cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.515n9k9
title: Data from: Timing of perineuronal nets development in the zebra finch song control system correlates with developmental song learning

description: The appearance of perineuronal nets (PNN) represents one of the mechanisms
 that contribute to the closing of sensitive periods for neural plasticity.
 This relationship has mostly been studied in the ocular dominance model in
 rodents. Previous studies also indicated that PNN might control neural
 plasticity in the song control system (SCS) of songbirds. To further
 elucidate this relationship, we quantified PNN expression and their
 localization around parvalbumin interneurons at key time-points during
 ontogeny in both male and female zebra finches and correlated these data
 with the well-described development of song in this species. We also
 extended these analyses to the auditory system. The development of PNN
 during ontogeny correlated with song crystallization although the timing
 of PNN appearance in the four main telencephalic song control nuclei
 slightly varied between nuclei in agreement with the established role
 these nuclei play during song learning. Our data also indicate that very
 few PNN develop in the secondary auditory forebrain areas even in adult
 birds, which may allow constant adaptation to a changing acoustic
 environment by allowing synaptic reorganization during adulthood.
description: ZFontogenesiCountingPVPNNallsectionsExcel file containing all raw data for numbers of PV and PNN in all nuclei investigated
DOI: 10.5061/dryad.bs1f7c3
title: Data from: Comparing convenience and probability sampling for urban ecology applications

description: 1. Urban forest ecosystems confer multiple ecosystem services. There is
 thus a need to quantify ecological characteristics in terms of community
 structure and composition so that benefits can be better understood in
 ecosystem service models. Efficient sampling and monitoring methods are
 crucial in this process. 2. Full tree inventories are scarce due to time
 and financial constraints, thus a variety of sampling methods exist.
 Modern vegetation surveys increasingly use stratified-random plot-based
 sampling to reduce the bias associated with convenience sampling, even
 though the latter can save time and increase species richness scores. The
 urban landscape, with a high degree of conspecific clustering and high
 species diversity, provides a unique biogeographical case for comparing
 these two methodological approaches. 3. We use two spatially extensive
 convenience samples of the urban forest of Meran (Italy) and compare the
 community structure, tree characteristics and ecosystem service provision
 with 200 random circular plots. 4. The convenience sampling resulted in a
 higher species diversity, incorporating more rare species. This is a
 result of covering more area per unit sampling time. Pseudorandom
 sub-plots were compared to the random plots revealing similar Shannon
 diversity and sampling comparability indices. Measured tree variables
 (diameter at breast height, height, tree-crown width, height to crown
 base) were similar between the two methods, as were ecosystem service
 model outputs. 5. Synthesis and applications. The results suggest that
 convenience sampling may be a time and money saving alternative to random
 sampling as long as stratification by land-use type is incorporated into
 the design. The higher species richness can potentially improve the
 accuracy of urban ecological models, which rely on species-specific
 functional traits.
description: Data_archiveRaw data for three separate urban forest samples of the city of Meran in Northern Italy. One is a random sample following I-tree protocol, one is a public tree inventory managed by the council of Meran and one is a convenience sample. The random and convenience samples also contain information on DBH, height, canopy width, tree condition, light exposure, canopy integrity, landtype.
DOI: 10.5061/dryad.g4f4790
title: Data from: Demography and rapid local adaptation shape Creole cattle genome diversity in the tropics

description: The introduction of Iberian cattle in the Americas after Columbus’ arrival
 imposed high selection pressures on a limited number of animals over a
 brief period of time. Knowledge of the genomic regions selected during
 this process may help in enhancing climatic resilience and sustainable
 animal production. We first determined taurine and indicine contributions
 to the genomic structure of modern Creole cattle. Second, we inferred
 their demographic history using approximate Bayesian computation (ABC),
 linkage disequilibrium (LD), and Ne Slope (NeS) analysis. Third, we
 performed whole genome scans for selection signatures based on
 cross-population extended haplotype homozygosity (XP-EHH) and population
 differentiation (FST) to disentangle the genetic mechanisms involved in
 adaptation and phenotypic change by a rapid and major environmental
 transition. To tackle these questions, we combined SNP array data (~54,000
 SNPs) in Creole breeds with their modern putative Iberian ancestors.
 Reconstruction of the population history of Creoles from the end of the
 15th century indicated a major demographic expansion until the
 introduction of zebu and commercial breeds into the Americas ~180 years
 ago, coinciding with a drastic Ne contraction. NeS analysis provided
 insights into short-term complexity in population change and depicted a
 decrease/expansion episode at the end of the ABC-inferred expansion, as
 well as several additional fluctuations in Ne with the attainment of the
 current small Ne only towards the end of the 20th century. Selection
 signatures for tropical adaptation pinpointed the thermoregulatory slick
 hair coat region, identifying a new candidate gene (GDNF), as well as
 novel candidate regions involved in immune function, behavioural
 processes, iron metabolism and adaptation to new feeding conditions. The
 outcomes from this study will help in future-proofing farm animal genetic
 resources (FAnGR) by providing molecular tools that allow selection for
 improved cattle performance, resilience and welfare under climate change.
description: Pitt2018EvolAppThe folder includes the SNP array data of 29 cattle samples newly genotyped and the synchronized and filtered 33,342 SNPs dataset analysed in the manuscript.
DOI: 10.5061/dryad.tt6h5h1
title: Geo-referenced crop-nutrient response function dataset for Tropical Africa

description: The profit potential for a given investment in fertilizer use can be
 estimated using representative crop nutrient response functions. Where
 response data is scarce, determination of representative response
 functions can be strengthened by using results from homologous crop
 growing conditions. Maize (Zea mays L.) nutrient response functions were
 selected from the Optimization of Fertilizer Recommendations in Africa
 (OFRA) database of 5500 georeferenced response functions determined from
 field research conducted in Sub-Saharan Africa. Three methods for defining
 inference domains for selection of response functions were compared. Use
 of the OFRA Inference Tool (OFRA-IT; http://agronomy.unl.edu/OFRA)
 resulted in greater specificity of maize N, P, and K response functions
 with higher R2 values indicating superiority compared with using the
 Harvest Choice Agroecological Zones (HC-AEZ) and the recommendation
 domains of the Global Yield Gap Atlas project (GYGA-RD). The OFRA-IT
 queries three soil properties in addition to climate-related properties
 while the latter two options use climate properties only. The OFRA-IT was
 generally insensitive to changes in criteria ranges of 20–25% used in
 queries suggesting value in using wider criteria ranges compared with the
 default for information scarce crop nutrient response functions.
description: GeorefCropNutrientResponseFunctions for Tropical Africa
DOI: 10.5061/dryad.3d7c900
title: Data from: Soluble hexamethyl-substituted subphthalocyanine as a dopant-free hole transport material for planar perovskite solar cells

description: Boron subphthalocyanine (SubPc) has special physical and chemical
 properties, originating from its non-centrosymmetric, near-planar taper
 structure and large conjugated system; it can act as an alternative to the
 small molecule hole-transporting material
 2,2’,7,7’-tetrakis-(N,N-di-p-methoxyphenylamine)-9,9’-spirobifluorene in
 perovskite solar cells. To achieve a higher solubility in common organic
 solvents and a more suitable highest occupied molecular orbital (HOMO)
 energy level that aligns with the valence band of the perovskite material,
 a SubPc molecule with a hexamethyl substitution at its peripheral position
 (Me6-SubPc) was successfully designed and synthesized in a one-step
 method. Completely solution processed perovskite solar cells were
 fabricated with only a small hysteresis, a power conversion efficiency
 (PCE) of 6.96% and Voc of 0.986 V.
description: Me6-SubPc single
 crystal
DOI: 10.6084/m9.figshare.30587573
title: Global marine deflection of the vertical and gravity anomaly models derived from ICESat-2 laser altimeter data:SDUST2024DOV­_IS2 and SDUST2024GRA_IS2

description: This dataset provides global 1-arcminute gridded models of marine gravity anomalies and deflections of the vertical derived from ICESat-2 laser altimetry. The products cover the global oceans from 80°S to 88°N and longitudes from 0° to 360°E, referenced to the TOPEX/Poseidon ellipsoid.The file <b>SDUST2024GRA_IS2.nc</b> contains the global marine gravity anomaly model on a 1′ × 1′ grid. It includes three variables: <i>lon</i> and <i>lat</i>, which are one-dimensional coordinate vectors, and <i>gra</i>, a 10080 × 21600 array representing marine gravity anomalies in milligals (mGal).The file <b>SDUST2024DOV_IS2.nc</b> provides the global marine deflection of the vertical (DOV) model on the same spatial grid. It includes four variables: <i>lon</i>, <i>lat</i>, <i>dov_ns</i> (meridional component), and <i>dov_ew</i> (prime-vertical component). The DOV arrays have the same dimensions as the gravity anomaly grid, and all values are reported in microradians (µrad).The models were derived exclusively from ICESat-2 ATL12 photon data. We implemented an optimized fusion strategy that combines the meridional component estimated from along-track geoid gradients with the prime-vertical component estimated from cross-track geoid gradients, yielding a directionally balanced DOV model. This fusion improves component-wise accuracy and enhances the stability and overall accuracy of the gravity anomaly inversion.<b>Uncertainty and Validation:</b> The accuracy of the data products has been rigorously assessed using independent validation datasets. The marine gravity anomaly model (SDUST2024GRA_IS2) was validated against NCEI shipborne gravity measurements, achieving a global standard deviation of approximately 5.71 mGal. For the deflection of the vertical (SDUST2024DOV_IS2) model, the estimated uncertainty is characterized by standard deviations of 3.34 µrad for the meridional component and 3.69 µrad for the prime-vertical component, as evaluated against the SIO V32.1 benchmark.<b>Code Availability:</b> The code for data processing is available on GitHub: https://github.com/XinLiu1969/Calculate-DOV-and-gravity-anomalies"
DOI: 10.6084/m9.figshare.30587573.v1
title: Global marine deflection of the vertical and gravity anomaly models derived from ICESat-2 laser altimeter data:SDUST2024DOV­_IS2 and SDUST2024GRA_IS2

description: This dataset provides global 1-arcminute gridded models of marine gravity anomalies and deflections of the vertical derived from ICESat-2 laser altimetry. The products cover the global oceans from 80°S to 88°N and longitudes from 0° to 360°E, referenced to the TOPEX/Poseidon ellipsoid.The file <b>SDUST2024GRA_IS2.nc</b> contains the global marine gravity anomaly model on a 1′ × 1′ grid. It includes three variables: <i>lon</i> and <i>lat</i>, which are one-dimensional coordinate vectors, and <i>gra</i>, a 10080 × 21600 array representing marine gravity anomalies in milligals (mGal).The file <b>SDUST2024DOV_IS2.nc</b> provides the global marine deflection of the vertical (DOV) model on the same spatial grid. It includes four variables: <i>lon</i>, <i>lat</i>, <i>dov_ns</i> (meridional component), and <i>dov_ew</i> (prime-vertical component). The DOV arrays have the same dimensions as the gravity anomaly grid, and all values are reported in microradians (µrad).The models were derived exclusively from ICESat-2 ATL12 photon data. We implemented an optimized fusion strategy that combines the meridional component estimated from along-track geoid gradients with the prime-vertical component estimated from cross-track geoid gradients, yielding a directionally balanced DOV model. This fusion improves component-wise accuracy and enhances the stability and overall accuracy of the gravity anomaly inversion.<b>Uncertainty and Validation:</b> The accuracy of the data products has been rigorously assessed using independent validation datasets. The marine gravity anomaly model (SDUST2024GRA_IS2) was validated against NCEI shipborne gravity measurements, achieving a global standard deviation of approximately 5.71 mGal. For the deflection of the vertical (SDUST2024DOV_IS2) model, the estimated uncertainty is characterized by standard deviations of 3.34 µrad for the meridional component and 3.69 µrad for the prime-vertical component, as evaluated against the SIO V32.1 benchmark.<b>Code Availability:</b> The code for data processing is available on GitHub: https://github.com/XinLiu1969/Calculate-DOV-and-gravity-anomalies"
DOI: 10.5061/dryad.98jh446
title: Data from: Population genomics and morphometric assignment of western honey bees (Apis mellifera L.) in the Republic of South Africa

description: Backgrounds: Apis mellifera scutellata and A.m. capensis (the Cape honey
 bee) are western honey bee subspecies indigenous to the Republic of South
 Africa (RSA). Both bees are important for biological and economic reasons.
 First, A.m. scutellata is the invasive "African honey bee" of
 the Americas and exhibits a number of traits that beekeepers consider
 undesirable. They swarm excessively, are prone to absconding (vacating the
 nest entirely), usurp other honey bee colonies, and exhibit heightened
 defensiveness. Second, Cape honey bees are socially parasitic bees; the
 workers can reproduce thelytokously. Both bees are indistinguishable
 visually. Therefore, we employed Genotyping-by-Sequencing (GBS), wing
 geometry and standard morphometric approaches to assess the genetic
 diversity and population structure of these bees to search for diagnostic
 markers that can be employed to distinguish between the two subspecies.
 Results: Apis mellifera scutellata possessed the highest mean number of
 polymorphic SNPs (among 2,449 informative SNPs) with minor allele
 frequencies &gt;0.05 (Np = 88%). The RSA honey bees generated a high
 level of expected heterozygosity (Hexp = 0.24). The mean genetic
 differentiation (FST; 6.5%) among the RSA honey bees revealed that
 approximately 93% of the genetic variation was accounted for within
 individuals of these subspecies. Two genetically distinct clusters (K = 2)
 corresponding to both subspecies were detected by Model-based Bayesian
 clustering and supported by Principal Coordinates Analysis (PCoA)
 inferences. Selected highly divergent loci (n = 83) further reinforced a
 distinctive clustering of two subspecies across geographical origins,
 accounting for approximately 83% of the total variation in the PCoA plot.
 The significant correlation of allele frequencies at divergent loci with
 environmental variables suggested that these populations are adapted to
 local conditions. Only 17 of 48 wing geometry and standard morphometric
 parameters were useful for clustering A.m. capensis, A.m. scutellata, and
 hybrid individuals. Conclusions: We produced a minimal set of 83 SNP loci
 and 17 wing geometry and standard morphometric parameters useful for
 identifying the two RSA honey bee subspecies by genotype and phenotype. We
 found that genes involved in neurology/behavior and development/growth are
 the most prominent heritable traits evolved in the functional evolution of
 honey bee populations in RSA.
description: Population genomics of
 Honey bee from South AfricaGenotyping-By-Sequencing
 data of 474 honey bees from South Africa and a reference western honey
 beeHoney
 bee GBS.vcf
DOI: 10.5061/dryad.mq85r61
title: Data from: Optimized flocking of autonomous drones in confined environments

description: We address a fundamental issue of collective motion of aerial robots: how
 to ensure that large flocks of autonomous drones seamlessly navigate in
 confined spaces. The numerous existing flocking models are rarely tested
 on actual hardware because they typically neglect some crucial aspects of
 multirobot systems. Constrained motion and communication capabilities,
 delays, perturbations, or the presence of barriers should be modeled and
 treated explicitly because they have large effects on collective behavior
 during the cooperation of real agents. Handling these issues properly
 results in additional model complexity and a natural increase in the
 number of tunable parameters, which calls for appropriate optimization
 methods to be coupled tightly to model development. In this paper, we
 propose such a flocking model for real drones incorporating an
 evolutionary optimization framework with carefully chosen order parameters
 and fitness functions. We numerically demonstrated that the induced swarm
 behavior remained stable under realistic conditions for large flock sizes
 and notably for large velocities. We showed that coherent and realistic
 collective motion patterns persisted even around perturbing obstacles.
 Furthermore, we validated our model on real hardware, carrying out field
 experiments with a self-organized swarm of 30 drones. This is the largest
 of such aerial outdoor systems without central control reported to date
 exhibiting flocking with collective collision and object avoidance. The
 results confirmed the adequacy of our approach. Successfully controlling
 dozens of quadcopters will enable substantially more efficient task
 management in various contexts involving drones.
description: Flight logs of drone
 swarmsFlight logs from four
 swarm flights with 30 autonomous outdoor drones performing synchronized
 self-organized collective motion within a virtually bounded area. Flight
 logs are in .gpx format.flight_logs.zip
DOI: 10.5061/dryad.g38g40b
title: Data from: Exploring and visualising spaces of tree reconciliations

description: Tree reconciliation is the mathematical tool that is used to investigate
 the coevolution of organisms, such as hosts and parasites. A common
 approach to tree reconciliation involves specifying a model that assigns
 costs to certain events, such as cospeciation, and then tries to find a
 mapping between two specified phylogenetic trees which minimises the total
 cost of the implied events. For such models, it has been shown that there
 may be a huge number of optimal solutions, or at least solutions that are
 close to optimal. It is therefore of interest to be able to systematically
 compare and visualise whole collections of reconciliations between a
 specified pair of trees. In this paper, we consider various metrics on the
 set of all possible reconciliations between a pair of trees, some that
 have been defined before but also new metrics that we shall propose. We
 show that the diameter for the resulting spaces of reconciliations can in
 some cases be determined theoretically, information that we use to
 normalise and compare properties of the metrics. We also implement the
 metrics and compare their behaviour on several host parasite datasets,
 including the shapes of their distributions. In addition, we show that in
 combination with multidimensional scaling, the metrics can be useful for
 visualising large collections of reconciliations, much in the same way as
 phylogenetic tree metrics can be used to explore collections of
 phylogenetic trees. Implementations of the metrics can be downloaded from:
 https://team.inria.fr/erable/en/team-members/blerina-sinaimeri/reconciliation-distances/
description: Exploring and
 visualising spaces of tree reconciliations: Supplementary Material I
 (Proofs)supplementary-material-2018-04-18.pdfsupplementary-material-IIsupplementary-material-2018-04-18.pdf
DOI: 10.5061/dryad.t8c88vh
title: Data from: Flexible decision-making in grooming partner choice in sooty mangabeys and chimpanzees

description: Living in permanent social groups forces animals to make decisions about
 when, how and with whom to interact, requiring decisions to be made that
 integrate multiple sources of information. Changing social environments
 can influence this decision-making process by constraining choice or
 altering the likelihood of a positive outcome. Here, we conceptualised
 grooming as a choice situation where an individual chooses one of a number
 of potential partners. Studying two wild populations of sympatric primate
 species, sooty mangabeys (Cercocebus atys atys) and Western chimpanzees
 (Pan troglodytes verus), we tested what properties of potential partners
 influenced grooming decisions, including their relative value based on
 available alternatives and the social relationships of potential partners
 with bystanders who could observe the outcome of the decision. Across
 1,529 decision events, multiple partner attributes (e.g. dominance ranks,
 social relationship quality, reproductive state, partner sex) influenced
 choice. Individuals preferred to initiate grooming with partners of
 similar global rank, but this effect was driven by a bias towards partners
 with a high rank compared to other locally available options. Individuals
 also avoided grooming partners who had strong social relationships with at
 least one bystander. Results indicated flexible decision-making in
 grooming interactions in both species, based on a partner’s value given
 the local social environment. Viewing partner choice as a value-based
 decision-making process allows researchers to compare how different
 species solve similar social problems.
description: Data
 Model1Data for Models 1-1 and
 1-2Data
 Model2Data for Models 2-1 and
 2-2Script Model 1 and
 2Scripts necessary to
 analyse Models 1 and 2
DOI: 10.5061/dryad.d69512q
title: Data from: The Palaeozoic colonization of the water column and the rise of global nekton

description: The colonization of the water column is among the most important
 transformations in the evolution of animal life and global ecosystems. The
 Devonian Nekton Revolution (DNR) has been identified as a major
 macroevolutionary event signifying the sudden occupation of the water
 column by independent radiations of swimming animals. Using new data, an
 expanded taxonomic coverage, sample standardization, and increased
 ecological resolution, we reanalysed the timing, duration, and magnitude
 of this event. We find that nekton and eunekton were well established
 prior to the Devonian and did not diversify dramatically during any
 Palaeozoic interval. Relative nektic diversity and occurrences decreased
 rather than increased during the Devonian. Eunektic diversity and
 occurrences increased throughout the Palaeozoic, but this rise was
 protracted and cannot be attributed to any single interval. Our new data
 indicate that the metazoan colonization of the water column was
 considerably more complex and gradual than previously understood.
description: Whalen & Briggs -
 Supplementary Data FileEcomorphological
 assignments for each genus with references, justifications, relative
 confidence scores, and additional informationWhalen & Briggs 2018 -
 Supplementary Data File.xlsx