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799 results for “abundance data”
Data from: Abundance and morphometry changes across the high-mountain lake-size gradient in the tropical Andes of Southern Ecuador
The number, size, and shape of lakes are key determinants of the ecological functionality of a lake district. The lake area scaling relationships with lake number and volume enable upscaling biogeochemical processes and spatially considering organisms' metapopulation dynamics. These relationships vary regionally depending on the geomorphological context, particularly in the range of lake area <1 km2 and mountainous regions. The Cajas Massif (Southern Ecuador) holds a tropical mountain lake district with 5955 water bodies. The number of lakes deviates from a power law relationship with the lake area at both ends of the size range; similarly to the distributions found in temperate mountain ranges. The deviation of each distribution tail does not respond to the same cause. The marked relief limits the size of the largest lakes at high altitudes, whereas ponds are prompt to a complete infilling. A bathymetry survey of 202 lakes, selected across the full-size range, revealed a volume-area scaling coefficient larger than those found for other lake areas of glacial origin but softer relief. Water renewal time is not consistently proportional to the lake area due to the volume-area variation in midsize lakes. The 85% of the water surface is in lakes >104 m2 and 50% of the water resources are held in a few ones (∼10) deeper than 18 m. Therefore, midlakes and large lakes are by far more biogeochemically relevant than ponds and shallow lakes in this tropical mountain lake district.
Data from: Taxonomic identification bias does not drive patterns of abundance and diversity in theropod dinosaurs
<p>The ability of palaeontologists to correctly diagnose and classify new fossil species from incomplete morphological data is fundamental to our understanding of evolution. Different parts of the vertebrate skeleton have different likelihoods of fossil preservation and varying amounts of taxonomic information, which could bias our interpretations of fossil material. Substantial previous research has focused on the diversity and macroevolution of non-avian theropod dinosaurs. Theropods provide a rich dataset for analysis of the interactions between taxonomic diagnosability and fossil preservation. We use specimen data and formal taxonomic diagnoses to create a new metric, the Likelihood of Diagnosis (LoD), which quantifies the diagnostic likelihood of fossil species in relation to bone preservation potential. We use this to assess whether a taxonomic identification bias impacts the non-avian theropod fossil record. We find the patterns of differential species abundance and clade diversity are not a consequence of their relative diagnosability. Although there are other factors that bias the theropod fossil record, our results suggest patterns of relative abundance and diversity for theropods might be more representative of Mesozoic ecology than often considered.</p>
Data from: Which species, how many, and from where: Integrating habitat suitability, population genomics, and abundance estimates into species reintroduction planning
Extirpated organisms are reintroduced into their former ranges worldwide to combat species declines and biodiversity losses. The growing field of reintroduction biology provides guiding principles for reestablishing populations, though criticisms remain regarding limited integration of initial planning, modeling frameworks, interdisciplinary collaborations, and multi-species approaches. We used an interdisciplinary, multi-species, quantitative framework to plan reintroductions of three fish species into Abrams Creek, Great Smoky Mountains National Park, USA. We first assessed the appropriateness of habitat at reintroduction sites for banded sculpin (Cottus carolinae), greenside darter (Etheostoma blennioides), and mottled sculpin (Cottus bairdii) using species distribution modeling. Next, we evaluated the relative suitability of nine potential source stock sites using population genomics, abundance estimates, and multiple-criteria decision analysis (MCDA) based on known correlates of reintroduction success. Species distribution modeling identified mottled sculpin as a poor candidate, but banded sculpin and greenside darter as suitable candidates for reintroduction based on species-habitat relationships and habitats available in Abrams Creek. Genotyping by sequencing revealed acceptable levels of genetic diversity at all candidate source stock sites, identified population clusters, and allowed for estimating the number of fish that should be included in translocations. Finally, MCDA highlighted priorities among candidate source stock sites that were most likely to yield successful reintroductions based on differential weightings of habitat assessment, population genomics, and the number of fish available for translocation. Our integrative approach represents a unification of multiple recent advancements in the field of reintroduction biology and highlights the benefit of shifting away from simply choosing nearby populations for translocation to an information-based science with strong a priori planning coupled with several suggested posteriori monitoring objectives. Our framework can be applied to optimize reintroduction successes for a multitude of organisms and advances the science of reintroduction biology by simultaneously addressing a variety of past criticisms of the field.
Data from: Predator abundance drives the association between exploratory personality and foraging habitat risk in a wild marine meso-predator.
<p>1. In recent years, the incorporation of lower levels of organization to the understanding of population ecology, has led to an increase in interest for animal personality and individual foraging specialization. Despite these topics investigating comparable phenomena, i.e. individual consistency in behavior and in food resource use respectively, they have rarely been investigated together.</p> <p>2. Food resource use is thought to be at the interface between personality and life-history. More explorative individuals in a population, for example, are thought to increase encounter rates with food resources and consequently have faster growth than less explorative conspecifics.</p> <p>3. Such hypotheses have so far only received partial support, and the link between personality and life-history is increasingly speculated to be plastic and dependent on spatio-temporal variation in ecological conditions. Intra-specific competition and/or predation risk, for example are known to influence foraging specialization.</p> <p>4. Here, we investigated the relationship between exploration personality of juvenile lemon sharks (<i>Negaprion brevirostris</i>) (measured in captivity) and foraging habitat use (high risk vs low risk; measured via stable isotope analysis in the field) in relation to conspecific and predator abundance.</p> <p>5. We identified predator abundance as the main driver for the association between foraging habitat and exploration personality. When predators were less abundant, increased exploration was associated with foraging in riskier habitats. When predator abundance increased, an inverse relationship occurred, with less explorative individuals using more dangerous habitat.</p> <p>6. We conclude that the relationship between personality and resource use is plastic and context dependent, which could explain the inconclusive results of previous studies investigating links between personality and life-history.</p>
Data from: Characterization of the abiotic drivers of abundance of nearshore Arctic fishes
<p><span>Fish are critical ecologically and socioeconomically for subsistence economies in the Arctic, an ecosystem undergoing unprecedented environmental change. Our understanding of the responses of nearshore Arctic fishes to environmental change is inadequate because of limited research on the physicochemical drivers of abundance occurring at a fine scale. Here, high-frequency <i>in-situ </i>measurements of pH, temperature, salinity, and dissolved oxygen were paired with daily fish catches in nearshore Alaskan waters of the Beaufort Sea. </span><span>This dataset includes hourly measurements of pH, temperature, salinity, and dissolved oxygen, which were collected and calibrated according to best practices in chemical oceanography, and daily catch-per-unit-effort data for 18 nearshore Arctic fish species paired with daily averaged oceanographic data.</span></p>
Cannot see the diversity for all the species: evaluating inclusion criteria for local species lists when using abundant citizen science data
Abundant citizen science data on species occurrences is becoming increasingly available and enables identifying composition of communities occurring at multiple sites with high temporal resolution. However, for species displaying temporary patterns of local occurrences, i.e. that are transient to some sites, biodiversity measures are clearly dependent on the criteria used to include species into local species lists. Using abundant opportunistic citizen science data from frequently visited wetlands we investigated the sensitivity of α- and β-diversity estimates to the use raw vs. detection-corrected data and to the use of inclusion criteria for species presence reflecting alternative site use. We tested 7 inclusion criteria (with varying number of days required to be present) on time series of daily occurrence status during a breeding season of 90 days for 77 wetland bird species. We show that even when opportunistic presence-only observation data is abundant, raw data may not produce reliable local species richness estimates and rank sites very differently in terms of species richness. Furthermore, occupancy model based - and - diversity estimates were sensitive to the inclusion criteria used. Total species lists (all species observed at least once during a season) may therefore mask diversity differences among sites in local communities of species, by e.g. including vagrant species on potentially breeding communities and change the relative rank order of sites in terms of species richness. Very high sampling effort does not necessarily free opportunistic data from its inherent bias and can produce a pattern in which many species are observed at least once almost everywhere, thus leading to a possible paradox: the large amount of biological information may hinder its usefulness. Therefore, when prioritizing among sites to manage or preserve species diversity estimates need to be carefully related to relevant inclusion criteria depending on the diversity estimate in focus.
Data from: An assessment of sampling designs using SCR analyses to estimate abundance of boreal caribou
<p class="List1"><span>Accurately estimating abundance is a critical component of monitoring and recovery of rare and elusive species. Spatial capture-recapture (SCR) models are an increasingly popular method for robust estimation of ecological parameters. We provide an analytical framework to assess results from empirical studies to inform SCR sampling design, using both simulated and empirical data from non-invasive genetic sampling of seven boreal caribou populations (<i>Rangifer tarandus caribou</i>) which varied in range size and estimated population density. We use simulated population data with varying levels of clustered distributions to quantify the impact of non-independence of detections on density estimates, and empirical datasets to explore the influence of varied sampling intensity on the relative bias and precision of density estimates. Simulations revealed that clustered distributions of detections did not significantly impact relative bias or precision of density estimates. The genotyping success rate of our empirical dataset (n = 7,210 samples) was 95.1%, and 1,755 unique individuals were identified. Analysis of the empirical data indicated that reduced sampling intensity had a greater impact on density estimates in smaller ranges. The number of captures and spatial recaptures were strongly correlated with precision, but not absolute relative bias. The best sampling designs did not differ with estimated population density but differed between large and small ranges. We provide an efficient framework implemented in R to estimate the detection parameters required when designing SCR studies. The framework can be used when designing a monitoring program to minimize effort and cost while maximizing effectiveness, which is critical for informing wildlife management and conservation.</span></p>
Figure 2. Abundance data for S in Life history of the spider Selenops occultus Mello-Leitão (Araneae, Selenopidae) from Brazil with notes on the natural history of the genus
Figure 2. Abundance data for S. occultus plotted together with the average monthly precipitation and minimum and maximum temperatures for each month during which the study took place. The numbers in the black circles are the total number of S. occultus collected during each month.
Data from: Effectiveness of signs of activity as relative abundance indices for wild boar
<p><span>Population growth in wild boars and feral pigs (</span><i><span>Sus scrofa</span></i><span>) has negative environmental and economic implications worldwide. Accordingly, it is necessary to monitor population trends for appropriate management. Despite the potential for bias, relative abundance indices based on signs of activity </span><span><span>have the potential to be </span></span><span>practical, low-cost monitoring tools for data collection at a local scale and over large areas. However, few studies have examined the effectiveness of specific signs as measures of relative wild boar abundance </span><span><span>in comparison with reliable density estimates.</span></span><span> In this study, we examined whether three activity signs (digging marks, rubbing marks, and fecal pellet groups) could be used as relative abundance indices for wild boar. In particular, we conducted transect surveys for signs of activity as well as camera trap surveys from September 2017 to January 2018 at six sites in Hyogo Prefecture and eight sites in Chiba Prefecture, Japan. We modeled the relations between the number of activity signs and wild boar densities or </span><span><span>abundances</span></span><span> estimated from camera trap data </span><span><span>in a hierarchical framework</span></span><span>. Fecal pellet counts are a well-established method for estimating the abundance of herbivores, including wild boar; however, we found few fecal pellet groups in our study area, and the counts were not related to wild boar densities. Instead, we found that digging marks were strongly associated with estimates of wild boar density. Although fluctuations in the number of digging marks may be affected by factors other than boar density, including environmental conditions and seasonality, our results suggest that digging marks are an effective relative abundance index for evaluations of the spatial patterns of wild boar in Japan.</span></p>
Fish abundance data in forest steppe and grassland river networks in Mongolia
<p>Fish abundance data (fish per m) collected during the MACRO project in Mongolia. We collected fish assemblages in river networks of two different ecoregions, the Forest Steppe (FS) and Grassland (G), in 2017 and 2019.</p>
Data set of 1) plant abundance in the herb layer and 2) Shrub and tree composition and structure following forest management along a chronosequence
<p>In each site (1200 m²), three circular plots (400 m²) were established (total of 198 plots). Data presented here for 1) plant of the herb layer and 2) shrub and tree are grouped by site (addition of three plots). </p> <p>In the herb layer, total plant species identity and abundance (percentage cover) were sampled in each plot using eight circular micro-plots of 4 m². Data were collected in 2016 and 2017, between June and August. To minimize seasonal variability and allow detection of early spring species, plants (identity and abundance) in the herb layer were measured twice (once in June to early-July, and once in late-July to August).</p> <p>For tree, in each plot, species identity, diameter at breast height (DBH, 1.3 m) and locations of each tree > 9.1 cm DBH were determined. In each plot, species identity and DBH of shrubs and small trees (DBH range: 1.1 to 9.1 cm) were measured in three circular micro-plots of 25 m². Data that were related to the shrub-canopy layer included all trees and shrubs with DBH > 1.1 cm. Here, in each site, forest composition and structure is represented by different combinations of DBH classes (1.1-4 cm, 4-9.1 cm, 9.1-20 cm, 20-35 cm, >35 cm) and species.</p> <p>Plant community composition and abundance were assessed in unmanaged forests (sites of old-growth forest > 100 years, with dominant and co-dominant trees older than 200 years, and no obvious sign of past harvesting), and in even-aged and uneven-aged managed forests along a chronosequence (< 5 years, 15 years, 30 years after forest harvesting).</p>
Data from: Honey bees are the most abundant visitors to Australian watermelon but native stingless bees are equally effective as pollinators
<p><span>Despite the benefits of a diverse approach to crop pollination, global food production remains reliant on a low diversity of managed pollinators, especially </span>the European honey bee (<em>Apis mellifera</em>). To facilitate more robust pollinator management and improve the resilience of the production system, it is necessary to understand regional variation in the pollination ecology of global food crops. Watermelon (<em>Citrullus lanatus</em> (Thunb.) Matsum. & Nakai) is a highly insect pollinator-dependent crop and even though it is grown globally across many different climate zones, little is known about its pollination ecology across the diverse growing regions of Australia, spanning from the tropics to the arid zone. We compared the species composition, visitation rates, and effectiveness of the dominant floral visitors on 15 farms across five major watermelon-growing regions of Australia. We found that insect species composition differed significantly among regions, but honey bees were the dominant watermelon flower visitor, with relative abundance varying from 73 - 94%. However, native bees (including stingless bees <em>Tetragonula</em> sp., and bees from Families Megachilidae, and Halictidae such as <em>Lasioglossum</em>, <em>Homalictus</em>, <em>Lipotriches</em>), and flies (particularly Syrphidae sp.) also visited and transferred pollen onto watermelon flowers. In particular, native stingless bees were common visitors in several growing regions and deposited similar amounts of pollen to honey bees. Our findings indicate that the Australian watermelon industry utilizes honey bees, but the diverse assemblage of available native pollinating taxa provides an additional opportunity for growers in specific growing regions. These native taxa may be encouraged in the production system by deploying managed populations (e.g. native stingless bee colonies), employing pollinator-safe land management practices, as well as exploring methods for increasing the efficiency of managed honey bee colonies.</p>
Monitoring small mammal abundance using NEON data: Are calibrated indices useful?
<p>Small mammals are important to the functioning of ecological communities with changes to their abundances used to track impacts of environmental change. While capture-recapture estimates of absolute abundance are preferred, indices of abundance continue to be used in cases of limited sampling, rare species with little data, or unmarked individuals. Improvement to indices can be achieved by calibrating them to absolute abundance but their reliability across years, sites, or species is unclear. To evaluate this, we used the US National Ecological Observatory Network (NEON) capture-recapture data for 63 small mammal species over 46 sites from 2013–2019. We generated 17,155 absolute abundance estimates using capture-recapture analyses and compared these to two standard abundance indices, and three types of calibrated indices. We found that neither raw abundance indices nor index calibrations were reliable approximations of absolute abundance, with raw indices less correlated with absolute abundance than index calibrations (raw indices overall R<sup>2</sup> < 0.5, index calibration overall R<sup>2</sup> > 0.6). Performance of indices and index calibrations varied by species, with those having higher and less variable capture probabilities performing best. We conclude that indices and index calibration methods should be used with caution with a count of individuals being the best index to use, especially if it can be calibrated with capture probability. None of the indices we tested should be used for comparing different species due to high variation in capture probabilities. Hierarchical models that allow for sharing of capture probabilities over species or plots (i.e., joint likelihood models) may offer a better solution to mitigate the cost and effort of large-scale small mammal sampling while still providing robust estimates of abundance.</p>
Data for: Genomic heterozygosity is associated with parasite abundance, but the effects are not mediated by host condition
<p>Whether, when, and how genetic diversity buffers individuals and populations against infectious disease risk is a critical and open question for understanding wildlife disease and zoonotic disease risk. Several, but not all, studies have found negative relationships between infection and heterozygosity in wildlife. Since they can host multiple zoonotic infections, we sampled a population of wild deer mice (<em>Peromyscus maniculatus</em>), sequenced their genomes, and examined their fecal samples for coccidia and nematode eggs. We analyzed coccidia infection status, abundance, and coinfection status in relation to per-locus and per-individual measures of heterozygosity, as well as identified SNPs associated with infection status. Since heterozygosity might affect host condition, and condition is known to affect immunity, it was included as a co-variate in the per-individual analyses and as response variable in relation to heterozygosity. Not only did coccidia-infected individuals have lower levels of genome-wide per-locus diversity across all metrics, but we found an inverse relationship between genomic diversity and severity of coccidia infection. We also found weaker evidence that coinfected individuals had lower levels of private allelic variation than all other groups. In the per-individual analyses, relationships between heterozygosity and infection were marginal but followed the same negative trends. Condition was negatively correlated with infection, but was not associated with heterozygosity, suggesting that effects of heterozygosity on infection were not mediated by host condition in this system. Association tests identified multiple loci involved in the inflammatory response, with a particular role for NF-κB signaling, supporting previous work on the genetic basis of coccidia resistance. Taken together, we find that increased genome-wide neutral diversity, the presence of specific genetic variants, and improved condition positively impact infection status. Our results underscore the importance of considering host genomic variation as a buffer against infection, especially in systems that can harbor zoonotic diseases.</p>
SCUBA belt transects for abundance data H. cochlea and H. aequicostatus
<p>Marine symbioses are integral to the persistence of ecosystem functioning in coral reefs. Solitary corals of the species <em>Heteropsammia cochlea</em> and <em>Heterocyathus aequicostatus </em>have been observed to live in symbiosis with the sipunculan worm<em> Aspidosiphon muelleri muelleri</em>, which inhabits a cavity within the coral, in Zanzibar (Tanzania). The symbiosis of these photosymbiotic corals enables the coral holobiont to move, in fine to coarse unconsolidated substrata, a process termed as "walking". This allows the coral to escape sediment cover in turbid conditions which is crucial for these light-dependent species. An additional commensalistic symbiosis of this coral-worm holobiont is found between the <em>Aspidosiphon </em>worm and the cryptoendolithic bivalve <em>Jousseaumiella </em>sp., which resides within the cavity of the coral skeleton. To understand the morphological alterations caused by these symbioses, interspecific relationships, with respect to the carbonate structures between these three organisms, are documented using high-resolution imaging techniques (scanning electron microscopy and µCT scanning). Documenting multi-layered symbioses can shed light on how morphological plasticity interacts with environmental conditions to contribute to species persistence.</p>
Small rodent abundance and rainfall data
<p><span>Rodent outbreaks or irruptions in semiarid Chile are associated with rainfall pulses driven by the El Niño Southern Oscillation (ENSO). During the last decade, </span><span>north-central Chile has experienced an almost uninterrupted sequence of dry years, the so-called megadrought, which had led to a new ecological situation in this region. We employ a diagnostic approach to analyze the abundance of data regarding two rodent species, <em>Phyllotis</em> <em>darwini</em> and <em>Abrothrix</em> <em>olivacea</em>, using a 33-yr time series spanning from 1987 to 2019. Our population dynamic models provide evidence of competitive interactions within and among both species of rodents. This result is novel since rainfall variability influences the degree of interspecific competition and is asymmetric. The diagnostic approach used here offers a way to develop simple population models that are useful for understanding the causes of population fluctuations and for predicting population changes under a climate change scenario. </span></p>
UCYN-A1 nifH gene abundance data from SCOPE-Gradients 2019 cruise
<p>Surface UCYN-A1 nifH gene abundance data from the April 2019 SCOPE-Gradients 2019 cruise (http://scope.soest.hawaii.edu/data/gradients/gradients.html). Sample collection followed methods described in Gradoville et al. 2020 (Limnology and Oceanography), but included near-surface water sampling from the ship's clean underway line ("Underway") and trace-metal clean tow-fish (Tow-fish) in addition to CTD sampling. nifH genes of the UCYN-A1 phylotype were enumerated using ddPCR according to the methods described by Gradoville et al. 2021 (Environmental Microbiology). Average and standard deviations from two replicate bottles are provided.</p>
Data for: Higher abundance of adult pike in Baltic Sea coastal areas adjacent to restored wetlands compared to reference bays
<p><span>The abundance of pike, a keystone top-predator, has declined dramatically in the Baltic Sea since the 1990s likely owing to recruitment failure. It has been proposed that wetland restoration can aid the recovery of the pike stock by increasing the number of recruits produced by anadromous populations. Yet, no previous studies have addressed whether wetland restorations are associated with higher abundances of adult pike in the coastal habitat. To address this, we performed standardised rod-and-reel survey fishing in paired bays with and without wetlands across three coastal areas and three years. To estimate dispersal and the contribution of wetland pike to the coastal stock, we tagged captured pike with passive integrated responders (PIT) and employed PIT-reader stations in wetland inlets. The results showed that pike abundances were on average 90% higher in bays with an adjacent wetland although the effect varied among areas. Moreover, PIT-data uncovered that wetland pike constituted a high proportion of the pike found in adjacent coastal habitats and that some wetland fish dispersed up to 10 km. These results support that wetland restoration is a valuable tool to aid the coastal pike stock and ultimately restore the function and services of the coastal ecosystem.</span></p>
Data and code corresponding to: Contemporary evolution rivals the effects of rhizobium abundance on soil nitrogen availability in experimental mesocosms
<p>Because genotypes within a species commonly differ in traits that influence other species, whole communities, or even ecosystem functions, evolutionary change within one key species may affect community and ecosystem processes. Here we use experimental mesocosms to test how the evolution of reduced cooperation in rhizobium mutualists in response to 20 years of nitrogen fertilization compares to the effects of rhizobium abundance on soil nitrogen availability and plant community composition and diversity. The evolution of reduced rhizobium cooperation caused reductions in soil nitrogen that were as strong, or even stronger, than substantially reducing rhizobium mutualist abundance in a community. Effects of both rhizobium evolution and rhizobium inoculation on legume dominance, plant community composition, and plant species diversity were much smaller in magnitude, but suggest that rhizobium evolution can alter the relative abundance of plant functional groups. Our findings indicate that the consequences of rapid microbial evolution for ecosystems and communities can rival the effects resulting from the presence or abundance of keystone mutualists.</p>
Bold Park reptile species capture data for: Decadal abundance patterns in an isolated urban reptile assemblage: Monitoring under a changing climate
<p class="MsoNormal"><span>Fenced pitfall trapping in four sampling sites <span>representing different habitats and fire history</span> over the primary reptile activity period for 35 consecutive years with over 17000 individuals captured during 3300 days of sampling; the trapping regime was modified for the last 28 years.</span></p>
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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.