cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6rc405m
title: Data from: The relative contribution of natural landscapes and human-mediated factors on the connectivity of a noxious invasive weed

description: Examining how the landscape may influence gene flow is at the forefront of
 understanding population differentiation and adaptation. Such
 understanding is crucial in light of ongoing environmental changes and the
 elevated risk of ecosystems alteration. In particular, knowledge of how
 humans may influence population structure is imperative to allow for
 informed decisions in management and conservation as well as to gain a
 better understanding of anthropogenic impacts on the interplay between
 gene flow, genetic drift and selection. Here we use genome-wide molecular
 markers to characterize the population genetic structure and connectivity
 of Ipomoea purpurea (Convolvulaceae), a noxious invasive weed. We,
 likewise, assess the interaction between natural and human-driven
 influences on genetic differentiation among populations. Our analyses find
 that human population density is an important predictor of pairwise
 population differentiation, suggesting that the agricultural and/or
 horticultural trade may be involved in maintaining some level of
 connectivity across distant agricultural fields. Climatic variation
 appears as an additional predictor of genetic connectivity in this
 species. We discuss the implications of these results and highlight future
 research needed to disentangle the mechanistic processes underlying
 population connectivity of weeds.
description: Alvarado-Serrano et
 al_I_purpurea_SNPdataSet of filtered SNPs (in
 vcf format) used.Alvarado-Serrano et
 al_I_purpurea_SSRdataSSR dataset (in genalex
 format) used.Alvarado-Serrano et
 al_landscape_variablesAscii files for all 8
 natural and anthropogenic variables used in the
 analyses.landscape_variables.zip
DOI: 10.5061/dryad.j09c05c
title: Data from: Adaptation to reef habitats through selection on the coral animal and its associated microbiome

description: Spatially adjacent habitats on coral reefs can represent highly distinct
 environments, often harbouring different coral communities. Yet, certain
 coral species thrive across divergent environments. It is unknown whether
 the forces of selection are sufficiently strong to overcome the
 counteracting effects of the typically high gene flow over short
 distances, and for local adaptation to occur. We screened the coral genome
 (using restriction-site-associated sequencing [RAD-seq]), and
 characterized both the dinoflagellate photosymbiont and tissue-associated
 prokaryote microbiomes (using metabarcoding) of a reef flat and slope
 population of the reef-building coral, Pocillopora damicornis, at two
 locations on Heron Island in the southern Great Barrier Reef. Reef flat
 and slope populations were separated by &lt;100 m horizontally and ~5
 m vertically and the two study locations were separated by ~1 km. For the
 coral host, genetic divergence between habitats was much greater than
 between locations, suggesting limited gene flow between the flat and slope
 populations. Consistent with environmental selection, outlier loci
 primarily belonged to the conserved, minimal cellular stress response,
 likely reflecting adaptation to the different temperature and irradiance
 regimes on the reef flat and slope. Similarly, the prokaryote community
 differed across both habitat and, to a lesser extent, location, whereas
 the dinoflagellate photosymbionts differed by habitat but not location.
 The observed intra-specific diversity associated with divergent habitats
 supports that environmental adaptation involves multiple members of the
 coral holobiont. Adaptive alleles or microbial associations present in
 coral populations from the environmentally-variable reef flat may provide
 a source of adaptive variation for assisted evolution approaches, through
 assisted gene flow, artificial cross-breeding or probiotic inoculations,
 with the aim to increase climate resilience in the slope populations.
description: pdam_2fVCF data file for unique genotypes only, ie excluding clone matespdam_wclon_2fVCF data file for all samples, including clone mates
DOI: 10.15468/wdp283
title: IAS pilot - Observations of alien plant species using a vehicle-mounted camera system in Flanders (Belgium)

description: IAS pilot - Observations of alien plant species using a vehicle-mounted camera system in Flanders (Belgium) is an occurrence dataset published by the Research Institute for Nature and Forest (INBO). It is part of the Biodiversa IAS pilot project (2023-2027), that implemented the monitoring of invasive alien plants using a vehicle-mounted camera system in various countries across Europe. Specifically, the CamAlien camera system (Dyrmann et al. 2024) was mounted on a car to capture images of the roadside vegetation. Data have been standardized to Darwin Core. Issues with the dataset can be reported at https://github.com/inbo/ias-pilot/issues.Images from the cameras were processed with image recognition algorithms provided through Pl@ntNet (Espitalier et al. 2025). For the current dataset, only pre-selected species of regional importance were retained, and occurrences (images) with insufficient confidence were filtered out.We have released this dataset to the public domain under a Creative Commons Zero waiver. We would appreciate it if you follow the INBO norms for data use (https://www.inbo.be/en/norms-data-use) when using the data. If you have any questions regarding this dataset, don't hesitate to contact us via the contact information provided in the metadata or via opendata@inbo.be.This dataset was published as open data for the IAS pilot project (funded by Biodiversa+) and the OneSTOP project (funded by Horizon Europe), with technical support provided by the Research Institute for Nature and Forest (INBO).
DOI: 10.5061/dryad.m2s1735
title: Data from: A multispecies coalescent model for quantitative traits

description: We present a multispecies coalescent model for quantitative traits that
 allows for evolutionary inferences at micro- and macroevolutionary scales.
 A major advantage of this model is its ability to incorporate genealogical
 discordance underlying a quantitative trait. We show that discordance
 causes a decrease in the expected trait covariance between more closely
 related species relative to more distantly related species. If unaccounted
 for, this outcome can lead to an overestimation of a trait's
 evolutionary rate, to a decrease in its phylogenetic signal, and to errors
 when examining shifts in mean trait values. The number of loci controlling
 a quantitative trait appears to be irrelevant to all trends reported, and
 discordance also affected discrete, threshold traits. Our model and
 analyses point to the conditions under which different methods should fare
 better or worse, in addition to indicating current and future approaches
 that can mitigate the effects of discordance.
description: Quantitative traits
 simulated under three-taxon phylogenyR workspace containing
 simulated quantitative traits (3 species).5_15_25_50_100loci_rnorm_3spp_w_1ind_ils_1-2-3-4-5_t4.RDataQuantitative traits simulated under five-taxon phylogenyR workspace containing simulated quantitative traits (5 species).5_15_25_50_100loci_rnorm_5spp_w_1ind_ils_1-2-3-4-5_t4.RDataPlottable objectsR workspace containing objects for producing plots.quant_trait_plotting_objs_t4_elife.RData
DOI: 10.5061/dryad.5147g9s
title: Data from: An affordable apparatus for fine‐controlled emulation of buzzing frequencies of bees for the testing hypothesis in buzz interactions

description: 1. The buzzing foraging behavior of female bees for pollen harvesting
 called the attention of early pollination biologists. Flower-types that
 demand this buzzing behavior comprise about 20.000 species of different
 and phylogenetically unrelated plant taxa, suggesting that it had
 independently evolved many times among the flowering plants. Between the
 late 70’s and early 80’s, theoretical papers had modeled the energetics of
 buzz-pollination, but, up to this moment, no hypothesis was experimentally
 tested concerning the theoretical basis of the energetics of
 buzz-pollination. 2. We present a cost-eﬀective and simple apparatus,
 including a digital and highly accurate frequency generator, and a device
 for the transference of buzz-frequency energy to the receptive floral
 unity. The receptive floral unities may comprise the entire or partial
 androecium, or the tubular corolla, or, in some cases, the whole flower.
 3. This apparatus can be easily used both laboratory and field conditions
 of research, since natural air currents are avoided, and the response of
 pollen liberation can be quantitatively measured by pollen grain counts
 that can be captured by adhesion in slide poured with an isosmotic
 lactate-glycerin media. 4. The maximum displacement of the hardwire
 beam/claw system was 0.1170 ± 0.0006mm @ 150Hz; 0.021 ± 0.003 mm @ 250 Hz;
 0.010 ± 0.001 mm @350 Hz; 0.0058 ± 0.0001 mm @ 450 Hz and 0.0082 ± 0.0005
 mm @ 55 0Hz. 5. Hypothesis contrasting frequency emission and pollen
 liberation measured as pollen-grain counts may be tested in a species
 flower-type by simple linear regression, if pollen counts are normally
 distributed, or ordinal logistic regression, with non-normal counts. The
 comparison among different flower-type requirements can be tested through
 appropriate statistical methods for both normally and non-normally
 distributed pollen grain counts.
description: data_f_150Displacement measured at 150 Hzdata_f_250Displacement at 250 Hzdata_f_350Displacement at 350 Hzdata_f_450Displacement at 450 Hzdata_f_550Displacement at 550 Hz
DOI: 10.5061/dryad.1139fm7
title: Data from: Accurate genomic prediction of Coffea canephora in multiple environments using whole-genome statistical models

description: Genomic selection have been proposed as the standard method to predict
 breeding values in animal and plant breeding. Although some crops have
 benefited from this methodology, studies in Coffea are still emerging. To
 date, there have been no studies of how well genomic prediction models
 work across populations and environments for different complex traits in
 coffee. Considering that predictive models are based on biological and
 statistical assumptions, it is expected that their performance vary
 depending on how well these assumptions align with the true genetic
 architecture of the phenotype. To investigate this, we used data from two
 recurrent selection populations of Coffea canephora, evaluated in two
 locations, and single nucleotide polymorphisms identified by
 Genotyping-by-Sequencing. In particular, we evaluated the performance of
 13 statistical approaches to predict three important traits in the coffee
 — production of coffee beans, leaf rust incidence and yield of green
 beans. Analyses were performed for predictions within-environment, across
 locations and across populations to assess the reliability of genomic
 selection. Overall, differences in the prediction accuracy of the
 competing models were small, although the Bayesian methods showed a modest
 improvement over other methods, at the cost of more computation time. As
 expected, predictive accuracy for within-environment analysis, on average,
 were higher than predictions across locations and across populations. Our
 results support the potential of genomic selection to reshape traditional
 plant breeding schemes. In practice, we expect to increase the genetic
 gain per unit of time by reducing the length cycle of recurrent selection
 in coffee.
description: SNPs and phenotypes in
 Coffea canephora populationThis dataset contains
 the genotypic and phenotypic information used in the whole-genomic
 statistical models for Coffea canephora. In the original manuscript, two
 populations of recurrent selection were genotyped and three traits -
 coffee bean production, incidence of rust and yield of green beans - were
 evaluated in two locations. Genotypic data (SNPs identified using the
 Genotyping-by-Sequencing approach) for both populations are stored in two
 .csv files (-1,0,1 format). Phenotype data for both populations are also
 stored in two .csv files. The values stored in the phenotypic files are
 phenotypes adjusted for linear effects of environmental covariates and
 other experimental covariates.data_set.zip
DOI: 10.5061/dryad.g24c6b6
title: Data from: Recent prey capture experience and dynamic habitat quality mediate short-term foraging site fidelity in a seabird

description: Foraging site fidelity allows animals to increase their efficiency by
 returning to profitable feeding areas. However, the mechanisms
 underpinning why animals “stay” or “switch” sites have rarely been
 investigated. Here we explore how habitat quality and prior prey capture
 experience influence short-term site fidelity by the little penguin
 (Eudyptula minor). Using 88 consecutive foraging trips by 20 brooding
 penguins, we found that site fidelity was higher after foraging trips
 where environmental conditions were favourable, and after trips where prey
 capture success was high. When penguins exhibited lower site fidelity, the
 number of prey captures relative to the previous trip increased,
 suggesting that switches in foraging location were an adaptive strategy in
 response to low prey capture rates. Penguins foraged closer to where other
 penguins foraged on the same day than they did to the location of their
 own previous foraging site, and caught more prey when they foraged close
 together. This suggests that penguins aggregated flexibly when prey was
 abundant and accessible. Our results illustrate how foraging predators can
 integrate information about prior experience with contemporary information
 such as social cues. This gives insight into how animals combine
 information adaptively to exploit changing prey distribution in a dynamic
 environment.
description: Penguin_locations_ssmLocations estimated from little penguin GPS tracks Sep-Nov 2016, interpolated to a 30 s interval using a state-space model (bsam, Ian Jonsen).locsdf.csvPrey Capture eventsUnique prey capture events by little penguins in 2016 identified by applying a support vector machine algorithm to raw accelerometry tracks to identify prey handling behavior, then applying a broken stick model to identify "unique" prey capture events. For more details see Carroll et al. 2014 Journal of Experimental BiologyuniqueEvents.csv
DOI: 10.5061/dryad.pd33j50
title: Data from: Simulation of the nodal flow of mutant embryos with small number of cilia: comparison of mechanosensing and vesicle transport hypotheses

description: Left-right (L-R) asymmetry in the body plan is determined by nodal flow in
 vertebrate embryos. Shinohara et al. used Dpcd and Rfx3 mutant mouse
 embryos and showed that only a few cilia were sufficient to achieve L-R
 asymmetry. However, the mechanism underlying the breaking of symmetry by
 such weak ciliary flow is unclear. The flow-mediated signals related to
 L-R asymmetry have not been clarified; there are two models for L-R
 symmetry breaking: vesicle transport and mechanosensing. In this study, we
 developed a computational model of the node system reported by Shinohara
 et al. and examined feasibilities of two hypotheses with a small number of
 cilia. With the small number of rotating cilia, flow was induced locally
 and global strong flow was not observed in the node. Particles were then
 effectively transported only when they were close to the cilia, and
 particle transport was strongly dependent on the ciliary positions.
 Although the maximum wall shear rate was also influenced by ciliary
 position, the mean wall shear rate at the perinodal wall increased
 monotonically with the number of cilia. We also investigated membrane
 tension of immotile cilia, which is relevant to the regulation of
 mechanotransduction. The results indicated that tension of about 0.1 uN/m
 was exerted at the base even when the fluid shear rate was applied about
 0.1 1/s. The area of high tension was also localised at the upstream side,
 and negative tension appeared at the downstream side. Such localisation
 may be useful to sense the flow direction at the periphery, as
 time-averaged anticlockwise circulation was induced in the node by
 rotation of a few cilia. Our numerical results support the mechanosensing
 hypothesis, and we expect that our study will stimulate further
 experimental investigations of mechanotransduction in the near future.
description: Nodal flow with 2
 rotating ciliaVelocity field within
 the node with two rotating ciliamovie1.movNodal flow with 6 ciliaVelocity field within the node with 6 rotating ciliamovie2.movVesicle transport simulationNeutrally buoyant 100 particles were randomly distributed at the initialmovie3.movWall shear rate distributionWall shear rate distribution during one period.movie4.mov
DOI: 10.5061/dryad.n62t1hm
title: Data from: A redescription of Orovenator mayorum (Sauropsida, Diapsida) using high-resolution μCT and the consequences for early amniote phylogeny

description: The earliest known neodiapsid Orovenator mayorum from the early Permian of
 Oklahoma is redescribed using high-resolution μCT, revealing remarkable
 details of the skull anatomy. Our findings are relevant to both
 palaeoecology (suggesting burrowing and nocturnality) and phylogeny.
 Orovenator and other sauropsids share at least 16 character states with
 varanopids, many of which were not recognised by previous studies. These
 include a rounded subnarial shelf of the premaxilla, a posterodorsal
 extension of the external naris, the asymmetrical bifurcation of the
 anterior vomer, and a prominent dorsomedial shelf of the surangular. This
 exceptional degree of similarity between Orovenator and varanopids (a
 nominally synapsid clade) questions our current understanding of
 relationships among early amniotes. We test this by including Orovenator
 in a phylogenetic data matrix used in an earlier study to differentiate
 between early diapsids and synapsids, and find a monophyletic clade of
 Orovenator + varanopids within Diapsida. Recent phylogenetic research on
 early amniote evolution has focused on resolving intra-clade affiliations
 rather than the interrelationships of major taxonomic groups.
 Nevertheless, the relative incompleteness of existing phylogenetic
 character lists for early amniotes can only be remedied by detailed
 cross-clade assessment. We therefore suggest that early amniote
 relationships require further scrutiny before we can confidently accept or
 reject our new phylogenetic hypothesis.
description: Supplement
 3Measurements of OMNH
 74606 and 74607Supplement
 2Scoring of Orovenator
 mayorum for the character list of Reisz et al. 2010Supplement
 1A
 virtual reconstruction of the scleral ring and orbit of Orovenator mayorum
 and the measurement of dimensions.
DOI: 10.5061/dryad.sq28254
title: Data from: Nuclear genetic analysis of the red fox across its trans-Pacific range

description: The red fox (Vulpes vulpes) occurs on multiple continents in diverse
 habitats, making it an informative system for evolutionary genomic
 research. However, its phylogeography remains unclear. Previously,
 mitochondrial DNA and small numbers of nuclear loci provided discordant
 views. Both markers indicated deep divergence (~ 0.5 MY) between Eurasian
 and southern North American populations but differed in the apparent
 continental affinity of Alaskan red foxes, implying some degree of gene
 exchange during secondary contact (~0.1 MY). We assayed &gt;173,000
 nuclear genomic sites in 52 red foxes, along with 2 Rueppell’s (V.
 rueppellii) foxes and a gray wolf (Canis lupus) using the Illumina
 CanineHD BeadChip. We obtained 5,107 SNPs that were polymorphic in the
 foxes. Consistent with the Afro-Eurasian origins of red foxes, genetic
 diversity was higher in Eurasian than North American samples. Phylogenetic
 trees indicated that Alaskan and southern North American red foxes formed
 a monophyletic group nested within the Eurasian clade. However, admixture
 models suggested Alaskan red foxes contained up to 40% Eurasian ancestry.
 We hypothesize that North American red foxes either hybridized with
 Eurasian foxes in Beringia at the start of the last glaciation or merged
 with a Beringian population after the last glaciation. Future work is
 needed to test between these scenarios and assess speciation.
description: 4Dryad_14Sept2017SNP genotypes
DOI: 10.5061/dryad.9mj8mt5
title: Data from: Climate and host plant associations shaped the evolution of ceutorhynch weevils throughout the Cenozoic

description: Using molecular phylogenetic data and methods we infer divergence times
 and diversification patterns for the weevil subfamily Ceutorhynchinae in
 the context of host-plant associations and global climate over
 evolutionary time. We detected four major diversification shifts that
 correlate with both host shifts and major climate events. Ceutorhynchinae
 experienced an increase in diversification rate at ~53 Ma, during the
 Early Eocene Climate Optimum, coincident with a host shift to Lamiaceae. A
 second major diversification phase occurred at the end of the Eocene (~34
 Ma). This contrasts with the overall deterioration in climate equability
 at the Eocene-Oligocene boundary, but tracks the diversification of
 important host plant clades in temperate (higher) latitudes, leading to
 increased diversification rates in the weevil clades infesting temperate
 hosts. A third major phase of diversification is correlated with the
 rising temperatures of the Late Oligocene Warming Event (~26.5 Ma);
 diversification rates then declined shortly after the Middle Miocene
 Climate Transition (~14.9 Ma). Our results indicate that biotic and
 abiotic factors together explain the evolution of Ceutorhynchinae better
 than each of these drivers viewed in isolation.
description: EVOLUTION_Letsch_et_al
DOI: 10.5061/dryad.45747rs
title: Data from: The induction of the fibroblast extracellular senescence metabolome is a dynamic process

description: Cellular senescence is often associated with irreparable DNA double strand
 breaks (IrrDSBs) which accumulate with chronological age (IrrDSBsen). The
 removal of senescent cells ameliorates several age-related diseases in
 mice but the translation of these findings into a clinical setting would
 be aided by the characterisation of non-invasive biomarkers of senescent
 cells. Several serum metabolites are independent indicators of
 chronological age and some of these accumulate outside senescent
 fibroblasts independently of cell cycle arrest, repairable DNA breaks and
 cell size (the extracellular senescence metabolome, or ESM). The
 post-mitotic phase of senescence is dynamic, making the detection of
 senescent cells in vivo difficult. An unbiased metabolomic screen of the
 IrrDSBsen fibroblast ESM also showed differences in the times of
 initiation and maintenance of different metabolites but generally the ESM
 altered progressively over the 20 day study period unlike the reported
 transcriptional profiles. This more detailed analysis of IrrDSBsen
 identified several new ESM metabolites that are associated with
 chronological ageing. Targeted analysis of citrate confirmed the dynamic
 nature of this metabolite in two cell lines and revealed its independence
 from the senescence effector p16INK4A. These data will aid our
 understanding of metabolic signatures of ageing and their relationship to
 cellular senescence and IrrDSBs.
description: Metabolomic changes
 during radiation-induced senescence in oral fibroblastsThe data contains an
 explanation of the data. The heat maps based on the Welch's T test
 although the paper used the unpaired test. The original scale raw data.
 Pathway sorted box plots.QMUL-02-10VW CDT
 (final).xls