cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n95k3
title: Data from: Hormonally mediated increases in sex-biased gene expression accompany the breakdown of between-sex genetic correlations in a sexually dimorphic lizard

description: The evolution of sexual dimorphism is predicted to occur through
 reductions in between-sex genetic correlations (rmf) for shared traits,
 but the physiological and genetic mechanisms that facilitate these
 reductions remain largely speculative. Here, we use a paternal
 half-sibling breeding design in captive brown anole lizards (Anolis
 sagrei) to show that the development of sexual size dimorphism is mirrored
 by the ontogenetic breakdown of rmf for body size and growth rate. Using
 transcriptome data from the liver (which integrates growth and
 metabolism), we show that sex-biased gene expression also increases
 dramatically between ontogenetic stages bracketing this breakdown of rmf.
 Ontogenetic increases in sex-biased expression are particularly evident
 for genes involved in growth, metabolism, and cell proliferation,
 suggesting that they contribute to both the development of sexual
 dimorphism and the breakdown of rmf. Mechanistically, we show that
 treatment of females with testosterone stimulates the expression of
 male-biased genes while inhibiting the expression of female-biased genes,
 thereby inducing male-like phenotypes at both organismal and
 transcriptomic levels. Collectively, our results suggest that sex-specific
 modifiers such as testosterone can orchestrate sex-biased gene expression
 to facilitate the phenotypic development of sexual dimorphism while
 simultaneously reducing genetic correlations that would otherwise
 constrain the independent evolution of the sexes.
description: ReadMe file explaining
 data in other fileslegend.txtPedigree used in animal model analysesIndividual ID numbers with sire and dam ID numbersexumped2.txtSize data for quantitative genetic analysesData used for animal model analyses of size and mass across 6 age classesexumdat2.txtGrowth rates for quantitative genetic analysesRates of instantaneous growth in length and mass across 5 age intervals for use in animal model analysesexumdat2growth3.txtGrowth curve parameters for quantitatvie genetic analysesParameters estimated from Von Bertalanffy growth trajectories for use in animal model analysesexumvonbertdat.txtAccession numbers for NCBI Short Read ArchiveTable providing accession numbers for samples used in RNAseq analyses.Asagrei_RNAseq_NCBIaccessioning_20Oct2016.xlsxNormalized expression data for juveniles and subadultsNormalized counts per million for transcriptome comparisons of juvenile and subadult males and femalesAsagrei_unique_cpm_juvsub.csvNormalized expression data for juveniles with testosterone treatmentNormalized counts per million for transcriptome data from juvenile males and females with a control implant (blank) or a testosterone implant (T)Asagrei_unique_cpm_juv.csv
DOI: 10.5061/dryad.6fq75
title: Data from: Epidemiological models to control the spread of information in marine mammals

description: Socially transmitted wildlife behaviours that create human–wildlife
 conflict are an emerging problem for conservation efforts, but also
 provide a unique opportunity to apply principles of infectious disease
 control to wildlife management. As an example, California sea lions
 (Zalophus californianus) have learned to exploit concentrations of
 migratory adult salmonids below the fish ladders at Bonneville Dam,
 impeding endangered salmonid recovery. Proliferation of this foraging
 behaviour in the sea lion population has resulted in a controversial
 culling programme of individual sea lions at the dam, but the impact of
 such culling remains unclear. To evaluate the effectiveness of current and
 alternative culling strategies, we used network-based diffusion analysis
 on a long-term dataset to demonstrate that social transmission is
 implicated in the increase in dam-foraging behaviour and then studied
 different culling strategies within an epidemiological model of the
 behavioural transmission data. We show that current levels of lethal
 control have substantially reduced the rate of social transmission, but
 failed to effectively reduce overall sea lion recruitment. Earlier
 implementation of culling could have substantially reduced the extent of
 behavioural transmission and, ultimately, resulted in fewer animals being
 culled. Epidemiological analyses offer a promising tool to understand and
 control socially transmissible behaviours.
description: AstoriaCountData_Obs&PredColumns are time in weeks, predicted number of sea lions at Astoria using B-splines of order 6 (PredCount), and observed weekly counts (ObsCount).post2008MatrixAssociation matrix from 2008 and onPre2008MatrixAssociation matrix prior to 2008asoc2_dryadAssociation matrix for the entire time frame
DOI: 10.5061/dryad.1r45h
title: Data from: Pollinator adaptation and the evolution of floral nectar sugar composition

description: A longstanding debate concerns whether nectar sugar composition evolves as
 an adaptation to pollinator dietary requirements or whether it is
 ‘phylogenetically constrained’. Here we use a modeling approach to
 evaluate the hypothesis that nectar sucrose proportion (NSP) is an
 adaptation to pollinators. We analyze ~2,100 species of asterids, spanning
 several plant families and pollinator groups (PGs), and show that the
 hypothesis of adaptation cannot be rejected: NSP evolves toward two
 optimal values, high NSP for specialist-pollinated and low NSP for
 generalist-pollinated plants. However, the inferred adaptive process is
 weak, suggesting that adaptation to PG only provides a partial explanation
 for how nectar evolves. Additional factors are therefore needed to fully
 explain nectar evolution and we suggest that future studies might
 incorporate floral shape and size and the abiotic environment into the
 analytical framework. Further, we show that NSP and PG evolution are
 correlated – in a manner dictated by pollinator behavior. This contrasts
 with the view that a plant necessarily has to adapt its nectar composition
 to ensure pollination but rather suggests that pollinators adapt their
 foraging behavior or dietary requirements to the nectar sugar composition
 presented by the plants. Finally, we document unexpectedly sucrose-poor
 nectar in some specialized nectarivorous bird-pollinated plants from the
 Old World, which might represent an overlooked form of pollinator
 deception. Thus, our broad study provides several new insights into how
 nectar evolves and we conclude by discussing why maintaining the
 conceptual dichotomy between adaptation and constraint might be unhelpful
 for advancing this field.
description: Abrahamczyk_et_al_JEB_DataS1Literature sources consulted for generating the asterid summary phylogenyAbrahamczyketal_SI_Data1.docAbrahamczyk_et_al_JEB_DataS2Nectar sugar composition and concentration and pollinator group for each species newly analyzed for this study; *Nectar samples collected in the wild are highlighted (*); Literature sources for published data analyzed in this studyAbrahamczyketal_SI_Data2.doc
DOI: 10.5281/zenodo.17423483
title: Constructive Patterns for Human-Centered Tech Hiring

description: This repository accompanies the study “Constructive Patterns for Human-Centered Tech Hiring”. Through 22 semi-structured interviews with early-career software engineer and thematic analysis of over 470 candidate experiences, the study identifies 22 Constructive Patterns (CPs) that characterize human-centered hiring practices, such as transparent job advertisements, specific feedback, respectful communication, and framing recruitment as a two-way process.

The materials included here provide supporting documentation for the study:





Participants Characterization




Online R&S CP Codebook




Informed Consent Form




Interview Guide
DOI: 10.5281/zenodo.17423484
title: Constructive Patterns for Human-Centered Tech Hiring

description: This repository accompanies the study “Constructive Patterns for Human-Centered Tech Hiring”. Through 22 semi-structured interviews with early-career software engineer and thematic analysis of over 470 candidate experiences, the study identifies 22 Constructive Patterns (CPs) that characterize human-centered hiring practices, such as transparent job advertisements, specific feedback, respectful communication, and framing recruitment as a two-way process.

The materials included here provide supporting documentation for the study:





Participants Characterization




Online R&S CP Codebook




Informed Consent Form




Interview Guide
DOI: 10.5061/dryad.5ch51
title: Data from: Correlations between axial stiffness and microstructure of a species of bamboo

description: Bamboo is a ubiquitous monocotyledonous flowering plant and is a member of
 the true grass family Poaceae. In many parts of the world, it is widely
 used as a structural material especially in scaffolding and buildings. In
 spite of its wide use, there is no accepted methodology for standardizing
 a species of bamboo for a particular structural purpose. The task of
 developing structure–property correlations is complicated by the fact that
 bamboo is a hierarchical material whose structure at the nanoscopic level
 is not very well explored. However, we show that as far as stiffness is
 concerned, it is possible to obtain reliable estimates of important
 structural properties like the axial modulus from the knowledge of certain
 key elements of the microstructure. Stiffness of bamboo depends most
 sensitively on the size and arrangement of the fibre sheaths surrounding
 the vascular bundles and the arrangement of crystalline cellulose
 microfibrils in their secondary cell walls. For the species of bamboo
 studied in this work, we have quantitatively determined the radial
 gradation that the arrangement of fibres renders to the structure. The
 arrangement of the fibres gives bamboo a radially graded property
 variation across its cross section.
description: Sayyad_Mannan_et_al
DOI: 10.5061/dryad.412gv
title: Data from: Postcopulatory sexual selection influences baculum evolution in primates and carnivores

description: The extreme morphological variability of the baculum across mammals is
 thought to be the result of sexual selection (particularly, high levels of
 postcopulatory selection). However, the evolutionary trajectory of the
 mammalian baculum is little studied and evidence for the adaptive function
 of the baculum has so far been elusive. Here, we use Markov chain Monte
 Carlo methods implemented in a Bayesian phylogenetic framework to
 reconstruct baculum evolution across the mammalian class and investigate
 the rate of baculum length evolution within the primate order. We then
 test the effects of testes mass (postcopulatory sexual selection),
 polygamy, seasonal breeding and intromission duration on the baculum in
 primates and carnivores. The ancestral mammal did not have a baculum, but
 both ancestral primates and carnivores did. No relationship was found
 between testes mass and baculum length in either primates or carnivores.
 Intromission duration correlated with baculum presence over the course of
 primate evolution, and prolonged intromission predicts significantly
 longer bacula in extant primates and carnivores. Both polygamous and
 seasonal breeding systems predict significantly longer bacula in primates.
 These results suggest the baculum plays an important role in facilitating
 reproductive strategies in populations with high levels of postcopulatory
 sexual selection.
description: Primate Data (10k
 Trees)Primate data on baculum
 presence, intromission duration, mating system and breeding
 seasonality.Carnivora Data (10k
 Trees)Carnivore data on
 baculum presence and intromission durationPrimate Data (Mammal
 Supertree)Primate data on baculum
 presenceCarnivora Data (Mammal
 Supertree)Carnivora data on
 baculum presence.Chiroptera Data (Mammal
 Supertree)Chiroptera data on
 baculum presence.Rodentia Data (Mammal
 Supertree)Rodentia data on baculum
 presence.
DOI: 10.5061/dryad.kn871
title: Data from: Monitoring of plant-environment interactions by high throughput FTIR spectroscopy of pollen

description: Fourier transform infrared (FTIR) spectroscopy enables chemical analysis
 of pollen samples for plant phenotyping to study plant–environment
 interactions, such as influence of climate change or pathogens. However,
 current approach, such as microspectroscopy and attenuated total
 reflection spectroscopy, does not allow for high-throughput protocols.
 This study at hand suggests a new spectroscopic method for high-throughput
 characterization of pollen. Samples were measured as thin films of pollen
 fragments using a Bruker FTIR spectrometer with a high-throughput
 eXTension (HTS-XT) unit employing 384-well plates. In total, 146 pollen
 samples, belonging to 31 different pollen species of Fagaceae and
 Betulaceae and collected during three consecutive years (2012–2014) at
 locations in Croatia, Germany and Norway, were analysed. Critical steps in
 the sample preparation and measurement, such as variabilities between
 technical replicates, between microplates and between spectrometers, were
 studied. Measurement variations due to sample preparation, microplate
 holders and instrumentation were low, and thus allowed differentiation of
 samples with respect to phylogeny and biogeography. The spectral
 variability for a range of Fagales species (Fagus, Quercus, Betula,
 Corylus, Alnus and Ostrya) showed high-species-specific differences in
 pollen's chemical composition due to either location or year.
 Statistically significant inter-annual and locational differences in the
 pollen spectra indicate that pollen chemical composition has high
 phenotypic plasticity and is influenced by local climate conditions. The
 variations in composition are connected to lipids, proteins, carbohydrates
 and sporopollenins that play crucial roles in cold and desiccation
 tolerance, protection against UV radiation and as material and energy
 reserves. The results of this study demonstrate the value of
 high-throughput FTIR approach for the systematic collection of data on
 ecosystems. The novel FTIR approach offers fast, reliable and economical
 screening of large number of samples by semi-automated methodology. The
 high-throughput approach could provide crucial understanding on
 plant–climate interactions with respect to biochemical variation within
 genera, species and populations.
description: READMEMain info on
 datasamplesList of the pollen sampleswavenumbersFTIR wavenumbers for spectral dataZHTSFTIR spectra (Absorbance values) of pollen samples
DOI: 10.5061/dryad.0s3t5
title: Data from: Potentially adaptive mitochondrial haplotypes as a tool to identify divergent nuclear loci

description: 1. Genetic tools are commonly used for conservation and management of
 at-risk species. Individuals are often sampled from mixtures composed of
 many populations, which creates a need to assign individuals to their
 source. This can be problematic when the genetic divergence among source
 populations is weak but can be improved using adaptive genetic loci, which
 should show stronger levels of divergence. 2. We previously reported a
 signature of positive selection in the mitochondrial-encoded ND5 subunit
 of complex I in diverse taxa. The respiratory machinery of the
 mitochondria in salmonids is composed of more than 80 nuclear genes and
 there is substantial interaction between nuclear and mitochondrial
 expressed gene products. Recent studies report adaptive variation in
 mitochondrial function as well as co-evolution between mitochondrial and
 nuclear genomes. We used potentially adaptive ND5-based mitochondrial
 haplotypes to identify nuclear loci that would display increased levels of
 genetic divergence compared to neutral nuclear loci in chum salmon
 (Oncorhynchus keta). Populations in a geographic area the size of France
 have previously demonstrated weak genetic divergence even after
 substantial discovery efforts by multiple laboratories for allozymes,
 microsatellites and SNPs over the last two decades. 3. We used RAD-based
 Next-Generation Sequencing and identified a nuclear-encoded subunit of
 mitochondrial complex I that was a significant FST outlier and 14 other
 divergent markers that improve genetic assignment of individuals to their
 population of origin relative to assignments based on neutral markers
 alone. 4. This work demonstrates how a known adaptive marker can be
 leveraged to increase the probability of identifying divergent markers for
 applied genetics tools that may be biologically linked to it.
description: Garvin et al. 2016
 RAD_Tag_DataThis file contains the
 19,098, 200bp RAD-tags that were produced. For each RAD-tag, the variable
 nucleotide (potential SNP) is listed for each individual and individuals
 are grouped by collection. The colored boxes at the top identify the
 mutation that was found in the mitochondrial DNA for that particular
 individual.
DOI: 10.5061/dryad.f7h12
title: Data from: Poor adherence to guidelines for preventing central line-associated bloodstream infections (CLABSI): results of a worldwide survey

description: Background: Central line-associated bloodstream infections (CLABSI) are a
 cause of increased morbidity and mortality, and are largely preventable.
 We documented attitudes and practices in intensive care units (ICUs) in
 2015 in order to assess compliance with CLABSI prevention guidelines.
 Methods: Between June and October 2015, an online questionnaire was made
 available to medical doctors and nurses working in ICUs worldwide. We
 investigated practices related to central line (CL) insertion, maintenance
 and measurement of CLABSI-related data following the SHEA guidelines as a
 standard. We computed weighted estimates for high, middle and low-income
 countries using country population as a weight. Only countries providing
 at least 10 complete responses were included in these estimates. Results:
 Ninety five countries provided 3407 individual responses; no low income,
 14 middle income (MIC) and 27 high income (HIC) countries provided 10 or
 more responses. Of the total respondents, 80% (MIC, SE = 1.5) and 81%
 (HIC, SE = 1.0) reported availability of written clinical guidelines for
 CLABSI prevention in their ICU; 23% (MIC,SE = 1.7) and 62% (HIC,SE = 1.4)
 reported compliance to the following (combined) recommendations for CL
 insertion: hand hygiene, full barrier precaution, chlorhexidine
 &gt;0.5%, no topic or systemic antimicrobial prophylaxis; 60%
 (MIC,SE = 2.0) and 73% (HIC,SE = 1.2) reported daily assessment for the
 need of a central line. Most considered CLABSI measurement key to quality
 improvement, however few were able to report their CLABSI rate.
 Heterogeneity between countries was high and country specific results are
 made available. Conclusions: This study has identified areas for
 improvement in CLABSI prevention practices linked to CL insertion and
 maintenance. Priorities for intervention differ between countries.
description: CLABSIsurvey2Data file including the responses to the CLABSI survey per country. The survey explores practices in CLABSI preventive actions and measurement, but also attitudes towards measurement of outcomes of these preventive activities. For confidentiality reasons, 100 records from 46 countries having provided less than 5 replies have been removed from the dataset. This dataset therefore has 3,307 records from 49 different countries.
DOI: 10.5061/dryad.b56d4
title: Data from: Movement tactics of a mobile predator in a meta-ecosystem with fluctuating resources: the arctic fox in the High Arctic

description: Animal movement is a fundamental process shaping ecosystems at multiple
 levels, from the fate of individuals to global patterns of biodiversity.
 The spatio-temporal dynamic of food resources is a major driver of animal
 movement and generates patterns ranging from range residency to migration
 and nomadism. Arctic tundra predators face a strongly fluctuating
 environment marked by cyclic microtine populations, high seasonality, and
 the potential availability of sea ice, which gives access to marine
 resources in winter. This type of relatively poor and highly variable
 environment can promote long-distance movements and resource tracking in
 mobile species. Here, we investigated the winter movements of the arctic
 fox, a major tundra predator often described as a seasonal migrant or
 nomad. We used six years of Argos satellite telemetry data collected on 66
 adults from Bylot Island (Nunavut, Canada) tracked during the sea ice
 period. We hypothesized that long-distance movements would be influenced
 by spatio-temporal changes in resource availability and individual
 characteristics. Despite strong annual and seasonal changes in resource
 abundance and distribution, we found that a majority of individuals
 remained resident, especially those located in an area characterized by
 highly predictable pulse resources (goose nesting colony) and abundant
 cached food items (eggs). Foxes compensated terrestrial food shortage by
 commuting to the sea ice rather than using long-distance tracking or
 moving completely onto the sea ice for winter. Individual characteristics
 also influenced movement patterns: age positively influenced the
 propensity to engage in nomadism, suggesting older foxes may be driven out
 of their territories. Our results show how these mammalian predators can
 adjust their movement patterns to favor range residency despite strong
 spatio-temporal fluctuations in food resources. Understanding the movement
 responses of predators to prey dynamics helps identifying the scales at
 which they work, which is a critical aspect of the functioning and
 connectivity among meta-ecosystems.
description: Raw Argos data of arctic
 foxes from Bylot IslandThis dataset contains
 the Argos locations of arctic foxes tracked from July 2007 to May 2013 (66
 individuals, 97 fox-years); the file is provided in txt format. More
 information is provided in the joined ReadMe file.Raw_Argos_Data_Laietal_Oikos.txt
DOI: 10.5281/zenodo.18387531
title: Widespread seasonal transition in snow effects on vegetation growth across the Tibetan Plateau

description: Code and data for "Widespread seasonal transition in snow effects on vegetation growth across the Tibetan Plateau"
DOI: 10.5061/dryad.v5t1m
title: Data from: Male mate choice, male quality, and the potential for sexual selection on female traits under polygyny.

description: Observations of male mate choice are increasingly common, even in species
 with traditional sex roles. In addition, female traits that bear the
 hallmarks of secondary sexual characters are increasingly reported. These
 concurrent empirical trends have led to the repeated inference that, even
 under polygyny, male mate choice is a mechanism of sexual selection on
 female traits. It is often either assumed or argued that in these cases
 females are competing for males of superior “quality”; females might
 experience sexual selection under polygyny if they compete for mates that
 provide either direct or indirect benefits. However, the theoretical
 foundation of this testable hypothesis remains largely uninvestigated. We
 develop a population genetic model to probe the logic of this hypothesis
 and demonstrate that, contrary to common inferences, male mate choice,
 variation in male quality (in the form of a direct fecundity benefit to
 females), and female ornamentation can coexist in a population without any
 sexual selection on female ornamentation taking place at all. Furthermore,
 even in a “best case scenario” where high quality males with a preference
 for ornamented females are able to mate disproportionately more often with
 them, the evolution of female traits by sexual selection may be relatively
 weak. We discuss the implication of these findings for ongoing empirical
 and theoretical research on the evolution of sexual-signaling in females.
description: Mathematica code for
 basic modelDevelops recursion
 equations for basic model in standard population genetic
 notation.DryadFile_BasicModel.nb