cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.xgxd254k9
title: Prey preferences of the coyote (Canis latrans) throughout its North American distribution

description: The coyote Canis latrans is one of the most studied species in North
 America with at least 510 papers on its diet alone. While this research
 has yielded excellent reviews of what coyotes eat, it has been inadequate
 to draw deeper conclusions because no synthesis to date has considered
 prey availability. We accounted for prey availability by investigating the
 prey preferences of coyotes across the species’ distribution using the
 traditional Jacobs’ index method, as well as the new iterative preference
 averaging method on scats and biomass. We found that coyotes preferred
 Dall’s sheep Ovis dalli, white-tailed deer Odocoileus virginianus, eastern
 cottontail rabbits Sylvilagus floridanus and California voles Microtus
 californicus, which yielded a predator to preferred prey ratio of 1:2. We
 also found that coyotes avoided preying on other small mammals, including
 carnivorans and arboreal species. There was strong concordance between the
 traditional and iterative preference averaging method on scats, but this
 pattern was not detected when biomass was considered. General linear
 models revealed coyotes preferred to prey upon larger species that were
 riskier to hunt, reflecting their ability to hunt in groups, and were
 least likely to hunt solitary species. Coyotes increasingly preferred mule
 deer O. hemionus and snowshoe hares Lepus americanus at higher latitudes,
 whereas black-tailed jackrabbit Lepus californicus were increasingly
 preferred towards the tropics. Mule deer were increasingly preferred at
 higher coyote densities, while black-tailed jackrabbit were increasingly
 avoided at higher coyote densities. Coyote predation could constrain the
 realized niche of prey species at the predator species’ distributional
 limits through their increased efficiency of predation reflected in
 increased prey preference values. These results are integral to improved
 understandings of coyote ecology and can inform predictive analyses
 allowing for spatial variation, which ultimately will lead to better
 understandings about the coyote’s ecological role across different
 ecosystems.
description: Data was sourced from the literature.
description: Data were collated in Microsoft Excel
DOI: 10.5061/dryad.2fqz612sg
title: Survey data of the health literacy on COVID-19 and COVID-19 vaccination in Indonesia

description: Introduction: Health literacy on COVID-19 and COVID-19 vaccination is
 valuable during the pandemic. The objective of this study was to determine
 the levels of health literacy about the COVID-19 vaccine and vaccination
 (Vaccine and Vaccination literacy—VL) in the Indonesian adult general
 population, assessing the perceptions of the respondents/interviewees
 about current adult immunization and beliefs about vaccination in general,
 and analyzing correlations of these variables with the VL
 levels.  Methods: A rapid survey was administered via the web.
 Data were analyzed using descriptive and inferential stats; the internal
 consistency of the VL scales was assessed through Cronbach’s alpha
 coefficient, and a Principal Component Analysis (PCA) was conducted to
 investigate how the questions of the functional and interactive-critical
 VL scales were related to one another and whether the underlying
 components (factors) and each question’s load on the components could be
 identified as anticipated. An alpha level lesser than 0.05 was considered
 significant. Results: Answers to functional- and interactive/ critical- VL
 questions showed good/ acceptable internal consistency (Cronbach’s alpha =
 0.817 and 0.699, respectively), lowest values observed were 0.806 for
 functional scale and 0.640 for the interactive-critical scale. PCA showed
 two components accounting for 52.45% of the total variability.
 Approximately 60% of respondents were females (n=686). Almost all
 respondents used the internet to seek information regarding COVID-19 and
 COVID-19 vaccination. Many used at least one social media actively with
 74.4% of respondents sometimes believing the validity of this information.
 Conclusions: High scores were observed in both functional- and
 interactive/ critical-VL, and were quite balanced between genders in the
 prior VL and higher in females for the latter; these were also closely
 related to the educational level and age group. It is crucial to increase
 public health literacy on managing the pandemic.
DOI: 10.5061/dryad.wh70rxwr6
title: Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads

description: Mammal declines across northern Australia are one of the major
 biodiversity loss events occurring globally. There has been no regional
 assessment of the implications of these species declines for genomic
 diversity. To address this, we conducted a species-wide assessment of
 genomic diversity in the northern quoll (Dasyurus hallucatus), an
 Endangered marsupial carnivore. We used next-generation sequencing methods
 to genotype 10,191 SNPs in 352 individuals from across a 3220 km length of
 the continent, investigating patterns of population genomic structure and
 diversity, and identifying loci showing signals of putative selection. We
 found strong heterogeneity in the distribution of genomic diversity across
 the continent, characterised by (1) biogeographic barriers driving
 hierarchical population structure through long-term isolation, and (2)
 severe reductions in diversity resulting from population declines,
 exacerbated by the spread of introduced toxic cane toads (Rhinella
 marina). These results warn of a large ongoing loss of genomic diversity
 and associated adaptive capacity as mammals decline across northern
 Australia. Encouragingly, populations of the northern quoll established on
 toad-free islands by translocations appear to have maintained most of the
 initial genomic diversity after 16 years. By mapping patterns of genomic
 diversity within and among populations, and investigating these patterns
 in the context of population declines, we can provide conservation
 managers with data critical to informed decision-making. This includes the
 identification of populations that are candidates for genetic management,
 the importance of remnant island and insurance/translocated populations
 for the conservation of genetic diversity, and the characterisation of
 putative evolutionarily significant units.
description: We use next-generation sequencing methods to genotype 10,191 SNPs
 in 352 northern quoll individuals from across a 3220 km length of the
 continent. We investigate patterns of population genomic structure and
 diversity, and identify loci showing signals of putative selection.
 Detailed methodological information is provided in the raw data, metadata
 files, scripts, and published manuscript that relate to this
 dataset.
description: Bioinformatic scripts are mostly run in command line format on
 Linux systems, using BWA v0.7.17, SAMTOOLS v1.7-1, ANGSD v0.93.
 R scripts including most genomic analyses and figure production
 were run using R version 4.1 in RStudio 2022.07.0+548 "Spotted
 Wakerobin" Release for Windows. Demographic and
 temporal trends were analysed using BEAST, SNeP v1.1, StairwayPlot
 v2.
DOI: 10.5061/dryad.ngf1vhhxc
title: Data for: Epistatic effects between amino acid insertions and substitutions mediate toxin-resistance of vertebrate Na+, K+-ATPases

description: The recurrent evolution of resistance to cardiotonic steroids (CTS) across
 diverse animals most frequently involves convergent amino-acid
 substitutions in the H1-H2 extracellular loop of Na+, K+-ATPase (NKA).
 Previous work revealed that hystricognath rodents (e.g. chinchilla) and
 pterocliform birds (sandgrouse) have convergently evolved amino-acid
 insertions in the H1-H2 loop, but their functional significance was not
 known. Using protein engineering, we show that these insertions have
 distinct effects on CTS resistance in homologs of each of the two species
 that strongly depend on intramolecular interactions with other residues.
 Removing the insertion in the chinchilla NKA unexpectedly increases CTS
 resistance and decreases NKA activity. In the sandgrouse NKA, the amino
 acid insertion and substitution Q111R both contribute to an augmented CTS
 resistance without compromising ATPase activity levels. Molecular docking
 simulations provide additional insight into the biophysical mechanisms
 responsible for the context-specific mutational effects on CTS
 insensitivity of the enzyme. Our results highlight the diversity of
 genetic substrates that underlie CTS insensitivity in vertebrate NKA and
 reveal how amino-acid insertions can alter the phenotypic effects of point
 mutations at key sites in the same protein domain.
DOI: 10.5061/dryad.k0p2ngfbn
title: Niche overlap between two large herbivores across landscape variability using dietary eDNA metabarcoding: Raw sequences of European bison and red deer – Bialowieza

description: Understanding the trophic ecology of herbivore species is key to assess
 their environmental requirements and to improve management policies, but
 measuring their trophic interactions remains challenging. Among the
 methods available, quantifying the plant composition of a species'
 diet provides a detailed picture of how species exploit the resources in
 their environment and their associated niche overlap. Yet, most studies
 focusing on herbivore trophic ecology ignore the influence that landscape
 variability may have. Here, we studied how landscape variability
 influences trophic interactions through niche partitioning. We used eDNA
 metabarcoding to quantify the diet composition of two large herbivores of
 the Bialowieza Forest, red deer (Cervus elaphus) and European bison (Bison
 bonasus, hereafter referred to as bison) to investigate how increasing
 habitat quality and predation risk in their environment influence their
 diet composition and niche partitioning. We found red deer to have an
 overall greater diet variability and lower niche overlap within species
 compared to bison. Moreover, our findings indicate herbivore interactions
 are non-homogeneous across the landscape. Higher habitat quality was
 associated with higher niche overlap only within bison. We also detected
 an increase in niche overlap with increasing predation risk within red
 deer, indicating they modify their diet choice as a reaction to wolf
 predation risk. This study provides evidence of eDNA dietary metabarcoding
 as a useful tool for wildlife management to assess the status of species
 in an ecosystem based on known environmental factors. We suggest future
 studies to integrate the environments' variability when studying
 trophic ecology of herbivores to capture the whole extent of species
 interaction in order to improve conservation and management guidelines.
DOI: 10.5061/dryad.mpg4f4r34
title: Data from: Resident-disperser differences and genetic variability affect communities in microcosms

description: Dispersal is a key process mediating ecological and evolutionary dynamics.
 Its effects on the dynamics of spatially-structured systems, population
 genetics, or species range distribution can depend on phenotypic
 differences between dispersing and non-dispersing individuals. However,
 scaling up the importance of resident-disperser differences to communities
 and ecosystems has rarely been considered, in spite of intraspecific
 phenotypic variability being an important factor mediating community
 structure and productivity. Here, we used the ciliate Tetrahymena
 thermophila, in which phenotypic traits are known to differ between
 residents and dispersers, to test (i) whether these resident-disperser
 differences affect biomass and composition in competitive communities
 composed of four other Tetrahymena species, and (ii) whether these effects
 are genotype-dependent. We found that dispersers led to lower community
 biomass compared to residents. This effect was highly consistent across
 the twenty T. thermophila genotypes used, despite intraspecific
 variability in resident-disperser phenotypic differences. We also found a
 significant genotypic effect on biomass production, showing that
 intraspecific variability has consequences for communities. Our study
 suggests that individual dispersal strategy can scale up to community
 productivity in a predictable way, opening new perspectives to the
 functioning of spatially structured ecosystems.
description: Data were analysed using R software.
DOI: 10.5061/dryad.6q573n620
title: Hypothalamic interaction with reward-related regions during subjective evaluation of foods

description: The reward system implemented in the midbrain, ventral striatum,
 orbitofrontal cortex, and ventromedial prefrontal cortex evaluates and
 compares various types of rewards given to the organisms. It has been
 suggested that autonomic factors influence reward-related processing via
 the hypothalamus, but how the hypothalamus modulates the reward system
 remains elusive. In this functional magnetic resonance imaging study, the
 hypothalamus was parcellated into individual hypothalamic nuclei
 performing different autonomic functions using boundary mapping
 parcellation analyses. The effective interaction during subjective
 evaluation of foods in a reward task was then investigated between the
 human hypothalamic nuclei and the reward-related regions. We found
 significant brain activity decrease in the paraventricular nucleus (PVH)
 and lateral nucleus in the hypothalamus in food evaluation compared with
 monetary evaluation. A psychophysiological interaction analysis revealed
 dual interactions between the PVH and (1) midbrain region and (2)
 ventromedial prefrontal cortex, with the former correlated with the
 stronger tendency of participants toward food-seeking. A dynamic causal
 modeling analysis further revealed unidirectional interactions from the
 PVH to the midbrain and ventromedial prefrontal cortex. These results
 suggest that the PVH in the human hypothalamus interacts with the
 reward-related regions in the cerebral cortex via multiple pathways (i.e.,
 the midbrain pathway and ventromedial prefrontal pathway) to evaluate
 rewards for subsequent decision-making.
description: Higher-resolution fMRI images were collected to investigate the
 effective interaction between the human hypothalamic nuclei and the
 regions in the reward system. We also collected the resting-state
 functional images to parcellate the medial hypothalamus into individual
 nuclei. The brain activity in individual hypothalamic nuclei was examined
 during the evaluation of food rewards compared to monetary rewards. The
 neural pathways toward the reward-related regions were then explored using
 effective connectivity analyses.
DOI: 10.5061/dryad.rn8pk0pf6
title: Optimal vaccination at high reproductive numbers: sharp transitions and counterintuitive allocations

description: Optimization of vaccine allocations among different segments of a
 heterogeneous population is important for enhancing the effectiveness of
 vaccination campaigns in reducing the burden of epidemics. Intuitively, it
 would seem that allocations designed to minimize infections should
 prioritize those with the highest risk of being infected and infecting
 others. This prescription is well supported by vaccination theory, e.g.
 when the vaccination campaign aims to reach herd immunity. In this work,
 we show, however, that for vaccines providing partial protection (leaky
 vaccines) and for sufficiently high values of the basic reproduction
 number, intuition is overturned: the optimal allocation minimizing the
 number of infections prioritizes the vaccination of those who are least
 likely to be infected. The work combines numerical investigations,
 asymptotic analysis for a general model, and complete mathematical
 analysis in a two-group model. The results point to important
 considerations in managing vaccination campaigns for infections with high
 transmissibility.
description: The MATLAB source code, including all data and parameters used to
 produce the graphs presented in this work, is available on GitHub at https://github.com/NGavish/HighR0 or Zenodo at https://doi.org/10.5281/zenodo.6962689. The contact matrices used in the code were obtained from [Citation 28; PLOS Computational Biology, e1009098]. There are provided as .mat files under the subdirectory /CountryData and under the names xxx_data.mat where xxx is the country code. Pre-computed data files are provided as .mat files under the subdirectory /data.  By default, the graphs are produced from pre-computed simulation output. See Usage Notes for instructions on producing the graphs without relying on these pre-computed data files.
description: The file main.m produces all graphs presented in this work. By
 default, the graphs are produced from pre-computed simulation output.  To
 run a full computation of simulations modify line 11 of main.m.
DOI: 10.5061/dryad.tqjq2bw30
title: Input data and model implementation from: How do terrestrial wildlife communities respond to small-scale Acacia plantations embedded in harvested tropical forest?

description: To offset the declining timber supply from shifting towards more
 sustainable forestry practices, industrial tree plantations are expanding
 in tropical production forests. The conversion of natural forest to tree
 plantation is generally associated with loss of biodiversity and shifts
 toward more generalist and disturbance tolerant communities; but effects
 of mixed-landuse landscapes integrating natural and plantation forest
 remain little understood. Using camera traps, we surveyed the
 medium-to-large bodied terrestrial wildlife community across two
 mixed-land-use forest management areas in Sarawak, Malaysia Borneo which
 include areas dedicated for logging of natural forest and adjacent planted
 Acacia forests. We analysed data from a 25-wildlife species community
 using a Bayesian community occupancy model to assess species richness and
 species-specific occurrence responses to Acacia plantations at a broad
 scale, and to remote-sensed local habitat conditions within the different
 forest land-use types. All species were estimated to occur in both
 land-use types, but species-level percent area occupied and predicted
 average local species richness were slightly higher in the natural forest
 management areas compared to licensed planted forest. Similarly,
 occupancy-based species diversity profiles and defaunation indices for
 both a full community and only threatened and endemic species suggested
 the diversity and occurrence were slightly higher in the natural forest
 management areas. At the local scale, forest quality was the most
 prominent predictor of species occurrence. These associations with forest
 quality varied among species but were predominantly positive. Our results
 highlight the ability of a mixed-land-use landscape with small-scale
 Acacia plantations embedded in natural forest to retain terrestrial
 wildlife communities while providing an alternate source of timber.
 Nonetheless, there was a tendency towards reduced biodiversity in planted
 forests, which would likely be more pronounced in plantations that are
 larger or embedded in a less natural matrix.
DOI: 10.25349/d9r89j
title: Sub-Lithospheric Small-Scale Convection Tomographically Imaged Beneath the Pacific Plate

description: Small-scale convection beneath the oceanic plates has been invoked to
 explain off-axis non-plume volcanism, departure from simple seafloor
 depth-age relationships, and intraplate gravity lineations. We deployed
 thirty broadband OBS stations on ~40 Ma Pacific seafloor in a region
 notable for gravity anomalies, measured by satellite altimetry, elongated
 parallel to plate motion. P-wave teleseismic tomography reveals
 alternating upper mantle velocity anomalies on the order of ±2%, aligned
 with the gravity lineations. These features, which correspond to ~300-500
 ˚K lateral temperature contrast, and possible hydrous or carbonatitic
 partial melt, are – surprisingly – strongest between 150 and 260 km depth,
 indicating rapid vertical motions through a low-viscosity asthenospheric
 channel. Coherence and admittance analysis of gravity and
 topography using new multibeam bathymetry soundings substantiates
 the presence of mantle density variations, and forward modelling predicts
 gravity anomalies that qualitatively match observed lineations. This study
 provides observational support for small-scale convective rolls beneath
 the oceanic plates.
DOI: 10.5061/dryad.q83bk3jmg
title: Sexual conflict does not maintain female colour polymorphism in a territorial damselfly

description: Female-limited dimorphism is commonly hypothesized to be an adaptation
 resulting from male harassment or sexual conflict over female mating rate.
 We examined whether males discriminate be- tween female colour morphs of
 the beautiful Hawaiian damselfly, Megalagrion calliphya, in order to
 evaluate whether male harassment could explain the existence and/or
 maintenance of this dimorphism. Previous studies of this species suggest
 that spatially varying ecological selection maintains the dimorphism, but
 these hypotheses are not mutually exclusive. Here, we used a common method
 of measuring male behaviour towards secured females at mating sites under
 naturally occurring conditions, using five populations that range in
 male-like female morph frequency from 0 to 0.86. We found very low rates
 of interaction in a total of 64 one-hour trials, and male behaviour
 towards females did not differ significantly between colour morphs. By
 comparing the populations that vary in female morph fre- quency, we found
 no evidence of frequency-dependent sexual selection on colour, suggesting
 that this polymorphism is maintained by selective forces other than sexual
 conflict.
DOI: 10.15468/dl.7gk5fu
title: Occurrence Download

description: A dataset containing 502 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Heliophorus sena"
 ]
}

 The dataset includes 502 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003270-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.