cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8m7t2
title: Data from: Repeated evolution of tricellular (and bicellular) pollen

description: Premise of study: Male gametophytes of seed plants are sexually immature
 at the time they are dispersed as pollen, but approximately 30% of
 flowering plants have tricellular pollen containing fully formed sperm at
 anthesis. The classic study of Brewbaker (1967: American Journal of Botany
 54: 1069–1083) provided a powerful confirmation of the long-standing
 hypothesis that tricellular pollen had many parallel and irreversible
 origins within angiosperms. We readdressed the main questions of that
 study with modern comparative phylogenetic methods. Methods: We used our
 own and more recent reports to greatly expand the Brewbaker data set. We
 modeled trait evolution for 2511 species on a time-calibrated angiosperm
 phylogeny using (1) Binary State Speciation and Extinction (BiSSE), which
 accounts for the effect of species diversification rates on character
 transition rates and, (2) the hidden rates model (HRM), which incorporates
 variation in transition rates across a phylogeny. Key results: Seventy
 percent of species had bicellular pollen. BiSSE found a 1.9-fold higher
 bicellular to tricellular transition rate than in the reverse direction,
 and bicellular lineages had a 1.8-fold higher diversification rate than
 tricellular lineages. HRM found heterogeneity in evolutionary rates, with
 bidirectional transition rates in three of four rate classes. Conclusions:
 The tricellular condition is not irreversible. Pollen cell numbers are
 maintained at intermediate frequencies because lower net diversification
 rates of tricellular lineages are counterbalanced by slower state shifts
 to the bicellular condition. That tricellular lineages diversify slowly
 and give rise to bicellular lineages slowly reflects a linkage between the
 evolution of sporophyte lifestyles and the developmental lability of male
 gametophytes.
description: Pollen cell number
 databaseThis file contains the
 full database on pollen cell numbers, including the restricted database
 used in all analyses, and lists of taxa that were discarded or that had
 their trait states modified for the analysis.WilliamsEtAl.AJB2014.pollen.cell.number.database.xlsxWilliamsEtAl.AJB2014.ScriptsA compressed directory containing the raw scripts and related files used for the analyses. All scripts are included, even those used for exploratory analyses, for completeness.
DOI: 10.5061/dryad.j7260
title: Data from: Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates

description: Linking variation in quantitative traits to variation in the genome is an
 important, but challenging task in the study of life-history evolution.
 Linkage maps provide a valuable tool for the unravelling of such
 trait-gene associations. Moreover, they give insight into recombination
 landscapes and between- species karyotype evolution. Here we used genotype
 data, generated from a 10k SNP-chip, of over 2000 individuals to produce
 high-density linkage maps of the great tit (Parus major), a passerine
 bird, which serves as a model species for ecological and evolutionary
 questions. We created independent maps from two distinct populations: a
 captive F2-cross from The Netherlands (NL) and a wild population from the
 United Kingdom (UK). The two maps contained 6554 SNPs in 32 linkage
 groups, spanning 2010 cM and 1917 cM for the NL and UK populations
 respectively, and were similar in size and marker order. Subtle levels of
 heterochiasmy within and between chromosomes were remarkably consistent
 between the populations, suggesting that local departures from sex-equal
 recombination rates have evolved. This key and surprising result would
 have been impossible to detect if only one population was mapped. A
 comparison with zebra finch Taeniopygia guttata, chicken Gallus gallus and
 the green anole lizard Anolis carolinensis genomes provided further
 insight into the evolution of avian karyotypes.
description: SNP_INFO_DATA_2013_09_23NL_genotpes_PEDUK_genotypes_PED
DOI: 10.5061/dryad.hg375
title: Data from: Genomic diversity of a nectar yeast clusters into metabolically, but not geographically, distinct lineages

description: Both dispersal limitation and environmental sorting can affect genetic
 variation in populations, but their contribution remains unclear,
 particularly in microbes. We sought to determine the contribution of
 geographic distance (as a proxy for dispersal limitation) and phenotypic
 traits (as a proxy for environmental sorting), including morphology,
 metabolic ability, and interspecific competitiveness, to the genotypic
 diversity in a nectar yeast species, Metschnikowia reukaufii. To measure
 genotypic diversity, we sequenced the genomes of 102 strains of M.
 reukaufii isolated from the floral nectar of hummingbird-pollinated shrub,
 Mimulus aurantiacus, along a 200-km coastline in California. Intraspecific
 genetic variation showed no detectable relationship with geographic
 distance, but could be grouped into three distinct lineages that
 correlated with metabolic ability and interspecific competitiveness.
 Despite ample evidence for strong competitive interactions within and
 among nectar yeasts, a full spectrum of the genotypic and phenotypic
 diversity observed across the 200-km coastline was represented even at a
 scale as small as 200 m. Furthermore, more competitive strains were not
 necessarily more abundant. These results suggest that dispersal limitation
 and environmental sorting might not fully explain intraspecific diversity
 in this microbe and highlight the need to also consider other ecological
 factors such as trade-offs, source-sink dynamics, and niche modification.
description: filtered SNP set used
 for population structure and clustering analysisThese SNPs were called
 from 109 Metchnikowia sp whole genomes mapped to MR_a10 reference genome
 using GATK best practices guidelines. Hard filtering of initial SNPs was
 performed using the GATK variant filtration tool (v3.4) and VCFtools
 (v1.5) as per best practices (Danecek et al. 2011), using the following
 parameters: base quality = 20, quality by depth = 2.0, mapping quality =
 30, Fisher strand bias = 60, mapping quality rank sum =-12.5, and
 ReadPosRankSum = -8.0. Post InDel removal, the SNP set consisting 1.27
 million SNPs across 109 strains was further filtered to exclude:
 non-bi-allelic SNPs, a minor allele frequency below 0.05 and polymorphisms
 with more than 50% missing data. To resolve SNPs in linkage, a window size
 of 50 SNPs advanced by 5 SNPS at a time and an r2 threshold of 0.5 was
 used. The final set of high confidence SNPs consisted of 88, 192
 polymorphisms. See attached scripts.Dhami_et_al_final_SNPset.vcf.gzDhamietal-MEC-Rerefence-mappingMapping to reference genomes.Dhamietal-MEC-duplicate-removal-gvcf-callingRMDUP_and_RAW_GVCF_all_masterSNP calling and duplicate removalDhamietal-MEC-hardfilteringSNP filteringDhamietal-MEC-vcftools_filteringSNP filtering 2Dhamietal-MEC-fastStructurePopulation structure analysis
DOI: 10.5061/dryad.5n92p
title: Data from: Pellets of proof: first glimpse of the dietary composition of adult odonates as revealed by metabarcoding of feces

description: Recent advances in molecular techniques allow us to resolve the diet of
 unstudied taxa. Odonates are potentially important top-down regulators of
 many insects. Yet, to date, our knowledge of odonate prey use is based
 mainly on limited observations of odonates catching or eating their prey.
 In this study, we examine the potential use of metabarcoding in
 establishing the diet of three adult odonate species (Lestes sponsa,
 Enallagma cyathigerum, and Sympetrum danae) at a site in southwestern
 Finland. To this purpose, we compared three different methods for
 extracting DNA from fecal samples: the Macherey-Nagel Nucleospin XS kit, a
 traditional salt extraction, and the Zymo Research Fecal Microprep kit.
 From these extracts, we amplified group-specific mitochondrial markers
 (COI and 16S rRNA) from altogether 72 odonate individuals, and compared
 them to comprehensive reference libraries. The three odonate species show
 major overlap in diet, with no significant differences between individuals
 of different size and/or gender, reflecting opportunistic foraging of
 adult odonates. Of a total of 41 different prey species detected, the most
 frequently consumed ones were Diptera, with additional records of six
 other orders. Based on our data, the best DNA extraction method is the
 traditional salt extraction, as it provides the most information on prey
 content while also being the most economical. To our knowledge, this is
 the first study to resolve the species-level diet of adult odonates. Armed
 with the appropriate methodological caveats, we are ready to examine the
 ecological role of odonates in both terrestrial and aquatic food webs, and
 in transferring subsidies between these two realms.
description: COI
 ZOTUsQuality-trimmed,
 adapter-trimmed, dereplicated, chimera-filtered and denoised sequences
 amplified from odonate faecal DNA COI region.COI_denoised.fa16S ZOTUsQuality-trimmed, adapter-trimmed, dereplicated, chimera-filtered and denoised sequences amplified from odonate faecal DNA COI region.16S_denoised.faCombined readmap for 16S and COITable with the number of reads assigned to each prey species per each sample for either of the two gene regions (16S and COI).Combined_readmap.csvFASTQ filesThe raw FASTQ files produced in the study. The files are compressed using gzip and collected to a tar-ball.Dragon15.tar
DOI: 10.5061/dryad.153b8
title: Data from: Population structure and reticulate evolution of Saccharomyces eubayanus and its lager-brewing hybrids

description: Reticulate evolution can be a major driver of diversification into new
 niches, especially in disturbed habitats and at the edges of ranges.
 Industrial fermentation strains of yeast provide a window into these
 processes, but progress has been hampered by a limited understanding of
 the natural diversity and distribution of Saccharomyces species and
 populations. For example, lager beer is brewed with Saccharomyces
 pastorianus, an alloploid hybrid of S. cerevisiae and S. eubayanus, a
 species only recently discovered in Patagonia, Argentina. Here we report
 that genetically diverse strains of S. eubayanus are readily isolated from
 Patagonia, demonstrating that the species is well established there.
 Analyses of multi-locus sequence data strongly suggest that there are two
 diverse and highly differentiated Patagonian populations. S. eubayanus
 alleles present among hybrid European brewing strains had strikingly low
 diversity, suggesting they were drawn from a small subpopulation that is
 closely related to one of the Patagonian populations. For the first time,
 we also report the rare isolation of S. eubayanus outside of Patagonia, in
 Wisconsin, USA. In contrast to the clear population differentiation in
 Patagonia, the North American strains represent a recent and possibly
 transient admixture of the two Patagonian populations. These complex and
 varied reticulation events are not adequately captured by conventional
 phylogenetic methods and required analyses of Bayesian concordance factors
 and phylogenetic networks to accurately summarize and interpret. These
 findings show how genetically diverse eukaryotic microbes can produce rare
 but economically important hybrids with low genetic diversity when they
 migrate from their natural ecological context.
description: Peris_et_al_MEC-13-1430
DOI: 10.5281/zenodo.18381037
title: Fusion of LiDAR and AIS Data for Improved Maritime Object Detection - test dataset

description: Maritime autonomous systems require robust perception to address the high rate of human-error-caused accidents in the maritime domain. We present a hybrid detection framework combining YOLO11-based neural network detection on bird's-eye-view LiDAR projections with deterministic algorithms for identifying isolated floating objects and coast-anchored vessels. Our approach achieves significantly improved recall on real marina data compared to neural network detection alone. We further integrate AIS data using Kalman filtering and path matching, demonstrating high matching accuracy under realistic noise conditions. The system operates at real-time rates on modest GPU hardware, making it suitable for autonomous navigation applications.
DOI: 10.5281/zenodo.18381038
title: Fusion of LiDAR and AIS Data for Improved Maritime Object Detection - test dataset

description: Maritime autonomous systems require robust perception to address the high rate of human-error-caused accidents in the maritime domain. We present a hybrid detection framework combining YOLO11-based neural network detection on bird's-eye-view LiDAR projections with deterministic algorithms for identifying isolated floating objects and coast-anchored vessels. Our approach achieves significantly improved recall on real marina data compared to neural network detection alone. We further integrate AIS data using Kalman filtering and path matching, demonstrating high matching accuracy under realistic noise conditions. The system operates at real-time rates on modest GPU hardware, making it suitable for autonomous navigation applications.
DOI: 10.5061/dryad.18v5d
title: Data from: Artificial light at night confounds broad-scale habitat use by migrating birds

description: With many of the world's migratory bird populations in alarming
 decline, broad-scale assessments of responses to migratory hazards may
 prove crucial to successful conservation efforts. Most birds migrate at
 night through increasingly light-polluted skies. Bright light sources can
 attract airborne migrants and lead to collisions with structures, but
 might also influence selection of migratory stopover habitat and thereby
 acquisition of food resources. We demonstrate, using multi-year weather
 radar measurements of nocturnal migrants across the northeastern U.S.,
 that autumnal migrant stopover density increased at regional scales with
 proximity to the brightest areas, but decreased within a few kilometers of
 brightly-lit sources. This finding implies broad-scale attraction to
 artificial light while airborne, impeding selection for extensive forest
 habitat. Given that high-quality stopover habitat is critical to
 successful migration, and hindrances during migration can decrease
 fitness, artificial lights present a potentially heightened conservation
 concern for migratory bird populations.
description: EL_dataData table with response and predictor variable data for BGAM model.
DOI: 10.5061/dryad.1447866
title: Data from: Environmental heterogeneity amplifies behavioural response to a temporal cycle

description: Resource acquisition is integral to maximise fitness, however in many
 ecosystems this requires adaptation to resource abundance and
 distributions that seldom stay constant. For predators, prey availability
 can vary at fine spatial and temporal scales as a result of changes in the
 physical environment, and therefore selection should favour individuals
 that can adapt their foraging behaviour accordingly. The tidal cycle is a
 short, yet predictable, temporal cycle, which can influence prey
 availability at temporal scales relevant to movement decisions. Here, we
 ask whether black-legged kittiwakes (Rissa tridactyla) can adjust their
 foraging habitat selection according to the tidal cycle using GPS tracking
 studies at three sites of differing environmental heterogeneity. We used a
 hidden Markov model to classify kittiwake behaviour, and analysed habitat
 selection during foraging. As expected for a central-place forager, we
 found that kittiwakes preferred to forage nearer to the breeding colony.
 However, we also show that habitat selection changed over the 12.4-hour
 tidal cycle, most likely because of changes in resource availability.
 Furthermore, we observed that environmental heterogeneity was associated
 with amplified changes in kittiwake habitat selection over the tidal
 cycle, potentially because environmental heterogeneity drives greater
 resource variation. Both predictable cycles and environmental
 heterogeneity are ubiquitous. Our results therefore suggest that,
 together, predictable cycles and environmental heterogeneity may shape
 predator behaviour across ecosystems.
description: Kittiwake locations for
 habitat selectionData comprises of used
 locations from GPS tracking, and 10 available locations for each used
 locations selected randomly from within foraging range of kittiwakes in R
 statistical software, as detailed in Oikos manuscript. Here we give all
 GPS locations, however analyses in paper were subset to foraging only
 points based on state defined by HMM model. See README file for column
 details.Data_Kit_HS.csv
DOI: 10.15472/0wrrjo
title: Monitoreos de fauna y flora silvestre en el área de explotación de hidrocarburos campo Quifa, Puerto Gaitán-Meta años 2023 - 2025

description: Durante los últimos años, los estudios encaminados a reconocer la diversidad y riqueza de los ecosistemas han venido incrementando ya que permiten identificar, monitorear y controlar los daños causados a los recursos naturales. Por lo general este tipo de estudios busca efectuar un seguimiento y monitoreo contante de los cambios que se vienen presentando entorno a los ecosistemas prestando principal atención en los factores abióticos y bióticos. Para efectuar estos monitoreos de forma efectiva se hace necesaria contar con investigaciones y estudios de flora y fauna, que permitan conocer a una escala detallada las condiciones y estado de los ecosistemas que se están evaluando.En ese sentido, y dando cumplimiento a la resolución 261 de 2013, se llevó a cabo el estudio de caracterización florística sobre el Campo Quifa siendo esta una de las unidades de seguimiento y monitoreo establecidas por la empresa Frontera Energy como áreas de compensación florística por los impactos ocasionados a causa de sus actividades industriales, y un monitoreo de fauna realizado a tres grupos faunísticos anfibios-reptiles (herpetos), aves y mamíferos, el cual partió de la implementación de técnicas de muestreo acordes con las propuestas por la autoridad ambiental para su caracterización.Este conjunto de datos consta de 785 registros biológicos que fueron tomados en julio del 2023 en el área de explotación de Hidrocarburos Quifa, localizada en la región de la Orinoquía, vereda Santa Helena, municipio de Puerto Gaitán, departamento del Meta. Se realizó un monitoreo en el año 2024, donde se evaluó fauna y flora, que consta de 1884 registros biológicos que fueron tomados en el mes de marzo del año 2024, en las áreas aledañas a la zona de explotación de hidrocarburos campo Quifa , ubicada en Puerto Gaitán, Meta. Abarca una cobertura taxonómica distribuida en cuatro clases para fauna y una para flora: Aves (506), Amphibia (81), Reptilia (66), Mammalia (51) para fauna, Equisetopsida (1180) para flora. Los registros se agrupan en 41 órdenes, 81 familias, 165 géneros y 183 especies.Adicionalmente se realizó un monitoreo de flora y fauna en el año 2025, constando de 3.314 registros biológicos tomados en Octubre del 2025. La cobertura taxonómica abarca 6 clases para fauna y 4 para flora, presentandose así: Amphibia (292), Aves (268), Reptilia (84), Mammalia (260) para fauna y Liliopsida (1077), Lycopodiopsida (7), Magnoliopsida (1300), Polypodiopsida (26) para flora. Los registros se agrupan en 52 órdenes, 127 familias, 280 géneros y 376 especies.
DOI: 10.5061/dryad.3cp54
title: Data from: Analysis of potential ischemic effect of intravitreal bevacizumab on unaffected retina in treatment-naïve macular edema due to branch retinal vein occlusion: a prospective, interventional case-series

description: Background: To study potential ischemic effects of intravitreal
 Bevacizumab (IVB) on unaffected retina in treatment-naive eyes with
 macular edema secondary to branch retinal vein occlusion (BRVO) and
 contralateral eyes secondary to systemic absorption. Methods and Findings:
 Prospective, interventional series included 27 treatment-naive eyes with
 BRVO and macular edema. Exclusion criteria: Eyes with diabetic
 retinopathy, glaucoma, vasculitides, papilledema or systemic neurologic
 condition. Subjects underwent complete ophthalmological examination
 including fluoroscein angiography (FA), optical coherence tomography (OCT)
 and multifocal electroretinogram (mf-ERG). All subjects received single
 1.25 mg/0.05ml IVB injection. Two observers measured all parameters;
 inter-observer agreements were expressed as kappa values. Paired t-test
 was used to compare values at baseline and follow-up. The statistical
 analysis was done using SPSS for Windows, Version 14.0. (Chicago, SPSS
 Inc.) Presenting mean CFT (central foveal thickness) was 499.5(+/-229.7)
 μm, mean BCVA (best corrected visual acuity) was 0.64(+/-0.41) logMAR. At
 last follow-up, mean CFT was 267.9(+/-159.3) μm (P&lt;0.001), 95% CI
 [127.18, 422.32]; mean BCVA was 0.28(+/-0.24) logMAR. Respectively, mean
 N1 and P1 amplitudes of mfERG in 'unaffected quadrant' at
 presentation were -6.10(+/-4.00) nV/deg2 and 17.17(+/-11.54)nV/deg2; and
 -5.33(+/-1.30)nV/deg2 and 15.29(+/-4.69)nV/deg2 at final follow-up (P =
 0.631 and 0.197, respectively), (95% CIs [-0.93, 1.42] and [-4.22, 1.08]
 respectively). In fundus quadrant of fellow eyes corresponding to
 unaffected quadrant in treated eyes, mean N1 and P1 amplitudes at
 presentation were -5.39(+/-1.56)nV/deg2 and 15.89(+/-3.89)nV/deg2; and
 -5.39(+/-1.90)nV/deg2 and 15.9(+/-5.52)nV/deg2 (P = 0.380 and 0.208), (95%
 CIs [-0.57, 1.28] and [-4.1, 1.1]) at last follow-up, respectively.
 Limitations: This study analysed the effects with a single injection of
 bevacizumab. However, whether ischemic adverse effects will emerge with
 repeated IVB injections as a consequence of cumulative dosing needs
 further investigation. The setting of our study being a tertiary care
 centre, the numbers of fresh BRVO cases without prior intervention were
 limited. Thus, the limitations of our study include a small sample size
 with a small follow-up period. No major ocular/systemic adverse event was
 observed in the study period. Conclusion: No evidence of progressive
 ischaemia attributable to single bevacizumab treatment was observed in
 this study. However, a larger prospective study involving subjects with
 cumulative dosing of bevacizumab and a longer follow-up could provide a
 better understanding of the potential ischaemic effects of bevacizumab or
 other anti-VEGF agents.
description: 20160827Fluorescein20160827mfERG20160827OCT