cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8ks41
title: Data from: Manipulating virulence factor availability can have complex consequences for infections

description: Given the rise of bacterial resistance against antibiotics, we urgently
 need alternative strategies to fight infections. Some propose we should
 disarm rather than kill bacteria, through targeted disruption of their
 virulence factors. It is assumed that this approach (i) induces weak
 selection for resistance because it should only minimally impact bacterial
 fitness, and (ii) is specific, only interfering with the virulence factor
 in question. Given that pathogenicity emerges from complex interactions
 between pathogens, hosts, and their environment, such assumptions may be
 unrealistic. To address this issue in a test case, we conducted
 experiments with the opportunistic human pathogen Pseudomonas aeruginosa,
 where we manipulated the availability of a virulence factor, the
 iron-scavenging pyoverdine, within the insect host Galleria mellonella. We
 observed that pyoverdine availability was not stringently predictive of
 virulence, and affected bacterial fitness in non-linear ways. We show that
 this complexity could partly arise because pyoverdine availability affects
 host responses and alters the expression of regulatorily linked virulence
 factors. Our results reveal that virulence-factor manipulation feeds back
 on pathogen and host behavior, which in turn affects virulence. Our
 findings highlight that realizing effective and evolutionarily robust
 anti-virulence therapies will ultimately require deeper engagement with
 the intrinsic complexity of host-pathogen systems.
description: RawData_EvolAppl_Weigert_et_al_2016All raw data are collected in this file with self explanatory treatment names and a short technical description.
DOI: 10.5061/dryad.ng75r
title: Data from: Description of a new microphthalmous species of Pterostichus Bonelli, 1810 (Coleoptera: Carabidae) from southwestern Oregon and key to species of the subgenus Leptoferonia Casey, 1918

description: Pterostichus (Leptoferonia) hackerae sp. nov. is described based on a
 single male specimen with its type locality No Name Cave, Josephine Co.,
 Oregon. This is the seventh species of microphthalmous Leptoferonia Casey,
 1918 to be described, and based on the analysis of DNA data, it is found
 to be most closely related to another microphthalmous species, P. rothi
 (Hatch, 1951). A second specimen and location for P. (Leptoferonia) enyo
 Will, 2007, also a microphthalmous species, is reported. Analysis of DNA
 sequence data (28S rDNA and COI mtDNA) places P. enyo as sister to the
 more southern microphthalmous species P. (Leptoferonia) caligans Horn,
 1891. A modified version of the key by Hacker (1968) is presented,
 allowing for identification of all known species of Leptoferonia.
description: KWill leptoferonia data
 filesMesquite NEXUS files,
 aligned and concatenated, MrBayes files, and TNT run
 files.
DOI: 10.5061/dryad.ph2p2
title: Data from: Seasonal detours by soaring migrants shaped by wind regimes along the East Atlantic Flyway

description: Avian migrants often make substantial detours between their seasonal
 destinations. It is likely some species do this to make the most of
 predictable wind regimes along their respective flyways. We test this
 hypothesis by studying orientation behaviour of a long-distance soaring
 migrant in relation to prevailing winds along the East Atlantic Flyway. We
 tracked 62 migratory journeys of 12 adult European Honey Buzzards Pernis
 apivorus with GPS loggers. Hourly fixes were annotated with local wind
 vectors from a global atmospheric model to determine orientation
 behaviours with respect to the buzzards’ seasonal goal destinations. This
 enabled us to determine hot spots where buzzards overdrifted and
 overcompensated for side winds. We then determined whether winds along the
 buzzards’ detours differed from winds prevailing elsewhere in the flyway.
 Honey Buzzards cross western Africa using different routes in autumn and
 spring. In autumn, they overcompensated for westward winds to circumvent
 the Atlas Mountains on the eastern side and then overdrifted with
 south-westward winds while crossing the Sahara. In spring, however, they
 frequently overcompensated for eastward winds to initiate a westward
 detour at the start of their journey. They later overdrifted with side
 winds north-westward over the Sahel and north-eastward over the Sahara,
 avoiding adverse winds over the central Sahara. We conclude that Honey
 Buzzards make seasonal detours to utilize more supportive winds further en
 route and thereby expend less energy while crossing the desert. Lifelong
 tracking studies will be helpful to elucidate how honey buzzards and other
 migrants learn complex routes to exploit atmospheric circulation patterns
 from local to synoptic scales.
description: Vansteelant-etal-JAE_processeddataContains all GPS tracking data, wind conditions extracted for each fix from ECMWF, and calculated values for the ratio of sideward movement vs sidewind and classification of orientation behaviours.
DOI: 10.5061/dryad.37sb7
title: Data from: The speed–curvature power law in Drosophila larval locomotion

description: We report the discovery that the locomotor trajectories of Drosophila
 larvae follow the power-law relationship between speed and curvature
 previously found in the movements of human and non-human primates. Using
 high-resolution behavioural tracking in controlled but naturalistic
 sensory environments, we tested the law in maggots tracing different
 trajectory types, from reaching-like movements to scribbles. For most but
 not all flies, we found that the law holds robustly, with an exponent
 close to three-quarters rather than to the usual two-thirds found in
 almost all human situations, suggesting dynamic effects adding on purely
 kinematic constraints. There are different hypotheses for the origin of
 the law in primates, one invoking cortical computations, another
 viscoelastic muscle properties coupled with central pattern generators.
 Our findings are consistent with the latter view and demonstrate that the
 law is possible in animals with nervous systems orders of magnitude
 simpler than in primates. Scaling laws might exist because natural
 selection favours processes that remain behaviourally efficient across a
 wide range of neural and body architectures in distantly related species.
description: data_Larvae_Overshoot_conditionX and Y raw centroid and tail positions of individual Drosophila melanogaster larvae (n=42) in the overshoot condition (orbiting around an odor source) tracked at 7Hz and at the spatial resolution specified in the file— see manuscript for more details.data_Larvae_Approach_conditionX and Y raw centroid and tail positions of individual Drosophila melanogaster larvae (n=40) in the approach condition (reaching an odor source from afar) tracked at 7Hz and at the spatial resolution specified in the file— see manuscript for more details.data_Larvae_Dispersal_conditionX and Y raw centroid and tail positions of individual Drosophila melanogaster larvae (n=41) in the dispersal condition (foraging in the absence of olfactory cues) tracked at 7Hz and at the spatial resolution specified in the file— see manuscript for more details.
DOI: 10.5061/dryad.qc2fm
title: Data from: Horses in the Cloud: big data exploration and mining of fossil and extant Equus (Mammalia: Equidae)

description: Extant species of the genus Equus (e.g., horses, asses, and zebras) have a
 widespread distribution today on all continents except Antarctica. Extinct
 species of Equus represented by fossils were likewise widely distributed
 in the Pliocene and even more so during the Pleistocene. In order to
 understand the efficacy of “big data” for (paleo)biogeographic analyses,
 location records (latitude, longitude) and fossil occurrences for the
 genus Equus were mined and further explored from six databases, including
 iDigBio, Paleobiology Database, VertNet, BISON, Neotoma, and GBIF. These
 were chosen from a priori knowledge of where relevant data might be
 aggregated. We also realized that these databases have different
 objectives and data sources and therefore would provide a useful
 comparative study of the widespread taxon Equus in space and time. The
 mining of Equus data from these six sources yielded a combined total of
 123.8 K location records, including 116.2K fossil specimens. These include
 individual points that are unique, that is, only occurring in one of these
 databases, and those that are duplicated in multiple databases. Of the six
 databases, three (iDigBio, Paleobiology Database, and GBIF) were judged to
 be the most useful in the Equus use case. Most of the databases are biased
 toward North American records, thus limiting the reconstruction of the
 actual distribution of the genus Equus in space and time outside of this
 continent. Although Equus has a large number of digitally accessible
 records, fundamentally interesting questions pertaining to evolutionary
 dynamics and extinction geography are still a challenge for these kinds of
 biodiversity databases due primarily to the lack of sufficiently dense and
 precise temporal data.
description: Supp Doc 1
 FINALDescription of the Equus
 search results for three big databases, i.e., VertNet, BISON, and
 Neotoma.Supp Doc 2
 FINALThis is a discussion of
 a previous search for Equus in which downloaded data from GBIF were
 incorrectly transposed, resulting in spurious locations on the world
 map.
DOI: 10.5061/dryad.mt16j
title: Data from: Genetic and genomic evidence of niche partitioning and adaptive radiation in mountain pine beetle fungal symbionts

description: Bark beetles form multipartite symbiotic associations with blue stain
 fungi (Ophiostomatales, Ascomycota). These fungal symbionts play an
 important role during the beetle's life cycle by providing
 nutritional supplementation, overcoming tree defences and modifying host
 tissues to favour brood development. The maintenance of stable
 multipartite symbioses with seemingly less competitive symbionts in
 similar habitats is of fundamental interest to ecology and evolution. We
 tested the hypothesis that the coexistence of three fungal species
 associated with the mountain pine beetle is the result of niche
 partitioning and adaptive radiation using SNP genotyping coupled with
 genotype–environment association analysis and phenotypic characterization
 of growth rate under different temperatures. We found that genetic
 variation and population structure within each species is best explained
 by distinct spatial and environmental variables. We observed both common
 (temperature seasonality and the host species) and distinct (drought, cold
 stress, precipitation) environmental and spatial factors that shaped the
 genomes of these fungi resulting in contrasting outcomes. Phenotypic
 intraspecific variations in Grosmannia clavigera and Leptographium
 longiclavatum, together with high heritability, suggest potential for
 adaptive selection in these species. By contrast, Ophiostoma montium
 displayed narrower intraspecific variation but greater tolerance to
 extreme high temperatures. Our study highlights unique phenotypic and
 genotypic characteristics in these symbionts that are consistent with our
 hypothesis. By maintaining this multipartite relationship, the bark
 beetles have a greater likelihood of obtaining the benefits afforded by
 the fungi and reduce the risk of being left aposymbiotic. Complementarity
 among species could facilitate colonization of new habitats and survival
 under adverse conditions.
description: Data
 fileExcel workbook
 containing the SNP data, environmental data and growth data for G.
 clavigera, L. leptographium and O. montium.BSF_dryad.xls
DOI: 10.6084/m9.figshare.31157603
title: the Bayesian script for the constrained analysis from A new polyglyphanodontian lizard from the Upper Cretaceous of southern China implies a complex evolutionary history of the clade

description: Data S2 Bayesian unconstrained 20250930.txt
DOI: 10.6084/m9.figshare.31157603.v1
title: the Bayesian script for the constrained analysis from A new polyglyphanodontian lizard from the Upper Cretaceous of southern China implies a complex evolutionary history of the clade

description: Data S2 Bayesian unconstrained 20250930.txt
DOI: 10.5061/dryad.r4g74
title: Data from: Chimpanzee females queue but males compete for social status

description: Dominance hierarchies are widespread in animal social groups and often
 have measureable effects on individual health and reproductive success.
 Dominance ranks are not static individual attributes, however, but instead
 are influenced by two independent processes: 1) changes in hierarchy
 membership and 2) successful challenges of higher-ranking individuals.
 Understanding which of these processes dominates the dynamics of rank
 trajectories can provide insights into fitness benefits of within-sex
 competition. This question has yet to be examined systematically in a wide
 range of taxa due to the scarcity of long-term data and a lack of
 appropriate methodologies for distinguishing between alternative causes of
 rank changes over time. Here, we expand on recent work and develop a new
 likelihood-based Elo rating method that facilitates the systematic
 assessment of rank dynamics in animal social groups, even when interaction
 data are sparse. We apply this method to characterize long-term rank
 trajectories in wild eastern chimpanzees (Pan troglodytes schweinfurthii)
 and find remarkable sex differences in rank dynamics, indicating that
 females queue for social status while males actively challenge each other
 to rise in rank. Further, our results suggest that natal females obtain a
 head start in the rank queue if they avoid dispersal, with potential
 fitness benefits.
description: Female agonistic
 interactionsfemale_ago.xlsMale agonistic interactionsmale_ago.xlsFemale presence gridLists each date of study period and presence/absence of each adult female. This allows the calculation of relative ranks on each date based on Elo scores.female_presence.xlsMale presence gridLists each date of study period and presence/absence of each adult male. This allows the calculation of relative ranks on each date based on Elo scores.male_presence.xlsOptimized elo rating R codeCommented R code used for modeling Elo scores, corresponding to models 1-3 in manuscript. Includes code for import of sample data files to allow rerunning of models.Elo_code.pdf
DOI: 10.6084/m9.figshare.31157609
title: the phylogenetic matrix in nex. format from A new polyglyphanodontian lizard from the Upper Cretaceous of southern China implies a complex evolutionary history of the clade

description: Data S1 131nex-order.nex
DOI: 10.6084/m9.figshare.31157609.v1
title: the phylogenetic matrix in nex. format from A new polyglyphanodontian lizard from the Upper Cretaceous of southern China implies a complex evolutionary history of the clade

description: Data S1 131nex-order.nex
DOI: 10.5061/dryad.1qh4c
title: Data from: The core planar cell polarity gene, Vangl2, directs adult corneal epithelial cell alignment and migration

description: This study shows that the core planar cell polarity (PCP) genes direct the
 aligned cell migration in the adult corneal epithelium, a stratified
 squamous epithelium on the outer surface of the vertebrate eye. Expression
 of multiple core PCP genes was demonstrated in the adult corneal
 epithelium. PCP components were manipulated genetically and
 pharmacologically in human and mouse corneal epithelial cells in vivo and
 in vitro. Knockdown of VANGL2 reduced the directional component of
 migration of human corneal epithelial (HCE) cells without affecting speed.
 It was shown that signalling through PCP mediators, dishevelled,
 dishevelled-associated activator of morphogenesis and Rho-associated
 protein kinase directs the alignment of HCE cells by affecting
 cytoskeletal reorganization. Cells in which VANGL2 was disrupted tended to
 misalign on grooved surfaces and migrate across, rather than parallel to
 the grooves. Adult corneal epithelial cells in which Vangl2 had been
 conditionally deleted showed a reduced rate of wound-healing migration.
 Conditional deletion of Vangl2 in the mouse corneal epithelium ablated the
 normal highly stereotyped patterns of centripetal cell migration in vivo
 from the periphery (limbus) to the centre of the cornea. Corneal opacity
 owing to chronic wounding is a major cause of degenerative blindness
 across the world, and this study shows that Vangl2 activity is required
 for directional corneal epithelial migration.
description: Figure
 2Prism files for Figure 2
 - see read me.Figure
 S3Prism Files for Fig. S3
 - see read me.Figure
 S4Prism Files for Figure
 S4 - see read meFigure
 3AFigure
 3BFigure
 3CFigure
 3DFigure
 4AFigure
 4BFigure
 4CFigure
 4DFigure
 4EFigure
 4FPRISM
 FILES
DOI: 10.6084/m9.figshare.31157615
title: the Bayesian script for the unconstrained analysis from A new polyglyphanodontian lizard from the Upper Cretaceous of southern China implies a complex evolutionary history of the clade

description: Data S3 Bayesian constrained 20250930.txt
DOI: 10.6084/m9.figshare.31157615.v1
title: the Bayesian script for the unconstrained analysis from A new polyglyphanodontian lizard from the Upper Cretaceous of southern China implies a complex evolutionary history of the clade

description: Data S3 Bayesian constrained 20250930.txt
DOI: 10.5061/dryad.kv072
title: Data from: Anthropogenic disruption of the night sky darkness in urban and rural areas

description: The growing emissions of artificial light to the atmosphere are producing,
 among other effects, a significant increase of the night sky brightness
 (NSB) above its expected natural values. A permanent sensor network has
 been deployed in Galicia (northwest of Iberian peninsula) to monitor the
 anthropogenic disruption of the night sky darkness in a countrywide area.
 The network is composed of 14 detectors integrated in automated weather
 stations of MeteoGalicia, the Galician public meteorological agency.
 Zenithal NSB readings are taken every minute and the results are openly
 available in real time for researchers, interested stakeholders and the
 public at large through a dedicated website. The measurements allow one to
 assess the extent of the loss of the natural night in urban, periurban,
 transition and dark rural sites, as well as its daily and monthly time
 courses. Two metrics are introduced here to characterize the disruption of
 the night darkness across the year: the significant magnitude (m1/3) and
 the moonlight modulation factor (γ). The significant magnitude shows that
 in clear and moonless nights the zenithal night sky in the analysed urban
 settings is typically 14–23 times brighter than expected from a nominal
 natural dark sky. This factor lies in the range 7–8 in periurban sites,
 1.6–2.5 in transition regions and 0.8–1.6 in rural and mountain dark sky
 places. The presence of clouds in urban areas strongly enhances the amount
 of scattered light, easily reaching amplification factors in excess of 25,
 in comparison with the light scattered in the same places under clear sky
 conditions. The periodic NSB modulation due to the Moon, still clearly
 visible in transition and rural places, is barely notable at periurban
 locations and is practically lost at urban sites.
description: GalicianNightSkyBrightnessData_2015Each data file, in txt format, corresponds to a measurement site and contains, in seven columns, the following raw data: Day, Month, Year, Hour, Minute, and Second (in UTC time), and the recorded sky bightness in mag/arcsec^2. An additional file ("Offsets.txt") contains the correction factors to relate the measurements of all sensors to the synthetic common reference sensor of the network.NightSkyBrightnessData_2015.zip
DOI: 10.5061/dryad.22vg4
title: Data from: Does biomass growth increase in the largest trees? Flaws, fallacies and alternative analyses

description: The long-standing view that biomass growth in trees typically follows a
 rise-and-fall unimodal pattern has been challenged by studies concluding
 that biomass growth increases with size even among the largest stems in
 both closed forests and in open competition-free environments. We
 highlight challenges and pitfalls that influence such interpretations. The
 ability to observe and calibrate biomass change in large stems requires
 adequate data regarding these specific stems. Data checking and control
 procedures can bias estimates of biomass growth and generate false
 increases with stem size. It is important to distinguish aggregate and
 individual-level trends: a failure to do so results in flawed
 interpretations. Our assessment of biomass growth in 706 tropical forest
 stems indicates that individual biomass growth patterns often plateau for
 extended periods, with no significant difference in the number of stems
 indicating positive and negative trends in all but one of the 14 species.
 Nonetheless, when comparing aggregate growth during the most recent five
 years, 13 out of our 14 species indicate that biomass growth increases
 with size even among the largest sizes. Thus, individual and aggregate
 patterns of biomass growth with size are distinct. Claims concerning
 general biomass growth patterns for large trees remain unconvincing. We
 suggest how future studies can improve our knowledge of growth patterns in
 and among large trees.
description: Population_level(5yr)This data file contains mean data for 706 trees (14 species) over the period 2006-2010. This data was used or all population level analyses.Individual_levelThis data file contains tree-ring data of 706 individual trees belonging 14 tree species described in the paper above. This data was used for all individual level analyses.
DOI: 10.5061/dryad.n3r35
title: Data from: Genetic hitchhiking and resistance evolution to transgenic Bt toxins: insights from the African stalk borer Busseola fusca (Noctuidae)

description: Since transgenic crops expressing Bacillus thuringiensis (Bt) toxins were
 first released, resistance evolution leading to failure in control of
 pests populations has been observed in a number of species. Field
 resistance of the moth Busseola fusca was acknowledged 8 years after Bt
 maize was introduced in South Africa. Since then, field resistance of this
 corn borer has been observed at several locations, raising questions about
 the nature, distribution and dynamics of the resistance trait. Using
 genetic markers, our study identified four outlier loci clearly associated
 with resistance. In addition, genetic structure at neutral loci reflected
 extensive gene flow among populations. A realistically parameterised model
 suggests that resistance could travel in space at speed of several
 kilometres a year. Markers at outlier loci delineated a geographic region
 associated with resistance spread. This was an area of approximately
 100 km radius, including the location where resistance was first reported.
 Controlled crosses corroborated these findings and showed significant
 differences of progeny survival on Bt plants depending on the origin of
 the resistant parent. Last, our study suggests diverse resistance
 mutations, which would explain the widespread occurrence of resistant
 larvae in Bt fields across the main area of maize production in South
 Africa.
description: AFLP outlier
 lociThe columns of the table
 correspond to the outlier loci presented in Campagne et al. 2016
 (Heredity). Rows, correspond to individuals (described in the file
 sample-info.txt).non-outlier-loci.txtnon-outlier-lociThe columns of the table correspond to the non-outlier loci presented in Campagne et al. 2016 (Heredity). Rows, correspond to individuals (described in the file sample-info.txt).sample information'Field.ID' corresponds to the field numbers/IDs in which a larvae was sampled; 'Type.of.field', describes whether the field sampled was Bt maize (i.e., Bt) or a non-Bt crop (maize or sorghum, i.e., nBt).sample-info.txt