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580 results for “pattern analysis”
Figure 12 from: Shimizu S, Broad GR, Maeto K (2020) Integrative taxonomy and analysis of species richness patterns of nocturnal Darwin wasps of the genus Enicospilus Stephens (Hymenoptera, Ichneumonidae, Ophioninae) in Japan. ZooKeys 990: 1-144. https://doi.org/10.3897/zookeys.990.55542
Figure 12 Enicospilus capensis (Thunberg, 1824) (HT ♀ of E. yanagiharai (Sonan, 1940)) A habitus B head, frontal view C head, dorsal view D head, lateral view E mesosoma, lateral view F central part of fore wing.
Figure 11 from: Shimizu S, Broad GR, Maeto K (2020) Integrative taxonomy and analysis of species richness patterns of nocturnal Darwin wasps of the genus Enicospilus Stephens (Hymenoptera, Ichneumonidae, Ophioninae) in Japan. ZooKeys 990: 1-144. https://doi.org/10.3897/zookeys.990.55542
Figure 11 Enicospilus acutus Shimizu, sp. nov. ♀ from Japan (PT) A habitus B head, frontal view C head, dorsal view D head, lateral view E mesosoma, lateral view F central part of fore wing.
Figure 1 from: Shimizu S, Broad GR, Maeto K (2020) Integrative taxonomy and analysis of species richness patterns of nocturnal Darwin wasps of the genus Enicospilus Stephens (Hymenoptera, Ichneumonidae, Ophioninae) in Japan. ZooKeys 990: 1-144. https://doi.org/10.3897/zookeys.990.55542
Figure 1 Field collection A High Intensity Discharge (HID) light trap equipment used by the first author B nocturnal insects attracted to the HID light on a white sheet.
Figure 10 from: Shimizu S, Broad GR, Maeto K (2020) Integrative taxonomy and analysis of species richness patterns of nocturnal Darwin wasps of the genus Enicospilus Stephens (Hymenoptera, Ichneumonidae, Ophioninae) in Japan. ZooKeys 990: 1-144. https://doi.org/10.3897/zookeys.990.55542
Figure 10 Enicospilus aciculatus (Taschenberg, 1875) ♀ from Japan A habitus B head, frontal view C head, dorsal view D head, lateral view E mesosoma, lateral view F central part of fore wing.
Figure 40 from: Shimizu S, Broad GR, Maeto K (2020) Integrative taxonomy and analysis of species richness patterns of nocturnal Darwin wasps of the genus Enicospilus Stephens (Hymenoptera, Ichneumonidae, Ophioninae) in Japan. ZooKeys 990: 1-144. https://doi.org/10.3897/zookeys.990.55542
Figure 40 Enicospilus riukiuensis (Matsumura & Uchida, 1926) ♀ from Japan A habitus B head, frontal view C head, dorsal view D head, lateral view E mesosoma, lateral view F central part of fore wing.
Figure 37 from: Shimizu S, Broad GR, Maeto K (2020) Integrative taxonomy and analysis of species richness patterns of nocturnal Darwin wasps of the genus Enicospilus Stephens (Hymenoptera, Ichneumonidae, Ophioninae) in Japan. ZooKeys 990: 1-144. https://doi.org/10.3897/zookeys.990.55542
Figure 37 Enicospilus puncticulatus Tang, 1990 ♀ from Japan A habitus B head, frontal view C head, dorsal view D head, lateral view E mesosoma, lateral view F central part of fore wing.
Figure 45 from: Shimizu S, Broad GR, Maeto K (2020) Integrative taxonomy and analysis of species richness patterns of nocturnal Darwin wasps of the genus Enicospilus Stephens (Hymenoptera, Ichneumonidae, Ophioninae) in Japan. ZooKeys 990: 1-144. https://doi.org/10.3897/zookeys.990.55542
Figure 45 Enicospilus shinkanus (Uchida, 1928) ♀ from Japan A habitus B head, frontal view C head, dorsal view D head, lateral view E mesosoma, lateral view F central part of fore wing.
Figure 33 from: Shimizu S, Broad GR, Maeto K (2020) Integrative taxonomy and analysis of species richness patterns of nocturnal Darwin wasps of the genus Enicospilus Stephens (Hymenoptera, Ichneumonidae, Ophioninae) in Japan. ZooKeys 990: 1-144. https://doi.org/10.3897/zookeys.990.55542
Figure 33 Enicospilus nigropectus Cameron, 1905 ♀ from Japan A habitus B head, frontal view C head, dorsal view D head, lateral view E mesosoma, lateral view F central part of fore wing.
A meta-analysis of tropical land-use change effects on the soil microbiome: emerging patterns and knowledge gaps
<p>Modifications to vegetation and soil due to changes in land use have the potential to alter the soil microbiome, with consequences for carbon and nutrient cycling. Despite the important function of soil microorganisms, little is known about their response to land-use change, especially in tropical regions where current rates of land conversion are greatest. The aim of this meta-analysis was to examine how land-use change influences soil microbial properties in tropical ecosystems and to identify current trends and knowledge gaps in the literature. We identified 83 published paired studies that reported data on microbial biomass, abundance, composition, and enzyme activity under representative land-use changes in the tropics. We calculated response ratios for studies that compared the following: reference forests to (a) agriculture, (b) pastures, (c) plantations, and (d) secondary forests. Here you will find all the raw and clean data used for the meta-analysis. </p>
Data from: Image Calibration and Analysis Toolbox – a free software suite for measuring reflectance, colour, and pattern objectively and to animal vision
1. Quantitative measurements of colour, pattern, and morphology are vital to a growing range of disciplines. Digital cameras are readily available and already widely used for making these measurements, having numerous advantages over other techniques, such as spectrometry. However, off-the-shelf consumer cameras are designed to produce images for human viewing, meaning that their uncalibrated photographs cannot be used for making reliable, quantitative measurements. Many studies still fail to appreciate this, and of those scientists who are aware of such issues, many are hindered by a lack usable tools for making objective measurements from photographs. 2. We have developed an image processing toolbox that generates images that are linear with respect to radiance from the RAW files of numerous camera brands, and can combine image channels from multispectral cameras, including additional ultraviolet photographs. Images are then normalised using one or more grey standards to control for lighting conditions. This enables objective measures of reflectance and colour using a wide range of consumer cameras. Furthermore, if the camera's spectral sensitivities are known, the software can convert images to correspond to the visual system (cone-catch values) of a wide range of animals, enabling human and non-human visual systems to be modelled. The toolbox also provides image analysis tools that can extract luminance (lightness), colour, and pattern information. Furthermore, all processing is performed on 32-bit floating point images rather than commonly used 8-bit images. This increases precision and reduces the likelihood of data loss through rounding error or saturation of pixels, while also facilitating the measurement of objects with shiny or fluorescent properties. 3. All cameras tested using this software were found to demonstrate a linear response within each image and across a range of exposure times. Cone-catch mapping functions were highly robust, converting images to several animal visual systems and yielding data that agreed closely with spectrometer-based estimates. 4. Our imaging toolbox is freely available as an addition to the open source ImageJ software. We believe that it will considerably enhance the appropriate use of digital cameras across multiple areas of biology, in particular researchers aiming to quantify animal and plant visual signals.
Data from: Boundary strength analysis: combining colour pattern geometry and coloured patch visual properties for use in predicting behaviour and fitness
1.Colour patterns are used by many species to make decisions that ultimately affect their Darwinian fitness. Colour patterns consist of a mosaic of patches that differ in geometry and visual properties. Although traditionally pattern geometry and colour patch visual properties are analysed separately, these components are likely to work together as a functional unit. Despite this, the combined effect of patch visual properties, patch geometry, and the effects of the patch boundaries on animal visual systems, behaviour and fitness are relatively unexplored. 2.Here we describe Boundary Strength Analysis (BSA), a novel way to combine the geometry of the edges (boundaries among the patch classes) with the receptor noise estimate (ΔS) of the intensity of the edges. The method is based upon known properties of vertebrate and invertebrate retinas. The mean and SD of ΔS (mΔS, sΔS) of a colour pattern can be obtained by weighting each edge class ΔS by its length, separately for chromatic and achromatic ΔS. This assumes those colour patterns, or parts of the patterns used in signalling, with larger mΔS and sΔS are more stimulating and hence more salient to the viewers. BSA can be used to examine both colour patterns and visual backgrounds. 3.BSA was successful in assessing the estimated conspicuousness of colour pattern variants in two species, guppies (Poecilia reticulata) and Gouldian finches (Erythrura gouldiae), both polymorphic for patch colour, luminance and geometry. 3D representations of the ΔS of patch edges (Fort Diagrams) of both species show that there is little or negative geometric correspondence between the chromatic and achromatic edges. All individuals have mΔS > 1.5 for both chromatic and achromatic measures, indicating the high within‐pattern contrast expected for display signals. In contrast from what one would expect from sexual selection, all guppies have mΔS less than expected from random contacts between all pairs of patch colour/luminance classes. The correlation between chromatic and luminance ΔS is negative in both species but zero when correlating all possible kinds of edges between the colours of each species and morph indicating non‐random colour geometry. 4.The pattern difference between chromatic and achromatic edges in both species reveals the possibility that chromatic and achromatic edges could function differently. The smaller than random expected mΔS values in guppies suggests an anti‐predator function because guppies are never found without predators. Moreover, mΔS could vary with predation intensity within and among species. BSA can be applied to any colour pattern used in intraspecific and interspecific behaviour. Seven predictions and four questions about colour patterns are presented. 5.In species which are very convex, both chromatic and luminance mΔS change with viewing angle; geometry of signalling is as important as signal geometry.
Data from: The ontogeny of plant defense and herbivory: characterizing general patterns using meta-analysis
Defense against herbivores often changes dramatically as plants develop. Hypotheses based on allocation theory and herbivore selection patterns predict that defense should either increase or decrease, respectively, across ontogeny, and previous research partly supports both predictions. Thus, it remains unclear which pattern is more common and what factors contribute to variability among studies. We conducted a meta-analysis of 116 published studies reporting ontogenetic patterns in plant defense traits and herbivory. Patterns varied depending on plant life form (woody, herbaceous, grass), type of herbivore (insect, mollusk, mammal), and type of defense trait (secondary chemistry, physical defense, tolerance). In woody plants, chemical defense increased during the seedling stage, followed by an increase in physical defenses during the vegetative juvenile stage. Mammalian herbivores showed a strong preference for mature compared to juvenile tissues in woody plants. Herbs experienced a significant increase in secondary chemistry across the entire ontogenetic trajectory, although the magnitude of increase was greatest during the seedling stage. Correspondingly, mollusks preferred young compared to older herbs. Future research investigating growth/defense trade-offs, allometry, herbivore selection patterns, and ecological costs, would shed light on the mechanisms driving the ontogenetic patterns observed.
Data from: Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution
Over half of all vertebrates are "fishes", which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a full sample of all bony fishes. Here we conducted a comprehensive phylogenetic study on an unprecedented combination of broad taxonomic sampling of actinopterygian and sarcopterygian lineages (with a chondrichthyan outgroup) using a molecular data set of 21 independent loci. These data yielded a resolved phylogenetic hypothesis for extant Osteichthyes, including 1) reciprocally monophyletic Sarcopterygii and Actinopterygii, as currently understood, with polypteriforms as the first diverging lineage within Actinopterygii; 2) a monophyletic group containing gars and bowfin (= Holostei) as sister group to Teleostei; and 3) the earliest diverging lineage among teleosts being Elopomorpha, rather than Osteoglossomorpha. Relaxed-clock dating analysis employing a set of 24 newly applied fossil calibrations reveals divergence times that are more consistent with paleontological estimates than previous studies. Establishing a new phylogenetic pattern with accurate divergence dates for bony fishes illustrates several areas where the fossil record is incomplete and provides critical new insights on diversification of this important vertebrate group.
Data from: Paternity analysis of wood turtles (Glyptemys insculpta) reveals complex mating patterns
Mating system characteristics are of great importance as they may influence male and female reproductive success and reproductive isolation. The wood turtle (Glyptemys insculpta) is a terrestrial freshwater species listed as endangered by the International Union for Conservation of Nature. Considering its conservation status and the paucity of information currently available on parentage relationship for the species, we performed a microsatellite analysis to study the mating system of wood turtles in the Shawinigan River (Québec). We sampled 38 clutches over two years (14 in 2006 and 24 in 2007), for a total of 248 offspring genotyped with seven microsatellite loci. The reconstructed genotypes of the fathers revealed that reproductive success in the sampled clutches varied greatly between males and are positively correlated with the number of mates and clutches sired. Frequency of multiple paternity was estimated at 37% through a consensus of three different estimation methods. Positive correlation was observed between the genetic diversity of clutches and the number of fathers. Repeat paternity, however, was observed in 88% of the clutches by the same female in successive years, which suggests either a frequent use of sperm storage, or re-mating with the same partner in successive years.
Data from: Multiple pairwise analysis of non-homologous centromere coupling reveals preferential chromosome size-dependent interactions and a role for bouquet formation in establishing the interaction pattern
During meiosis, chromosomes undergo a homology search in order to locate their homolog to form stable pairs and exchange genetic material. Early in prophase, chromosomes associate in mostly non-homologous pairs, tethered only at their centromeres. This phenomenon, conserved through higher eukaryotes, is termed centromere coupling in budding yeast. Both initiation of recombination and the presence of homologs are dispensable for centromere coupling (occurring in spo11 mutants and haploids induced to undergo meiosis) but the presence of the synaptonemal complex (SC) protein Zip1 is required. The nature and mechanism of coupling have yet to be elucidated. Here we present the first pairwise analysis of centromere coupling in an effort to uncover underlying rules that may exist within these non-homologous interactions. We designed a novel chromosome conformation capture (3C)-based assay to detect all possible interactions between non-homologous yeast centromeres during early meiosis. Using this variant of 3C-qPCR, we found a size-dependent interaction pattern, in which chromosomes assort preferentially with chromosomes of similar sizes, in haploid and diploid spo11 cells, but not in a coupling-defective mutant (spo11 zip1 haploid and diploid yeast). This pattern is also observed in wild-type diploids early in meiosis but disappears as meiosis progresses and homologous chromosomes pair. We found no evidence to support the notion that ancestral centromere homology plays a role in pattern establishment in S. cerevisiae post-genome duplication. Moreover, we found a role for the meiotic bouquet in establishing the size dependence of centromere coupling, as abolishing bouquet (using the bouquet-defective spo11 ndj1 mutant) reduces it. Coupling in spo11 ndj1 rather follows telomere clustering preferences. We propose that a chromosome size preference for centromere coupling helps establish efficient homolog recognition.
Data from: Genomic analysis suggests KITLG is responsible for a roan pattern in two Pakistani goat breeds
The roan coat color pattern is described as the presence of white hairs intermixed with pigmented hairs. This kind of pigmentation pattern has been observed in many domestic species, including the goat. The molecular mechanisms and inheritance that underlie this pattern are known for some species and the KITLG gene has been shown associated with this phenotype. To date, no research effort has been done to find the gene(s) that controls roan coat color pattern in goats. In the present study, after genotyping with the GoatSNP50 BeadChip, 35 goats that showed a roan pattern and that belonged to two Pakistan breeds (Group A) were analyzed and then compared to 740 goats of 39 Italian and Pakistan goats breeds that did not have the same coat color pattern (Group B). Run of homozygosity-based and XP-EHH analyses were used to identify unique genomic regions potentially associated with the roan pattern. A total of 3 regions on chromosomes 5, 6 and 12 were considered unique among the group A versus B group comparisons. The A region > 1.7 Mb on chromosome 5 was the most divergent between the two groups. This region contains six genes, including the KITLG gene. Our findings support the hypothesis that the KITLG gene may be associated with the roan phenotype in goats.
Data from: QTL and quantitative genetic analysis of beak morphology reveals patterns of standing genetic variation in an Estrildid finch
The intra- and interspecific diversity of avian beak morphologies is one of the most compelling examples for the power of natural selection acting on a morphological trait. The development and diversification of the beak has also become a textbook example for evolutionary developmental biology, and variation in expression levels of several genes is known to causally affect beak shape. However, until now no genomic polymorphisms have been identified that are related to beak morphology in birds. QTL mapping does reveal the location of causal polymorphisms, albeit with poor spatial resolution. Here we estimate heritability and genetic correlations for beak length, depth and width and perform a QTL linkage analysis for these traits based on 1,404 informative single nucleotide polymorphisms genotyped in a four generation pedigree of 992 captive zebra finches (Taeniopygia guttata). Beak size, relative to body size, was sexually dimorphic (larger in males). Heritability estimates ranged from 0.47 for beak length to 0.74 for beak width. QTL mapping revealed four to five regions of significant or suggestive genome-wide linkage for each of the three beak dimensions (nine different regions in total). Eight out of eleven genes known to influence beak morphology are located in these nine peak regions. Five QTL do not cover known candidates demonstrating that yet unknown genes or regulatory elements may influence beak morphology in the zebra finch.
Data from: Patterns and processes in complex landscapes: testing alternative biogeographic hypotheses through integrated analysis of phylogeography and community ecology in Hawai'i
The Island of Hawai'i is a dynamic assemblage of five volcanoes with wet forest habitat currently existing in four distinct natural regions that vary in area, age, and geographic isolation. In this complex landscape, alternative assumptions of the relative importance of specific habitat characteristics on evolutionary and ecological processes predict strikingly different general patterns of local diversity and regional similarity. In this study we compare alternative a priori hypotheses against observed patterns within two distinct biological systems and scales: community composition of wet forest vascular plant species and mitochondrial and nuclear genes of Drosophila sproati, a wet forest restricted endemic. All observed patterns display strong and similar regional structuring, with the greatest local diversity found in Kohala and the windward side of Mauna Loa, the least in Ka'ū and Kona, and a distinctive pattern of regional similarity that likely reflects the historical development of this habitat on the island. These observations largely corroborate a biogeographic model that integrates multiple lines of evidence, including climatic reconstruction, over those relying on single measures, such as current habitat configuration or substrate age. This method of testing alternative hypotheses across biological systems and scales is an innovative approach for understanding complex landscapes and should prove valuable in diverse biogeographic systems.
Data from: Patterns and drivers of intraspecific variation in avian life history along elevational gradients: a meta-analysis
Elevational gradients provide powerful natural systems for testing hypotheses regarding the role of environmental variation in the evolution of life-history strategies. Case studies have revealed shifts towards slower life histories in organisms living at high elevations yet no synthetic analyses exist of elevational variation in life-history traits for major vertebrate clades. We examined (i) how life-history traits change with elevation in paired populations of bird species worldwide, and (ii) which biotic and abiotic factors drive elevational shifts in life history. Using three analytical methods, we found that fecundity declined at higher elevations due to smaller clutches and fewer reproductive attempts per year. By contrast, elevational differences in traits associated with parental investment or survival varied among studies. High-elevation populations had shorter and later breeding seasons, but longer developmental periods implying that temporal constraints contribute to reduced fecundity. Analyses of clutch size data, the trait for which we had the largest number of population comparisons, indicated no evidence that phylogenetic history constrained species-level plasticity in trait variation associated with elevational gradients. The magnitude of elevational shifts in life-history traits were largely unrelated to geographic (altitude, latitude), intrinsic (body mass, migratory status), or habitat covariates. Meta-population structure, methodological issues associated with estimating survival, or processes shaping range boundaries could potentially explain the nature of elevational shifts in life-history traits evident in this data set. We identify a new risk factor for montane populations in changing climates: low fecundity will result in lower reproductive potential to recover from perturbations, especially as fewer than half of the species experienced higher survival at higher elevations.
Data from: A phylogenetic analysis of macroevolutionary patterns in fermentative yeasts
When novel sources of ecological opportunity are available, physiological innovations can trigger adaptive radiations. This could be the case of yeasts (Saccharomycotina), in which an evolutionary novelty is represented by the capacity to exploit simple sugars from fruits (fermentation). During adaptive radiations, diversification and morphological evolution are predicted to slow-down after early bursts of diversification. Here, we performed the first comparative phylogenetic analysis in yeasts, testing the "early burst" prediction on species diversification and also on traits of putative ecological relevance (cell-size and fermentation versatility). We found that speciation rates are constant during the time-range we considered (ca., 150 millions of years). Phylogenetic signal of both traits was significant (but lower for cell-size), suggesting that lineages resemble each other in trait-values. Disparity analysis suggested accelerated evolution (diversification in trait values above Brownian Motion expectations) in cell-size. We also found a significant phylogenetic regression between cell-size and fermentation versatility (R2 = 0.10), which suggests correlated evolution between both traits. Overall, our results do not support the early burst prediction both in species and traits, but suggest a number of interesting evolutionary patterns, that warrant further exploration. For instance, we show that the Whole Genomic Duplication that affected a whole clade of yeasts, does not seems to have a statistically detectable phenotypic effect at our level of analysis. In this regard, further studies of fermentation under common-garden conditions combined with comparative analyses are warranted.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.