cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1zcrjdfqt
title: Goat collective decisions

description: For group-living animals to remain cohesive they must agree on where to
 travel. Theoretical models predict shared group decisions should be
 favoured, and a number of empirical examples support this. However, the
 behavioural mechanisms that underpin shared decision-making are not fully
 understood. Groups may achieve consensus of direction by active
 communication of individual preferences (i.e. voting), or by responding to
 each other’s orientation and movement (i.e. copying). For example, African
 buffalo (Syncerus caffer) are reported to use body orientation to vote and
 indicate their preferred direction to achieve a consensus on travel
 direction, whilst golden shiners (Notemigonus
 crysoleucas) achieve consensus of direction by responding to the
 movement cues of their neighbours. Here, we present a conceptual model
 (supported by agent-based simulations) that allows us to distinguish
 patterns of motion that represent voting or copying. We test our model
 predictions using high-resolution GPS and magnetometer data collected from
 a herd of free-ranging goats (Capra aegagrus hircus) in the Namib Desert,
 Namibia. We find that decisions concerning travel direction were more
 consistent with individuals copying one another’s motion and find no
 evidence to support the use of voting with body orientation. Our findings
 highlight the role of simple behavioural rules for collective decision
 making by animal groups.
description: Heading_data.RData provides animal orientation for each
 individual and event across the study. Data were collected using
 magnetometers and accelerometers attached to goats. Full methods for
 transforming these data into animal orientation can be found in the
 Supplemental Material for the manuscript. 
 Loc_data.RData provides GPS fixes for each individual at each
 timestep (1 second) for the events of interest across the
 study.    Heading data contains the
 following column names: "event"   "id"    
  "time"    "heading"
 "event" refers to the identified collective
 decision "id" to the individual
 goat "time" is the number of seconds since
 January 1st 1970 (standard notation)
 "heading" refers to the animal orientation with respect
 to north     Loc
 data contains the additional column names:"lat" 
 "lon"  Which refer to the latitude and
 longitude of the individual goat as read from their GPS collar.
DOI: 10.5061/dryad.np5hqbzrb
title: Data from: Are British urban foxes (Vulpes vulpes) ‘bold’? The importance of understanding human-wildlife interactions in urban areas

description: Urban fox behaviour recorded during an extensive field experiment in
 Bristol, UK. We examined two different but inter-related
 behaviours, both of which influence a fox's propensity to
 take risks. Neophobia affects a fox's reaction to
 novelty in the environment, and wariness its reaction to potential
 threats. We investigated how social status and foraging social context
 influenced both behaviours in Bristol’s fox population. For further
 information please see Padovani et al. 2021.  
description: Two excel spreadsheets.
 "Padovani_et_al_Behavioural_Data.xlsx" details
 neophobia and wariness behaviour per fox individual, with behaviour
 captured through 12 variables that represent different aspects of urban
 fox hesitation and avoidance behaviour. Recording season, fox social
 group, and foraging social context (alone/with other foxes present) is
 also recorded. PC1 and PC2 values emerging from a principal components
 analysis of the 12 behavioural variables are also listed. The "Total
 Behaviour - Neophobia" tab represents behaviour in response to the
 neophobia stimulus, irrespective of foraging social context. The
 "Total Behaviour - Wariness" tab represents behaviour in
 response to the wariness stimulus, irrespective of foraging social
 context. The "Social Context - Neophobia" tab represents
 behaviour in response to the neophobia stimulus, and in response to
 foraging social context. The "Social Context - Wariness" tab
 represents behaviour in response to the wariness stimulus, and in response
 to foraging social context. Descriptions of column headings are provided
 on the "Variable Definitions" tab.
 "Padovani_et_al_Habituation_Data.xlsx" details a subset
 of the neophobia and wariness behaviours recorded in
 "Padovani_et_al_Behavioural_Data.xlsx", with these behaviours
 broken down across days 1, 2, and 4 of the neophobia and wariness tests.
 These data were used to determine if any habituation occured to the
 neophobia or wariness stimuli as the tests progressed. The
 "Neophobia" tab represents behaviour in response to the
 neophobia stimulus. Missing values indicate that a fox did not forage in
 the test circle on that day. The "Wariness" tab represents
 behaviour in response to the wariness stimulus. Missing values indicate
 that a fox did not forage in the test circle on that day. Descriptions of
 column headings are provided on the "Variable Definitions"
 tab. For further details on all experimental processes,
 variables, and stastical analyses, see Padovani <em>et
 al.</em> 2021.
DOI: 10.5061/dryad.d7wm37q09
title: Patterns, predictors, and consequence of dominance in hybrids

description: Compared to those of their parents, are the traits of first-generation
 (F1) hybrids typically intermediate, biased toward one parent, or
 mismatched for alternative parental phenotypes? And how does hybrid trait
 expression affect fitness? To address this empirical gap, we compiled data
 from 198 studies in which traits were measured in a common environment for
 two parent taxa and their F1 hybrids. We find that individual traits in
 F1s are, on average, halfway between the parental midpoint and one
 parental value (e.g., hybrid trait values are 0.75 if parents'values
 are 0 &1). When considering pairs of traits together, a
 hybrid's bivariate phenotype tends to resemble one parent (pairwise
 parent-bias) about 50 % more than the other while also exhibiting a
 similar magnitude of mismatch due to different traits having dominance in
 conflicting directions. We detect no phylogenetic signal nor an effect of
 parental genetic distance on dominance or mismatch. Using data from an
 experimental field planting of recombinant hybrid sunflowers, we
 illustrate that pairwise parent-bias improves fitness whereas pairwise
 mismatch reduces fitness. In sum, our study has three major conclusions.
 First, hybrids between ecologically divergent natural populations are not
 phenotypically intermediate but rather exhibit substantial mismatch while
 also resembling one parent more than the other. Second, dominance and
 mismatch do not seem to be governed by general rules but rather by the
 idiosyncratic evolutionary trajectories of individual traits in individual
 populations or species. Finally, selection against hybrids likely results
 from selection against both intermediate and mismatched phenotypes.
description: The systematic review data were compiled from the literature
 (many datasets came from emailing authors). The sunflower data were
 collected by Ken Whitney & co. All details given in text. Data are
 raw, as collected, in the 'raw_data.'
description: Everything should work well if directories are established using
 the .Rproj file in RStudio. See meta-data and readme file for further
 instructions. Email me (kthomp1063@gmail.com) with any queries. Data
 collection for follow-up projects is ongoing, and if you are interested in
 the most current dataset please contact me. I'd be happy to
 collaborate and/or share the updated dataset.
DOI: 10.5061/dryad.1g1jwsttr
title: Data from: The influence of disorder on the exciton spectra in two-dimensional structures

description: We study the joint effect of disorder and Coulomb interaction screening on
 the exciton spectra in two-dimensional (2D) structures. These can be van
 der Waals structures or heterostructures of organic (polymeric)
 semiconductors as well as inorganic substances like transition metal
 dichalcogenides. We consider 2D screened hydrogenic problem with Rytova -
 Keldysh interaction by means if so-called fractional Scrodinger equation.
 Our main finding is that above synergy between screening and disorder
 either destroys the exciton (strong screening) or promote the creation of
 a bound state, leading to its collapse in the extreme case. Our second
 finding is energy levels crossing, i.e. the degeneracy (with respect to
 index µ) of the exciton eigenenergies at certain discrete value of
 screening radius. Latter effects may also be related to the quantum
 manifestations of chaotic exciton behavior in above 2D semiconductor
 structures. Hence, they should be considered in device applications, where
 the interplay between dielectric screening and disorder is important.
DOI: 10.5061/dryad.x69p8czgv
title: Selective extinctions resulting from random habitat destruction lead to under‐estimates of local and regional biodiversity loss in a manipulative field experiment

description: Land-use change is a significant cause of anthropogenic extinctions, which
 are likely to continue and accelerate as habitat conversion proceeds in
 most biomes. One way to understand the effects of habitat loss on
 biodiversity is through improved tools for predicting the number and
 identity of species losses in response to habitat loss. There are
 relatively few methods for predicting extinctions and even fewer
 opportunities for rigorously assessing the quality of these predictions.
 In this paper we address these issues by applying a new method based on
 rarefaction to predict species losses after random, but aggregated,
 habitat loss. We compare predictions from three rarefaction models,
 individual-based, sample-based, and spatially-clustered, to those derived
 from a commonly-used extinction estimation method, the Species-Area
 Relationship (SAR). We apply each method to a mesocosm experiment, in
 which we aim to predict species richness and extinctions of arthropods
 immediately following 50% habitat loss. While each model produced
 strikingly accurate predictions of species richness immediately after the
 habitat loss disturbance, each model significantly underestimated the
 number of extinctions occurring at both the local (within-mesocosm) and
 regional (treatment-wide) scales. Despite the stochastic nature of our
 small-scale, short-term, and randomly applied habitat loss experiment, we
 found surprisingly clear evidence for extinction selectivity, for example
 when abundant species with low extinction probabilities were extirpated
 following habitat loss. The important role played by selective extinction
 even in this contrived experimental system suggests that ecologically
 driven, trait-based extinctions play an equally important role to
 stochastic extinction, even when the disturbance itself has no clear
 selectivity. As a result, neutrally stochastic null models such as the SAR
 and rarefaction are likely to underestimate extinctions caused by habitat
 loss. Nevertheless, given the difficulty of predicting extinctions, null
 models provide useful benchmarks for conservation planning by providing
 minimum estimates and probabilities of species extinctions.
description: The master dataset (GoldenrodData_Master.xlsx) contains abundance
 and occupancy data of arthropod communities for each sampling period of
 the experiment described in the associated manuscript. Taxa are identified
 to morphospecies or the lowest taxonomic unit possible. Each of the
 available R scripts corresponds to a different analysis outlined in the
 associated manuscript (for more information, see
 README_AlmeidaEtAlGCB.docx).
description: To reproduce the analyses from the associated manuscript, follow
 the workflow outlined in the provided ReadMe file
 (README_AlmeidaEtAlGCB.docx).
DOI: 10.5061/dryad.m905qfv03
title: Buck Creek fish samplings

description: Buck Creek is a spring-fed, cool-water tributary of the West Fork White
 River, Indiana. The Muncie Bureau of Water Quality sampled fishes and
 monitored water temperature in Buck Creek annually from 1986-2018. For
 this study, we utilized long-term fish data from the Bureau of Water
 Quality to evaluate spatial and temporal changes in the fish assemblages
 of Buck Creek in Delaware County, Indiana, USA. Non-metric
 multidimensional scaling (NMDS) was used to describe changes in the fish
 assemblages over space and time. Linear mixed-effects models were used to
 evaluate the relationship between environmental factors and the fish
 assemblages. The spatial NMDS results were separated in distinct groups of
 upstream and downstream assemblages. This was characterized by a shift of
 headwater specialists shifting to large-river species. The temporal NMDS
 results were separated into distinct annual assemblages. This was
 characterized by a drop in pollution-tolerant species and an increase in
 intolerant species. Our findings indicate that the fish assemblages have
 improved in Buck Creek over space and time.
description: Data was collected annually from 1986 to 2018 by the Muncie
 Bureau of Water Quality with tote-barge and backpack electrofishing
 units.  It has been processed for use in various
 analyses such non-metric multidimensional scaling and linear mixed-effects
 modeling. 
description: There are no missing values. All data is within the file.
DOI: 10.5061/dryad.51c59zw6v
title: Which enemies mediate distance- and density-dependent mortality of tree seeds and seedlings? A meta-analysis of fungicide, insecticide, and exclosure studies

description: Conspecific negative distance- and density-dependence is believed to be
 one of the most important mechanisms controlling forest community assembly
 and species diversity globally. SoilPlant pathogens, and insect and
 mammalian herbivores, are the most common natural enemy types that have
 been implicated in this phenomenon, but their relative importancegeneral
 effects at different plant life stages isare still unclear. Here, we
 conduct a meta-analysis of studies that involved robust manipulative
 experiments, using fungicides, insecticides, and exclosures, to assess the
 contributions of different natural enemy types to distance- and
 density-dependent effects at seed and seedling stages. We found that
 natural enemies cause stronger distance- and density-dependent mortality
 caused by natural enemies was most likely at the seedling stage than the
 seed stage. Fungicide treatments can change significantand was greater at
 higher mean annual temperatures. Seedling mortality was significantly
 weakened when fungi were removed. By contrast, negative distance- and
 density-dependent mortality to non-significance at the seedling stage.
 Negative conspecific distance- and density-dependence is not a general
 pattern at the seed stage. High seed mass reduced distance- and
 density-dependent mortality. Seed studies excluding only large mammals
 found significant negative conspecific distance-dependent mortality, but
 exclusion of all mammals resulted in a non-significant mortality.effect of
 conspecifics. Our study suggests that soilplant pathogens are a major
 cause of distance- and density-dependent mortality at the seedling stage,
 althoughwhile the impacts of herbivores on seedlings have been
 understudied. At the seed stage, large and small mammals respectively
 weaken and enhance negative conspecific distance-dependent mortality.
 Future research should identify specific agents of mortality, investigate
 the interactions among different enemy types, and assess how global change
 drivers may affect the dynamics of natural enemies and thus influence the
 strength of conspecific distance- and density-dependence.
DOI: 10.5061/dryad.34tmpg4j1
title: Gene flow increases phylogenetic structure and inflates cryptic species estimations: a case study on widespread Philippine puddle frogs (Occidozyga laevis)

description: In cryptic amphibian complexes, there is a growing trend to equate high
 levels of genetic structure with hidden cryptic species diversity.
 Typically, phylogenetic structure and distance-based approaches are used
 to demonstrate the distinctness of clades and justify the recognition of
 new cryptic species. However, this approach does not account for gene
 flow, spatial, and environmental processes that can obfuscate phylogenetic
 inference and bias species delimitation. As a case study, we sequenced
 genome-wide exons and introns to evince the processes that underlie the
 diversification of Philippine Puddle Frogs—a group that is widespread,
 phenotypically conserved, and exhibits high levels of geographically-based
 genetic structure. We showed that widely adopted tree- and distance-based
 approaches inferred up to 20 species, compared to genomic analyses that
 inferred an optimal number of five distinct genetic groups. Using a suite
 of clustering, admixture, and phylogenetic network analyses, we
 demonstrate extensive admixture among the five groups and elucidate two
 specific ways in which gene flow can cause overestimations of species
 diversity: (1) admixed populations can be inferred as distinct lineages
 characterized by long branches in phylograms; and (2) admixed lineages can
 appear to be genetically divergent, even from their parental populations
 when simple measures of genetic distance are used. We demonstrate that the
 relationship between mitochondrial and genome-wide nuclear p-distances is
 decoupled in admixed clades, leading to erroneous estimates of genetic
 distances and, consequently, species diversity. Additionally, genetic
 distance was also biased by spatial and environmental processes. Overall,
 we showed that high levels of genetic diversity in Philippine Puddle Frogs
 predominantly comprise metapopulation lineages that arose through complex
 patterns of admixture, isolation-by-distance, and isolation-by-environment
 as opposed to species divergence. Our findings suggest that speciation may
 not be the major process underlying the high levels of hidden diversity
 observed in many taxonomic groups and that widely-adopted tree- and
 distance-based methods overestimate species diversity in the presence of
 gene flow.
DOI: 10.5061/dryad.p2ngf1vpd
title: Nonlinear dynamic model and rollover threshold of a liquid tank semi-trailer

description: A refined dynamic model of a tractor-semitrailer, including the nonlinear
 tire force and tank swing force, is established, and the fluid force and
 torque in the liquid tank are obtained through simulation by using the
 fluid mechanics software Fluent. Two kinds of tests, the tire corner
 stiffness test and tire roll stiffness test, are designed and performed
 using the KHAT flat bed test rig for tires, and a nonlinear model of the
 tire is obtained. The driving vehicle body state and handling stability of
 the liquid tank semi-trailer are studied through the model. The roll angle
 and lateral accelerationare used as the rollover characterization
 parameters. The dynamic lateral load transfer rate (LTR) is used as the
 rollover index to characterize the rollover threshold. The conclusions are
 of great significance for running status monitoring, rollover early
 warning and rollover avoidance controlfor liquid tank semi-trailers.
description: The movement law data of the tank is  obtained by FLUENT
 simulation;<br> Other vehicle parameter motion laws data are 
 obtained through the joint simulation of SIMULINK and FLUENT.
DOI: 10.5061/dryad.h18931zjn
title: Data from: Bobbing and fin-flicking in a small benthic fish

description: Most anti-predator strategies increase survival of individuals by
 signalling to predators, by reducing the chances of being recognised as
 prey, or by bewildering a predator's perception. In fish, bobbing and
 fin-flicking are commonly considered as pursuit‑deterrent behaviours that
 signal a predator that it has been detected and thus lost its
 surprise-attack advantage. Yet, very few studies assessed whether such
 behavioural traits are restricted to the visual presence of a predator. In
 this study, we used the yellow black-headed
 triplefin Tripterygion delaisi to investigate the
 association between these behaviours and the visual exposure to (1) a
 black scorpionfish predator (Scorpaena porcus), (2) a stone of a size
 similar to that of S. porcus, (3) a conspecific, and 4) a
 harmless heterospecific combtooth blenny (Parablennius sanguinolentus). We
 used a laboratory-controlled experiment with freshly caught fish designed
 to test for differences in visual cues only. Distance kept by the focal
 fish to each stimulus, frequency of bobbing and fin-flicking were
 recorded. Triplefins kept greater distance from the stimulus compartment
 when a scorpionfish predator was visible. Bobbing was more frequent in the
 visual presence of a scorpionfish, but also shown towards the other
 stimuli. However, fin flicks were equally abundant across all stimuli.
 Both behaviours decreased in frequency over time suggesting that triplefin
 become gradually comfortable in a non-changing new environment. We discuss
 why bobbing and fin-flicking are not exclusive pursuit‑deterrent
 behaviours in this species, and propose additional non-exclusive functions
 such as enhancing depth perception by parallax motion (bobbing) or
 signalling vigilance (fin‑flicking).
DOI: 10.5061/dryad.v15dv41v3
title: Deep eutectic solvent-based emulsification liquid-liquid microextraction coupled with HPLC-UV for the analysis of phenoxy acid herbicides in paddy field water samples

description: An emulsification liquid-liquid microextraction (ELLME) method was
 successfully developed using phenolic based deep eutectic solvent (DES) as
 an extraction solvent for the determination of phenoxy acid herbicides,
 dicamba and MCPA in environmental water samples. Five different phenolics
 based DES were successfully synthesized by using phenol (DES 1),
 2-chlorophenol (DES 2), 3-chlorophenol (DES 3), 4-chlorophenol (DES 4) and
 3,4-dichlorophenol (DES 6) as the hydrogen-bond donor (HBD) and choline
 chloride as the hydrogen-bond acceptor (HBA). The DESs were mixed at a 1:2
 ratio. A homogenous solution (clear solution) was observed upon the
 completion of the successful synthesis. The synthesized DESs were
 characterised by using FTIR and NMR. Under optimum ELLME
 conditions (50 µL of DES 2 as extraction solvent; 100 µL of THF as
 emulsifier solvent; pH 2; extraction time; 5 min), enrichment factor (EF)
 obtained for dicamba and MCPA were 43.1 and 59.7, respectively. Limit of
 detection (LOD) and limit of quantification (LOQ) obtained for dicamba was
 1.66 and 5.03 µg/L respectively, meanwhile for MCPA was 1.69 and 5.12
 µg/L, respectively. The developed ELLME-DES method was applied on paddy
 field water samples, with extraction recoveries in the range of 27-91% for
 dicamba and 82-96% for MCPA.
description: A 1.5 mL of ultrapure water containing 0.1 mg L<sup>-1</sup> of dicamba and MCPA of pH 2 was transferred into a centrifuge tube. 100 µL of DES (extraction solvent) and THF (emulsifier solvent) were added to the sample. The tube was placed on the vortex mixer at 2500 rpm for 5 min. The solution was cloudy after vortexing which was caused by the aggregation of DES droplet from the aqueous phase. The targeted analytes were simultaneously extracted to the DES phase during this process. The solution was then centrifuge at 3400 rpm for 10 min to separate the DES phase from the aqueous phase. The extract was dried under a steady stream of nitrogen gas at room temperature and reconstitute with 25 µL of mobile phase before being injected into HPLC system. All data obtained from HPLC analysis were interpolated through a calibration curve to determine the enrichment factor and recovery.