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The most basic behavioural states of animals can be described as active or passive. However, while high-resolution observations of activity patterns can provide insights into the ecology of animal species, few methods are able to measure the activity of individuals of small taxa in their natural environment. We present a novel approach in which the automated VHF radio-tracking of small vertebrates fitted with lightweight transmitters (< 0.2 g) is used to distinguish between active and passive behavioural states.
A dataset containing > 3 million VHF signals was used to train and test a random forest model in the assignment of either active or passive behaviour to individuals from two forest-dwelling bat species (Myotis bechsteinii (n = 50) and Nyctalus leisleri (n = 20)). The applicability of the model to other taxonomic groups was demonstrated by recording and classifying the behaviour of a tagged bird and by simulating the effect of different types of vertebrate activity with the help of humans carrying transmitters. The random forest model successfully classified the activity states of bats as well as those of birds and humans, although the latter were not included in model training (F-score 0.96–0.98).
The utility of the model in tackling ecologically relevant questions was demonstrated in a study of the differences in the daily activity patterns of the two bat species. The analysis showed a pronounced bimodal activity distribution of N. leisleri over the course of the night while the night-time activity of M. bechsteinii was relatively constant. These results show that significant differences in the timing of species activity according to ecological preferences or seasonality can be distinguished using our method.
Our approach enables the assignment of VHF signal patterns to fundamental behavioural states with high precision and is applicable to different terrestrial and flying vertebrates. To encourage the broader use of our radio-tracking method, we provide the trained random forest models together with an R-package that includes all necessary data-processing functionalities. In combination with state-of-the-art open-source automated radio-tracking, this toolset can be used by the scientific community to investigate the activity patterns of small vertebrates with high temporal resolution, even in dense vegetation.
Tree water relations of mature oaks in southwest Germany under extreme drought stress in summer 2018
(2021)
Mature oak stands of different tree height at four sandy valley river sites (Quercus robur) and one south-exposed schist slope (Qu. petraea) in the middle Rhine and lower Main valley were studied from early summer 2017 (normal wet year) until the end of 2018 (extremely hot and dry year). Tree water relations (ΨPD, RWC, sap flow rates) were monitored together with soil water relations, LAI and leaf chl content. In two sandy sites with presumed continuous capillary water access from the groundwater aquifer, sap flow rates of the large trees (30 m) and estimated canopy conductance decreased to about 50% of the maximum value in the course of summer 2018, but recovered in autumn. At two other sites, with smaller trees (14–24 m) and presumed interrupted capillary water access during mid-summer 2018, sap flow rates and canopy conductance broke down completely and trees shed a large proportion of leaves in summer. In one of these sites, ΨPD decreased (reversibly) to -4 MPa, one of the lowest values reported in the literature for central Europe, and tree damage resulted not only in extreme leaf shedding, but also in susceptibility to uprooting (in 2 out of 5 measured trees) by thunderstorm gusts in autumn 2018. At the schist slope site, where oaks reached the lowest height and stand density of all sites, sap flow rates remained similar to the values found at the presumed capillary-water supplied sandy sites, indicating access to rock fissure water even at the peak of the drought period. Our findings corroborate the prediction from vegetation modelling that several Qu. robur stands in the Rhine-Main valleys will be prone to severe forest dieback in the forthcoming decades.
In search for practical silvicultural management tools to identify alternative tree species for predicted Central European climate conditions, a cross-species survey with five evergreen, semi-evergreen, and deciduous Quercus taxa with contrasting morphological leaf traits was performed. Fast chlorophyll fluorescence induction of PSII and relative leaf chlorophyll contents were performed to assess the overall plant vitality at any point in time during two complete vegetation periods in consecutive years (2012 and 2013). Maximum photochemical efficiency of PSII and the performance index on absorption base showed a very conservative relationship to each other and a similar intra-annual progress in all deciduous species, but with a different speed of increase and decrease during leaf development and senescence and thus a different length of vegetation period. The intra-annual variability of OJIP and chlorophyll content parameters is considered with respect to the practicability of measurements in the field for management purposes.
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.
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.
Phylogenetic analyses of nuclear and mitochondrial genomes indicate that polar bears captured the brown bear mitochondrial genome 160,000 years ago, leading to an extinction of the original polar bear mitochondrial genome. However, mitochondrial DNA occasionally integrates into the nuclear genome, forming pseudogenes called numts (nuclear mitochondrial integrations). Screening the polar bear genome identified only 13 numts. Genomic analyses of two additional ursine bears and giant panda indicate that all except one of the discovered numts entered the bear lineage at least 14 million years ago. However, short read genome assemblies might lead to an under-representation of numts or other repetitive sequences. Our findings suggest low integration rates of numts in bears and a loss of the original polar bear mitochondrial genome.
The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome-wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
Motivation Expert curation to differentiate between functionally diverged homologs and those that may still share a similar function routinely relies on the visual interpretation of domain architecture changes. However, the size of contemporary data sets integrating homologs from hundreds to thousands of species calls for alternate solutions. Scoring schemes to evaluate domain architecture similarities can help to automatize this procedure, in principle. But existing schemes are often too simplistic in the similarity assessment, many require an a-priori resolution of overlapping domain annotations, and those that allow overlaps to extend the set of annotations sources cannot account for redundant annotations. As a consequence, the gap between the automated similarity scoring and the similarity assessment based on visual architecture comparison is still too wide to make the integration of both approaches meaningful.
Results Here, we present FAS, a scoring system for the comparison of multi-layered feature architectures integrating information from a broad spectrum of annotation sources. Feature architectures are represented as directed acyclic graphs, and redundancies are resolved in the course of comparison using a score maximization algorithm. A benchmark using more than 10,000 human-yeast ortholog pairs reveals that FAS consistently outperforms existing scoring schemes. Using three examples, we show how automated architecture similarity assessments can be routinely applied in the benchmarking of orthology assignment software, in the identification of functionally diverged orthologs, and in the identification of entries in protein collections that most likely stem from a faulty gene prediction.
Mosquito species belonging to the genus Aedes have attracted the interest of scientists and public health officers because of their capacity to transmit viruses that affect humans. Some of these species were brought outside their native range by means of trade and tourism and then colonised new regions thanks to a unique combination of eco-physiological traits. Considering mosquito physiological and behavioural traits to understand and predict their population dynamics is thus a crucial step in developing strategies to mitigate the local densities of invasive Aedes populations. Here, we synthesised the life cycle of four invasive Aedes species (Ae. aegypti, Ae. albopictus, Ae. japonicus and Ae. koreicus) in a single multi-scale stochastic modelling framework which we coded in the R package dynamAedes. We designed a stage-based and time-discrete stochastic model driven by temperature, photo-period and inter-specific larval competition that can be applied to three different spatial scales: punctual, local and regional. These spatial scales consider different degrees of spatial complexity and data availability by accounting for both active and passive dispersal of mosquito species as well as for the heterogeneity of the input temperature data. Our overarching aim was to provide a flexible, open-source and user-friendly tool rooted in the most updated knowledge on the species’ biology which could be applied to the management of invasive Aedes populations as well as to more theoretical ecological inquiries.
Mosquito species belonging to the genus Aedes have attracted the interest of scientists and public health officers for their invasive species traits and efficient capacity of transmitting viruses affecting humans. Some of these species were brought outside their native range by human activities such as trade and tourism, and colonised new regions thanks to a unique combination of eco-physiological traits.
Considering mosquito physiological and behavioural traits to understand and predict the spatial and temporal population dynamics is thus a crucial step to develop strategies to mitigate the local densities of invasive Aedes populations.
Here, we synthesised the life cycle of four invasive Aedes species (Ae. aegypti, Ae. albopictus, Ae. japonicus and Ae. koreicus) in a single multi-scale stochastic modelling framework which we coded in the R package dynamAedes. We designed a stage-based and time-discrete stochastic model driven by temperature, photo-period and inter-specific larval competition that can be applied to three different spatial scales: punctual, local and regional. These spatial scales consider different degrees of spatial complexity and data availability, by accounting for both active and passive dispersal of mosquito species as well as for the heterogeneity of the input temperature data.
Our overarching aim was to provide a flexible, open-source and user-friendly tool rooted in the most updated knowledge on species biology which could be applied to the management of invasive Aedes populations as well as for more theoretical ecological inquiries.