cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pc866t1k3
title: Data from: Structural colours in diverse Mesozoic insects

description: Structural colours, nature’s most pure and intense colours, originate when
 light is scattered via nanoscale modulations of the refractive index.
 Original colours in fossils illuminate the ecological interactions among
 extinct organisms and functional evolution of colours. Here we report
 multiple examples of vivid metallic colours in diverse insects from
 mid-Cretaceous amber. Scanning and transmission electron microscopy
 revealed a smooth outer surface and five alternating electron-dense and
 electron-lucent layers in the epicuticle of a fossil wasp, suggesting that
 multilayer reflectors, the most common biophotonic nanostructure in
 animals and even plants, are responsible for the exceptional preservation
 of colour in amber fossils. Based on theoretical modeling of the
 reflectance spectra, a reflective peak of wavelength of 514 nm was
 calculated, corresponding to the bluish green colour observed under white
 light. The green to blue structural colours in fossil wasps, beetles, and
 a fly most likely functioned as camouflage, although other functions such
 as thermoregulation cannot be ruled out. This discovery not only provides
 critical evidence of evolution of structural colours in arthropods, but
 also sheds light on the preservation potential of nanostructures of
 ancient animals through geological time.
description: For standard observation, fossils were polished using different
 grades of sandpaper and diatomite powder, to get as close to the
 inclusions as possible without damaging them. Where it aided observation,
 some pieces were polished into very thin slices, making the insect
 inclusions clearly observable and the surrounding amber matrix almost
 transparent in bright light. Photographs against various backgrounds were
 taken using a Canon EOS 5D Mark III digital camera, equipped with a Canon
 MP-E 65 mm macro lens (F2.8, 1–5X), and with an attached Canon MT-24EX
 twin flash. Focus stacking software (Zerene Stacker, Version 1.04) was
 used to increase the depth of field. The resultant images were edited in
 Photoshop only to correct brightness and contrast. Two amber-entombed
 wasps (metallic coloured and silvery) were selected for ultrastructural
 analysis of the cuticles. Ultrathin (70 nm thick) sections were cut with a
 Diatome 3 mm 45° diamond knife, mounted on formvar-coated copper grids,
 and air dried. Unstained sections were imaged using a JEM-2100 Plus
 transmission electron microscope (at Nanjing Institute of Geography and
 Limnology, Chinese Academy of Sciences) at 80 keV. The sectioned samples
 were mounted on stubs with double-sided carbon tape. The sectioned surface
 was imaged with a LEO 1530 VP analytical scanning electron microscope
 controlled by JEOL InTouchScope version 1.05A software, using the
 variable-pressure secondary electron detector at low vacuum and at 18
 keV.
DOI: 10.5061/dryad.msbcc2fv7
title: Can time-to-detection models with fewer survey replicates provide a robust alternative to traditional site-occupancy models?

description: Occupancy models are widely used in ecology because they explicitly
 separate the observation and state processes and hence account for
 imperfect species detection. Traditional occupancy models that record
 detection/non-detection (DND) of a species typically rely on either
 spatial or temporal  survey replication to estimate model
 parameters. Recording the time until a species is first encountered after
 starting a survey is often possible with little extra effort and such
 time-to-detection (TTD) surveys may be more efficient than pure DND
 surveys. Using continuous time data, TTD occupancy models can in theory
 estimate occupancy and detection parameters using a single TTD survey.
 These models therefore have the potential to drastically reduce the
 logistical effort and costs associated with traditional occupancy survey
 designs. However, the robustness and general applicability of TTD models
 has not been widely addressed and their effectiveness in different study
 systems remains unknown. We use simulations and bird data of 63 species
 from a field study in the Karoo region of South Africa to explicitly
 compare estimates of occupancy, detection and species richness between DND
 and TTD models under various levels of survey replication and for species
 with different occupancy and detection characteristics. Simulations
 revealed that for inconspicuous species (low detection probability) single
 survey TTD models can perform better or equally as well as DND models with
 a higher number of replicates. This effect was attenuated in widespread
 species (high occupancy probability). The benefits of TTD models were more
 pronounced at low survey replicates and performance of the two methods
 converged quickly as the number of survey replicates increased. The
 difference in model performance related to precision around estimates
 while the bias in parameter means was fairly low. However, results from
 the field data showed that a single TTD survey was not adequate to
 reliably estimate occupancy, detection and species richness; especially in
 rare and inconspicuous species. Increasing the number of TTD surveys to
 two replicates improved the models substantially. Our results demonstrate
 the general utility of TTD surveys depends on the characteristics of the
 species considered in the study. A single TTD survey may be sufficient in
 some study designs but is unlikely to be sufficient in most multi-species
 field scenarios where communities are made up of species that have a wide
 range of detection and occupancy probabilities. TTD surveys do provide
 benefits however in that data can be used to construct detection curves
 which can be used to guide survey effort in the design of future studies.
DOI: 10.5061/dryad.18931zcsr
title: Climate change and maladaptive wing shortening in a long-distance migratory bird

description: Contemporary phenotypic trends associated with global change are widely
 documented, but whether such trends always denote trait optimization under
 changed conditions remains obscure. Natural selection has shaped the wings
 of long-distance migratory birds to minimize the costs of transport, and
 new optimal wing shapes could be promoted by migration patterns altered
 due to global change. Alternatively, wing shape could vary as a correlated
 response to selection on other traits favoured in a changing environment,
 eventually moving away from the optimal shape for migration and increasing
 transport costs. Data from 20 years of monitoring of two Common
 Nightingale (Luscinia megarhynchos) populations breeding in central Spain,
 where environmental conditions for breeding have deteriorated during the
 last decades due to increased summer drought, show that birds have reduced
 wing length relative to body size over the period 1995-2014. However,
 long-winged nightingales survived their first round-trip migration better,
 and the shorter the average wing length of individuals, the stronger the
 survival-associated natural selection favouring longer wings. Maladaptive
 short wings may have arisen because the mortality costs of migration are
 outweighed by reproductive benefits accrued by short-winged nightingales
 in these populations. Assuming that the phenotypic integration of
 morphological and reproductive adaptations of migratory birds has a
 genetic basis, we hypothesize that the maladaptive trend towards shorter
 wings may be a correlated response to selection for moderate breeding
 investment in drying habitat. Our results provide evidence that
 contemporary phenotypic change may deviate average trait values from their
 optima, thereby increasing our understanding of the ecological constraints
 underpinning adaptation to rapid global change.
description: According to the journal
 (The Auk) policy about the ethical re-use of data, and considering the
 effort that the members of the SEO-Monticola ringing group put in
 assembling this database, we would appreciate that anyone interested in
 re-using the data to contact the corresponding author in order to agree to
 a collaboration when appropriate. Analyses reported in this article
 can be reproduced using the data provided. In the README for databases.txt
 you can find a description of the variables included in each database
 file. Missing values are designated as NA.
DOI: 10.5061/dryad.8kprr4xjs
title: Immunological changes in nestlings growing under predation risk

description: Predation is one of the most relevant selective forces in nature. However,
 the physiological mechanisms behind anti‐predator strategies have been
 overlooked, despite their importance to understand predator‐prey
 interactions. In this context, the immune system could be especially
 revealing due to its relationship with other critical functions and its
 ability to enhance prey's probabilities of survival to a
 predator's attack. Developing organisms (e.g. nestlings) are
 excellent models to study this topic because they suffer a high predation
 pressure while undergoing the majority of their development, which
 maximizes potential trade‐offs between immunity and other biological
 functions. Using common blackbirds (Turdus merula) as model species, we
 experimentally investigated whether an elevated nest predation risk during
 the nestling period affects nestlings’ immunity and its possible
 interactions with developmental conditions (i.e. body condition and
 growth). Experimental nestlings modified some components of their
 immunity, but only when considering body condition and growth rate,
 indicating a multifaceted immunological response to predation risk and an
 important mediator role of nestlings’ developmental conditions. Predation
 risk induced a suppression of IgY but an increase in lymphocytes in
 nestlings with poor body condition. In addition, experimental but not
 control nestlings showed a negative correlation between growth and
 heterophils, demonstrating that nest predation risk can affect the
 interaction between growth and immunity. This study highlights the
 importance of immunity in anti‐predator response in nestlings and shows
 the relevance of including physiological components to the study of
 predation risk.  
description: These data refer to the immunological parameters analysed in
 order to detect the differences between nestlings of control (C) and
 treatment (T) groups. All the immunological components are
 reported, together with body condition (BMI) and growth rate
 (KT).
DOI: 10.6084/m9.figshare.31158847
title: VolE: A Point-cloud Framework for Food 3D Reconstruction and Volume Estimation

description: Accurate food volume estimation is crucial for medical nutrition management and health monitoring applications. However, existing methods for estimating food volume are often constrained by the use of monocular data. They typically rely on specialised hardware such as 3D scanners, gather sensor-specific information such as depth data, or depend on camera calibration with reference objects. In this paper, we present VolE, a novel framework that leverages mobile device-driven 3D reconstruction to estimate food volume. VolE captures images and camera locations in free motion to generate precise 3D models, thanks to AR-capable mobile devices. To achieve real-world measurement, VolE is a reference- and depth-free framework that leverages food video segmentation for food mask generation. We also introduce a new food dataset encompassing the challenging scenarios absent in the previous benchmarks. Our experiments demonstrate that VolE outperforms the existing volume estimation techniques across multiple datasets by achieving 2.22\% MAPE, highlighting its superior performance in food volume estimation.
DOI: 10.6084/m9.figshare.31158847.v1
title: VolE: A Point-cloud Framework for Food 3D Reconstruction and Volume Estimation

description: Accurate food volume estimation is crucial for medical nutrition management and health monitoring applications. However, existing methods for estimating food volume are often constrained by the use of monocular data. They typically rely on specialised hardware such as 3D scanners, gather sensor-specific information such as depth data, or depend on camera calibration with reference objects. In this paper, we present VolE, a novel framework that leverages mobile device-driven 3D reconstruction to estimate food volume. VolE captures images and camera locations in free motion to generate precise 3D models, thanks to AR-capable mobile devices. To achieve real-world measurement, VolE is a reference- and depth-free framework that leverages food video segmentation for food mask generation. We also introduce a new food dataset encompassing the challenging scenarios absent in the previous benchmarks. Our experiments demonstrate that VolE outperforms the existing volume estimation techniques across multiple datasets by achieving 2.22\% MAPE, highlighting its superior performance in food volume estimation.
DOI: 10.5061/dryad.n5tb2rbs8
title: Community structure of vascular epiphytes: a neutral perspective

description: Vascular epiphytes form a diverse group of almost 30,000 species, yet
 theory concerning their community structure is still largely lacking. We
 therefore employed simple models of biodiversity, (near-)neutral models,
 to study to what extent they can explain their community structure. With
 recently developed tools for (near-)neutral models we analyzed species
 abundance data from many samples in Central and South America which we
 divided into four metacommunities (Mesoamerica, Central America, Amazonia
 and Paraná). For each metacommunity we considered two subsets differing in
 dispersal syndrome: an animal-dispersed guild and a wind-dispersed guild.
 We considered three models differing in the underlying speciation mode.
 Across all metacommunities, we found observed patterns to be
 indistinguishable from patterns generated by neutral or near-neutral
 processes. Furthermore, we found that subdivision in different dispersal
 guilds was often supported, with recruitment limitation being stronger for
 animal-dispersed species than for wind-dispersed species. This is the
 first time that (near-)neutral theory has been applied to epiphyte
 communities. Future efforts with additional data sets and more refined
 models are expected to further improve our understanding of community
 structure in epiphytes and will have to test the generality of our
 findings.
description: Data was collected from the literature. 
 Processing was performed using R.
description: See README files for further information
DOI: 10.5061/dryad.pk0p2ngjn
title: Epistasis, inbreeding depression and the evolution of self-fertilization

description: Inbreeding depression resulting from partially recessive deleterious
 alleles is thought to be the main genetic factor preventing
 self-fertilizing mutants from spreading in outcrossing hermaphroditic
 populations. However, deleterious alleles may also generate an advantage
 to selfers in terms of more efficient purging, while the effects of
 epistasis among those alleles on inbreeding depression and mating system
 evolution remain little explored. In this paper, we use a general model of
 selection to disentangle the effects of different forms of epistasis
 (additive-by-additive, additive-by-dominance and dominance-by-dominance)
 on inbreeding depression and on the strength of selection for selfing.
 Models with fixed epistasis across loci, and models of stabilizing
 selection acting on quantitative traits (generating distributions of
 epistasis) are considered as special cases. Besides its effects on
 inbreeding depression, epistasis may increase the purging advantage
 associated with selfing (when it is negative on average), while the
 variance in epistasis favors selfing through the generation of linkage
 disequilibria that increase mean fitness. Approximations for the strengths
 of these effects are derived, and compared with individual-based
 simulation results.
description: See README files for further information
DOI: 10.5061/dryad.2rbnzs7jc
title: Metabolic syndrome and risk of lung cancer: An analysis of Korean National Health Insurance Corporation database

description: Introduction: Metabolic syndrome is known to increase the risk of several
 cancers. However, the association between lung cancer and metabolic
 syndrome remains unclear. Thus, we investigated the impact of metabolic
 syndrome on the incidence of lung cancer. Methods: This study enrolled
 participants in a health screening program provided by the Korean National
 Health Insurance Service between January 2009 and December 2012. The
 incidence of lung cancer was observed until December 2016. We analyzed the
 risk of lung cancer according to the presence of metabolic syndrome,
 metabolic syndrome components, and number of metabolic syndrome
 components. Results: During the study, 45,635 new cases of lung cancer
 were recorded among 9,586,753 participants. The presence of metabolic
 syndrome and all its components was positively associated with the risk of
 lung cancer in males after multivariate adjustment (hazard ratio (HR) of
 metabolic syndrome 1.15, 95% confidence interval (CI) = 1.12–1.18). The
 risk of lung cancer increased with the number of components present. The
 effect of metabolic syndrome on the increasing risk of lung cancer is may
 be higher in underweight male ever smokers than in other participants.
 Conclusion: Metabolic syndrome was associated with an increased risk of
 lung cancer in males. Moreover, the higher the number of metabolic
 syndrome components, the higher the risk of lung cancer.
DOI: 10.5061/dryad.qz612jmb0
title: Data from: Stay home, stay safe: site familiarity reduces predation risk in a large herbivore in two contrasting study sites

description: 1. Restricting movements to familiar areas should increase individual
 fitness as it provides animals with information about the spatial
 distribution of resources and predation risk. While the benefits of
 familiarity for locating resources have been reported previously, the
 potential value of familiarity for predation avoidance has been accorded
 less attention. It has been suggested that familiarity should be
 beneficial for anti-predator behaviour when direct cues of predation risk
 are unclear and do not allow prey to identify well defined spatial
 refuges. However, to our knowledge, this hypothesis has yet to be tested.
 2. Here, we assessed how site familiarity, measured as the intensity of
 use of a given location, is associated with the probability of roe deer
 (Capreolus capreolus) being killed by two predators with contrasting
 hunting tactics, the Eurasian lynx (Lynx lynx) and human hunters. While
 risk of human hunting was confined to open habitats, risk of lynx
 predation was more diffuse, with no clear refuge areas. 3. We estimated
 cause-specific mortality rates in a competing risk framework for 212
 GPS-collared roe deer in two ecologically distinct areas of Central Europe
 to test the hypothesis that the daily risk of being killed by lynx or
 hunters should be lower in areas of high familiarity. 4. We found strong
 evidence that site familiarity reduces the risk of being predated by lynx,
 whereas the evidence that the risk of being hunted is linked to site
 familiarity was weak. 5. We suggest that local knowledge about small scale
 differences in predation risk and information about efficient escape
 routes affect an individual’s ability to avoid or escape an attack by an
 ambush predator. Our study emphasises the role of site familiarity in
 determining the susceptibility of prey to predation. Further research will
 be required to better understand how a cognitive map of individual spatial
 information is beneficial for avoiding predation in the arms race that
 drives the predator-prey shell game.
description: The roe deer location data were collected from radio-collared
 animals in the two study sites Bernese (Switzerland) and Bavaria
 (Germany). Kill locations were collected through systematic searches of
 GPS clusters of radio-collared lynx. The data was processed as described
 in detail in the method section of the article.
description: The datasets provided can
 be used to repeat the analyses described in the article. We provide the
 processed raw dataset, meaning that for some fields of the competing risk
 datset some rows (i.e. coverhunt and coverhunttime - see ReadMe file)
 contain missing values which were omitted in the analysis. Raw data are also available
 through the EURODEER platform. Anyone is welcome to join the EURODEER
 project and obtain an access to the database after contacting the persons
 in charge (see https://eurodeer.org/contacts/).
DOI: 10.5061/dryad.6wwpzgmtx
title: Highways are a threat for giant armadillos (Priodontes maximus) that underpasses can mitigate

description: We report 22 records of giant armadillo roadkill on Brazilian highways in
 the Cerrado, Pantanal and Amazon biomes illustrating that highways are a
 threat to this species. However, we also documented the species using
 underpasses, demonstrating that these structures could help to reduce the
 risk of roadkill for giant armadillos.
description: In the Pantanal and Cerrado, in the state of Mato Grosso do Sul,
 a total of 1,337 km of highways (BR-262, MS-040 and BR-267) were monitored
 every 2 weeks for 29 months between February 2017 and December, totaling
 92,364 km. In addition, Citizen science data was also collected as regular
 road users were encouraged to contact the researchers to report roadkill.
 Information about giant armadillo roadkill was also obtained from data
 published in academic journals, from Environmental Military Police and
 from an electronic journal. In the Amazon, a giant armadillo roadkill was
 recorded opportunistically along the highway PA-275 highway in the Carajás
 National Forest.
description: A total of 22 giant armadillos were registered as roadkill on 11
 highways of Brazil between 2007 and 2020. This included 20 giant
 armadillos in the Cerrado, one in the Pantanal and one in the Amazon. On
 Mato Grosso do Sul highways in the Cerrado and Pantanal, 11,199 carcasses
 of animals were recorded, representing over one animal per 10 km, but only
 two giant armadillos. Another nine giant armadillo were recorded outside
 the monitoring (two opportunistically and six through reports from people
 confirmed by researchers). Also in the Cerrado, five individuals were
 reported by Hannibal <i>et al.</i> (2018), two by Rocha
 <i>et al.</i> (2018), one by Environmental Military Police of
 Goiás, one by Environmental Military Police of Tocantins and one published
 by an electronic journal Alcinopolis.com in Mato Grosso do Sul. In the
 Amazon, one individual was recorded on the PA-275 highway, in Carajás
 National Forest.