cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vq83bk3xv
title: The departure between constant-rate birth-death and empirically inferred diversification processes

description: Birth-death models (BDMs) are stochastic processes describing the
 processes of speciation and extinction through time and across taxa and
 are widely used in biology for inference of evolutionary timescales.
 Previous research has highlighted how the expected trees under BDMs tend
 to differ from empirical trees with respect to indices such as the amount
 of phylogenetic imbalance. However, our understanding of how trees differ
 between BDMs and empirical inferences remains incomplete. In this study,
 we demonstrate how four different constant-rate BDM scenarios influence
 tree shape and branch-length characteristics of phylogenetic trees, using
 a wide range of topology and branch-length indices. Comparison of BDM
 expectations against a comprehensive empirical dataset of 1,189 empirical
 trees shows that the dominant form of model inadequacy in BDMs is in
 failing to accommodate large amounts of phylogenetic imbalance in
 empirical processes. We also find that empirical trees tend to have
 significantly greater depth, lower stemminess, and longer shortest pendant
 edge lengths than BD-simulated trees. The results also indicate that
 accounting for the sampling fraction is the single most important
 parameter for accommodating empirical stemminess and branch lengths.
 Overall, our findings demonstrate the limitations of BDM priors when
 inferring the shape and structural characteristics of phylogenetic trees,
 highlighting the importance of novel methods that account for a broader
 tree space and secondarily reduce any possible bias in branch length
 estimation.
DOI: 10.3886/e244708
title: Ethical Leadership and Algorithmic Dehumanization: The Role of Psychological Safety and Monitoring Intensity

description: Algorithmic management has transformed contemporary work by enhancing efficiency through data-driven monitoring and control, yet it often produces unintended human costs, including employee experiences of dehumanization. While prior research has documented these effects, little is known about whether internal organizational mechanisms can mitigate them. Drawing on dehumanization theory, we examine perceived ethical leadership as a rehumanizing antecedent in algorithmically managed work contexts. We propose and test a moderated mediation model in which ethical leadership reduces employees’ perceived algorithmic dehumanization by fostering psychological safety. Moreover, we argue that this indirect effect is contingent on the intensity of algorithmic monitoring, such that the rehumanizing role of ethical leadership becomes stronger under conditions of high monitoring. Using multi-wave survey data from employees working under algorithmic management, we find that ethical leadership is negatively related to algorithmic dehumanization, both directly and indirectly through psychological safety. Consistent with our theorizing, this indirect effect is amplified when employees perceive higher levels of algorithmic monitoring intensity. These findings contribute to research on algorithmic management and ethical leadership by identifying leadership as a critical internal resource for restoring humanness in technologically mediated work and highlighting psychological safety as a key mechanism through which this process occurs.
DOI: 10.5061/dryad.c59zw3rcp
title: Fitting and evaluating univariate and multivariate models of within-lineage evolution

description: The nature of phenotypic evolution within lineages is central to many
 unresolved questions in paleontology and evolutionary biology. Analyses of
 evolutionary time-series of ancestor-descendant populations in the fossil
 record are likely to make important contributions to many of these
 debates. However, the limited number of models that have been applied to
 these types of data may restrict our ability to interpret phenotypic
 evolution in the fossil record. Using uni- and multivariate models of
 trait evolution that make different assumptions regarding the dynamics of
 the adaptive landscape, I evaluate contrasting hypotheses to explain
 evolution of size in the radiolarian Eucyrtidium calvertense and armor in
 the stickleback Gaserosteus doryssus. Body size evolution in E.
 calvertense is best explained by a model where the lineage evolves as a
 consequence of a shift in the adaptive landscape that coincides with the
 initiation of neosympatry with its sister lineage. Multivariate evolution
 of armor traits in a stickleback lineage (Gasterosteus doryssus) shows
 evidence of adaptation towards independent optima on the adaptive
 landscape at the same time as traits change in a correlated fashion. The
 fitted models are available in an R package evoTS, which builds on the
 commonly used paleoTS framework.
DOI: 10.3886/e244708v1
title: Ethical Leadership and Algorithmic Dehumanization: The Role of Psychological Safety and Monitoring Intensity

description: Algorithmic management has transformed contemporary work by enhancing efficiency through data-driven monitoring and control, yet it often produces unintended human costs, including employee experiences of dehumanization. While prior research has documented these effects, little is known about whether internal organizational mechanisms can mitigate them. Drawing on dehumanization theory, we examine perceived ethical leadership as a rehumanizing antecedent in algorithmically managed work contexts. We propose and test a moderated mediation model in which ethical leadership reduces employees’ perceived algorithmic dehumanization by fostering psychological safety. Moreover, we argue that this indirect effect is contingent on the intensity of algorithmic monitoring, such that the rehumanizing role of ethical leadership becomes stronger under conditions of high monitoring. Using multi-wave survey data from employees working under algorithmic management, we find that ethical leadership is negatively related to algorithmic dehumanization, both directly and indirectly through psychological safety. Consistent with our theorizing, this indirect effect is amplified when employees perceive higher levels of algorithmic monitoring intensity. These findings contribute to research on algorithmic management and ethical leadership by identifying leadership as a critical internal resource for restoring humanness in technologically mediated work and highlighting psychological safety as a key mechanism through which this process occurs.
DOI: 10.5061/dryad.6wwpzgn37
title: Data from: Effective population size in a partially clonal plant is not predicted by the number of genetic individuals

description: Estimating effective population size (Ne) is important for theoretical and
 practical applications in evolutionary biology and conservation.
 Nevertheless, estimates of Ne in organisms with complex
 life-history traits remain scarce because of the challenges associated
 with estimation methods. Partially clonal plants capable of both
 vegetative (clonal) growth and sexual reproduction are a common group of
 organisms for which the discrepancy between the apparent number of
 individuals (ramets) and the number of genetic individuals (genets) can be
 striking, and it is unclear how this discrepancy relates to Ne.
 In this study, we analysed two populations of the orchid Cypripedium
 calceolus to understand how the rate of clonal vs. sexual reproduction
 affected Ne. We genotyped &gt;1,000 ramets at microsatellite
 and SNP loci, and estimated contemporary Ne with the
 linkage disequilibrium method, starting from the theoretical expectation
 that variance in reproductive success among individuals caused by clonal
 reproduction and by constraints on sexual reproduction would
 lower Ne. We considered factors potentially affecting our
 estimates, including different marker types and sampling strategies, and
 the influence of pseudoreplication in genomic datasets
 on Ne confidence intervals. The magnitude
 of Ne/Nramets and Ne/Ngenets ratios we provide may be
 used as reference points for other species with similar life-history
 traits. Our findings demonstrate that Ne in partially
 clonal plants cannot be predicted based on the number of genets generated
 by sexual reproduction, because demographic changes over time can strongly
 influence Ne. This is especially relevant in species of
 conservation concern, in which population declines may not be detected by
 only ascertaining the number of genets.
description: Please see README.md and related manuscript.
DOI: 10.5061/dryad.j0zpc86jp
title: Data for: Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast

description: Optimized nutrient utilization is crucial for the progression of
 microorganisms in competing communities. Here we investigate how different
 budding yeast species and ecological isolates have established divergent
 preferences for two alternative sugar substrates: Glucose, which is
 fermented preferentially by yeast, and galactose, which is alternatively
 used upon induction of the relevant GAL metabolic genes. We
 quantified the dose-dependent induction of the GAL1 gene encoding the
 central galactokinase enzyme, and found that a very large diversification
 exists between different yeast ecotypes and species. The sensitivity of
 GAL1 induction correlates with the growth performance of the respective
 yeasts with the alternative sugar. We further define some of the
 mechanisms, which have established different glucose/galactose consumption
 strategies in representative yeast strains by modulating the activity of
 the Gal3 inducer. (1) Optimal galactose consumers, such as Saccharomyces
 uvarum, contain a hyperactive GAL3 promoter, sustaining highly sensitive
 GAL1 expression, which is not further improved upon repetitive galactose
 encounters. (2) Desensitized galactose consumers, such as S. cerevisiae
 Y12, contain a less sensitive Gal3 sensor, causing a shift of the
 galactose response towards higher sugar concentrations even in galactose
 experienced cells. (3) Galactose insensitive sugar consumers, such as S.
 cerevisiae DBVPG6044, contain an interrupted GAL3 gene, causing extremely
 reluctant galactose consumption, which however still is improved upon
 repeated galactose availability. In summary, different yeast strains and
 natural isolates have evolved galactose utilization strategies, which
 cover the whole range of possible sensitivities by modulating the
 expression and/or activity of the inducible galactose sensor Gal3.
description: Unprocessed raw obtained from continuous readings (luminescence
 or absorbance) using automated microplate readers.
DOI: 10.15468/dl.4ce986
title: Occurrence Download

description: A dataset containing 5091 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-76.94101 5.47048,-74.24749 5.47048,-74.24749 8.76323,-76.94101 8.76323,-76.94101 5.47048))",
 "HasGeospatialIssue is false",
 "TaxonKey is Capito hypoleucus"
 ]
}

 The dataset includes 5091 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003471-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3n5tb2rn5
title: Data for: A selfish genetic element and its suppressor causes abnormalities to testes in a fly

description: Selfish genetic elements (SGEs), specifically X-chromosome meiotic drive
 (XCMD), create huge conflicts within a host’s genome and can have profound
 effects on fertility. Suppressors are a common evolutionary response to
 XCMD to negate its costs. However, whether suppressors themselves can
 cause negative non-target effects remains understudied. Here, we examine
 whether the intragenomic conflicts created by XCMD and its suppressor
 affect gonad morphology in Drosophila subobscura. We found significant
 differences in testes, seminal vesicle, and accessory gland size depending
 on whether a male carried a non-driving X chromosome, an XCMD, and if the
 XCMD was suppressed. We also found the first evidence of abnormal testes
 development that is specifically associated with a suppressor of XCMD.
 Unlike other studies, our evidence suggests that XCMD in D. subobscura
 creates major abnormalities to male gonads. These abnormalities are most
 frequent if both XCMD and its suppressor are both present. While costs of
 suppression have importance in theoretical models, they have largely been
 ignored in empirical XCMD systems. Overall, this study highlights that
 genetic conflict, created by SGEs and their suppressors, is a potent
 evolutionary force that can have major impacts on gonad development and
 gametogenesis.
description: This data was collected from images using ImageJ.
 Here, we present the relative measurements used for final data
 analyses in the paper (in most cases these came from two measured
 organs). See the README.md file for details of the data
 set.
DOI: 10.5281/zenodo.12801421
title: CIANNA V1.0 release example network models

description: Set of pre-trained artificial network models to be used with CIANNA examples associated with the V-1.0 release of the framework.See related works for more information, or go to https://github.com/Deyht/CIANNA for the latest version of the related framework.The provided files are in binary format and are only useful for loading with CIANNA.
DOI: 10.15468/dl.m2j9b7
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Fraxinus mandshurica"
 ]
}

 The dataset includes 60 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003472-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12801420
title: CIANNA V1.0 release example network models

description: Set of pre-trained artificial network models to be used with CIANNA examples associated with the V-1.0 release of the framework.See related works for more information, or go to https://github.com/Deyht/CIANNA for the latest version of the related framework.The provided files are in binary format and are only useful for loading with CIANNA.
DOI: 10.5061/dryad.mpg4f4r49
title: Rum and Argyll red deer genotype files

description: The red deer population inhabiting the north block of the Isle of Rum,
 Scotland (57°0’N, 6°20’W) has been studied at an individual level since
 1971 and was the main focus of this study. After quality control 39,587
 autosomal SNPs genotyped in 3046 individuals were retained for analysis.
 This study also used equivalent genotype data for 157 individuals from a
 mainland population of red deer from Argyll, Scotland. Data files are in
 plink readable format (.bed .bim .fam) and include a .txt file with
 estimated SNP positions in centimorgans (cM). If you plan to analyse the
 data, we request that you inform us, see README file for more
 information. 
description: DNA was extracted from ear punches from calves captured soon
 after birth or darted adults, post-mortem tissue or cast antlers (See
 Huisman et al (2016) for full details). DNA samples were genotyped at
 50,541 attempted SNP loci on the Cervine Illumina 50K BeadChip (Brauning,
 2015). SNP genotypes were clustered and scored using Illumina GenomeStudio
 v2.0, and were subject to quality control with the following parameters:
 SNP minor allele frequency (MAF) &gt; 0.001, ID genotyping success
 &gt; 0.9, and SNP genotyping success &gt; 0.99.
 For the Argyll dataset details of sample collection and DNA
 extraction can be found in McFarlane et al (2020). Samples were genotyped
 as above and quality control was carried out by McFarlane et al (2020) as
 above with the exception of SNP genotyping success &gt;0.9.
DOI: 10.5061/dryad.z08kprrht
title: Exploring the effect of industrial agglomeration on income inequality in China

description: Income inequality is a good indicator reflecting the quality of
 people's livelihood. There are many studies on the determinants of
 income inequality. However, few have studied the impacts of industrial
 agglomeration on income inequality, and even fewer have studied the
 spatial correlation of income inequality. The goal of this paper is to
 investigate the impact of China’s industrial agglomeration on income
 inequality from a spatial perspective. Using data on China’s 31 provinces
 from 2003 to 2020 and the spatial panel Durbin model, our results show
 that industrial agglomeration and income inequality present an inverted
 “U-shape” relationship, proving that they are non-linear changes. As the
 degree of industrial agglomeration increases, income inequality will rise;
 after it reaches a certain value, income inequality will drop. Therefore,
 the Chinese government and enterprises had better pay attention to the
 spatial distribution of industrial agglomeration, thereby reducing
 China's regional income inequality.
description: These data originate from the 2004–2021 China Statistical
 Yearbook, China Labour Statistical Yearbook and China Population and
 Employment Statistics Yearbook. Using data on
 China's 31 provinces from 2003 to 2020, the spatial panel Durbin
 model is adopted to explore the impact of industrial agglomeration on
 income inequality in China.
DOI: 10.15468/dl.454rk5
title: Occurrence Download

description: A dataset containing 14658 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tapirus terrestris"
 ]
}

 The dataset includes 14658 records from 199 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003473-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.n02v6wx1w
title: Intraguild predation is increased in areas of low prey diversity in a generalist predator community

description: 1. Niche differentiation and intraguild predation (IGP) can allow
 ecologically similar species to coexist, although it is unclear which
 coexistence mechanism predominates in consumer communities. Until now, a
 limited ability to quantify diets from metabarcoding data has precluded
 the use of sequencing data to determine the relative importance of these
 mechanisms. 2. Here, we pair a recent metabarcoding quantification
 approach with stable isotope analysis to examine diet composition in a
 wolf spider community. 3. We compare the prevalence of resource
 partitioning and IGP in these spiders, and test whether factors that
 influence foraging performance, including individual identity, morphology,
 prey community, and environmental conditions, can explain variation in
 diet composition and IGP. 4. Extensive IGP is likely the primary
 coexistence mechanism in this community, and other factors to which
 foraging variation is often attributed do not explain diet composition and
 IGP here. Rather, IGP increases as prey diversity decreases. 5. Foragers
 are driven to IGP where resource niches are limited. We highlight the need
 to examine how drivers of predator-prey interaction strengths translate
 into foraging in natural systems.
description: Data collection described in the manuscript methods.
DOI: 10.5061/dryad.8gtht76t5
title: Data from: Rewilding in Southeast Asia: Singapore as a case study

description: Re-establishing extirpated wildlife – or ‘rewilding’ – is touted as a way
 to restore biodiversity and ecosystem processes, but we lack real-world
 examples of this process, particularly in Southeast Asia. Here we use a
 decade of aggregated camera trap data, N-mixture occupancy models, and
 input from local wildlife experts to describe the unassisted
 recolonization of two native large herbivores in Singapore. Sambar deer
 (Rusa unicolor) escaped from captivity (private or public zoos) in the
 1970s and contemporary camera trap data show they have only colonized
 nearby forest fragments and their abundance remains low. Wild pigs (Sus
 scrofa), in contrast, naturally recolonized by swimming from Malaysia in
 the 1990s and have rapidly expanded their range and abundance across
 Singapore. While wild pigs have not recolonized all viable green spaces
 yet, their trajectory indicates they soon will. We also note that a third
 ungulate, the muntjac deer (Muntiacus muntjak), was captured in camera
 trapping in 2014 and 2015 but was never recorded afterward despite
 increased sampling effort, and thus we do not focus on their presumably
 unsuccessful recolonization. The divergent rewilding trajectories between
 sambar deer and wild pigs suggest different conservation outcomes and
 management requirements. Sambar deer may restore lost plant-animal
 interactions such as herbivory and seed dispersal without requiring
 significant management. Wild pigs, in contrast, have reached high numbers
 rapidly and may require active management to avoid hyperabundance and
 negative ecological impacts in regions such as Singapore that lack both
 hunting and large predators.
DOI: 10.5061/dryad.7pvmcvdz5
title: Species distribution data and distribution of private and public protected areas in Cerrado, Brazil

description: Here we present the models of 103 threatened vertebrates (Anphibia,
 Reptile, Birds and Mammals) from the Cerrado in Brazil and all information
 about spatial distribution of private and public conservation protected
 areas that is a part of an article about the value of private areas to
 conservation.
description: Species distribution data was fitted based on the most recent
 occurrence database and using the ENMTML R-package. We use the 19 climatic
 data from WORDCLIM, four different algorithms for fit, and control for
 overprediction using M-SDM techniques. Distribution of
 private areas was rasterized from the original shapefile data from the CAR
 (Cadastro Ambiental Rural) of Brazil. So, the information in each cell is
 the area of each category of private land in the cell. Distribution of
 conservation units follows the same reasoning. 
description: All data was developed and produced using R, specifically the
 library "raster."
DOI: 10.5061/dryad.qbzkh18nj
title: Data for: Microglia phagocytosis determines the volume and function of the rat Sexually Dimorphic Nucleus of the Preoptic Area

description: The Sexually Dimorphic Nucleus of the Preoptic Area (SDN-POA) is the
 oldest and most robust sex difference reported in mammalian brain and is
 singular for its presence across a wide range of species from rodents to
 ungulates to man. This small collection of Nissl dense neurons is reliably
 larger in volume in males. Yet, despite its notoriety and intense
 interrogation, both the mechanism establishing the sex difference and the
 functional role of the SDN have remained elusive. Convergent evidence from
 rodent studies led to the conclusion that testicular androgens aromatized
 to estrogens are neuroprotective in males and that higher apoptosis
 (naturally occurring cell death) in females determines their smaller SDN.
 In several species, including humans, a smaller SDN correlates with a
 preference for mating with males. We report here that this volume
 difference is dependent upon a participatory role of phagocytic microglia
 which engulf more neurons in the female SDN and assure their destruction .
 Selectively blocking microglia phagocytosis temporarily spared neurons
 from apoptotic death and increased SDN volume in females without hormone
 treatment. Increasing the number of neurons in the SDN in neonatal females
 resulted in loss of preference for male odors in adulthood, an effect
 paralleled by dampened excitation of SDN neurons as evidenced by reduced
 IEG expression when exposed to male urine. Thus, the mechanism
 establishing a sex difference in SDN volume includes an essential role for
 microglia, and SDN function as a regulator of sexual partner preference is
 confirmed.