Find research datasets worth reusing

opennotspecifiedApr 2020View details →

FIGURE 6. Unidentified species and Ceramaster grenadensis. A. Unidentified genus and species 1 in New species, occurrence records and observations of predation by deep-sea Asteroidea (Echinodermata) from the North Atlantic by NOAA ship Okeanos Explorer

FIGURE 6. Unidentified species and Ceramaster grenadensis. A. Unidentified genus and species 1, NW Florida Escarpment, Gulf of Mexico, 2178 m. B. C. grenadensis in situ feeding. Unidentified stalks emerging from below (indicated with arrows). Richardson Scarp, North Atlantic. 897 m C. C. grenadensis feeding on coral rubble. Richardson Scarp, North Atlantic. 954 m D. C. grenadensis with yellow scale worm associate (indicated by arrow). Okeanos Ridge, 734 m.

opennotspecifiedJun 2020View details →

FIGURE 3. Eumunida turbulenta n in New occurrences of squat lobsters of the genus Eumunida Smith, 1883 (Decapoda Eumunididae) in New Caledonia, the Solomon Islands and Papua-New Guinea with the description of a new species

FIGURE 3. Eumunida turbulenta n. sp., holotype, ov. F 16.0 mm, Chesterfield Islands (MNHN-IU-2014-23780). A, right P1, dorsal. B, right P1, ventral. C, right P2, lateral. D, right P2 dactylus, lateral. E, right P3, lateral. F, right P4, lateral. Scale: A–C, E, F = 2.0 mm; D = 1.0 mm.

opennotspecifiedJun 2020View details →

FIGURE 2. Eumunida turbulenta n in New occurrences of squat lobsters of the genus Eumunida Smith, 1883 (Decapoda Eumunididae) in New Caledonia, the Solomon Islands and Papua-New Guinea with the description of a new species

FIGURE 2. Eumunida turbulenta n. sp., A–E, H, holotype, ov. F 16.0 mm, Chesterfield Islands (MNHN-IU-2014-23780); F, E. annulosa, F 16.0 mm, New Caledonia (MNHN-IU-2014-23761); G, E. sternomaculata, F 14.7 mm, New Caledonia (MNHN- IU-2011-4533). A, carapace and abdomen, dorsal. B, carapace, right side, lateral. C, sternal plastron. D, telson. E–G, left antenna, ventral. H, right Mxp3 ischium to carpus, lateral. Scale: A–D = 2.0 mm; E–H = 1.0 mm.

opencc-zeroOct 2020View details →

Morning glory species co-occurrence is associated with asymmetrically decreased and cascading reproductive isolation

Hybridization between species can affect the strength of the reproductive barriers that separate those species. Two extensions of this effect are: (1) the expectation that asymmetric hybridization or gene flow will have asymmetric effects on reproductive barrier strength and (2) the expectation that local hybridization will affect only local reproductive barrier strength and could therefore alter within-species compatibility. We tested these hypotheses in a pair of morning glory species that exhibit asymmetric gene flow from highly selfing Ipomoea lacunosa into mixed-mating I. cordatotriloba in regions where they co-occur. Because of the direction of this gene flow, we predicted that reproductive barrier strength would be more strongly affected in I. cordatotriloba than I. lacunosa. We also predicted that changes to reproductive barriers in sympatric I. cordatotriloba populations would affect compatibility with allopatric populations of that species. We tested these predictions by measuring the strength of a reproductive barrier to seed set across the species' ranges. Consistent with our first prediction, we found that sympatric and allopatric I. lacunosa produce the same number of seeds in crosses with I. cordatotriloba, whereas crosses between sympatric I. cordatotriloba and I. lacunosa are more successful than crosses between allopatric I. cordatotriloba and I. lacunosa. This difference in compatibility appears to reflect an asymmetric decrease in the strength of the barrier to seed set in sympatric I. cordatotriloba, which could be caused by I. lacunosa alleles that have introgressed into I. cordatotriloba. We further demonstrated that changes to sympatric I. cordatotriloba have decreased its ability to produce seeds with allopatric populations of the same species, in line with our second prediction. Thus, in a manner analogous to cascade reinforcement, we suggest that introgression associated with hybridization not only influences between-species isolation but can also contribute to isolation within a species.

opencc-zeroJan 2021View details →

Remotely sensed forest understory density and nest predator occurrence interact to predict suitable breeding habitat and the occurrence of a resident boreal bird species

Habitat suitability models (HSM) based on remotely sensed data are useful tools in conservation work. However, they typically use species occurrence data rather than robust demographic variables, and their predictive power is rarely evaluated. These shortcomings can result in misleading guidance for conservation. Here, we develop and evaluate a HSM based on correlates of long term breeding success of an open nest building boreal forest bird, the Siberian jay. In our study site in northern Sweden, nest failure of this permanent resident species is driven mainly by visually hunting corvids that are associated with human settlements. Parents rely on understory nesting cover as protection against these predators. Accordingly, our HSM includes a light detection and ranging (LiDAR) based metric of understory density around the nest and the distance of the nest to the closest settlement to predict breeding success. It reveals that a high understory density 15-80 m around nests is associated with increased breeding success in territories close to settlements (<1.5 km). Farther away from human settlements breeding success is highest at nest sites with a more open understory providing a favourable warmer microclimate. We validated this HSM by comparing the predicted breeding success with landscape-wide census data on Siberian jay occurrence. The correlation between breeding success and occurrence was strong up to 40 km around the study site. However, the HSM appears to overestimate breeding success in regions with a milder climate, and therefore higher corvid numbers. Our findings suggest that maintaining patches of small diameter trees may provide a cost-effective way to restore the breeding habitat for Siberian jays up to 1.5 km from human settlements. This distance is expected to increase in the warmer, southern, and coastal range of the Siberian jay where the presence of other corvids is to a lesser extent restricted to settlements.

FIGURES 35–39 in Megarthrus of China. Part 3. Comments on the occurrence of Megarthrus nitidulus Kraatz, 1857 in China, and description of a new species, with notes on teratology and phoretic acari in the genus (Coleoptera: Staphylinidae: Proteininae)

FIGURES 35–39. Megarthrusheise sp. nov. withanalpedicelsof deutonymphsof Uropodina mites: headandanteriorpartof pronotum of the same specimen in dorsal (35) and oblique (36) views with pedicel on left eye; elytra andabdomen in dorsal view of specimen with pedicels on elytra and abdomen (37); pronotum in dorsal view of specimen with pedicel on pronotum (38); elytra in latetal view of specimen with pedicel on elytra (39). Scale bar = 0.2 mm; up = 35–36, 38–39; down = 37.

FIGURES 29–34 in Megarthrus of China. Part 3. Comments on the occurrence of Megarthrus nitidulus Kraatz, 1857 in China, and description of a new species, with notes on teratology and phoretic acari in the genus (Coleoptera: Staphylinidae: Proteininae)

FIGURES 29–34. Megarthrus heise sp. nov.: antenna (29); male, protibia and protarsus (30); head of male (31) and female (32) in dorsal view; male: apex of abdomen in lateral (33) and dorsal (34) views (T VI = tergite VI, T VII = basal part of abnormal tergite VII, T VII' = posterior part of abnormal tergite VI, T VIII = tergite VIII. Scale bars: 29–32 = 0.1 mm; 33–34 = 0.2 mm.

FIGURES 1–3 in Megarthrus of China. Part 3. Comments on the occurrence of Megarthrus nitidulus Kraatz, 1857 in China, and description of a new species, with notes on teratology and phoretic acari in the genus (Coleoptera: Staphylinidae: Proteininae)

FIGURES 1–3. Megarthrusheise sp. nov., habitus, male: dorsal (1), ventral (2), andlateral (3) views. Scalebar = 0.5 mm.

FIGURES 22–28 in Megarthrus of China. Part 3. Comments on the occurrence of Megarthrus nitidulus Kraatz, 1857 in China, and description of a new species, with notes on teratology and phoretic acari in the genus (Coleoptera: Staphylinidae: Proteininae)

FIGURES 22–28. Megarthrus heise sp. nov., female: genital segments, ventral part in dorsal (22) and lateral (23) views, and dorsal part (24) in ventral view; sternite VIII in ventral view (25); outline of pronotum (26); tergite VIII in dorsal (27) and lateral (28) views. Scale bars: a = 0.2 mm; b–c = 0.1 mm.

FIGURES 10–21 in Megarthrus of China. Part 3. Comments on the occurrence of Megarthrus nitidulus Kraatz, 1857 in China, and description of a new species, with notes on teratology and phoretic acari in the genus (Coleoptera: Staphylinidae: Proteininae)

FIGURES 10–21. Megarthrus heise sp. nov., male: mesotibia in lateral (10) and ventral (11) views; abdominal tergite VIII in lateral (12) and dorsal (21) views; protrochanter and profemur in lateral view (13); mesotrochanter and mesofemur in lateral view (14); metatrochanter and metafemur in lateral view (17–19); metatibia in lateral (15) and ventral (16) views; abdominal sternite VIII in ventral view (20). Scale bar = 0.1 mm.

opencc-zeroDec 2018View details →

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.

opencc-zeroDec 2016View details →

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.

opencc-zeroDec 2017View details →

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.

opencc-zeroDec 2015View details →

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.

opencc-zeroSep 2019View details →

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.

opencc-zeroDec 2016View details →

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.

opencc-zeroDec 2015View details →

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.

opencc-zeroDec 2017View details →

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.

opencc-zeroDec 2016View details →

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.