cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.612jm644s
title: Sighting data and tactile events logged from mixed-group underwater interactions

description: Interactions between mammalian social groups are generally antagonistic as
 individuals in groups cooperate to defend resources from non-members.
 Members of the family Delphinidae inhabit a three-dimensional habitat
 where resource defense is usually impractical. Here, we describe a
 long-term partial fusion of two communities of Atlantic spotted dolphins
 (Stenella frontalis). The northern community, studied for 30 years,
 immigrated 160 km to the range of the southern community, observed for 20
 years. Both communities featured fission-fusion grouping patterns,
 strongest associations between adult males, and frequent affiliative
 contact between individuals. For the five-year period following the
 immigration, we found members of all age classes and both sexes in mixed
 groups, but there was a strong bias toward finding immigrant males in
 mixed groups. Some association levels between males, and males and
 females, from different communities were as high as the highest
 within-community associations. Affiliative contacts indicate that these
 individuals were forming bonds, likely for future mating opportunities.
 The mixing of two separate social groups with new bond formation is rare
 in terrestrial mammal groups. Such mixing between spotted dolphin groups
 suggests that adaptations to respond aggressively to ‘outsiders’ is
 diminished in this species and possibly other ecologically similar
 dolphins.
description: The first file contains group composition data logged from our
 field sighting logs with dolphin identities collected from underwater
 still photos and video. These data were used to conduct association
 analyses. The second file contains tactile contact events logged from
 underwater video specifically from mixed sightings (sightings including
 resident and immigrant dolphins). These data were used to conduct
 chi-square tests using basic code in R. See
 DCP_SIGHTING_TACTILE_DATAreadme.txt file for further details.
description: See DCP_SIGHTING_TACTILE_DATAreadme.txt file.
DOI: 10.5061/dryad.7pvmcvdv4
title: A general swimming response in exhausted obligate swimming fish

description: Marine organisms normally swim at elevated speeds relative to cruising
 speeds only during strenuous activity, such as predation or escape. We
 measured swimming speeds of 29 ram ventilating sharks from 10 species and
 of three Atlantic bluefin tunas immediately after exhaustive exercise
 (fighting a capture by hook-and-line), and unexpectedly found all
 individuals exhibited a uniform mechanical response, with swimming speed
 initially 2 times higher than the cruising speeds reached approximately 6
 hours later. We hypothesised that elevated swimming behaviour is a means
 to increase energetic demand and drive the removal of lactate accumulated
 during capture via oxidation. To explore this hypothesis, we estimated the
 mechanical work that must have been spent by an animal to elevate its swim
 speed, and then showed that the amount of lactate that could have been
 oxidized to fuel it comprises a significant portion of the amount of
 lactate normally observed in fishes after exhaustive exercise. An estimate
 for the full energetic cost of the catch-and-release event ensued.
DOI: 10.5061/dryad.mw6m905z0
title: The evolution of antagonistic and mutualistic traits in the yucca-yucca moth obligate pollination mutualism

description: Dataset used to analyze the rates of evolution of mouthparts used for
 pollination and egg-laying morphology in yucca moths.  Dataset
 includes the morphological measurements, the phylogenetic tree, and the
 species means for the evolutionary rates test.
description: The dataset was collected via morphological measurements using a
 hand caliper and measurements under a microscope.
DOI: 10.5061/dryad.bg79cnpc1
title: Outcrossing rates in an experimentally admixed population of self-compatible and self-incompatible Arabidopsis lyrata

description: AbstractThe transition to self-compatibility from self-incompatibility is
 often associated with high rates of self-fertilization, which can restrict
 gene flow among populations and cause reproductive isolation of
 self-compatible (SC) lineages. Secondary contact between SC and
 self-incompatible (SI) lineages might re-establish gene flow if SC
 lineages remain capable of outcrossing. By contrast, intrinsic features of
 SC plants that reinforce high rates of self-fertilization could maintain
 evolutionary divergence between lineages. Arabidopsis lyrata subsp. lyrata
 is characterized by multiple origins of self-compatibility and high rates
 of self-fertilization in SC-dominated populations. It is unclear whether
 these high rates of selfing by SC plants have intrinsic or extrinsic
 causes. We estimated outcrossing rates and examined patterns of pollinator
 movement for 38 SC and 40 SI maternal parents sampled from an admixed
 array of 1509 plants sourced from six SC and six SI populations grown
 under uniform density. Although plants from SI populations had higher
 outcrossing rates (mean tm = 0.78 ± 0.05 SE) than plants from SC
 populations (mean tm = 0.56 ± 0.06 SE), outcrossing rates among SC plants
 were substantially higher than previous estimates from natural
 populations. Patterns of pollinator movement appeared to contribute to
 lower outcrossing rates for SC plants; we estimated that 40% of floral
 visits were geitonogamous (between flowers of the same plant). The
 relatively high rates of outcrossing for SC plants under standardized
 conditions indicate that selfing rates in natural SC populations of A.
 lyrata are facultative and driven by extrinsic features of A. lyrata,
 including patterns of pollinator movement.
DOI: 10.5061/dryad.6hdr7sr29
title: Data from: A low-latitude species pump: Peripheral isolation, parapatric speciation and mating-system evolution converge in a marine radiation

description: Geologically recent radiation can shed light on speciation processes, but
 incomplete lineage sorting and introgressive gene flow render accurate
 evolutionary reconstruction and interpretation challenging. Independently
 evolving metapopulations of low-dispersal taxa may provide an additional
 level of phylogeographic information, given sufficiently broad sampling
 and genome-wide sequencing. Evolution in the marine brown algal genus
 Fucus in the south-eastern Atlantic was shaped by Quaternary
 climate-driven range shifts. Over this timescale, divergence and
 speciation occurred against a background of expansion-contraction cycles
 from multiple refugia, together with mating-system shifts from outcrossing
 (dioecy) to selfing hermaphroditism. We tested the hypothesis that
 peripheral isolation of range edge (dioecious) F. vesiculosus led to
 parapatric speciation and radiation of hermaphrodite lineages. Species
 tree methods using 876 single-copy nuclear genes and extensive geographic
 coverage produced conflicting topologies with respect to geographic clades
 of F. vesiculosus. All methods, however, revealed a new and early
 diverging hermaphrodite species, Fucus macroguiryi sp. Nov. Both the
 multispecies coalescent and polymorphism-aware models (in contrast to
 concatenation) support sequential paraphyly in F. vesiculosus resulting
 from distinct evolutionary processes. Our results support 1) peripheral
 isolation of the southern F. vesiculosus clade prior to parapatric
 speciation and radiation of hermaphrodite lineages – a “low latitude
 species pump”. 2) Directional introgressive gene flow into F. vesiculosus
 around the present-day secondary contact zone (sympatric-allopatric
 boundary) between dioecious/hermaphrodite lineages as hermaphrodites
 expanded northwards, as supported by concordance analysis and statistical
 tests of introgression. Species boundaries in the extensive sympatric
 range are likely maintained by reproductive system (selfing in
 hermaphrodites) and reinforcement.
description: Alignment files used in the article "A low-latitude
 species pump: Peripheral isolation, parapatric speciation and
 mating-system evolution converge in a marine radiation"
 alignment_files_Fucus.zip
DOI: 10.5061/dryad.f1vhhmgz8
title: Intraspecific interaction of host plants leads to concentrated distribution of a specialist herbivore through metabolic alterations in the leaves

description: 1. Recent studies suggest that changes in leaf traits due to interactions
 between plants affect resource utilisation by and the distribution of
 herbivores. However, this has not yet been confirmed experimentally. Here,
 we investigated the effects of phenotypic plasticity in leaf traits of
 Rumex obtusifolius (host plant) in response to intra- and interspecific
 interaction on the distribution of two leaf beetles, Gastrophysa
 atrocyanea (specialist herbivore) and Galerucella grisescens (generalist
 herbivore). 2. We investigated the local population density of R.
 obtusifolius plants and the presence of leaf beetles on the plants at five
 study sites. Leaf chemicals (condensed tannins and total phenolics) were
 compared between aggregated and solitary R. obtusifolius plants. To
 clarify the effects of the interaction environment of R. obtusifolius
 plants on their leaf traits and on resource utilisation by the leaf
 beetles, we compared leaf chemicals and preferences of adult leaf beetles
 among treatments where R. obtusifolius experienced intraspecific
 interaction, interspecific interaction, or no interaction in cultivation
 experiments. Finally, we evaluated the independent and combined effects of
 patch size and intraspecific interaction on leaf beetle distribution in
 mesocosm experiments. 3. In the field, the presence of the specialist leaf
 beetle G. atrocyanea was positively correlated with the local population
 density (rosette overlap ratio) of R. obtusifolius plants; however, there
 was no correlation in the case of the generalist leaf beetle G.
 grisescens. In the cultivation experiments, plants in the intraspecific
 interaction treatment increased their leaf contents of condensed tannins
 and total phenolics, and G. atrocyanea consumed more of these leaves than
 leaves in other treatments. Similar results were observed in the field. In
 the mesocosm experiments, larger numbers of G. atrocyanea were distributed
 on R. obtusifolius plants exposed to below-ground intraspecific
 interaction than on plants not exposed to intraspecific interaction. 4.
 Our results provide experimental evidence that leaf-trait changes in
 response to intraspecific interaction between host plants influence
 specialist herbivore distribution. This highlights the need to integrate
 plant–plant interactions into our understanding of plant–animal
 interactions.
DOI: 10.5061/dryad.3j9kd51kg
title: EL57 - Rhizoctonia solani seedling resistance

description: Intermediate files required for analysis of data associated with EL57
 population. (Select and Sequence (SnS) of a segregating sugar beet
 population provides genomic perspective of host resistance to seedling
 Rhizoctonia solani infection)
description: Methods can be found in the paper: Select and
 Sequence (SnS) of a segregating sugar beet population provides genomic
 perspective of host resistance to seedling Rhizoctonia solani
 infection Paul Galewski , Andrew Funk and J Mitchell
 McGrath<br>Front. Plant Sci. doi: 10.3389/fpls.2021.785267
description: Description of files: AlleleFreq.txt - Allele
 frequency data for resistant, susceptible and unselected beet
 populations. Biallelic.vcf - Filtered vcf with only the
 biallelic sites used for analysis. DeltaAF.txt  -
 Changes in allele frequency between seleted and unseleted beet
 populations DeltaAF_Signifiant.txt  -  Significant
 changes in allele frequency between seleted and unseleted beet
 populations FST.txt  - Divergence between beet
 populations selected for Rhizoctonia resistance
 Manta_SV.vcf -  Structural variation detected using the program
 Manta FST_24.txt  - Fst calculated within a 24bp
 sliding window Multiallelic.vcf  - Multiallelic
 variation, not used in statistical analysis but importnat to understanding
 causal variation SNPeff.vcf - vcf file annotated using
 SNPeff EL10_2_final_assembly.fa - EL10.2 referance
 sequence EL10_2_final_protien.fasta - EL10.2 protien
 sequences EL10_2_final_cDNA.fasta - EL10.2 cDNA
 sequences EL10_2_final.gff - EL10.2 referance
 annotation (Liftoff from EL10.1)
DOI: 10.5061/dryad.c866t1g87
title: Variations and controlling factors of soil denitrification rate

description: The denitrification process profoundly affects soil nitrogen (N)
 availability and generates its byproduct, nitrous oxide, as a potent
 greenhouse gas. There are large uncertainties in predicting global
 denitrification because its controlling factors remain elusive. In this
 study, we compiled 4301 observations of denitrification rates across a
 variety of terrestrial ecosystems from 214 papers published in the
 literature. The averaged denitrification rate was
 3516.3 ± 91.1 µg N kg−1 soil day−1. The highest denitrification rate was 4242.3 ± 152.3 µg N kg−1 soil day−1 under humid subtropical climates, and the lowest was 965.8 ± 150.4 µg N kg−1 under dry climates. The denitrification rate increased with temperature, precipitation, soil carbon and N contents, as well as microbial biomass carbon and N, but decreased with soil clay contents. The variables related to soil N contents (e.g., nitrate, ammonium, and total N) explained the variation of denitrification more than climatic and edaphic variables (e.g., mean annual temperature (MAT), soil moisture, soil pH, and clay content) according to structural equation models. Soil microbial biomass carbon, which was influenced by soil nitrate, ammonium, and total N, also strongly influenced denitrification at a global scale. Collectively, soil N contents, microbial biomass, pH, texture, moisture, and MAT accounted for 60% of the variation in global denitrification rates. The findings suggest that soil N contents and microbial biomass are strong predictors of denitrification at the global scale.
description: We collected the available
 denitrification rate from published papers. The screening of articles was
 conducted using two platforms: Web of Science (http://apps.webofknowledge.com) and China National Knowledge Infrastructure Database (http://www.cnki.net).
DOI: 10.5061/dryad.j3tx95xfx
title: Data from: What drives diversification? Range expansion tops climate, life history, habitat, and size in lizards and snakes

description: Aim: A major challenge in ecology and evolutionary biology is to explain
 the dramatic differences in species richness among clades. Much variation
 in richness is explained by differences in diversification rates among
 clades, and variation in diversification rates is often linked to various
 traits. But what types of traits are most important for explaining
 diversification? Here, we compared the impacts of different types of
 traits on diversification rates among lizard and snake families, and
 tested predictions about the relative importance of ecology vs.
 morphology, static vs. dynamic traits, and alpha vs. beta niche traits.
 Location: Global. Time period: Recent to ~200 million years ago. Major
 taxa studied: Squamata. Methods: We compared the relative impacts of
 traits related to biogeography (range size, range expansion), climate,
 life history (viviparity), microhabitat, and morphology (body-size) on
 diversification rates among all 72 family-level clades of squamates. We
 compiled data on traits, and tested for relationships between traits and
 diversification rates using phylogenetic multiple regression models.
 Results: The best-fitting model explained ~60% of the variation in
 diversification rates across squamate families. This model included only
 microhabitat (proportion of arboreal species) and a novel, dynamic,
 ecological/biogeographic beta-niche trait (rate of range expansion), which
 explained most variance. Other variables had more variable or
 non-significant contributions, including rates of climatic-niche change.
 Rates of range expansion were related to species richness, larger body
 size, and faster rates of climatic-niche change. Main conclusions:
 Overall, we provide possibly the most comprehensive comparison of the
 types of traits that can drive diversification. We also help explain
 diversity patterns in one of the largest vertebrate clades. We show that
 the rate of range expansion is the most important variable for explaining
 diversification rates and richness patterns in squamates. We also identify
 traits that help explain variation in rates of range expansion among
 clades.
DOI: 10.5061/dryad.jwstqjq9x
title: Active neural coordination of motor behaviors with internal states

description: The brain must continuously coordinate skeletomuscular movements with
 internal physiological states like arousal, but how is this coordination
 achieved? One possibility is that brain simply reacts to changes in
 external and/or internal signals. Another possibility is that it is
 actively coordinating both external and internal activities. We used
 functional ultrasound imaging to capture a large medial section of the
 brain, including multiple cortical and subcortical areas, in marmoset
 monkeys while monitoring their spontaneous movements and cardiac activity.
 By analyzing the causal ordering of these different time-series, we found
 that information flowing from the brain to movements and heart rate
 fluctuations were significantly greater than in the opposite direction.
 The brain areas involved in this external versus internal coordination
 were spatially distinct but also extensively interconnected. Temporally,
 the brain alternated between network states for this regulation. These
 findings suggest that the brain’s dynamics actively and efficiently
 coordinate motor behavior with internal physiology.
DOI: 10.5061/dryad.ffbg79cwb
title: Data from: Deep learning unlocks X‐ray microtomography segmentation of multiclass microdamage in heterogeneous materials

description: Four-dimensional quantitative characterization of heterogeneous materials
 using in situ synchrotron radiation computed tomography can reveal 3D
 sub-micron features, particularly damage, evolving under load, leading to
 improved materials. However, dataset size and complexity increasingly
 require time-intensive and subjective semi-automatic segmentations. Here,
 we present the first deep learning (DL) convolutional neural network (CNN)
 segmentation of multiclass microscale damage in heterogeneous bulk
 materials, teaching on advanced aerospace-grade composite damage using
 ≈65,000 (trained) human-segmented tomograms. The trained CNN machine
 segments complex and sparse (&lt;&lt;1% of volume) composite
 damage classes to ≈99.99% agreement, unlocking both objectivity and
 efficiency, with nearly 100% of the human time eliminated, which
 traditional rule-based algorithms do not approach. The trained machine is
 found to perform as well or better than the human due to
 ‘machine-discovered’ human segmentation error, with machine improvements
 manifesting primarily as new damage discovery and segmentation
 augmentation/extension in artifact-rich tomograms. Interrogating a
 high-level network hyperparametric space on two material configurations,
 we find DL to be a disruptive approach to quantitative structure-property
 characterization, enabling high-throughput knowledge creation (accelerated
 by two orders of magnitude) via generalizable, ultra-high-resolution
 feature segmentation.
description: See Methods section and Supporting Information associated
 with corresponding Advanced Materials paper (DOI:
 10.1002/adma.202107817).
description: Database of thirty high-resolution synchrotron radiation computed
 tomography scans of advanced composites, wherein each scan is represented
 in a zipped file containing both raw tomographic images (TIFF) and
 corresponding trained-human annotations of polymer damage (TIFF), used in
 the development of deep learning datasets for semantic segmentation via
 the instructions outlined in the ReadMe document. Additional usage details
 can be found in the corresponding Advanced Materials paper (DOI:
 10.1002/adma.202107817).
DOI: 10.5281/zenodo.18392389
title: Influence of a reversible chemical reaction on viscous fingering with partially miscible fluids
DOI: 10.5281/zenodo.18392390
title: Influence of a reversible chemical reaction on viscous fingering with partially miscible fluids
DOI: 10.5061/dryad.r4xgxd2dv
title: Habitat mediates coevolved but not novel species interactions

description: On-going recovery of native predators has the potential to alter species
 interactions, with community and ecosystem wide implications. We estimated
 co-occurrence of three species of conservation and management interest
 from a multi-species citizen science camera trap survey. We demonstrate
 fundamental differences in novel and co-evolved predator-prey interactions
 that are mediated by habitat. Specifically, we demonstrate that
 anthropogenic habitat modification had no influence on the expansion of
 the recovering native pine marten in Ireland, nor does it affect the
 predator’s suppressive influence on an invasive prey species, the grey
 squirrel. In contrast, the direction of the interaction between the pine
 marten and a native prey species, the red squirrel, is dependent on
 habitat. Pine martens had a positive influence on red squirrel occurrence
 at a landscape scale, especially in native broadleaved woodlands. However,
 in areas dominated by non-native conifer plantations, the pine marten
 reduced red squirrel occurrence. These findings suggest that following the
 recovery of a native predator, the benefits of competitive release are
 spatially structured and habitat specific. The potential for past and
 future landscape modification to alter established interactions between
 predators and prey has global implications in the context of the on-going
 recovery of predator populations in human-modified landscapes.
description: A survey spanning a five-year period documenting the occurrence
 of pine marten and grey and red squirrel was conducted throughout Northern
 Ireland between 2015 and 2020. The survey was repeated three times,
 initially in 2015 with 332 sites surveyed by citizen scientists provided
 with camera traps and trained for their consistent use (for full
 Methodology see Twining et al. 2021). This survey was repeated in 2018
 with 172 sites, and in 2020 with 207 sites using the same methods. At each
 site, a single camera trap was deployed at a point randomly selected by
 the surveyor within an independent 1km grid. Cameras were installed at
 head height on a tree overlooking a wooden squirrel feeder erected on an
 adjacent tree. Feeders were baited with peanuts and sunflower seeds in
 2015 and 2020, but just sunflower seeds in 2018. Cameras were set to take
 three images per trigger with a 1s reset time. Camera traps were deployed
 for 7 - 14 days at each location (mean = 10.3 days) after which cameras
 were retrieved for data extraction and species identification. Detection
 records were created for each species over the recording period.
description: Dates not sampled are replaced with NA's
 Each row the detection - non detection .csvs aligns with the same
 line on the associated site level covariate file