cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q3j60
title: Data from: Neighborhood defense gene similarity effects on tree performance: a community transcriptomic approach

description: The structure and dynamics of ecological communities are ultimately the
 outcome of the differential demographic rates of individuals. Individual
 growth and mortality rates largely result from the interaction between an
 organism's phenotype and the abiotic and biotic environment.
 Functional traits have been used extensively over the past decade to
 elucidate links among phenotypes, demography and community dynamics. A
 fundamental weakness of most functional trait approaches is the use of
 ‘soft’ traits associated with resource acquisition to examine how
 neighbourhood similarity affects tree survival and growth. However, these
 ‘soft’ traits are unlikely to be good predictors of similarities among
 co-occurring species. Less easily measured aspects of organismal function
 – such as those related to defence – have frequently gone unmeasured. This
 is particularly problematic for testing important hypotheses in forest
 ecology, such as the Janzen–Connell hypothesis where focal trees are
 expected to be at a disadvantage if their neighbours share the same
 natural enemies. A potential alternative to functional trait approaches is
 to quantify the transcriptomic or functional genomic similarity of
 species. Such analyses are now possible in natural systems where de novo
 transciptome assemblies can be used to conduct functional phylogenomic
 analyses where homologous gene trees are produced. Using demographic plot
 data for 21 species from a North American forest dynamic plot, we conduct
 a community functional phylogenomic analysis of a plant community to
 elucidate the similarity in defence response genes across species. This
 similarity was then used to ask whether the similarity in defence genes of
 heterospecific species in the local neighbourhood of a focal individual
 tree influences its growth and mortality rates. The results show that
 individual growth rates are higher when surrounded by dissimilar
 heterospecific species for 16 of 27 defence genes analysed. Additionally,
 survival rates are increased when an individual is in a neighbourhood with
 dissimilar species for 4 of the 27 defence genes studied. Lastly, strong
 conspecific effects were found in all analyses, underscoring that future
 analyses investigating the genetic variation and differential expression
 of defence-related genes in neighbourhoods may prove important. Synthesis.
 In summary, this research leverages recent advances in RNA sequencing and
 bioinformatics to conduct community-wide transcriptomic analyses and
 analyses of defence-related gene similarity across a tree community. The
 results demonstrate that defence gene similarity in neighbourhoods often
 does have negative effects on individual demographic performance as
 predicted by the Janzen–Connell hypothesis.
description: ComDataMatrix.20mThe community data matrix from the study with 20x20 quadrats as rows and species as columns.
DOI: 10.5061/dryad.76ks0
title: Data from: Does learning or instinct shape habitat selection?

description: Habitat selection is an important behavioural process widely studied for
 its population-level effects. Models of habitat selection are, however,
 often fit without a mechanistic consideration. Here, we investigated
 whether patterns in habitat selection result from instinct or learning for
 a population of grizzly bears (Ursus arctos) in Alberta, Canada. We found
 that habitat selection and relatedness were positively correlated in
 female bears during the fall season, with a trend in the spring, but not
 during any season for males. This suggests that habitat selection is a
 learned behaviour because males do not participate in parental care: a
 genetically predetermined behaviour (instinct) would have resulted in
 habitat selection and relatedness correlations for both sexes. Geographic
 distance and home range overlap among animals did not alter correlations
 indicating that dispersal and spatial autocorrelation had little effect on
 the observed trends. These results suggest that habitat selection in
 grizzly bears are partly learned from their mothers, which could have
 implications for the translocation of wildlife to novel environments.
description: Genotype
 dataIndividual ID, sex, and
 15 microsatellite lociBear_genotypes_working_AS.xlsx
DOI: 10.6084/m9.figshare.29115725
title: A survey of the occurrence and possible functions of low-amplitude songs in owls

description: Low-amplitude vocalisations have only recently begun to receive evolutionary attention, mainly in studies focused on diurnal birds. Owls, as nocturnal and forest-dwelling birds, seem promising for investigating the evolution of these signals, which may play an important role in short-range communication in low-light conditions. Here, we survey the occurrence of low-amplitude vocalisations in owls, combining a synthesis of bibliographic records with original acoustic analyses of audio recordings. We found low-amplitude vocalisations in 63 (25.6%) of all 246 owl species, including 31 species with low-amplitude territorial songs. Low-amplitude songs were typically emitted in response to territorial intrusion, and gradually transitioned into broadcast (high-amplitude) songs. We observed significant acoustic differences between these two song types, which could not be explained by bioacoustic trade-offs alone, suggesting the influence of social selection. We found no evidence that low-amplitude songs are aggressive signals in owls. A recently proposed ‘prospecting signal’ hypothesis, suggesting that low-amplitude songs serve to elicit a response from nearby but unseen rivals, seems compatible with our findings, and deserves further testing. Our study not only advances knowledge about low-amplitude singing in owls, but also proposes owls as a valuable model for further studies of low-amplitude signalling, offering suggestions for future experimental approaches.
DOI: 10.6084/m9.figshare.29115725.v1
title: A survey of the occurrence and possible functions of low-amplitude songs in owls

description: Low-amplitude vocalisations have only recently begun to receive evolutionary attention, mainly in studies focused on diurnal birds. Owls, as nocturnal and forest-dwelling birds, seem promising for investigating the evolution of these signals, which may play an important role in short-range communication in low-light conditions. Here, we survey the occurrence of low-amplitude vocalisations in owls, combining a synthesis of bibliographic records with original acoustic analyses of audio recordings. We found low-amplitude vocalisations in 63 (25.6%) of all 246 owl species, including 31 species with low-amplitude territorial songs. Low-amplitude songs were typically emitted in response to territorial intrusion, and gradually transitioned into broadcast (high-amplitude) songs. We observed significant acoustic differences between these two song types, which could not be explained by bioacoustic trade-offs alone, suggesting the influence of social selection. We found no evidence that low-amplitude songs are aggressive signals in owls. A recently proposed ‘prospecting signal’ hypothesis, suggesting that low-amplitude songs serve to elicit a response from nearby but unseen rivals, seems compatible with our findings, and deserves further testing. Our study not only advances knowledge about low-amplitude singing in owls, but also proposes owls as a valuable model for further studies of low-amplitude signalling, offering suggestions for future experimental approaches.
DOI: 10.6084/m9.figshare.29314468
title: Evaluating the influencers of acoustic indices in a zoo soundscape

description: Acoustic indices are promising tools for ecoacoustic studies and may be useful in zoos for passive acoustic monitoring of enclosures and their inhabitants. To validate their suitability for these applications, it is important to understand how different sounds in the environment affect them. Zoos have unique soundscapes with anthropogenic sounds such as human voices and mechanical noises often prevalent alongside high levels of animal-produced sounds; however, the influence of these sounds on acoustic indices in zoos has yet to be studied. This study investigates how different sound types recorded in aviaries at Chester Zoo in 2019 and 2020 affected three widely used acoustic indices: the Sonic Heterogeneity Index (SHI), the Acoustic Entropy Index (H), and the Normalised Difference Soundscape Index (NDSI). All three indices increased with avian vocalisations; H and SHI increased with human voices; only H increased with non-vocal anthropophonic sounds; SHI and NDSI increased with non-vocal biophonic sounds; and SHI increased but H decreased with the sound of wind. Because each index captures sound types in different ways, using all three in conjunction may provide researchers and practitioners with a more detailed understanding of the acoustic environments in zoos and other anthropogenically dominated environments.
DOI: 10.6084/m9.figshare.29314468.v1
title: Evaluating the influencers of acoustic indices in a zoo soundscape

description: Acoustic indices are promising tools for ecoacoustic studies and may be useful in zoos for passive acoustic monitoring of enclosures and their inhabitants. To validate their suitability for these applications, it is important to understand how different sounds in the environment affect them. Zoos have unique soundscapes with anthropogenic sounds such as human voices and mechanical noises often prevalent alongside high levels of animal-produced sounds; however, the influence of these sounds on acoustic indices in zoos has yet to be studied. This study investigates how different sound types recorded in aviaries at Chester Zoo in 2019 and 2020 affected three widely used acoustic indices: the Sonic Heterogeneity Index (SHI), the Acoustic Entropy Index (H), and the Normalised Difference Soundscape Index (NDSI). All three indices increased with avian vocalisations; H and SHI increased with human voices; only H increased with non-vocal anthropophonic sounds; SHI and NDSI increased with non-vocal biophonic sounds; and SHI increased but H decreased with the sound of wind. Because each index captures sound types in different ways, using all three in conjunction may provide researchers and practitioners with a more detailed understanding of the acoustic environments in zoos and other anthropogenically dominated environments.
DOI: 10.5061/dryad.sq633
title: Data from: Historic disturbance regimes promote tree diversity only under low browsing regimes in eastern deciduous forest

description: Eastern deciduous forests are changing in species composition and
 diversity outside of classical successional trajectories. Three
 disturbance mechanisms appear central to this phenomenon: fire frequency
 is reduced, canopy gaps are smaller, and browsers are more abundant. Which
 factor is most responsible is a matter of great debate and remains
 unclear, at least partly because few studies have simultaneously
 investigated more than one process. We conducted a large-scale experiment
 in mesophytic forests of West Virginia, USA, to test three key hypotheses:
 (1) the fire hypothesis (fire suppression limits diversity to few
 shade-tolerant, fire-intolerant species that replace and suppress many
 fire-tolerant species); (2) the gap hypothesis (small gaps typical of
 today's forests promote dominance of a few shade-tolerant species);
 and (3) the browsing hypothesis (overbrowsing by deer limits diversity to
 a few unpalatable species). We tested these hypotheses using a factorial
 experiment that manipulated surface fire, large canopy gap formation (gap
 size 255 m2), and browsing by deer, and we followed the fates of
 &gt;28 000 seedlings and saplings for five years. Understory tree
 communities in control plots were dominated (up to 90%) by Fagus
 grandifolia, averaging little more than two species, whereas overstories
 were diverse, with 10–15 species. Fire, large canopy gaps, and browsing
 all dramatically affected understory composition. However, our findings
 challenge views that fire and large canopy gaps can maintain or promote
 diversity, because browsers reduced the benefits of gaps and created
 depauperate understories following fire. Consequently, two major
 disturbances that once promoted tree diversity no longer do so because of
 browsing. Our findings appear to reconcile equivocal views on the role of
 fire and gaps. If browsers are abundant, these two disturbances either
 depress diversity or are less effective. Alternatively, with browsers
 absent, these disturbances promote diversity (three- to fivefold). Our
 results apply to large portions of eastern North America where deer are
 overabundant, and we provide compelling experimental evidence that
 historical disturbance regimes in combination with low browsing regimes
 typical of pre-European settlement forests could maintain high tree
 species diversity. However, restoring disturbances without controlling
 browsing may be counterproductive.
description: MWERF 2004
 SeedlingsSeedling data for Mead
 Westvaco Experimental Forest, collected 2004. Headings are MP = main plot
 (site or block), SP = subplot (experimental unit) SPEC = species (see
 species codes file), FIRE = fire trt, GAP = gap trt, DEER = deer trt,
 N_seedlings = number of seedlings per plot.MWERF 2004
 SaplingsSee MWERF 2004 Seedlings
 data for description of headingsSpecies
 ListSpecies codes for the
 other files
DOI: 10.5061/dryad.k78f6
title: Data from: Divergence in DNA photorepair efficiency among genotypes from contrasting UV radiation environments in nature

description: Populations of organisms routinely face abiotic selection pressures, and a
 central goal of evolutionary biology is to understand the mechanistic
 underpinnings of adaptive phenotypes. Ultraviolet radiation (UVR) is one
 of earth’s most pervasive environmental stressors, potentially damaging
 DNA in any organism exposed to solar radiation. We explored mechanisms
 underlying differential survival following UVR exposure in genotypes of
 the water flea Daphnia melanica derived from natural ponds of differing in
 UVR intensity. The UVR tolerance of a D. melanica genotype from a high-UVR
 habitat depended on the presence of visible and UV-A light wavelengths
 necessary for photoenzymatic repair of DNA damage, a repair pathway widely
 shared across the tree of life. We then measured the acquisition and
 repair of cyclobutane pyrimidine dimers, the primary form of UVR-caused
 DNA damage, in D. melanica DNA following experimental UVR exposure. We
 demonstrate that genotypes from high-UVR habitats repair DNA damage faster
 than genotypes from low-UVR habitats in the presence of visible and UV-A
 radiation necessary for photoenzymatic repair, but not in dark treatments.
 Because differences in repair rate only occurred in the presence of
 visible and UV-A radiation, we conclude that differing rates of DNA
 repair, and therefore differential UVR tolerance, are a consequence of
 variation in photoenzymatic repair efficiency. We then rule out a simple
 gene expression hypothesis for the molecular basis of differing repair
 efficiency, as expression of the CPD photolyase gene photorepair did not
 differ among D. melanica lineages, both in the presence and absence of
 UVR.
description: Source pond GPS
 coordinatesSource_pond_GPS_coordinates.txtSurvival_dataData shown in Fig. 1. Number of starting animals and number of surviving animals after UV-B exposure and subsequent exposure to photorepair radiation (light) or no radiation (dark).DNA damage dataData shown in Fig 2A & 2B, with statistical results shown in Table 1. Data are absorbance values from ELISA for cyclobutane pyrimidine dimers (CPDs) in DNA.DNA_damage_data.csvqPCR data for photorepair geneRaw Ct (cycle threshold) values from quantitative PCR, used to calculate relative expression values for photorepair gene shown in Fig. 3. Loci abbreviations are as follows: phr = photorepair, EF1A = elongation factor 1-alpha (reference gene), ATUB = alpha-tubulin (reference gene), G3PD = glyceraldegyde-3-phosphate dehydrogenase (reference gene)qPCR_for_photorepair_gene.csvDNA damage data (dark treatment)Data shown in Fig 2C. Data are absorbance values from ELISA for cyclobutane pyrimidine dimers (CPDs) in DNA.DNA_damage_dark_data.csvCarotenoid contentCarotenoid data shown in figure in Supporting Information.carotenoid_data.csv
DOI: 10.15468/dl.wfrsk6
title: Occurrence Download

description: A dataset containing 831 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Agarista salicifolia",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 831 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001187-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3n451
title: Data from: The role of neighborhood environment in promoting risk factors of cardiovascular disease among young adults: data from middle to high income population in an Asian megacity

description: Background: Modifiable risk factors of cardiovascular diseases (CVD) have
 their triggers in the neighborhood environments of communities. Studying
 the environmental triggers for CVD risk factors is important to understand
 the situation in a broader perspective. Young adults are influenced the
 most by the environment profile around them hence it is important to study
 this subset of the population. Methods: This was a descriptive study
 conducted using the EPOCH research tool designed by the authors of the
 PURE study. The study population consisted of young adults aged 18-25 in
 two areas of Karachi. The study setting was busy shopping malls frequented
 by young adults in the particular community being studied. Results: Our
 total sample size was 120 individuals, who consented to be interviewed by
 our interviewers. Less than 50% of the population recognized some form of
 restriction regarding smoking in their communities. The largest
 contributor to tobacco advertising was actors smoking in movies and TV
 shows with 89% responses from both communities. Only 11.9% of the
 individuals disapproved of smoking cigarettes among men with wide
 acceptance of ‘sheesha’ across all age groups. Advertising for smoking and
 junk food was more frequent as compared to smoking cessation, healthy diet
 and exercise in both the areas. Unhealthy food items were more easily
 available in contrast to healthier options. The cost of healthy snack food
 options including vegetables and fruits was higher than sugary drinks and
 foods. Conclusion: This assessment showed that both communities were
 exposed to environments that promote risk factors for cardiovascular
 diseases.
description: Raw Data for the study
 "The Role of Neighborhood Environment in Promoting Risk Factors of
 Cardiovascular Disease among Young Adults: Data from Middle to High Income
 Population in an Asian Megacity"The file includes values
 that were used for all statistical and qualitative analysis and
 tables.CVD
 Study.sav
DOI: 10.5061/dryad.7978
title: Data from: Rapid parallel evolution of aberrant traits in the diversification of the Gulf of Guinea white-eyes (Aves, Zosteropidae)

description: Archipelago-endemic bird radiations are familiar to evolutionary
 biologists as key illustrations of evolutionary patterns. However, such
 radiations are in fact rare events. White-eyes (Zosteropidae) are birds
 with an exceptionally high colonization and speciation potential; they
 have colonized more islands globally than any other passerine group and
 include the most species-rich bird genus. The multiplication of white-eye
 island-endemics has been consistently attributed to independent
 colonisations from the mainland; the white-eyes of the Gulf of Guinea
 archipelago had been seen as a classic case, spanning as great a breadth
 of phenotypic diversity as the family worldwide. Contrary to this
 hypothesis, our molecular phylogenetic analysis places the Gulf of Guinea
 white-eyes in just two radiations, one grouping all five oceanic island
 taxa and the other grouping continental island and land bridge taxa.
 Numerous ‘aberrant’ phenotypes (traditionally grouped in the genus
 Speirops) have evolved independently over a short space of time from
 non-aberrant (Zosterops) phenotypes; the most phenotypically divergent
 species have separated as recently as 0.22 Ma. These radiations rival
 those of Darwin’s finches and the Hawaiian honeycreepers in terms of the
 extent of adaptive radiation per unit time, both in terms of species
 numbers and phenotypic diversity. Tempo and patterns of morphological
 divergence are strongly supportive of an adaptive radiation in the oceanic
 islands driven by ecological interactions between sympatric white-eyes.
 Here, very rapid phenotypic evolution mainly affected taxa derived from
 the youngest wave of colonization, in accordance with the model of
 asymmetric divergence due to resource competition in sympatry.
description: Microsatellite
 genotyping of the Gulf of Guinea white-eyes and the Cape white-eye
 (Zosteropidae)Zosteropidae-Gulf of
 Guinea-microsatellites.txt
DOI: 10.5061/dryad.f8h7h
title: Data from: Paleobiology of the basal hydrochoerine Cardiomys Ameghino, 1885 (Rodentia, Caviomorpha, late Miocene, South America) as inferred from its postcranial anatomy

description: Extinct Hydrochoerinae traditionally included within “Cardiomyinae”
 (Cavioidea, Caviidae) are caviomorph rodents well-represented in the late
 Miocene-late Pliocene of Argentina, but their paleobiology has been
 investigated little. The postcranium of these rodents is poorly-known and
 has not been considered in morpho-functional or systematic studies. Here,
 we provide the first description of the postcranium of the basal
 hydrochoerine Cardiomys Ameghino, 1885, based on a well preserved specimen
 from the late Miocene of Central Argentina, and evaluate its
 paleobiological and systematic implications. A morpho-functional study and
 a character mapping analysis were performed. We concluded that most of its
 postcranial features are neither adaptations to a specialized
 cursoriality, as in some extant cavioids, nor major modifications
 associated with swimming, as in extant capybaras. Cardiomys exhibits
 several features (high humeral distal articular surface, perforated
 olecranon fossa, proximal radius cranially located with respect to the
 ulna, subrectangular-shaped radial head with flattened ulnar facet,
 calcaneocuboid joint distally located with respect to the
 astragalonavicular joint) that allow us to consider it as an ambulatory
 caviid. Among cavioids, some features of Cardiomys are more similar to
 those of Hydrochoerus Brisson, 1762 (lateral coronoid process reduced,
 humeral capitular tail well-differentiated, capitular tail facet of the
 radial head well-developed and relatively short craniodistally, plantar
 process of the navicular massive and short). Other postcranial features
 (relatively longer and more gracile Mt III and phalanges, straight caudal
 border of the ulna) suggest that Cardiomys would have been a generalized
 hydrochoerine, as was also indicated by its dental and cranial characters.
description: Candela et al.
 Supplemental Data 1Supplemental Data 1.-
 List of cavioid specimens examined.Candela et al.
 Supplemental Data 2Characters and character
 states definitionsCandela et al.
 Supplemental Data 3Data
 matrix