cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q2bvq83p5
title: Influence of microhabitat, fecundity, and parental care on the evolution of sexual size dimorphism in Caribbean Eleutherodactylus frogs

description: Rensch's rule suggests that sexual size dimorphism (SSD) increases
 with species size when males are the larger sex, whereas it decreases when
 females are the larger sex. However, the process responsible for this
 pattern remains obscure. SSD can result from sexual selection, such as
 intra-sexual competition for access to mates, or from natural selection,
 due to resource partitioning or fecundity selection. We studied SSD in
 Caribbean Eleutherodactylus frogs using phylogenetic
 comparative methods to investigate the influence of microhabitat,
 fecundity, and parental care. Our results show that in
 Caribbean Eleutherodactylus, females tend to be larger and,
 contrary to Rensch’s rule, dimorphism increases with species size. SSD was
 not related to microhabitat use. However, SSD was positively correlated
 with fecundity, mediated by a greater increase in female size. SSD was
 also influenced by parental care, suggesting that male care promotes
 larger male size and reduces the female bias in SSD. As suggested for
 other anurans, female-biased SSD in
 Caribbean Eleutherodactylus results from fecundity
 selection, although the magnitude is countered by increased male size in
 species with paternal care. Our results highlight the importance of
 considering various selective forces that may act in concert to influence
 the evolution of sexual size dimorphism.
description: Data was collected from museum specimens.
DOI: 10.5061/dryad.jsxksn0dc
title: Excel data coding file for child welfare reform scoping review

description: While there have been ongoing calls to reform child welfare so that it
 better meets children’s and families’ needs, to date there have been no
 comprehensive summaries of child welfare reform strategies. For this
 systematic scoping review, we summarized authors’ recommendations for
 improving child welfare. We conducted a systematic search (2010 to 2021)
 and included published reviews that addressed authors’ recommendations for
 improving child welfare for children, youth, and families coming into
 contact with child welfare in high-income countries. A total of 4,758
 records was identified by the systematic search, 685 full-text articles
 were screened for eligibility, and 433 reviews were found to be eligible
 for this scoping review. Reviews were theoretically divided, with some
 review authors arguing for reform efforts at the macro level (e.g.,
 addressing poverty) and others arguing for reform efforts at the practice
 level (e.g., implementing evidence-based parenting programs). Reform
 efforts across socioecological levels were summarized in this scoping
 review. An important next step is to formulate what policy solutions are
 likely to lead to the greatest improvement in safety and well-being for
 children and families involved in child welfare.
description: For this systematic scoping review we: 1) conducted a systematic
 search, 2) summarized the number of reviews published, type of review, and
 populations included in reviews and 3) thematically analyzed the primary
 theme and author recommendations for child welfare reform. The Excel data
 coding file counts the number of reviews in each of these
 areas.   
description: This data set is an Excel file, so Excel is required to open the
 data files.
DOI: 10.5061/dryad.4j0zpc8fz
title: Estimation of reinforced urn processes under left-truncation and right-censoring

description: We propose a nonparametric estimator for bivariate left-truncated and
 right-censored (LTRC) observations that combines the
 Expectation-Maximization (EM) algorithm and the Reinforced Urn Process
 (RUP). The resulting Expectation-Reinforcement (ER) algorithm allows for
 the inclusion of experts' knowledge in the form of a prior
 distribution, thus belonging to the class of Bayesian models. This can be
 relevant in applications where the data is incomplete, due to biases in
 the sampling process, as in the case of left-truncation and
 right-censoring. With this new approach, the distribution of the
 truncation variables is also recovered, granting further insight into
 those biases, and playing an important role in applications like prevalent
 cohort studies. The estimators are tested numerically using artificial and
 empirical datasets and compared with other methodologies such as copula
 models and the Kaplan-Meier estimator.
description: The simulated data was generated by the authors, while the
 empirical Canadian data was obtained from Prof. E. W. Frees, to whom one
 may be referred to get access to said data. Therefore, this dataset
 contains only the synthetic data and not the empirical one.
 The synthetic data consists of 10000 observations of bivariate
 left-truncated and right-censored samples. Each observation contains the
 two (possibly censored) observed values (X and Y), the two truncation
 values (TX and TY), the two censoring indicators deltaX and deltaY (we use
 the convention: 1 for uncensored and 0 for censored), and finally the
 difference between TY and TX, TY-TX. This makes a total of 7 variables per
 observation. Clearly, only the first 6 variables are
 independent. The distributions of each variable, as
 well as the specific censoring and truncation mechanisms, can be found in
 the script generate_ltrc_data.py. Due to differences in the pseudo-random
 sequences, running the aforementioned script may yield different datasets
 than the one we provide, but because the underlying distributions are the
 same, the statistical properties should also be the same, up to numerical
 errors. The code to generate the simulated data can be
 accessed in the public repository https://github.com/LuisSouto/Expectation-Reinforcement, or in the attached code, specifically the generate_ltrc_data.py Python script.
description: The main routines are implemented in C++, while the data
 generation and the post-analysis of the results are in written in Python.
 No special libraries are required to run the Python code (apart from the
 standard numpy, matplotlib, scipy, etc.). A small part of the C++ code
 requires the Boost library, but this is only a few lines of code and can
 be easily changed to not require said library.
DOI: 10.5061/dryad.69p8cz953
title: Intraspecific trait variation in a dryland tree species corresponds to regional climate gradients

description: Aim: Intraspecific trait variation is fundamental to understanding a
 species’ adaptive capacity. Assessing phenotypic variation at different
 ecological scales is useful for evaluating species’ vulnerability to
 changing environmental conditions. Here we quantify the ecological scale
 of variation of phenotypic functional traits for a widespread dryland tree
 species in the western United States, Pinus monophylla, and evaluate the
 strength of trait-environment relationships across spatial gradients and
 in response to interannual variability in weather conditions. Location:
 Western United States Taxon: Conifer tree (Pinaceae): Pinus monophylla
 Methods: Nine reproductive and foliar morphological traits were measured
 from 23 sampling locations in nine mountain ranges, stratified across
 broad-scale gradients of precipitation timing and quantity and local
 gradients of elevation. We partitioned trait variation within and among
 nested ecological scales (mountain range, site, tree, and tree growth
 year). We then used multivariate methods to quantify the association
 between environmental variables and ecological trade-offs associated with
 both reproductive and foliar traits. Results: Most variation was explained
 at the scale of individual trees (18–46%) and between growth years
 (20–30%), with smaller but variable contributions at the scale of sites
 (8–25%) and mountain ranges (0–15%). Trait values had low correlation with
 environmental variables (13%); however, 94% of the trait-environment
 covariance was explained by two major axes of variation: (1) the
 drought-stress gradient covarying with reproductive traits, and (2)
 precipitation patterns covarying with foliar morphology. Main conclusions:
 High levels of individual trait variation indicate within-population
 adaptive capacity. Consistent relationships among range-wide patterns of
 foliar and reproductive traits and broad-scale climate gradients provide
 indirect evidence of local adaptation and may inform seed sourcing for
 restoration or the potential for assisted migration efforts.
 Quantification of intraspecific trait variation across multiple ecological
 scales is important for understanding the potential climate change
 response of dryland tree species.
DOI: 10.5061/dryad.qz612jmk2
title: Data from: Shifts in mutation bias promote mutators by altering the distribution of fitness effects

description: Recent experimental evidence demonstrates that shifts in mutational
 biases, for example increases in transversion frequency, can change the
 distribution of fitness effects of mutations (DFE). In particular,
 reducing or reversing a prevailing bias can increase the probability that
 a de novo mutation is beneficial. It has also been shown that mutator
 bacteria are more likely to emerge if the beneficial mutations they
 generate have a larger effect-size than observed in the wildtype. Here, we
 connect these two results, demonstrating that mutator strains that reduce
 or reverse a prevailing bias have a positively-shifted DFE, which in turn
 can dramatically increase their emergence probability. Since changes in
 mutation rate and bias are often coupled through the gain and loss of DNA
 repair enzymes, our results predict that the invasion of mutator strains
 will be facilitated by shifts in mutation bias that offer improved access
 to previously under-sampled beneficial mutations.
DOI: 10.5061/dryad.x95x69pnf
title: Landscape-scale drivers of liana load across a Southeast Asian forest canopy differ to the Neotropics

description: Lianas (woody vines) are a key component of tropical forests, known to
 reduce forest carbon storage and sequestration and to be increasing in
 abundance. Analysing how and why lianas are distributed in forest canopies
 at landscape scales will help us determine the mechanisms driving changes
 in lianas over time. This will improve our understanding of liana ecology
 and projections of tropical forest carbon storage now and into the future.
 Despite competing hypotheses on the mechanisms driving spatial patterning
 of lianas, few studies have integrated multiple tree-level biotic and
 abiotic factors in an analytical framework. None have done so in the
 Palaeotropics, which are biogeographically and evolutionarily distinct
 from the Neotropics, where most research on lianas has been conducted. We
 used an unoccupied aerial system (UAS; drone) to assess liana load in
 50-ha of Palaeotropical forest canopy in Southeast Asia. We obtained data
 on hypothesised drivers of liana spatial distribution in the forest
 canopy, including disturbance, tree characteristics, soil chemistry, and
 topography, from the UAS, from airborne LiDAR, and from ground surveys. We
 integrated these in a comprehensive analytical framework to extract
 variables at an individual-tree level and evaluated the relative strengths
 of the hypothesised drivers and their ability to predict liana
 distributions through boosted regression tree (BRT) modeling. Tree height
 and distance to canopy gaps were the two most important predictors of
 liana load, with relative contribution values in BRT models of 34.60%
  45.39% and 7.93% - 10.19%, respectively. Our results suggest
 that taller trees were less often and less heavily infested by lianas than
 shorter trees, opposite to Neotropical findings. Lianas also occurred more
 often, and to a greater extent, in tree crowns close to canopy gaps and to
 neighbouring trees with lianas in their crown. Synthesis: Despite their
 known importance and prevalence in tropical forests, lianas are not well
 understood, particularly in the Palaeotropics. Examining 2,428 trees
 across 50-ha of Palaeotropical forest canopy in Southeast Asia, we find
 support for the hypothesis that canopy gaps promote liana infestation. Our
 finding that liana presence and load declined with tree height, opposite
 to well-established Neotropical findings, suggests a fundamental
 difference between Neotropical and Southeast Asian forests. Considering
 that most liana literature has focused on the Neotropics, this highlights
 the need for additional studies in other biogeographic regions to clarify
 potential differences and enable us to better understand liana impacts on
 tropical forest ecology, carbon storage and sequestration.
DOI: 10.5061/dryad.cnp5hqc7r
title: Data from: Metabarcoding of trap nests reveals differential impact of urbanization on cavity-nesting bee and wasp communities

description: Urbanization is affecting arthropod communities worldwide, for example by
 changing the availability of food resources. However, the strength and
 direction of a community’s response are species-specific and depend on the
 species’ trophic level. Here, we investigated interacting species at
 different trophic levels in nests of cavity-nesting bees and wasps along
 two urbanization gradients in four German cities using trap nests. We
 analyzed bee and wasp diversity and their trophic interaction partners by
 metabarcoding the DNA of bee pollen and preyed arthropods found in wasp
 nests. We found that the pollen richness increased with increasing
 distance from city centers and at sites characterized by a high percentage
 of impervious and developed surfaces, while the richness of pollinators
 was unaffected by urbanization. In contrast, species richness of wasps,
 but not their arthropod prey, was highest at sites with low levels of
 urbanization. However, the community structure of wasp prey changed with
 urbanization at both local and regional scales. Throughout the study area,
 the community of wasps consisted of specialists, while bee species were
 generalists. Our results suggest that Hymenoptera and their food resources
 are negatively affected by increasing urbanization. However, to understand
 the distribution patterns of both, wasps and bees in urban settings other
 factors besides food availability should be considered.
description: Arthropod and pollen samples
 were collected from trap nests at 18 locations situated in the cities of
 Berlin, Cologne, Frankfurt, and Hamburg and were selected to represent an
 urban-rural gradient. Traps consisted of 20 cm long bundles of reed and
 bamboo in PVC tubes (diameter 11 cm; reed cavity diameter ranged
 1-16mm).  Arthropod remains (faeces, undigested prey
 tissue) and pollen of a maximum of three brood cells was extracted and
 stored individually in 2 mL microcentrifuge tubes at -18°C until further
 processing. Living larva, pupa, and imago were reared (8 weeks at 6°C,
 subsequent weeks at 20°C until development was completed) allowing later
 morphological species identification.
 Arthropod and pollen samples
 were subjected to DNA-extraction followed by two-stage PCR
 protocol to build the DNA libraries for next-generation sequencing.
 Primer pair
 mlCOIintF/jgHCO2198
 (Leray et al., 2013, Geller, Meyer, Parker, & Hawk,
 2013) were used for amplification of athropod prey, primer pair ITS3/ITS4 (White, Bruns, Lee, & Taylor, 1990) for
 pollen samples.  Bioinformatic analysis was performed following
 the steps described in the file
 MetabarcodingTrapnests_pipe_2021_DRYAD.sh
DOI: 10.5061/dryad.w6m905qsm
title: Genetic diversity, genetic differentiation and demographic history of Cryptomeria (Cupressaceae), a Tertiary relict plant in East Asia based on RAD sequencing

description: Genetic structure and distribution patterns of modern floras are strongly
 affected by climatic change and geographical isolation. In the present
 study, we applied restriction-site-associated DNA sequencing (RAD-seq) to
 analyze the genetic structure and to simulate the demographic history of
 two extant Cryptomeria species in
 Japan (C. japonica) and Southeastern China
 (C. japonica var. sinensis). Thirteen natural
 populations representing the entire species distributed in East
 Asia were collected from Japan and China.
 At the species level, the genetic diversity of
 Cryptomeria was moderate (Ho = 0.217, He =
 0.203) with a significant genetic differentiation among
 populations (85.30%, P &lt; 0.001), especially between Japan and China
 lineages (FST = 0.147). Except for the Lushan
 (LS) population in China, all populations were clustered
 into two lineages (Japanese and Chinese), which was consistent with their
 geographical distribution. Approximate Bayesian
 computations (ABC) model indicated that the current two
 geographical lineages diverged from a common ancestral lineage
 and that their divergence time was about
 0.417 ~ 0.139 million years ago
 (Mya). Geographical isolation, climate change
 in the Quaternary, and human disturbance
 played important roles in genetic variation and
 distribution patterns of Cryptomeria in East Asia. Our results
 shed light on the speciation processes of
 Cryptomeria and provide a reference for the conservation
 of this species.
DOI: 10.5061/dryad.8w9ghx3qr
title: Data from: Temporal change in floral availability leads to periods of resource limitation and affects diet specificity in a generalist pollinator

description: Generalist species are core components of ecological networks and crucial
 for the maintenance of biodiversity. Generalised species and networks are
 expected to be more resilient, therefore understanding the dynamics of
 specialisation and generalisation in ecological networks is a key focus in
 a time of rapid global climate change. Whilst diet generalisation is
 frequently studied, our understanding of how it changes over time is
 limited. We explore temporal variation in diet specificity in the honeybee
 (Apis mellifera), using pollen DNA metabarcoding of honey samples, through
 the foraging season, over two years. We find that overall, honeybees are
 generalists that visit a wide range of plants, but there is temporal
 variation in the degree of specialisation. Temporal specialisation of
 honeybee colonies corresponds to periods of resource limitation,
 identified as a lack of honey stores. Honeybees experience a lack of
 preferred resources in June when switching from flowering trees in spring
 to shrubs and herbs in summer. Investigating temporal patterns in
 specialisation can identify periods of resource limitation that may lead
 to species and network vulnerability. Diet specificity must therefore be
 explored at different temporal scales in order to fully understand species
 and network stability in the face of ecological change.
description: All data files are .csv. R scripts are provided for graphical and
 statistical analysis.
DOI: 10.5061/dryad.hmgqnk9m8
title: CO2-fertilisation enhances resilience to browsing in the recruitment phase of an encroaching savanna tree

description: 1. CO2-fertilisation is implicated in the widespread and significant woody
 encroachment of savannas due to CO2-stimulated increases in belowground
 reserves that enhance sapling regrowth after fire. However, the effect of
 CO2 concentration ([CO2]) on tree responses to the other major disturbance
 in savannas, herbivory, is poorly understood. Herbivory responses cannot
 be predicted from fire responses, as herbivore effects occur earlier
 during establishment and are moderated by plant palatability and defence
 rather than below-ground carbon accumulation. 2. The relationship between
 herbivory and [CO2] is explored here using a widespread,
 strongly-encroaching savanna tree, Vachellia karroo. Using
 greenhouse-grown seedlings under past- through to predicted future-[CO2]
 (180–1000 ppm) and field-grown seedlings under ambient [CO2], we assessed
 plant survival, growth, defence and palatability. 3. Increasing [CO2]
 improves the tolerance of greenhouse-grown seedlings to herbivory by
 stimulating growth and allowing a critical size-threshold associated with
 survival to be reached earlier, thereby decreasing the probability of
 fatal herbivory during the vulnerable recruitment phase. Elevated [CO2]
 also decreases the time taken to reach a second size-threshold linked to
 accelerated recovery of field-grown seedlings following herbivory.
 Seedling growth responses to increasing [CO2] are non-linear, suggesting
 that historic growth- and survival enhancements are smaller than those
 predicted for the future. Increasing [CO2] is associated with greater
 resistance to herbivores (more branched shoot architecture) but not leaf
 palatability (C:N ratio) or defence (leaf tannins and spine density). 4.
 Increasing V. karroo densities already constitute a major land management
 problem in southern African savannas. However, encroachment by this
 species, and likely other savanna tree species, may be greatly exacerbated
 under future [CO2], as tolerance to herbivory at the recruitment stage is
 further enhanced.
DOI: 10.5061/dryad.5mkkwh78v
title: Complex plumages spur rapid color diversification in kingfishers (Aves: Alcedinidae)

description: Colorful signals in nature provide some of the most stunning examples of
 rapid phenotypic evolution. Yet, studying color pattern evolution has been
 historically difficult owing to differences in perceptual ability of
 humans and analytical challenges with studying how complex color patterns
 evolve. Island systems can provide a natural laboratory for testing
 hypotheses about the direction and magnitude (i.e., rate) of phenotypic
 change. A recent study of bird coloration found that the plumages of
 island species are darker and less complex than continental species.
 Whether such shifts in plumage complexity are associated with increased
 rates of color evolution on islands remains unknown. Here, we use
 geometric morphometric techniques to test the hypothesis that plumage
 complexity and island insularity interact to influence color diversity in
 a species-rich and cosmopolitan clade of colorful birds—kingfishers (Aves:
 Alcedinidae). In particular, we test three predictions: i) plumage
 complexity enhances interspecific rates of color evolution, ii) plumage
 complexity is lower on islands, and iii) rates of plumage color evolution
 are higher within island systems. Our results show that more complex
 plumages result in more diverse colors among species and that island
 species have higher rates of color evolution. Importantly, we found that
 island species did not have more complex plumages than their continental
 relatives. Thus, complexity may be a key innovation that facilitates
 response to relaxed (or divergent) selection pressures on islands. Lack of
 strong support for competition-driving rates of evolution along different
 color axes hints at an allopatric model of color evolution in which
 species adapt to local conditions on different islands. This study
 demonstrates how a truly multivariate treatment of color data can reveal
 evolutionary patterns that might otherwise go unnoticed.
description: This data was collected with a UV-Vis spectrophotometer.