cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.948j3
title: Data from: Parentage and sibship inference from markers in polyploids

description: Many plants and some animal species are polyploids. Non-disomically
 inherited markers (e.g. microsatellites) in such species cannot be
 analysed directly by standard population genetics methods developed for
 diploid species. One solution is to transform the polyploid codominant
 genotypes to pseudo diploid dominant genotypes, which can then be analysed
 by standard methods for various purposes such as spatial genetic
 structure, individual relatedness and relationship. Although this data
 transformation approach has been used repeatedly in the literature, no
 systematic study has been conducted to investigate how efficient it is,
 how much marker information is lost and thus how much analysis accuracy is
 reduced. More specifically, it is unknown whether or not the transformed
 data can be used to infer parentage and sibship jointly, and how different
 sampling schemes (number and polymorphism of markers, number of
 individuals) and ploidy level affect the inference accuracy. This study
 analyzes both simulated and empirical data to examine the effects of
 polyploid levels, actual pedigree structures, and marker number and
 polymorphism on the accuracy of joint parentage and sibship assignments in
 polyploid species. We show that sibship, parentage and selfing rates in
 polyploids can be inferred accurately from a typical set of microsatellite
 loci. We also show that inferences can be substantially improved by
 allowing for a small genotyping error rate to accommodate the distortion
 in assumed Mendelian inheritance of the converted markers when large
 sibship groups are involved. The results are discussed in the context of
 polyploid data analysis in molecular ecology.
description: Sturgeon polyploid
 microsatellite genotypesmulti-locus
 microsatllite genotypes for non-mendelian loci scored for lake sturgeon
 (Acipenser fulvescens) from Black Lake, MichiganSturgeon.txt
DOI: 10.5281/zenodo.18385143
title: Replication Data and Code for: "Ethical AI in Healthcare: Insights from European Policy Discourses"

description: Data and R Scripts for Topic Modeling of EU Artificial Intelligence Policy Discourse
DOI: 10.5281/zenodo.18385144
title: Replication Data and Code for: "Ethical AI in Healthcare: Insights from European Policy Discourses"

description: Data and R Scripts for Topic Modeling of EU Artificial Intelligence Policy Discourse
DOI: 10.5061/dryad.83t3c
title: Data from: Social evolution of toxic metal bioremediation in Pseudomonas aeruginosa.

description: Bacteria are often iron-limited, and hence produce extracellular
 iron-scavenging siderophores. A crucial feature of siderophore production
 is that it can be an altruistic behaviour (individually costly but
 benefitting neighbouring cells), thus siderophore producers can be invaded
 by non-producing social ‘cheats’. Recent studies have shown that
 siderophores can also bind other heavy metals (such as Cu and Zn), but in
 this case siderophore chelation actually reduces metal uptake by bacteria.
 These complexes reduce heavy metal toxicity, hence siderophore production
 may contribute to toxic metal bioremediation. Here, we show that
 siderophore production in the context of bioremediation is also an
 altruistic trait and can be exploited by cheating phenotypes in the
 opportunistic pathogen Pseudomonas aeruginosa. Specifically, we show that
 in toxic copper concentrations (i) siderophore non-producers evolve de
 novo and reach high frequencies, and (ii) producing strains are fitter
 than isogenic non-producing strains in monoculture, and vice versa in
 co-culture. Moreover, we show that the evolutionary effect copper has on
 reducing siderophore production is greater than the reduction observed
 under iron-limited conditions. We discuss the relevance of these results
 to the evolution of siderophore production in natural communities and
 heavy metal bioremediation.
description: Social evolution of
 toxic metal bioremediation in Pseudomonas aeruginosaAll analysis was carried
 out in R. W.cheat was used as our response variable in our competition
 experiment. This is taken as the cheat malthusian parameter/ wild type
 malthusian parameter. If W&gt;1 cheats are said to 'invade' the
 populationdryad-updated.zip
DOI: 10.15468/dl.dspcq9
title: Occurrence Download

description: A dataset containing 19274626 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((17.36153 58.62073,19.12552 58.62073,19.12552 59.9559,17.36153 59.9559,17.36153 58.62073))"
 ]
}

 The dataset includes 19274626 records from 622 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001318-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jc00c
title: Data from: The pace of plant community change is accelerating in remnant prairies

description: Patterns of biodiversity are changing rapidly. “Legacy studies” use
 historical data to document changes between past and present communities,
 revealing long-term trends that can often be linked to particular drivers
 of ecological change. However, a single pair of historical samples cannot
 ascertain whether rates of change are consistent or whether the impact and
 identity of drivers have shifted. Using data from a second resurvey of 47
 Wisconsin prairie remnants, we show that the pace of community change has
 increased with shifts in the strength of particular drivers. Annual rates
 of local colonization and extinction accelerated by 129 and 214%,
 respectively, between 1950 and 1987 and between 1987 and 2012. Two
 anthropogenic drivers—patch area and fire history—increased in importance
 between these periods. As the strength and number of anthropogenic forces
 increase, rates of biodiversity change are likely to accelerate in other
 ecosystems as well.
description: Data from: The pace of
 plant community change is accelerating in remnant
 prairiesData for colonizations
 (Col) and extinctions (Extinc) were calculated from three surveys of
 remnant prairies in 1950, 1987 and 2012. Data for drivers were obtained
 from records of previous surveys and from land managers. Numerical suffix
 1 corresponds to the period between the 1950 and 1987 (first and second)
 surveys, while 2 corresponds to the period between the 1987 and 2012
 (second and third) surveys. The second tab contains functional trait data.
 Functional trait values for each species were obtained from Leach and
 Givnish 1996.Alstad_ScienceAdvances_DryadData.xlsx
DOI: 10.5061/dryad.f4mc7
title: Data from: The adaptive capacity of lake food webs: from individuals to ecosystems

description: Aquatic ecosystems support size structured food webs, wherein
 predator-prey body sizes span orders of magnitude. As such, these food
 webs are replete with extremely generalized feeding strategies, especially
 among the larger bodied, higher trophic position taxa. The movement scale
 of aquatic organisms also generally increases with body size and trophic
 position. Together, these body size, mobility, and foraging relationships
 suggest that organisms lower in the food web generate relatively distinct
 energetic pathways by feeding over smaller spatial areas. Concurrently,
 the potential capacity for generalist foraging and spatial coupling of
 these pathways often increases, on average, moving up the food web toward
 higher trophic levels. We argue that these attributes make for a food web
 architecture that is inherently ‘adaptive’ in its response to
 environmental conditions. This is because variation in lower trophic level
 dynamics is dampened by the capacity of predators to flexibly alter their
 foraging behavior. We argue that empirical, theoretical, and applied
 research needs to embrace this inherently adaptive architecture if we are
 to understand the relationship between structure and function in the face
 of ongoing environmental change. Toward this goal, we discuss empirical
 patterns in the structure of lake food webs to suggest that ecosystems
 change consistently, from individual traits to the structure of whole food
 webs, under changing environmental conditions. We then explore an
 empirical example to reveal that explicitly unfolding the mechanisms that
 drive these adaptive responses offers insight into how human-driven
 impacts, such as climate change, invasive species, and fisheries harvest,
 ought to influence ecosystem structure and function (e.g., stability,
 secondary productivity, maintenance of major energy pathways). We end by
 arguing that such a directed food web research program promises a powerful
 across-scale framework for more effective ecosystem monitoring and
 management.
description: Dolson et al 2009
 unpublished dataPreviously unpublished
 lake shape, Lake Trout weight and Lake Trout catch per unit effort (CPUE)
 data gathered as part of a study described in Dolson et al. 2009 (see
 citation for all sampling and study lake information). Full citation:
 Dolson, R., K. McCann, N. Rooney, and M. Ridgway. 2009. Lake morphometry
 predicts the degree of habitat coupling by a mobile predator. Oikos
 118:1230-1238.Dolson et al unpublished
 data.xlsx
DOI: 10.5061/dryad.jk111
title: Data from: Sweat bees on hot chillies: provision of pollination services by native bees in traditional slash-and-burn agriculture in the Yucatán Peninsula of tropical Mexico

description: Traditional tropical agriculture often entails a form of slash-and-burn
 land management that may adversely affect ecosystem services such as
 pollination, which are required for successful crop yields. The Yucatán
 Peninsula of Mexico has a &gt;4000 year history of traditional
 slash-and-burn agriculture, termed ‘milpa’. Hot ‘Habanero’ chilli is a
 major pollinator-dependent crop that nowadays is often grown in
 monoculture within the milpa system. We studied 37 local farmers’ chilli
 fields (sites) to evaluate the effects of landscape composition on bee
 communities. At 11 of these sites, we undertook experimental pollination
 treatments to quantify the pollination of chilli. We further explored the
 relationships between landscape composition, bee communities and
 pollination service provision to chilli. Bee species richness,
 particularly species of the family Apidae, was positively related to the
 amount of forest cover. Species diversity decreased with increasing
 proportion of crop land surrounding each sampling site. Sweat bees of the
 genus Lasioglossum were the most abundant bee taxon in chilli fields and,
 in contrast to other bee species, increased in abundance with the
 proportion of fallow land, gardens and pastures which are an integral part
 of the milpa system. There was an average pollination shortfall of 21% for
 chilli across all sites; yet the shortfall was unrelated to the proportion
 of land covered by crops. Rather, chilli pollination was positively
 related to the abundance of Lasioglossum bees, probably an important
 pollinator of chilli, as well indirectly to the proportion of fallow land,
 gardens and pastures that promote Lasioglossum abundance. Synthesis and
 applications. Current, low-intensity traditional slash-and-burn (milpa)
 agriculture provides Lasioglossum spp. pollinators for successful chilli
 production – fallow land, gardens and pasture therefore need to be valued
 as important habitats for these and related ground-nesting bee species.
 However, the negative impact of agriculture on total bee species diversity
 highlights how agricultural intensification is likely to reduce
 pollination services to crops, including chilli. Indeed, natural forest
 cover is vital in tropical Yucatán to maintain a rich assemblage of bee
 species and the provision of pollination services for diverse crops and
 wild flowers.
description: Script for CCA analysis
 and visualizationFile with the script for
 execute the CCA analysis and visualize the resultsccascriptPlandaverde.txtenvironment300Environmental data for the 300 m scale for the CCA analysisSpeciesabundance and identity of species for the CCA analysisdata for SEM allData containing landscape proportion and abundance and richness (Chao-1 corrected) for the most abundant bees and for transect, pan traps and total dataset.dataforsemallb.txt
DOI: 10.5061/dryad.n42h0
title: Data from: Correcting for missing and irregular data in home-range estimation

description: Home-range estimation is an important application of animal tracking data
 that is frequently complicated by autocorrelation, sampling irregularity,
 and small effective sample sizes. We introduce a novel, optimal weighting
 method that accounts for temporal sampling bias in autocorrelated tracking
 data. This method corrects for irregular and missing data, such that
 oversampled times are downweighted and undersampled times are upweighted
 to minimize error in the home-range estimate. We also introduce
 computationally efficient algorithms that make this method feasible with
 large datasets. Generally speaking, there are three situations where
 weight optimization improves the accuracy of home-range estimates: with
 marine data, where the sampling schedule is highly irregular, with duty
 cycled data, where the sampling schedule changes during the observation
 period, and when a small number of home-range crossings are observed,
 making the beginning and end times more independent and informative than
 the intermediate times. Using both simulated data and empirical examples
 including reef manta ray, Mongolian gazelle, and African buffalo, optimal
 weighting is shown to reduce the error and increase the spatial resolution
 of home-range estimates. With a conveniently packaged and computationally
 efficient software implementation, this method broadens the array of
 datasets with which accurate space-use assessments can be made.
description: Mongolian gazelle
 movementslocations of a single
 individualgazelle.csv
DOI: 10.5061/dryad.c2n66
title: Physiological maturity at a critical life‐history transition and flight ability at fledging

description: Developmental maturity (e.g. body condition, body mass) at major
 life-history transitions is known to affect fitness across a wide range of
 taxa. Fledging (leaving the nest), a major life-history transition in
 birds, is associated with high post-fledging mortality and is widely
 assumed to be related to poor initial flight ability of fledglings, which,
 in turn, might be related to developmental maturity at fledging. We
 investigated individual variation in developmental maturity of both
 somatic and physiological traits at this critical life-history transition
 in different ecological contexts (year, first or second broods) to
 determine the importance of physiological traits related to
 oxygen-carrying capacity (haematocrit, haemoglobin) for individual
 variation in initial flight ability at fledging. Haemoglobin concentration
 and haematocrit at fledging had much higher variance than somatic traits
 and were more variable across ecological contexts. Furthermore, fledgling
 haemoglobin concentration was the least developmentally mature of all
 traits (on average, only 78% of adult concentration). Fledglings from
 second broods, which are known to have lower post-fledging survival, were
 less developmentally mature than fledglings from first broods for all
 traits (except tarsus), with haematocrit and haemoglobin concentration
 being the most developmentally immature traits (in first vs. second
 broods, haematocrit: 47·1% vs. 40·9%; haemoglobin: 13·3 vs. 11·6 g dL−1).
 Models predicting individual variation in two aspects of initial flight
 ability (total energy gain, take-off angle) were significantly improved
 when physiological traits (in particular haemoglobin) were incorporated
 into models based on somatic traits.
description: File name:
 chickdatadryad; physiological, somatic, and flight trait values for all
 chicks in the study, as well as covariate data like minutes handled and
 time of day sampled (d21time). More details available in
 SupplementalDryadInfo file. File name:
 SupplementalDryadInfo; descriptions of column headers for chickdatadryad,
 and notes about NA values, use of data, etc. File name: AdultValuesDryad;
 adult measurements for all individual adults used in the study to
 calculate average adult values, the average adult value was used to
 generate Table 1 of Results section
DOI: 10.5061/dryad.ft70n
title: Data from: Ornament complexity is correlated with sexual selection: (a comment on Raia et al., "Cope's rule and the universal scaling law of ornament complexity")

description: Raia et al. propose that the evolution of the shape and complexity of
 animal ornaments (e.g., deer antlers) can be explained by interspecific
 variation in body size and is not influenced by sexual selection. They
 claim to show that ornament complexity is related to body size by an
 0.25-power law and argue that this finding precludes a role for sexual
 selection in the evolution of ornament complexity. However, their study
 does not test alternative hypotheses and mismeasures antler shape
 allometry by omitting much of the published data. We show that an index of
 sexual selection (sexual size dimorphism) is positively correlated with
 size-corrected antler complexity and that the allometric slope of
 complexity is substantially greater than 0.25, contra Raia et al. We
 conclude that sexual selection and physical constraints both affect the
 evolution of antler shape.
description: Holman and Bro-Jorgensen
 - R script for analyses and figuresR script used for
 analyses and figure-making. Has lots of annotation to explain what it
 does.Reply to Raia et al -
 Dryad dataThis is our raw data,
 for use with the attached R file.
DOI: 10.15468/dl.kuwp43
title: Occurrence Download

description: A dataset containing 227 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aspilanta oinophylla"
 ]
}

 The dataset includes 227 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001354-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6kn05
title: Data from: Estimating resource preferences of a native bumblebee: the effects of availability and use-availability models on preference estimatess

description: Identifying resource preference is considered essential for developing
 targeted conservation plans but, for many species, questions remain about
 the best way to estimate preference. Resource preferences for bees are
 particularly difficult to determine as the resources they collect, nectar
 and pollen, are challenging to estimate availability and collection.
 Resources are traditionally measured at the flower or inflorescence level,
 but these measures of availability do not correspond to the resources
 actually used by bees. Additionally, it is unclear as to whether common
 models including availability are appropriate for bees which may target
 resources regardless of available quantities. Here we first compare two
 common hypotheses of resource use – the ‘random use hypothesis’ and the
 ‘linear preferences hypothesis’ – using three different measures of
 availability (pollen, flower and inflorescence) – to determine if one
 measure of availability was better for understanding bee pollen use. Next,
 the superior model using availability was compared to a novel model of bee
 pollen use the ‘target use hypothesis’. This model assumes that bees
 target some resources regardless of how much of each resource is available
 (but assuming resources are present at a site), and thus models preference
 without availability data. Of the models including availability, the
 linear preference model using inflorescence availability best explained
 the pollen use data. This suggests that bumblebee pollen use is non-random
 and that cues to identify and locate resources (i.e. display size and
 quantity) may be more important than the quantity of the resource
 available (i.e. pollen availability). Additionally, in most cases the
 target use model explained the data equal to or better than the other
 models suggesting bee resource use may be better modeled without measured
 availability data compared to linear models. These results could be
 important for expanding resource use analysis of bees that are difficult
 to quantify availability.
description: pollen collection by
 beeNumber of pollen grains
 collected by each bee used in the study. NA's were entered for
 impossible combinations due to lack of availability at a
 site.pollen
 collection raw.csvInflorescence
 availabilityNumber of inflorescences
 of each plant species counted at each unique Site-date
DOI: 10.5061/dryad.7v1hq
title: Data from: Extreme fertilisation bias towards freshly inseminated sperm in a species exhibiting prolonged female sperm storage

description: The storage of sperm by females across successive reproductive cycles is
 well documented in internal fertilisers, yet the fate of stored sperm when
 they compete with ‘new’ sperm to fertilise a female’s eggs has rarely been
 considered. This gap in our understanding is likely due to the logistical
 difficulties of controlling behavioural interactions during or after
 mating, which in turn may influence how many sperm are inseminated and how
 stored sperm are ultimately utilised during successive bouts of sperm
 competition with freshly inseminated sperm. Here, we use artificial
 insemination (AI) in guppies (Poecilia reticulata), a polyandrous
 livebearing poeciliid fish exhibiting prolonged sperm storage by females,
 to overcome these challenges. The use of AI enables us to control
 potential differential maternal effects (e.g. behaviourally mediated
 cryptic female choice) and specifically test for post-copulatory paternity
 biases that favour either stored or fresh sperm when they compete to
 fertilise eggs. Our paternity analyses revealed the almost complete
 dominance of freshly inseminated sperm over stored sperm, supporting
 previous studies reporting similar patterns following natural matings
 across successive brood cycles. However, our use artificial inseminations,
 which excluded behavioural interactions between males and females, most
 likely generated a far stronger pattern of fresh sperm precedence compared
 to those reported in previous studies, possibly implicating ‘cryptic’
 forms of selection by females that may sometimes bolster the success of
 stored sperm.
description: data
 dryaddata on paternity
 success of stored vs fresh sperm in the guppy (an internally fertilising
 fish with prolonged sperm storage). Stored sperm were from a previous
 reproductive cycle (i.e. female produced one brood with 'stored'
 sperm and was then successively artificially inseminated with the
 'fresh' sperm). Experimental design was fully balanced, so that
 the sperm from the same male were used both in the 'stored' and
 'fresh' conditions. See text and Figure 2 for further details on
 the experimental design.