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Feeding exclusively on blood, vampire bats represent the only obligate sanguivorous lineage among mammals. To uncover genomic changes associated with adaptations to this unique dietary specialization, we generated a new haplotype-resolved reference-quality genome of the common vampire bat (Desmodus rotundus) and screened 26 bat species for genes that were specifically lost in the vampire bat lineage. We discovered previously-unknown gene losses that relate to metabolic and physiological changes, such as reduced insulin secretion (FFAR1, SLC30A8), limited glycogen stores (PPP1R3E), and a distinct gastric physiology (CTSE). Other gene losses likely reflect the biased nutrient composition (ERN2, CTRL) and distinct pathogen diversity of blood (RNASE7). Interestingly, the loss of REP15 likely helped vampire bats to adapt to high dietary iron levels by enhancing iron excretion and the loss of the 24S-hydroxycholesterol metabolizing enzyme CYP39A1 could contribute to their exceptional cognitive abilities. Finally, losses of key cone phototransduction genes (PDE6H, PDE6C) suggest that these strictly-nocturnal bats completely lack cone-based vision. These findings enhance our understanding of vampire bat biology and the genomic underpinnings of adaptations to sanguivory.
Vampire bats are the only mammals that feed exclusively on blood. To uncover genomic changes associated with this dietary adaptation, we generated a haplotype-resolved genome of the common vampire bat and screened 27 bat species for genes that were specifically lost in the vampire bat lineage. We found previously unknown gene losses that relate to reduced insulin secretion (FFAR1 and SLC30A8), limited glycogen stores (PPP1R3E), and a unique gastric physiology (CTSE). Other gene losses likely reflect the biased nutrient composition (ERN2 and CTRL) and distinct pathogen diversity of blood (RNASE7) and predict the complete lack of cone-based vision in these strictly nocturnal bats (PDE6H and PDE6C). Notably, REP15 loss likely helped vampire bats adapt to high dietary iron levels by enhancing iron excretion, and the loss of CYP39A1 could have contributed to their exceptional cognitive abilities. These findings enhance our understanding of vampire bat biology and the genomic underpinnings of adaptations to blood feeding.
Smut fungi are well-suited to investigate the ecology and evolution of plant pathogens, as they are strictly biotrophic, yet cultivable on media. Here we report the genome sequence of Melanopsichium pennsylvanicum, closely related to Ustilago maydis and other Poaceae-infecting smuts, but parasitic to a dicot plant. To explore the evolutionary patterns resulting from host adaptation after this huge host jump, the genome of M. pennsylvanicum was sequenced and compared to the genomes of Ustilago maydis, Sporisorium reilianum, and Ustilago hordei. While all four genomes had a similar completeness in CEGMA analyses, gene absence was highest in M. pennsylvanicum, and most pronounced in putative secreted proteins, which are often considered as effector candidates. In contrast, the amount of private genes was similar among the species, highlighting that gene loss rather than gene gain is the hallmark of adaptation after the host jump to the dicot host. Our analyses revealed a trend of putative effectors to be next to another putative effector, but the majority of these are not in clusters and thus the focus on pathogenicity clusters might not be appropriate for all smut genomes. Positive selection studies revealed that M. pennsylvanicum has the highest number and proportion of genes under positive selection. In general, putative effectors showed a higher proportion of positively selected genes than non-effector candidates. The 248 putative secreted effectors found in all four smut genomes might constitute a core set needed for pathogenicity, while those 92 that are found in all grass-parasitic smuts, but have no ortholog in M. pennsylvanicum might constitute a set of effectors important for successful colonization of grass hosts.
Background: We evaluated the sensitivity of the D-statistic, a parsimony-like method widely used to detect gene flow between closely related species. This method has been applied to a variety of taxa with a wide range of divergence times. However, its parameter space and thus its applicability to a wide taxonomic range has not been systematically studied. Divergence time, population size, time of gene flow, distance of outgroup and number of loci were examined in a sensitivity analysis.
Result: The sensitivity study shows that the primary determinant of the D-statistic is the relative population size, i.e. the population size scaled by the number of generations since divergence. This is consistent with the fact that the main confounding factor in gene flow detection is incomplete lineage sorting by diluting the signal. The sensitivity of the D-statistic is also affected by the direction of gene flow, size and number of loci. In addition, we examined the ability of the f-statistics, fˆGf^G and fˆhomf^hom, to estimate the fraction of a genome affected by gene flow; while these statistics are difficult to implement to practical questions in biology due to lack of knowledge of when the gene flow happened, they can be used to compare datasets with identical or similar demographic background.
Conclusions: The D-statistic, as a method to detect gene flow, is robust against a wide range of genetic distances (divergence times) but it is sensitive to population size. The D-statistic should only be applied with critical reservation to taxa where population sizes are large relative to branch lengths in generations.
The recent advances in molecular methods and data processing have facilitated research on anisakid nematodes. While most research efforts were made regarding the genus Anisakis, since this genus is held responsible for the majority of reported clinical signs, there is still a demand for data on the genus Pseudoterranova. Several case studies of severe invasive anisakidosis affecting various organs caused by species of the P. decipiens complex have been described. To better understand the way these parasites might infest their fish host, we examined whether parasite location within the fish host affects gene expression. A de novo assembly of the transcriptome of Pseudoterranova bulbosa, isolated from North Atlantic cod, was analysed for patterns of differential gene expression between samples taken from liver and viscera. We additionally searched for homologs to known nematode allergens, to give a first estimate of the potential allergenicity of P. bulbosa. There was a subtle difference in the gene expression of samples taken from liver and viscera. Seventy genes were differentially expressed, 32 genes were upregulated in parasites isolated from liver and 38 genes were upregulated in parasites from viscera. Homologs of five nematode allergens were identified among the genes expressed by P. bulbosa. Our transcriptome of P. bulbosa will be a valuable resource for further meta-analyses and resequencing projects.
Fungi indirectly affect plant root architecture by modulating soil volatile organic compounds
(2018)
The plant-growth modulating effect of microbial volatile organic compounds (VOCs) has been demonstrated repeatedly. This has most often been performed by exposing plants to VOC released by microbes grown on nutrient rich media. Here, we used soil instead to grow fungi of the Fusarium genus and investigate how VOCs emitted by this system influenced the development of Arabidopsis plants. The volatile profiles of Fusarium strains grown in soil and malt extract were also compared. Our results demonstrate that distinct volatile signatures can be attributed to different Fusarium genetic clades but also highlight a major influence of the growth medium on volatile emission. Furthermore, all soil-grown Fusarium isolates increased primary root length in Arabidopsis by decreasing VOC concentrations in soil. This result represents a major paradigm shift in plant-microbe interactions since growth modulating effects have been attributed so far to the emission and not the consumption of volatile signals.
Background: Dispersal rates, i.e. the effective number of dispersing individuals per unit time, are the product of dispersal capacity, i.e. a species physiological potential for dispersal, dispersal behaviour, i.e. the decision to leave a habitat patch in favour of another, and connectivity of occupied habitat. Dispersal of species that are highly specialised to a certain habitat is thus strongly limited by habitat availability. Additionally, species inhabiting very stable environments may adopt a sedentary life-style. Both factors should lead to strong genetic differentiation in highly specialised species inhabiting stable environments. These two factors apply to our model species Rhyacophila pubescens a highly specialised freshwater insect that occurs in tufa springs, a very stable habitat. Results: We examined the genetic population structure and phylogeography using range-wide mtCOI sequence and AFLP data from 333 individuals of R. pubescens. We inferred the location of Pleistocene refugia and postglacial colonisation routes of R. pubescens, and examined ongoing local differentiation. Our results indicate intraregional differentiation with a high number of locally endemic haplotypes, that we attributed to habitat specificity and low dispersal rates of R. pubescens. We observed high levels of genetic diversity south of the Alps and genetic impoverishment north of the Alps. Estimates of migrants placed the refugium and the source of the colonisation in the Dauphine Alps (SW Alps). Conclusions: This is the first example of an aquatic insect with a colonisation route along the western margin of the Alps to the Central European highlands. The study also shows that specialisation to a stable environment may have promoted a behavioural shift to decreased dispersal rates, leading to stronger local population differentiation than in less specialised aquatic insects. Alternatively, the occurrence of highly specialised tufa spring habitats may have been more widespread in the past, leading to range regression and fragmentation among present day R. pubescens populations.
Forensic entomology
(2017)
For many members of the forensic community, insects still have an exotic status. This may be one reason why forensic entomology, the analysis of insect evidence for forensic and legal purposes, has not yet achieved the significance it deserves in forensic sciences. The present special issue may help to change that. ...
In Benin, people have a rich ethnobotanical knowledge of plant species, reflecting the cultural and ecological diversity of their environment. Several studies were focused on the question of how valuable are plant species for local communities. However, there has been very little research interest in the orchid species in spite of the importance of orchids in the livelihood of the local people. This study examined the use and differences in knowledge of local people of orchids in the Sudanian zone of Benin. An ethnobotanical study was conducted amongst the four main socio-economic and ethnic groups from six villages around the Pendjari Biosphere Reserve in Benin. One hundred and sixty people participated in this study. Data were gathered using semi-structured individual interviews and analysed using quantitative ethnobotanical methods. 29 different types of use were recorded and can be grouped into four main use categories: medicinal, veterinary, spiritual and food. There were differences in orchid utilization among the ethnic groups, gender and age. The knowledge of orchid uses was significantly affected by the ethnic group and the age of the respondent. Unlike young educated generations, most adults and elders, especially women, had a more comprehensive knowledge of orchid uses. Calyptrochilum christianum, the most used orchid, was mentioned in more than 50% of the types of orchid use. The Gourmantché and Waama tribe had more knowledge on orchid use whereas the Berba tribe had less knowledge. Three orchid species (Habenaria cirrhata, Eulophia horsfallii and Nervilia bicarinata) were reported as food. Orchids had low use value ranging from 0.01 (Eulophia spp) to 0.2 (C. christianum). The controlled access to the biosphere reserve and rural exodus can explain the lack of indigenous knowledge transfer of orchid use and value from elders to the young generation.
Plant communities provide floral resource-landscapes for pollinators. Yet, it is insufficiently understood how these landscapes shape pollinator-mediated interactions among multiple plant species. Here, we study how pollinators and the seed set of plants respond to the distribution of a floral resource (nectar sugar) in space and across plant species, inflorescences and flowering phenologies. In a global biodiversity hotspot, we quantified floral resource-landscapes on 27 sites of 4 ha comprising 127,993 shrubs of 19 species. Visitation rates of key bird pollinators strongly depended on the phenology of site-scale resource amounts. Seed set of focal plants increased with resources of conspecific neighbours and with site-scale resources, notably with heterospecific resources of lower quality (less sugar per inflorescence). Floral resources are thus a common currency determining how multiple plant species interact via pollinators. These interactions may alter conditions for species coexistence in plant communities and cause community-level Allee effects that promote extinction cascades.
Biological invasions are frequently studied topics in ecological research. Unfortunately, within invasion ecology parasite-associated aspects such as parasite impacts on new environments and on local host populations are less well-studied. Round gobies migrating from the Ponto-Caspian region into the Rhine River system are heavily infested with the Ponto-Caspian acanthocephalan parasite Pomphorhynchus laevis. As shown by experimental infestations the acanthocephalans occur as pre-adults in host-encapsulated cysts within the internal organs of the migrating gobies, but remain infective for their definitive host chub. Recently, we described the occurrence of larvae of another parasite, the invasive eel swim bladder nematode Anguillicola crassus, in these Pomphorhynchus cysts. In the present study, we could prove the infectivity of the nematode larvae for European eels for the first time. After experimental inoculation of Pomphorhynchus cysts occasionally infested with A. crassus larvae, the nematodes grow to maturity and reproduce whereas all P. laevis were unviable. We therefore postulate that the nematode larvae behave like immunological hitchhikers that follow a “Trojan horse strategy” in order to avoid the paratenic host’s immune response. Accordingly, the interaction between both invasive parasites gives first evidence that the invasional meltdown hypothesis may also apply to parasites.
During field work along a transect in the Cordillera Central of western Panama between 2008 and 2010, we detected several populations of amphibian species which are considered as “Endangered” or “Critically Endangered” by the IUCN. Some of these species had suffered from serious population declines, probably due to chytridiomycosis, but all are generally threatened by habitat loss. We detected 53% of the Endangered and 56% of the Critically Endangered amphibian species that have previously been reported from within the investigated area. We report on findings of species that have not been found in Panama for many years, and provide locality data of newly discovered populations. There is a need to create a new protected area in the Cerro Colorado area of the Serranía de Tabasará, where we found 15% of the Endangered and Critically Endangered amphibian species known to Panama.
Divergent selection between ecologically dissimilar habitats promotes local adaptation, which can lead to reproductive isolation (RI). Populations in the Poecilia mexicana species complex have independently adapted to toxic hydrogen sulfide and show varying degrees of RI. Here, we examined the variation in the mate choice component of prezygotic RI. Mate choice tests across drainages (with stimulus males from another drainage) suggest that specific features of the males coupled with a general female preference for yellow color patterns explain the observed variation. Analyses of male body coloration identified the intensity of yellow fin coloration as a strong candidate to explain this pattern, and common-garden rearing suggested heritable population differences. Male sexual ornamentation apparently evolved differently across sulfide-adapted populations, for example because of differences in natural counterselection via predation. The ubiquitous preference for yellow color ornaments in poeciliid females likely undermines the emergence of strong RI, as female discrimination in favor of own males becomes weaker when yellow fin coloration in the respective sulfide ecotype increases. Our study illustrates the complexity of the (partly non-parallel) pathways to divergence among replicated ecological gradients. We suggest that future work should identify the genomic loci involved in the pattern reported here, making use of the increasing genomic and transcriptomic datasets available for our study system.
Feeding type and development drive the ingestion of microplastics by freshwater invertebrates
(2017)
Microscopic plastic items (microplastics) are ubiquitously present in aquatic ecosystems. With decreasing size their availability and potential to accumulate throughout food webs increase. However, little is known on the uptake of microplastics by freshwater invertebrates. To address this, we exposed species with different feeding strategies to 1, 10 and 90 µm fluorescent polystyrene spheres (3–3 000 particles mL−1). Additionally, we investigated how developmental stages and a co-exposure to natural particles (e.g., food) modulate microplastic ingestion. All species ingested microplastics in a concentration-dependent manner with Daphnia magna consuming up to 6 180 particles h−1, followed by Chironomus riparius (226 particles h−1), Physella acuta (118 particles h−1), Gammarus pulex (10 particles h−1) and Lumbriculus variegatus (8 particles h−1). D. magna did not ingest 90 µm microplastics whereas the other species preferred larger microplastics over 1 µm in size. In C. riparius and D. magna, size preference depended on the life stage with larger specimens ingesting more and larger microplastics. The presence of natural particles generally reduced the microplastics uptake. Our results demonstrate that freshwater invertebrates have the capacity to ingest microplastics. However, the quantity of uptake depends on their feeding type and morphology as well as on the availability of microplastics.
Background: Factors and processes shaping the population structure and spatial distribution of genetic diversity across a species' distribution range are important in determining the range limits. We comprehensively analysed the influence of recurrent and historic factors and processes on the population genetic structure, mating system and the distribution of genetic variability of the pulmonate freshwater snail Radix balthica. This analysis was based on microsatellite variation and mitochondrial haplotypes using Generalised Linear Statistical Modelling in a Model Selection framework. Results: Populations of R. balthica were found throughout North-Western Europe with range margins marked either by dispersal barriers or the presence of other Radix taxa. Overall, the population structure was characterised by distance independent passive dispersal mainly along a Southwest-Northeast axis, the absence of isolation-by-distance together with rather isolated and genetically depauperated populations compared to the variation present in the entire species due to strong local drift. A recent, climate driven range expansion explained most of the variance in genetic variation, reducing at least temporarily the genetic variability in this area. Other factors such as geographic marginality and dispersal barriers play only a minor role. Conclusions: To our knowledge, such a population structure has rarely been reported before. It might nevertheless be typical for passively dispersed, patchily distributed taxa (e.g. freshwater invertebrates). The strong local drift implied in such a structure is expected to erode genetic variation at both neutral and coding loci and thus probably diminish evolutionary potential. This study shows that the analysis of multiple factors is crucial for the inference of the processes shaping the distribution of genetic variation throughout species ranges. Additional files Additional file 1: Distribution of Radix taxa. Spatial distribution of the Radix MOTU as defined in Pfenninger et al. 2006 plus an additional, newly discovered taxon. This map is the basis for the inference of the species range of R. balthica. Additional file 2: Sampling site table and spatial distribution of diversity indices, selfing estimates and inferred population bottlenecks for R. balthica. Table of sampling site code, geographical position in decimal degrees latitude and longitude, number of individuals analysed with microsatellites (Nnuc), expected heterozygosity (HE) and standard deviation across loci, mean rarefied number of alleles per microsatellite locus (A) and their standard deviation, number of individuals analysed for mitochondrial variation (Nmt), rarefied number of mitochondrial COI haplotypes (Hmt), number of individuals measured for body size (Nsize). Figures A1 - A3 show a graphical representation of the spatial distribution of He, Hmt and, s, respectively. Additional file 3: Assessment of environmental marginality. PCA (principle component analysis) on 35 climatic parameters for the period from 1960 - 2000 from publicly availableWorldClim data. Additional file 4: Inference of a recent climate driven range expansion in R. balthica. Analysis of the freshwater benthos long term monitoring data of the Swedish national monitoring databases at the Swedish University of Agricultural Sciences SLU with canonical correspondence analysis.
Background: Replicate population pairs that diverge in response to similar selective regimes allow for an investigation of (a) whether phenotypic traits diverge in a similar and predictable fashion, (b) whether there is gradual variation in phenotypic divergence reflecting variation in the strength of natural selection among populations, (c) whether the extent of this divergence is correlated between multiple character suites (i.e., concerted evolution), and (d) whether gradual variation in phenotypic divergence predicts the degree of reproductive isolation, pointing towards a role for adaptation as a driver of (ecological) speciation. Here, we use poeciliid fishes of the genera Gambusia and Poecilia that have repeatedly evolved extremophile lineages able to tolerate high and sustained levels of toxic hydrogen sulfide (H2S) to answer these questions.
Results: We investigated evolutionary divergence in response to H2S in Gambusia spp. (and to a lesser extent Poecilia spp.) using a multivariate approach considering the interplay of life history, body shape, and population genetics (nuclear miscrosatellites to infer population genetic differentiation as a proxy for reproductive isolation). We uncovered both shared and unique patterns of evolution: most extremophile Gambusia predictably evolved larger heads and offspring size, matching a priori predictions for adaptation to sulfidic waters, while variation in adult life histories was idiosyncratic. When investigating patterns for both genera (Gambusia and Poecilia), we found that divergence in offspring-related life histories and body shape were positively correlated across populations, but evidence for individual-level associations between the two character suites was limited, suggesting that genetic linkage, developmental interdependencies, or pleiotropic effects do not explain patterns of concerted evolution. We further found that phenotypic divergence was positively correlated with both environmental H2S-concentration and neutral genetic differentiation (a proxy for gene flow).
Conclusions: Our results suggest that higher toxicity exerts stronger selection, and that divergent selection appears to constrain gene flow, supporting a scenario of ecological speciation. Nonetheless, progress toward ecological speciation was variable, partially reflecting variation in the strength of divergent selection, highlighting the complexity of selective regimes even in natural systems that are seemingly governed by a single, strong selective agent.
Our knowledge of early evolution of snakes is improving, but all that we can infer about the evolution of modern clades of snakes such as boas (Booidea) is still based on isolated bones. Here, we resolve the phylogenetic relationships of Eoconstrictor fischeri comb. nov. and other booids from the early-middle Eocene of Messel (Germany), the best-known fossil snake assemblage yet discovered. Our combined analyses demonstrate an affinity of Eoconstrictor with Neotropical boas, thus entailing a South America-to-Europe dispersal event. Other booid species from Messel are related to different New World clades, reinforcing the cosmopolitan nature of the Messel booid fauna. Our analyses indicate that Eoconstrictor was a terrestrial, medium- to large-bodied snake that bore labial pit organs in the upper jaw, the earliest evidence that the visual system in snakes incorporated the infrared spectrum. Evaluation of the known palaeobiology of Eoconstrictor provides no evidence that pit organs played a role in the predator–prey relations of this stem boid. At the same time, the morphological diversity of Messel booids reflects the occupation of several terrestrial macrohabitats, and even in the earliest booid community the relation between pit organs and body size is similar to that seen in booids today.
Fossil dental remains are an archive of unique information for paleobiological studies. Computed microtomography based on X-ray microfocus sources (X-μCT) and Synchrotron Radiation (SR-μCT) allow subtle quantification at the micron and sub-micron scale of the meso- and microstructural signature imprinted in the mineralized tissues, such as enamel and dentine, through high-resolution “virtual histology”. Nonetheless, depending on the degree of alterations undergone during fossilization, X-ray analyses of tooth tissues do not always provide distinct imaging contrasts, thus preventing the extraction of essential morphological and anatomical details. We illustrate here by three examples the successful application of neutron microtomography (n-μCT) in cases where X-rays have previously failed to deliver contrasts between dental tissues of fossilized specimen.
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.
Songs in passerine birds are important for territory defense and mating. Speciation rates in oscine passerines are so high, due to cultural evolution, that this bird lineage makes up half of the extant bird species. Leaf warblers are a speciose Old-World passerine family of limited morphological differentiation, so that songs are even more important for species delimitation. We took 16 sonographic traits from song recordings of 80 leaf warbler taxa and correlated them with 15 potentially explanatory variables, pairwise, and in linear models. Based on a well-resolved molecular phylogeny of the same taxa, all pairwise correlations were corrected for relatedness with phylogenetically independent contrasts and phylogenetic generalized linear models were used. We found a phylogenetic signal for most song traits, but a strong one only for the duration of the longest and of the shortest element, which are presumably inherited instead of learned. Body size of a leaf warbler species is a constraint on song frequencies independent of phylogeny. At least in this study, habitat density had only marginal impact on song features, which even disappeared through phylogenetic correction. Maybe most leaf warblers avoid the deterioration through sound propagation in dense vegetation by singing from exposed perches. Latitudinal (and longitudinal) extension of the breeding ranges was correlated with most song features, especially verse duration (longer polewards and westwards) and complexity (lower polewards). Climate niche or expansion history might explain these correlations. The number of different element types per verse decreases with elevation, possibly due to fewer resources and congeneric species at higher elevations.
The study of organisms with restricted dispersal abilities and presence in the fossil record is particularly adequate to understand the impact of climate changes on the distribution and genetic structure of species. Trochoidea geyeri (Soós 1926) is a land snail restricted to a patchy, insular distribution in Germany and France. Fossil evidence suggests that current populations of T. geyeri are relicts of a much more widespread distribution during more favourable climatic periods in the Pleistocene. Results: Phylogeographic analysis of the mitochondrial 16S rDNA and nuclear ITS-1 sequence variation was used to infer the history of the remnant populations of T. geyeri. Nested clade analysis for both loci suggested that the origin of the species is in the Provence from where it expanded its range first to Southwest France and subsequently from there to Germany. Estimated divergence times predating the last glacial maximum between 25–17 ka implied that the colonization of the northern part of the current species range occurred during the Pleistocene. Conclusion: We conclude that T. geyeri could quite successfully persist in cryptic refugia during major climatic changes in the past, despite of a restricted capacity of individuals to actively avoid unfavourable conditions.
We demonstrate how a classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. A cave-dwelling centipede, Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae), found in a remote karst region in Knin, Croatia, is the first eukaryotic species for which, in addition to the traditional morphological description, we provide a fully sequenced transcriptome, a DNA barcode, detailed anatomical X-ray microtomography (micro-CT) scans, and a movie of the living specimen to document important traits of its ex-situ behaviour. By employing micro-CT scanning in a new species for the first time, we create a high-resolution morphological and anatomical dataset that allows virtual reconstructions of the specimen and subsequent interactive manipulation to test the recently introduced ‘cybertype’ notion. In addition, the transcriptome was recorded with a total of 67,785 scaffolds, having an average length of 812 bp and N50 of 1,448 bp (see GigaDB). Subsequent annotation of 22,866 scaffolds was conducted by tracing homologs against current available databases, including Nr, SwissProt and COG. This pilot project illustrates a workflow of producing, storing, publishing and disseminating large data sets associated with a description of a new taxon. All data have been deposited in publicly accessible repositories, such as GigaScience GigaDB, NCBI, BOLD, Morphbank and Morphosource, and the respective open licenses used ensure their accessibility and re-usability.
Erratum to doi:10.1186/s13071-016-1853-2
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.
Human exposure to endocrine disruptors is well documented by biomonitoring data. However, this information is limited to few chemicals like bisphenol A or phthalate plasticizers. To account for so-far unidentified endocrine disruptors and potential mixture effects we employ bioassays to detect endocrine activity in foodstuff and consequently characterize the integrated exposure to endocrine active compounds. Recently, we reported a broad contamination of commercially available bottled water with estrogenic activity and presented evidence for the plastic packaging being a source of this contamination. In continuation of that work, we here compare different sample preparation methods to extract estrogen-like compounds from bottled water. These data demonstrate that inappropriate extraction methods and sample treatment may lead to false-negative results when testing water extracts in bioassays. Using an optimized sample preparation strategy, we furthermore present data on the estrogenic activity of bottled water from France, Germany, and Italy: eleven of the 18 analyzed water samples (61.1%) induced a significant estrogenic response in a bioassay employing a human carcinoma cell line (MCF7, E-Screen). The relative proliferative effects ranged from 19.8 to 50.2% corresponding to an estrogenic activity of 1.9-12.2 pg estradiol equivalents per liter bottled water. When comparing water of the same spring that is packed in glass or plastic bottles made of polyethylene terephthalate (PET), estrogenic activity is three times higher in water from plastic bottles. These data support the hypothesis that PET packaging materials are a source of estrogen-like compounds. Furthermore, the findings presented here conform to previous studies and indicate that the contamination of bottled water with endocrine disruptors is a transnational phenomenon.
Background, aim, and scope Food consumption is an important route of human exposure to endocrine-disrupting chemicals. So far, this has been demonstrated by exposure modeling or analytical identification of single substances in foodstuff (e.g., phthalates) and human body fluids (e.g., urine and blood). Since the research in this field is focused on few chemicals (and thus missing mixture effects), the overall contamination of edibles with xenohormones is largely unknown. The aim of this study was to assess the integrated estrogenic burden of bottled mineral water as model foodstuff and to characterize the potential sources of the estrogenic contamination. Materials, methods, and results In the present study, we analyzed commercially available mineral water in an in vitro system with the human estrogen receptor alpha and detected estrogenic contamination in 60% of all samples with a maximum activity equivalent to 75.2 ng/l of the natural sex hormone 17beta-estradiol. Furthermore, breeding of the molluskan model Potamopyrgus antipodarum in water bottles made of glass and plastic [polyethylene terephthalate (PET)] resulted in an increased reproductive output of snails cultured in PET bottles. This provides first evidence that substances leaching from plastic food packaging materials act as functional estrogens in vivo. Discussion and conclusions Our results demonstrate a widespread contamination of mineral water with xenoestrogens that partly originates from compounds leaching from the plastic packaging material. These substances possess potent estrogenic activity in vivo in a molluskan sentinel. Overall, the results indicate that a broader range of foodstuff may be contaminated with endocrine disruptors when packed in plastics. Keywords Endocrine disrupting chemicals - Estradiol equivalents - Human exposure - In vitro effects - In vivo effects - Mineral water - Plastic bottles - Plastic packaging - Polyethylene terephthalate - Potamopyrgus antipodarum - Yeast estrogen screen - Xenoestrogens
The impact of climate change that comes with a dramatic increase of long periods of extreme summer drought associated with heat is a fundamental challenge for European forests. As a result, forests are expected to shift their distribution patterns toward north-east, which may lead to a dramatic loss in value of European forest land. Consequently, unraveling key processes that underlie drought stress tolerance is not only of great scientific but also of utmost economic importance for forests to withstand future heat and drought wave scenarios. To reveal drought stress-related molecular patterns we applied cross-species comparative transcriptomics of three major European oak species: the less tolerant deciduous pedunculate oak (Quercus robur), the deciduous but quite tolerant pubescent oak (Q. pubescens), and the very tolerant evergreen holm oak (Q. ilex). We found 415, 79, and 222 differentially expressed genes during drought stress in Q. robur, Q. pubescens, and Q. ilex, respectively, indicating species-specific response mechanisms. Further, by comparative orthologous gene family analysis, 517 orthologous genes could be characterized that may play an important role in drought stress adaptation on the genus level. New regulatory candidate pathways and genes in the context of drought stress response were identified, highlighting the importance of the antioxidant capacity, the mitochondrial respiration machinery, the lignification of the water transport system, and the suppression of drought-induced senescence - providing a valuable knowledge base that could be integrated in breeding programs in the face of climate change.
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.
West African Savanna ecosystems are undergoing severe changes in their vegetation composition due to the impact of human land use and changes in climatic conditions. This study aims to examine the effect of climate, land use, and their interaction on species richness and composition of West African herbaceous vegetation. Plot based vegetation sampling was done in Burkina Faso. Specific richness and diversity indices were used to determine the effect of land use, climate, and their interaction. An importance value was computed to determine herbaceous species dominating the communities. Frequency of species is used to examine their distribution pattern. The results showed that climate significantly influenced herbaceous specific richness more than land use. However, land use had a significant effect on herbaceous vegetation composition. Herbaceous species diversity changed with environmental conditions. The floristic composition of dominant species is driven by both climate and land use. The frequency of distribution demonstrated that herbaceous species occurrences were more influenced by the mixed effect of climate and land use than their separate effects. Occasional and rare species are the most important part of herbaceous vegetation. Thus heterogeneity of Savanna ecosystem and vulnerability of herbaceous species are high.
We welcome critical appraisals that help to provide balance; however, Dietrich et al. gave an unjustified reproach. We feel that Dietrich’s position is severely compromised because he serves as an expert for the bisphenol A (BPA) Industry Group (Brussels, Belgium). We would like to respond to the issues raised by Dietrich et al., as well as to their oversights and inappropriate interpretations of our findings...
Municipal wastewater contains nutrients valuable for a reuse in agriculture and can be the source of a multitude of chemicals used in private households and industry, too. As many of these chemicals are incompletely degraded during wastewater treatment, their residues remain partly in sewage sludge and partly in treated wastewater. Concerns are linked particularly to the so called micropollutants, i.e. anthropogenic organic substances such as personal care products, pharmaceuticals and biocides, for which scarce data on their degradability and environmental fate and particularly on their ecotoxicity are available. Thus, when reusing treated wastewater and sewage sludge for irrigation or as soil amendment for a sustainable land and water management, these wastewater-borne pollutants may enter soil, groundwater and surface water. The present work therefore aimed at assessing potential ecotoxic effects on aquatic and terrestrial organisms of reusing treated wastewater and sewage sludge. To this end, established as well as newly developed experimental approaches were used to investigate the problem on several levels. Individual wastewater-borne substances, samples from field study sites and samples from a soil column experiment simulating prolonged wastewater irrigation were examined.
At the start of the experimental work, the ecotoxicity of climbazole was characterised towards five aquatic and five terrestrial test organisms. Climbazole is an azole antimycotic agent applied in cosmetics and anti-dandruff shampoos and was recently detected in relatively high concentrations in treated wastewater and sewage sludge. In the present work climbazole was found to be particularly toxic towards plants such as water lentils with effective concentrations comparable to those of agricultural azole fungicides. Dwarfism, that is reduced shoot elongation observed in plants, pointed at a specific, phytohormone inhibiting mode of action of climbazole. Furthermore, the expected influence of the soil pH on the phytotoxicity of climbazole was experimentally confirmed.
Based on the findings for climbazole, two additional azole antimycotics, ketoconazole and fluconazole, and the regularly in sewage sludge detected biocide benzyldimethyldodecyl-ammonium chloride (BDDA) were investigated for their toxicity towards plants.
In aqueous medium, an increasing phytotoxicity from fluconazole to BDDA, ketoconazole and climbazole was observed, while in soil, phytotoxicity increased from BDDA to ketoconazole, climbazole and fluconazole. The relatively low terrestrial toxicity of BDDA and ketoconazole probably resulted from their strong binding to soil as well as their good biodegradability. To render the exposure scenario more realistic, sewage sludge was co-applied with the four test substances in a parallel test run. However, as no detectable influence on their effective concentrations was found, it can be assumed that the current practice of assessing sewage sludge borne substances with biotests in standard soil is sufficiently realistic. In a further study, different advanced sludge-treatment technologies were assessed for their efficacy in reducing pollutants. Results from the present work indicated that effects assessed in terrestrial short term biotests only seldom correlated with the concentrations of certain pollutants. Rather, a negative correlation of the stability of the sludges, determined by the ratio of volatile to total solids, to their ecotoxicity was seen.
Another aspect of the present work was the design and performance of an experimental approach to assess the environmental risk of a long-term irrigation with treated wastewater concerning the quality of soil and water in a prospective way, i.e. before the installation at field scale. For the simulation of a continuous irrigation corresponding to approximately 30 years, a percolation apparatus was developed and four different soils were percolated with treated wastewater for three months. Acute and chronic biotests with nine test organisms from different trophic levels (green algae, water lentils and water fleas as well as oilseed rape, oats, bacteria, spring tails, enchytraeids and earthworms) were used to assess the soil percolates as well as the soils with and without percolation. These investigations were accompanied by a comprehensive chemical monitoring conducted by project partners. Results indicated that the soil passage, that is the percolation through the soil, generally improved the quality of the treated wastewater as habitat for aquatic organisms which was visible by a reduction of its phytotoxicity. However, in some cases it deteriorated the water quality, probably resulting from the leaching of metals from pre-contaminated soil. A deteriorated habitat quality of the soil after the percolation with treated wastewater was observed for several test organisms and soils. In the same, mainly peaty soils, the highest accumulation of wastewater-borne micropollutants and of zinc was measured. Yet, their concentrations did not correlate to the observed biological effects. Moreover, data on ecotoxicity were only available for a small fraction of the detected substances so that their concentrations could not successfully be used to predict expected biological effects.
The experimental approach used in the present work demonstrated to be an adequate tool to support the prospective evaluation of environmental risks of treated wastewater irrigation. Overall, it can be concluded that the reuse of treated wastewater on soil can improve the quality of treated wastewater but that this can come at the cost of deteriorating the quality of the soil. As these risks cannot be generalised, a comprehensive biotest battery as well as chemical analysis should be used to assess them on a case-specific basis for each respective wastewater and the respective soil.
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 subfamily Bromelioideae is one of the most diverse groups among the neotropical Bromeliaceae. Previously, key innovations have been identified which account for the extraordinary radiation and species richness of this subfamily, especially in the so-called core Bromelioideae. However, in order to extend our understanding of the evolutionary mechanisms, the genomic mechanisms (e.g. polyploidy, dysploidy) that potentially underlie this accelerated speciation also need to be tested. Here, using PI and DAPI staining and flow cytometry we estimated genome size and GC content of 231 plants covering 30 genera and 165 species and combined it with published data. The evolutionary and ecological significance of all three genomic characters was tested within a previously generated dated phylogenetic framework using ancestral state reconstructions, comparative phylogenetic methods, and multiple regressions with climatic variables. The absolute genome size (2C) of Bromelioideae varied between 0.59 and 4.11 pg, and the GC content ranged between 36.73 and 41.43%. The monoploid genome sizes (Cx) differed significantly between core and early diverging lineages. The occurrence of dysploidy and polyploidy was, with few exceptions, limited to the phylogenetically isolated early diverging tank-less lineages. For Cx and GC content Ornstein–Uhlenbeck models outperformed the Brownian motion models suggesting adaptive potential linked to the temperature conditions. 2C-values revealed different rates of evolution in core and early diverging lineages also related to climatic conditions. Our results suggest that polyploidy is not associated with higher net diversification and fast radiation in core bromelioids. On the other hand, although coupled with higher extinction rates, dysploidy, polyploidy, and resulting genomic reorganizations might have played a role in the survival of the early diverging bromelioids in hot and arid environments.
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.
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.
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.
Since the 1980s, advances in wastewater treatment technology have led to considerably improved surface water quality in the urban areas of many high income countries. However, trace concentrations of organic wastewater-associated contaminants may still pose a key environmental hazard impairing the ecological quality of surface waters. To identify key impact factors, we analyzed the effects of a wide range of anthropogenic and environmental variables on the aquatic macroinvertebrate community. We assessed ecological water quality at 26 sampling sites in four urban German lowland river systems with a 0–100% load of state-of-the-art biological activated sludge treated wastewater. The chemical analysis suite comprised 12 organic contaminants (five phosphor organic flame retardants, two musk fragrances, bisphenol A, nonylphenol, octylphenol, diethyltoluamide, terbutryn), 16 polycyclic aromatic hydrocarbons, and 12 heavy metals. Non-metric multidimensional scaling identified organic contaminants that are mainly wastewater-associated (i.e., phosphor organic flame retardants, musk fragrances, and diethyltoluamide) as a major impact variable on macroinvertebrate species composition. The structural degradation of streams was also identified as a significant factor. Multiple linear regression models revealed a significant impact of organic contaminants on invertebrate populations, in particular on Ephemeroptera, Plecoptera, and Trichoptera species. Spearman rank correlation analyses confirmed wastewater-associated organic contaminants as the most significant variable negatively impacting the biodiversity of sensitive macroinvertebrate species. In addition to increased aquatic pollution with organic contaminants, a greater wastewater fraction was accompanied by a slight decrease in oxygen concentration and an increase in salinity. This study highlights the importance of reducing the wastewater-associated impact on surface waters. For aquatic ecosystems in urban areas this would lead to: (i) improvement of the ecological integrity, (ii) reduction of biodiversity loss, and (iii) faster achievement of objectives of legislative requirements, e.g., the European Water Framework Directive.
Methods using environmental DNA to explore and analyze biodiversity from previously unexplored habitats and ecosystems have become increasingly popular in recent years. This is particularly due to the potential reduction in necessary taxonomic expertise, the opportunity to assess microorganismal communities, and decreased time investments required to cover large spatial extents. In forests, the surface of tree bark is an important habitat for epiphytic diversity. Because of the large surface area rich in micro-niches, the seasonal stability of the substrate, and the longevity of trees, tree bark surfaces provide an ideal habitat for many species. Yet, we lack a comprehensive understanding of their communities and the environmental drivers behind the community assembly. These missing links hinder the exploration of the forest microbiome as a whole and limits our understanding of functions of a large forest habitat and its connections to other forest microbiomes. With a holistic eDNA metabarcoding approach, encompassing samples of three major taxonomic groups (e.g. bacteria, fungi, and green algae), as well as simultaneous collections from multiple forest habitats we can contribute to closing these gaps and increase our knowledge of the forest microbiome.
My dissertation is set within the framework of the Biodiversity Exploratories and was conducted in four parts: I. the establishment of an eDNA metabarcoding workflow to reveal the local diversity of the bark surface microbiome; II. the upscaling of the method to large geographic and environmental gradients to uncover the drivers of the microbiome; III. the integration of soil and bark samples to investigate compositional differences in two important forest habitats; IV. the evaluation of eDNA metabarcoding as a tool for biodiversity assessments of lichen diversity in forests.
In the first part, I developed a simple, cost-effective and fast sampling strategy to acquire eDNA samples from the bark of trees in forest ecosystems. Using readily available medical-specimen-collection swabs I sampled bark surfaces of individual trees in Central German forests and used metabarcoding to amplify marker genes of green algae, fungi and bacteria. From the sequencing reads I calculated the first diversity estimates of the major organismal groups of bark surface microbiomes from Central European forests. Overall the methodology produced reliable results, allowing for an expanded sampling in the second part.
In the second part of the dissertation, I expanded the sampling based on the results of part one. I collected bark surface samples from the three regions of the Biodiversity Exploratories covering large spatial and environmental gradients representative for Central European forests. The collection included composite samples from 150 plots and over 750 trees. Utilizing measurements of climatic and forest structure variables provided by the Biodiversity Exploratories, as well as my own community data, I identified the biotic and abiotic drivers behind alpha and beta diversity of the bark surface microbiome.
In the third part, I studied the differences between the bark surface as an unexplored and the soil as an example of a well characterized forest microbiome. Using only the fungal part of the large sampling campaign and soil samples obtained from the same plots at the same time, I assessed the commonalities and differences of the micro-communities of these distinct forest niches. Furthermore, I included two coniferous and one deciduous tree species to examine, if the effect of tree species, previously shown for soil microbiomes, also holds true for the bark surface.
In the last part of my dissertation, I used eDNA in a more applied way as a tool in biodiversity assessments of lichenized fungi. I compared the results from eDNA metabarcoding to an expert floristic mapping conducted in the same plots in 2007/2008. I assigned functional guilds to the fungal taxa obtained in the large sampling campaign and used a subset that was assigned as lichenized fungi.
In conclusion, I showed that eDNA metabarcoding is a valuable tool to reveal the unknown diversity of microorganisms in forest ecosystems. In particular, my results advance our understanding of the bark surface microbiome, an underexplored habitat within forests. The tightly linked interactions of the three major microbial groups underline that studies need to take holistic approaches across multiple taxonomic groups to deepen our understanding of processes governing the assembly of microbiomes. Results from my dissertation may serve as a foundation to inform hypotheses addressing the functions of forest microbiomes. The massive diversity data collected may also contribute to closing the gap in our understanding of macro-organisms and micro-organisms with respect to diversity distributions and patterns of richness, and serve as a baseline for predictions of biodiversity responses under future anthropogenic change.
Panama is a megadiverse country that together with Costa Rica constitutes Lower Central America (LCA). Western Panama's Cordillera Central accounts for the eastern part of the LCA highlands shared between these countries. The aim of the present study is to compile the most complete and updated picture possible of the taxonomy, diversity, and distribution of reptiles that occur from 500 m asl upwards along the Talamanca and Tabasará ranges. These two continuous mountain ridges account for the western two-thirds of the Cordillera Central between the Costa Rican border and 81°W Including specimens collected four own research travels, I morphologically examined more than 1800 specimens, analyzed 16S and/or COI barcodes of 300 specimens, and performed a thorough search in literature and databases to obtain locality records for specimens and species occurrences. My complete occurrence dataset comprises 14620 georeferenced occurrence records in three quality categories. Conceivable occurrences of species not yet documented from a given area are evaluated on the basis of existing data either as "plausible" or "possible". I provide all datasets which I generated for this study in Appendices. The previously published descriptions of Dactyloa ginaelisae Lotzkat, Hertz, Bienentreu & Köhler 2013, Norops benedikti (Lotzkat, Bienentreu, Hertz & Köhler 2011), Sibon perissostichon Köhler, Lotzkat & Hertz 2010, and Sibon noalamina Lotzkat, Hertz & Köhler 2012 are included in the present work. In the course of integrative taxonomic analyses, I classify 15 genealogical lineages revealed by DNA barcoding within 7 anole species as Deep Conspecific Lineages (DCLs) because they lack consistent morphological differences to their nominal conspecifics. I provisionally classify 18 mitochondrial lineages found within six other anole species as Unconfirmed Genealogical Lineages (UGLs) pending adequate analyses of their morphological variation. I regard the two additional UGLs Celestus sp. and Geophis sp. and the two Confirmed Genealogical Lineages (CGLs) Lepidoblepharis sp. 1 and 2 to represent undescribed species. My taxonomic analyses yield the hitherto most comprehensive survey of the variability exhibited by dozens of reptile species in western Panama. The 16S and/or COI barcodes I provide represent 65 species recognized herein and constitute the first DNA barcode reference library for LCA reptiles. The reptile fauna of Panama comprises 265 species, including the four UGLs and CGLs mentioned above and characterized for the first time in this study, as well as Dendrophidion crybelum Cadle 2012 whose presence in the country I consider plausible. My occurrence dataset reveals that 160 of these species have been documented to occur in my study area. Adding the 20 species whose occurrence therein I consider plausible, I report the total species richness of the Talamanca and Tabasará ranges as comprising 180 species representing 81 genera in 25 families. With 178.8 species per 10 000 km2, the relative species richness of the area is extremely high even in a tropical context. In view of their overall documented distribution, I regard the presence of 27 additional species in my study area as possible. For the 180 species occurring in my study area I provide standardized species accounts that, together with the taxonomic results, for the first time permit the doubtless identification of all 180 species, and illustrate 168 of these with color photographs. Concerning biogeography, my georeferenced dataset yields noteworthy distribution extensions for many species. Moreover, I present the hitherto most comprehensive, detailed, and reproducible assessments of the distribution patterns, historical origins, and conservation as well as of the occurrence among physiographic regions, climatic and altitudinal belts, political subdivisions, and protected areas, for my study area's reptile fauna. With 65 species, more than a third of the fauna is endemic to LCA. Among these, 42 Talamancan highland endemics are restricted to the LCA highlands, in the case of 16 small-scale highland endemics with documented ranges spanning less than 100 km. I assess many of these endemics as endangered. The fact that several of these species do not occur in any protected area renders the establishment of additional conservation areas necessary, especially in the central Serranía de Tabasará. Distributional range boundaries shared among different clades of highland anoles indicate physiographic and climatic barriers that may have effected in situ speciation within these lineages. As the largest study on Panamanian reptile diversity assembled to date, the present dissertation considerably increases our knowledge on the reptiles along the Cordillera Central and beyond, and thus constitutes a solid basis for future studies.
Soil degradation can have an impact on the soil microbiota, but its specific effects on soil fungal communities are poorly understood. In this work, we studied the impact of soil degradation on the richness and diversity of communities of soil fungi, including three different degrees of degradation in Germany and Panama. Soil fungi were isolated monthly using the soil-sprinkling method for 8 months in Germany and 3 months in Panama, and characterized by morphological and molecular data. Soil physico-chemical properties were measured and correlated with the observed values of fungal diversity. We isolated a total of 71 fungal species, 47 from Germany, and 32 from Panama. Soil properties were not associated with fungal richness, diversity, or composition in soils, with the exception of soil compaction in Germany. The geographic location was a strong determinant of the soil fungal species composition although in both countries there was dominance by members of the orders Eurotiales and Hypocreales. In conclusion, the results of this work do not show any evident influence of soil degradation on communities of soil fungi in Germany or Panama.
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%).
Sponges play a key role in Antarctic marine benthic community structure and dynamics and are often a dominant component of many Southern Ocean benthic communities. Understanding the drivers of sponge distribution in Antarctica enables us to understand many of general benthic biodiversity patterns in the region. The sponges of the Antarctic and neighbouring oceanographic regions were assessed for species richness and biogeographic patterns using over 8,800 distribution records. Species-rich regions include the Antarctic Peninsula, South Shetland Islands, South Georgia, Eastern Weddell Sea, Kerguelen Plateau, Falkland Islands and north New Zealand. Sampling intensity varied greatly within the study area, with sampling hotspots found at the Antarctic Peninsula, South Georgia, north New Zealand and Tierra del Fuego, with limited sampling in the Bellingshausen and Amundsen seas in the Southern Ocean. In contrast to previous studies we found that eurybathy and circumpolar distributions are important but not dominant characteristics in Antarctic sponges. Overall Antarctic sponge species endemism is ~43%, with a higher level for the class Hexactinellida (68%). Endemism levels are lower than previous estimates, but still indicate the importance of the Polar Front in isolating the Southern Ocean fauna. Nineteen distinct sponge distribution patterns were found, ranging from regional endemics to cosmopolitan species. A single, distinct Antarctic demosponge fauna is found to encompass all areas within the Polar Front, and the sub-Antarctic regions of the Kerguelen Plateau and Macquarie Island. Biogeographical analyses indicate stronger faunal links between Antarctica and South America, with little evidence of links between Antarctica and South Africa, Southern Australia or New Zealand. We conclude that the biogeographic and species distribution patterns observed are largely driven by the Antarctic Circumpolar Current and the timing of past continent connectivity.
Reproductive isolation among locally adapted populations may arise when immigrants from foreign habitats are selected against via natural or (inter-)sexual selection (female mate choice). We asked whether also intrasexual selection through male-male competition could promote reproductive isolation among populations of poeciliid fishes that are locally adapted to extreme environmental conditions [i.e., darkness in caves and/or toxic hydrogen sulphide (H(2)S)]. We found strongly reduced aggressiveness in extremophile P. oecilia mexicana, and darkness was the best predictor for the evolutionary reduction of aggressiveness, especially when combined with presence of H(2)S. We demonstrate that reduced aggression directly translates into migrant males being inferior when paired with males from non-sulphidic surface habitats. By contrast, the phylogenetically old sulphur endemic P. sulphuraria from another sulphide spring area showed no overall reduced aggressiveness, possibly indicating evolved mechanisms to better cope with H(2)S.
Reporting on the first locality in Bocas del Toro province of extreme western Panama, we extend the known geographic distribution of the lizard Leposoma rugiceps (Cope, 1869) about 275 km westwards from the nearest locality in Panamá province. We provide photos of Panamanian specimens, comment on their morphology, and map the distribution of this binational endemism.
We report new localities for the lizard Anolis salvini Boulenger, 1885, along the Pacific slopes of the Cordillera Central in Chiriquí province and the Comarca Ngöbe-Buglé of western Panama. These records extend the known geographic distribution of this species about 70 km eastwards. They also extend the known vertical distribution approximately 70 m uphill. Additionally, we provide the first record for the Caribbean slopes, an updated distribution map, photos of specimens from different localities, an analysis of a distress call, and comments on the morphology of this species.
We report on new localities for Anolis gruuo Köhler, Ponce, Sunyer and Batista, 2007 along the Serranía de Tabasará in the Comarca Ngöbe-Buglé and Veraguas province of western Panama. These records extend the known geographic distribution of this lizard about 80 km eastward, and the known vertical distribution approximately 40 m lower and 630 m higher. We provide photos of specimens from different localities and comment on their morphology. Only the easternmost populations of this Panamanian endemic live inside a protected area.
In China and other countries of East Asia, so-called Ling-zhi or Reishi mushrooms are used in traditional medicine since several centuries. Although the common practice to apply the originally European name ‘Ganoderma lucidum’ to these fungi has been questioned by several taxonomists, this is still generally done in recent publications and with commercially cultivated strains. In the present study, two commercially sold strains of ‘G. lucidum’, M9720 and M9724 from the company Mycelia bvba (Belgium), are compared for their fruiting body (basidiocarp) morphology combined with molecular phylogenetic analyses, and for their secondary metabolite profile employing an ultra-performance liquid chromatography–electrospray ionization mass spectrometry (UPLC–ESIMS) in combination with a high resolution electrospray ionization mass spectrometry (HR-ESI-MS). According to basidiocarp morphology, the strain M9720 was identified as G. lucidum s.str. whereas M9724 was determined as Ganoderma lingzhi. In molecular phylogenetic analyses, the M9720 ITS and beta-tubulin sequences grouped with sequences of G. lucidum s.str. from Europe whereas those from M9724 clustered with sequences of G. lingzhi from East Asia. We show that an ethanol extract of ground basidiocarps from G. lucidum (M9720) contains much less triterpenic acids than found in the extract of G. lingzhi (M9724). The high amount of triterpenic acids accounts for the bitter taste of the basidiocarps of G. lingzhi (M9724) and of its ethanol extract. Apparently, triterpenic acids of G. lucidum s.str. are analyzed here for the first time. These results demonstrate the importance of taxonomy for commercial use of fungi.
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.
Scholars have debated the taxonomic identity of isolated primate teeth from the Asian Pleistocene for over a century, which is complicated by morphological and metric convergence between orangutan (Pongo) and hominin (Homo) molariform teeth. Like Homo erectus, Pongo once showed considerable dental variation and a wide distribution throughout mainland and insular Asia. In order to clarify the utility of isolated dental remains to document the presence of hominins during Asian prehistory, we examined enamel thickness, enamel-dentine junction shape, and crown development in 33 molars from G. H. R. von Koenigswald's Chinese Apothecary collection (11 Sinanthropus officinalis [= Homo erectus], 21 “Hemanthropus peii,” and 1 “Hemanthropus peii” or Pongo) and 7 molars from Sangiran dome (either Homo erectus or Pongo). All fossil teeth were imaged with non-destructive conventional and/or synchrotron micro-computed tomography. These were compared to H. erectus teeth from Zhoukoudian, Sangiran and Trinil, and a large comparative sample of fossil Pongo, recent Pongo, and recent human teeth. We find that Homo and Pongo molars overlap substantially in relative enamel thickness; molar enamel-dentine junction shape is more distinctive, with Pongo showing relatively shorter dentine horns and wider crowns than Homo. Long-period line periodicity values are significantly greater in Pongo than in H. erectus, leading to longer crown formation times in the former. Most of the sample originally assigned to S. officinalis and H. erectus shows greater affinity to Pongo than to the hominin comparative sample. Moreover, enamel thickness, enamel-dentine junction shape, and a long-period line periodicity value in the “Hemanthropus peii” sample are indistinguishable from fossil Pongo. These results underscore the need for additional recovery and study of associated dentitions prior to erecting new taxa from isolated teeth.