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90 results for “species occurrence data”
Data from: Revisiting the relative growth rate hypothesis for gymnosperm and angiosperm species co‐occurrence
Premise of the study: It is unclear to what extent the co-occurrence of angiosperm and gymnosperm species in some marginal ecosystems is explained by reduced growth in angiosperms due to carbon (C) limitation, and by high stress tolerance in gymnosperms associated with lack of vessels and resource conservation. Methods: We examined growth patterns and traits associated with C balance in four evergreen angiosperm species (including one vesselless species, Drimys winteri) and three gymnosperm tree species of a cold-temperate rainforest in southern Chile. We measured the mean basal area increment for the first 50 (BAI50) and the last 10 years (BAI10), wood density, leaf lifespan, and non-structural carbohydrate (NSC) concentrations in different organs. Key results: BAI50 was 6-fold higher in angiosperms than in gymnosperms, and c. 4-fold higher in Drimys than in the fastest growing gymnosperm. BAI10 and aboveground NSC concentrations were significantly higher and leaf lifespan lower in angiosperms than in gymnosperms; these differences though were largely driven by the slow growth and low NSC concentrations of the Cupressaceae species (Pilgerodendron uviferum), while the two Podocarpaceae showed similar BAI10 and NSC concentrations to angiosperms. In angiosperms, NSC and starch concentrations were generally higher in species with lower BAI10, indicating no severe C limitation. Conclusions: The co-occurrence of angiosperms and gymnosperms in cold-temperate rainforests of southern Chile is not explained by growth disadvantages and C limitation in angiosperms. High leaf longevity, but not lack of vessels, appeared to favor resource conservation and C balance in some gymnosperms (Podocarpaceae). In compliance with data protection regulations, please contact the publication office if you would like to have your personal information removed from the database.
Data from: Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards
Genetic diversity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic diversity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 individuals spanning 76 nominal species of Australian scincid lizards in the genus Ctenotus. To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based species delimitation to delineate 83 species-level lineages within the genus for downstream analyses. We then used these genetic data to infer levels of within-population genetic diversity. Using a phylogenetically informed approach, we tested whether variation in genetic diversity could be explained by population size, environmental heterogeneity or historical demography. We find that the strongest predictor of genetic diversity is a novel proxy for census population size: the number of vouchered occurrences in museum databases. However, museum occurrences only explain a limited proportion of the variance in genetic diversity, suggesting that genetic diversity might be difficult to predict at shallower phylogenetic scales.
Data from: Understanding co-occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM)
A primary goal of ecology is to understand the fundamental processes underlying the geographic distributions of species. Two major strands of ecology – habitat modelling and community ecology – approach this problem differently. Habitat modellers often use species distribution models (SDMs) to quantify the relationship between species' and their environments without considering potential biotic interactions. Community ecologists, on the other hand, tend to focus on biotic interactions and, in observational studies, use co‐occurrence patterns to identify ecological processes. Here, we describe a joint species distribution model (JSDM) that integrates these distinct observational approaches by incorporating species co‐occurrence data into a SDM. JSDMs estimate distributions of multiple species simultaneously and allow decomposition of species co‐occurrence patterns into components describing shared environmental responses and residual patterns of co‐occurrence. We provide a general description of the model, a tutorial and code for fitting the model in R. We demonstrate this modelling approach using two case studies: frogs and eucalypt trees in Victoria, Australia. Overall, shared environmental correlations were stronger than residual correlations for both frogs and eucalypts, but there were cases of strong residual correlation. Frog species generally had positive residual correlations, possibly due to the fact these species occurred in similar habitats that were not fully described by the environmental variables included in the JSDM. Eucalypt species that interbreed had similar environmental responses but had negative residual co‐occurrence. One explanation is that interbreeding species may not form stable assemblages despite having similar environmental affinities. Environmental and residual correlations estimated from JSDMs can help indicate whether co‐occurrence is driven by shared environmental responses or other ecological or evolutionary process (e.g. biotic interactions), or if important predictor variables are missing. JSDMs take into account the fact that distributions of species might be related to each other and thus overcome a major limitation of modelling species distributions independently.
Data from: Species interactions in occurrence data for a community of tick-transmitted pathogens
Interactions between species of ticks, their realised range of hosts, the pathogens they carry and transmit, as well as the geographical distribution of species in the Western Palearctic, have been obtained based on evidence published between 1970–2014. These relationships were linked to remotely-sensed features of temperature and vegetation and used to extract the network of interactions among the organisms. The resulting datasets were focussed on niche overlap among ticks and hosts, species interactions and the fraction of the environmental niche where tick-borne pathogens may circulate, as a result of interactions and environmental trait overlap. The presented datasets provide a valuable resource for researchers of tick-borne pathogens, as they conciliate the abiotic and biotic sides of their niche, allowing exploration of the importance of each species of vertebrate reservoir in the circulation of tick-transmitted pathogens at intervals of the environmental niche.
Data from: Predicting species occurrences with habitat network models
1. Biodiversity conservation requires modelling tools capable of predicting the presence or absence (i.e. occurrence-state) of species in habitat patches. Local habitat characteristics of a patch (lh), the cost of traversing the landscape matrix between patches (weighted connectivity; (wc), and the position of the patch in the habitat network topology (nt) all influence occurrence-state. Existing models are data demanding or consider only local habitat characteristics. We address these shortcomings and present a network-based modelling approach, which aims to predict species occurrence-state in habitat patches using readily available presence-only records. 2. For the tree frog Hyla arborea on the Swiss Plateau, we delineated habitat network nodes from an ensemble habitat suitability model, and used different cost surfaces to generate the edges of three networks: one limited only by dispersal distance (Uniform), another incorporating traffic, and a third based on inverse habitat suitability. For each network, we calculated explanatory variables representing the three categories (lh, wc and nt). The response variable, occurrence-state, was parametrized by a sampling-intensity procedure assessing observations of comparable species over a threshold of patch visits. The explanatory variables from the three networks and an additional non-topological model were related to the response variable with boosted regression trees. 3. The habitat network models had a similar fit; they all outperformed the non-topological model. Habitat suitability index ((lh) was the most important predictor in all networks, followed by third-order neighborhood (nt). Patch size (lh) was unimportant in all three networks. 4. We found that topological variables of habitat networks are relevant for the prediction of species occurrence-state, a step-forward from models considering only local habitat characteristics. For any habitat patch, occurrence-state is most prominently influenced by its habitat suitability, and then by the number of patches in a wide neighborhood. Our approach is generic and can be applied to multiple species in different habitats.
Data from: Disentangling biotic interactions, environmental filters, and dispersal limitation as drivers of species co-occurrence
A key focus in ecology is to search for community assembly rules. Here we compare two community modelling frameworks that integrate a combination of environmental and spatial data to identify positive and negative species associations from presence-absence matrices, and incorporate an additional comparison using joint species distribution models (JSDM). The frameworks use a dichotomous logic tree that distinguishes dispersal limitation, environmental requirements, and interspecific interactions as causes of segregated or aggregated species pairs. The first framework is based on a classical null model analysis complemented by tests of spatial arrangement and environmental characteristics of the sites occupied by the members of each species pair (Classic framework). The second framework, (SDM framework) implemented here for the first time, builds on the application of environmentally-constrained null models (or JSDMs) to partial out the influence of the environment, and includes an analysis of the geographical configuration of species ranges to account for dispersal effects. We applied these approaches to examine plot-level species co-occurrence in plant communities sampled along a wide elevation gradient in the Swiss Alps. According to the frameworks, the majority of species pairs were randomly associated, and most of the non-random positive and negative species associations could be attributed to environmental filtering and/or dispersal limitation. These patterns were partly detected also with JSDM. Biotic interactions were detected more frequently in the SDM framework, and by JSDM, than in the Classic framework. All approaches detected species aggregation more often than segregation, perhaps reflecting the important role of facilitation in stressful high-elevation environments. Differences between the frameworks may reflect the explicit incorporation of elevational segregation in the SDM framework and the sensitivity of JSDM to the environmental data. Nevertheless, all methods have the potential to reveal general patterns of species co-occurrence for different taxa, spatial scales, and environmental conditions.
Data from: Dynamic species co-occurrence networks require dynamic biodiversity surrogates
In conservation it is inevitable that surrogates be selected to represent the occurrence of hard–to–find species and find priority locations for management. However, species co–occurrence can vary over time. Here we demonstrate how temporal dynamics in species co–occurrence influence the ability of managers to choose the best surrogate species. We develop an efficient optimisation formulation that selects the optimal set of complementary surrogate species from any co–occurrence network. We apply it to two Australian datasets on successional bird responses to disturbances of revegetation and fire. We discover that a surprisingly small number of species are required to represent the majority of species co–occurrences at any one time. Because co–occurrence patterns are temporally dynamic, the optimal set of surrogates, and the number of surrogates required to achieve a desired surrogacy power, depend on sampling effort and the successional state of a system. Overlap in optimal sets of surrogates for representing 70% of co–occurring species ranges from zero to 57% depending on when the surrogacy decision is made. Surrogate sets representing early successional communities over–estimate the power of surrogacy decisions at later times. Our results show that in dynamic systems, optimal surrogates might be selected in different ways: (1) use short–term monitoring to choose a larger number of static less–informative surrogates; (2) use long–term monitoring to choose a smaller number of static high–power surrogates that may poorly represent early successional co–occurrence; (3) develop adaptive surrogate selection frameworks with high short–term and long–term surrogacy power that update surrogate sets and capture temporal dynamics in species co–occurrence. Our results suggest vigilance is needed when selecting surrogates for other co–occurring species in dynamic landscapes, as selected surrogates from one time may have reduced effectiveness at a different time. Ultimately, decisions that fail to acknowledge dynamic species co–occurrence will lead to uninformative or redundant surrogates.
Data from: Fine scale waterbody data improve prediction of waterbird occurrence despite coarse species data
While modelling habitat suitability and species distribution, ecologists must deal with issues related to the spatial resolution of species occurrence and environmental data. Indeed, given that the spatial resolution of species and environmental datasets range from centimeters to hundreds of kilometers, it underlines the importance of choosing the optimal combination of resolutions to achieve the highest possible modelling prediction accuracy. We evaluated how the spatial resolution of land cover/waterbody datasets (meters to 1 km) affect waterbird habitat suitability models based on atlas data (grid cell of 12×11 km). We hypothesized that the area, perimeter and number of waterbodies computed from high resolution datasets would explain distributions of waterbirds better because coarse resolution datasets omit small waterbodies affecting species occurrence. Specifically, we investigated which spatial resolution of waterbodies better explain the distribution of seven waterbirds nesting on ponds/lakes with areas ranging from 0.1 ha to hundreds of hectares. Our results show that the area and perimeter of waterbodies derived from high resolution datasets (raster data with 30 m resolution, vector data corresponding with map scale 1:10,000) explain the distribution of the waterbirds better than those calculated using less accurate datasets despite the coarse grain of the species data. Taking into account the spatial extent (global vs regional) of the datasets, we found the Global Inland Waterbody Dataset to be the most suitable for modelling distribution of waterbirds. In general, we recommend using land cover data of a resolution sufficient to capture the smallest patches of the habitat suitable for a given species' presence for both fine and coarse grain habitat suitability and distribution modelling.
Data from: On the occurrence of three non-native cichlid species including the first record of a feral population of Pelmatolapia (Tilapia) mariae (Boulenger, 1899) in Europe
Thermally influenced freshwater systems provide suitable conditions for non-native species of tropical and subtropical origin to survive and form proliferating populations beyond their native ranges. In Germany, non-native convict cichlids (Amatitlania nigrofasciata) and tilapia (Oreochromis sp.) have established populations in the Gillbach, a small stream that receives warm water discharge from a local power plant. Here, we report on the discovery of spotted tilapia (Pelmatolapia mariae) in the Gillbach, the first record of a reproducing population of this species in Europe. It has been hypothesized that Oreochromis sp. in the Gillbach are descendants of aquaculture escapees and our mtDNA analysis found both O. mossambicus and O. niloticus maternal lineages, which are commonly used for hybrids in aquaculture. Convict cichlids and spotted tilapia were most probably introduced into the Gillbach by aquarium hobbyists. Despite their high invasiveness worldwide, we argue that all three cichlid species are unlikely to spread and persist permanently beyond the thermally influenced range of the Gillbach river system. However, convict cichlids from the Gillbach are known to host both native and non-native fish parasites and thus, non-native cichlids may constitute threats to the native fish fauna. We therefore strongly recommend continuous monitoring of the Gillbach and similar systems.
FIGURES 15–26. 15–19, Pagodula concepcionensis n in New data on recently described Chilean trophonines (Gastropoda: Muricidae), description of a new species and notes of their occurrence at a cold seep site
FIGURES 15–26. 15–19, Pagodula concepcionensis n.sp.; 15–16, Chile, off Concepción, 36°21.75'S, 73°43.55'W, 726–865m, holotype MNHNCL201648, 19mm; 17–18, Chile, off Concepción, 36°21.46'S, 73°44.08'W, 930m, paratype IRSNB IG 30559/565, 19.5mm; 19, Protoconch (holotype) Scale bar 0.5mm; 20–21, Pagodula cf. concepcionensis; Chile, off Concepción, 36°21.46'S, 73°44.08'W, 930m, RH, 21.13mm; 22–24, Trophon veronicae Pastorino, 1999, off southern Chile, 46°00'S, 83°59'W, 742m, holotype USNM 880195, 52.2mm (photo courtesy G. Pastorino). Scale bar: 200µm; 25, Protoconch of Pagodula aculeata (Watson, 1882) (RH). Scale bar: 0.5mm; 26, Protoconch of P. verrillii (Bush, 1893) (RH). Scale bar: 0.5mm.
FIGURES 36–37. 36 in New data on recently described Chilean trophonines (Gastropoda: Muricidae), description of a new species and notes of their occurrence at a cold seep site
FIGURES 36–37. 36, Radula of Boreotrophon cepula (Sowerby, 1880), Kuriles Islands (scale bar: 10µm); 37, Radula of Pagodula aculeata (Watson, 1883), Brazil (scale bar: 10µm).
FIGURES 1–14. 1–4 in New data on recently described Chilean trophonines (Gastropoda: Muricidae), description of a new species and notes of their occurrence at a cold seep site
FIGURES 1–14. 1–4, Trophon condei Houart, 2003; 1, Chile, Ancud, trawled in 1350m, holotype IRSNBIG 29715/512, 61.4mm; 2, Chile, 36°21.65'S, 73°44.42'W, 900904m (AGT 5), JS, 41.6mm; 3–4, Chile, off Concepción, 36°21.46'S, 73°44.08'W, 930m, MNHNCL201646, 41.8mm; 5–10, Trophon ceciliae Houart, 2003; 5–6, Chile, trawled off Caldera, III Región, 434m, coll. E. Garcia, nr 25029, 43.9mm; 7–8, Chile, off Concepción, 36°21.46'S, 73°44.08'W, 930m, JS, 28.7mm (juvenile); 9, Chile, Antofagasta, 1000m, holotype MNHN Moll 4544, 41.5m; 10, Chile, Antofagasta, 1300m, paratype RH, 16.5mm (juvenile); 11–14, Trophon vangoethemi Houart, 2003; 11–12, Chile, trawled off Itata, north of Concepción, in about 350m, Holotype IRSNB IG 29715/ 513, 16.9mm; 13–14, Chile, off Concepción, 36º10.50' S, 73º35.95'W, 563–613m, JS, 13. 14.8mm; 14: 16.8mm.
FIGURES 27–35. 27–29 in New data on recently described Chilean trophonines (Gastropoda: Muricidae), description of a new species and notes of their occurrence at a cold seep site
FIGURES 27–35. 27–29, Coronium wilhelmense (RamírezBohme, 1981); 27–28, Chile, off Valdivia, 39°50'S, 74°30'W, 500m, JS, 18.4mm; 29, Protoconch. Scale bar: 0.5mm; 30, Protoconch of Trophon acanthodes (Watson, 1882) [syntype BM(NH)] 1887.2.9.570. Scale bar: 0.5mm; 31–32, Trophon vangoethemi; 31, Operculum, Chile, off Concepción, 36º10.50' S, 73º35.95' W, 563–613m (scale bar: 1.2mm); 32, Radula, male, same locality (scale bar: 60µm); 33, Radula of Trophon condei, female, off Concepción, Chile, (Sta. AGT 1, 11/30/2003), 36°21.46'S, 73°44.08'W, 930m, (scale bar: 120µm); 34–35, Radula of Pagodula concepcionensis n.sp., female, off Concepción, Chile, (Sta. AGT 1, 11/30/2003), 36°21.46'S, 73°44.08'W, 930m, (scale bar: 60µm).
Data from "Elevation affects both the occurrence of ungulate browsing and its effect on tree seedling growth for four major tree species in European mountain forests"
<p>This repository contains the field data used in the paper from Bernard et al. on the interactive effect of elevation and ungulate browsing on tree regeneration. This dataset is associated with a github repository containing the code to run the analyses of the paper, publicly available at https://github.com/jbarrere3/BaccaraPaper</p>
Data from: Fauxcurrence: simulating multi-species occurrences for null models in species distribution modelling and biogeography
<p>This dataset contains GPS coordinates of occurrences from 22 species from Sulawesi, Indonesia. It was used in the manuscript "Fauxcurrence: simulating multi-species occurrences for null models in species distribution modelling and biogeography" to demonstrate the utility of the fauxcurrence R package (<a href="https://github.com/ogosborne/fauxcurrence">https://github.com/ogosborne/fauxcurrence)</a>.</p>
Actual and predicted distributions of Adoxotoma and Helpis, triangles: actual distribution from field data, and predicted distribution based upon bioclimatic profile for each genus. Growing shade intensity illustrates likelihood of occurrence. in A new genus and five new species of Astieae (Araneae: Salticidae) from Australia, with remarks on distribution
Actual and predicted distributions of Adoxotoma and Helpis, triangles: actual distribution from field data, and predicted distribution based upon bioclimatic profile for each genus. Growing shade intensity illustrates likelihood of occurrence.
Data from: Occurrence of the isopod Archaeoniscus coreaensis new species from the Lower Cretaceous Jinju Formation, Korea
The fossil isopod crustacean genus Archaeoniscus has been known to occur in England, France and Germany during the Upper Jurassic, and in Mexico and Egypt during the Lower Cretaceous. The morphology of this genus is unique in having dorsoventrally compressed body, the cephalon set deeply into the first pereionite, pleon as wide as pereion, and a broad semicircular pleotelson. These features have resulted in placing the classification of the genus in the monotypic family Archaeoniscidae. However, due to the lack of detailed morphological data, suprafamilial classification of this genus has remained unclear, as well as its ecology and lifestyle. Here we report Archaeoniscus coreaensis n. sp. from the Jinju Formation, Gyeongsang Basin, Korea. The occurrence of Archaeoniscus in the East Asia implies that the genus may have had a worldwide distribution. The Gyeongsang Basin was a Cretaceous backarc basin, which consists of exclusively non-marine sedimentary sequences. The occurrence of this genus, therefore, indicates that Archaeoniscus successfully adapted to a freshwater ecosystem as well. Detailed anatomy including antennulae, antennae, pereiopods, and uropods was observed from well-preserved multiple specimens, which allows better understanding of the morphology of Archaeoniscus. The axial structure in the posterior part of the body, which was previously interpreted as a unique brood pouch characterizing the family, turned out to be a remnant of the hindgut. Females of all isopods and most of the members of the superorder Peracarida have a thoracic ventral brood pouch, modified from the thoracic coxal endites. Based on the morphology of the largely unmodified ambulatory pereiopods of A. coreaensis, the possibility of Archaeoniscus being ectoparasitic is discounted. Instead, the flattened body and the form of limbs of A. coreaensis would have been suitable for a benthic lifestyle.
Occurrence data download from GBIF for 115 tree species in Burundi
<p>Cleaned occurrence data from GBIF for 115 tree species in Burundi </p>
Data from: Understanding co-occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM)
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Data from: Distorted views of biodiversity: spatial and temporal bias in species occurrence data
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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.
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DANDI Archive for NWB datasets
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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.