Refine
Year of publication
Document Type
- Article (269)
- Preprint (8)
- Part of Periodical (4)
- Book (3)
- Contribution to a Periodical (3)
- Doctoral Thesis (3)
- Conference Proceeding (1)
- Review (1)
Language
- English (278)
- German (11)
- Multiple languages (3)
Has Fulltext
- yes (292)
Is part of the Bibliography
- no (292) (remove)
Keywords
- climate change (9)
- Invasive species (7)
- Phylogeny (6)
- Biodiversity (5)
- Biogeography (5)
- phylogeny (5)
- taxonomy (5)
- Climate change (4)
- Ecological modelling (4)
- West Africa (4)
Institute
- Biodiversität und Klima Forschungszentrum (BiK-F) (292) (remove)
Prof. Karin Böhning-Gaese, seit 2010 Direktorin des Senckenberg Biodiversität und Klima Forschungszentrums in Frankfurt am Main und Professorin an der Goethe-Universität, wurde in den Rat für Nachhaltige Entwicklung berufen. Das 15-köpfige Gremium berät die Bundesregierung, erarbeitet Beiträge zur Fortentwicklung der Nachhaltigkeitsstrategie, veröffentlicht Stellungnahmen zu Einzelthemen und soll zur öffentlichen Bewusstseinsbildung und zur gesellschaftlichen Debatte über Nachhaltigkeit beitragen.
The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome-wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
Aim: Predicting future changes in species richness in response to climate change is one of the key challenges in biogeography and conservation ecology. Stacked species distribution models (S‐SDMs) are a commonly used tool to predict current and future species richness. Macroecological models (MEMs), regression models with species richness as response variable, are a less computationally intensive alternative to S‐SDMs. Here, we aim to compare the results of two model types (S‐SDMS and MEMs), for the first time for more than 14,000 species across multiple taxa globally, and to trace the uncertainty in future predictions back to the input data and modelling approach used.
Location: Global land, excluding Antarctica.
Taxon: Amphibians, birds and mammals.
Methods: We fitted S‐SDMs and MEMs using a consistent set of bioclimatic variables and model algorithms and conducted species richness predictions under current and future conditions. For the latter, we used four general circulation models (GCMs) under two representative concentration pathways (RCP2.6 and RCP6.0). Predicted species richness was compared between S‐SDMs and MEMs and for current conditions also to extent‐of‐occurrence (EOO) species richness patterns. For future predictions, we quantified the variance in predicted species richness patterns explained by the choice of model type, model algorithm and GCM using hierarchical cluster analysis and variance partitioning.
Results: Under current conditions, species richness predictions from MEMs and S‐SDMs were strongly correlated with EOO‐based species richness. However, both model types over‐predicted areas with low and under‐predicted areas with high species richness. Outputs from MEMs and S‐SDMs were also highly correlated among each other under current and future conditions. The variance between future predictions was mostly explained by model type.
Main conclusions: Both model types were able to reproduce EOO‐based patterns in global terrestrial vertebrate richness, but produce less collinear predictions of future species richness. Model type by far contributes to most of the variation in the different future species richness predictions, indicating that the two model types should not be used interchangeably. Nevertheless, both model types have their justification, as MEMs can also include species with a restricted range, whereas S‐SDMs are useful for looking at potential species‐specific responses.
Vegetation responds to drought through a complex interplay of plant hydraulic mechanisms, posing challenges for model development and parameterization. We present a mathematical model that describes the dynamics of leaf water-potential over time while considering different strategies by which plant species regulate their water-potentials. The model has two parameters: the parameter λ describing the adjustment of the leaf water potential to changes in soil water potential, and the parameter Δψww describing the typical ‘well-watered’ leaf water potentials at non-stressed (near-zero) levels of soil water potential. Our model was tested and calibrated on 110 time-series datasets containing the leaf- and soil water potentials of 66 species under drought and non-drought conditions. Our model successfully reproduces the measured leaf water potentials over time based on three different regulation strategies under drought. We found that three parameter sets derived from the measurement data reproduced the dynamics of 53% of an drought dataset, and 52% of a control dataset [root mean square error (RMSE) < 0.5 MPa)]. We conclude that, instead of quantifying water-potential-regulation of different plant species by complex modeling approaches, a small set of parameters may be sufficient to describe the water potential regulation behavior for large-scale modeling. Thus, our approach paves the way for a parsimonious representation of the full spectrum of plant hydraulic responses to drought in dynamic vegetation models.
Recent phylogenomic studies have failed to conclusively resolve certain branches of the placental mammalian tree, despite the evolutionary analysis of genomic data from 32 species. Previous analyses of single genes and retroposon insertion data yielded support for different phylogenetic scenarios for the most basal divergences. The results indicated that some mammalian divergences were best interpreted not as a single bifurcating tree, but as an evolutionary network. In these studies the relationships among some orders of the super-clade Laurasiatheria were poorly supported, albeit not studied in detail. Therefore, 4775 protein-coding genes (6,196,263 nucleotides) were collected and aligned in order to analyze the evolution of this clade. Additionally, over 200,000 introns were screened in silico, resulting in 32 phylogenetically informative long interspersed nuclear elements (LINE) insertion events.
The present study shows that the genome evolution of Laurasiatheria may best be understood as an evolutionary network. Thus, contrary to the common expectation to resolve major evolutionary events as a bifurcating tree, genome analyses unveil complex speciation processes even in deep mammalian divergences. We exemplify this on a subset of 1159 suitable genes that have individual histories, most likely due to incomplete lineage sorting or introgression, processes that can make the genealogy of mammalian genomes complex.
These unexpected results have major implications for the understanding of evolution in general, because the evolution of even some higher level taxa such as mammalian orders may sometimes not be interpreted as a simple bifurcating pattern.
Wetlands such as bogs, swamps, or freshwater marshes are hotspots of biodiversity. For 5.1 million km2 of inland wetlands, the dynamics of area and water storage, which strongly impact biodiversity and ecosystem services, were simulated using the global hydrological model WaterGAP. For the first time, the impacts of both human water use and man‐made reservoirs (WUR) and future climate change (CC) on wetlands around the globe were quantified. WUR impacts are concentrated in arid/semiarid regions, where WUR decreased mean wetland water storage by more than 5% on 8.2% of the mean wetland area during 1986–2005 (Am), with highest decreases in groundwater depletion area. Using output of three climate models, CC impacts on wetlands were quantified, distinguishing unavoidable impacts [i.e., at 2 °C global warming (GW)] from avoidable impacts (difference between 3 °C and 2 °C impacts). Even unavoidable CC impacts are projected to be much larger than WUR impacts, also in arid/semiarid regions. On most wetland area with reliable estimates, avoidable CC impacts are more than twice as large as unavoidable impacts. In case of 2 °C GW, half of Am is estimated to be unaffected by mean storage changes of more than 5%, but only one third in case of 3 °C GW. Temporal variability of water storage will increase for most wetlands. Wetlands in dry regions will be affected the most, particularly by water storage decreases in the dry season. Different from wealthier countries, low‐income countries will dominantly suffer from a decrease in wetland water storage due to CC.
Network graphs have become a popular tool to represent complex systems composed of many interacting subunits; especially in neuroscience, network graphs are increasingly used to represent and analyze functional interactions between multiple neural sources. Interactions are often reconstructed using pairwise bivariate analyses, overlooking the multivariate nature of interactions: it is neglected that investigating the effect of one source on a target necessitates to take all other sources as potential nuisance variables into account; also combinations of sources may act jointly on a given target. Bivariate analyses produce networks that may contain spurious interactions, which reduce the interpretability of the network and its graph metrics. A truly multivariate reconstruction, however, is computationally intractable because of the combinatorial explosion in the number of potential interactions. Thus, we have to resort to approximative methods to handle the intractability of multivariate interaction reconstruction, and thereby enable the use of networks in neuroscience. Here, we suggest such an approximative approach in the form of an algorithm that extends fast bivariate interaction reconstruction by identifying potentially spurious interactions post-hoc: the algorithm uses interaction delays reconstructed for directed bivariate interactions to tag potentially spurious edges on the basis of their timing signatures in the context of the surrounding network. Such tagged interactions may then be pruned, which produces a statistically conservative network approximation that is guaranteed to contain non-spurious interactions only. We describe the algorithm and present a reference implementation in MATLAB to test the algorithm’s performance on simulated networks as well as networks derived from magnetoencephalographic data. We discuss the algorithm in relation to other approximative multivariate methods and highlight suitable application scenarios. Our approach is a tractable and data-efficient way of reconstructing approximative networks of multivariate interactions. It is preferable if available data are limited or if fully multivariate approaches are computationally infeasible.
Animal tracking and biologging devices record large amounts of data on individual movement behaviors in natural environments. In these data, movement ecologists often view unexplained variation around the mean as “noise” when studying patterns at the population level. In the field of behavioral ecology, however, focus has shifted from population means to the biological underpinnings of variation around means. Specifically, behavioral ecologists use repeated measures of individual behavior to partition behavioral variability into intrinsic among-individual variation and reversible behavioral plasticity and to quantify: a) individual variation in behavioral types (i.e. different average behavioral expression), b) individual variation in behavioral plasticity (i.e. different responsiveness of individuals to environmental gradients), c) individual variation in behavioral predictability (i.e. different residual within-individual variability of behavior around the mean), and d) correlations among these components and correlations in suites of behaviors, called ‘behavioral syndromes’. We here suggest that partitioning behavioral variability in animal movements will further the integration of movement ecology with other fields of behavioral ecology. We provide a literature review illustrating that individual differences in movement behaviors are insightful for wildlife and conservation studies and give recommendations regarding the data required for addressing such questions. In the accompanying R tutorial we provide a guide to the statistical approaches quantifying the different aspects of among-individual variation. We use movement data from 35 African elephants and show that elephants differ in a) their average behavior for three common movement behaviors, b) the rate at which they adjusted movement over a temporal gradient, and c) their behavioral predictability (ranging from more to less predictable individuals). Finally, two of the three movement behaviors were correlated into a behavioral syndrome (d), with farther moving individuals having shorter mean residence times. Though not explicitly tested here, individual differences in movement and predictability can affect an individual’s risk to be hunted or poached and could therefore open new avenues for conservation biologists to assess population viability. We hope that this review, tutorial, and worked example will encourage movement ecologists to examine the biology of individual variation in animal movements hidden behind the population mean.
The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information.
Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo-diversity metrics based on their mathematical form within these three dimensions and identify ‘anchor’ representatives: for α-diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.
The caddisfly subfamily Drusinae BANKS comprises roughly 100 species inhabiting mountain ranges in Europe, Asia Minor and the Caucasus. A 3-gene phylogeny of the subfamily previously identified three major clades that were corroborated by larval morphology and feeding ecologies: scraping grazers, omnivorous shredders and filtering carnivores. Larvae of filtering carnivores exhibit unique head capsule complexities, unknown from other caddisfly larvae. Here we assess the species-level relationships within filtering carnivores, hypothesizing that head capsule complexity is derived from simple shapes observed in the other feeding groups. We summarize the current systematics and taxonomy of the group, clarify the systematic position of Cryptothrix nebulicola, and present a larval key to filtering carnivorous Drusinae. We infer relationships of all known filtering carnivorous Drusinae and 34 additional Drusinae species using Bayesian species tree analysis and concatenated Bayesian phylogenetic analysis of 3805bp of sequence data from six gene regions (mtCOI5-P, mtCOI3-P, 16S mrDNA, CADH, WG, 28S nrDNA), morphological cladistics from 308 characters, and a total evidence analysis. All analyses support monophyly of the three feeding ecology groups but fail to fully resolve internal relationships. Within filtering carnivores, variation in head setation and frontoclypeus structure may be associated with progressive niche adaptation, with less complex species recovered at a basal position. We propose that diversification of complex setation and frontoclypeus shape represents a recent evolutionary development, hypothetically enforcing speciation and niche specificity within filtering carnivorous Drusinae.
Fire is the primary disturbance factor in many terrestrial ecosystems. Wildfire alters vegetation structure and composition, affects carbon storage and biogeochemical cycling, and results in the release of climatically relevant trace gases including CO2, CO, CH4, NOx, and aerosols. One way of assessing the impacts of global wildfire on centennial to multi-millennial timescales is to use process-based fire models linked to dynamic global vegetation models (DGVMs). Here we present an update to the LPJ-DGVM and a new fire module based on SPITFIRE that includes several improvements to the way in which fire occurrence, behaviour, and the effects of fire on vegetation are simulated. The new LPJ-LMfire model includes explicit calculation of natural ignitions, the representation of multi-day burning and coalescence of fires, and the calculation of rates of spread in different vegetation types. We describe a new representation of anthropogenic biomass burning under preindustrial conditions that distinguishes the different relationships between humans and fire among hunter-gatherers, pastoralists, and farmers. We evaluate our model simulations against remote-sensing-based estimates of burned area at regional and global scale. While wildfire in much of the modern world is largely influenced by anthropogenic suppression and ignitions, in those parts of the world where natural fire is still the dominant process (e.g. in remote areas of the boreal forest and subarctic), our results demonstrate a significant improvement in simulated burned area over the original SPITFIRE. The new fire model we present here is particularly suited for the investigation of climate–human–fire relationships on multi-millennial timescales prior to the Industrial Revolution.
Recently, new soil data maps were developed, which include vertical soil properties like soil type. Implementing those into a multilayer Soil-Vegetation-Atmosphere-Transfer (SVAT) scheme, discontinuities in the water content occur at the interface between dissimilar soils. Therefore, care must be taken in solving the Richards equation for calculating vertical soil water fluxes. We solve a modified form of the mixed (soil water and soil matric potential based) Richards equation by subtracting the equilibrium state of soil matrix potential ψE from the hydraulic potential ψh. The sensitivity of the modified equation is tested under idealized conditions. The paper will show that the modified equation can handle with discontinuities in soil water content at the interface of layered soils.
The lichen-forming genus Pertusaria under its current circumscription is polyphyletic and its phylogenetic affiliations are uncertain. Here we study the species of the genera Pertusaria and Varicellaria which containlecanoric acid as major constituent, have disciform apothecia, strongly amyloid asci, non-amyloid hymenial gel, 1-2-spored asci, and 1- or 2-celled ascospores with thick, 1-layered walls. We infer phylogenetic relationships using maximum likelihood and Bayesian analyses based on four molecular loci (mtSSU, nuLSU rDNA, and the protein-coding, nuclear RPB1 and MCM7 genes). Our results show that the lecanoric acid-containing species form a well-supported, monophyletic group, which is only distantly related to Pertusaria s.str. The phylogenetic position of this clade is unclear, but placement in Pertusaria s.str. is rejected using alternative hypothesis testing. The circumscription of the genus Varicellaria is enlarged to also include species with non-septate ascospores. Seven species are accepted in the genus: Varicellaria culbersonii (Vězda) Schmitt & Lumbsch, comb. nov., Varicellaria hemisphaerica (Flörke) Schmitt & Lumbsch, comb. nov., Varicellaria kasandjeffii (Szatala) Schmitt & Lumbsch, comb. nov., Varicellaria lactea (L.) Schmitt & Lumbsch, comb. nov., Varicellaria philippina (Vain.) Schmitt & Lumbsch, comb. nov., Varicellaria rhodocarpa (Körb.) Th. Fr., and Varicellaria velata (Turner) Schmitt & Lumbsch, comb. nov. A key to the species of Varicellaria is provided.
One of the major problems in evolutionary biology is to elucidate the relationships between historical events and the tempo and mode of lineage divergence. The development of relaxed molecular clock models and the increasing availability of DNA sequences resulted in more accurate estimations of taxa divergence times. However, finding the link between competing historical events and divergence is still challenging. Here we investigate assigning constrained-age priors to nodes of interest in a time-calibrated phylogeny as a means of hypothesis comparison. These priors are equivalent to historic scenarios for lineage origin. The hypothesis that best explains the data can be selected by comparing the likelihood values of the competing hypotheses, modelled with different priors. A simulation approach was taken to evaluate the performance of the prior-based method and to compare it with an unconstrained approach. We explored the effect of DNA sequence length and the temporal placement and span of competing hypotheses (i.e. historic scenarios) on selection of the correct hypothesis and the strength of the inference. Competing hypotheses were compared applying a posterior simulation analogue of the Akaike Information Criterion and Bayes factors (obtained after calculation of the marginal likelihood with three estimators: Harmonic Mean, Stepping Stone and Path Sampling). We illustrate the potential application of the prior-based method on an empirical data set to compare competing geological hypotheses explaining the biogeographic patterns in Pleurodeles newts. The correct hypothesis was selected on average 89% times. The best performance was observed with DNA sequence length of 3500-10000 bp. The prior-based method is most reliable when the hypotheses compared are not temporally too close. The strongest inferences were obtained when using the Stepping Stone and Path Sampling estimators. The prior-based approach proved effective in discriminating between competing hypotheses when used on empirical data. The unconstrained analyses performed well but it probably requires additional computational effort. Researchers applying this approach should rely only on inferences with moderate to strong support. The prior-based approach could be applied on biogeographical and phylogeographical studies where robust methods for historical inferences are still lacking.
A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes)
(2013)
Background: Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf, and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass.
Results: Here we provide the first mitochondrial DNA sequence data of red foxes from central Asia (Siberia), and new sequences from several European populations. In a range-wide synthesis of 729 red fox mitochondrial control region sequences, including 677 previously published and 52 newly obtained sequences, this manuscript describes the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. In a 335 bp alignment we found in total 175 unique haplotypes. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene.
Conclusions: The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic. Both brown bears and red foxes colonized Japan’s northern island Hokkaido at least three times, all lineages being most closely related to different mainland lineages. Red foxes, grey wolves, and brown bears thus represent an interesting case where species that occupy similar ecological niches also exhibit similar phylogeographic histories.
Molecular phylogenetic studies of Moraea Mill. and the inclusion of Barnardiella Goldblatt, Galaxia Thunb., Gynandriris Parl., Hexaglottis Vent., Homeria Vent. and Roggeveldia Goldblatt in the genus have rendered the existing infrageneric classification, dating from 1976, in need of substantial revision. In particular, subg. Moraea and subg. Vieusseuxia have been shown to be paraphyletic. We propose a new infrageneric classification, based, as far as current data permit, on phylogenetic principles. Monophyletic subgenera and sections are circumscribed based on molecular phylogenies alone or in combination with morphological considerations. We recognize 11 subgenera, 15 sections and three series, arranged as follows in phylogenetic sequence: Plumarieae; Visciramosae (with sect. Multifoliae and sect. Visciramosae); Moraea (with sect. Moraea and sect. Polyphyllae); Galaxia (with ser. Unguiculatae, ser. Eurystigma and ser. Galaxia); Monocephalae; Acaules; Polyanthes (with sect. Serpentinae, sect. Deserticola, sect. Hexaglottis, sect. Gynandriris, sect. Polyanthes and sect. Pseudospicatae); Grandifl orae; Vieusseuxia (with sect. Integres, sect. Vieusseuxia and sect. Villosae); and Homeria (with sect. Stipanthera, sect. Flexuosae, sect. Homeria and sect. Conantherae). Most are moderately to well circumscribed at the morphological level either by floral or vegetative characters, except subg. Moraea, which includes a small number of unspecialized species apparently not linked by any apomorphic features. With over 27 new species described in the past 25 years and another 60 transferred to the genus, Moraea now includes 214 species. We provide a full taxonomic synopsis of the genus.
Demographic change is supposed to be the most important indirect driver for changing biodiversity. In this article, a systematic review of 148 studies was conducted to examine the scientific evidence for this relationship and to identify potential gaps in research. We explored the spatial distribution of studies, the categories addressed with respect to biodiversity and demographic change, and the ways in which their relationships were conceptualised (spatially and temporally) and valued. The majority of studies were carried out in Africa, Europe and North America. Our analysis confirms the trend that demographic phenomena were mostly found to negatively influence biodiversity. However, a considerable number of studies also point towards impacts that were context dependent, either positive or negative under certain circumstances. In addition to that we identified significant gaps in research. In particular, there is a lack of addressing (1) other demographic aspects such as population decline, age structure or gender differences, (2) spatial variability of, e.g. human population growth, (3) long-term effects of demographic processes, and (4) the context dependency (e.g. regulations/law enforcement, type of human activities, and choice of scale or proxy). We conclude there is evidence that the relationship between biodiversity and demographic change is much more complex than expected and so far represented in research. Thus, we call for a social–ecological biodiversity research that particularly focusses on the functional relation between biodiversity and human activities, namely the different types, context, and interdependent dynamics (spatial and temporal) of this complex relation.
A tale of two seasons: The link between seasonal migration and climatic niches in passerine birds
(2020)
The question of whether migratory birds track a specific climatic niche by seasonal movements has important implications for understanding the evolution of migration, the factors affecting species' distributions, and the responses of migrants to climate change. Despite much research, previous studies of bird migration have produced mixed results. However, whether migrants track climate is only one half of the question, the other being why residents remain in the same geographic range year-round. We provide a literature overview and test the hypothesis of seasonal niche tracking by evaluating seasonal climatic niche overlap across 437 migratory and resident species from eight clades of passerine birds. Seasonal climatic niches were based on a new global dataset of breeding and nonbreeding ranges. Overlap between climatic niches was quantified using ordination methods. We compared niche overlap of migratory species to two null expectations, (a) a scenario in which they do not migrate and (b) in comparison with the overlap experienced by closely related resident species, while controlling for breeding location and range size. Partly in accordance with the hypothesis of niche tracking, we found that the overlap of breeding versus nonbreeding climatic conditions in migratory species was greater than the overlap they would experience if they did not migrate. However, this was only true for migrants breeding outside the tropics and only relative to the overlap species would experience if they stayed in the breeding range year-round. In contrast to the hypothesis of niche tracking, migratory species experienced lower seasonal climatic niche overlap than resident species, with significant differences between tropical and nontropical species. Our study suggests that in seasonal nontropical environments migration away from the breeding range may serve to avoid seasonally harsh climate; however, different factors may drive seasonal movements in the climatically more stable tropical regions.
A world dataset on the geographic distributions of Solenidae razor clams (Mollusca: Bivalvia)
(2019)
Background: Using this dataset, we examined the global geographical distributions of Solenidae species in relation to their endemicity, species richness and latitudinal ranges and then predicted their distributions under future climate change using species distribution modelling techniques (Saeedi et al. 2016a, Saeedi et al. 2016b). We found that the global latitudinal species richness in Solenidae is bi-modal, dipping at the equator most likely derived by high sea surface temperature (Saeedi et al. 2016b). We also found that most of the Solenidae species will shift their distribution ranges polewards due to global warming (Saeedi et al. 2016a). We also provided a comprehensive review of the taxon to test whether the latitudinal gradient in species richness was uni-modal with a peak in the tropics or northern hemisphere or asymmetric and bimodal as proposed previously (Chaudhary et al. 2016).
New information: This paper presents an integrated global geographic distribution dataset for 77 Solenidae taxa, including 3,034 geographic distribution records. This dataset was compiled after a careful data-collection and cleaning procedure over four years. Data were collected using field sampling, literature and from open-access databases. Then all the records went through quality control procedures such as validating the taxonomy of the species by examining and re-identifying the specimens in museum collections and using taxonomic and geographic data quality control tools in the World Register of Marine Species (WoRMS) and the r-OBIS package (Provoost and Bosch 2017). This dataset can thus be further used for taxonomical and biogeographical studies of Solenidae.
Background: Many fungal species occur across a variety of habitats. Particularly lichens, fungi forming symbioses with photosynthetic partners, have evolved remarkable tolerances for environmental extremes. Despite their ecological importance and ubiquity, little is known about the genetic basis of adaption in lichen populations. Here we studied patterns of genome-wide differentiation in the lichen-forming fungus Lasallia pustulata along an altitudinal gradient in the Mediterranean region. We resequenced six populations as pools and identified highly differentiated genomic regions. We then detected gene-environment correlations while controlling for shared population history and pooled sequencing bias, and performed ecophysiological experiments to assess fitness differences of individuals from different environments.
Results: We detected two strongly differentiated genetic clusters linked to Mediterranean and temperate-oceanic climate, and an admixture zone, which coincided with the transition between the two bioclimates. High altitude individuals showed ecophysiological adaptations to wetter and more shaded conditions. Highly differentiated genome regions contained a number of genes associated with stress response, local environmental adaptation, and sexual reproduction.
Conclusions: Taken together our results provide evidence for a complex interplay between demographic history and spatially varying selection acting on a number of key biological processes, suggesting a scenario of ecological speciation.
Parasites of the nematode genus Anisakis are associated with aquatic organisms. They can be found in a variety of marine hosts including whales, crustaceans, fish and cephalopods and are known to be the cause of the zoonotic disease anisakiasis, a painful inflammation of the gastro-intestinal tract caused by the accidental consumptions of infectious larvae raw or semi-raw fishery products. Since the demand on fish as dietary protein source and the export rates of seafood products in general is rapidly increasing worldwide, the knowledge about the distribution of potential foodborne human pathogens in seafood is of major significance for human health. Studies have provided evidence that a few Anisakis species can cause clinical symptoms in humans. The aim of our study was to interpolate the species range for every described Anisakis species on the basis of the existing occurrence data. We used sequence data of 373 Anisakis larvae from 30 different hosts worldwide and previously published molecular data (n = 584) from 53 field-specific publications to model the species range of Anisakis spp., using a interpolation method that combines aspects of the alpha hull interpolation algorithm as well as the conditional interpolation approach. The results of our approach strongly indicate the existence of species-specific distribution patterns of Anisakis spp. within different climate zones and oceans that are in principle congruent with those of their respective final hosts. Our results support preceding studies that propose anisakid nematodes as useful biological indicators for their final host distribution and abundance as they closely follow the trophic relationships among their successive hosts. The modeling might although be helpful for predicting the likelihood of infection in order to reduce the risk of anisakiasis cases in a given area.
Acetobacterium woodii utilizes the Wood‐Ljungdahl pathway for reductive synthesis of acetate from carbon dioxide. However, A. woodii can also perform non‐acetogenic growth on 1,2‐propanediol (1,2‐PD) where instead of acetate, equal amounts of propionate and propanol are produced as metabolic end products. Metabolism of 1,2‐PD occurs via encapsulated metabolic enzymes within large proteinaceous bodies called bacterial microcompartments. While the genome of A. woodii harbours 11 genes encoding putative alcohol dehydrogenases, the BMC‐encapsulated propanol‐generating alcohol dehydrogenase remains unidentified. Here, we show that Adh4 of A. woodii is the alcohol dehydrogenase required for propanol/ethanol formation within these microcompartments. It catalyses the NADH‐dependent reduction of propionaldehyde or acetaldehyde to propanol or ethanol and primarily functions to recycle NADH within the BMC. Removal of adh4 gene from the A. woodii genome resulted in slow growth on 1,2‐PD and the mutant displayed reduced propanol and enhanced propionate formation as a metabolic end product. In sum, the data suggest that Adh4 is responsible for propanol formation within the BMC and is involved in redox balancing in the acetogen, A. woodii.
Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play an essential role in comparative genomics and phylogenomic analyses. With the continued sequencing of organisms across the tree of life, the data are available to reconstruct the unique evolutionary histories of tens of thousands of gene families. Accurate reconstruction of these histories, however, is a challenging computational problem, and the focus of the Quest for Orthologs Consortium. We review the recent advances and outstanding challenges in this field, as revealed at a symposium and meeting held at the University of Southern California in 2017. Key advances have been made both at the level of orthology algorithm development and with respect to coordination across the community of algorithm developers and orthology end-users. Applications spanned a broad range, including gene function prediction, phylostratigraphy, genome evolution, and phylogenomics. The meetings highlighted the increasing use of meta-analyses integrating results from multiple different algorithms, and discussed ongoing challenges in orthology inference as well as the next steps toward improvement and integration of orthology resources.
Background: Aedes albopictus and Ae. japonicus are two of the most widespread invasive mosquito species that have recently become established in western Europe. Both species are associated with the transmission of a number of serious diseases and are projected to continue their spread in Europe.
Methods: In the present study, we modelled the habitat suitability for both species under current and future climatic conditions by means of an Ensemble forecasting approach. We additionally compared the modelled MAXENT niches of Ae. albopictus and Ae. japonicus regarding temperature and precipitation requirements.
Results: Both species were modelled to find suitable habitat conditions in distinct areas within Europe: Ae. albopictus within the Mediterranean regions in southern Europe, Ae. japonicus within the more temperate regions of central Europe. Only in few regions, suitable habitat conditions were projected to overlap for both species. Whereas Ae. albopictus is projected to be generally promoted by climate change in Europe, the area modelled to be climatically suitable for Ae. japonicus is projected to decrease under climate change. This projection of range reduction under climate change relies on the assumption that Ae. japonicus is not able to adapt to warmer climatic conditions. The modelled MAXENT temperature niches of Ae. japonicus were found to be narrower with an optimum at lower temperatures compared to the niches of Ae. albopictus.
Conclusions: Species distribution models identifying areas with high habitat suitability can help improving monitoring programmes for invasive species currently in place. However, as mosquito species are known to be able to adapt to new environmental conditions within the invasion range quickly, niche evolution of invasive mosquito species should be closely followed upon in future studies.
The Asian tiger mosquito Aedes albopictus, native to South East Asia, is listed as one of the worst invasive vector species worldwide. In Europe the species is currently restricted to Southern Europe, but due to the ongoing climate change, Ae. albopictus is expected to expand its potential range further northwards. In addition to modelling the habitat suitability for Ae. albopictus under current and future climatic conditions in Europe by means of the maximum entropy approach, we here focused on the drivers of the habitat suitability prediction. We explored the most limiting factors for Aedes albopictus in Europe under current and future climatic conditions, a method which has been neglected in species distribution modelling so far. Ae. albopictus is one of the best-studied mosquito species, which allowed us to evaluate the applied Maxent approach for most limiting factor mapping. We identified three key limiting factors for Ae. albopictus in Europe under current climatic conditions: winter temperature in Eastern Europe, summer temperature in Southern Europe. Model findings were in good accordance with commonly known establishment thresholds in Europe based on climate chamber experiments and derived from the geographical distribution of the species. Under future climatic conditions low winter temperature were modelled to remain the most limiting factor in Eastern Europe, whereas in Central Europe annual mean temperature and summer temperatures were modelled to be replaced by summer precipitation, respectively, as most limiting factors. Changes in the climatic conditions in terms of the identified key limiting factors will be of great relevance regarding the invasive potential of the Ae. albopictus. Thus, our results may help to understand the key drivers of the suggested range expansion under climate change and may help to improve monitoring programmes. The applied approach of investigating limiting factors has proven to yield valuable results and may also provide valuable insights into the drivers of the prediction of current and future distribution of other species. This might be particularly interesting for other vector species that are of increasing public health concerns.
The Alpine Region, constituting the Alps and the Dinaric Alps, has played a major role in the formation of current patterns of biodiversity either as a contact zone of postglacial expanding lineages or as the origin of genetic diversity. In our study, we tested these hypotheses for two widespread, sympatric microgastropod taxa - Carychium minimum O.F. Müller, 1774 and Carychium tridentatum (Risso, 1826) (Gastropoda, Eupulmonata, Carychiidae) - by using COI sequence data and species potential distribution models analyzed in a statistical phylogeographical framework. Additionally, we examined disjunct transatlantic populations of those taxa from the Azores and North America. In general, both Carychium taxa demonstrate a genetic structure composed of several differentiated haplotype lineages most likely resulting from allopatric diversification in isolated refugial areas during the Pleistocene glacial periods. However, the genetic structure of Carychium minimum is more pronounced, which can be attributed to ecological constraints relating to habitat proximity to permanent bodies of water. For most of the Carychium lineages, the broader Alpine Region was identified as the likely origin of genetic diversity. Several lineages are endemic to the broader Alpine Region whereas a single lineage per species underwent a postglacial expansion to (re)colonize previously unsuitable habitats, e.g. in Northern Europe. The source populations of those expanding lineages can be traced back to the Eastern and Western Alps. Consequently, we identify the Alpine Region as a significant 'hot-spot' for the formation of genetic diversity within European Carychium lineages. Passive dispersal via anthropogenic means best explains the presence of transatlantic European Carychium populations on the Azores and in North America. We conclude that passive (anthropogenic) transport could mislead the interpretation of observed phylogeographical patterns in general.
Molluscs are the second most species-rich phylum in the animal kingdom, yet only 11 genomes of this group have been published so far. Here, we present the draft genome sequence of the pulmonate freshwater snail Radix auricularia. Six whole genome shotgun libraries with different layouts were sequenced. The resulting assembly comprises 4,823 scaffolds with a cumulative length of 910 Mb and an overall read coverage of 72×. The assembly contains 94.6% of a metazoan core gene collection, indicating an almost complete coverage of the coding fraction. The discrepancy of ∼690 Mb compared with the estimated genome size of R. auricularia (1.6 Gb) results from a high repeat content of 70% mainly comprising DNA transposons. The annotation of 17,338 protein coding genes was supported by the use of publicly available transcriptome data. This draft will serve as starting point for further genomic and population genetic research in this scientifically important phylum.
High-throughput metabarcoding studies on fungi and other eukaryotic microorganisms are rapidly becoming more frequent and more complex, requiring researchers to handle ever increasing amounts of raw sequence data. Here, we provide a flexible pipeline for pruning and analyzing fungal barcode (ITS rDNA) data generated as paired-end reads on Illumina MiSeq sequencers. The pipeline presented includes specific steps fine-tuned for ITS, that are mostly missing from pipelines developed for prokaryotes. It (1) employs state of the art programs and follows best practices in fungal high-throughput metabarcoding; (2) consists of modules and scripts easily modifiable by the user to ensure maximum flexibility with regard to specific needs of a project or future methodological developments; and (3) is straightforward to use, also in classroom settings. We provide detailed descriptions and revision techniques for each step, thus giving the user maximum control over data treatment and avoiding a black-box approach. Employing this pipeline will improve and speed up the tedious and error-prone process of cleaning fungal Illumina metabarcoding data.
The Culex pipiens complex encompasses five species and subspecies of the genus Culex. Over time, a multitude of morphologically indistinguishable species has been assigned to this complex with several species being classified as important vectors for different diseases. Some species of this complex hibernate in subterranean habitats, and it has been proven that viruses can survive this phase of hibernation. However, studies focusing on the environmental requirements, ecology and spatial and temporal distribution patterns of mosquitos in underground habitats are sparse. Here, we investigate the main environmental factors and dependencies of Culex, considering the number of individuals and survival probabilities in underground habitats during the winter months. Methods. Since the State of Hesse, Germany harbors about 3500 to 4000 subterranean shelters ample availability of subterranean habitats there provides a good opportunity to conduct detailed investigations of the Culex pipiens complex. In this study, we identified a sample of 727 specimens of overwintering females within the Culex pipiens complex from 52 different underground sites collected over a period of 23 years using qPCR. A complete data set of samplings of hibernating mosquitos from 698 subterranean habitats in Central Germany over the same period was available to study the spatial and temporal patterns and the effect of temperature and precipitation conditions on these hibernating populations using a generalized linear model (GLM). Results. Our qPCR-results show, similar to aboveground studies of mosquitos, that Culex pipiens pipiens and Culex torrentium occur sympatrically. On the other hand, Culex pipiens molestus occurred very rarely. The GLM revealed no shifts in species composition over time, but different preferences for subterranean hibernacula, chemical effects on overwintering populations as well as effects of annual and seasonal mean temperature and precipitation during the active phase from March to November. Cx. p. pipiens and Cx. torrentium are the most common species within Hessian caves and other underground habitats during winter. They co-occur with different frequency without any patterns in species composition. Weather conditions influence the number of overwintering mosquitos during the activity phase. Depending on cave parameters, the number of mosquitos decreases during the winter months.
The turnover time of terrestrial carbon (τ) controls the global carbon cycle – climate feedback and, yet, is poorly simulated by the current Earth System Models (ESMs). In this study, by assessing apparent carbon turnover time as the ratio between carbon stocks and fluxes, we provide a new, updated ensemble of diagnostic terrestrial carbon turnover times and associated uncertainties on a global scale using multiple, state-of-the-art, observation-based datasets of soil organic carbon stock (Csoil), vegetation biomass (Cveg) and gross primary productivity (GPP). Using this new ensemble, we estimated the global average τ to be 42$% &' years when the full soil depth is considered, longer than the previous estimates of 23$) &* years. Only considering the top 1 m (assuming maximum active layer depth is up to 1 meter) of soil carbon in circumpolar regions yields a global τ of 35$) &' years. Csoil in circumpolar regions account for two thirds of the total uncertainty in global τ estimates, whereas Csoil in non-circumpolar contributes merely 9.38%. GPP (2.25%) and Cveg (0.05%) contribute even less to the total uncertainty. Therefore, the high uncertainty in Csoil is the main factor behind the uncertainty in global τ, as reflected in the larger range of full-depth Csoil (3152-4372 PgC). The uncertainty is especially high in circumpolar regions with a behaviour of ESMs which could contribute to uncertainty reductions in future projections of the carbon cycle - climate feedback. The dataset of the terrestrial turnover time ensemble (DOI: 10.17871/bgitau.201911) is openly available from the data portal: https://doi.org/10.17871/bgitau.201911 (Fan et al., 2019) uncertainty of 50% and the spatial correlations among different datasets are also low compared to other regions. Overall, we argue that current global datasets do not support robust estimates of τ globally, for which we need clarification on variations of Csoil with soil depth and stronger estimates of Csoil in circumpolar regions. Despite the large variation in both magnitude and spatial patterns of τ, we identified robust features in the spatial patterns of τ that emerge regardless of soil depth and differences in data sources of Csoil, Cveg and GPP. Our findings show that the latitudinal gradients of τ are consistent across different datasets and soil depth. Furthermore, there is a strong consensus on the negative correlation between τ and temperature along latitude that is stronger in temperate zones (30ºN-60ºN) than in subtropical and tropical zones (30ºS30ºN). The identified robust patterns can be used to infer the response of τ to climate and for constraining contemporaneous behaviour of ESMs which could contribute to uncertainty reductions in future projections of the carbon cycle - climate feedback. The dataset of the terrestrial turnover time ensemble (DOI:10.17871/bgitau.201911) is openly available from the data portal: https://doi.org/10.17871/bgitau.201911 (Fan et al., 2019).
The turnover time of terrestrial ecosystem carbon is an emergent ecosystem property that quantifies the strength of land surface on the global carbon cycle–climate feedback. However, observation- and modeling-based estimates of carbon turnover and its response to climate are still characterized by large uncertainties. In this study, by assessing the apparent whole ecosystem carbon turnover times (τ) as the ratio between carbon stocks and fluxes, we provide an update of this ecosystem level diagnostic and its associated uncertainties in high spatial resolution (0.083∘) using multiple, state-of-the-art, observation-based datasets of soil organic carbon stock (Csoil), vegetation biomass (Cveg) and gross primary productivity (GPP). Using this new ensemble of data, we estimated the global median τ to be 43+7−7 yr (median+difference to percentile 75−difference to percentile 25) when the full soil is considered, in contrast to limiting it to 1 m depth. Only considering the top 1 m of soil carbon in circumpolar regions (assuming maximum active layer depth is up to 1 m) yields a global median τ of 37+3−6 yr, which is longer than the previous estimates of 23+7−4 yr (Carvalhais et al., 2014). We show that the difference is mostly attributed to changes in global Csoil estimates. Csoil accounts for approximately 84 % of the total uncertainty in global τ estimates; GPP also contributes significantly (15 %), whereas Cveg contributes only marginally (less than 1 %) to the total uncertainty. The high uncertainty in Csoil is reflected in the large range across state-of-the-art data products, in which full-depth Csoil spans between 3362 and 4792 PgC. The uncertainty is especially high in circumpolar regions with an uncertainty of 50 % and a low spatial correlation between the different datasets (0.2<r<0.5) when compared to other regions (0.6<r<0.8). These uncertainties cast a shadow on current global estimates of τ in circumpolar regions, for which further geographical representativeness and clarification on variations in Csoil with soil depth are needed. Different GPP estimates contribute significantly to the uncertainties of τ mainly in semiarid and arid regions, whereas Cveg causes the uncertainties of τ in the subtropics and tropics. In spite of the large uncertainties, our findings reveal that the latitudinal gradients of τ are consistent across different datasets and soil depths. The current results show a strong ensemble agreement on the negative correlation between τ and temperature along latitude that is stronger in temperate zones (30–60∘ N) than in the subtropical and tropical zones (30∘ S–30∘ N). Additionally, while the strength of the τ–precipitation correlation was dependent on the Csoil data source, the latitudinal gradients also agree among different ensemble members. Overall, and despite the large variation in τ, we identified robust features in the spatial patterns of τ that emerge beyond the differences stemming from the data-driven estimates of Csoil, Cveg and GPP. These robust patterns, and associated uncertainties, can be used to infer τ–climate relationships and for constraining contemporaneous behavior of Earth system models (ESMs), which could contribute to uncertainty reductions in future projections of the carbon cycle–climate feedback. The dataset of τ is openly available at https://doi.org/10.17871/bgitau.201911 (Fan et al., 2019).
Future climate change is predicted to advance faster than the postglacial warming. Migration may therefore become a key driver for future development of biodiversity and ecosystem functioning. For 140 European plant species we computed past range shifts since the last glacial maximum and future range shifts for a variety of Intergovernmental Panel on Climate Change (IPCC) scenarios and global circulation models (GCMs). Range shift rates were estimated by means of species distribution modelling (SDM). With process-based seed dispersal models we estimated species-specific migration rates for 27 dispersal modes addressing dispersal by wind (anemochory) for different wind conditions, as well as dispersal by mammals (dispersal on animal's coat – epizoochory and dispersal by animals after feeding and digestion – endozoochory) considering different animal species. Our process-based modelled migration rates generally exceeded the postglacial range shift rates indicating that the process-based models we used are capable of predicting migration rates that are in accordance with realized past migration. For most of the considered species, the modelled migration rates were considerably lower than the expected future climate change induced range shift rates. This implies that most plant species will not entirely be able to follow future climate-change-induced range shifts due to dispersal limitation. Animals with large day- and home-ranges are highly important for achieving high migration rates for many plant species, whereas anemochory is relevant for only few species.
Brachiopod shells are the most widely used geological archive for the reconstruction of the temperature and the oxygen isotope composition of Phanerozoic seawater. However, it is not conclusive whether brachiopods precipitate their shells in thermodynamic equilibrium. In this study, we investigated the potential impact of kinetic controls on the isotope composition of modern brachiopods by measuring the oxygen and clumped isotope compositions of their shells. Our results show that clumped and oxygen isotope compositions depart from thermodynamic equilibrium due to growth rate-induced kinetic effects. These departures are in line with incomplete hydration and hydroxylation of dissolved CO2. These findings imply that the determination of taxon-specific growth rates alongside clumped and bulk oxygen isotope analyses is essential to ensure accurate estimates of past ocean temperatures and seawater oxygen isotope compositions from brachiopods.
Repeated Quaternary glaciations have significantly shaped the present distribution and diversity of several European species in aquatic and terrestrial habitats. To study the phylogeography of freshwater invertebrates, patterns of intraspecific variation have been examined primarily using mitochondrial DNA markers that may yield results unrepresentative of the true species history. Here, population genetic parameters were inferred for a montane aquatic caddisfly, T hremma gallicum , by sequencing a 658‐bp fragment of the mitochondrial CO 1 gene, and 12,514 nuclear RAD loci. T . gallicum has a highly disjunct distribution in southern and central Europe, with known populations in the Cantabrian Mountains, Pyrenees, Massif Central, and Black Forest. Both datasets represented rangewide sampling of T. gallicum . For the CO 1 dataset, this included 352 specimens from 26 populations, and for the RAD dataset, 17 specimens from eight populations. We tested 20 competing phylogeographic scenarios using approximate Bayesian computation (ABC ) and estimated genetic diversity patterns. Support for phylogeographic scenarios and diversity estimates differed between datasets with the RAD data favouring a southern origin of extant populations and indicating the Cantabrian Mountains and Massif Central populations to represent highly diverse populations as compared with the Pyrenees and Black Forest populations. The CO 1 data supported a vicariance scenario (north–south) and yielded inconsistent diversity estimates. Permutation tests suggest that a few hundred polymorphic RAD SNP s are necessary for reliable parameter estimates. Our results highlight the potential of RAD and ABC‐based hypothesis testing to complement phylogeographic studies on non‐model species.
La biodiversité comprend la plénitude de la vie dans toutes ses formes. Sa protection et son usage durable doivent ainsi être une partie intégrante d’une politique orientée vers l’avenir et ancrer de plus en plus dans la conscience politique et publique. La condition préalable pour cela est une meilleure compréhension des effets des actions humaines sur la biodiversité et une connaissance plus approfondie de sa valeur. La recherche scientifique contribue de façon indispensable à la préservation des biomes, des espèces et gènes. Elle ne se limite pas à fournir les connaissances fondamentales qui sont nécessaires pour arrêter le progrès de la disparition de la biodiversité. Bien plus, ce sont les chercheurs eux-mêmes qui, ensemble avec leurs partenaires locaux, élaborent des stratégies pour un usage durable de la biodiversité. Explorer la flore et la faune du continent africain, et mesurer les changements observés dans leur milieu naturel afin de les réduire, tels sont les objectifs de BIOTA (Biodiversity Monitoring Transect Analysis in Africa / Transect d´Analyse du suivi de la Biodiversité en Afrique de l´Ouest). Ce réseau de recherche a été créé en 1999 ensemble par les chercheurs africains et allemands. Vu la grande importance de BIOTA, cette initiative est non seulement financée par le Ministère fédérale de l’Education et de la Recherche, mais entre-temps aussi par plusieurs Etats africains et institutions partenaires. «BIOTA Ouest» a été lancé au début de 2001. Parmi les résultats de cette coopération réussie figurent le centre de biodiversité à Ouagadougou (Burkina Faso) et l’Atlas «BIOTA Ouest» actuel. Je me réjouis de l’apparition de cet atlas, qui constitue une vue d’ensemble compréhensive aussi bien que compréhensible des nombreux résultats de recherche et recommandations pratiques, car la biodiversité est une condition essentielle pour le fonctionnement de l’écosystème et, partant, le fondement de la vie humaine et de l’activité économique.
La biodiversité comprend la plénitude de la vie dans toutes ses formes. Sa protection et son usage durable doivent ainsi être une partie intégrante d’une politique orientée vers l’avenir et ancrer de plus en plus dans la conscience politique et publique. La condition préalable pour cela est une meilleure compréhension des effets des actions humaines sur la biodiversité et une connaissance plus approfondie de sa valeur. La recherche scientifique contribue de façon indispensable à la préservation des biomes, des espèces et gènes. Elle ne se limite pas à fournir les connaissances fondamentales qui sont nécessaires pour arrêter le progrès de la disparition de la biodiversité. Bien plus, ce sont les chercheurs eux-mêmes qui, ensemble avec leurs partenaires locaux, élaborent des stratégies pour un usage durable de la biodiversité. Explorer la flore et la faune du continent africain, et mesurer les changements observés dans leur milieu naturel afin de les réduire, tels sont les objectifs de BIOTA (Biodiversity Monitoring Transect Analysis in Africa / Transect d´Analyse du suivi de la Biodiversité en Afrique de l´Ouest). Ce réseau de recherche a été créé en 1999 ensemble par les chercheurs africains et allemands. Vu la grande importance de BIOTA, cette initiative est non seulement financée par le Ministère fédérale de l’Education et de la Recherche, mais entre-temps aussi par plusieurs Etats africains et institutions partenaires. «BIOTA Ouest» a été lancé au début de 2001. Parmi les résultats de cette coopération réussie figurent le centre de biodiversité à Ouagadougou (Burkina Faso) et l’Atlas «BIOTA Ouest» actuel. Je me réjouis de l’apparition de cet atlas, qui constitue une vue d’ensemble compréhensive aussi bien que compréhensible des nombreux résultats de recherche et recommandations pratiques, car la biodiversité est une condition essentielle pour le fonctionnement de l’écosystème et, partant, le fondement de la vie humaine et de l’activité économique.
La biodiversité comprend la plénitude de la vie dans toutes ses formes. Sa protection et son usage durable doivent ainsi être une partie intégrante d’une politique orientée vers l’avenir et ancrer de plus en plus dans la conscience politique et publique. La condition préalable pour cela est une meilleure compréhension des effets des actions humaines sur la biodiversité et une connaissance plus approfondie de sa valeur. La recherche scientifique contribue de façon indispensable à la préservation des biomes, des espèces et gènes. Elle ne se limite pas à fournir les connaissances fondamentales qui sont nécessaires pour arrêter le progrès de la disparition de la biodiversité. Bien plus, ce sont les chercheurs eux-mêmes qui, ensemble avec leurs partenaires locaux, élaborent des stratégies pour un usage durable de la biodiversité. Explorer la flore et la faune du continent africain, et mesurer les changements observés dans leur milieu naturel afin de les réduire, tels sont les objectifs de BIOTA (Biodiversity Monitoring Transect Analysis in Africa / Transect d´Analyse du suivi de la Biodiversité en Afrique de l´Ouest). Ce réseau de recherche a été créé en 1999 ensemble par les chercheurs africains et allemands. Vu la grande importance de BIOTA, cette initiative est non seulement financée par le Ministère fédérale de l’Education et de la Recherche, mais entre-temps aussi par plusieurs Etats africains et institutions partenaires. «BIOTA Ouest» a été lancé au début de 2001. Parmi les résultats de cette coopération réussie figurent le centre de biodiversité à Ouagadougou (Burkina Faso) et l’Atlas «BIOTA Ouest» actuel. Je me réjouis de l’apparition de cet atlas, qui constitue une vue d’ensemble compréhensive aussi bien que compréhensible des nombreux résultats de recherche et recommandations pratiques, car la biodiversité est une condition essentielle pour le fonctionnement de l’écosystème et, partant, le fondement de la vie humaine et de l’activité économique.
Ursine bears are a mammalian subfamily that comprises six morphologically and ecologically distinct extant species. Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial phylogeny. Evolutionary processes such as incomplete lineage sorting and introgression can cause gene tree discordance and complicate phylogenetic inferences, but are not accounted for in phylogenetic analyses of concatenated data. We generated a high-resolution data set of autosomal introns from several individuals per species and of Y-chromosomal markers. Incorporating intraspecific variability in coalescence-based phylogenetic and gene flow estimation approaches, we traced the genealogical history of individual alleles. Considerable heterogeneity among nuclear loci and discordance between nuclear and mitochondrial phylogenies were found. A species tree with divergence time estimates indicated that ursine bears diversified within less than 2 My. Consistent with a complex branching order within a clade of Asian bear species, we identified unidirectional gene flow from Asian black into sloth bears. Moreover, gene flow detected from brown into American black bears can explain the conflicting placement of the American black bear in mitochondrial and nuclear phylogenies. These results highlight that both incomplete lineage sorting and introgression are prominent evolutionary forces even on time scales up to several million years. Complex evolutionary patterns are not adequately captured by strictly bifurcating models, and can only be fully understood when analyzing multiple independently inherited loci in a coalescence framework. Phylogenetic incongruence among gene trees hence needs to be recognized as a biologically meaningful signal.
Allgemein ist anerkannt, dass gute Kompensationsprojekte nicht nur Kohlenstoff festlegen, sondern möglichst weitere Nachhaltigkeitsleistungen aufweisen, die jedoch bisher bei der Durchführung und der Bewertung der Projekte häufig nicht angemessen berücksichtigt werden. In der vorliegenden Untersuchung wird erhoben, ob brauchbare Indikatoren vorliegen, die zur Bewertung weiterer ökologischer und sozialer Nutzen derartiger Projekte verwendet werden können.
Um den Kritiken gegenüber Waldprojekten zu begegnen, sollten Indikatoren zur Bewertung der Projekte möglichst so gewählt werden, dass sich mit ihnen auch räumliche Verlagerungseffekte erfassen lassen. Ebenso wichtig ist die Betrachtung ausreichender Zeiträume Waldprojekte haben aufgrund der langen Lebensdauer von Bäumen eine längere Laufzeit, als sie derzeit in vielen Bewertungssystemen berücksichtigt wird. Der langfristige Sequestrierungseffekt eines Projektes hängt entscheidend davon ab, ob das Holz alter Bäume im Wald wieder in den Kohlenstoffkreislauf kommt oder dem Wald entzogen wird. Bei ausschließlicher energetischer Nutzung des Holzes und auch bei Verarbeitung zu Zellstoff, Papier und Pappe wird kurze Zeit nach der Holzernte wieder Kohlendioxid freigesetzt. Dagegen schlagen langlebige Nutzungen des Holzes und insbesondere eine tatsächliche Substitution von Produkten aus Erdöl und Erdgas positiv zu Buche.
Wichtige Zusammenhänge bestehen zwischen dem Kohlendioxid-Minderungspotential von Waldprojekten und deren erheblichen ökologischen und sozialen Nutzen; diese entstehen bei optimalem Management in einer Art Ko-Produktion und sollten bewusst gestaltet werden; entsprechende Trade-offs sind bekannt.
Für die Beschreibung der gesamtökologischen und der sozialen Leistungen von Waldprojekten kann weitgehend auf bereits bekannten Kriterien aufgebaut werden; sie sollten aber um die Betrachtung der relevanten Ökosystemdienstleistungen ergänzt werden. Die Kohlenstofffestlegung ist eng mit zahlreichen dieser Ökosystemdienstleistungen (z.B. Humusbildung, Pufferungspotential gegenüber Stickstoff usw.) verknüpft. Waldprojekte mit hoher Biodiversität sind zudem in der Regel besser in der Lage, das Kriterium der Permanenz eines Kohlenstofflagers zu erfüllen. Auch lassen sich über die Ökosystemdienstleistungen bisher ausgeblendete sozio-kulturelle Dimensionen besser als bisher einbeziehen.
Auf diese Weise lässt sich die Darstellung der Nachhaltigkeitsleistung von Waldprojekten auf eine breitere Basis als bisher stellen – sowohl in ökologischer als auch in sozialer Hinsicht können die Kriterienkataloge der bisherigen Standards erweitert werden, die besonders auf Umweltwirkungen und sozioökonomische Effekte abheben. In den meisten Fällen sind bereits ausreichend geeignete Indikatoren bzw. Parameter vorhanden, um weitere wichtige Leistungen der Waldprojekte nachvollziehbar zu beschreiben. Für einige der betrachteten Dimensionen und Kriterien sind bisher noch keine Indikatoren vorhanden; zumeist gibt es aber auch dort Parameter, die Situationen anzeigen, welche unter Umständen genauer betrachtet werden müssten.
Bisher liegen keine allgemein anerkannten Standards hinsichtlich der Nachhaltigkeitskriterien von Waldprojekten vor. Eine neuerliche Debatte über eine Erweiterung des Kriteriensets ist notwendig, damit die zugehörigen Leistungsindikatoren allgemein akzeptiert werden. Diese Diskussion sollte jenseits der Nachhaltigkeitsleistungen der Waldprojekte selbst auch deren Vergleichbarkeit mit technischen Kompensationsprojekten im Blick haben. Die Kriteriendebatte war bisher durch die technischen Projekte dominiert und leider auch auf deren Bewertung verengt. Anders als technische Projekte haben Waldprojekte häufig sowohl für den Naturhaushalt als auch für die Gesellschaft viele weitere Nutzen, die eine nachhaltige Entwicklung begünstigen. Diese werden aber bisher nur unzureichend für die Qualitätssicherung und Kommunikation der Projekte genutzt.
Analog zum Gold Standard (GS) sollten die diskutierten Kriterien zu einem Standard für Waldprojekte verknüpft werden, mit dem sich die Nachhaltigkeitsleistungen dieser Kompensationsprojekte verlässlich bestimmen und überprüfen lassen. In Testläufen könnten die identifizierten Kriterien und Indikatorvorschläge erprobt und dabei modifiziert bzw. verfeinert werden.
To quantify water flows between groundwater (GW) and surface water (SW) as well as the impact of Abstract. To quantify water flows between groundwater (GW) and surface water (SW) as well as the impact of capillary rise on evapotranspiration by global hydrological models (GHMs), it is necessary to replace the bucket-like linear GW reservoir model typical for hydrological models with a fully integrated gradient-based GW flow model. Linear reservoir models can only simulate GW discharge to SW bodies, provide no information on the location of the GW table and assume that there is no GW flow among grid cells. A gradient-based GW model simulates not only GW storage but also hydraulic head, which together with information on SW table elevation enables the quantification of water flows from GW to SW and vice versa. In addition, hydraulic heads are the basis for calculating lateral GW flow among grid cells and capillary rise.
G³M is a new global gradient-based GW model with a spatial resolution of 5' that will replace the current linear GW reservoir in the 0.5° WaterGAP Global Hydrology Model (WGHM). The newly developed model framework enables inmemory coupling to WGHM while keeping overall runtime relatively low, allowing sensitivity analyses and data assimilation. This paper presents the G³M concept and specific model design decisions together with results under steady-state naturalized conditions, i.e. neglecting GW abstractions. Cell-specific conductances of river beds, which govern GW-SW interaction, were determined based on the 30'' steady-state water table computed by Fan et al. (2013). Together with an appropriate choice for the effective elevation of the SW table within each grid cell, this enables a reasonable simulation of drainage from GW to SW such that, in contrast to the GW model of de Graaf et al. (2015, 2017), no additional drainage based on externally provided values for GW storage above the floodplain is required in G³M. Comparison of simulated hydraulic heads to observations around the world shows better agreement than de Graaf et al. (2015). In addition, G³M output is compared to the output of two established macro-scale models for the Central Valley, California, and the continental United States, respectively. As expected, depth to GW table is highest in mountainous and lowest in flat regions. A first analysis of losing and gaining rivers and lakes/wetlands indicates that GW discharge to rivers is by far the dominant flow, draining diffuse GW recharge, such that lateral flows only become a large fraction of total diffuse and focused recharge in case of losing rivers and some areas with very low GW recharge. G³M does not represent losing rivers in some dry regions. This study presents the first steps towards replacing the linear GW reservoir model in a GHM while improving on recent efforts, demonstrating the feasibility of the approach and the robustness of the newly developed framework.
1. Recent research highlights the ecological importance of individual variation in behavioural predictability. Individuals may not only differ in their average expression of a behavioural trait (their behavioural type) and in their ability to adjust behaviour to changing environmental conditions (individual plasticity), but also in their variability around their average behaviour (predictability). However, quantifying behavioural predictability in the wild has been challenging due to limitations of acquiring sufficient repeated behavioural measures.
2. We here demonstrate how common biologging data can be used to detect individual variation in behavioural predictability in the wild and reveal the coexistence of highly predictable individuals along with unpredictable individuals within the same population.
3. We repeatedly quantified two behaviours—daily movement distance and diurnal activity—in 62 female brown bears Ursus arctos tracked across 187 monitoring years. We calculated behavioural predictability over the short term (50 consecutive monitoring days within 1 year) and long term (across monitoring years) as the residual intra-individual variability (rIIV) of behaviour around the behavioural reaction norm. We tested whether predictability varies systematically across average behavioural types and whether it is correlated across functionally distinct behaviours, that is, daily movement distance and amount of diurnal activity.
4. Brown bears showed individual variation in behavioural predictability from predictable to unpredictable individuals. For example, the standard deviation around the average daily movement distance within one monitoring year varied up to fivefold from 1.1 to 5.5 km across individuals. Individual predictability for both daily movement distance and diurnality was conserved across monitoring years. Individual predictability was correlated with behavioural type where individuals which were on average more diurnal and mobile were also more unpredictable in their behaviour. In contrast, more nocturnal individuals moved less and were more predictable in their behaviour. Finally, individual predictability in daily movement distance and diurnality was positively correlated, suggesting that individual predictability may be a quantitative trait in its own regard that could evolve and is underpinned by genetic variation.
5. Unpredictable individuals may cope better with stochastic events and unpredictability may hence be an adaptive behavioural response to increased predation risk.
Biosynthetic gene content of the "Perfume Lichens" Evernia prunastri and Pseudevernia furfuracea
(2019)
Lichen-forming fungi produce a vast number of unique natural products with a wide variety of biological activities and human uses. Although lichens have remarkable potential in natural product research and industry, the molecular mechanisms underlying the biosynthesis of lichen metabolites are poorly understood. Here we use genome mining and comparative genomics to assess biosynthetic gene clusters and their putative regulators in the genomes of two lichen-forming fungi, which have substantial commercial value in the perfume industry, Evernia prunastri and Pseudevernia furfuracea. We report a total of 80 biosynthetic gene clusters (polyketide synthases (PKS), non-ribosomal peptide synthetases and terpene synthases) in E. prunastri and 51 in P. furfuracea. We present an in-depth comparison of 11 clusters, which show high homology between the two species. A ketosynthase (KS) phylogeny shows that biosynthetic gene clusters from E. prunastri and P. furfuracea are widespread across the Fungi. The phylogeny includes 15 genomes of lichenized fungi and all fungal PKSs with known functions from the MIBiG database. Phylogenetically closely related KS domains predict not only similar PKS architecture but also similar cluster architecture. Our study highlights the untapped biosynthetic richness of lichen-forming fungi, provides new insights into lichen biosynthetic pathways and facilitates heterologous expression of lichen biosynthetic gene clusters.
To improve data availability and exchange in the area of the WAP complex, West Africa’s largest continuous area of reserves, we set up a citizen science project on the iNaturalist platform, allowing contribution of observations, ideally documented by photographs and/or sounds. Along with the project we created a number of online field guides for the local flora. Within only two months, 852 observations of 312 species have been assembled. We expect this dataset to further grow in the future and complement existing data sets from scientific collections and surveys.
During the Holocene, North American ice sheet collapse and rapid sea-level rise reconnected the Black Sea with the global ocean. Rapid meltwater releases into the North Atlantic and associated climate change arguably slowed the pace of Neolithisation across southeastern Europe, originally hypothesized as a catastrophic flooding that fueled culturally-widespread deluge myths. However, we currently lack an independent record linking the timing of meltwater events, sea-level rise and environmental change with the timing of Neolithisation in southeastern Europe. Here, we present a sea surface salinity record from the Northern Aegean Sea indicative of two meltwater events at ~8.4 and ~7.6 kiloyears that can be directly linked to rapid declines in the establishment of Neolithic sites in southeast Europe. The meltwater events point to an increased outflow of low salinity water from the Black Sea driven by rapid sea level rise >1.4 m following freshwater outbursts from Lake Agassiz and the final decay of the Laurentide ice sheet. Our results shed new light on the link between catastrophic sea-level rise and the Neolithisation of southeastern Europe, and present a historical example of how coastal populations could have been impacted by future rapid sea-level rise.
Plant pathogenic smut fungi in the broader sense can be divided into the Ustilaginomycetes, which cause classical smut symptoms with masses of blackish spores being produced in a variety of angiosperms, and the Exobasidiomycetes, which are often less conspicuous, as many do not shed large amounts of blackish spores. The leaf-spot causing members of the genus Entyloma (Entylomatales, Exobasidiomycetes) belong to the latter group. Currently, 172 species that all infect eudicots are included in the genus. Vánky (2012) recognised five Entyloma species on species of Ranunculus s.lat. Two have been reported only from Ficaria verna s.lat., while three, E. microsporum, E. ranunculi-repentis, E. verruculosum, have been reported to have a broad host range, encompassing 30, 26, and 5 species of Ranunculus, respectively. This broad host range is in contrast to the generally high host specificity assumed for species of Entyloma, indicating that they may represent complexes of specialised species. The aim of this study was to investigate Entyloma on Ranunculus s.lat. using multigene phylogenies and morphological comparisons. Phylogenetic analyses on the basis of up to four loci (ITS, atp2, ssc1, and map) showed a clustering of Entyloma specimens according to host species. For some of these Entyloma lineages, names not currently in use were available and reinstated. In addition, Entyloma microsporum s.str. is neotypified. Six novel species are described in this study, namely, Entyloma jolantae on Ranunculus oreophilus, E. klenkei on R. marginatus, E. kochmanii on R. lanuginosus, E. piepenbringiae on R. polyanthemos subsp. nemorosus (type host) and R. repens, E. savchenkoi on R. paludosus, and E. thielii on R. montanus. For all species diagnostic bases and morphological characteristics are provided. The results in this study once more highlight the importance of detailed re-investigation of broad host-range pathogens of otherwise specialised plant pathogen groups.
Causes of maladaptation
(2019)
Evolutionary biologists tend to approach the study of the natural world within a framework of adaptation, inspired perhaps by the power of natural selection to produce fitness advantages that drive population persistence and biological diversity. In contrast, evolution has rarely been studied through the lens of adaptation's complement, maladaptation. This contrast is surprising because maladaptation is a prevalent feature of evolution: population trait values are rarely distributed optimally; local populations often have lower fitness than imported ones; populations decline; and local and global extinctions are common. Yet we lack a general framework for understanding maladaptation; for instance in terms of distribution, severity, and dynamics. Similar uncertainties apply to the causes of maladaptation. We suggest that incorporating maladaptation‐based perspectives into evolutionary biology would facilitate better understanding of the natural world. Approaches within a maladaptation framework might be especially profitable in applied evolution contexts – where reductions in fitness are common. Toward advancing a more balanced study of evolution, here we present a conceptual framework describing causes of maladaptation. As the introductory article for a Special Feature on maladaptation, we also summarize the studies in this Issue, highlighting the causes of maladaptation in each study. We hope that our framework and the papers in this Special Issue will help catalyze the study of maladaptation in applied evolution, supporting greater understanding of evolutionary dynamics in our rapidly changing world.
In global hydrological models, groundwater (GW) is typically represented by a bucket-like linear groundwater reservoir. Reservoir models, however, (1) can only simulate GW discharge to surface water (SW) bodies but not recharge from SW to GW, (2) provide no information on the location of the GW table, and (3) assume that there is no GW flow among grid cells. This may lead, for example, to an underestimation of groundwater resources in semiarid areas where GW is often replenished by SW or to an underestimation of evapotranspiration where the GW table is close to the land surface. To overcome these limitations, it is necessary to replace the reservoir model in global hydrological models with a hydraulic head gradient-based GW flow model.
We present G3M, a new global gradient-based GW model with a spatial resolution of 5′ (arcminutes), which is to be integrated into the 0.5∘ WaterGAP Global Hydrology Model (WGHM). The newly developed model framework enables in-memory coupling to WGHM while keeping overall runtime relatively low, which allows sensitivity analyses, calibration, and data assimilation. This paper presents the G3M concept and model design decisions that are specific to the large grid size required for a global-scale model. Model results under steady-state naturalized conditions, i.e., neglecting GW abstractions, are shown. Simulated hydraulic heads show better agreement to observations around the world compared to the model output of de Graaf et al. (2015). Locations of simulated SW recharge to GW are found, as is expected, in dry and mountainous regions but areal extent of SW recharge may be underestimated. Globally, GW discharge to rivers is by far the dominant flow component such that lateral GW flows only become a large fraction of total diffuse and focused recharge in the case of losing rivers, some mountainous areas, and some areas with very low GW recharge. A strong sensitivity of simulated hydraulic heads to the spatial resolution of the model and the related choice of the water table elevation of surface water bodies was found. We suggest to investigate how global-scale groundwater modeling at 5′ spatial resolution can benefit from more highly resolved land surface elevation data.
Premise of the study: Polymorphic microsatellite markers were developed for the lichen species Cetraria aculeata (Parmeliaceae) to study fine-scale population diversity and phylogeographic structure.
Methods and Results: Using Illumina HiSeq and MiSeq, 15 fungus-specific microsatellite markers were developed and tested on 81 specimens from four populations from Spain. The number of alleles ranged from four to 13 alleles per locus with a mean of 7.9, and average gene diversities varied from 0.40 to 0.73 over four populations. The amplification rates of 10 markers (CA01– CA10) in populations of C. aculeata exceeded 85%. The markers also amplified across a range of closely related species, except for locus CA05, which did not amplify in C. australiensis and C. "panamericana," and locus CA10 which did not amplify in C. australiensis.
Conclusions: The identified microsatellite markers will be used to study the genetic diversity and phylogeographic structure in populations of C. aculeata in western Eurasia.
Pertusarialean lichens include more than 300 species belonging to several independent phylogenetic lineages. Only some of these phylogenetic clades have been comprehensively sampled for molecular data, and formally described as genera. Here we present a taxonomic treatment of a group of pertusarialean lichens formerly known as "Pertusaria amara-group", "Monomurata-group", or "Variolaria-group", which includes widespread and well-known taxa such as P. amara, P. albescens, or P. ophthalmiza. We generated a 6-locus data set with 79 OTUs representing 75 species. The distinction of the Variolaria clade is supported and consequently, the resurrection of the genus Lepra is followed. Thirty-five new combinations into Lepra are proposed and the new species Lepra austropacifica is described from mangroves in the South Pacific. Lepra is circumscribed to include species with disciform ascomata, a weakly to non-amyloid hymenial gel, strongly amyloid asci without clear apical amyloid structures, containing 1 or 2, single-layered, thin-walled ascospores. Chlorinated xanthones are not present, but thamnolic and picrolichenic acids occur frequently, as well as orcinol depsides. Seventy-one species are accepted in the genus. Although the distinction of the genus from Pertusaria is strongly supported, the relationships of Lepra remain unresolved and the genus is tentatively placed in Pertusariales incertae sedis.
The most basic behavioural states of animals can be described as active or passive. However, while high-resolution observations of activity patterns can provide insights into the ecology of animal species, few methods are able to measure the activity of individuals of small taxa in their natural environment. We present a novel approach in which the automated VHF radio-tracking of small vertebrates fitted with lightweight transmitters (< 0.2 g) is used to distinguish between active and passive behavioural states.
A dataset containing > 3 million VHF signals was used to train and test a random forest model in the assignment of either active or passive behaviour to individuals from two forest-dwelling bat species (Myotis bechsteinii (n = 50) and Nyctalus leisleri (n = 20)). The applicability of the model to other taxonomic groups was demonstrated by recording and classifying the behaviour of a tagged bird and by simulating the effect of different types of vertebrate activity with the help of humans carrying transmitters. The random forest model successfully classified the activity states of bats as well as those of birds and humans, although the latter were not included in model training (F-score 0.96–0.98).
The utility of the model in tackling ecologically relevant questions was demonstrated in a study of the differences in the daily activity patterns of the two bat species. The analysis showed a pronounced bimodal activity distribution of N. leisleri over the course of the night while the night-time activity of M. bechsteinii was relatively constant. These results show that significant differences in the timing of species activity according to ecological preferences or seasonality can be distinguished using our method.
Our approach enables the assignment of VHF signal patterns to fundamental behavioural states with high precision and is applicable to different terrestrial and flying vertebrates. To encourage the broader use of our radio-tracking method, we provide the trained random forest models together with an R-package that includes all necessary data-processing functionalities. In combination with state-of-the-art open-source automated radio-tracking, this toolset can be used by the scientific community to investigate the activity patterns of small vertebrates with high temporal resolution, even in dense vegetation.
he most basic behavioural states of animals can be described as active or passive. While high-resolution observations of activity patterns can provide insights into the ecology of animal species, few methods are able to measure the activity of individuals of small taxa in their natural environment. We present a novel approach in which a combination of automatic radiotracking and machine learning is used to distinguish between active and passive behaviour in small vertebrates fitted with lightweight transmitters (<0.4 g).
We used a dataset containing >3 million signals from very-high-frequency (VHF) telemetry from two forest-dwelling bat species (Myotis bechsteinii [n = 52] and Nyctalus leisleri [n = 20]) to train and test a random forest model in assigning either active or passive behaviour to VHF-tagged individuals. The generalisability of the model was demonstrated by recording and classifying the behaviour of tagged birds and by simulating the effect of different activity levels with the help of humans carrying transmitters. The model successfully classified the activity states of bats as well as those of birds and humans, although the latter were not included in model training (F1 0.96–0.98).
We provide an ecological case-study demonstrating the potential of this automated monitoring tool. We used the trained models to compare differences in the daily activity patterns of two bat species. The analysis showed a pronounced bimodal activity distribution of N. leisleri over the course of the night while the night-time activity of M. bechsteinii was relatively constant. These results show that subtle differences in the timing of species' activity can be distinguished using our method.
Our approach can classify VHF-signal patterns into fundamental behavioural states with high precision and is applicable to different terrestrial and flying vertebrates. To encourage the broader use of our radiotracking method, we provide the trained random forest models together with an R package that includes all necessary data processing functionalities. In combination with state-of-the-art open-source automated radiotracking, this toolset can be used by the scientific community to investigate the activity patterns of small vertebrates with high temporal resolution, even in dense vegetation.
Background: Despite its largely mountainous terrain for which this Himalayan country is a popular tourist destination, Nepal is now endemic for five major vector-borne diseases (VBDs), namely malaria, lymphatic filariasis, Japanese encephalitis, visceral leishmaniasis and dengue fever. There is increasing evidence about the impacts of climate change on VBDs especially in tropical highlands and temperate regions. Our aim is to explore whether the observed spatiotemporal distributions of VBDs in Nepal can be related to climate change.
Methodology: A systematic literature search was performed and summarized information on climate change and the spatiotemporal distribution of VBDs in Nepal from the published literature until December 2014 following providing items for systematic review and meta-analysis (PRISMA) guidelines.
Principal findings: We found 12 studies that analysed the trend of climatic data and are relevant for the study of VBDs, 38 studies that dealt with the spatial and temporal distribution of disease vectors and disease transmission. Among 38 studies, only eight studies assessed the association of VBDs with climatic variables. Our review highlights a pronounced warming in the mountains and an expansion of autochthonous cases of VBDs to non-endemic areas including mountain regions (i.e., at least 2,000 m above sea level). Furthermore, significant relationships between climatic variables and VBDs and their vectors are found in short-term studies.
Conclusion: Taking into account the weak health care systems and difficult geographic terrain of Nepal, increasing trade and movements of people, a lack of vector control interventions, observed relationships between climatic variables and VBDs and their vectors and the establishment of relevant disease vectors already at least 2,000 m above sea level, we conclude that climate change can intensify the risk of VBD epidemics in the mountain regions of Nepal if other non-climatic drivers of VBDs remain constant.
Natural products can contribute to abiotic stress tolerance in plants and fungi. We hypothesize that biosynthetic gene clusters (BGCs), the genomic elements that underlie natural product biosynthesis, display structured differences along elevation gradients. We analysed biosynthetic gene variation in natural populations of the lichen-forming fungus Umbilicaria pustulata. We collected a total of 600 individuals from the Mediterranean and cold-temperate climates. Population genomic analyses indicate that U. pustulata contains three clusters that are highly differentiated between the Mediterranean and cold-temperate populations. One entire cluster is exclusively present in cold-temperate populations, and a second cluster is putatively dysfunctional in all cold-temperate populations. In the third cluster variation is fixed in all cold-temperate populations due to hitchhiking. In these two clusters the presence of consistent allele frequency differences among replicate populations/gradients suggests that selection rather than drift is driving the pattern. We advocate that the landscape of fungal biosynthetic genes is shaped by both positive and hitchhiking selection. We demonstrate, for the first time, the presence of climate-associated BGCs and BGC variations in lichen-forming fungi. While the associated secondary metabolites of the candidate clusters are presently unknown, our study paves the way for targeted discovery of natural products with ecological significance.
Little work has been done on large-scale patterns of stream insect richness in China. We explored the influence of climatic and catchment-scale factors on stream insect (Ephemeroptera, Plecoptera, Trichoptera; EPT) richness across mid-latitude China. We assessed the predictive ability of climatic, catchment land cover and physical structure variables on genus richness of EPT, both individually and combined, in 80 mid-latitude Chinese streams, spanning a 3899-m altitudinal gradient. We performed analyses using boosted regression trees and explored the nature of their influence on richness patterns. The relative importance of climate, land cover, and physical factors on stream insect richness varied considerably between the three orders, and while important for Ephemeroptera and Plecoptera, latitude did not improve model fit for any of the groups. EPT richness was linked with areas comprising high forest cover, elevation and slope, large catchments and low temperatures. Ephemeroptera favoured areas with high forest cover, medium-to-large catchment sizes, high temperature seasonality, and low potential evapotranspiration. Plecoptera richness was linked with low temperature seasonality and annual mean, and high slope, elevation and warm-season rainfall. Finally, Trichoptera favoured high elevation areas, with high forest cover, and low mean annual temperature, seasonality and aridity. Our findings highlight the variable role that catchment land cover, physical properties and climatic influences have on stream insect richness. This is one of the first studies of its kind in Chinese streams, thus we set the scene for more in-depth assessments of stream insect richness across broader spatial scales in China, but stress the importance of improving data availability and consistency through time.
Background: Polyploidy and apomixis are important factors influencing plant distributions often resulting in range shifts, expansions and geographical parthenogenesis. We used the Ranunculus auricomus complex as a model to asses if the past and present distribution and climatic preferences were determined by these phenomena.
Results: Ecological differentiation among diploids and polyploids was tested by comparing the sets of climatic variables and distribution modelling using 191 novel ploidy estimations and 561 literature data. Significant differences in relative genome size on the diploid level were recorded between the “auricomus” and “cassubicus” groups and several new diploid occurrences were found in Slovenia and Hungary. The current distribution of diploids overlapped with the modelled paleodistribution (22 kyr BP), except Austria and the Carpathians, which are proposed to be colonized later on from refugia in the Balkans. Current and historical presence of diploids from the R. auricomus complex is suggested also for the foothills of the Caucasus. Based on comparisons of the climatic preferences polyploids from the R. auricomus complex occupy slightly drier and colder habitats than the diploids.
Conclusions: The change of reproductive mode and selection due to competition with the diploid ancestors may have facilitated the establishment of polyploids within the R. auricomus complex in environments slightly cooler and drier, than those tolerated by diploid ancestors. Much broader distribution of polyploid apomicts may have been achieved due to faster colonization mediated by uniparental reproductive system.
Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods.
Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal -arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods – BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence.
Active species reintroduction is an important conservation tool when aiming for the restoration of biological communities and ecosystems. The effective monitoring of reintroduction success is a crucial factor in this process. Here, we used a combination of environmental DNA (eDNA) techniques and species distribution models (SDMs) to evaluate the success of recent reintroductions of the freshwater fish Alburnoides bipunctatus in central Germany. We built SDMs without and with eDNA presence data to locate further suitable reintroduction sites and potentially overlooked populations of the species. We successfully detected eDNA of A. bipunctatus at all reintroduction sites, as well as several adjacent sites mostly in downstream direction, which supports the success of reintroduction efforts. eDNA‐based species detection considerably improved SDMs for A. bipunctatus, which allowed to identify species presence in previously unknown localities. Our results confirm the usefulness of eDNA techniques as standard tool to monitor reintroduced fish populations. We propose that combining eDNA with SDMs is a highly effective approach for long‐term monitoring of reintroduction success in aquatic species.
The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 μatm) and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2.
Social insects dominate arthropod communities worldwide due to cooperation and division of labor in their societies. This, however, makes them vulnerable to exploitation by social parasites, such as slave‐making ants. Slave‐making ant workers pillage brood from neighboring nests of related host ant species. After emergence, host workers take over all nonreproductive colony tasks, whereas slavemakers have lost the ability to care for themselves and their offspring. Here, we compared transcriptomes of different developmental stages (larvae, pupae, and adults), castes (queens and workers), and sexes of two related ant species, the slavemaker Temnothorax americanus and its host Temnothorax longispinosus. Our aim was to investigate commonalities and differences in group‐specific transcriptomes, whereupon across‐species differences possibly can be explained by their divergent lifestyles. Larvae and pupae showed the highest similarity between the two species and upregulated genes with enriched functions of translation and chitin metabolism, respectively. Workers commonly upregulated oxidation‐reduction genes, possibly indicative of their active lifestyle. Host workers, but not workers of the slavemaker, upregulated a “social behavior” gene. In slavemaker queens and workers, genes associated with the regulation of transposable elements were upregulated. Queens of both species showed transcriptomic signals of anti‐aging mechanisms, with hosts upregulating various DNA repair pathways and slavemaker queens investing in trehalose metabolism. The transcriptomes of males showed enriched functions for quite general terms realized in different genes and pathways in each species. In summary, the strong interspecific commonalities in larvae, pupae, and workers were reflected in the same enriched Gene Ontology (GO) terms. Less commonalities occurred in the transcriptomes of queens and males, which apparently utilize different pathways to achieve a long life and sperm production, respectively. We found that all analyzed groups in this study show characteristic GO terms, with similar patterns in both species.
The adaptive response of Sorghum bicolor landraces from Egypt to drought stress and following recovery was analyzed using two-dimensional difference gel electrophoresis, 2D-DIGE. Physiological measurements and proteome alterations of accession number 11434, drought tolerant, and accession number 11431, drought sensitive, were compared to their relative control values after drought stress and following recovery. Differentially expressed proteins were analysed by Matrix assisted laser desorption ionisation time-of-flight mass spectrometry, MALDI-TOF-MS. Alterations in protein contents related to the energy balance, metabolism (sensu Mewes et al. 1997), and chaperons were the most apparent features to elucidate the differences between the drought tolerant and sensitive accessions. Further alterations in the levels of proteins related to transcription and protein synthesis are discussed.
Ceraceosorus bombacis is an early-diverging lineage of smut fungi and a pathogen of cotton trees (Bombax ceiba). To study the evolutionary genomics of smut fungi in comparison with other fungal and oomycete pathogens, the genome of C. bombacis was sequenced and comparative genomic analyses were performed. The genome of 26.09 Mb encodes for 8,024 proteins, of which 576 are putative-secreted effector proteins (PSEPs). Orthology analysis revealed 30 ortholog PSEPs among six Ustilaginomycotina genomes, the largest groups of which are lytic enzymes, such as aspartic peptidase and glycoside hydrolase. Positive selection analyses revealed the highest percentage of positively selected PSEPs in C. bombacis compared with other Ustilaginomycotina genomes. Metabolic pathway analyses revealed the absence of genes encoding for nitrite and nitrate reductase in the genome of the human skin pathogen Malassezia globosa, but these enzymes are present in the sequenced plant pathogens in smut fungi. Interestingly, these genes are also absent in cultivable oomycete animal pathogens, while nitrate reductase has been lost in cultivable oomycete plant pathogens. Similar patterns were also observed for obligate biotrophic and hemi-biotrophic fungal and oomycete pathogens. Furthermore, it was found that both fungal and oomycete animal pathogen genomes are lacking cutinases and pectinesterases. Overall, these findings highlight the parallel evolution of certain genomic traits, revealing potential common evolutionary trajectories among fungal and oomycete pathogens, shaping the pathogen genomes according to their lifestyle.
Projections of future changes in runoff can have important implications for water resources and flooding. In this study, runoff projections from ISI-MIP (Inter-sectoral Impact Model Intercomparison Project) simulations forced with HadGEM2-ES bias-corrected climate data under the Representative Concentration Pathway 8.5 have been analysed. Projections of change from the baseline period (1981–2010) to the future (2070–2099) from a number of different ecosystems and hydrological models were studied. The differences between projections from the two types of model were looked at globally and regionally. Typically, across different regions the ecosystem models tended to project larger increases and smaller decreases in runoff than the hydrological models. However, the differences varied both regionally and seasonally. Sensitivity experiments were also used to investigate the contributions of varying CO2 and allowing vegetation distribution to evolve on projected changes in runoff. In two out of four models which had data available from CO2 sensitivity experiments, allowing CO2 to vary was found to increase runoff more than keeping CO2 constant, while in two models runoff decreased. This suggests more uncertainty in runoff responses to elevated CO2 than previously considered. As CO2 effects on evapotranspiration via stomatal conductance and leaf-area index are more commonly included in ecosystems models than in hydrological models, this may partially explain some of the difference between model types. Keeping the vegetation distribution static in JULES runs had much less effect on runoff projections than varying CO2, but this may be more pronounced if looked at over a longer timescale as vegetation changes may take longer to reach a new state.
The implementation of HTS (high-throughput sequencing) approaches is rapidly changing our understanding of the lichen symbiosis, by uncovering high bacterial and fungal diversity, which is often host-specific. Recently, HTS methods revealed the presence of multiple photobionts inside a single thallus in several lichen species. This differs from Sanger technology, which typically yields a single, unambiguous algal sequence per individual. Here we compared HTS and Sanger methods for estimating the diversity of green algal symbionts within lichen thalli using 240 lichen individuals belonging to two species of lichen-forming fungi. According to HTS data, Sanger technology consistently yielded the most abundant photobiont sequence in the sample. However, if the second most abundant photobiont exceeded 30% of the total HTS reads in a sample, Sanger sequencing generally failed. Our results suggest that most lichen individuals in the two analyzed species, Lasallia hispanica and L. pustulata, indeed contain a single, predominant green algal photobiont. We conclude that Sanger sequencing is a valid approach to detect the dominant photobionts in lichen individuals and populations. We discuss which research areas in lichen ecology and evolution will continue to benefit from Sanger sequencing, and which areas will profit from HTS approaches to assessing symbiont diversity.
With the change to one scientific name for pleomorphic fungi, generic names typified by sexual and asexual morphs have been evaluated to recommend which name to use when two names represent the same genus and thus compete for use. In this paper, generic names in Pucciniomycotina and Ustilaginomycotina are evaluated based on their type species to determine which names are synonyms. Twenty-one sets of sexually and asexually typified names in Pucciniomycotina and eight sets in Ustilaginomycotina were determined to be congeneric and compete for use. Recommendations are made as to which generic name to use. In most cases the principle of priority is followed. However, eight generic names in the Pucciniomycotina, and none in Ustilaginomycotina, are recommended for protection: Classicula over Naiadella, Gymnosporangium over Roestelia, Helicobasidium over Thanatophytum and Tuberculina, Melampsorella over Peridermium, Milesina over Milesia, Phragmidium over Aregma, Sporobolomyces over Blastoderma and Rhodomyces, and Uromyces over Uredo. In addition, eight new combinations are made: Blastospora juruensis, B. subneurophyla, Cronartium bethelii, C. kurilense, C. sahoanum, C. yamabense, Milesina polypodii, and Prospodium crusculum combs. nov.
Protein disulfide isomerases (PDIs) support endoplasmic reticulum redox protein folding and cell-surface thiol-redox control of thrombosis and vascular remodeling. The family prototype PDIA1 regulates NADPH oxidase signaling and cytoskeleton organization, however the related underlying mechanisms are unclear. Here we show that genes encoding human PDIA1 and its two paralogs PDIA8 and PDIA2 are each flanked by genes encoding Rho guanine-dissociation inhibitors (GDI), known regulators of RhoGTPases/cytoskeleton. Evolutionary histories of these three microsyntenic regions reveal their emergence by two successive duplication events of a primordial gene pair in the last common vertebrate ancestor. The arrangement, however, is substantially older, detectable in echinoderms, nematodes, and cnidarians. Thus, PDI/RhoGDI pairing in the same transcription orientation emerged early in animal evolution and has been largely maintained. PDI/RhoGDI pairs are embedded into conserved genomic regions displaying common cis-regulatory elements. Analysis of gene expression datasets supports evidence for PDI/RhoGDI coexpression in developmental/inflammatory contexts. PDIA1/RhoGDIα were co-induced in endothelial cells upon CRISP-R-promoted transcription activation of each pair component, and also in mouse arterial intima during flow-induced remodeling. We provide evidence for physical interaction between both proteins. These data support strong functional links between PDI and RhoGDI families, which likely maintained PDI/RhoGDI microsynteny along > 800-million years of evolution.
The fossil record is widely informative about evolution, but fossils are not systematically used to study the evolution of stem-cell-driven renewal. Here, we examined evolution of the continuous growth (hypselodonty) of rodent molar teeth, which is fuelled by the presence of dental stem cells. We studied occurrences of 3,500 North American rodent fossils, ranging from 50 million years ago (mya) to 2 mya. We examined changes in molar height to determine whether evolution of hypselodonty shows distinct patterns in the fossil record, and we found that hypselodont taxa emerged through intermediate forms of increasing crown height. Next, we designed a Markov simulation model, which replicated molar height increases throughout the Cenozoic and, moreover, evolution of hypselodonty. Thus, by extension, the retention of the adult stem cell niche appears to be a predictable quantitative rather than a stochastic qualitative process. Our analyses predict that hypselodonty will eventually become the dominant phenotype.
The degradation of natural forests to modified forests threatens subtropical and tropical biodiversity worldwide. Yet, species responses to forest modification vary considerably. Furthermore, effects of forest modification can differ, whether with respect to diversity components (taxonomic or phylogenetic) or to local (α-diversity) and regional (β-diversity) spatial scales. This real-world complexity has so far hampered our understanding of subtropical and tropical biodiversity patterns in human-modified forest landscapes. In a subtropical South African forest landscape, we studied the responses of three successive plant life stages (adult trees, saplings, seedlings) and of birds to five different types of forest modification distinguished by the degree of within-forest disturbance and forest loss. Responses of the two taxa differed markedly. Thus, the taxonomic α-diversity of birds was negatively correlated with the diversity of all plant life stages and, contrary to plant diversity, increased with forest disturbance. Conversely, forest disturbance reduced the phylogenetic α-diversity of all plant life stages but not that of birds. Forest loss neither affected taxonomic nor phylogenetic diversity of any taxon. On the regional scale, taxonomic but not phylogenetic β-diversity of both taxa was well predicted by variation in forest disturbance and forest loss. In contrast to adult trees, the phylogenetic diversity of saplings and seedlings showed signs of contemporary environmental filtering. In conclusion, forest modification in this subtropical landscape strongly shaped both local and regional biodiversity but with contrasting outcomes. Phylogenetic diversity of plants may be more threatened than that of mobile species such as birds. The reduced phylogenetic diversity of saplings and seedlings suggests losses in biodiversity that are not visible in adult trees, potentially indicating time-lags and contemporary shifts in forest regeneration. The different responses of taxonomic and phylogenetic diversity to forest modifications imply that biodiversity conservation in this subtropical landscape requires the preservation of natural and modified forests.
Australia has experienced dramatic declines and extinctions of its native rodent species over the last 200 years, particularly in southern Australia. In the tropical savanna of northern Australia significant declines have occurred only in recent decades. The later onset of these declines suggests that the causes may differ from earlier declines in the south. We examine potential regional effects (northern versus southern Australia) on biological and ecological correlates of range decline in Australian rodents. We demonstrate that rodent declines have been greater in the south than in the tropical north, are strongly influenced by phylogeny, and are consistently greater for species inhabiting relatively open or sparsely vegetated habitat. Unlike in marsupials, where some species have much larger body size than rodents, body mass was not an important predictor of decline in rodents. All Australian rodent species are within the prey-size range of cats (throughout the continent) and red foxes (in the south). Contrary to the hypothesis that mammal declines are related directly to ecosystem productivity (annual rainfall), our results are consistent with the hypothesis that disturbances such as fire and grazing, which occur in non-rainforest habitats and remove cover used by rodents for shelter, nesting and foraging, increase predation risk. We agree with calls to introduce conservation management that limits the size and intensity of fires, increases fire patchiness and reduces grazing impacts at ecological scales appropriate for rodents. Controlling feral predators, even creating predator-free reserves in relatively sparsely-vegetated habitats, is urgently required to ensure the survival of rodent species, particularly in northern Australia where declines are not yet as severe as those in the south.
Marine oomycetes are highly diverse, globally distributed, and play key roles in marine food webs as decomposers, food source, and parasites. Despite their potential importance in global ocean ecosystems, marine oomycetes are comparatively little studied. Here, we tested if the primer pair cox2F_Hud and cox2-RC4, which is already well-established for phylogenetic investigations of terrestrial oomycetes, can also be used for high-throughput community barcoding. Community barcoding of a plankton sample from Brudenell River (Prince Edward Island, Canada), revealed six distinct oomycete OTU clusters. Two of these clusters corresponded to members of the Peronosporaceae—one could be assigned to Peronospora verna, an obligate biotrophic pathogen of the terrestrial plant Veronica serpyllifolia and related species, the other was closely related to Globisporangium rostratum. While the detection of the former in the sample is likely due to long-distance dispersal from the island, the latter might be a bona fide marine species, as several cultivable species of the Peronosporaceae are known to withstand high salt concentrations. Two OTU lineages could be assigned to the Saprolegniaceae. While these might represent marine species of the otherwise terrestrial genus, it is also conceivable that they were introduced on detritus from the island. Two additional OTU clusters were grouped with the early-diverging oomycete lineages but could not be assigned to a specific family. This reflects the current underrepresentation of cox2 sequence data which will hopefully improve with the increasing interest in marine oomycetes.
The data provided is related to the article "Phylogenetic analyses of gazelles reveal repeated transitions of key ecological traits and provide novel insights into the origin of the genus Gazella". The data is based on 48 tissue samples of all nine extant species of the genus Gazella, namely Gazella gazella, Gazella arabica, Gazella bennettii, Gazella cuvieri, Gazella dorcas, Gazella leptoceros, Gazella marica, Gazella spekei, and Gazella subgutturosa and four related taxa (Saiga tatarica, Antidorcas marsupialis, Antilope cervicapra and Eudorcas rufifrons). It comprises alignments of sequences of a cytochrome b data set and of six nuclear intron markers. For the latter new primers were designed based on cattle and sheep genomes. Based on these alignments phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood methods. Furthermore, ancestral character states (inferred with BayesTraits 1.0) and ancestral ranges based on a Dispersal-Extinction-Cladogenesis model were estimated and results׳ files were stored within this article.
Temporal variation in the detectability of a species can bias estimates of relative abundance if not handled correctly. For example, when effort varies in space and/or time it becomes necessary to take variation in detectability into account when data are analyzed. We demonstrate the importance of incorporating seasonality into the analysis of data with unequal sample sizes due to lost traps at a particular density of a species. A case study of count data was simulated using a spring-active carabid beetle. Traps were ‘lost’ randomly during high beetle activity in high abundance sites and during low beetle activity in low abundance sites. Five different models were fitted to datasets with different levels of loss. If sample sizes were unequal and a seasonality variable was not included in models that assumed the number of individuals was log-normally distributed, the models severely under- or overestimated the true effect size. Results did not improve when seasonality and number of trapping days were included in these models as offset terms, but only performed well when the response variable was specified as following a negative binomial distribution. Finally, if seasonal variation of a species is unknown, which is often the case, seasonality can be added as a free factor, resulting in well-performing negative binomial models. Based on these results we recommend (a) add sampling effort (number of trapping days in our example) to the models as an offset term, (b) if precise information is available on seasonal variation in detectability of a study object, add seasonality to the models as an offset term; (c) if information on seasonal variation in detectability is inadequate, add seasonality as a free factor; and (d) specify the response variable of count data as following a negative binomial or over-dispersed Poisson distribution.
Increasing atmospheric CO2 stimulates photosynthesis which can increase net primary production (NPP), but at longer timescales may not necessarily increase plant biomass. Here we analyse the four decade-long CO2-enrichment experiments in woody ecosystems that measured total NPP and biomass. CO2 enrichment increased biomass increment by 1.05 ± 0.26 kg C m−2 over a full decade, a 29.1 ± 11.7% stimulation of biomass gain in these early-secondary-succession temperate ecosystems. This response is predictable by combining the CO2 response of NPP (0.16 ± 0.03 kg C m−2 y−1) and the CO2-independent, linear slope between biomass increment and cumulative NPP (0.55 ± 0.17). An ensemble of terrestrial ecosystem models fail to predict both terms correctly. Allocation to wood was a driver of across-site, and across-model, response variability and together with CO2-independence of biomass retention highlights the value of understanding drivers of wood allocation under ambient conditions to correctly interpret and predict CO2 responses.
Sucrose is known to repress the translation of Arabidopsis thaliana AtbZIP11 transcript which encodes a protein belonging to the group of S (S - stands for small) basic region-leucine zipper (bZIP)-type transcription factor. This repression is called sucrose-induced repression of translation (SIRT). It is mediated through the sucrose-controlled upstream open reading frame (SC-uORF) found in the AtbZIP11 transcript. The SIRT is reported for 4 other genes belonging to the group of S bZIP in Arabidopsis. Tobacco tbz17 is phylogenetically closely related to AtbZIP11 and carries a putative SC-uORF in its 5′-leader region. Here we demonstrate that tbz17 exhibits SIRT mediated by its SC-uORF in a manner similar to genes belonging to the S bZIP group of the Arabidopsis genus. Furthermore, constitutive transgenic expression of tbz17 lacking its 5′-leader region containing the SC-uORF leads to production of tobacco plants with thicker leaves composed of enlarged cells with 3–4 times higher sucrose content compared to wild type plants. Our finding provides a novel strategy to generate plants with high sucrose content.
Tropical forest soils are a significant source for the greenhouse gas N2O as well as for NO, a precursor of tropospheric ozone. However, current estimates are uncertain due to the limited number of field measurements. Furthermore, there is considerable spatial and temporal variability of N2O and NO emissions due to the variation of environmental conditions such as soil properties, vegetation characteristics and meteorology. In this study we used a process-based model (ForestDNDC-tropica) to estimate N2O and NO emissions from tropical highland forest (Nyungwe) soils in southwestern Rwanda. To extend the model inputs to regional scale, ForestDNDC-tropica was linked to an exceptionally large legacy soil dataset. There was agreement between N2O and NO measurements and the model predictions though the ForestDNDC-tropica resulted in considerable lower emissions for few sites. Low similarity was specifically found for acidic soil with high clay content and reduced metals, indicating that chemo-denitrification processes on acidic soils might be under-represented in the current ForestDNDC-tropica model. The results showed that soil bulk density and pH are the most influential factors driving spatial variations in soil N2O and NO emissions for tropical forest soils. The area investigated (1113 km2) was estimated to emit ca. 439 ± 50 t N2O-N yr−1 (2.8–5.5 kg N2O-N ha−1 yr−1) and 244 ± 16 t NO-N yr−1 (0.8–5.1 kg N ha−1 yr−1). Consistent with less detailed studies, we confirm that tropical highland rainforest soils are a major source of atmospheric N2O and NO.
Since few decades there is a broad debate about the so called ecological crisis. The debate had its highlight at the Rio-Conference in 1992. This conference was also the starting point for a wide range of political efforts concerned with a broad spectrum of biodiversity issues. Insofar, the term ‘biodiversity’ is not one of the natural sciences, but one which is inherently connected with questions of good human life. This article argues that the question for the good life predominantly fulfills a heuristic function and is to be answered in light of certain societal relations to nature. Furthermore, in light of these societal relations to nature it is argued for a virtue ethical approach with respect to the individual good life, whereas concerning the scale of societal aspects transdisciplinarity is identified as the appropriate research mode, which addresses both societal and scientific issues.
New geochemical data from the Malawi Rift (Chiwondo Beds, Karonga Basin) fill a major spatial gap in our knowledge of hominin adaptations on a continental scale. Oxygen (δ18O), carbon (δ13C), and clumped (Δ47) isotope data on paleosols, hominins, and selected fauna elucidate an unexpected diversity in the Pleistocene hominin diet in the various habitats of the East African Rift System (EARS). Food sources of early Homo and Paranthropus thriving in relatively cool and wet wooded savanna ecosystems along the western shore of paleolake Malawi contained a large fraction of C3 plant material. Complementary water consumption reconstructions suggest that ca. 2.4 Ma, early Homo (Homo rudolfensis) and Paranthropus (Paranthropus boisei) remained rather stationary near freshwater sources along the lake margins. Time-equivalent Paranthropus aethiopicus from the Eastern Rift further north in the EARS consumed a higher fraction of C4 resources, an adaptation that grew more pronounced with increasing openness of the savanna setting after 2 Ma, while Homo maintained a high versatility. However, southern African Paranthropus robustus had, similar to the Malawi Rift individuals, C3-dominated feeding strategies throughout the Early Pleistocene. Collectively, the stable isotope and faunal data presented here document that early Homo and Paranthropus were dietary opportunists and able to cope with a wide range of paleohabitats, which clearly demonstrates their high behavioral flexibility in the African Early Pleistocene.
Global climate change is one of the major driving forces for adaptive shifts in migration and breeding phenology and possibly impacts demographic changes if a species fails to adapt sufficiently. In Western Europe, pied flycatchers (Ficedula hypoleuca) have insufficiently adapted their breeding phenology to the ongoing advance of food peaks within their breeding area and consequently suffered local population declines. We address the question whether this population decline led to a loss of genetic variation, using two neutral marker sets (mitochondrial control region and microsatellites), and one potentially selectively non-neutral marker (avian Clock gene). We report temporal changes in genetic diversity in extant populations and biological archives over more than a century, using samples from sites differing in the extent of climate change. Comparing genetic differentiation over this period revealed that only the recent Dutch population, which underwent population declines, showed slightly lower genetic variation than the historic Dutch population. As that loss of variation was only moderate and not observed in all markers, current gene flow across Western and Central European populations might have compensated local loss of variation over the last decades. A comparison of genetic differentiation in neutral loci versus the Clock gene locus provided evidence for stabilizing selection. Furthermore, in all genetic markers, we found a greater genetic differentiation in space than in time. This pattern suggests that local adaptation or historic processes might have a stronger effect on the population structure and genetic variation in the pied flycatcher than recent global climate changes.
The ancestors to the Australian marsupials entered Australia around 60 (54-72) million years ago from Antarctica, and radiated into the four living orders Peramelemorphia, Dasyuromorphia, Diprotodontia and Notoryctemorphia. The relationship between the four Australian marsupial orders has been a long-standing question, because different phylogenetic studies were not able to consistently reconstruct the same topology. Initial in silico analysis of the Tasmanian devil genome and experimental screening in the seven marsupial orders revealed 20 informative transposable element insertions for resolving the inter- and intraordinal relationships of Australian and South American orders. However, the retrotransposon insertions support three conflicting topologies regarding Peramelemorphia, Dasyuromorphia and Notoryctemorphia, indicating that the split between the three orders may be best understood as a network. This finding is supported by a phylogenetic re-analysis of nuclear gene sequences, using a consensus network approach that allows depicting hidden phylogenetic conflict, otherwise lost when forcing the data into a bifurcating tree. The consensus network analysis agrees with the transposable element analysis in that all possible topologies regarding Peramelemorphia, Dasyuromorphia, and Notoryctemorphia in a rooted four-taxon topology are equally well supported. In addition, retrotransposon insertion data supports the South American order Didelphimorphia being the sistergroup to all other living marsupial orders. The four Australian orders originated within three million years at the Cretaceous-Paleogene boundary. The rapid divergences left conflicting phylogenetic information in the genome possibly generated by incomplete lineage sorting or introgressive hybridisation, leaving the relationship among Australian marsupial orders unresolvable as a bifurcating process million years later.
An updated inventory of the Bromeliaceae for Costa Rica is presented including citations of representative specimens for each species. The family comprises 18 genera and 198 species in Costa Rica, 32 species being endemic to the country. Additional 36 species are endemic to Costa Rica and Panama. Only 4 of the 8 bromeliad subfamilies occur in Costa Rica, with a strong predominance of Tillandsioideae (7 genera/150 spp.; 75.7% of all bromeliad species in Costa Rica). 124 species (62.6%) grow exclusively epiphytic, additional 59 spp. (29.8%) are facultative epiphytes. The most diverse genus is Werauhia, with 59 species (29.8% of the Costa Rican bromeliad flora), followed by Tillandsia with 40 species (20.2%) and Guzmania with 28 spp. (8.6%).
Background: One aspect of premating isolation between diverging, locally-adapted population pairs is female mate choice for resident over alien male phenotypes. Mating preferences often show considerable individual variation, and whether or not certain individuals are more likely to contribute to population interbreeding remains to be studied. In the Poecilia mexicana-species complex different ecotypes have adapted to hydrogen sulfide (H2S)-toxic springs, and females from adjacent non-sulfidic habitats prefer resident over sulfide-adapted males. We asked if consistent individual differences in behavioral tendencies (animal personality) predict the strength and direction of the mate choice component of premating isolation in this system.
Results: We characterized focal females for their personality and found behavioral measures of ‘novel object exploration’, ‘boldness’ and ‘activity in an unknown area’ to be highly repeatable. Furthermore, the interaction term between our measures of exploration and boldness affected focal females’ strength of preference (SOP) for the resident male phenotype in dichotomous association preference tests. High exploration tendencies were coupled with stronger SOPs for resident over alien mating partners in bold, but not shy, females. Shy and/or little explorative females had an increased likelihood of preferring the non-resident phenotype and thus, are more likely to contribute to rare population hybridization. When we offered large vs. small conspecific stimulus males instead, less explorative females showed stronger preferences for large male body size. However, this effect disappeared when the size difference between the stimulus males was small.
Conclusions: Our results suggest that personality affects female mate choice in a very nuanced fashion. Hence, population differences in the distribution of personality types could be facilitating or impeding reproductive isolation between diverging populations depending on the study system and the male trait(s) upon which females base their mating decisions, respectively.
Don't poke the bear : using tracking data to quantify behavioural syndromes in elusive wildlife
(2018)
Animal personality traits and the emergence of behavioural syndromes, i.e. between-individual correlation of behaviours, are commonly quantified from behavioural observations in controlled environments. Subjecting large and elusive wildlife to controlled test situations is, however, rarely possible, suggesting that ecologists should exploit alternative measures of behaviours for quantifying differences between individuals. Our goal was to test whether movement and space use data can be used to quantify behavioural syndromes in the wild. We quantified six behaviours from GPS and dual motion sensor tracking devices of 46 adult female brown bears followed in southcentral Sweden over the summer and early autumn. As well as daily travel distance, an indicator for activity, and daily displacement, an indicator for exploration, we quantified four behaviours that increase a bear's likelihood of encountering humans and could thus serve as indicators for boldness: diurnality, selection for roads and selection for two open habitat types, bogs and clearcuts, with low lateral cover. We tested (1) whether behaviours showed repeatable between-individual variation (animal personality) and (2) whether behaviours were correlated between individuals and thus formed a behavioural syndrome. Repeatability of behaviours ranged from 0.16 to 0.61 confirming between-individual variation in movement, activity and space use. A multivariate mixed model revealed significant positive correlations between travel distance, displacement and diurnality, suggesting the existence of an activity–exploration and potentially partial boldness syndrome in our bear population. Selection for exposed or human-frequented habitats were uncorrelated with the activity–exploration syndrome and with each other, albeit there was a trend for stronger road avoidance by bears that readily used clearcuts. We show that large tracking data sets can be used to quantify between-individual correlation in spatial behaviours. We suggest that delineating behavioural types from wildlife tracking data will be of increasing interest because of the importance of animal personality for ecological processes, wildlife conservation and human–wildlife coexistence.
Downsizing of animal communities due to defaunation is prevalent in many ecosystems. Yet, we know little about its consequences for ecosystem functions such as seed dispersal. Here, we use eight seed-dispersal networks sampled across the Andes and simulate how downsizing of avian frugivores impacts structural network robustness and seed dispersal. We use a trait-based modeling framework to quantify the consequences of downsizing-relative to random extinctions-for the number of interactions and secondary plant extinctions (as measures of structural robustness) and for long-distance seed dispersal (as a measure of ecosystem function). We find that downsizing leads to stronger functional than structural losses. For instance, 10% size-structured loss of bird species results in almost 40% decline of long-distance seed dispersal, but in less than 10% of structural loss. Our simulations reveal that measures of the structural robustness of ecological networks underestimate the consequences of animal extinction and downsizing for ecosystem functioning.
Diatoms are thought to provide about 40% of total global photosynthesis and diatoms of the genus Coscinodiscus are an important, sometimes dominant, cosmopolitan component of the marine diatom community. The oomycete parasitoid Lagenisma coscinodisci is widespread in the northern hemisphere on its hosts in the genus Coscinodiscus. Because of its potential ecological importance, it would be a suitable pathogen model to investigate plankton/parasite interactions, but the species cannot be cultivated on media without its host, so far. Thus, it was the aim of this study to explore the potential of dual culture of host and pathogen in the laboratory and to optimise cultivation to ensure a long-term cultivation of the pathogen. Here, we report successful cultivation of a single spore strain of L. coscinodisci (Isla), on several Coscinodiscus species and strains, as well as the establishment of a cultivation routine with Coscinodiscus granii (CGS1 and CG36), which enabled us to maintain the single spore strain for more than 3 years in 6 cm Petri dishes and 10 ml tissue culture flasks. This opens up the opportunity to study the processes and mechanism in plankton/parasitoid interactions under controlled conditions.
Mosquito species belonging to the genus Aedes have attracted the interest of scientists and public health officers for their invasive species traits and efficient capacity of transmitting viruses affecting humans. Some of these species were brought outside their native range by human activities such as trade and tourism, and colonised new regions thanks to a unique combination of eco-physiological traits.
Considering mosquito physiological and behavioural traits to understand and predict the spatial and temporal population dynamics is thus a crucial step to develop strategies to mitigate the local densities of invasive Aedes populations.
Here, we synthesised the life cycle of four invasive Aedes species (Ae. aegypti, Ae. albopictus, Ae. japonicus and Ae. koreicus) in a single multi-scale stochastic modelling framework which we coded in the R package dynamAedes. We designed a stage-based and time-discrete stochastic model driven by temperature, photo-period and inter-specific larval competition that can be applied to three different spatial scales: punctual, local and regional. These spatial scales consider different degrees of spatial complexity and data availability, by accounting for both active and passive dispersal of mosquito species as well as for the heterogeneity of the input temperature data.
Our overarching aim was to provide a flexible, open-source and user-friendly tool rooted in the most updated knowledge on species biology which could be applied to the management of invasive Aedes populations as well as for more theoretical ecological inquiries.
Mosquito species belonging to the genus Aedes have attracted the interest of scientists and public health officers because of their capacity to transmit viruses that affect humans. Some of these species were brought outside their native range by means of trade and tourism and then colonised new regions thanks to a unique combination of eco-physiological traits. Considering mosquito physiological and behavioural traits to understand and predict their population dynamics is thus a crucial step in developing strategies to mitigate the local densities of invasive Aedes populations. Here, we synthesised the life cycle of four invasive Aedes species (Ae. aegypti, Ae. albopictus, Ae. japonicus and Ae. koreicus) in a single multi-scale stochastic modelling framework which we coded in the R package dynamAedes. We designed a stage-based and time-discrete stochastic model driven by temperature, photo-period and inter-specific larval competition that can be applied to three different spatial scales: punctual, local and regional. These spatial scales consider different degrees of spatial complexity and data availability by accounting for both active and passive dispersal of mosquito species as well as for the heterogeneity of the input temperature data. Our overarching aim was to provide a flexible, open-source and user-friendly tool rooted in the most updated knowledge on the species’ biology which could be applied to the management of invasive Aedes populations as well as to more theoretical ecological inquiries.
State-of-the-art general circulation models (GCMs) are tested and challenged by the ability to reproduce paleoclimate key intervals. In order to account for climate changes associated with soil dynamics we have developed a soil scheme, which is asynchronously coupled to a state-of-the-art atmosphere ocean GCM with dynamic vegetation. We test the scheme for conditions representative of a warmer (mid-Holocene, 6 kyr before present, BP) and colder (Last Glacial Maximum, 21 kyr BP) than pre-industrial climate. The computed change of physical soil properties (i.e. albedo, water storage capacity, and soil texture) for these different climates leads to amplified global climate anomalies. Especially regions like the transition zone of desert/savannah and taiga/tundra, exhibit an increased response as a result of the modified soil treatment. In comparison to earlier studies, the inclusion of the soil feedback pushes our model simulations towards the warmer end in the range of mid-Holocene studies and beyond current estimates of global cooling during the Last Glacial Maximum based on PMIP2 (Paleoclimate Modelling Intercomparison Project 2) studies. The main impact of the interactive soil scheme on the climate response is governed by positive feedbacks, including dynamics of vegetation, snow, sea ice, local water recycling, which might amplify forcing factors ranging from orbital to tectonic timescales.
Ecological networks are more sensitive to plant than to animal extinction under climate change
(2016)
Impacts of climate change on individual species are increasingly well documented, but we lack understanding of how these effects propagate through ecological communities. Here we combine species distribution models with ecological network analyses to test potential impacts of climate change on >700 plant and animal species in pollination and seed-dispersal networks from central Europe. We discover that animal species that interact with a low diversity of plant species have narrow climatic niches and are most vulnerable to climate change. In contrast, biotic specialization of plants is not related to climatic niche breadth and vulnerability. A simulation model incorporating different scenarios of species coextinction and capacities for partner switches shows that projected plant extinctions under climate change are more likely to trigger animal coextinctions than vice versa. This result demonstrates that impacts of climate change on biodiversity can be amplified via extinction cascades from plants to animals in ecological networks.
The Asian tiger mosquito, Aedes albopictus (Diptera: Culicidae, SKUSE), is an important threat to public health due to its rapid spread and its potential as a vector. The eggs of Ae. albopictus are the most cold resistant life stage and thus, the cold hardiness of eggs is used to predict the future occurrence of the species in distribution models. However, the mechanism of cold hardiness has yet to be revealed. To address this question, we analyzed the layers of diapausing and cold acclimatized eggs of a temperate population of Ae. albopictus in a full factorial test design using transmission electron microscopy. We reviewed the hypotheses that a thickened wax layer or chorion is the cause of cold hardiness but found no evidence. As a result of the induced diapause, the thickness of the dark endochorion as a layer of high electron density and thus an assumed location for waxes was decreasing. We therefore hypothesized a qualitative alteration of the wax layer due to compaction. Cold acclimation was causing an increase in the thickness of the middle serosa cuticle indicating a detachment of serosa membrane from the endochorion as a potential adaptation strategy to isolate inoculating ice formations in the inter-membranous space.
Marine nematodes of the genus Anisakis are common parasites of a wide range of aquatic organisms. Public interest is primarily based on their importance as zoonotic agents of the human Anisakiasis, a severe infection of the gastro-intestinal tract as result of consuming live larvae in insufficiently cooked fish dishes. The diverse nature of external impacts unequally influencing larval and adult stages of marine endohelminth parasites requires the consideration of both abiotic and biotic factors. Whereas abiotic factors are generally more relevant for early life stages and might also be linked to intermediate hosts, definitive hosts are indispensable for a parasite’s reproduction. In order to better understand the uneven occurrence of parasites in fish species, we here use the maximum entropy approach (Maxent) to model the habitat suitability for nine Anisakis species accounting for abiotic parameters as well as biotic data (definitive hosts). The modelled habitat suitability reflects the observed distribution quite well for all Anisakis species, however, in some cases, habitat suitability exceeded the known geographical distribution, suggesting a wider distribution than presently recorded. We suggest that integrative modelling combining abiotic and biotic parameters is a valid approach for habitat suitability assessments of Anisakis, and potentially other marine parasite species.
Trypanosoma cruzi, the causative agent of Chagas disease, colonizes the gut of triatomine insects, including Rhodnius prolixus. It is believed that this colonization upsets the microbiota that are normally present, presumably switching the environment to one more favorable for parasite survival. It was previously thought that one particular bacterium, Rhodococcus rhodnii, was essential for insect survival due to its ability to produce vital B-complex vitamins. However, these bacteria are not always identified in great abundance in studies on R. prolixus microbiota. Here we sequenced the microbiota of the insect anterior midgut using shotgun metagenomic sequencing in order to obtain a high-resolution snapshot of the microbes inside at two different time points and under two conditions; in the presence or absence of parasite and immediately following infection, or three days post-infection. We identify a total of 217 metagenomic bins, and recovered one metagenome-assembled genome, which we placed in the genus Dickeya. We show that, despite Rhodococcus being present, it is not the only microbe capable of synthesizing B-complex vitamins, with the genes required for biosynthesis present in a number of different microbes. This work helps to gain a new insight into the microbial ecology of R. prolixus.
Erratum to doi:10.1186/s13071-016-1853-2
The accurate knowledge of the groundwater storage variation (ΔGWS) is essential for reliable water resource assessment, particularly in arid and semi-arid environments (e.g., Australia, the North China Plain (NCP)) where water storage is significantly affected by human activities and spatiotemporal climate variations. The large-scale ΔGWS can be simulated from a land surface model (LSM), but the high model uncertainty is a major drawback that reduces the reliability of the estimates. The evaluation of the model estimate is then very important to assess its accuracy. To improve the model performance, the terrestrial water storage variation derived from the Gravity Recovery And Climate Experiment (GRACE) satellite mission is commonly assimilated into LSMs to enhance the accuracy of the ΔGWS estimate. This study assimilates GRACE data into the PCRaster Global Water Balance (PCR-GLOBWB) model. The GRACE data assimilation (DA) is developed based on the three-dimensional ensemble Kalman smoother (EnKS 3D), which considers the statistical correlation of all extents (spatial, temporal, vertical) in the DA process. The ΔGWS estimates from GRACE DA and four LSM simulations (PCR-GLOBWB, the Community Atmosphere Biosphere Land Exchange (CABLE), the Water Global Assessment and Prognosis Global Hydrology Model (WGHM), and World-Wide Water (W3)) are validated against the in situ groundwater data. The evaluation is conducted in terms of temporal correlation, seasonality, long-term trend, and detection of groundwater depletion. The GRACE DA estimate shows a significant improvement in all measures, notably the correlation coefficients (respect to the in situ data) are always higher than the values obtained from model simulations alone (e.g., ~0.15 greater in Australia, and ~0.1 greater in the NCP). GRACE DA also improves the estimation of groundwater depletion that the models cannot accurately capture due to the incorrect information of the groundwater demand (in, e.g., PCR-GLOBWB, WGHM) or the unavailability of a groundwater consumption routine (in, e.g., CABLE, W3). In addition, this study conducts the inter-comparison between four model simulations and reveals that PCR-GLOBWB and CABLE provide a more accurate ΔGWS estimate in Australia (subject to the calibrated parameter) while PCR-GLOBWB and WGHM are more accurate in the NCP (subject to the inclusion of anthropogenic factors). The analysis can be used to declare the status of the ΔGWS estimate, as well as itemize the possible improvements of the future model development.
Evaluation of radiation components in a global freshwater model with station-based observations
(2016)
In many hydrological models, the amount of evapotranspired water is calculated using the potential evapotranspiration (PET) approach. The main driver of several PET approaches is net radiation, whose downward components are usually obtained from meteorological input data, whereas the upward components are calculated by the model itself. Thus, uncertainties can be large due to both the input data and model assumptions. In this study, we compare the radiation components of the WaterGAP Global Hydrology Model, driven by two meteorological input datasets and two radiation setups from ERA-Interim reanalysis. We assess the performance with respect to monthly observations provided by the Baseline Surface Radiation Network (BSRN) and the Global Energy Balance Archive (GEBA). The assessment is done for the global land area and specifically for energy/water limited regions. The results indicate that there is no optimal radiation input throughout the model variants, but standard meteorological input datasets perform better than those directly obtained by ERA-Interim reanalysis for the key variable net radiation. The low number of observations for some radiation components, as well as the scale mismatch between station observations and 0.5° × 0.5° grid cell size, limits the assessment.
BACKGROUND: Current biodiversity patterns are considered largely the result of past climatic and tectonic changes. In an integrative approach, we combine taxonomic and phylogenetic hypotheses to analyze temporal and geographic diversification of epigean (Carychium) and subterranean (Zospeum) evolutionary lineages in Carychiidae (Eupulmonata, Ellobioidea). We explicitly test three hypotheses: 1) morphospecies encompass unrecognized evolutionary lineages, 2) limited dispersal results in a close genetic relationship of geographical proximally distributed taxa and 3) major climatic and tectonic events had an impact on lineage diversification within Carychiidae.
RESULTS: Initial morphospecies assignments were investigated by different molecular delimitation approaches (threshold, ABGD, GMYC and SP). Despite a conservative delimitation strategy, carychiid morphospecies comprise a great number of unrecognized evolutionary lineages. We attribute this phenomenon to historic underestimation of morphological stasis and phenotypic variability amongst lineages. The first molecular phylogenetic hypothesis for the Carychiidae (based on COI, 16S and H3) reveals Carychium and Zospeum to be reciprocally monophyletic. Geographical proximally distributed lineages are often closely related. The temporal diversification of Carychiidae is best described by a constant rate model of diversification. The evolution of Carychiidae is characterized by relatively few (long distance) colonization events. We find support for an Asian origin of Carychium. Zospeum may have arrived in Europe before extant members of Carychium. Distantly related Carychium clades inhabit a wide spectrum of the available bioclimatic niche and demonstrate considerable niche overlap.
CONCLUSIONS: Carychiid taxonomy is in dire need of revision. An inferred wide distribution and variable phenotype suggest underestimated diversity in Zospeum. Several Carychium morphospecies are results of past taxonomic lumping. By collecting populations at their type locality, molecular investigations are able to link historic morphospecies assignments to their respective evolutionary lineage. We propose that rare founder populations initially colonized a continent or cave system. Subsequent passive dispersal into adjacent areas led to in situ pan-continental or mountain range diversifications. Major environmental changes did not influence carychiid diversification. However, certain molecular delimitation methods indicated a recent decrease in diversification rate. We attribute this decrease to protracted speciation.
Background: The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species’ survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed element (SINE) retroposons.
Results: The temporal history of Tasmanian devil SINEs, elucidated using a transposition in transposition analysis, indicates that WSINE1, a CORE-SINE present in around 200,000 copies, is the most recently active element. Moreover, we discovered a new subtype of WSINE1 (WSINE1b) that comprises at least 90% of all Tasmanian devil WSINE1s. The frequencies of WSINE1 subtypes differ in the genomes of two of the other Australian marsupial orders. A co-segregation analysis indicated that at least 66 subfamilies of WSINE1 evolved during the evolution of Dasyuromorphia. Using a substitution rate derived from WSINE1 insertions, the ages of the subfamilies were estimated and correlated with a newly established phylogeny of Dasyuromorphia. Phylogenetic analyses and divergence time estimates of mitochondrial genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus) around 14 million years ago.
Conclusions: The radiation and abundance of CORE-SINEs in marsupial genomes indicates that they may be a major player in the evolution of marsupials. It is evident that the early phases of evolution of the carnivorous marsupial order Dasyuromorphia was characterized by a burst of SINE activity. A correlation between a speciation event and a major burst of retroposon activity is for the first time shown in a marsupial genome.