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Data from: Combining human acceptance and habitat suitability in a unified socio-ecological suitability model: a case study of the wolf in Switzerland
Habitat suitability models (HSMs) are commonly used in conservation practise to assess the potential of an area to be occupied and colonised. A major limitation of these models, however, is the omission of spatially explicit understanding of human acceptance towards the focal species. As wildlife is more and more subject to human-dominated landscapes, ignoring the sociological component will result in misrepresentation of the observed processes and inappropriate management. We distributed 10 000 questionnaires across Switzerland and identified key socio-demographical factors correlated with human acceptance of the wolf. We then created a spatially explicit acceptance model based on geo-referenced socio-demographical, social and geographical information. Finally, we combined our acceptance model with a HSM to obtain a unified socio-ecological suitability model, which included human and ecological components. We showed that the key factors associated with human acceptance were perception of how harmful the wolf is, interest in wolf-related issues, need for livestock protection, and fear of the wolf. Perceived harmfulness was in turn correlated with direct and indirect experience with the wolf, and level of education. Our acceptance map predicted decreasing acceptance with increasing altitude of residency and proximity to locations of confirmed wolf presence. This resulted in the overall opposition to the wolf for the Alpine region, albeit substantial regional differences. We found little spatial overlap (6% of Switzerland) between areas where the wolf was accepted and areas of suitable habitat. These areas of socio-ecological suitability were concentrated in the Jura Mountains and in the eastern and southern Alps, and were absent in the western and central Alps. Particularly in the Jura region, which is yet to be colonised, management of human acceptance will be a crucial conservation target. Synthesis and applications. We developed an integrative, socio-ecological approach that allowed us to accurately reproduce recent wolf recolonisation. We anticipate our framework to be a powerful tool to reliably evaluate overall suitable habitats and predict short to medium-term range expansion for species whose distribution is also dependent on human attitudes. Because our approach is sensitive to both the ecological and human component, it is ideally suited to identify key regions where proactive and targeted socio-ecological management plans are needed.
Data from: Wind farms affect the occurrence, abundance and population trends of small passerine birds: the case of the Dupont's lark
1.The assessment of the effects of wind farms on bird populations is commonly based on collision fatality records. This could undervalue the effect of wind farms on small-sized birds. We evaluate the effect of wind turbines on occurrence, abundance and population trends of a threatened small passerine species, the Dupont's lark Chersophilus duponti. To our knowledge, this is one of the first studies addressing the effect of wind farms on population trends using time series data from multiple wind farms. 2.We estimated population trends by fitting a switching linear trend model with the software TRIM (Trend & Indices for Monitoring data). We used multiannual data surveys of five populations in the presence of wind farms and nine in their absence (2008–2016 period). Furthermore, we fitted a logistic and a negative binomial regression model to test the effect of wind farm proximity on species occurrence and abundance in 2016, respectively. We incorporated local connectivity and habitat availability estimates in both models as predictors. 3.Results showed a negative trend overall, but that was significantly more regressive in the presence of wind farms: 21.0% versus 5.8% average annual decline in the absence of wind farms. 4.Dupont's lark occurrence and abundance in 2016 were negatively affected by measures of population isolation and positively affected by the distance to wind farms. 5.These results highlight the negative effect of isolation and wind farm proximity on Dupont's lark population parameters. Taking into account the metapopulation structure exhibited by the species in the study area, this work established a 4.5 km threshold distance from wind farms, beyond which Dupont's lark populations should be unaffected. 6.Synthesis and applications. This work highlights the negative impact of wind farms on small-sized birds and provides a 4.5 km threshold distance that should be taken into account in the design of future wind energy projects. Moreover, we suggest an analytical approach based on population trends, species abundance and occurrence variation in relation to wind farms, useful for the assessment of wind farm impacts on small-sized birds.
Data from: Shifting niches of marine predators due to human exploitation: the diet of the South American sea lion (Otaria flavescens) since the late Holocene as a case study
Stable isotope ratios of carbon and nitrogen in archaeological and modern bone samples have been used to reconstruct the dietary changes of the South American sea lion Otaria flavescens from the late Holocene to the present in the southwestern Atlantic. We sampled bones from archaeological sites in northern-central and southern Patagonia, Argentina, and bones housed in modern scientific collections. Additionally, we analyzed the stable isotope ratios in ancient and modern shells of intertidal molluscs to explore changes in the isotope baseline and allow comparison between bone samples from different periods after correction for baseline shifts. Results confirmed the trophic plasticity of the South American sea lion, demonstrated the much larger impact of modern exploitation of marine resources as compared with that of hunter-gatherers, and underscored the dissimilarity between the past and modern niches of exploited species. These conclusions are supported by the rather stable diet of South American sea lions during several millennia of aboriginal exploitation, in both northern-central and southern Patagonia, and the dramatic increase in trophic level observed during the twentieth century. The recent increase in trophic level might be related to the smaller population size resulting from modern sealing and the resulting reduced intraspecific competition. These results demonstrate how much can be learned about the ecology of modern species thanks to retrospective studies beyond the current, anthropogenically modified setting where ecosystem structure is totally different from that in the pristine environments where current species evolved.
Data from: Testing the potential of DNA barcoding in vertebrate radiations: the case of the littoral cichlids (Pisces, Perciformes, Cichlidae) from Lake Tanganyika
We obtained 398 cytochrome c oxidase subunit I barcodes of 96 morphospecies of Lake Tanganyika (LT) cichlids from the littoral zone. The potential of DNA barcoding in these fishes was tested using both species identification and species delineation methods. The best match (BM) and best close match (BCM) methods were used to evaluate the overall identification success. For this, three libraries were analysed in which the specimens were categorized into Operational Taxonomic Units (OTU) in three alternative ways: (A) morphologically distinct, including undescribed, species, (B) valid species and (C) complexes of morphologically similar or closely related species. For libraries A, B and C, 73, 73 and 96% (BM) and 72, 70 and 94% (BCM) of the specimens were correctly identified. Additionally, the potential of two species delineation methods was tested. The General Mixed Yule Coalescent (GMYC) analysis suggested 70 hypothetical species, while the Automatic Barcode Gap Discovery (ABGD) method revealed 115 putative species. Although the ABGD method had a tendency to oversplit, it outperformed the GMYC analysis in retrieving the species. In most cases where ABGD suggested oversplitting, this was due to intraspecific geographical variation. The failure of the GMYC method to retrieve many species could be attributed to discrepancies between mitochondrial gene trees and the evolutionary histories of LT cichlid species. Littoral LT cichlids have complex evolutionary histories that include instances of hybridization, introgression and rapid speciation. Nevertheless, although the utility of DNA barcoding in identification is restricted to the level of complexes, it has potential for species discovery in cichlid radiations.
Data from: Species discrimination of co-occurring small fossil mammals: a case study of the Cretaceous-Paleogene multituberculate genus Mesodma
The mammalian fossil record is largely composed of isolated teeth and tooth-bearing elements. In vertebrate microfossil assemblages with closely related, co-occurring species of mammals, it can be difficult to identify isolated teeth to species level because morphological differences among species may be slight and based on a single tooth position. Here we investigate the utility of the allegedly diagnostic lower fourth premolar (p4) for species-level identification in the genus Mesodma (Multituberculata, Neoplagiaulacidae). We conducted linear and geometric morphometrics on 86 p4s representing four Cretaceous-Paleogene (K-Pg) species of Mesodma that are common in deposits of the western interior of North America. Although Mesodma has been extensively discussed in the literature, these four species overlap considerably in p4 size and shape, making species-level identifications challenging. Using linear measurements, landmarks, and semilandmarks, we quantified p4 size and shape to understand morphological variation across the genus and uncover practical sources of morphological differentiation among the species represented here. Our results indicate (1) size is more important than shape for identifying p4s of Mesodma species; p4 shape varies across the genus, but cannot be used alone to identify isolated p4s to species; (2) M. garfieldensis and M. thompsoni cannot be distinguished from each other using p4 size or shape; we therefore subsume M. garfieldensis within M. thompsoni; and (3) M. formosa increased in size across the K-Pg boundary. In light of these results, we recommend that taxonomic diagnoses relying on isolated teeth incorporate quantitative analyses of morphology whenever possible to increase the accuracy of species-level identifications and paleofaunal studies that employ them.
Data from: Ancient vicariance and climate-driven extinction explain continental-wide disjunctions in Africa: the case of the Rand Flora genus Canarina (Campanulaceae)
Transoceanic distributions have attracted the interest of scientists for centuries. Less attention has been paid to the evolutionary origins of 'continent-wide' disjunctions, in which related taxa are distributed across isolated regions within the same continent. A prime example is the 'Rand Flora' pattern, which shows sister taxa disjunctly distributed in the continental margins of Africa. Here, we explore the evolutionary origins of this pattern using the genus Canarina, with three species: C. canariensis, associated with the Canarian laurisilva, and C. eminii and C. abyssinica, endemic to the Afromontane region in East Africa, as case study. We infer phylogenetic relationships, divergence times and the history of migration events within Canarina using Bayesian inference on a large sample of chloroplast and nuclear sequences. Ecological niche modelling was employed to infer the climatic niche of Canarina through time. Dating was performed with a novel nested approach to solve the problem of using deep time calibration points within a molecular dataset comprising both above-species and population-level sampling. Results show C. abyssinica as sister to a clade formed by disjunct C. eminii and C. canariensis. Miocene divergences were inferred among species, whereas infraspecific divergences fell within the Pleistocene–Holocene periods. Although C. eminii and C. canariensis showed a strong genetic geographic structure, among-population divergences were older in the former than in the latter. Our results suggest that Canarina originated in East Africa and later migrated across North Africa, with vicariance and aridification-driven extinction explaining the 7000 km/7 million year divergence between the Canarian and East African endemics.
Data from: Paleo-islands as refugia and sources of genetic diversity within volcanic archipelagos: The case of the widespread endemic Canarina canariensis (Campanulaceae)
Geographical isolation by oceanic barriers and climatic stability has been postulated as some of the main factors driving diversification within volcanic archipelagos. However, few studies have focused on the effect that catastrophic volcanic events have had on patterns of within-island differentiation in geological time. This study employed data from the chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine the patterns of genetic variation in Canarina canariensis, an iconic plant species associated with the endemic laurel forest of the Canary Islands. We found a strong geographical population structure, with a first divergence around 0.8 Ma that has Tenerife as its central axis and divides Canarian populations into eastern and western clades. Genetic diversity was greatest in the geologically stable 'palaeo-islands' of Anaga, Teno and Roque del Conde; these areas were also inferred as the ancestral location of migrant alleles towards other disturbed areas within Tenerife or the nearby islands using a Bayesian approach to phylogeographical clustering. Oceanic barriers, in contrast, appear to have played a lesser role in structuring genetic variation, with intra-island levels of genetic diversity larger than those between-islands. We argue that volcanic eruptions and landslides after the merging of the palaeo-islands 3.5 Ma played key roles in generating genetic boundaries within Tenerife, with the palaeo-islands acting as refugia against extinction, and as cradles and sources of genetic diversity to other areas within the archipelago.
Data from: Dealing with allometry in linear and geometric morphometrics: a taxonomic case study in the Leporinus cylindriformis group (Characiformes: Anostomidae) with description of a new species from Suriname
To achieve maximum efficacy, taxonomic studies that seek to distinguish amongst species must first account for allometric shape variation within species. Two recently developed software packages (SMATR and MorphoJ) offer regression-based allometric approaches that are notable for their statistical power and ease of use and that may prove highly useful to taxonomists working with linear or geometric morphometric data. We investigate species delimitation of the slender-bodied fishes in the Leporinus cylindriformis group using these programs and demonstrate the utility of the allometric corrections that they provide. Without allometric correction, many pairs of species are difficult to distinguish on the basis of morphometrics, but once regressions are used to account for marked allometric variation within species, most of the recognized species in this group can be readily distinguished with linear or geometric morphometrics, particularly using variation in the depth of the body. Both approaches returned congruent patterns of separation amongst putative species, but the geometric approach in MorphoJ distinguished amongst four more pairs of species than did the linear approach in SMATR and appears to provide slightly more statistical power. Based on distinctive morphometrics, meristics, and coloration, a highly elongate species of Leporinus from the Suriname, Corantijn, and Coppename rivers of Suriname is described herein as a new species, Leporinus apollo sp. nov. The unique L. cylindriformis holotype from Porto de Moz, Brazil differs in morphology, meristics, and pigmentation from specimens commonly referred to that species from the main basin of the Amazon; the latter specimens may represent an additional undescribed species. The L. cylindriformis holotype itself may represent a rare species or a specimen collected at the edge of its native range. Measurements of the holotype and paratype of Leporinus niceforoi, which were collected in the Amazonian slope of Colombia, differ substantially from similarly pigmented and putatively conspecific specimens from Amazonian portions of Ecuador and Peru. Recently collected specimens from Colombia are needed to determine whether the observed morphometric variation encompassed by the current concept of L. niceforoi indicates a morphocline within a single species, suggests the presence of multiple cryptic species, or results from shrinkage of the types. In all these cases, linear or geometric morphometric data can reliably differentiate amongst species, but only after one accounts for allometric shape variation. The new SMATR and MorphoJ software packages both offer easy and effective approaches to such allometrically informed taxonomy, and may prove useful to any systematist working on taxa that change shape as they grow.
Figure 1 in Wolves in sheep's clothing: three new cases of aggressive mimicry in Red Sea coral reef fishes
Figure 1. New records of mimicry in the Red Sea: (a) juvenile Diploprion drachi, a mimic of (b) Meiacanthus nigrolineatus; (c) juvenile Epinephelus leucogrammicus, a mimic of (d) Larabicus quadrilineatus; (e) juvenile Plectropomus marisrubri, a mimic of (f) Cheilinus quinquecinctus. (Photos: Luiz A. Rocha).
Figure 2. A in Wolves in sheep's clothing: three new cases of aggressive mimicry in Red Sea coral reef fishes
Figure 2. A juvenile Epinephelus leucogrammicus embedded in a cleaning station with Larabicus quadrilineatus. (Photo: Luiz A. Rocha).
Schizophrenia and Bartonella spp. infection: A pilot case–control study
<p>Recently, infections with emerging zoonotic bacteria of the genus Bartonella have been reported in association with a range of CNS symptoms. Currently, it remains unknown if Bartonella spp. infection is associated with symptoms of schizophrenia/schizoaffective disorder (SCZ/SAD). The objective of this study was to determine if there is an association between Bartonella species infection and SCZ/SAD. A secondary objective was to determine if SCZ/SAD symptoms were more severe among participants with documented Bartonella spp. infection. Using a case–control study design, 17 cases and 13 controls were evaluated with a series of clinical and cognitive assessments. Blood samples were collected and tested for Bartonella spp. infection using serological, microbiological, and molecular techniques. People with SCZ/SAD were more likely than healthy volunteers to have Bartonella spp. DNA in their bloodstream, with 11 of 17 cases (65%) positive by Bartonella spp. droplet digital PCR (ddPCR). In comparison, only one healthy volunteer was Bartonella spp. ddPCR positive (8%, p = 0.0024). Based on serology, Bartonella spp. exposure was common among people with SCZ/SAD (12 of 17) as well as among healthy volunteers (12 of 13), with no significant difference between the groups ( p = 0.196). Within the case group of people with SCZ/SAD, there was no significant difference in SCZ/SAD severity scores between people with and without ddPCR evidence of Bartonella spp. infection. This pilot study provides preliminary evidence in support of future investigations that should examine a potential contribution of Bartonella spp. infection to SCZ/SAD.</p>
Figure 3 in Amphibian taxonomy: early 21st century case studies
Figure 3. (a) Bar plot depicting number of new species of Amphibia described during 2015–2019 from global biodiversity hotspots. (b) Map depicting the distribution of hotspots that new amphibians were described from during 2015–2019. (c) Bar plot depicting number of new species of Amphibia described from broad geographical regions during 2015–2019. Europe and Central Asia have been combined due to geographic proximity and small sample sizes from Central Asia (N = 1).
Figure 2 in Amphibian taxonomy: early 21st century case studies
Figure 2. (a) Bar plot depicting number of new species of Amphibia described from each family across three extant orders (Anura, Caudata, and Gymnophiona) during 2015–2019. (b) Relationship between the number of new species described from each family and the overall number of species known from each family according to Frost (2020). Data have been fitted with a linear smoother using the 'lm' function from ggplot2 (Wickham 2016).
Figure 1 in Amphibian taxonomy: early 21st century case studies
Figure 1. (a) Description of new species of Amphibia from 2004 to 2019. Note that the number of species described has been similar during this timeframe and that there is no clear trend of increase or decrease. Data obtained amphibiaweb.org. (b) Types of data used to describe new species of Amphibia from 2015 to 2019. See text for definitions of data types. Proportion is out of 732 new species surveyed for our study. (c) Proportion of integrative studies (using two or more lines of evidence) to describe species of Amphibia from 2015 to 2019. Proportion is out of 732 new species surveyed for our study. Note general increase over the survey period. (d) Approximate DNA sequence alignment lengths used to describe species of Amphibia from 2015 to 2019 for mitochondrial (mtDNA) and nuclear DNA (nDNA). Alignment lengths have been Log10-transformed. Note increase in size of nDNA datasets in 2019.
Development of a versatile source apportionment analysis based on positive matrix factorization: a case study of the seasonal variation of organic aerosol sources in Estonia
<p>This work presents an advanced source apportionment approach that estimates the uncertainties of the positive matrix factorization model. The selection of the environmentally meaningful solutions is challenging in such models and a systematic approach to identify and sort the factors is important. We applied this method to a novel data set covering one yearly cycle at three sites in Estonia. The main results showed that biomass burning dominates in winter, while biogenic sources prevail in summer.</p>
Supplementary material 1 from: Mesibov R (2020) A second remarkable case of parapatry in a Tasmanian millipede genus (Diplopoda, Polydesmida, Dalodesmidae). In: Korsós Z, Dányi L (Eds) Proceedings of the 18th International Congress of Myriapodology, Budapest, Hungary. ZooKeys 930: 89-101. https://doi.org/10.3897/zookeys.930.38031
Specimen data for Tasmaniosoma armatum Verhoeff, 1936, T. clarksonorum Mesibov, 2010, T. orientale Mesibov, 2010 and specimens not yet identifiable as T. armatum or T. orientale
Spectacles case
WWII artefact #31A Source: Objaverse 1.0 / Sketchfab
Card Case 2
For more information about this item visit: https://bhpsite.org/ Source: Objaverse 1.0 / Sketchfab
A Chinese female Morvan patient with LGI1 and CASPR2 antibodies: a case report
<p>Video 1. shaking of the toes and myokymia of lower limbs.</p>
Trasncripts and Survey from Case Study of Small Collaboration
<p>To identify the particularities of the small collaboration we used an exploratory case study methodology. The case study followed an embedded case study design and we collected data via semi-structured interviews and the SDR’s logs. In the study, we explored three topics: the scientific collaboration process, the collaboration’s data-sharing practices and attitudes.</p> <p>We found that, on the topic of collaboration, the collaborations suffered the common problems of geographically distributed collaborations. In terms of data- sharing practices and attitudes, we found that collaborators were solely motivated by extrinsic incentives. They showed a very restricted awareness of potential benefits, and sharing only occurred under low risk scenarios.</p> <p>We begin this section with the description of the exploratory study. We then present the results and a discussion of this exploration and propose three empirical claims.</p> <p> </p>
ScienceDex guides
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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.