Institutes
Refine
Document Type
- Article (27) (remove)
Language
- English (27)
Has Fulltext
- yes (27)
Is part of the Bibliography
- no (27)
Keywords
- Ecology (5)
- Biodiversity (3)
- Biogeography (2)
- Ecological modelling (2)
- Species distribution modelling (2)
- Arctic Ocean (1)
- Benthos (1)
- Biological anthropology (1)
- Biotechnology (1)
- Canis lupus (1)
- Canis lupus familiaris (1)
- Castor bean tick (1)
- Climate change (1)
- Climatic conditions (1)
- Coevolution (1)
- Community ecology (1)
- Conservation biology (1)
- Crustacea (1)
- Deep sea (1)
- Direct seeding (1)
- Diseases (1)
- Drug discovery (1)
- Earth sciences (1)
- Ecological niche modelling (1)
- Ecological requirements (1)
- Ecosystem Services (1)
- Environmental sciences (1)
- Evolutionary biology (1)
- Hematophagous arthropods (1)
- Host-parasite interaction (1)
- Hybridization (1)
- Infectious diseases (1)
- Intestinal bacterial community (1)
- Ixodes ricinus (1)
- Land cover (1)
- Life-Satisfaction (1)
- Limnology (1)
- Mawson Bank (1)
- Maxent (1)
- Metagenomic shotgun sequencing (1)
- Microbiology (1)
- Microscopy (1)
- Molecular biology (1)
- Montane forest (1)
- Museum samples (1)
- Myotis bechsteinii (1)
- NW Pacific (1)
- Nature Contributions to People (1)
- Nature Valuation (1)
- Nature conservation (1)
- Non-invasive sampling (1)
- Nyctalus leisleri (1)
- Pathogenesis (1)
- Pelagic (1)
- Phylogenetics (1)
- Plant sciences (1)
- Podocarpus National Park (1)
- Population dynamics (1)
- Psychology (1)
- Quercus frainetto (1)
- Quercus pubescens (1)
- Range expansion (1)
- Robert Koch Institute (1)
- Ross Sea (1)
- SNP genotyping (1)
- Secondary metabolites (1)
- Seed sowing experiment (1)
- Seedling establishment (1)
- Shallow water (1)
- Simuliidae (1)
- Social sciences (1)
- Species richness (1)
- Subjective Well-Being (1)
- Tick-borne diseases (1)
- Triatominae (1)
- Tropical forest restoration (1)
- Trypanosoma cruzi (1)
- Trypanosoma rangeli (1)
- Vector-host-interaction (1)
- Viral infection (1)
- Weather conditions (1)
- animal movement (1)
- arid climate (1)
- assembly gaps (1)
- assisted migration (1)
- automated radiotelemetry system (1)
- barrier (1)
- bats (1)
- behaviour (1)
- benchmarking (1)
- benthic fauna (1)
- biodiversity protection (1)
- birds (1)
- chlorophyll fluorescence (1)
- community composition (1)
- conservation (1)
- conservation funding (1)
- conservation planning (1)
- decision making (1)
- deep sea (1)
- depth (1)
- distribution (1)
- diurnal variation (1)
- fence (1)
- gas exchange (1)
- generalised additive models (1)
- genome assembly (1)
- genomic diversity (1)
- global change (1)
- inbreeding (1)
- long sequencing reads (1)
- long-term protection (1)
- machine learning (1)
- memory (1)
- migration (1)
- morphology (1)
- navigation (1)
- nomadism (1)
- northern giraffe (1)
- population genomics (1)
- population structure (1)
- post-2020 biodiversity targets (1)
- random forest (1)
- runs of homozygosity (1)
- search (1)
- shallow water (1)
- silicate (1)
- small animals (1)
- stairway plot (1)
- strategic site selection (1)
- tRackIT (1)
- ungulate (1)
Institute
- Senckenbergische Naturforschende Gesellschaft (27) (remove)
Background: Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples.
Results: Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations.
Conclusions: We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the third-generation backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales.
Combinatorial CRISPR-Cas screens have advanced the mapping of genetic interactions, but their experimental scale limits the number of targetable gene combinations. Here, we describe 3Cs multiplexing, a rapid and scalable method to generate highly diverse and uniformly distributed combinatorial CRISPR libraries. We demonstrate that the library distribution skew is the critical determinant of its required screening coverage. By circumventing iterative cloning of PCR-amplified oligonucleotides, 3Cs multiplexing facilitates the generation of combinatorial CRISPR libraries with low distribution skews. We show that combinatorial 3Cs libraries can be screened with minimal coverages, reducing associated efforts and costs at least 10-fold. We apply a 3Cs multiplexing library targeting 12,736 autophagy gene combinations with 247,032 paired gRNAs in viability and reporter-based enrichment screens. In the viability screen, we identify, among others, the synthetic lethal WDR45B-PIK3R4 and the proliferation-enhancing ATG7-KEAP1 genetic interactions. In the reporter-based screen, we identify over 1,570 essential genetic interactions for autophagy flux, including interactions among paralogous genes, namely ATG2A-ATG2B, GABARAP-MAP1LC3B and GABARAP-GABARAPL2. However, we only observe few genetic interactions within paralogous gene families of more than two members, indicating functional compensation between them. This work establishes 3Cs multiplexing as a platform for genetic interaction screens at scale.
Size and shape variation of molar crowns in primates plays an important role in understanding how species adapted to their environment. Gorillas are commonly considered to be folivorous primates because they possess sharp cusped molars which are adapted to process fibrous leafy foods. However, the proportion of fruit in their diet can vary significantly depending on their habitats. While tooth morphology can tell us what a tooth is capable of processing, tooth wear can help us to understand how teeth have been used during mastication. The objective of this study is to explore if differences in diet at the subspecies level can be detected by the analysis of molar macrowear. We analysed a large sample of second lower molars of Grauer’s, mountain and western lowland gorilla by combining the Occlusal Fingerprint Analysis method with other dental measurements. We found that Grauer’s and western lowland gorillas are characterised by a macrowear pattern indicating a larger intake of fruit in their diet, while mountain gorilla’s macrowear is associated with the consumption of more folivorous foods. We also found that the consumption of herbaceous foods is generally associated with an increase in dentine and enamel wear, confirming the results of previous studies.
Background: Long sequencing reads allow increasing contiguity and completeness of fragmented, short-read–based genome assemblies by closing assembly gaps, ideally at high accuracy. While several gap-closing methods have been developed, these methods often close an assembly gap with sequence that does not accurately represent the true sequence.
Findings: Here, we present DENTIST, a sensitive, highly accurate, and automated pipeline method to close gaps in short-read assemblies with long error-prone reads. DENTIST comprehensively determines repetitive assembly regions to identify reliable and unambiguous alignments of long reads to the correct loci, integrates a consensus sequence computation step to obtain a high base accuracy for the inserted sequence, and validates the accuracy of closed gaps. Unlike previous benchmarks, we generated test assemblies that have gaps at the exact positions where real short-read assemblies have gaps. Generating such realistic benchmarks for Drosophila (134 Mb genome), Arabidopsis (119 Mb), hummingbird (1 Gb), and human (3 Gb) and using simulated or real PacBio continuous long reads, we show that DENTIST consistently achieves a substantially higher accuracy compared to previous methods, while having a similar sensitivity.
Conclusion: DENTIST provides an accurate approach to improve the contiguity and completeness of fragmented assemblies with long reads. DENTIST's source code including a Snakemake workflow, conda package, and Docker container is available at https://github.com/a-ludi/dentist. All test assemblies as a resource for future benchmarking are at https://bds.mpi-cbg.de/hillerlab/DENTIST/.
In the framework of the PNRA (Italian National Antarctic Research Program) project CARBONANT focusing on biogenic carbonates and held in January–February 2002, several Ross Sea banks were sampled to obtain samples of biogenic carbonates. In the Mawson Bank, species belonging to the isopod genus Chaetarcturus Brandt, 1990 were recorded, including a specimen that did not match any described species. In this paper we describe Chaetarcturus cervicornis sp. n., which is characterized by supraocular spines and two pairs of tubercle-like protrusions on the cephalothorax. The new species is very similar to C. bovinus (Brandt & Wägele, 1988) and C. adareanus (Hodgson, 1902), but has a clearly different spine pattern. The study of the species of the genus Chaetarcturus in the Ross Sea contributes to increase our knowledge on the diversity of the Antarcturidae in the Southern Ocean. Ross Sea banks seem to hold an interesting and not-well-known fauna, deserving attention in future research.
Oaks may contribute to the stabilization of European forests under climate change. We utilized two common gardens established in contrasting growth regimes, in Greece (Olympiada) and Germany (Schwanheim), to compare the diurnal photosynthetic performance of a Greek and an Italian provenance of two Mediterranean oaks (Quercus pubescens and Q. frainetto) during the 2019 growing season. Although the higher radiation in the southern common garden led to a strong midday depression of chlorophyll a fluorescence parameters (maximum quantum efficiency of PSII, performance index on absorption basis), comparable light-saturated net photosynthetic rates were achieved in both study areas. Moreover, both species and provenances exhibited analogous responses. Q. pubescens had enhanced chlorophyll a fluorescence traits but similar photosynthetic rates compared to Q. frainetto, whereas the provenances did not differ. These findings indicate the high photosynthetic efficiency of both oaks under the current climate in Central Europe and their suitability for assisted migration schemes.
The Culex pipiens complex encompasses five species and subspecies of the genus Culex. Over time, a multitude of morphologically indistinguishable species has been assigned to this complex with several species being classified as important vectors for different diseases. Some species of this complex hibernate in subterranean habitats, and it has been proven that viruses can survive this phase of hibernation. However, studies focusing on the environmental requirements, ecology and spatial and temporal distribution patterns of mosquitos in underground habitats are sparse. Here, we investigate the main environmental factors and dependencies of Culex, considering the number of individuals and survival probabilities in underground habitats during the winter months. Methods. Since the State of Hesse, Germany harbors about 3500 to 4000 subterranean shelters ample availability of subterranean habitats there provides a good opportunity to conduct detailed investigations of the Culex pipiens complex. In this study, we identified a sample of 727 specimens of overwintering females within the Culex pipiens complex from 52 different underground sites collected over a period of 23 years using qPCR. A complete data set of samplings of hibernating mosquitos from 698 subterranean habitats in Central Germany over the same period was available to study the spatial and temporal patterns and the effect of temperature and precipitation conditions on these hibernating populations using a generalized linear model (GLM). Results. Our qPCR-results show, similar to aboveground studies of mosquitos, that Culex pipiens pipiens and Culex torrentium occur sympatrically. On the other hand, Culex pipiens molestus occurred very rarely. The GLM revealed no shifts in species composition over time, but different preferences for subterranean hibernacula, chemical effects on overwintering populations as well as effects of annual and seasonal mean temperature and precipitation during the active phase from March to November. Cx. p. pipiens and Cx. torrentium are the most common species within Hessian caves and other underground habitats during winter. They co-occur with different frequency without any patterns in species composition. Weather conditions influence the number of overwintering mosquitos during the activity phase. Depending on cave parameters, the number of mosquitos decreases during the winter months.