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The swine plasma metabolome chronicles "many days" biological timing and functions linked to growth
(2016)
The paradigm of chronobiology is based almost wholly upon the daily biological clock, or circadian rhythm, which has been the focus of intense molecular, cellular, pharmacological, and behavioral, research. However, the circadian rhythm does not explain biological timings related to fundamental aspects of life history such as rates of tissue/organ/body size development and control of the timing of life stages such as gestation length, age at maturity, and lifespan. This suggests that another biological timing mechanism is at work. Here we focus on a "many days" (multidien) chronobiological period first observed as enigmatic recurring growth lines in developing mammalian tooth enamel that is strongly associate with all adult tissue, organ, and body masses as well as life history attributes such as gestation length, age at maturity, weaning, and lifespan, particularly among the well studied primates. Yet, knowledge of the biological factors regulating the patterning of mammalian life, such as the development of body size and life history structure, does not exist. To identify underlying molecular mechanisms we performed metabolome and genome analyses from blood plasma in domestic pigs. We show that blood plasma metabolites and small non-coding RNA (sncRNA) drawn from 33 domestic pigs over a two-week period strongly oscillate on a 5-day multidien rhythm, as does the pig enamel rhythm. Metabolomics and genomics pathway analyses actually reveal two 5-day rhythms, one related to growth in which biological functions include cell proliferation, apoptosis, and transcription regulation/protein synthesis, and another 5-day rhythm related to degradative pathways that follows three days later. Our results provide experimental confirmation of a 5-day multidien rhythm in the domestic pig linking the periodic growth of enamel with oscillations of the metabolome and genome. This association reveals a new class of chronobiological rhythm and a snapshot of the biological bases that regulate mammalian growth, body size, and life history.
This article reports on the second Young Environmental Scientists Meeting that was hosted from 28 February to 2 March 2011 by the Institute for Environmental Research at RWTH Aachen University, Germany. This extraordinary meeting was again initiated and organized by the Student Advisory Council under the umbrella of Society of Environmental Toxicology and Chemistry Europe. A movie about the meeting and the abstracts of poster and platform presentations are freely available as supplemental material of this article.
The process of ecological speciation drives the evolution of locally adapted and reproductively isolated populations in response to divergent natural selection. In Southern Mexico, several lineages of the freshwater fish species of the genus Poecilia have independently colonized toxic, hydrogen sulfide-rich springs. Even though ecological speciation processes are increasingly well understood in this system, aligning the taxonomy of these fish with evolutionary processes has lagged behind. While some sulfide spring populations are classified as ecotypes of Poecilia mexicana, others, like P. sulphuraria, have been described as highly endemic species. Our study particularly focused on elucidating the taxonomy of the long described sulfide spring endemic, Poecilia thermalis Steindachner 1863, and investigates if similar evolutionary patterns of phenotypic trait divergence and reproductive isolation are present as observed in other sulfidic species of Poecilia. We applied a geometric morphometric approach to assess body shape similarity to other sulfidic and non-sulfidic fish of the genus Poecilia. We also conducted phylogenetic and population genetic analyses to establish the phylogenetic relationships of P. thermalis and used a population genetic approach to determine levels of gene flow among Poecilia from sulfidic and non-sulfidic sites. Our results indicate that P. thermalis' body shape has evolved in convergence with other sulfide spring populations in the genus. Phylogenetic analyses placed P. thermalis as most closely related to one population of P. sulphuraria, and population genetic analyses demonstrated that P. thermalis is genetically isolated from both P. mexicana ecotypes and P. sulphuraria. Based on these findings, we make taxonomic recommendations for P. thermalis. Overall, our study verifies the role of hydrogen sulfide as a main factor shaping convergent, phenotypic evolution and the emergence of reproductive isolation between Poecilia populations residing in adjacent sulfidic and non-sulfidic environments.
Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
Global change effects on biodiversity and human wellbeing call for improved long-term environmental data as a basis for science, policy and decision making, including increased interoperability, multifunctionality, and harmonization. Based on the example of two global initiatives, the International Long-Term Ecological Research (ILTER) network and the Group on Earth Observations Biodiversity Observation Network (GEO BON), we propose merging the frameworks behind these initiatives, namely ecosystem integrity and essential biodiversity variables, to serve as an improved guideline for future site-based long-term research and monitoring in terrestrial, freshwater and coastal ecosystems. We derive a list of specific recommendations of what and how to measure at a monitoring site and call for an integration of sites into co-located site networks across individual monitoring initiatives, and centered on ecosystems. This facilitates the generation of linked comprehensive ecosystem monitoring data, supports synergies in the use of costly infrastructures, fosters cross-initiative research and provides a template for collaboration beyond the ILTER and GEO BON communities.
Despite prevailing arid conditions, the diversity of terrestrial and freshwater biota in the Middle East is amazingly high and marine biodiversity is among the highest on Earth. Th roughout the Region, threats to the environment are moderate to severe. Despite the outstanding economic and ecological importance of biological diversity, the capacity in biodiversity-related research and academic education is inadequate. The "Middle Eastern Biodiversity Network" (MEBN), founded in 2006 by six universities and research institutes in Iran, Jordan, Germany, Lebanon and Yemen was designed to fi ll this gap. An integrated approach is taken to upgrade biodiversity research and education in order to improve regional ecosystem conservation and management capacities. A wide range of activities are carried out in the framework of the Network, including capacity building in biological collection management and professional natural history curatorship, developing university curricula in biodiversity, conducting scientifi c research, organising workshops and conferences on Middle Eastern biodiversity, and translating the results of biodiversity research into conservation and sustainable development. Keywords: Middle Eastern biodiversity, nature museums, biodiversity research, biodiversity education, biodiversity conservation, biodiversity networks
Background: The angiosperm family Bromeliaceae comprises over 3.500 species characterized by exceptionally high morphological and ecological diversity, but a very low genetic variation. In many genera, plants are vegetatively very similar which makes determination of non flowering bromeliads difficult. This is particularly problematic with living collections where plants are often cultivated over decades without flowering. DNA barcoding is therefore a very promising approach to provide reliable and convenient assistance in species determination. However, the observed low genetic variation of canonical barcoding markers in bromeliads causes problems.
Result. In this study the low-copy nuclear gene Agt1 is identified as a novel DNA barcoding marker suitable for molecular identification of closely related bromeliad species. Combining a comparatively slowly evolving exon sequence with an adjacent, genetically highly variable intron, correctly matching MegaBLAST based species identification rate was found to be approximately double the highest rate yet reported for bromeliads using other barcode markers.
Conclusion. In the present work, we characterize Agt1 as a novel plant DNA barcoding marker to be used for barcoding of bromeliads, a plant group with low genetic variation. Moreover, we provide a comprehensive marker sequence dataset for further use in the bromeliad research community.
Southern African protected areas (PAs) harbour a great diversity of animals, which represent a large potential for wildlife tourism. In this region, global change is expected to result in vegetation changes, such as bush encroachment and increases in vegetation density. However, little is known on the influence of vegetation structure on wildlife tourists’ wildlife viewing experience and satisfaction. In this study, we collected data on vegetation structure and perceived mammal densities along 196 road transects (each 5 km long) and conducted a social survey with 651 questionnaires across four PAs in three Southern African countries. Our objectives were 1) to assess visitors’ attitude towards vegetation, 2) to test the influence of perceived mammal density and vegetation structure on the easiness to spot animals, and 3) on visitors’ satisfaction during their visit to PAs. Using a Boosted Regression Tree procedure, we found mostly negative non-linear relationships between vegetation density and wildlife tourists’ experience, and positive relationships between perceived mammal densities and wildlife tourists’ experience. In particular, wildlife tourists disliked road transects with high estimates of vegetation density. Similarly, the easiness to spot animals dropped at thresholds of high vegetation density and at perceived mammal densities lower than 46 individuals per road transect. Finally, tourists’ satisfaction declined linearly with vegetation density and dropped at mammal densities smaller than 26 individuals per transect. Our results suggest that vegetation density has important impacts on tourists’ wildlife viewing experience and satisfaction. Hence, the management of PAs in savannah landscapes should consider how tourists perceive these landscapes and their mammal diversity in order to maintain and develop a sustainable wildlife tourism.
It is commonly assumed that the colonization of restored river reaches by fish depends on the regional species pools; however, quantifications of the relationship between the composition of the regional species pool and restoration outcome are lacking. We analyzed data from 18 German river restoration projects and adjacent river reaches constituting the regional species pools of the restored reaches. We found that the ability of statistical models to describe the fish assemblages established in the restored reaches was greater when these models were based on ‘biotic’ variables relating to the regional species pool and the ecological traits of species rather than on ‘abiotic’ variables relating to the hydromorphological habitat structure of the restored habitats and descriptors of the restoration projects. For species presence in restored reaches, ‘biotic’ variables explained 34% of variability, with the occurrence rate of a species in the regional species pool being the most important variable, while ’abiotic’ variables explained only the negligible amount of 2% of variability. For fish density in restored reaches, about twice the amount of variability was explained by ‘biotic’ (38%) compared to ‘abiotic’ (21%) variables, with species density in the regional species pool being most important. These results indicate that the colonization of restored river reaches by fish is largely determined by the assemblages in the surrounding species pool. Knowledge of species presence and abundance in the regional species pool can be used to estimate the likelihood of fish species becoming established in restored reaches.
The German postgraduate degree program in ecotoxicology (SETAC GLB and GDCh) : a success story
(2016)
This article gives a comprehensive overview on the strategy, the development and the progress of the German postgraduate degree program in ecotoxicology (SETAC GLB and GDCh). The program soon prompted positive results: more than 10 years now the courses had an average enrolment rate of 90 %, and employment-seeking graduates from the first courses mostly succeeded in quickly finding employment relevant to their training. With over 450 students enrolled to date, the degree program contributes significantly to the field of Environmental Chemistry and Ecotoxicology.
The gradual heterogeneity of climatic factors pose varying selection pressures across geographic distances that leave signatures of clinal variation in the genome. Separating signatures of clinal adaptation from signatures of other evolutionary forces, such as demographic processes, genetic drift, and adaptation to non-clinal conditions of the immediate local environment is a major challenge. Here, we examine climate adaptation in five natural populations of the harlequin fly Chironomus riparius sampled along a climatic gradient across Europe. Our study integrates experimental data, individual genome resequencing, Pool-Seq data, and population genetic modelling. Common-garden experiments revealed a positive correlation of population growth rates corresponding to the population origin along the climate gradient, suggesting thermal adaptation on the phenotypic level. Based on a population genomic analysis, we derived empirical estimates of historical demography and migration. We used an FST outlier approach to infer positive selection across the climate gradient, in combination with an environmental association analysis. In total we identified 162 candidate genes as genomic basis of climate adaptation. Enriched functions among these candidate genes involved the apoptotic process and molecular response to heat, as well as functions identified in other studies of climate adaptation in other insects. Our results show that local climate conditions impose strong selection pressures and lead to genomic adaptation despite strong gene flow. Moreover, these results imply that selection to different climatic conditions seems to converge on a functional level, at least between different insect species.
Background: Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white-rot of hardwood in forests of warm and mild climate. The ease of cultivation and fructification on solidified media as well as its archetypal mushroom fruit body morphology render A. aegerita a well-suited model for investigating mushroom developmental biology.
Results: Here, the genome of the species is reported and analysed with respect to carbohydrate active genes and genes known to play a role during fruit body formation. In terms of fruit body development, our analyses revealed a conserved repertoire of fruiting-related genes, which corresponds well to the archetypal fruit body morphology of this mushroom. For some genes involved in fruit body formation, paralogisation was observed, but not all fruit body maturation-associated genes known from other agaricomycetes seem to be conserved in the genome sequence of A. aegerita. In terms of lytic enzymes, our analyses suggest a versatile arsenal of biopolymer-degrading enzymes that likely account for the flexible life style of this species. Regarding the amount of genes encoding CAZymes relevant for lignin degradation, A. aegerita shows more similarity to white-rot fungi than to litter decomposers, including 18 genes coding for unspecific peroxygenases and three dye-decolourising peroxidase genes expanding its lignocellulolytic machinery.
Conclusions: The genome resource will be useful for developing strategies towards genetic manipulation of A. aegerita, which will subsequently allow functional genetics approaches to elucidate fundamentals of fruiting and vegetative growth including lignocellulolysis.
Background: Xanthophyllomyces dendrorhous is a basal agaricomycete with uncertain taxonomic placement, known for its unique ability to produce astaxanthin, a carotenoid with antioxidant properties. It was the aim of this study to elucidate the organization of its CoA-derived pathways and to use the genomic information of X. dendrorhous for a phylogenomic investigation of the Basidiomycota.
Results: The genome assembly of a haploid strain of Xanthophyllomyces dendrorhous revealed a genome of 19.50 Megabases with 6385 protein coding genes. Phylogenetic analyses were conducted including 48 fungal genomes. These revealed Ustilaginomycotina and Agaricomycotina as sister groups. In the latter a well-supported sister-group relationship of two major orders, Polyporales and Russulales, was inferred. Wallemia occupies a basal position within the Agaricomycotina and X. dendrorhous represents the basal lineage of the Tremellomycetes, highlighting that the typical tremelloid parenthesomes have either convergently evolved in Wallemia and the Tremellomycetes, or were lost in the Cystofilobasidiales lineage. A detailed characterization of the CoA-related pathways was done and all genes for fatty acid, sterol and carotenoid synthesis have been assigned.
Conclusions: The current study ascertains that Wallemia with tremelloid parenthesomes is the most basal agaricomycotinous lineage and that Cystofilobasidiales without tremelloid parenthesomes are deeply rooted within Tremellomycetes, suggesting that parenthesomes at septal pores might be the core synapomorphy for the Agaricomycotina. Apart from evolutionary insights the genome sequence of X. dendrorhous will facilitate genetic pathway engineering for optimized astaxanthin or oxidative alcohol production.
Microthlaspi erraticum is widely distributed in temperate Eurasia, but restricted to Ca2+-rich habitats, predominantly on white Jurassic limestone, which is made up by calcium carbonate, with little other minerals. Thus, naturally occurring Microthlaspi erraticum individuals are confronted with a high concentration of Ca2+ ions while Mg2+ ion concentration is relatively low. As there is a competitive uptake between these two ions, adaptation to the soil condition can be expected. In this study, it was the aim to explore the genomic consequences of this adaptation by sequencing and analysing the genome of Microthlaspi erraticum. Its genome size is comparable with other diploid Brassicaceae, while more genes were predicted. Two Mg2+ transporters known to be expressed in roots were duplicated and one showed a significant degree of positive selection. It is speculated that this evolved due to the pressure to take up Mg2+ ions efficiently in the presence of an overwhelming amount of Ca2+ ions. Future studies on plants specialized on similar soils and affinity tests of the transporters are needed to provide unequivocal evidence for this hypothesis. If verified, the transporters found in this study might be useful for breeding Brassicaceae crops for higher yield on Ca2+-rich and Mg2+ -poor soils.
Background: The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text.
Results: We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based on phenotype description patterns and automated reasoning to generate the FLOPO. The resulting ontology consists of 25,407 classes and is based on the PO and PATO. The classified ontology closely follows the structure of Plant Ontology in that the primary axis of classification is the observed plant anatomical structure, and more specific traits are then classified based on parthood and subclass relations between anatomical structures as well as subclass relations between phenotypic qualities.
Conclusions: The FLOPO is primarily intended as a framework based on which plant traits can be integrated computationally across all species and higher taxa of flowering plants. Importantly, it is not intended to replace established vocabularies or ontologies, but rather serve as an overarching framework based on which different application- and domain-specific ontologies, thesauri and vocabularies of phenotypes observed in flowering plants can be integrated.
There are 63 known species of Thecaphora (Glomosporiaceae, Ustilaginomycotina), a third of which occur on Asteraceae. These smut fungi produce yellowish-brown to reddish-brown masses of spore balls in specific, mostly regenerative, plant organs. A species of Thecaphora was collected in the flower heads of Anthemis chia (Anthemideae, Asteraceae) on Rhodes Island, Greece, in 2015 and 2017, which represents the first smut record of a smut fungus on a host plant species in this tribe. Based on its distinctive morphology, host species and genetic divergence, this species is described as Thecaphora anthemidis sp. nov. Molecular barcodes of the ITS region are provided for this and several other species of Thecaphora. A phylogenetic and morphological comparison to closely related species showed that Th. anthemidis differed from other species of Thecaphora. Thecaphora anthemidis produced loose spore balls in the flower heads and peduncles of Anthemis chia unlike other flower-infecting species.
Over the last century, humans from industrialized societies have witnessed a radical increase in some dental diseases. A severe problem concerns the loss of dental materials (enamel and dentine) at the buccal cervical region of the tooth. This “modern-day” pathology, called non-carious cervical lesions (NCCLs), is ubiquitous and worldwide spread, but is very sporadic in modern humans from pre-industrialized societies. Scholars believe that several factors are involved, but the real dynamics behind this pathology are far from being understood. Here we use an engineering approach, finite element analysis (FEA), to suggest that the lack of dental wear, characteristic of industrialized societies, might be a major factor leading to NCCLs. Occlusal loads were applied to high resolution finite element models of lower second premolars (P2) to demonstrate that slightly worn P2s envisage high tensile stresses in the buccal cervical region, but when worn down artificially in the laboratory the pattern of stress distribution changes and the tensile stresses decrease, matching the results obtained in naturally worn P2s. In the modern industrialized world, individuals at advanced ages show very moderate dental wear when compared to past societies, and teeth are exposed to high tensile stresses at the buccal cervical region for decades longer. This is the most likely mechanism explaining enamel loss in the cervical region, and may favor the activity of other disruptive processes such as biocorrosion. Because of the lack of dental abrasion, our masticatory apparatus faces new challenges that can only be understood in an evolutionary perspective.
The Arabidopsis arenosa complex is closely related to the model plant Arabidopsis thaliana. Species and subspecies in the complex are mainly biennial, predominantly outcrossing, herbaceous, and with a distribution range covering most parts of latitudes and the eastern reaches of Europe. In this study we present the first comprehensive evolutionary history of the A. arenosa species complex, covering its natural range, by using chromosome counts, nuclear AFLP data, and a maternally inherited marker from the chloroplast genome [trnL intron (trnL) and trnL/F intergenic spacer (trnL/F-IGS) of tRNALeu and tRNAPhe, respectively]. We unravel the broad-scale cytogeographic and phylogeographic patterns of diploids and tetraploids. Diploid cytotypes were exclusively found on the Balkan Peninsula and in the Carpathians while tetraploid cytotypes were found throughout the remaining distribution range of the A. arenosa complex. Three centers of genetic diversity were identified: the Balkan Peninsula, the Carpathians, and the unglaciated Eastern and Southeastern Alps. All three could have served as long-term refugia during Pleistocene climate oscillations. We hypothesize that the Western Carpathians were and still are the cradle of speciation within the A. arenosa complex due to the high species number and genetic diversity and the concurrence of both cytotypes there.
Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to the closely related polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using three different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains numerous uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to massive amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. The increasing evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow.
Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to large amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. Evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow.
There is increasing evidence that rapid phenotypic adaptation of quantitative traits is not uncommon in nature. However, the circumstances under which rapid adaptation of polygenic traits occurs are not yet understood. Building on previous concepts of soft selection, i.e. frequency and density dependent selection, I developed and tested the hypothesis that adaptation speed of a polygenic trait depends on the number of offspring per breeding pair in a randomly mating diploid population.
Using individual based modelling on a range of offspring per parent (2–200) in populations of various size (100–10000 individuals), I could show that the by far largest proportion of variance (42%) was explained by the offspring number, regardless of genetic trait architecture (10–50 loci, different locus contribution distributions). In addition, it was possible to identify the majority of the responsible loci and account for even more of the observed phenotypic change with a moderate population size.
The simulation results suggest that offspring numbers may a crucial factor for the adaptation speed of quantitative loci. Moreover, as large offspring numbers translates to a large phenotypic variance in the offspring of each parental pair, this genetic bet hedging strategy increases the chance to contribute to the next generation in unpredictable environments.
In recent decades the embryo of Gallus g. domesticus has been widely used as a model for the study of early sexual development and the potential impact of substances affecting development, including endocrine disrupting chemicals (EDCs). Since there is no standardized procedure available for experiments with the chicken embryo, the objective of our project is to expedite the protocol to assess the potential effects of EDCs on early sexual differentiation. The main aim of the present study was to systematically investigate the natural variability of individual developmental and histological key parameters in untreated and solvent-treated control groups, since this has been insufficiently addressed so far. A further aim was to provide robust values for all parameters investigated in control and substance experiments, using two known estrogenic compounds, bisphenol A (75/150/300 μg/g egg) and 17α-ethinylestradiol (20 ng/g egg). On embryonic day 1 eggs were injected with the estrogenic compounds. On embryonic day 19 histological gonadal data as well as morphological parameters were noted. In baseline experiments with control groups the selected endpoints showed reproducible results with low variabilities. Furthermore, gonadal endpoints responded sensitively to the treatment with the two model EDCs. Thus, these endpoints are recommended for the assessment of suspected EDCs in which the values provided for all parameters can serve as validity criteria in future experiments. The embryo of G. domesticus has shown to be a suitable alternative to currently accepted mammalian bioassays for the impact assessment of EDCs on reproductive tissues.
Although climate is known to be one of the key factors determining animal species distributions amongst others, projections of global change impacts on their distributions often rely on bioclimatic envelope models. Vegetation structure and landscape configuration are also key determinants of distributions, but they are rarely considered in such assessments. We explore the consequences of using simulated vegetation structure and composition as well as its associated landscape configuration in models projecting global change effects on Iberian bird species distributions. Both present-day and future distributions were modelled for 168 bird species using two ensemble forecasting methods: Random Forests (RF) and Boosted Regression Trees (BRT). For each species, several models were created, differing in the predictor variables used (climate, vegetation, and landscape configuration). Discrimination ability of each model in the present-day was then tested with four commonly used evaluation methods (AUC, TSS, specificity and sensitivity). The different sets of predictor variables yielded similar spatial patterns for well-modelled species, but the future projections diverged for poorly-modelled species. Models using all predictor variables were not significantly better than models fitted with climate variables alone for ca. 50% of the cases. Moreover, models fitted with climate data were always better than models fitted with landscape configuration variables, and vegetation variables were found to correlate with bird species distributions in 26–40% of the cases with BRT, and in 1–18% of the cases with RF. We conclude that improvements from including vegetation and its landscape configuration variables in comparison with climate only variables might not always be as great as expected for future projections of Iberian bird species.
Resting egg banks of microcrustaceans have been used to reconstruct the evolutionary and ecological history of species. However, recent studies provided evidence for a discrepancy between dormant propagules in the sediment and the planktonic population. This pattern raises two questions: First, what is the value of data on resting egg banks for population dynamics over time and second, which component of the reproductive cycle causes the observed inconsistency? In our study we focussed on the second question by comparing the taxon composition of a resting egg bank with the reproductive success of ex-ephippial hatchlings. Species and interspecific hybrid identification of dormant and hatched stages was achieved through the application of restriction fragment length polymorphism analysis of an internal transcribed spacer region. We found no significant deviation between the proportion of hatched Daphnia galeata, D. galeata x hyalina and D. hyalina individuals and the observed taxon composition of the resting egg bank. However, species and hybrids differed in their mode and relative success of reproduction. We conclude that the components of reproductive success in Daphnia contribute differentially to the fitness of species and interspecific hybrids. The discrepancy between resting egg banks and "active" planktonic populations results not from differential hatching of species but from the reproductive success of ex-ephippial females and the timing and frequency of sexual reproduction of the different taxa.
Responding to inadequate awareness of the outstanding importance of biodiversity, the BioFrankfurt network was founded in 2004 in the State of Hesse, Germany. It is presented here as a case study and may serve as a model for other parts of the world, such as the Middle East. In 2007, only about 26% of the German population were familiar with the term “Biodiversity”, and most of them only had a vague idea about its meaning. The BioFrankfurt network of institutions addressed this problem, raising public awareness and supporting research, education and conservation. A regional biodiversity education program has been developed and delivered to more than 500 schools. Since 2007, an innovative public relations campaign combines raising awareness on regional biodiversity issues with activities to improve the public image of the Frankfurt area. Because of its geographical focus, the network’s activities gained the attention of local and regional politicians and other decision makers, culminating in the joint establishment of a new Biodiversity and Climate Research Centre by BioFrankfurt member institutions. The success of current activities attracts interesting partners, resulting in challenging cooperation initiatives. The authors are convinced that the network’s concepts and activities have a great potential to profoundly enhance the notion and acceptance of biodiversity issues elsewhere. Keywords: BioFrankfurt, biodiversity network, education, public awareness, scientifi c communication
In over 100 genera of tropical angiosperms, one or more species possess specialised structures for housing ants. The longevity and intimacy of these associations has often facilitated an increasing specialisation of both the ants and the plants, leading to a number of highly specific and obligate symbioses. Early literature contained only few anecdotal reports of the ant genus Cladomyrma WHEELER inhabiting (unidentified) plants. This work presents the new findings on Cladomyrma and its host plants that accumulated over the last two decades. My studies of Cladomyrma reveal that there is a largely overlooked community of south-east Asian plant-ants and their associated plants. Currently the genus consists of at least 12 species. Cladomyrma has been thought to be restricted to the ever-wet part of the West Malesian floristic region, comprising the Malay Peninsula, Borneo, and Sumatra, but recent collections from Thailand and Vietnam indicate that species of the genus penetrate the seasonal tropical forests of Continental Asia. Cladomyrma inhabits 24 plant species belonging to a surprisingly extensive range of plant taxa: Callerya, Saraca, Spatholobus (Fabaceae), Crypteronia (Crypteroniaceae), Drypetes (Putranjivaceae), Ryparosa (Achariaceae), Strychnos (Loganiaceae), Neonauclea (Rubiaceae), Luvunga (Rutaceae) and Sphenodesme (Verbenaceae). In terms of taxonomic diversity on the genus and family level the range of hosts utilised by Cladomyrma is one of the broadest ever recorded for any live stem-nesting plant-ant lineage worldwide. This work provides a species-level overview of all Cladomyrma host plants known from Borneo, the Malay Peninsula and Sumatra, including descriptions of ant-housing structures (domatia), ant inhabitant identity, onset of colonisation during plant ontogeny, nest structure, occupancy rate, and considerations of results obtained from herbarium specimens. Both the regularity of ant association and the degree of morphological specialisation toward myrmecophytism are assessed. The behavioural traits of Cladomyrma are compatible with traits exhibited by other protective plant-ants. This work demonstrates that all species of Cladomyrma investigated (dianeae, maschwitzi, yongi, petalae) confer antiherbivore protection to young leaves of its host. The ants also attack and repell or kill herbivorous insect larvae encountered on young foliage. Cleaning behaviour appears to be a trait shared by all members of the genus, and the two species tested (maschwitzi, petalae) successfully removed termite eggs experimentally placed onto young leaves. Another trait common to all known species of the genus is that the ants preferentially patrol young shoots and leaves ('neophily'). These behavioural traits of Cladomyrma likely reduce stem damage and pathogenic infection of their host. The ants prune encroaching vegetation (tested in dianeae maschwitzi, petalae, yongi, observed in crypteroniae) and attack paper tape used to mark host plants (observed in andrei, dianeae, hobbyi, nudidorsalis, maschwitzi, yongi, petalae). If these traits combined translate into a better reproductive success of the hosts has yet to be verified. Evidence for lifetime fitness benefits is particularly difficult to quantify for the long-lived woody host plants of Cladomyrma. The predominant food source of Cladomyrma appears to be the honeydew of scale insects (Coccidae and Pseudococcidae) which the ants tend inside their nest cavities. Observations on scale insect acquisition by Cladomyrma foundress queens show that hemipteran trophobionts are not transported by the queens on their nuptial flight but they nevertheless arrive on the host plant independently of the ants. Entry into nest chambers is facilitated by small holes kept open by the foundress queen. Most Cladomyrma species have been recorded from only one or two (three) host plant species (andrei, crypteroniae, hobbyi, maschwitzi, nudidorsalis, scopulosa, yongi), but two species, Cladomyrma petalae and C. dianeae, are more catholic in their host usage; the first being a 'generalist' plant-ant colonising hosts across a broad taxonomic range, the second inhabiting several members of the genus Neonauclea. First results of host-choice experiments with C. petalae are presented and the potential mechanisms promoting host specificity are discussed. My studies of the Cladomyrma/plant associations indicate that codiversification and host shifts or host expansions, rather than cospeciation, shape the pattern of species interactions in this system. Finally, I propose a scenario in which three key traits of Cladomyrma –access to live stems, utilisation of indirect food rewards via trophobionts and 'neophily'– are hypothesised to favour niche differentiation and the acquisition of new hosts over evolutionary time.
Background: Mammalian fossils from the Eppelsheim Formation (Dinotheriensande) have been a benchmark for Neogene vertebrate palaeontology since 200 years. Worldwide famous sites like Eppelsheim serve as key localities for biochronologic, palaeobiologic, environmental, and mammal community studies. So far the formation is considered to be of early Late Miocene age (~9.5 Ma, Vallesian), representing the oldest sediments of the Rhine River. The stratigraphic unity of the formation and of its fossil content was disputed at times, but persists unresolved.
Principal Findings: Here we investigate a new fossil sample from Sprendlingen, composed by over 300 mammalian specimens and silicified wood. The mammals comprise entirely Middle Miocene species, like cervids Dicrocerus elegans, Paradicrocerus elegantulus, and deinotheres Deinotherium bavaricum and D. levius. A stratigraphic evaluation of Miocene Central European deer and deinothere species proof the stratigraphic inhomogenity of the sample, and suggest late Middle Miocene (~12.5 Ma) reworking of early Middle Miocene (~15 Ma) sediments. This results agree with taxonomic and palaeoclimatic analysis of plant fossils from above and within the mammalian assemblage. Based on the new fossil sample and published data three biochronologic levels within the Dinotheriensand fauna can be differentiated, corresponding to early Middle Miocene (late Orleanian to early Astaracian), late Middle Miocene (late Astaracian), and early Late Miocene (Vallesian) ages.
Conclusions/Significance: This study documents complex faunal mixing of classical Dinotheriensand fauna, covering at least six million years, during a time of low subsidence in the Mainz Basin and shifts back the origination of the Rhine River by some five million years. Our results have severe implications for biostratigraphy and palaeobiology of the Middle to Late Miocene. They suggest that turnover events may be obliterated and challenge the proposed ‘supersaturated’ biodiversity, caused by Middle Miocene superstites, of Vallesian ecosystems in Central Europe.
Metabolic critical temperatures define the range of ambient temperatures where endotherms are able to minimize energy allocation to thermogenesis. Examining the relationship between metabolic critical temperatures and basal metabolic rates (BMR) provides a unique opportunity to gain a better understanding of how animals respond to varying ambient climatic conditions, especially in times of ongoing and projected future climate change. We make use of this opportunity by testing the heat dissipation limit (HDL) theory, which hypothesizes that the maximum amount of heat a species can dissipate constrains its energetics. Specifically, we test the theory’s implicit prediction that BMR should be lower under higher metabolic critical temperatures. We analysed the relationship of BMR with upper and lower critical temperatures for a large dataset of 146 endotherm species using regression analyses, carefully accounting for phylogenetic relationships and body mass. We show that metabolic critical temperatures are negatively related with BMR in both birds and mammals. Our results confirm the predictions of the HDL theory, suggesting that metabolic critical temperatures and basal metabolic rates respond in concert to ambient climatic conditions. This implies that heat dissipation capacities of endotherms may be an important factor to take into account in assessments of species’ vulnerability to climate change.
The large number of species still to be discovered in fungi, together with an exponentially growing number of environmental sequences that cannot be linked to known taxa, has fuelled the idea that it might be necessary to formally name fungi on the basis of sequence data only. Here we object to this idea due to several shortcomings of the approach, ranging from concerns regarding reproducibility and the violation of general scientific principles to ethical issues. We come to the conclusion that sequence-based nomenclature is potentially harmful for mycology as a discipline. Additionally, a classification based on sequences as types is not within reach anytime soon, because there is a lack of consensus regarding common standards due to the fast pace at which sequencing technologies develop.
This study aims at characterizing the diversity and temporal changes of species richness and composition of fungi in an ecotone of a forest border and a meadow in the Taunus mountain range in Germany. All macroscopically visible, epigeous fungi and vascular plants were sampled monthly over three years, together with climatic variables like humidity and temperature that influence fungal diversity and composition as shown by previous studies. In this mosaic landscape, a total of 855 fungal species were collected and identified based on morphological features, the majority of which belonged to Ascomycota (51 %) and Basidiomycota (45 %). Records of fungal species and plant species (218) for this area yielded a fungus to plant species ratio of 4:1, with a plant species accumulation curve that reached saturation. The three years of monitoring, however, were not sufficient to reveal the total fungal species richness and estimation factors showed that a fungus to plant species ratio of 6:1 may be reached by further sampling efforts. The effect of climatic conditions on fungal species richness differed depending on the taxonomic and ecological group, with temporal patterns of occurrence of Basidiomycota and mycorrhizal fungi being strongly associated with temperature and humidity, whereas the other fungal groups were only weakly related to abiotic conditions. In conclusion, long-term, monthly surveys over several years yield a higher diversity of macroscopically visible fungi than standard samplings of fungi in autumn. The association of environmental variables with the occurrence of specific fungal guilds may help to improve estimators of fungal richness in temperate regions.
A strong decline and thinning of the Arctic sea-ice cover over the past five decades has been documented. The former multiyear sea-ice system has largely changed to an annual system and with it the dynamics of sea-ice transport across the Arctic Ocean. Less sea ice is reaching the Fram Strait and more ice and ice-transported material is released in the northern Laptev Sea and the central Arctic Ocean. This trend is expected to have a decisive impact on ice associated (“sympagic”) communities. As sympagic fauna plays an important role in transmitting carbon from the ice-water interface to the pelagic and benthic food webs, it is important to monitor its community composition under the changing environmental conditions. We investigated the taxonomic composition, abundance and distribution of sea-ice meiofauna (here heterotrophs >10 μm; eight stations) and under-ice fauna (here metazoans >300 μm; fourteen stations) in Arctic 1.5 year-old pack ice north of Svalbard. Sampling was conducted during spring 2015 by sea-ice coring and trawling with a Surface and Under-Ice Trawl. We identified 42 taxa associated with the sea ice. The total abundance of sea-ice meiofauna ranged between 580 and 17,156 ind.m–2 and was dominated by Ciliophora (46%), Copepoda nauplii (29%), and Harpacticoida (20%). In contrast to earlier studies in this region, we found no Nematoda and few flatworms in our sea-ice samples. Under-ice fauna abundance ranged between 15 and 6,785 ind.m–2 and was dominated by Appendicularia (58%), caused by exceptionally high abundance at one station. Copepoda nauplii (23%), Calanus finmarchicus (9%), and Calanus glacialis (6%) were also very abundant while sympagic Amphipoda were comparatively rare (0.35%). Both sympagic communities showed regional differences in community composition and abundance between shelf and offshore stations, but only for the under-ice fauna those differences were statistically significant. Selected environmental variables moderately explained variations in abundances of both faunas. The results of this study are consistent with predictions of diversity shifts in the new Arctic.
Seed harvesting from wild plant populations is key for ecological restoration, but may threaten the persistence of source populations. Consequently, several countries have set guidelines limiting the proportions of harvestable seeds. Here, we use high-resolution data from 298 plant species to model the demographic consequences of seed harvesting. We find that the current guidelines only protect some species, but are insufficient or overly restrictive for others. We show that the maximum possible fraction of seed harvesting is strongly associated with harvesting frequency and generation time of the target species, ranging from 100% in long-lived species to <1% in the most annuals. Our results provide quantitative basis to guide seed harvesting legislation based on species’ generation time and harvesting regime.
Competition over land is at the core of many sustainable development challenges in Myanmar: villagers, companies, governments, ethnic minority groups, civil society organisations and non-governmental organisations from local to the international level claim access to and decision-making power over the use of land. Therefore, this article investigates the actor interactions influencing land-use changes and their impacts on the supply of ecosystem services and human well-being. We utilise a transdisciplinary mixed-methods approach and the analytical lens of the social-ecological systems framework. Results reveal that the links between land-use changes, ecosystem services and human well-being are multifaceted; For example ecosystem services can decline, while human well-being increases. We explain this finding through three different pathways to impact (changes in the resource systems, the governance systems or the broader social, economic and political context). We conclude with implications of these results for future sustainable land governance.
Wild plant species are important nutritious supplements to otherwise nutrient poor diets of rural populations in West Africa. Consequently, a decline of wild food species has a direct negative impact on the nutritional status of local households. In this study, we firstly investigated the preferred wild food species in south-east Burkina Faso, their perceived change in abundance as well as their contribution to wild food income. Secondly, we studied how these species might be substituted in times of species shortfall. Thirdly, we investigated the impact of socio-economic variables on the substitution choice. We conducted 155 household interviews in two villages and found 21 wild food species. With a contribution of almost 70% to wild food income, Vitellaria paradoxa and Parkia biglobosa were economically most important. All species were considered declining to some degree. The wide range of cited substitutes for the ten most important wild food species indicates a great knowledge on alternative plant species in the area. For the majority, the substitution choice did not depend on socio-economic characteristics. Cited as surrogate for several important wild food species, the native tree Balanites aegyptiaca was the most important substitute species. Many valued wild food species were substituted with other highly valued wild food species and therefore the decline of one species can lead to a shortfall of another substitute. Thus, even though our results suggest that people are able to counteract the decrease or absence of wild food species, growing decline of one species would concurrently increase the pressure on other native food species.
Non-Timber Forest Products (NTFPs) make a major contribution to the livelihoods and diets of rural households in the savanna ecosystems of West Africa. However, land use change and climatic variability might affect their availability in the future. Based on a survey among 227 households in Northern Benin, we investigated local substitution patterns for the seeds of the three socio-economically most important NTFP-species in the region, Vitellaria paradoxa, Adansonia digitata and Parkia biglobosa, being major sources for protein, fat, and micronutrients in local daily diets. Our study compared substitution patterns between, firstly, three income groups, to assess whether a households’ socio-economic status has an influence on the choice of surrogates (low cost vs. more costly options). Secondly, we compared substitution patterns between the five major ethnic groups in the study region (the Fulani, the Bariba, the Ditammarie, the Kabiyé and the Yom). The choice of substitutes differed significantly across income groups. However, the poorest households clearly show to be the most vulnerable: up to 30 % of the sampled households stated they would lack an adequate replacement for the NTFPs in question. Furthermore, ethnic affiliation showed to have a considerable impact on the preferred alternative products due to underlying cultural traditions of plant use. Subsequently, aiming at maintaining – and enhancing – the local supply of V. paradoxa, P. biglobosa and A. digitata in order to secure their contributions to local diets, local land use policy should have a particular focus on their ethnic-conditioned use and particularly the specific requirements of the poorest community members.
Spatial and temporal processes shaping microbial communities are inseparably linked but rarely studied together. By Illumina 16S rRNA sequencing, we monitored soil bacteria in 360 stations on a 100 square meter plot distributed across six intra-annual samplings in a rarely managed, temperate grassland. Using a multi-tiered approach, we tested the extent to which stochastic or deterministic processes influenced the composition of local communities. A combination of phylogenetic turnover analysis and null modeling demonstrated that either homogenization by unlimited stochastic dispersal or scenarios, in which neither stochastic processes nor deterministic forces dominated, explained local assembly processes. Thus, the majority of all sampled communities (82%) was rather homogeneous with no significant changes in abundance-weighted composition. However, we detected strong and uniform taxonomic shifts within just nine samples in early summer. Thus, community snapshots sampled from single points in time or space do not necessarily reflect a representative community state. The potential for change despite the overall homogeneity was further demonstrated when the focus shifted to the rare biosphere. Rare OTU turnover, rather than nestedness, characterized abundance-independent β-diversity. Accordingly, boosted generalized additive models encompassing spatial, temporal and environmental variables revealed strong and highly diverse effects of space on OTU abundance, even within the same genus. This pure spatial effect increased with decreasing OTU abundance and frequency, whereas soil moisture – the most important environmental variable – had an opposite effect by impacting abundant OTUs more than the rare ones. These results indicate that – despite considerable oscillation in space and time – the abundant and resident OTUs provide a community backbone that supports much higher β-diversity of a dynamic rare biosphere. Our findings reveal complex interactions among space, time, and environmental filters within bacterial communities in a long-established temperate grassland.
In this report, we present the contributions, outcomes, ideas, discussions and conclusions obtained at the PaleoMaps Workshop 2019, that took place at the Institute of Geography of the University of Cologne on 23 and 24 September 2019. The twofold aim of the workshop was: (1) to provide an overview of approaches and methods that are presently used to incorporate paleoenvironmental information in human–environment interaction modeling applications, and building thereon; (2) to devise new approaches and solutions that might be used to enhance the reconstruction of past human–environmental interconnections. This report first outlines the presented papers, and then provides a joint protocol of the often extensive discussions that came up following the presentations or else during the refreshment intervals. It concludes by adressing the open points to be resolved in future research avenues, e.g., implementation of open science practices, new procedures for reviewing of publications, and future concepts for quality assurance of the often complex paleoenvironmental data. This report may serve as an overview of the state of the art in paleoenvironment mapping and modeling. It includes an extensive compilation of the basic literature, as provided by the workshop attendants, which will itself facilitate the necessary future research.
The Asian bush mosquito (Aedes japonicus japonicus, Theobald 1901) is an invasive culicid species which originates in Asia but is nowadays present in northern America and Europe. It is a competent vector for several human disease pathogens. In addition to the public health threat, this invasive species may also be an ecological threat for native container-breeding mosquitoes which share a similar larval habitat. Therefore, it is of importance to gain knowledge on ecological and eco-toxicological features of the Asian bush mosquito. However, optimal laboratory feeding conditions have not yet been established. Standardized feeding methods will be needed in assessing the impact of insecticides or competitional strength of this species. To fill this gap, we performed experiments on food quality and quantity for Ae. j. japonicus larvae. We found out that the commercial fish food TetraMin (Tetra, Melle, Germany) in a dose of 10 mg per larva is the most suitable food tested. We also suggest a protocol with a feeding sequence of seven portions for all larval stages of this species.
We study how species richness of arthropods relates to theories concerning net primary productivity, ambient energy, water-energy dynamics and spatial environmental heterogeneity. We use two datasets of arthropod richness with similar spatial extents (Scandinavia to Mediterranean), but contrasting spatial grain (local habitat and country). Samples of ground-dwelling spiders, beetles, bugs and ants were collected from 32 paired habitats at 16 locations across Europe. Species richness of these taxonomic groups was also determined for 25 European countries based on the Fauna Europaea database. We tested effects of net primary productivity (NPP), annual mean temperature (T), annual rainfall (R) and potential evapotranspiration of the coldest month (PETmin) on species richness and turnover. Spatial environmental heterogeneity within countries was considered by including the ranges of NPP, T, R and PETmin. At the local habitat grain, relationships between species richness and environmental variables differed strongly between taxa and trophic groups. However, species turnover across locations was strongly correlated with differences in T. At the country grain, species richness was significantly correlated with environmental variables from all four theories. In particular, species richness within countries increased strongly with spatial heterogeneity in T. The importance of spatial heterogeneity in T for both species turnover across locations and for species richness within countries suggests that the temperature niche is an important determinant of arthropod diversity. We suggest that, unless climatic heterogeneity is constant across sampling units, coarse-grained studies should always account for environmental heterogeneity as a predictor of arthropod species richness, just as studies with variable area of sampling units routinely consider area.
There is increasing evidence that climate change will have a severe impact on species’ distributions by altering the climatic conditions within their present ranges. Especially species inhabiting stream ecosystems are expected to be strongly affected due to warming temperatures and changes in precipitation patterns. The aim of this thesis was to
investigate how distributions of aquatic insects, i.e., benthic stream macroinvertebrates would be impacted by warming climates. The methods comprised of an ensemble forecasting technique based on species distribution models (SDMs) and climate change scenarios of the Intergovernmental Panel on Climate Change of the year 2080. Future model projections were generated for a wide variety of species from a number of taxonomic orders for two spatial scales: a stream network within the lower mountain ranges of Germany, and the entire territory across Europe. In addition, the effect of the modelling technique on habitat suitability projections was investigated by modifying the choice of study area (continuous area vs. stream network) and the choice of predictors (standard vs. corrected set).
Projections of future habitat suitability showed that potential climate-change impacts would be dependent on species’ thermal preferences, and with a similar pattern for both spatial scales. Future habitat suitability was projected to remain for most or all of the modelled species, and species were projected to track their climatically suitable conditions by shifting uphill along the river continuum within the lower mountain ranges, and into a north-easterly direction across Europe. Cold-adapted headwater and high-latitude species were projected to lose suitable habitats, whereas gains would be expected for warm-adapted river and low-latitude species along the river continuum and across Europe, respectively. Additionally, habitat specialist species in terms of endemics of the Iberian Peninsula were identified as potential climate-change losers, highlighting their restricted habitat availability and therefore vulnerability to warming climates.
The main findings of this thesis underline the high susceptibility of stream macroinvertebrates to ongoing climate change, and give insights into patterns of possible consequences due to changes in species’ habitat suitability. Concerning the methodology, a clear recommendation can be given for future modelling approaches of stream macroinvertebrates by building models within a stream network and with a careful choice of environmental predictors, to reduce uncertainties and thus to improve model projections.
The iconic Australasian kangaroos and wallabies represent a successful marsupial radiation. However, the evolutionary relationship within the two genera, Macropus and Wallabia, is controversial: mitochondrial and nuclear genes, and morphological data have produced conflicting scenarios regarding the phylogenetic relationships, which in turn impact the classification and taxonomy. We sequenced and analyzed the genomes of 11 kangaroos to investigate the evolutionary cause of the observed phylogenetic conflict. A multilocus coalescent analysis using ∼14,900 genome fragments, each 10 kb long, significantly resolved the species relationships between and among the sister-genera Macropus and Wallabia. The phylogenomic approach reconstructed the swamp wallaby (Wallabia) as nested inside Macropus, making this genus paraphyletic. However, the phylogenomic analyses indicate multiple conflicting phylogenetic signals in the swamp wallaby genome. This is interpreted as at least one introgression event between the ancestor of the genus Wallabia and a now extinct ghost lineage outside the genus Macropus. Additional phylogenetic signals must therefore be caused by incomplete lineage sorting and/or introgression, but available statistical methods cannot convincingly disentangle the two processes. In addition, the relationships inside the Macropus subgenus M. (Notamacropus) represent a hard polytomy. Thus, the relationships between tammar, red-necked, agile, and parma wallabies remain unresolvable even with whole-genome data. Even if most methods resolve bifurcating trees from genomic data, hard polytomies, incomplete lineage sorting, and introgression complicate the interpretation of the phylogeny and thus taxonomy.
Understanding the spatial and temporal dynamics of species assemblages is a main challenge in ecology. The mechanisms that shape species assemblages and their temporal fluctuations along tropical elevational gradients are particularly poorly understood. Here, we examined the spatio-temporal dynamics of bird assemblages along an elevational gradient in Ecuador. We conducted bird point counts at three elevations (1000, 2000 and 3000 m) on 18 1-ha plots and repeated the sampling eight times over two years (216 hours in total). For each plot, we obtained data of monthly temperatures and precipitation and recorded the overall resource availability (i.e., the sum of flower, fruit, and invertebrate resources). As expected, bird richness decreased from low to high elevations. Moreover, we found a significant decrease in bird abundance and richness and an increase in evenness between the most and least humid season at each of the three elevations. Climatic factors were more closely related to these temporal fluctuations than local resource availability. While temperature had significant positive effects on the abundance of birds at mid and high elevations, precipitation negatively affected bird abundance at low and mid elevations. Our study highlights that bird assemblages along tropical elevational gradients can show pronounced seasonal fluctuations. In particular, low temperatures and high precipitation seem to impose important constraints on birds. We conclude that potential changes in climate, due to global warming, are likely to affect the spatio-temporal dynamics of bird assemblages along tropical elevational gradients.
Understanding major causes of biodiversity and range dynamics requires research on evolutionary processes under consideration of environmental changes. In my thesis, I investigated the spatio-temporal evolution of the Neotropical tree genus Cedrela from the Meliaceae family by studying its genetic diversity, taxonomy, colonization history, climatic niche changes and dynamics of species distributions. My results show that climatic and geological changes are major drivers of biological diversification in Cedrela.
Over the last decades agroforestry parklands in Burkina Faso have come under increasing demographic as well as climatic pressures, which are threatening indigenous tree species that contribute substantially to income generation and nutrition in rural households. Analyzing the threats as well as the species vulnerability to them is fundamental for priority setting in conservation planning. Guided by literature and local experts we selected 16 important food tree species (Acacia macrostachya, Acacia senegal, Adansonia digitata, Annona senegalensis, Balanites aegyptiaca, Bombax costatum, Boscia senegalensis, Detarium microcarpum, Lannea microcarpa, Parkia biglobosa, Sclerocarya birrea, Strychnos spinosa, Tamarindus indica, Vitellaria paradoxa, Ximenia americana, Ziziphus mauritiana) and six key threats to them (overexploitation, overgrazing, fire, cotton production, mining and climate change). We developed a species-specific and spatially explicit approach combining freely accessible datasets, species distribution models (SDMs), climate models and expert survey results to predict, at fine scale, where these threats are likely to have the greatest impact. We find that all species face serious threats throughout much of their distribution in Burkina Faso and that climate change is predicted to be the most prevalent threat in the long term, whereas overexploitation and cotton production are the most important short-term threats. Tree populations growing in areas designated as ‘highly threatened’ due to climate change should be used as seed sources for ex situ conservation and planting in areas where future climate is predicting suitable habitats. Assisted regeneration is suggested for populations in areas where suitable habitat under future climate conditions coincides with high threat levels due to short-term threats. In the case of Vitellaria paradoxa, we suggest collecting seed along the northern margins of its distribution and considering assisted regeneration in the central part where the current threat level is high due to overexploitation. In the same way, population-specific recommendations can be derived from the individual and combined threat maps of the other 15 food tree species. The approach can be easily transferred to other countries and can be used to analyze general and species specific threats at finer and more local as well as at broader (continental) scales in order to plan more selective and efficient conservation actions in time. The concept can be applied anywhere as long as appropriate spatial data are available as well as knowledgeable experts.
Background: Worldwide, the number of recorded human hantavirus infections as well as the number of affected countries is on the rise. In Europe, most human hantavirus infections are caused by the Puumala virus (PUUV), with bank voles (Myodes glareolus) as reservoir hosts. Generally, infection outbreaks have been related to environmental conditions, particularly climatic conditions, food supply for the reservoir species and land use. However, although attempts have been made, the insufficient availability of environmental data is often hampering accurate temporal and spatially explicit models of human hantavirus infections.
Methods: In the present study, dynamics of human PUUV infections between 2001 and 2015 were explored using ArcGIS in order to identify spatio-temporal patterns.
Results: Percentage cover of forest area was identified as an important factor for the spatial pattern, whereas beech mast was found explaining temporal patterns of human PUUV infections in Germany. High numbers of infections were recorded in 2007, 2010 and 2012 and areas with highest records were located in Baden-Wuerttemberg (southwest Germany) and North Rhine-Westphalia (western Germany).
Conclusion: More reliable data on reservoir host distribution, pathogen verification as well as an increased awareness of physicians are some of the factors that should improve future human infection risk assessments in Germany.
Small-scale phenotypic differentiation along complex stream gradients in a non-native amphipod
(2019)
Background: Selective landscapes in rivers are made up by an array of selective forces that vary from source to downstream regions or between seasons, and local/temporal variation in fitness maxima can result in gradual spatio-temporal variation of phenotypic traits. This study aimed at establishing freshwater amphipods as future model organisms to study adaptive phenotypic diversification (evolutionary divergence and/or adaptive plasticity) along stream gradients.
Methods: We collected Gammarus roeselii from 16 sampling sites in the Rhine catchment during two consecutive seasons (summer and winter). Altogether, we dissected n = 1648 individuals and quantified key parameters related to morphological and life-history diversification, including naturally selected (e.g., gill surface areas) as well as primarily sexually selected traits (e.g., male antennae). Acknowledging the complexity of selective regimes in streams and the interrelated nature of selection factors, we assessed several abiotic (e.g., temperature, flow velocity) and biotic ecological parameters (e.g., conspecific densities, sex ratios) and condensed them into four principal components (PCs).
Results: Generalized least squares models revealed pronounced phenotypic differentiation in most of the traits investigated herein, and components of the stream gradient (PCs) explained parts of the observed differences. Depending on the trait under investigation, phenotypic differentiation could be ascribed to variation in abiotic conditions, anthropogenic disturbance (influx of thermally polluted water), or population parameters. For example, female fecundity showed altitudinal variation and decreased with increasing conspecific densities, while sexual dimorphism in the length of male antennae—used for mate finding and assessment—increased with increasing population densities and towards female-biased sex ratios.
Conclusions: We provide a comprehensive protocol for comparative analyses of intraspecific variation in life history traits in amphipods. Whether the observed phenotypic differentiation over small geographical distances reflects evolutionary divergence or plasticity (or both) remains to be investigated in future studies. Independent of the mechanisms involved, variation in several traits is likely to have consequences for ecosystem functions. For example, leaf-shredding in G. roeselii strongly depends on body size, which varied in dependence of several ecological parameters.
Although it has been suggested that temperature increase may alter the toxic potential of environmental pollutants, few studies have investigated the potential risk of chemical stressors for wildlife under Global Climate Change (GCC) impact. We applied a bifactorial multigeneration study in order to test if GCC conditions alter the effects of low pesticide concentrations on life history and genetic diversity of the aquatic model organism Chironomus riparius. Experimental populations of the species were chronically exposed to a low concentration of the fungicide pyrimethanil (half of the no-observed-adverse-effect concentration: NOAEC/2) under two dynamic present-day temperature simulations (11.0–22.7°C; 14.0–25.2°C) and one future scenario (16.5–28.1°C). During the 140-day multigeneration study, survival, emergence, reproduction, population growth, and genetic diversity of C. riparius were analyzed. Our results reveal that high temperature and pyrimethanil act synergistically on the midge C. riparius. In simulated present-day scenarios, a NOAEC/2 of pyrimethanil as derived from a life-cycle toxicity test provoked only slight-to-moderate beneficial or adverse effects on C. riparius. In contrast, exposure to a NOAEC/2 concentration of pyrimethanil at a thermal situation likely for a summer under GCC conditions uncovered adverse effects on mortality and population growth rate. In addition, genetic diversity was considerably reduced by pyrimethanil in the future scenario, but only slightly under current climatic conditions. Our multigeneration study under near-natural (climatic) conditions indicates that not only the impact of climate change, but also low concentrations of pesticides may pose a reasonable risk for aquatic insects in future.
The species composition of local communities varies in space, and its similarity generally decreases with increasing geographic distance between communities, a phenomenon known as distance decay of similarity. It is, however, not known how changes in local species composition affect ecological processes, that is, whether they lead to differences in the local composition of species' functional roles. We studied eight seed‐dispersal networks along the South American Andes and compared them with regard to their species composition and their composition of functional roles. We tested (1) if changes in bird species composition lead to changes in the composition of bird functional roles, and (2) if the similarity in species composition and functional‐role composition decreased with increasing geographic distance between the networks. We also used cluster analysis to (3) identify bird species with similar roles across all networks based on the similarity in the plants they consume, (i) considering only the species identity of the plants and (ii) considering the functional traits of the plants. Despite strong changes in species composition, the networks along the Andes showed similar composition of functional roles. (1) Changes in species composition generally did not lead to changes in the composition of functional roles. (2) Similarity in species composition, but not functional‐role composition, decreased with increasing geographic distance between the networks. (3) The cluster analysis considering the functional traits of plants identified bird species with similar functional roles across all networks. The similarity in functional roles despite the high species turnover suggests that the ecological process of seed dispersal is organized similarly along the Andes, with similar functional roles fulfilled locally by different sets of species. The high species turnover, relative to functional turnover, also indicates that a large number of bird species are needed to maintain the seed‐dispersal process along the Andes.
Background: Until recently, read lengths on the Solexa/Illumina system were too short to reliably assemble transcriptomes without a reference sequence, especially for non-model organisms. However, with read lengths up to 100 nucleotides available in the current version, an assembly without reference genome should be possible. For this study we created an EST data set for the common pond snail Radix balthica by Illumina sequencing of a normalized transcriptome. Performance of three different short read assemblers was compared with respect to: the number of contigs, their length, depth of coverage, their quality in various BLAST searches and the alignment to mitochondrial genes. Results: A single sequencing run of a normalized RNA pool resulted in 16,923,850 paired end reads with median read length of 61 bases. The assemblies generated by VELVET, OASES, and SeqMan NGEN differed in the total number of contigs, contig length, the number and quality of gene hits obtained by BLAST searches against various databases, and contig performance in the mt genome comparison. While VELVET produced the highest overall number of contigs, a large fraction of these were of small size (< 200bp), and gave redundant hits in BLAST searches and the mt genome alignment. The best overall contig performance resulted from the NGEN assembly. It produced the second largest number of contigs, which on average were comparable to the OASES contigs but gave the highest number of gene hits in two out of four BLAST searches against different reference databases. A subsequent meta-assembly of the four contig sets resulted in larger contigs, less redundancy and a higher number of BLAST hits. Conclusion: Our results document the first de novo transcriptome assembly of a non-model species using Illumina sequencing data. We show that de novo transcriptome assembly using this approach yields results useful for downstream applications, in particular if a meta-assembly of contig sets is used to increase contig quality. These results highlight the ongoing need for improvements in assembly methodology. Keywords: next generation sequencing; short read assembly; Mollusca