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Aim Temporal dynamics of biodiversity along tropical elevational gradients are unknown. We studied seasonal changes of Lepidoptera biodiversity along the only complete forest elevational gradient in the Afrotropics. We focused on shifts of species richness patterns, seasonal turnover of communities, and seasonal shifts of species’ elevational ranges, the latter often serving as an indicator of the global change effects on mountain ecosystems. Location Mount Cameroon, Cameroon. Taxon Butterflies and moths (Lepidoptera) Methods We quantitatively sampled nine groups of Lepidoptera by bait-trapping (16,800 trap-days) and light-catching (126 nights) at seven elevations evenly distributed along the elevational gradient from sea level (30 m asl) to timberline (2,200 m asl). Sampling was repeated in three seasons. Result Altogether, 42,936 specimens of 1,099 species were recorded. A mid-elevation peak of species richness was detected for all groups but Eupterotidae. This peak shifted seasonally for five groups, most of them ascending during the dry season. Seasonal shifts of species’ elevational ranges were mostly responsible for these diversity pattern shifts along elevation: we found general upward shifts in fruit-feeding butterflies, fruit-feeding moths and Lymantriinae from beginning to end of the dry season. Contrarily, Arctiinae shifted upwards during the wet season. The average seasonal shifts of elevational ranges often exceeded 100 metres and were even several times higher for numerous species. Main conclusion We report seasonal uphill and downhill shifts of several lepidopteran groups. The reported shifts can be driven by both delay in weather seasonality and shifts in resource availability, causing phenological delay of adult hatching and/or adult migrations. Such shifts may lead to misinterpretations of diversity patterns along elevation if seasonality is ignored. More importantly, considering the surprising extent of seasonal elevational shifts of species, we encourage taking account of such natural temporal dynamics while investigating the global climate change impact on communities of Lepidoptera in tropical mountains. The dataset was collected by two methodologies: 1/ bait-trapping and 2/ manual catching of target group at light. See Maicher et al. (2019) for details.

Bioluminescent beetles of the superfamily Elateroidea (fireflies, fire beetles, glow-worms) are the most speciose group of terrestrial light-producing animals. The evolution of bioluminescence in elateroids is associated with unusual morphological modifications, such as soft-bodiedness and neoteny, but the fragmentary nature of the fossil record discloses little about the origin of these adaptations. We report the discovery of a new bioluminescent elateroid beetle family from the mid-Cretaceous of northern Myanmar (ca. 99 Ma), Cretophengodidae fam. nov. Cretophengodes azari gen. et sp. nov. belongs to the bioluminescent lampyroid clade, and represents a transitional fossil linking the soft-bodied Phengodidae + Rhagophthalmidae clade and hard-bodied elateroids. The fossil male possesses a light organ on the abdomen which presumably served a defensive function, documenting a Cretaceous radiation of bioluminescent beetles coinciding with the diversification of major insectivore groups such as frogs and stem-group birds. The discovery adds a key branch to the elateroid tree of life and sheds light on the timing of the evolution of soft-bodiedness and historical biogeography of elateroid beetles. The Burmese amber specimen studied here originates from amber mines near the Noije Bum Hill (26°20' N, 96°36' E), Hukawng Valley, Kachin State, northern Myanmar. The specimen is deposited in the Nanjing Institute of Geology and Palaeontology (NIGP), Chinese Academy of Sciences, Nanjing, China. The amber piece was trimmed with a small table saw, ground with emery papers of different grain sizes, and finally polished with polishing powder. Photographs under incident light were taken with a Zeiss Discovery V20 stereo microscope. Widefield fluorescence images were captured with a Zeiss Axio Imager 2 light microscope combined with a fluorescence imaging system. Confocal images were obtained with a Zeiss LSM710 confocal laser scanning microscope. Images under incident light and widefield fluorescence were stacked in Helicon Focus 7.0.2 or Zerene Stacker 1.04. Confocal images were manually stacked in Adobe Photoshop CC. Images were further processed in Adobe Photoshop CC to enhance contrast. 

Predators attack conspicuous prey phenotypes that are present in the environment. Male display behaviour of conspicuous nuptial colouration becomes risky in the presence of a predator, and adult males face higher predation risk. High predation risk in one sex will lead to low survival and sex ratio bias in adult cohorts, unless the increased predation risk is compensated by higher escape rate. Here, we tested the hypothesis that sand lizards (Lacerta agilis) have sex-specific predation risk and escape rate. We expected the differences to manifest in changes in sex ratio with age, differences in frequency of tail autotomy, and in sex-specific survival rate. We developed a statistical model to estimate predation risk and escape rate, combining the observed sex ratio and frequency of tail autotomy with likelihood-based survival rate. Using a Bayesian framework, we estimated the model parameters. We projected the date of the tail autotomy events from growth rates derived from capture-recapture data measurements. We found statistically stable sex ratio in age groups, equal frequency of tail regenerates between sexes, and similar survival rate. Predation risk is similar between sexes, and escape rate increases survival by about 5%. We found low survival rate and a low number of tail autotomy events in females during months when sand lizards mate and lay eggs, indicating high predator pressure throughout reproduction. Our data show that gravid females fail to escape predation. The risks of reproduction season in an ectotherm are a convolution of morphological changes (conspicuous colouration in males, body allometry changes in gravid females), behaviour (nuptial displays), and environmental conditions which challenge lizard thermal performance. Performance of endotherm predators in cold spring months endangers gravid females more than displaying males in bright nuptial colouration.  Capture-recapture data of sand lizards (Lacerta agilis, Lacertidae, Reptilia) from Hustopeče, Czechia (48.93 N, 16.72 E). animal - identification of the animal; prefix indicates the latest possible year of hatching day - day of capture month - month of capture year - year of capture season - phase I started from the arousal from hibernation, and lasted until the first adult male started to lose nuptial colouration; phase II constituted the season after males started to lose nuptial colouration, and lasted until the beginning of hibernation sex - sex of the animal ventralia - number of scales in the second rows from the ventral medial line age - young animals were juveniles and subadults, the remaining animals were considered adult aged.month - approximate age of the animal in months regenerate - presence of tail regenerate predation.attempt - first record of tail regenerate or reduced tail length at recapture Lreg - tail regenerate length in mm; 0 - animal with intact tail, 0.01 - recent tail autotomy, no tail regenerate growth measurable tailL - tail length from cloaca to tail tip corrected for body length from rostrum to cloaca48.93 N, 16.72 E48.93 N, 16.72 E)

Rapid and reliable identification of insects is important in many contexts, from the detection of disease vectors and invasive species to the sorting of material from biodiversity inventories. Because of the shortage of adequate expertise, there has long been an interest in developing automated systems for this task. Previous attempts have been based on laborious and complex handcrafted extraction of image features, but in recent years it has been shown that sophisticated convolutional neural networks (CNNs) can learn to extract relevant features automatically, without human intervention. Unfortunately, reaching expert-level accuracy in CNN identifications requires substantial computational power and huge training datasets, which are often not available for taxonomic tasks. This can be addressed using feature transfer: a CNN that has been pretrained on a generic image classification task is exposed to the taxonomic images of interest, and information about its perception of those images is used in training a simpler, dedicated identification system. Here, we develop an effective method of CNN feature transfer, which achieves expert-level accuracy in taxonomic identification of insects with training sets of 100 images or less per category. Specifically, we extract rich representations of intermediate to high-level image features from the CNN architecture VGG16 pretrained on the ImageNet dataset. This information is fed into a linear support vector machine classifier, which is trained on the target problem. We tested the performance of our approach on two types of challenging taxonomic tasks: (1) identifying insects to higher groups when they are likely to belong to subgroups that have not been seen previously; and (2) identifying visually similar species that are difficult to separate even for experts. For the first task, our approach reaches > 92 % accuracy on one dataset (884 face images of 11 families of Diptera, all specimens representing unique species), and > 96 % accuracy on another (2936 dorsal habitus images of 14 families of Coleoptera, over 90 % of specimens belonging to unique species). For the second task, our approach outperforms a leading taxonomic expert on one dataset (339 images of three species of the Coleoptera genus Oxythyrea; 97 % accuracy), and both humans and traditional automated identification systems on another dataset (3845 images of nine species of Plecoptera larvae; 98.6 % accuracy). Reanalyzing several biological image identification tasks studied in the recent literature, we show that our approach is broadly applicable and provides significant improvements over previous methods, whether based on dedicated CNNs, CNN feature transfer, or more traditional techniques. Thus, our method, which is easy to apply, can be highly successful in developing automated taxonomic identification systems even when training datasets are small and computational budgets limited. valan2018_SUPPLEMENT.tarThis directory contains: * metadata to obtain images from the three novel datasets we designed for our study * notebooks with thorough evaluation of off-the-shelf approach for image classification based on a feature extraction with a single feed forward pass trough pretrained VGG16 * script to run on your own dataset with what we found to be optimal settings. You can also access it here https://github.com/valanm/off-the-shelf-insect-identificationSupplementary_Figure1Impact of concatenating globally max pooled (MAX) and globally average pooled (AVG) features on identification accuracy for datasets D1, D2, D3 and D4. We used input images of size 416x416 and features are extracted after 4th convolutional block (c4). Concatenation of MAX and AVG features resulted in accuracy somewhere between the global average pooling (performed the best in all cases) and global max pooling (performed the worst in all cases).valan2018_latex

Human-driven environmental changes can induce marked shifts in the functional structure of biological communities with possible repercussion on important ecosystem functions and services. At the same time it remains unclear to which extent these changes may differently affect various types of organisms. We investigated species richness and community functional structure of species assemblages at the landscape scale (1km2 plots) for two contrasting model taxa, i.e., plants (producers and sessile organisms) and birds (consumers and mobile organisms), along topography, climate, landscape heterogeneity, and land-use (agriculture and urbanization) gradients in a densely populated region of Switzerland. Our study revealed that agricultural and urban land uses drove marked shifts in the functional structure of biological communities compared to changes along climate and topography gradients, especially for plants, while for birds these changes were comparable. Agricultural and urban land uses enhanced divergence in traits related to resource use for birds (diet and nesting), growth forms, dispersal, and reproductive traits for plants, while it induced convergence in vegetative plant traits (plant height and leaf dry matter content). These results suggest that contrasting assembly patterns may arise within and across taxonomic groups along the same environmental gradients as result of distinct underlying processes and 'organism-specific' environmental perceptions. Our results further suggest a potential homogenization of biological communities, as well as low functional diversity and redundancy levels of bird assemblages in our human-dominated study region. This might potentially compromise the maintenance of key ecological processes under future environmental changes. SES for plant and bird functional traits based on 1000 randomizationsSES_Data.zip

Alignment - section Fumigati; concatenated data from benA, CaM, act and RPB2 loci, 76 taxaCombined dataset of benA, CaM, act and RPB2 sequences for 76 taxa belonging to section Fumigati. Aspergillus clavatus NRRL 1 (sect. Clavati) represents an outgroup. BenA: positions 1-534; CaM: positions 535-1231; act: positions 1232-1662; RPB2: positions 1663-2661.Fumigati benA caM actin RPB2 76 taxa.fasPhylogeny of Aspergillus sect. Fumigati inferred from combined data: benA, CaM, act and RPB2Phylogenetic relationships of the section Fumigati members inferred from Bayesian analysis of the combined, 4-gene data set of β-tubulin (benA), calmodulin (CaM), actin (act) and RNA polymerase II second largest subunit (RPB2) genes. Bayesian posterior probability (PP) and Maximum likelihood bootstrap support (BS) are appended to nodes; only PP ≥ 95% and BS ≥ 70% and are shown; lower supports are indicated with a hyphen, whereas asterisks indicate full support (1.00 PP or 100% BS); ex-type strains are designated by a superscript T; species names in quotes are considered synonyms. The tree is rooted with Aspergillus clavatus NRRL 1. The reproductive mode of each species is designated by icons before the species name (see legend).Aspergillus section Fumigati phylogeny.pdfCombined alignment: benA, CaM, act and RPB2 loci; Aspergillus viridinutans complexCombined dataset of benA, CaM, act and RPB2 sequences for 110 taxa belongmembers of Aspergillus viridinutans complex. Aspergillus lentulus NRRL 35552 represents an outgroup. BenA: positions 1-475; CaM: positions 476-1172; act: positions 1173-1516; RPB2: positions 1517-2483.BenA CaM actin RPB2 viridinutans complex Dryad.fasPhylogeny of Aspergillus viridinutans species complex phylogeny inferred from combined data: BenA, CaM, act, RPB2Phylogenetic relationships of the section Aspergillus viridinutans species complex members inferred from Bayesian analysis of the combined, 4-gene data set of β-tubulin (benA), calmodulin (CaM), actin (act) and RNA polymerase II second largest subunit (RPB2) genes. Bayesian posterior probability (PP) and Maximum likelihood bootstrap support (BS) are appended to nodes; only PP ≥ 90% and BS ≥ 70% and are shown; lower supports are indicated with a hyphen, whereas asterisks indicate full support (1.00 PP or 100% BS); ex-type strains are designated by a superscript T; species names in quotes are considered synonyms. The tree is rooted with Aspergillus lentulus NRRL 35552. The geographic origin, and reproductive mode with MAT idiomorph (if known) is designated by icons before the isolate number while substrate of origin is designated by icons after isolate number (see legend).Aspergillus viridinutans complex phylogeny.pdfAlignment - Aspergillus viridinutans complex, A. felis clade: concatenated data of act, benA, CaM, mcm7, RPB2 and tsr1Combined dataset of act, benA, CaM, mcm7, RPB2 and tsr1 sequences for 33 taxa belonging to Aspergillus viridinutans complex - A. felis clade only. act: positions 1-329; benA: positions 330-803; CaM: positions 804-1484; mcm7: positions 1485-2107; RPB2: positions 2108-3074; tsr1: positions 3075-3835.actin benA CaM mcm7 RPB2 tsr1 Dryad.fasSpecies delimitation in Aspergillus felis clade based on six genetic lociSchematic representation of results of species delimitation methods in Aspergillus felis clade based on six genetic loci. The results of multilocus method (STACEY) are compared to results of single-locus methods (mPTP, bGMYC, GMYC). The results of STACEY are shown as tree branches with different colours, while the results of single-locus methods are depicted with coloured bars highlighting congruence across methods. The displayed tree is derived from IQtree analysis based on a concatenated dataset and is used solely for the comprehensive presentation of the results from different methods. The species validation analysis results (BP&P) are appended to nodes and shown in gray bordered boxes; the values represent posterior probabilities calculated in three scenarios having different prior distributions of parameters θ (ancestral population size) and τ0 (root age). The top value represents the results of analysis with large ancestral population sizes and deep divergence: θ ~ G (1, 10) and τ0 ~ G (1, 10), the middle value ); large ancestral populations sizes and shallow divergences among species: θ ~ G (1, 10) and τ0 ~ G (2, 2000) and the bottom value small ancestral population sizes and shallow divergences among species: θ ~ G (2, 2000) and τ0 ~ G (2, 2000). Although Aspergillus fumigatus is the major agent of invasive aspergillosis, an increasing number of infections are caused by its cryptic species, especially A. lentulus and the A. viridinutans species complex (AVSC). Their identification is clinically relevant because of antifungal drug resistance and refractory infections. Species boundaries in the AVSC are unresolved since most species have uniform morphology and produce interspecific hybrids in vitro. Clinical and environmental strains from six continents (n = 110) were characterized by DNA se- quencing of four to six loci. Biological compatibilities were tested within and between major phylogenetic clades, and ascospore morphology was characterised. Species delimitation methods based on the multispecies coalescent model (MSC) supported recognition of ten species including one new species. Four species are confirmed op- portunistic pathogens; A. udagawae followed by A. felis and A. pseudoviridinutans are known from opportunistic human infections, while A. felis followed by A. udagawae and A. wyomingensis are agents of feline sino-orbital aspergillosis. Recently described human-pathogenic species A. parafelis and A. pseudofelis are synonymized with A. felis and an epitype is designated for A. udagawae. Intraspecific mating assay showed that only minor part of the heterothallic species can readily generate sexual morph in vitro. Interspecific mating assay revealed that five different species combinations were biologically compatible. Hybrid ascospores had atypical surface ornamentation and significantly different dimensions compared to parental species. This suggests that species limits in the AVSC are maintained by both pre- and post-zygotic barriers and these species display a great potential for rapid adapta- tion and modulation of its virulence. This study highlights that a sufficient number of strains representing genetic diversity within a species is essential for meaningful species boundaries delimitation in cryptic species complexes. MSC-based delimitation methods are robust and suitable tools for evaluation of boundaries between these species.

The database compiled of investment costs of houses completed by suppliers. Only unified houses are considered (standardised for repetition). Houses based on individual design are not included in the database.The database was compiled in the period from February to April 2020 and in the end, bids from 38 suppliers were considered. Only complete bids, including information. Also, the price of the project was considered to keep comparable bids, due to more than 48.6% of bids containing cost for the projects as well. All bids were available on the websites of house suppliers and included completed houses. The bids were not affected by location, and contained transportation and groundwork costs. Easy available terrain and good soil extractability was assumed for all houses, thus conditions of all bids can be considered comparable.

Background: Appetite and gastrointestinal hormones (GIHs) participate in energy homeostasis, feeding behavior and regulation of body weight. We demonstrated previously the superior effect of a hypocaloric diet regimen with lower meal frequency (B2) on body weight, hepatic fat content, insulin sensitivity and feelings of hunger compared to the same diet divided into six smaller meals a day (A6).Studies with isoenergetic diet regimens indicate that lower meal frequency should also have an effect on fasting and postprandial responses of GIHs.The aim of this secondary analysis was to explore the effect of two hypocaloric diet regimens on fasting levels of appetite and GIHs and on their postprandial responses after a standard meal. It was hypothesized that lower meal frequency in a reduced-energy regimen leading to greater body weight reduction and reduced hunger would be associated with decreased plasma concentrations of GIHs: gastric inhibitory peptide (GIP), glucagon-like peptide-1(GLP-1), peptide YY(PYY), pancreatic polypeptide (PP) and leptin and increased plasma concentration of ghrelin. The postprandial response of satiety hormones (GLP-1, PYY and PP) and postprandial suppression of ghrelin will be improved. Methods: In a randomized crossover study, 54 patients suffering from type 2 diabetes (T2D) underwent both regimens.The concentrations of GLP-1, GIP, PP, PYY, amylin, leptin and ghrelin were determined using multiplex immunoanalyses. Results: Fasting leptin and GIP decreased in response to both regimens with no difference between the treatments (p=0.37 and p=0.83, respectively). Fasting ghrelin decreased in A6 and increased in B2 (with difference between regimens p=0.023). Fasting PP increased in B2with no significant difference between regimens (p=0.17). Neither GLP-1 nor PYY did change in either regimen. The decrease in body weight correlated negatively with changes in fasting ghrelin (r=-0.4, p<0.043) and the postprandial reduction of ghrelin correlated positively with its fasting level (r=0.9, p<0.001). The postprandial responses of GIHs and appetite hormones were similar after both diet regimens. Conclusions: Both hypocaloric diet regimens reduced fasting leptin and GIP and postprandial response of GIP comparably. The postprandial responses of GIHs and appetite hormones were similar after both diet regimens. Eating only breakfast and lunch increased fasting plasma ghrelin more than the same caloric restriction split into six meals. The changes in fasting ghrelin correlated negatively with the decrease in body weight. These results suggest that for type 2 diabetic patients on a hypocaloric diet, eating larger breakfast and lunch may be more efficient than six smaller meals during the day. DatasetDATASET.xlsx

Environmentally induced epigenetic variation has been recently recognized as a possible mechanism allowing plants to rapidly adapt to novel conditions. Despite increasing evidence on the topic, little is known on how epigenetic variation affects responses of natural populations to changing climate. We studied the effects of experimental demethylation (DNA methylation is an important mediator of heritable control of gene expression) on performance of a clonal grass, Festuca rubra, coming from localities with contrasting temperature and moisture regimes. We compared performance of demethylated and control plants from different populations under two contrasting climatic scenarios and explored whether the response to demethylation depended on genetic relatedness of the plants. Demethylation significantly affected plant performance. Its effects interacted with population of origin and partly with conditions of cultivation. The effects of demethylation also varied between distinct genotypes with more closely related genotypes showing more similar response to demethylation. For belowground biomass, demethylated plants showed signs of adaptation to drought that were not apparent in plants that were naturally methylated. The results suggest that DNA methylation may modify the response of this species to moisture. DNA methylation may thus affect the ability of clonal plants to adapt to novel climatic conditions. Whether this variation in DNA methylation may also occur under natural conditions, however, remains to be explored. Despite the significant interactions between population of origin and demethylation, our data do not provide clear evidence that DNA methylation enabled adaptation to different environments. In fact, we obtained stronger evidence of local adaptation in demethylated than in naturally-methylated plants. As changes in DNA methylation may be quite dynamic, it is thus possible that epigenetic variation can mask plant adaptations to conditions of their origin due to pre-cultivation of the plants under standardized conditions. This possibility should be considered in future experiments exploring plant adaptations. Epig-dryadData on plant performance in the experiment