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539 results for “disentangling”
Disentangling the roles of plant functional diversity and plaint traits in regulating plant nitrogen accumulation and denitrification in freshwaters
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Data from: Disentangling the Pelomedusa complex using type specimens and historical DNA (Testudines: Pelomedusidae)
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Data from: Disentangling the role of phenotypic plasticity and genetic divergence in contemporary ecotype formation during a biological invasion
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Data from: Landscape does matter: disentangling founder effects from natural and human-aided post-introduction dispersal during an ongoing biological invasion
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Disentangling the effects of biomass and productivity in plant competition
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Defaunated and invaded insular tropical rainforests will not recover alone: recruitment limitation factors disentangled by hierarchical models of spontaneous and assisted regeneration
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Data from: Disentangling drivers of the abundance of coral reef fishes in the Western Indian Ocean
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Data from: Disentangling ecologically equivalent from neutral species: the mechanisms of population regulation matter
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Data from: Disentangling the effects of precipitation amount and frequency on the performance of 14 grassland species
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Data from: Reconstructing hyperdiverse food webs: gut content metabarcoding as a tool to disentangle trophic interactions on coral reefs
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Stresses affect inbreeding depression in complex ways: Disentangling stress-specific genetic effects from effects of initial size in plants
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Disentangling the effects of male age and mating history: contrasting effects of mating history on pre-copulatory mating behaviour and paternity success
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Data from: Disentangling the spatial and temporal causes of decline in a bird population
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Data from: DNA metabarcoding as a tool for disentangling food webs in agroecosystems
<p>Better knowledge of food webs and related ecological processes is fundamental to understanding the functional role of biodiversity in ecosystems. This is particularly true for pest regulation by natural enemies in agroecosystems. However, it is generally difficult to decipher the impact of predators as they often leave no direct evidence of their activity. Metabarcoding via high throughput sequencing (HTS) offers new opportunities for unraveling trophic linkages between generalist predators and their prey, and ultimately identifying key ecological drivers of natural pest regulation. Here, this approach proved effective in deciphering the diet composition of key predatory arthropods (nine species of spiders, carabid beetles, ants, etc. – 27 prey taxa), insectivorous birds (one species, <em>Ploceus cucullatus</em>- 13 prey taxa) and bats (one species, <em>Taphozous mauritianus</em> – 103 prey taxa) sampled in a millet-based agroecosystem in Senegal. Such information enabled to inform the diet breadth or preference of predators (e.g., mainly moths for bats), to design a qualitative trophic network and to identify patterns of intraguild predation across arthropod predators, insectivorous vertebrates and parasitoids. Appropriateness and limitations of the proposed molecular-based approach for assessing the diet of crop pest predators and trophic linkages are discussed.</p>
Data from: Disentangling the fundamental branching patterns of phylogenetic divergence to refine eco-phylogenetic analyses
Aim: Previous studies have shown that phylogenetic divergence (i.e. the average phylogenetic displacement between species in a community) is highly sensitive to the underlying branching patterns of phylogenies, suggesting that there is a need to integrate both facets of phylogenic information to obtain a better understanding of assemblage structure. Here, we formally conceptualize the three fundamental branching patterns that can drive phylogenetic divergence, and propose a method to identify their signature in the communities based on the MPD (mean pairwise distance) metric. Location: Global. Taxa: All. Methods: Our approach consists on the joint interpretation of two MPD-derived metrics that summarize the differential contribution of individual phylogenetic branches to the observed divergence, which serves to evaluate to what extent the later emerges from contrasting branching patterns. We conduct simulation analyses to compare our two metrics with eight classical descriptors of phylogenetic structure, and use multi-strata tropical plant communities along a gradient of land-use intensity (LUI) to further illustrate our method. Results: As expected, our metrics correlated to some extent with the classical descriptors of phylogenetic structure, although the relationships were complex and varied systematically with species richness and the specific combination of metric values considered. Consequently, the information provided by our two indexes was only partially captured by their most correlated classical descriptors. We detected differential signatures of the fundamental branching patterns in our real-world dataset, either across vegetation strata and also within strata along the LUI gradient, which provided greater insight into potential assembly mechanisms. Main conclusions: While the sole use of phylogenetic divergence may lead to spurious interpretations in eco-phylogenetic studies, our approach can help to obtain a better understanding of assemblage structure by systematically analyzing phylogenetic divergence in the light of its fundamental branching patterns.
Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations
The interactions between transposable elements (TEs) and their hosts constitute one of the most profound co-evolutionary processes found in nature. The population dynamics of TEs depends on factors specific to each TE families, such as the rate of transposition and insertional preference, the demographic history of the host and the genomic landscape. How these factors interact has yet to be investigated holistically. Here we are addressing this question in the green anole ( Anolis carolinensis ) whose genome contains an extraordinary diversity of TEs (including non-LTR retrotransposons, SINEs, LTR-retrotransposons and DNA transposons). We observe a positive correlation between recombination rate and TEs frequencies and densities for LINEs, SINEs and DNA transposons. For these elements, there was a clear impact of demography on TE frequency and abundance, with a loss of polymorphic elements and skewed frequency spectra in recently expanded populations. On the other hand, some LTR-retrotransposons displayed patterns consistent with a very recent phase of intense amplification. To determine how demography, genomic features and intrinsic properties of TEs interact we ran simulations using SLiM3. We determined that i) short TE insertions are not strongly counter-selected, but long ones are, ii) neutral demographic processes, linked selection and preferential insertion may explain positive correlations between average TE frequency and recombination, iii) TE insertions are unlikely to have been massively recruited in recent adaptation. We demonstrate that deterministic and stochastic processes have different effects on categories of TEs and that a combination of empirical analyses and simulations can disentangle these mechanisms.
Supplementary material 2 from: Laini A, Beermann AJ, Bolpagni R, Burgazzi G, Elbrecht V, Zizka VMA, Leese F, Viaroli P (2020) Exploring the potential of metabarcoding to disentangle macroinvertebrate community dynamics in intermittent streams. Metabarcoding and Metagenomics 4: e51433. https://doi.org/10.3897/mbmg.4.51433
Table S1, Figures S1–S5
Supplementary material 1 from: Laini A, Beermann AJ, Bolpagni R, Burgazzi G, Elbrecht V, Zizka VMA, Leese F, Viaroli P (2020) Exploring the potential of metabarcoding to disentangle macroinvertebrate community dynamics in intermittent streams. Metabarcoding and Metagenomics 4: e51433. https://doi.org/10.3897/mbmg.4.51433
Raw data
Disentangling interactions among mercury, immunity, and infection in a Neotropical bat community
<ol> <li>Contaminants such as mercury are pervasive and can have immunosuppressive effects on wildlife. Impaired immunity could be important for forecasting pathogen spillover risks, as many land-use changes that generate mercury contamination also bring wildlife into close contact with humans and domestic animals. However, the interactions among contaminants, immunity, and infection are difficult to study in natural systems, and empirical tests of possible directional relationships remain rare.</li> <li>We capitalized on extreme mercury variation in a diverse bat community in Belize to test association among contaminants, immunity, and infection. By comparing a previous dataset of bats sampled in 2014 with new data from 2017, representing a period of rapid agricultural land conversion, we first confirmed bat species more reliant on aquatic prey had higher fur mercury. Bats in the agricultural habitat also had higher mercury in recent years. We then tested covariation between mercury and cellular immunity and determined if such relationships mediated associations between mercury and common bacterial pathogens . As bat ecology can dictate exposure to mercury and pathogens, we also assessed species-specific patterns in mercury–infection relationships.</li> <li>Across the bat community, individuals with higher mercury had fewer neutrophils but not lymphocytes, suggesting stronger associations with innate immunity. However, the odds of infection for hemoplasmas and <i>Bartonella </i>spp. were generally lowest in bats with high mercury, and relationships between mercury and immunity did not mediate infection patterns. Mercury also showed species- and clade-specific relationships with infection, being associated with especially low odds for hemoplasmas in <i>Pteronotus mesoamericanus </i>and <i>Dermanura phaeotis</i>. For <i>Bartonella </i>spp., mercury was associated with particularly low odds in the genus <i>Pteronotus</i> but high odds in the Stenodermatinae.</li> <li> <i>Synthesis and application</i>: Lower general infection risk in bats with high mercury despite weaker innate defense suggests contaminant-driven loss of pathogen habitat (i.e., anemia) or vector mortality as possible causes. Greater attention to these potential pathways could help disentangle relationships among contaminants, immunity, and infection in anthropogenic habitats and help forecast disease risks. Our results also suggest contaminants may increase infection risk in some taxa but not others, emphasizing the importance of considering surveillance and management at different phylogenetic scales.</li> </ol>
Data from: Disentangling the costs of male harassment and the benefits of polyandry for females
Many studies quantify how polyandry affects female fitness by allowing females to mate with one or several males. But even if the number of matings is standardised, such studies conflate any costs of interacting with males with potential benefits of receiving sperm from multiple mates, obscuring the benefits of polyandry. We conducted a 2x2 factorial experiment on the mosquitofish, Gambusia holbrooki to quantify the independent effects of male harassment and polyandry. We artificially inseminated virgin females with sperm from either one or five males. Females were housed in the presence or absence of reproductively-ablated males who could harass, but not mate with them. Our design ensured that the number of males inseminating a female was independent of the level of male harassment and the number of matings she received. Females not housed with males were instead housed with immature females to maintain densities across treatments. Unexpectedly, females that experienced sexual harassment were more likely to give birth, had shorter gestation periods and gave birth to larger broods. Furthermore, polyandrous females were more likely than monandrous females to give birth, and their sons reached maturity faster than those of monandrous females. We found no detectable costs to females of male harassment when the direct costs of mating were absent and that, in the absence of mating costs, there are direct and indirect fitness benefits of being inseminated by multiple males. If the costs of the act of mating are small or absent, polyandry will benefit female G.holbrooki producing their first brood.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.