Asian species. Species tree analyses strongly support two deeply diverged subclades that have not previously been recognized, and these clades may warrant recognition as subgenera. Our analyses also strongly support four traditionally recognized species groups of Nycteris. Mitonuclear discordance regarding geographic population structure in Nycteris thebaica appears to result from male‐biased dispersal in this species. Our analyses, almost wholly based on museum voucher specimens, serve to identify species‐rank clades that can be tested with independent datasets, such as morphology, vocalizations, distributions, and ectoparasites. Our analyses highlight the need for a comprehensive revision of Nycteridae.     

Predicting food‐web structure with metacommunity models

Synthesis Metacommunity theory aims to elucidate the relative influence of local and regional‐scale processes in generating diversity patterns across the landscape. Metacommunity research has focused largely on assemblages of competing organisms within a single trophic level. Here, we test the ability of metacommunity models to predict the network structure of the aquatic food web found in the leaves of the northern pitcher plant Sarracenia purpurea. The species‐sorting and patch‐dynamics models most accurately reproduced nine food web properties, suggesting that local‐scale interactions play an important role in structuring Sarracenia food webs. Our approach can be applied to any well‐resolved food web for which data are available from multiple locations. The metacommunity framework explores the relative influence of local and regional‐scale processes in generating diversity patterns across the landscape. Metacommunity models and empirical studies have focused mostly on assemblages of competing organisms within a single trophic level. Studies of multi‐trophic metacommunities are predominantly restricted to simplified trophic motifs and rarely consider entire food webs. We tested the ability of the patch‐dynamics, species‐sorting, mass‐effects, and neutral metacommunity models, as well as three hybrid models, to reproduce empirical patterns of food web structure and composition in the complex aquatic food web found in the northern pitcher plant Sarracenia purpurea. We used empirical data to determine regional species pools and estimate dispersal probabilities, simulated local food‐web dynamics, dispersed species from regional pools into local food webs at rates based on the assumptions of each metacommunity model, and tested their relative fits to empirical data on food‐web structure. The species‐sorting and patch‐dynamics models most accurately reproduced nine food web properties, suggesting that local‐scale interactions were important in structuring Sarracenia food webs. However, differences in dispersal abilities were also important in models that accurately reproduced empirical food web properties. Although the models were tested using pitcher‐plant food webs, the approach we have developed can be applied to any well‐resolved food web for which data are available from multiple locations.     

Algivory in food webs of three temperate Andean rivers

Food web analyses have been fundamental in understanding community organization and ecosystem functioning. To date, a number of studies demonstrate that stream food webs depend to a large extent on allochthonous detritus, but there are more recent studies that show a high degree of autochthony. Our food‐web study was carried out in three Andean rivers (Coilaco, Guampoe and Trancura) within the catchment area of Toltén River in southern Chile. Based on the analyses of 4251 invertebrate gut contents, we found that these Andean stream food webs are dominated by herbivores (range: 50–73% of all species) supported by a species‐rich algal (basal) component, and characterized by a low proportion of omnivores (range: 8–27% of all species) and predatory species (range: 10–24%). Significant differences in the number of feeding links of the herbivores Meridialis diguillina and Antarctoperla michaelseni and the omnivore Smicridea chilensis were found between seasons. The spring herbivore Aubertoperla sp. showed significant differences between rivers. S. chilensis fed on 50 different prey items as compared with the herbivores whose maximum number of links ranged between 37 and 40. Web sizes ranged between 93 and 131 species and the proportion of top species was distinctly lower than those of basal (up to 0.651 in Coilaco River) and intermediate species. Direct connectance (links per species²) values were low and similar among rivers (range: 0.051–0.074), whereas mean food chain length ranged between 2.23 and 2.90. The distributions of web property values from the Andean rivers differed from those previously published. In contrast to previous predictions, mean food chain length in these Andean streams displayed a scale‐invariant pattern across different web sizes, but it was significantly related to the proportion of intermediate species.     

Time‐series models to quantify short‐term effects of meteorological conditions on bumblebee forager activity in agricultural landscapes

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