cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8j616
title: Data from: How a GNSS receiver is held may affect static horizontal position accuracy

description: The static horizontal position accuracy of a mapping-grade GNSS receiver
 was tested in two forest types over two seasons, and subsequently was
 tested in one forest type against open sky conditions in the winter
 season. The main objective was to determine whether the holding position
 during data collection would result in significantly different static
 horizontal position accuracy. Additionally, we wanted to determine whether
 the time of year (season), forest type, or environmental variables had an
 influence on accuracy. In general, the F4Devices Flint GNSS receiver was
 found to have mean static horizontal position accuracy levels within the
 ranges typically expected for this general type of receiver (3 to 5 m)
 when differential correction was not employed. When used under forest
 cover, in some cases the GNSS receiver provided a higher level of static
 horizontal position accuracy when held vertically, as opposed to held at
 an angle or horizontally (the more natural positions), perhaps due to the
 orientation of the antenna within the receiver, or in part due to
 multipath or the inability to use certain satellite signals. Therefore,
 due to the fact that numerous variables may affect static horizontal
 position accuracy, we only conclude that there is weak to moderate
 evidence that the results of holding position are significant. Statistical
 test results also suggest that the season of data collection had no
 significant effect on static horizontal position accuracy, and results
 suggest that atmospheric variables had weak correlation with horizontal
 position accuracy. Forest type was found to have a significant effect on
 static horizontal position accuracy in one aspect of one test, yet
 otherwise there was little evidence that forest type affected horizontal
 position accuracy. Since the holding position was found in some cases to
 be significant with regard to the static horizontal position accuracy of
 positions collected in forests, it may be beneficial to have an
 understanding of antenna positioning within the receiver to achieve the
 greatest accuracy during data collection.
description: Whitehall_Forest_GNSS_study_2013-2014This is the raw data collected by a F4Devices Flint GNSS receiver during two studies. The main goal was to determine whether the holding position during data collection would result in significantly different static horizontal position accuracy.
DOI: 10.5061/dryad.fp85d
title: Data from: Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities

description: Antibiotics leak constantly into environments due to widespread use in
 agriculture and human therapy. Although sublethal concentrations are well
 known to select for antibiotic-resistant bacteria, little is known about
 how bacterial evolution cascades through food webs, having indirect effect
 on species not directly affected by antibiotics (e.g. via population
 dynamics or pleiotropic effects). Here, we used an experimental evolution
 approach to test how temporal patterns of antibiotic stress, as well as
 migration within metapopulations, affect the evolution and ecology of
 microcosms containing one prey bacterium, one phage and two protist
 predators. We found that environmental variability, autocorrelation and
 migration had only subtle effects for population and evolutionary
 dynamics. However, unexpectedly, bacteria evolved greatest fitness
 increases to both antibiotics and enemies when the sublethal levels of
 antibiotics were highest, indicating positive pleiotropy. Crucially,
 bacterial adaptation cascaded through the food web leading to reduced
 predator-to-prey abundance ratio, lowered predator community diversity and
 increased instability of populations. Our results show that the presence
 of natural enemies can modify and even reverse the effects of antibiotics
 on bacteria, and that antibiotic selection can change the ecological
 properties of multitrophic microbial communities by having indirect
 effects on species not directly affected by antibiotics.
description: PopulationdynamicsEvolutionEcoEvodynamics
DOI: 10.5061/dryad.3f1tm
title: Data from: Initiation and spread of escape waves within animal groups

description: The exceptional reactivity of animal collectives to predatory attacks is
 thought to be owing to rapid, but local, transfer of information between
 group members. These groups turn together in unison and produce escape
 waves. However, it is not clear how escape waves are created from local
 interactions, nor is it understood how these patterns are shaped by
 natural selection. By startling schools of fish with a simulated attack in
 an experimental arena, we demonstrate that changes in the direction and
 speed by a small percentage of individuals that detect the danger initiate
 an escape wave. This escape wave consists of a densely packed band of
 individuals that causes other school members to change direction. In the
 majority of cases, this wave passes through the entire group. We use a
 simulation model to demonstrate that this mechanism can, through local
 interactions alone, produce arbitrarily large escape waves. In the model,
 when we set the group density to that seen in real fish schools, we find
 that the risk to the members at the edge of the group is roughly equal to
 the risk of those within the group. Our experiments and modelling results
 provide a plausible explanation for how escape waves propagate in nature
 without centralized control.
description: controls_dataData containing tracks for the control trialsgroups_dataData containing the tracks of the group trialssingles_dataData containing the tracks of the single fish trials
DOI: 10.5061/dryad.689v4
title: Data from: A microsatellite-based linkage map for song sparrows (Melospiza melodia)

description: Although linkage maps are important tools in evolutionary biology, their
 availability for wild populations is limited. The population of song
 sparrows (Melospiza melodia) on Mandarte Island, Canada, is among the more
 intensively studied wild animal populations. Its long-term pedigree data,
 together with extensive genetic sampling, have allowed the study of a
 range of questions in evolutionary biology and ecology. However, the
 availability of genetic markers has been limited. We here describe 191 new
 microsatellite loci, including 160 high-quality polymorphic autosomal, 7
 Z-linked and 1 W-linked markers. We used these markers to construct a
 linkage map for song sparrows with a total sex-averaged map length of 1731
 cM and covering 35 linkage groups, and hence, these markers cover most of
 the 38–40 chromosomes. Female and male map lengths did not differ
 significantly. We then bioinformatically mapped these loci to the zebra
 finch (Taeniopygia guttata) genome and found that linkage groups were
 conserved between song sparrows and zebra finches. Compared to the zebra
 finch, marker order within small linkage groups was well conserved,
 whereas the larger linkage groups showed some intrachromosomal
 rearrangements. Finally, we show that as expected, recombination frequency
 between linked loci explained the majority of variation in gametic phase
 disequilibrium. Yet, there was substantial overlap in gametic phase
 disequilibrium between pairs of linked and unlinked loci. Given that the
 microsatellites described here lie on 35 of the 38–40 chromosomes, these
 markers will be useful for studies in this species, as well as for
 comparative genomics studies with other species.
description: Pedigree and genotypes
 from Mandarte Island song sparrowsDam and sire for each
 individual (id) used in the publication in Molecular Ecology Resources
 together with their genotypes at 209 microsatellite loci (the two alleles
 of each marker are denoted by "a" and "b" appended to
 the marker name).GeneticsPedigree_Publication.xlsx
DOI: 10.5061/dryad.855m4
title: Data from: The genetic relatedness in groups of joint-nesting Taiwan Yuhinas: low genetic relatedness with preferences for male kin

description: The relative importance of direct and indirect fitness and, thus, the role
 of kinship in the evolution of social behavior is much debated. Studying
 the genetic relatedness of interacting individuals is crucial to improving
 our understanding of these issues. Here, we used a seven-year data set to
 study the genetic structure of the Taiwan yuhina (Yuhina brunneciceps), a
 joint-nesting passerine. Ten microsatellite loci were used to investigate
 the pair-wised relatedness among yuhina breeding group members. We found
 that the average genetic relatedness between same-sex group members was
 very low (0.069 for male dyads and 0.016 for female dyads). There was also
 a low ratio of closely-related kin (r&gt;0.25) in the cooperative
 breeding groups of yuhinas (21.59% and 9.68% for male and female dyads,
 respectively). However, the relatedness of male dyads within breeding
 groups was significantly higher than female dyads. Our results suggest
 that yuhina cooperation is maintained primarily by direct fitness benefits
 to individuals; however, kin selection might play a role in partner choice
 for male yuhinas. Our study also highlights an important, but often
 neglected, question: Why do animals form non-kin groups, if kin are
 available? We use biological market theory to propose an explanation for
 group formation of unrelated Taiwan yuhinas.
description: 97-04 yuhina
 ms_7loci_171birds_for_dryad_05181510 microsatellite
 genetic markers data from 171 Taiwan yuhina (Yuhina
 brunneiceps).yuhina_relatedness_for_dryad_051815This is relatedness matrix in yuhina breeding group.yuhina_extra_pair_offspring_for_dryad_051815Data of extra paired offsprings id and their assigned biological parents.
DOI: 10.5061/dryad.8323
title: Data from: Accelerated evolutionary rate of housekeeping genes in tunicates

description: Phylogenomics has recently revealed that tunicates represent the
 sister-group of vertebrates in the newly defined clade Olfactores.
 However, phylogenomic and comparative genomic studies have also suggested
 that tunicates are characterized by an elevated rate of molecular
 evolution and a high degree of genomic divergence. Despite the recurrent
 interest in the group, the picture of tunicate peculiar evolutionary
 dynamics is still fragmentary, as it mainly lies in studies focusing on
 only a few model species. In order to expand the available genomic data
 for the group, we used the high-throughput 454 technology to sequence the
 partial transcriptome of a previously unsampled tunicate, Microcosmus
 squamiger. This allowed us to get further insights into
 tunicate-accelerated evolution through a comparative analysis based on
 pertinent phylogenetic markers, i.e., a core of 35 housekeeping genes
 conserved across bilaterians. Our results showed that tunicates evolved on
 average about two times faster than the other chordates, yet the degree of
 this acceleration varied extensively upon genes and upon lineages.
 Appendicularia and Aplousobranchia were detected as the most divergent
 groups which were also characterized by highly heterogeneous substitution
 rates across genes. Finally, an estimation of the d (N)/d (S) ratio in
 three pairs of closely related taxa within Olfactores did not reveal
 strong differences between the tunicate and vertebrate lineages suggesting
 that for this set of housekeeping genes, the accelerated evolution of
 tunicates is plausibly due to an elevated mutation rate rather than to
 particular selective effects.
description: Tsagkogeorga-JMolEvol2010_ntNucleotide concatenation of 35 housekeeping genes for 28 metazoan taxa.Tsagkogeorga-JMolEvol2010_aaAmino acid concatenation of 35 housekeeping genes for 28 metazoan taxa.
DOI: 10.5061/dryad.t23n3
title: Data from: On the Helmert-blocking Technique: its acceleration by Block Choleski decomposition and formulae to insert observations into an adjusted network

description: The Helmert-blocking technique is a common approach to adjust large
 geodetic networks like Europeans and Brazilians. The technique is based
 upon a division of the network into partial networks called blocks. This
 way, the global network adjustment can be done by manipulating these
 blocks. Here we show alternatives to solve the block system that arises
 from the application of the technique. We show an alternative that
 optimizes its implementation as the elapsed processing time is decreased
 by about 33%. We also show that to insert observations into an adjusted
 network it is not necessary to readjust the whole network. We show the
 formulae to insert new observations into an adjusted network that are more
 efficient than simply readjusting the whole new network.
description: Data from: On the
 Helmert-blocking Technique: its acceleration by Block Choleski
 decomposition and formulae to insert observations into an adjusted
 networkIt contains the
 computation of stats and results of simulations besides the Fortran codes
 built.Data.rar
DOI: 10.82294/dvnkrdvtw
title: COPUS. Territorio: Cundinamarca. Sector: Educación. Año: 2023
title: Dato. Observación estructurada con el protocolo COPUS.

description: Información recopilada durante el año 2023 a partir de observaciones estructuradas realizadas con el protocolo COPUS, dirigidas a educadores artísticos pertenecientes a programas de formación en educación artística y cultural del sector del sector Educación (educación formal) en el departamento de Cundinamarca.
DOI: 10.5061/dryad.885c0
title: Data from: The role of social and ecological processes in structuring animal populations: a case study from automated tracking of wild birds

description: Both social and ecological factors influence population process and
 structure, with resultant consequences for phenotypic selection on
 individuals. Understanding the scale and relative contribution of these
 two factors is thus a central aim in evolutionary ecology. In this study,
 we develop a framework using null models to identify the social and
 spatial patterns that contribute to phenotypic structure in a wild
 population of songbirds. We used automated technologies to track 1053
 individuals that formed 73 737 groups from which we inferred a social
 network. Our framework identified that both social and spatial drivers
 contributed to assortment in the network. In particular, groups had a more
 even sex ratio than expected and exhibited a consistent age structure that
 suggested local association preferences, such as preferential attachment
 or avoidance. By contrast, recent immigrants were spatially partitioned
 from locally born individuals, suggesting differential dispersal
 strategies by phenotype. Our results highlight how different scales of
 social decision-making, ranging from post-natal dispersal settlement to
 fission–fusion dynamics, can interact to drive phenotypic structure in
 animal populations.
description: R Data file containing
 all data.RData file containing
 four variables: (1) description, (2) gbi, (3) birds, (4) group.info.
 'description' provides a brief overview of the data.
 'gbi' is the group by individual matrix that maps detections of
 individuals (each column is an individual) to groups (each row is a group,
 a 1 represents an individual occurring in that group).
 'group.info' contains all the metadata for groups detected using
 the Gaussian Mixture Model (start and end times, location, sampling
 period). 'birds' contains all the metadata for the individuals
 (age, sex, immigration status, pca score). Each row in 'birds'
 matches each column in 'gbi', and each row in
 'group.info' matches each row in 'gbi'. To access this
 file, users will need to download the freeware R package from
 (http://www.r-project.org).Farine_etal_data.RData
DOI: 10.5061/dryad.n43qf
title: Data from: Spatial distribution of fishes in a Northwest Atlantic ecosystem in relation to risk of predation by a marine mammal

description: 1. Numerous studies have shown that, at spatial scales of metres to
 several kilometres, animals balance the trade-off between foraging success
 and predation mortality by increasing their use of safer but less
 profitable habitats as predation risk increases. However, it is less clear
 whether prey respond similarly at the larger spatiotemporal scales of many
 ecosystems. 2. We determine whether this behaviour is evident in a large
 marine ecosystem, the southern Gulf of St. Lawrence (sGSL, 75 000 km2)
 over a 42-year period. This ecosystem is characterized by a recent
 increase in the abundance of a large marine predator, the grey seal
 (Halichoerus grypus Fabricius), by more than an order of magnitude. 3. We
 compared changes in spatial distribution over the 1971–2012 period between
 important prey of grey seals (Atlantic cod, Gadus morhua L.; white hake,
 Urophycis tenuis Mitchill; and thorny skate, Amblyraja radiata Donovan)
 and non-prey fishes. Distribution was modelled using generalized additive
 models incorporating spatially variable effects of predation risk, density
 dependence and water temperature. 4. Distributions of cod, hake and skate
 were strongly related to risk of predation by seals, with distribution
 shifting into lower risk areas as predation risk increased. Non-prey
 species did not show similar changes in habitat use. Spatial variation in
 fish condition suggests that these low-risk areas are also less profitable
 for cod and skate in terms of food availability. The effects of density
 dependence and water temperature were also important in models, but did
 not account for the changes in habitat use as the risk of predation
 increased. 5. These results indicate that these fish are able to assess
 and respond to spatial variation in predation risk at very large spatial
 scales. They also suggest that non-consumptive ‘risk’ effects may be an
 important component of the declines in productivity of seal prey in this
 ecosystem, and of the indirect effects at lower trophic levels.
description: JAE_DataArchive_SwainBenoîtHammillThis file provides tow-by-tow catch rates of selected fishes, an index of local risk of predation by grey seals and selected environmental information from an anuual bottom-trawl survey of the southern Gulf of St. Lawrence conducted each September since 1971. Please see the accompanying ReadMe file for further details.
DOI: 10.5061/dryad.d8h27
title: Data from: Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae

description: Dysosma species (Berberidaceae, Podophylloideae) are of great medicinal
 pharmacogenetic importance and used as model systems to study the drivers
 and mechanisms of species diversification of temperate plants in East
 Asia. Recently, we have sequenced the transcriptome of the low-elevation
 D. versipellis. In this study, we sequenced the transcriptome of the
 high-elevation D. aurantiocaulis and used comparative genomic approaches
 to investigate the transcriptome evolution of the two species. We
 retrieved 53 929 unigenes from D. aurantiocaulis by de novo transcriptome
 assemblies using the Illumina HiSeq 2000 platform. Comparing the
 transcriptomes of both species, we identified 4593 orthologs. Estimation
 of Ka/Ks ratios for 3126 orthologs revealed that none had a Ka/Ks
 significantly greater than 1, whereas 1273 (Ka/Ks &lt; 0.5, P &lt;
 0.05) were inferred to be under purifying selection. A total of 51 primer
 pairs were successfully designed from 461 EST-SSRs contained in 4593
 orthologs. Marker validation assay revealed that 26 (51%) and 41 (80.4%)
 produced clear fragments with the expected sizes in all Podophylloideae
 species. Specifically, 19 different sequences of CYP719A were identified
 from PCR-amplified genomic DNA of all 12 species of Podophylloideae using
 primers designed from the assembled transcripts. The data further
 indicated that CYP719A was likely subject to strong selective constraints
 maintaining only one copy per genome. In Dysosma, there was relaxed
 purifying selection or more positive selection for high-elevation species.
 Overall, this study has generated a wealth of molecular resources
 potentially useful for pharmacogenetic and evolutionary studies in Dysosma
 and allied taxa.
description: Available
 dataAssembled EST-SSR
 sequences, single-copy gene sequences and 3,126 gene sequences with Ka
 value, Ks value and Ka/Ks ratio. The files (alignment file,tree
 file,script file) for PAML estimates were included in the
 datasets.submission.zip
DOI: 10.5061/dryad.nm0v0
title: Data from: Automatic supporting system for regionalization of ventricular tachycardia exit site in implantable defibrillators

description: Electrograms stored in Implantable Cardioverter Defibrillators (ICD-EGM)
 have been proven to convey useful information for roughly determining the
 anatomical location of the Left Ventricular Tachycardia exit site (LVTES).
 Our aim here was to evaluate the possibilities from a machine learning
 system intended to provide an estimation of the LVTES anatomical region
 with the use of ICD-EGM in the situation where 12-lead electrocardiogram
 of ventricular tachycardia are not available. Several machine learning
 techniques were specifically designed and benchmarked, both from
 classification (such as Neural Networks (NN), and Support Vector Machines
 (SVM)) and regression (Kernel Ridge Regression) problem statements.
 Classifiers were evaluated by using accuracy rates for LVTES
 identification in a controlled number of anatomical regions, and the
 regression approach quality was studied in terms of the spatial
 resolution. We analyzed the ICD-EGM of 23 patients (18±10 EGM per patient)
 during left ventricular pacing and simultaneous recording of the spatial
 coordinates of the pacing electrode with a navigation system. Several
 feature sets extracted from ICD-EGM (consisting of times and voltages)
 were shown to convey more discriminative information than the raw
 waveform. Among classifiers, the SVM performed slightly better than NN. In
 accordance with previous clinical works, the average spatial resolution
 for the LVTES was about 3 cm, as in our system, which allows it to support
 the faster determination of the LVTES in ablation procedures. The proposed
 approach also provides with a framework suitable for driving the design of
 improved performance future systems.
description: Dataset of the automatic
 supporting system for regionalization of ventricular tachycardia exit site
 in implantable defibrillatorsThe data file
 “Regionalization.txt" consists of features (voltages and times) and
 the averaged beat waveform of the far-field and bipolar electrogram
 registered by implantable defibrillators during pacing in a pace-mapping
 protocol. In addition, the pacing site number, spatial position (half and
 coordinates), and type of tissue are also included. Details are provided
 in the manuscript and in the “Readme.txt” file.Regionalization.txt