cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2280gb5nx
title: Associated evolution of fruit size, fruit color and spines in Neotropical palms

description: Understanding how ecological interactions have shaped the evolutionary
 dynamics of species traits remains a challenge in evolutionary ecology.
 Combining trait evolution models and phylogenies, we analyzed the
 evolution of characters associated with seed dispersal (fruit size and
 color) and herbivory (spines) in Neotropical palms to infer the role of
 these opposing animal-plant interactions in driving evolutionary patterns.
 We found that the evolution of fruit color and fruit size were associated
 in Neotropical palms, supporting the adaptive interpretation of
 seed-dispersal syndromes and highlighting the role of frugivores in
 shaping plant evolution. Furthermore, we revealed a positive association
 between fruit size and the presence of spines on palm leaves, bracteas and
 stems. We hypothesize that interactions between palms and large-bodied
 frugivores/herbivores may explain the evolutionary relationship between
 fruit size and spines. Large-bodied frugivores, such as extinct megafauna,
 besides consuming the fruits and dispersing large seeds, may also have
 consumed the leaves or damaged the plants, thus simultaneously favoring
 the evolution of large fruits and defensive structures. Our findings show
 how current trait patterns can be understood as the result of the
 interplay between antagonistic and mutualistic interactions that have
 happened throughout the evolutionary history of a clade.
description: We built a dataset on palm traits using information from the
 literature. Most of the data on traits was obtained from Henderson et al.
 (1995). In cases where no information from Henderson et al. (1995) was
 found, we completed the dataset with information from Lorenzi et al.
 (2004). We classified palm species into two categories according to the
 predominant color of the mature fruit: "colorful fruits" (red,
 black and purple) and "dull-colored fruits" (green, yellow,
 brown and orange), reflecting colors that have been related to bird and
 mammal frugivory, respectively (Gautier-Hion et al. 1985, Nevo et al.
 2018a). We considered only the color of ripe fruits and discarded those
 species for which the information about color was ambiguous. We also
 classified all species according to the presence ("with spines")
 and absence ("spineless") of spines. We consider spines to be
 any stiff sharply pointed structure (Grubb 1992) that is present either at
 the stem, peduncular bract, rachis or petioles, which is often associated
 with defense specifically related to mammalian herbivory
 (Charles-Dominique et al. 2016).
description: Data used in the analyses containing fruit length (cm), fruit
 color and presence (1) or absence (0) of spines for each Neotropical palm
 species. Information on certain traits was Not Available (NA) for a few
 species.
DOI: 10.5061/dryad.905qftth0
title: Climate dependent heating efficiency in the common lizard

description: Regulation of body temperature is crucial for optimizing physiological
 performance in ectotherms. However, time allocated to behavioral
 thermoregulation is also time lost to engage in other activities. In a
 heterogeneous thermal environment, ectotherm life history strategies and
 fitness may reflect the effects of local habitat conditions on an
 individual’s time budget. Although local adaptation of thermoregulation
 has been well studied and is known to vary between species or populations,
 the effects of environment on biophysical adjustments remains elusive. In
 particular, there are limited data showing that rates of heating (i.e. the
 speed of body temperature gain) vary in response to environmental
 conditions. In this study, we explored the effect of environmental
 conditions on heating rates in the common lizard (Zootoca vivipara). We
 sampled lizards from 10 populations, in the Massif Central Mountain range
 of France, and measured whether differences in heating rates of
 individuals correlated with phenotypic characteristics (i.e. body
 condition and dorsal darkness) or abiotic characteristics (temperature and
 rainfall). Our results show that heat gain is faster for larger lizards
 but also for individuals from habitats with higher amount of
 precipitation. Altogether, they demonstrate that environmentally induced
 constraints can shape biophysical aspects of thermoregulation.
DOI: 10.5061/dryad.9zw3r22b5
title: Data from: Starvation causes female to male sex reversal through lipid metabolism in the teleost fish, medaka (Oryzias latipes)

description: Raw metabolome data from medaka larvae at five days post-hatching (dph).
 Hatching stage of medaka larvae were treated with normal feeding (fed),
 starvation (starved), Pank inhibitor (PI) and FAS inhibitor (C75) for five
 days. Water-soluble metabolites were extracted from the whole body and
 analyzed by CE-TOFMS, IC-FTMS and LC-MS/MS.
DOI: 10.5061/dryad.kd51c5b2w
title: Data from: Phylogenetic niche conservatism and variations in species diversity-climate relationships

description: Although contemporary climate has been identified as one of the major
 determinants of large-scale species diversity patterns, its effect on
 species diversity greatly varies among clades. Understanding the drivers
 of the variation in species diversity-climate relationships (DCRs) across
 clades, which is critical for developing general mechanisms underlying the
 effects of climate on species diversity patterns, remains a current
 challenge. Using newly compiled distribution data of 914 Rosaceae species
 in China and a dated genus-level phylogeny, we first assessed the DCRs for
 the entire family, the two major growth forms (woody vs. herbaceous), and
 each genus separately, and then explored the drivers underlying the
 variation in DCRs across different clades. We found that the DCRs
 significantly differed between woody and herbaceous plants and among
 different genera in this family. Closely-related genera had more similar
 species diversity patterns and DCRs than expected. Both the ancestral
 climate niches of different genera and the discrepancy between
 contemporary and ancestral climate niches explained the variations in DCR
 slopes across genera with high explanatory power, indicating the effect of
 niche conservatism on DCRs. Our study suggests that niche conservatism is
 a major driver of DCR variations between clades, which enhances our
 understanding of the mechanisms underlying large-scale species diversity
 patterns.
description: We provided the distribution of species richness of all plants,
 woody plants, herbacious plants, each genus and the climate data in each
 10 km × 10 km grid cell in China.
DOI: 10.5061/dryad.3ffbg79fd
title: Data from: RAD sequencing data reveal a radiation of willow species (Salix L., Salicaceae) in the Hengduan Mountains and adjacent areas

description: Radiation_of_willows_in_Hengduan_Mountains_He_et_al_2020 Demultiplexed
 Restriction-site Associated DNA (RAD) read data of 58 samples and four
 phylip files generated from RAD reads of 72 samples used in "RAD
 sequencing data reveal a radiation of willow species (Salix L.,
 Salicaceae) in the Hengduan Mountains and adjacent areas". The other
 relevant 14 samples from Wagner et al. (2018) are available at the
 National Center for Biotechnology Information SequenceReadArchive:
 BioProject ID PRJNA433286.
DOI: 10.5061/dryad.905qftth1
title: Tape lures swell bycatch on a Mediterranean island harbouring illegal bird trapping

description: Mediterranean islands provide shelter and sustenance for millions of
 migrating birds each year. Humans have historically exploited bird
 migration through hunting. In Cyprus, trapping birds during their
 migratory peak is considered a tradition, but has long been against the
 law. Illegal bird trapping is lucrative, however, with trappers using tape
 lures that broadcast birdsong to increase capture rates. It results in the
 slaughter of millions of birds each year. Yet, scientific studies
 quantifying capture rates of target and nontarget species using methods
 employed by trappers are lacking. Here, we show using playback experiments
 that tape lures lead to an order of magnitude greater capture rates of
 target species, but also significantly increase bycatch, which may include
 species of conservation concern. Conservation efforts focusing on
 minimizing illegal bird killing should also consider tape lures and their
 contribution to the overall impact of trapping on avian populations.
DOI: 10.15468/dl.3bc8gt
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Auchenoceros punctatus",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 49 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002275-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rjdfn2z7c
title: Cooking chicken at home: common or recommended approaches to judge doneness may not assure sufficient inactivation of pathogens

description: About one third of foodborne illness outbreaks in Europe are acquired in
 the home and eating undercooked poultry is among consumption practices
 associated with illness. The aim of this study was to investigate whether
 actual and recommended practices for monitoring chicken doneness are safe.
 Seventy-five European households from five European countries were
 interviewed and videoed while cooking chicken in their private kitchens,
 including young single men, families with infants/in pregnancy and elderly
 over seventy years. A cross-national web-survey collected cooking
 practices for chicken from 3969 households. In a laboratory kitchen,
 chicken breast fillets were injected with cocktails of Salmonella and
 Campylobacter and cooked to core temperatures between 55 and 70 °C.
 Microbial survival in the core and surface of the meat were determined. In
 a parallel experiment, core colour, colour of juice and texture were
 recorded. Finally, a range of cooking thermometers from the consumer
 market were evaluated. The field study identified nine practical
 approaches for deciding if the chicken was properly cooked. Among these,
 checking the colour of the meat was commonly used and perceived as a way
 of mitigating risks among the consumers. Meanwhile, chicken was perceived
 as hedonically vulnerable to long cooking time. The quantitative survey
 revealed that households prevalently check cooking status from the inside
 colour (49.6%) and/or inside texture (39.2%) of the meat. Young men rely
 more often on the outside colour of the meat (34.7%) and less often on the
 juices (16.5%) than the elderly (&gt;65 years old; 25.8% and 24.6%,
 respectively). The lab study showed that colour change of chicken meat
 happened below 60 °C, corresponding to less than 3 log reduction of
 Salmonella and Campylobacter. At a core temperature of 70 oC, pathogens
 survived on the fillet surface not in contact with the frying pan. No
 correlation between meat texture and microbial inactivation was found. A
 minority of respondents used a food thermometer, and a challenge with
 cooking thermometers for home use was long response time. In conclusion,
 the recommendations from the authorities on monitoring doneness of chicken
 and current consumer practices do not ensure reduction of pathogens to
 safe levels. For the domestic cook, determining doneness is both a
 question of avoiding potential harm and achieving a pleasurable meal. It
 is discussed how lack of an easy “rule-of-thumb” or tools to check safe
 cooking at consumer level, as well as national differences in
 contamination levels, food culture and economy make it difficult to
 develop international recommendations that are both safe and easily
 implemented.
DOI: 10.5061/dryad.tqjq2bvvq
title: Oligocene divergence of frogmouth birds (Podargidae) across Wallace’s line

description: Wallace’s Line demarcates the transition between the differentiated
 regional faunas of Asia and Australia. However, while patterns of biotic
 differentiation across these two continental landmasses and the
 intervening island groups (“Wallacea”) have been extensively studied,
 patterns of long-term dispersal and diversification across this region are
 less well understood. Frogmouths (Aves: Podargidae) are a relictual family
 of large nocturnal birds represented by three extant genera occurring
 respectively in Asia, “Sahul” (Australia and New Guinea), and the Solomon
 Islands, thus spanning Wallace’s Line. We used new mitochondrial genomes
 from each of the extant frogmouth genera to estimate the timeline of
 frogmouth evolution and dispersal across Wallace’s Line. Our results
 suggest that the three genera diverged and dispersed during the
 mid-Cenozoic between approximately 30 and 40 million years ago. These
 divergences are among the oldest inferred for any trans-Wallacean
 vertebrate lineage. In addition, our results reveal that the monotypic
 Solomons frogmouth (Rigidipenna inexpectata) is one of the most
 phylogenetically divergent endemic bird lineages in the south-west
 Pacific. We suggest that the contemporary distribution of exceptionally
 deep divergences among extant frogmouth lineages may be explained by
 colonisation of, and subsequent long-term persistence on, island arcs in
 the south-west Pacific during the Oligocene. These island arcs may have
 provided a pathway for biotic dispersal out of both Asia and Australia
 that preceeded the formation of extensive emergent landmasses in Wallacea
 by at least 10 million years.
description: Denovo generation of mitochondrial genomes from Toe Pad and Liver
 samples, combined with existing data compiled from GenBank.
DOI: 10.5061/dryad.g4f4qrfms
title: Testing trait plasticity over the range of spectral composition of sunlight in forb species differing in shade tolerance

description: Although sunlight is essential for plant growth and development, the
 relative importance of each spectral region in shaping functional traits
 is poorly understood, particularly in dynamic light environments such as
 forest ecosystems. We examined responses of 25 functional traits from
 groups of 11 shade-intolerant and 12 understorey shade-tolerant forb
 species grown outdoors under five filter treatments differing in spectral
 transmittance: (1) transmitting c 95% of solar radiation; (2) attenuating
 ultraviolet-B (UV-B); (3) attenuating all UV; (4) attenuating all UV and
 blue light; (5) attenuating all UV, blue, and green light. Our results
 show that UV-B radiation mainly affected the biochemical traits but blue
 light mainly affected the physiological traits irrespective of functional
 strategy, whereas green light affected both sets of traits. This would
 suggest that differentiation among suites of functional-trait responses
 proceeds according to light quality. Biomass accumulation was
 significantly increased by UV-A radiation (contrasting treatment (2) vs
 (3)) among shade-intolerant but decreased by blue light among
 shade-tolerant species; green and red light affected whole-plant
 morphological development differently according to functional groups.
 Shade-tolerant species were more plastic than shade-intolerant species in
 response to each spectral region that we examined except for UV-B
 radiation. Synthesis. Our results show that differences in the spectral
 composition of sunlight can drive functional trait expression irrespective
 of total irradiance received. The different responses of functional traits
 between functional groups imply that shade-tolerant and intolerant species
 have adapted to utilize spectral cues differently in their respective
 light environments.
DOI: 10.5061/dryad.8sf7m0cj5
title: Data from: Elements of metacommunity structure of diatoms and macroinvertebrates within stream networks differing in environmental heterogeneity

description: Aim: Idealized metacommunity structures (i.e. checkerboard, random,
 quasi-structures, nested, Clementsian, Gleasonian, and evenly spaced) have
 recently gained increasing attention, but their relationships with
 environmental heterogeneity and how they vary with organism groups remain
 poorly understood. Here we tested two main hypotheses: (1) gradient-driven
 patterns (Clementsian and Gleasonian) occur frequently in heterogeneous
 environments, and (2) small organisms (here, diatoms) are more likely to
 exhibit gradient-driven patterns than large organisms (here,
 macroinvertebrates). Location: Streams in three regions in China. Taxon:
 Diatoms and macroinvertebrates. Methods: The stream diatom and
 macroinvertebrate data, as well as the environmental data collected from
 the same set of sites were used to examine the idealized metacommunity
 structures via the elements of the metacommunity structure (EMS;
 coherence, turnover, and boundary clumping) analysis in three regions. We
 extended the traditional EMS approach by ordering sites along known
 environmental gradients. Results: We found that Clementsian
 structure with high degrees of coherence and turnover, and significantly
 positive clumping was typically observed in the high-heterogeneity
 regions, whereas randomness was prevalent in the low-heterogeneity region.
 Macroinvertebrates exhibited clearer Clementsian structures compared with
 diatoms, while diatoms showed more randomness compared with
 macroinvertebrates, indicating a stronger role of environmental filtering
 for macroinvertebrates than diatoms. In most cases, the results of the
 more novel EMS approach differed from the results of the traditional EMS
 technique. Main Conclusions: Our results suggested that the occurrence of
 different metacommunity structures may be related with the degree of
 regional environmental heterogeneity. However, diatom metacommunities were
 more random than those of macroinvertebrate, and such an unexpected result
 may result from different dispersal abilities between the two organism
 groups. In addition, we found that the novel EMS approach increased power
 in discerning metacommunity structure in comparison to the traditional EMS
 technique.
description: <strong>He et al_Journal of
 Biogeography</strong> Data are compiled in an
 Excel spreadsheet with 3 tabs containing the following information: 1)
 Presence-absence diatom species dataset, 2) Presence-absence
 macroinvertebrate taxon dataset, 3) Environmental dataset.
DOI: 10.5061/dryad.j3tx95x9b
title: Comparative morphology of shark pectoral fins

description: Sharks vary greatly in morphology, physiology, and ecology. Differences in
 whole body shape, swimming style, and physiological parameters have
 previously been linked to varied habitat uses. Along with whole body
 morphology, shark pectoral fins are also previously described to vary in
 both shape and skeleton; however, there are limited comparative data on
 external and skeletal morphology. Further, fins were previously
 categorized into two discrete groups based on the amount of skeletal
 support present: (1) aplesodic, where less than half of the fin is
 supported and (2) plesodic where greater than half of the fin is
 supported. These discrete classifications have been used to
 phylogenetically place species, though the methodology of classification
 is infrequently described, and the comparisons may not be valid.
 Additionally, our understanding of shark pectoral fin ecomorphology is
 limited by access to samples from a broad variety of species. In this
 study, we sampled fins from various families, orders, and ecological
 classifications. We examined the external morphology, skeletal extent, and
 cross-sectional shape of the cartilaginous elements. Using phylogenetic
 comparative methods, we show that fin morphology does not differ
 significantly when considering the level of relatedness between species,
 suggesting there may be some mechanical constraint. We also describe a
 range of skeletal extent, rather than two discrete categories. We find
 that fins are shaped like hydrofoils in cross-section, supporting
 hypotheses that fins may be lift producing structures in sharks. Finally,
 we find that a number of morphological variables such as number of
 radials, radial calcification and shape, and fin taper all correlate with
 skeletal extent. Within these morphospaces, we also describe that some
 orders/families tend to occupy certain areas with limited overlap. With
 this study, we demonstrate that there is some mechanical constraint
 limiting variations in shark pectoral fin morphology, but there are subtle
 differences that appear to occur within shark groups that share close
 phylogenetic relationships and similar biological parameters.
DOI: 10.5061/dryad.8sf7m0cj6
title: Data for: Calibration of individual-based models to epidemiological data: a systematic review

description: Calibrating or fitting an individual-based model (IBM) to data is a
 crucial step in model development. We performed a systematic review to
 provide an overview of calibration methods used in IBMs modelling
 infectious disease spread. We included articles if models stored
 individual-specific information and calibration involved running the model
 and comparing model output to population-level targets expressed as
 summary statistics. The dataset contains information for each of the
 included articles on model calibration methods, including; the
 parameter-search strategy, the goodness-of-fit measure, acceptance
 criteria, and stopping rules. Also, the dataset contains information on
 contextual variables for model calibration such as target statistics and
 parameters.
description: Information was collected independently by two reviewers for each
 article included using a prospectively developed form. Data was collected
 verbatim and was later categorised. The dataset contains this categorised
 information, accompanied by verbatim information where relevant. We
 revisited articles on which there was disagreement in the classification
 and discussed the dispute until we reached an agreement. Due to this fact,
 information about the category of the calibration method may be based on a
 later review of the article at which stage no extra verbatim information
 was collected. We collected information on the number
 of calibrated parameters, the number of fixed parameters, and the number
 of targets. We noted how information on these counts was reported in the
 articles (i.e. the number was explicitly provided, could be deduced from
 text or figures, was provided incompletely or was not provided). Users of
 the data need to take into account a limitation concerning the counts
 contained in the dataset; counts often had to be deduced from the article,
 a process that is prone to error. We advise against further analyses using
 these numbers. Please refer to the associated paper for
 a complete description of the methodology.
description: The dataset is self-contained. There are missing values within
 nested variables (i.e. if the previous column/variable has a certain
 level, the nested variable will contain extra information). There are
 missing values in variables with an "optional" nature.