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799 results for “abundance data”
Abundance Trend Indicator - Models, Prediction, Stacked Environmental Data and Training Set Similarity
<p># Readme</p> <p>These trained models can be used to predict the abundance trends of New Zealand's forest species and can be used together with the code in https://github.com/lnilya/abundance-trend-indicator</p> <p>Since the process of using the models requires coding expertise and some setting up, please make sure to reach out to ilya.shabanov@vuw.ac.nz for any questions. All files will require the code in the repository to be read and used. </p> <p>If you want to explore the results generated with these models, please visit https://ati-nz-predictions-7e6f3d514735.herokuapp.com/ for a user-friendly, interactive UI.</p> <p>## Contents</p> <p>_models: Contains the trained models (Artificial Neural Network (ANN), Random Forest (RF), SVMW (Support vector machine) and GLM (logistic regression)) at different degrees of noise filtering, different datasets and variable sets. The model files also contain test and training scores. To load the files please refer to the readme in the code repository: ttps://github.com/lnilya/abundance-trend-indicator</p> <p><br>_predictions/_environment: Contains the predictor variables for the study area (New Zealand, 1950-2019) that are needed by the models to make predictions. </p> <p>_predictions/_similarity: Contains the masks of areas that can be predicted by models and are similar to the training set.</p> <p>_predictions/_ati: Contain the predicted results for the abundance trend. These can be explored on https://ati-nz-predictions-7e6f3d514735.herokuapp.com/ </p> <p> </p>
U. peregrina Isotope and foraminiferal abundance data from eastern Arabian sea during last 40 kiloyear by Majumder et al. (2024)
<p>We present the stable isotope ratio in <em>Uvigerina peregrina</em>, the relative abundance of oxic and dysoxic-suboxic benthic foraminifera groups, and the relative abundance of <em>Globigerina bulloides</em> spanning between ~40,000 and 3,500 calibrated years before the present from the eastern Arabian Sea (EAS).</p>
Data for J-PLUS: Beyond spectroscopy III. Stellar parameters and elemental-abundance ratios for five million stars from DR3
<p>The table contains stellar atmospehric parameters (Teff, logg, [Fe/H]), luminosity classification, element abundance ratios ([C/Fe], [Mg/Fe] and [alpha/Fe]), distance and age for over five million stars derived using J-PLUS DR3 + Gaia EDR3.</p><p>It includes the following parameters:</p><p>ra: Right Ascension from J-PLUS DR3 (J2000)</p><p>dec: Declination from J-PLUS DR3 (J2000)</p><p>gl: Galactic longitude derived from ICRS coordinates</p><p>gb: Galactic latitude derived from ICRS coordinates</p><p>mag[12]: Magnitudes of J-PLUS twelve bands (r, g, i, z, u, J0378, J0395, J0410, J0430, J0515, J0660, J0861)</p><p>err_mag[12]&Uncertainties of magnitudes of J-PLUS twelve bands (r, g, i, z, u, J0378, J0395, J0410, J0430, J0515, J0660, J0861)</p><p>gp1/rp1/ip1: Magnitudes from Pan-STARRS1</p><p>err_gp1/rp1/ip1: Uncertainties of magnitudes from Pan-STARRS1</p><p>G/BP/RP: Magnitudes for the Gaia three bands from EDR3; note G represents a calibration-corrected G magnitude</p><p>err_G/BP/RP: Uncertainties of magnitudes for the three Gaia bands from EDR3</p><p>ebv_sfd: Value of E(B - V) from the extinction map of SFD98, corrected for a 14% systematic</p><p>[Fe/H]: Photometric metallicity</p><p>err_[Fe/H]: Uncertainty of photometric metallicity</p><p>flg_[Fe/H]: Quality flag of [Fe/H]</p><p>[C/Fe]: Photometric carbon-to-iron abundance ratio</p><p>err_[C/Fe]:Uncertainty of photometric carbon-to-iron abundance ratio</p><p>flg_[C/Fe]: Quality flag of [C/Fe]</p><p>[Mg/Fe]: Photometric magnesium-to-iron abundance ratio</p><p>err_[Mg/Fe]: Uncertainty of photometric magnesium-to-iron abundance ratio</p><p>flg_[Mg/Fe]: Quality flag of [Mg/Fe]</p><p>[alpha/Fe]: Photometric alpha-to-iron abundance ratio</p><p>err_[alpha/Fe]: Uncertainty of photometric alpha-to-iron abundance ratio</p><p>flg_[alpha/Fe]: Quality flag of [alpha/Fe]</p><p>Teff: Effective temperature</p><p>err_Teff: Uncertainty of effective temperature</p><p>logg: Surface gravity</p><p>err_logg: Uncertainty of surface gravity</p><p>dist: Distance </p><p>err_dist: Uncertainty of distance</p><p>flg_dist: Flag to indicate the method used to derive distance, which takes the values ``parallax", ``CMF", and ``NO"</p><p>age: Stellar age</p><p>err_age: Uncertainty of stellar age</p><p>rv: Radial velocity</p><p>err_rv: Uncertainty of radial velocity</p><p>flg_rv: Flag to indicate the source of radial velocity, which takes the values ``GALAH", ``APOGEE'', ``Gaia",``RAVE", ``LAMOST", ``SEGUE"</p><p>parallax: Parallax from {it Gaia} EDR3</p><p>err_parallax: Uncertainty of parallax from {it Gaia} EDR3</p><p>pmra: Proper motion in Right Ascension direction from Gaia EDR3</p><p>err_pmra: Uncertainty of proper motion in Right Ascension direction from Gaia EDR3</p><p>pmdec: Proper motion in Declination direction from Gaia EDR3</p><p>err_pmdec&Uncertainty of proper motion in Declination direction from Gaia EDR3</p><p>ruwe: Renormalised unit weight error from Gaia EDR3</p><p>type: Flag to indicate classifications of stars, which takes the values ``dwarf" and ``giant" </p><p>subtype: Flag to indicate further sub-classifications of dwarf stars, which takes the values ``TO", ``MS" and ``Binary"</p>
corrigendum: Data for [Changing abundance of magnetofossil morphologies in pelagic red clay around Minamitorishima, western North Pacific]
<p>There is an error in a file in the original upload (doi: 10.5281/zenodo.896990).</p> <p>Please refer to sratios-MR15E02PC12_corrected.xlsx for the proper data.</p> <p>Also, a supporting material is missing in the publication, which is included in this upload.</p>
Data for: Projected effects of climate-change-induced flow alterations on stream macroinvertebrate abundances
<p>Global change has the potential to affect river flow conditions which are fundamental determinants of physical habitats. Predictions of the effects of flow alterations on aquatic biota have mostly been assessed based on species ecological traits (e.g., current preferences), which are difficult to link to quantitative discharge data. Alternatively, we used empirically derived predictive relationships for species’ response to flow to assess the effect of flow alterations due to climate change in two contrasting central European river catchments. Predictive relationships were set up for 294 individual species based on (1) abundance data from 223 sampling sites in the Kinzig lower-mountainous catchment and 67 sites in the Treene lowland catchment, and (2) flow conditions at these sites described by five flow metrics quantifying the duration, frequency, magnitude, timing and rate of flow events using present-day gauging data. Species’ abundances were predicted for three periods: (1) baseline (1998–2017), (2) horizon 2050 (2046–2065) and (3) horizon 2090 (2080–2099) based on these empirical relationships and using high-resolution modeled discharge data for the present and future climate conditions. We compared the differences in predicted abundances among periods for individual species at each site, where the percent change served as a proxy to assess the potential species responses to flow alterations. Climate change was predicted to most strongly affect the low-flow conditions, leading to decreased abundances of species up to −42%. Finally combining the response of all species over all metrics indicated increasing overall species assemblage responses in 98% of the studied river reaches in both projected horizons and were significantly larger in the lower-mountainous Kinzig compared to the lowland Treene catchment. Such quantitative analyses of freshwater taxa responses to flow alterations provide valuable tools for predicting potential climate-change impacts on species abundances and can be applied to any stressor, species, or region.</p>
Sediment geochemistry, archaeal abundance and GDGT data from methane seep sediments offshore Southwest Taiwan
<p>Dataset for manuscript "Methane Index and TEX86 values in cold seep sediments: implications for paleo-environmental reconstructions" currently under review in Geochimica et Cosmochimica Acta. Parameters include methane gas concentration, sulfate concentration, total organic carbon, dissolved inorganic carbon, stable carbon isotopes of total organic and dissolved inorganic carbon, the abundances of archaea and ANME-1, glycerol dialkyl glycerol tetraethers (GDGTs) and their associated indices including the Methane Index, Branched Isoprenoid Index, Ring Index and TEX86. ANME1_gdgt_calculation datasheet shows the calculations based on which the ANME-1 GDGT relative distribution was inferred. Datasheets Flux Dive1, Flux Dive3 and Flux MD10-3280 contain the calculations of sulfate and dissolved inorganic carbon fluxes.</p>
The Data For Spatial Variations of Stellar Elemental Abundances in FIRE Simulations of Milky Way-Mass Galaxies: Patterns Today Mostly Reflect Those at Formation
<p>Spatial patterns of stellar elemental abundances encode rich information about a galaxy’s formation<br>history. We analyze the radial, vertical, and azimuthal variations of metals in stars, both today and at<br>formation, in the FIRE-2 cosmological simulations of Milky Way-mass galaxies, and we compare<br>with the Milky Way. Overall, spatial variations of stellar metallicities show only modest differences between formation and today; spatial variations today primarily reflect the conditions of stars at birth, with spatial redistribution of stars after birth contributing secondarily. </p> <p> </p> <p>This data abides by CC-BY.</p>
Data from: A functional diversity approach of crop sequences reveals that weed diversity and abundance show different responses to environmental variability
1. Combining several crop species and associated agricultural practices in a crop sequence has the potential to control weed abundance while promoting weed diversity in arable fields. However, how the variability of environmental conditions that arise from crop sequences affects weed diversity and abundance remains poorly understood, with most studies to-date simply opposing weed communities in monoculture and in crop rotation. Here, we describe crop sequences along gradients of disturbance and resource variability using a crop functional trait and associated agricultural practices. We tested the hypothesis that variability of disturbances reduces weed abundance while variability of resources promotes weed diversity. 2. We used functional Hill's numbers to compute crop sequence functional diversity based on sowing date, herbicide spectrum and crop height - these are the respective proxies of disturbance timings, disturbance types and light availability. Using a large-scale weed monitoring database, we assessed crop sequence diversity for 1045 crop sequences of five consecutive cropping seasons. We computed weed richness and abundance at pluri-annual (pool of weeds observed across five cropping seasons) and annual (pool of weeds observed during a winter cereal cropping season preceded by five cropping seasons) scales. We also accounted for herbicide and tillage intensities to test whether management intensity affects the response of weed diversity and abundance to crop sequence diversity. 3. At the pluri-annual scale, weed richness increased with the diversity of crop height and sowing date while weed abundance decreased with sowing date diversity. Annual weed richness decreased with sowing date diversity while annual weed abundance poorly relied on crop sequence diversity. 4. Synthesis and applications. This study establishes a scientific basis for designing crop sequences according to specific weed management goals. We show that farmers may enhance arable weed diversity on a pluri-annual scale by sequentially sowing crop species that differ in their competitive ability and sowing date. They may also achieve a better control of weed abundance by increasing the diversity of crop sowing dates across the crop sequence.
Data from: Early life history of deep-water gorgonian corals may limit their abundance
Deep-water gorgonian corals are long-lived organisms found worldwide off continental margins and seamounts, usually occurring at depths of ~200–1,000 m. Most corals undergo sexual reproduction by releasing a planktonic larval stage that disperses; however, recruitment rates and the environmental and biological factors influencing recruitment in deep-sea species are poorly known. Here, we present results from a 4-year field experiment conducted in the Gulf of Maine (northwest Atlantic) at depths of more than 650 m that document recruitment for 2 species of deep-water gorgonian corals, Primnoa resedaeformis and Paragorgia arborea. The abundance of P. resedaeformis recruits was high, and influenced by the structural complexity of the recipient habitat, but very few recruits of P. arborea were found. We suggest that divergent reproductive modes (P. resedaeformis as a broadcast spawner and P. arborea as a brooder) may explain this pattern. Despite the high recruitment of P. resedaeformis, severe mortality early on in the benthic stage of this species may limit the abundance of adult colonies. Most recruits of this species (more than 80%) were at the primary polyp stage, and less than 1% of recruits were at stage of 4 polyps or more. We propose that biological disturbance, possibly by the presence of suspension-feeding brittle stars, and limited food supply in the deep sea may cause this mortality. Our findings reinforce the vulnerability of these corals to anthropogenic disturbances, such as trawling with mobile gear, and the importance of incorporating knowledge on processes during the early life history stages in conservation decisions.
Data from: Microsatellite evidence for obligate autogamy, but abundant genetic variation in the herbaceous monocarp Lobelia inflata (Campanulaceae)
Although high levels of self-fertilization (>85%) are not uncommon in nature, organisms reproducing entirely through selfing are extremely rare. Predominant selfers are expected to have low genetic diversity because genetic variation is distributed among rather than within lineages, and is readily lost through genetic drift. We examined genetic diversity at 22 microsatellite loci in 105 individuals from a population of the semelparous herb Lobelia inflata L., and found (1) no evidence of heterozygosity through outcrossing, yet (2) high rates of genetic polymorphism (2-4 alleles per locus). Furthermore, this genetic variation among lineages was associated with phenotypic traits (e.g. flower colour, size at first flower). Coupled with previous work characterizing the fitness consequences of reproductive timing, our results suggest that temporal genotype-by-environment interaction may maintain genetic variation and, because genetic variation occurs only among lineages, this simple system offers a unique opportunity for future tests of this mechanism.
Data from: Linking genetic diversity and temporal fluctuations in population abundance of the introduced feral cat (Felis silvestris catus) on the Kerguelen Archipelago.
Linking temporal variations of genetic diversity, including allelic richness and heterozygosity, and spatio-temporal fluctuations in population abundance has emerged as an important tool for understanding demographic and evolutionary processes in natural populations. This so-called 'genetic monitoring' was conducted across 12 consecutive years (1996-2007) at three sites for the feral cat, introduced onto the Kerguelen Archipelago fifty years ago. Temporal changes in allelic richness and heterozygosity at 18 microsatellite DNA loci were compared to temporal changes in the adult population abundance index, obtained by typical demographic monitoring. No association was found at the island spatial scale but we observed an association between genetic diversity and adult population indices from year to year within each study site. More particularly, the magnitude of successive increases or decreases in the adult population abundance index appeared to be the major factor linking the trajectories of genetic diversity and adult population abundance indices. Natal dispersal and/or local recruitment, both facilitated by high juvenile survival when the adult population size is small, are proposed as the major demographic processes contributing to such an observed pattern. Finally, we suggested avoiding the use of the harmonic mean as an estimator of long-term population size to study the relationships between demographic fluctuations and heterozygosity in populations characterized by strong multi-annual density fluctuations.
Data from: Regional and local patterns of genetic variation and structure in yellow-necked mice − the roles of geographic distance, population abundance and winter severity
The goal of this study, conducted in seven large woodlands and three areas with small woodlots in north-eastern Poland in 2004-2008, was to infer genetic structure in yellow-necked mouse Apodemus flavicollis population and to evaluate the roles of environmental and population ecology variables in shaping the spatial pattern of genetic variation using 768 samples genotyped at 13 microsatellite loci. Genetic variation was very high in all studied regions. The primal genetic subdivision was observed between the northern and the southern parts of the study area, which harboured two major clusters and the intermediate area of highly admixed individuals. The probability of assignment of individual mice to the northern cluster increased significantly with lower temperatures of January and July and declined in regions with higher proportion of deciduous and mixed forests. Despite the detected structure, genetic differentiation among regions was very low. Fine-scale structure was shaped by the population density, whereas higher level structure was mainly shaped by geographic distance. Genetic similarity indices were highly influenced by mouse abundance (which positively correlated with the share of deciduous forests in the studied regions) and exhibited the greatest change between 0 and 1 km in the forests, 0 and 5 km in small woodlots. Isolation by distance pattern, calculated among regions, was highly significant but such relationship between genetic and geographic distance was much weaker, and held the linearity at very fine scale (~1.5 km), when analyses were conducted at individual level.
Data from: Predatory fish sounds can alter crab foraging behavior and influence bivalve abundance
The risk of predation can have large effects on ecological communities via changes in prey behaviour, morphology and reproduction. Although prey can use a variety of sensory signals to detect predation risk, relatively little is known regarding the effects of predator acoustic cues on prey foraging behaviour. Here we show that an ecologically important marine crab species can detect sound across a range of frequencies, probably in response to particle acceleration. Further, crabs suppress their resource consumption in the presence of experimental acoustic stimuli from multiple predatory fish species, and the sign and strength of this response is similar to that elicited by water-borne chemical cues. When acoustic and chemical cues were combined, consumption differed from expectations based on independent cue effects, suggesting redundancies among cue types. These results highlight that predator acoustic cues may influence prey behaviour across a range of vertebrate and invertebrate taxa, with the potential for cascading effects on resource abundance.
Data from: Comparison of fish detections, community diversity, and relative abundance using environmental DNA metabarcoding and traditional gears
Background <p>Detecting species at low abundance, including aquatic invasive species (AIS), is critical for making informed management decisions. Environmental DNA (eDNA) methods have become a powerful tool for rare or cryptic species detection; however, many eDNA assays offer limited utility for community‐level analyses due to their use of species‐specific (presence/absence) 'barcodes'. Metabarcoding methods provide information on entire communities based on sequencing of all taxon‐specific barcodes within an eDNA sample.</p> Aims <p>Evaluate measures of fish species detections, community diversity, and estimates of relative abundance based on eDNA metabarcoding and traditional fisheries sampling approaches in the context of fish community characterization and AIS survellience.</p> Materials and Methods <p>In 2016, eight limnologically diverse lakes (surface area range: 13 – 1,728 ha) in Michigan, USA were sampled using a variety of traditional fisheries gears to characterize fish community composition. Environmental DNAs from surface (33 ± 6, mean ± 1 SD) and benthic (14 ± 2) water samples from each lake were isolated and amplified for two metabarcoding markers (mitochondrial 12S and 16S rDNA loci) using fish‐specific primers. Fish species detected within each lake were determined by comparing the sequencing data to a database of sequences from native Michigan fish species and 19 AIS on the Michigan's Watch List.</p> Results <p>Analysis of species accumulation curves indicated multi‐locus eDNA metabarcoding assays can enhance species detection capacities and characterize 95% of a fish community in fewer sampling efforts than traditional gear (range: 2 – 62, median: 14). In addition, all AIS detected in traditional gear samples were also detected by eDNA, while some AIS detected by eDNA assays were absent from traditional gear samples.</p> Discussion <p>Results reported here are, in part, driven by the lack of species‐selectivity during eDNA sampling events. Given the efficacy of eDNA assays, we suggest multi‐locus eDNA metabarcoding assays be implemented in early detection efforts.</p>
Data from: Bee communities along a prairie restoration chronosequence: similar abundance and diversity, distinct composition
Recognition of the importance of bee conservation has grown in response to declines of managed honey bees and some wild bee species. Habitat loss has been implicated as a leading cause of declines, suggesting that ecological restoration is likely to play an increasing role in bee conservation efforts. In the Midwestern USA, restoration of tallgrass prairie has traditionally targeted plant community objectives without explicit consideration for bees. However, restoration of prairie vegetation is likely to provide ancillary benefits to bees through increased foraging and nesting resources. We investigated community assembly of bees across a chronosequence of restored eastern tallgrass prairies and compared patterns to those in control and reference habitats (old fields and prairie remnants, respectively). We collected bees for three years and measured diversity and abundance of in-bloom flowering plants, vegetation structure, ground cover, and surrounding land use as predictors of bee abundance and bee taxonomic and functional diversity. We found that site-level variables, but not site type or restoration age, were significant predictors of bee abundance (bloom diversity: p = 0.004, bare ground cover: p = 0.02) and bee diversity (bloom diversity: p = 0.01). There were significant correlations between overall composition of bee and blooming plant communities (mantel test: p = 0.002), and both plant and bee assemblages in restorations were intermediate between those of old fields and remnant prairies. Restorations exhibited high bee beta diversity, i.e., restored sites' bee assemblages were taxonomically and functionally differentiated from each other. This pattern was strong in younger restorations (< 20 years old), but absent from older restorations (> 20 years), suggesting restored prairie bee communities become more similar to one another and more similar to remnant prairie bee communities over time with the arrival of more species and functional groups of bees. Our results indicate that old fields, restorations, and remnants provide habitat for diverse and abundant bee communities, but continued restoration of old fields will help support and conserve bee communities more similar to reference bee communities characteristic of remnant prairies.
Data from: Diversity and abundance of macro‐invertebrates on abandoned cattle kraals in a semi‐arid savanna
Abandoned cattle (Bos taurus) kraals are sources of habitat heterogeneity in dystrophic semi‐arid African savannas with a strong positive effect on soil nutrients and plant productivity. However, little is known regarding how macro‐invertebrate assemblages vary between abandoned kraals and the surrounding savanna matrix. We tested whether herbaceous biomass and basal and aerial covers and soil nutrients have an effect on aboveground and belowground macro‐invertebrate assemblages. Twelve abandoned kraals were contrasted with their paired control plots for soil characteristics, herbaceous productivity, and macro‐invertebrate assemblages in Save Valley Conservancy, Zimbabwe. Abandoned kraals had significantly higher concentrations of soil nitrogen (N), phosphorus (P), potassium (K), and calcium (Ca) as well as herbaceous biomass and basal and aerial covers than control plots. Both aboveground and belowground macro‐invertebrate species richness were higher on abandoned kraals. However, only belowground macro‐invertebrate diversity (Shannon H′ and Hill number 1) was significantly higher on abandoned kraals. Soil nutrients and herbaceous productivity had positive and significant correlations with the dominant taxa (Coleoptera, Hymenoptera, Hemiptera, Isoptera, and Myriapoda) on abandoned kraals. These results add to the growing body of evidence that abandoned kraals exert significant effects on savanna spatial heterogeneity years later, with implications on ecosystem processes and functioning.
Data from: An empirical and mechanistic explanation of abundance-occupancy relationships for a critically endangered nomadic migrant
The positive abundance-occupancy relationship (AOR) is a pervasive pattern in macroecology. Similarly, the association between occupancy (or probability of occurrence) and abundance is also usually assumed to be positive and in most cases constant. Examples of AORs for nomadic species with variable distributions are extremely rare. Here we examined temporal and spatial trends in the AOR over seven years for a critically endangered nomadic migrant which relies on dynamic pulses in food availability to breed. We predicted a negative temporal relationship, where local mean abundances increase when the number of occupied sites decreases, and a positive relationship between local abundances and the probability of occurrence. We also predicted that these patterns are largely attributable to spatiotemporal variation in food abundance. The temporal AOR was significantly negative and annual food availability was significantly positively correlated with the number of occupied sites, but negatively correlated with abundance. Thus, as food availability decreased, local densities of birds increased, and vice-versa. The abundance - probability of occurrence relationship was positive and non-linear, but varied between years due to differing degrees of spatial aggregation caused by changing food availability. Importantly, high abundance (or occupancy) did not necessarily equate to high quality habitat and may be indicative of resource bottlenecks or exposure to other processes affecting vital rates. Our results provide a rare empirical example that highlights the complexity of AORs for species that target aggregated food resources in dynamic environments.
Data from: Impact of urbanization on abundance and phenology of caterpillars and consequences for breeding in an insectivorous bird
Urbanization can have marked effects on plant and animal populations' phenology, population size, predator-prey interactions and reproductive success. These aspects are rarely studied simultaneously in a single system, and some are rarely investigated, e.g. how insect phenology responds to urban development. Here, we study a tri-trophic system of trees – phytophagous insects (caterpillars) – insectivorous birds (great tits) to assess how urbanization influences i) the phenology of each component of this system, ii) insect abundance and iii) avian reproductive success. We use data from two urban and two forest sites in Hungary, central Europe, collected over four consecutive years. Despite a trend of earlier leaf emergence in urban sites there is no evidence for an earlier peak in caterpillar abundance. Thus, contrary to the frequently stated prediction in the literature, the earlier breeding of urban bird populations is not associated with an earlier peak in caterpillar availability. Despite this the seasonal dynamics of caterpillar biomass exhibited striking differences between habitat types with a single clear peak in forests, and several much smaller peaks in urban sites. Caterpillar biomass was higher in forests than urban areas across the entire sampling period, and between 8.5 and 24 times higher during the first brood's chick-rearing period. This higher biomass was not associated with taller trees in forest sites, or with tree species identity, and occurred despite most of our focal trees being native to the study area. Urban great tits laid smaller clutches, experienced more frequent nestling mortality from starvation, reared fewer offspring to fledging age, and their fledglings had lower body mass. Our study strongly indicates that food limitation is responsible for lower avian reproductive success in cities, which is driven by reduced availability of the preferred nestling diet, i.e. caterpillars, rather than phenological shifts in the timing of peak food availability.
Data from: Snake venoms are integrated systems, but abundant venom proteins evolve more rapidly
Background: While many studies have shown that extracellular proteins evolve rapidly, how selection acts on them remains poorly understood. We used snake venoms to understand the interaction between ecology, expression level, and evolutionary rate in secreted protein systems. Venomous snakes employ well-integrated systems of proteins and organic constituents to immobilize prey. Venoms are generally optimized to subdue preferred prey more effectively than non-prey, and many venom protein families manifest positive selection and rapid gene family diversification. Although previous studies have illuminated how individual venom protein families evolve, how selection acts on venoms as integrated systems, is unknown. Results: Using next-generation transcriptome sequencing and mass spectrometry, we examined microevolution in two pitvipers, allopatrically separated for at least 1.6 million years, and their hybrids. Transcriptomes of parental species had generally similar compositions in regard to protein families, but for a given protein family, the homologs present and concentrations thereof sometimes differed dramatically. For instance, a phospholipase A 2 transcript comprising 73.4 % of the Protobothrops elegans transcriptome, was barely present in the P. flavoviridis transcriptome (<0.05 %). Hybrids produced most proteins found in both parental venoms. Protein evolutionary rates were positively correlated with transcriptomic and proteomic abundances, and the most abundant proteins showed positive selection. This pattern holds with the addition of four other published crotaline transcriptomes, from two more genera, and also for the recently published king cobra genome, suggesting that rapid evolution of abundant proteins may be generally true for snake venoms. Looking more broadly at Protobothrops, we show that rapid evolution of the most abundant components is due to positive selection, suggesting an interplay between abundance and adaptation. Conclusions: Given log-scale differences in toxin abundance, which are likely correlated with biosynthetic costs, we hypothesize that as a result of natural selection, snakes optimize return on energetic investment by producing more of venom proteins that increase their fitness. Natural selection then acts on the additive genetic variance of these components, in proportion to their contributions to overall fitness. Adaptive evolution of venoms may occur most rapidly through changes in expression levels that alter fitness contributions, and thus the strength of selection acting on specific secretome components.
Data from: Environmental factors influence both abundance and genetic diversity in a widespread bird species
Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N = 12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations.
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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.