cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m905qfv2q
title: Conceptualizing relationships among hyporheic exchange, storage, and water age: data represented in published figures

description: Hyporheic exchange is a key driver of ecosystem processes in streams, yet
 stream ecologists often fail to leverage detailed conceptual models
 developed by engineers and hydrologists describing the relationship
 between water storage, water balance, and water age (time elapsed
 since a conceptual parcel of water entered the hyporheic zone) in
 hyporheic zones.  In a companion paper (G.C. Poole et al.
 Hyporheic Hydraulic Geometry: Conceptualizing relationships among
 hyporheic exchange, storage, and water age, published in PLoS ONE;
 doi:10.1371/journal.pone.0262080), we provide visualizations of these
 relationships in an effort to allow non-hydrologists to grasp four primary
 concepts along with associated research and management implications: 1)
 the rate of hyporheic exchange, size of the hyporheic zone, and hyporheic
 water age are inexorably linked; 2) such linkages can be leveraged to
 build understanding of hyporheic processes; 3) the age distribution of
 hyporheic water and hyporheic discharge is heavily skewed toward young
 water ages -- at any temporal scale of observation (minutes, hours, days,
 or months) older hyporheic water is rare relative to younger water; 4) the
 age distribution of water discharged from any hyporheic zone is not the
 same as the age distribution of water stored within that hyporheic zone.
 The data set presented here represents the numerical values represented by
 the figures published in the companion paper.
description: Data used to support "nautilus plots" in the companion
 paper were calculated using the equations described in the companion
 paper. Data describing the behavior of a conservative
 tracer in an annular flume were derived from a salt slug release into an
 experimental flume, as described in the companion paper.
 Data describing the relationship between hyporheic water
 temperature, water age, and day of year represent a synthetic data set
 built on relationships between hyporheic water age and temperature along
 an idealized hyporheic flow path using relationships described in: Helton
 AM, Poole GC, Payn RA, Izurieta C, Stanford JA. <em>Scaling flow
 pathprocesses to fluvial landscapes: An integrated field and model
 assessment of temperature and dissolved oxygen dynamics in a
 river-floodplain-aquifer system</em>. Journal of Geophysical
 Research: Biogeosciences. 2012;117(G4). doi:10.1029/2012JG002025. Data comparing stream temperature, mean temperature of aquifer discharge, and mean temperature of stored hyporheic water were calculated using equations published in the companion paper.
description: Beyond the README file associated with this dataset, all
 additional information necessary to interpret the dataset are found in the
 companion paper: G.C. Poole et al., <em>Hyporheic
 Hydr</em><em>au</em><em>lic Geometry:
 Conceptualizing relationships among hyporheic exchange, storage, and water
 age</em>. PLOS ONE.  doi:10.1371/journal.pone.0262080.
DOI: 10.5061/dryad.c866t1g89
title: Long evolutionary history of an emerging fungal pathogen of diverse tree species in eastern Asia, Australia, and the Pacific Islands

description: Emerging plant pathogens have been increasing exponentially over the last
 century. To address this issue, it is critical to determine whether these
 pathogens are native to ecosystems or have been recently introduced.
 Understanding the ecological and evolutionary processes fostering
 emergence can help to manage their spread and predict
 epidemics/epiphytotics. Using restriction site-associated DNA sequencing
 data, we studied genetic relationships, pathways of spread, and
 evolutionary history of Phellinus noxius, an emerging
 root-rotting fungus of unknown origin, in eastern Asia, Australia, and the
 Pacific Islands. We analyzed patterns of genetic variation using Bayesian
 inference, maximum likelihood phylogeny, populations splits and mixtures
 measuring correlations in allele frequencies and genetic drift, and
 finally applied coalescent based theory using Approximate Bayesian
 computation (ABC) with supervised machine learning. Population structure
 analyses revealed five genetic groups with signatures of complex recent
 and ancient migration histories. The most probable scenario of ancient
 pathogen spread is movement from an unsampled population
 to Malaysia and the Pacific Islands, with subsequent spread to Taiwan and
 Australia. Furthermore, ABC analyses indicate P.
 noxius spread occurred thousands of generations ago,
 contradicting previous assumptions that this pathogen was recently
 introduced to multiple geographic regions. Our results suggest that recent
 emergence of P. noxiusin eastern Asia, Australia, and the Pacific
 Islands is likely driven by anthropogenic and natural disturbances, such
 as deforestation, land-use change, severe weather events, and/or
 introduction of exotic plants. This study provides a novel example of
 applying genome-wide allele frequency data to unravel dynamics of pathogen
 emergence under changing ecosystem conditions.
description: The dataset contains three input files obtained from raw RADseq
 reads with Stacks v.2 to generate results in our paper. It also contains
 configuration files of five DIYABC analyses performed with DIYABC Random
 Forest v.1.
description: Users will need sequence data () and some knowledge of
 linux.
DOI: 10.25338/b8h93c
title: Seminatural habitat surrounding farms promotes multifunctionality in avian ecosystem services

description: Farmland birds can suppress insect pests, but may also consume beneficial
 insects, damage crops, and potentially carry foodborne pathogens. As bird
 communities shift in response to farming practices, so too do the benefits
 (services) and costs (disservices) from birds. Understanding how and why
 ecosystem services and disservices covary can inform management
 interventions that enhance synergies, avoid tradeoffs, and promote
 multifunctionality. We investigated how farmland diversification practices
 influence the services and disservices provided by wild birds on 21
 California strawberry farms. Specifically, we coupled 285 bird surveys,
 metabarcoding, and other molecular analyses of ~1,000 fecal samples
 representing 55 bird species (mostly passerines) to determine which
 individuals consumed pests, natural enemies, and crops and carried
 foodborne pathogens. Then, we explored how farming practices shape
 ecosystem service bundles, or suites of consistently co-occurring
 services/disservices. Avian services and disservices were shaped by
 interactions between local farming practices and landscape context. We
 found that the amount of seminatural habitat surrounding each farm was the
 single most important driver of ecosystem services, with the best outcomes
 (highest multifunctionality) occurring on farms surrounded by seminatural
 habitat. Bundles were primarily influenced by landscape context.
 Increasing seminatural habitat around farms was associated with more
 multifunctional bird communities that maximized services and minimized
 disservices. However, not all tradeoffs were minimized in landscapes with
 more seminatural habitat, suggesting that specific farming contexts can
 exacerbate or mitigate tradeoffs as bird communities shift in response to
 diversification practices. Synthesis and applications: Though growers are
 often pressured to remove noncrop habitat to reduce food-safety risks, our
 work suggests that conserving habitat can support bird conservation,
 mitigate food-safety risks, and decrease crop damage from birds. More
 broadly, by considering the multiple roles that communities play in
 ecosystems, managers can simultaneously maximize services and minimize
 disservices to achieve multifunctionality.
description: README file describes the metadata for each of the data sets
 contained in this Dryad collection pertaining to the manuscript:
 "Seminatural habitat surrounding farms promotes multifunctionality in
 avian ecosystem services." Please see the manuscript and supporting
 information for methods on how the data were collected, processed, and
 analyzed. Geographic coordinates of farm locations were withheld to
 protect farmer privacy.
DOI: 10.5061/dryad.dfn2z353d
title: Humanization of wildlife gut microbiota in urban environments

description: Urbanization is rapidly altering Earth’s environments, demanding
 investigations of the impacts on resident wildlife. Here, we show that
 urban populations of coyotes (Canis latrans) and crested anole lizards
 (Anolis cristatellus) acquire gut microbiota constituents found in humans,
 including the gut bacterial lineages most significantly associated with
 urbanization in humans (e.g., Bacteroides). Comparisons of urban and rural
 wildlife and human populations revealed significant convergence of the gut
 microbiota among urban host populations. Remarkably, all microbial
 lineages found in humans that were overrepresented in urban wildlife
 relative to rural wildlife were also overrepresented in urban humans
 relative to rural humans. These results indicate parallel effects of
 urbanization on human and wildlife gut microbiota and suggest spillover of
 bacteria from humans into wildlife in cities
DOI: 10.5061/dryad.wstqjq2nw
title: Relaxed selection and the evolution of Chasmogamous flower of Impatiens capensis

description: We exploited ecotypic variation in Impatiens capensis to
 test the hypothesis that mutation accumulation accompanying relaxed
 selection on the chasmogamous (CH) flower leads to more variable flower
 shapes and smaller flowers. Sun ecotype populations of this species occur
 along sunny riverbanks and marshes and produce both CH and cleistogamous
 (CL) flowers, while shade ecotype populations occur in shady forest floors
 and produce only CL flowers. In the shade ecotype, it is assumed that
 selection on the CH flower has been relaxed. Seedlings from population
 samples of the two ecotypes exhibited different first internode growth
 responses to low ratio of red:far-red light characteristic of ecotypic
 differentiation to either sunny or shady conditions, helping to verify
 historical illumination conditions in the populations. We examined the CH
 floral mutation accumulation hypothesis by comparing the shape and size of
 the modified CH flower sepal under greenhouse conditions that triggered CH
 flowering in plants of both ecotypes. Contrary to our predictions,
 geometric morphometric analysis of sepal shape variation levels indicated
 little difference between the shade and sun ecotypes. We suggest that
 mutations that influence CH flower shape may have pleiotropic effects on
 structures or processes that remain under selection even when the CH
 flowers are not produced. On the other hand, sepal size was significantly
 smaller in the shade ecotype populations. In the case of CH sepal size,
 the mutational effects appear to be directional, towards the production of
 smaller sepals, and likely would be deleterious if shade ecotype plants
 encountered sunnier conditions where CH flowers could be
 produced.  
description: Please refer to the Methods and Results section of the article
 and to the README file.  The data files submitted include landmark and
 semi-landmark data for the flower, growth response to red-far red and
 control treatments of plants from different populations, and maternal
 effects testing.
description: Please refer to the Methods and Results sections of the article,
 and the Read_Me.txt file uploaded with the individual data
 files.
DOI: 10.5061/dryad.rn8pk0pc4
title: RNA-seq_NPC_FNZ_Day0-Day5

description: NPCs were treated with FNZ, harvested in Day 0, 1, 3, 5, respectively.
 Then total RNA was extracted with TRIzol. Libraries were prepared
 using an Illumina TruSeq RNA Sample Prep kit (FC-122-1001, Illumina)
 following the manufacturer’s instruction. The RNA-seq experiment was
 performed at Annoroad Gene Technology Co. Ltd. (Beijing, China).
DOI: 10.5061/dryad.pzgmsbcnv
title: Host-driven subspeciation in hedgehog fungus, Trichophyton erinacei, an emerging cause of human dermatophytosis

description: Trichophyton erinacei is a main cause of dermatophytosis in hedgehogs and
 is increasingly reported from human infections worldwide. This pathogen
 was originally described in the European hedgehog (Erinaceus europaeus)
 but is also frequently found in the African four-toed hedgehog (Atelerix
 albiventris), a popular pet animal worldwide. Little is known about the
 taxonomy and population genetics of this pathogen despite its increasing
 importance in clinical practice. Notably, whether there are different
 populations or even cryptic species associated with different hosts or
 geographic regions is not known. To answer these questions, we collected
 161 isolates, performed phylogenetic and population-genetic analyses,
 determined mating-type, and characterised morphology and physiology.
 Multigene phylogeny and microsatellite analysis supported T. erinacei as a
 monophyletic species, in contrast to highly incongruent single-gene
 phylogenies. Two main subpopulations, one specific mainly to Atelerix and
 second to Erinaceus hosts, were identified inside T. erinacei, and slight
 differences in the size of microconidia and antifungal susceptibilities
 were observed among them. Although the process of speciation into two
 lineages is ongoing in T. erinacei, there is still gene flow between these
 populations. Thus, we present T. erinacei as a single species, with
 notable intraspecies variability in genotype and phenotype. The data from
 wild hedgehogs indicated that sexual reproduction in T. erinacei and de
 novo infection of hedgehogs from soil are probably rare events and that
 clonal horizontal spread strongly dominates. The molecular typing approach
 used in this study represents a suitable tool for further epidemiological
 surveillance of this emerging pathogen in both animals and humans. The
 results of this study also highlighted the need to use a multigene
 phylogeny ideally in combination with other independent molecular markers
 to understand the species boundaries of dermatophytes.
DOI: 10.5061/dryad.h9w0vt4k5
title: Bocage landscape restricts the gene flow of pest vole populations

description: The population dynamics of most animal species inhabiting agroecosystems
 may be determined by landscape characteristics, with agricultural
 intensification and reduction of natural habitats influencing dispersal
 patterns. Increasing landscape complexity would thus benefit endangered
 species by providing different ecological niches, but it could also lead
 to undesired effects in species that can act as crop pests and disease
 reservoirs. We tested the hypothesis that a highly variegated landscape
 influences the dispersal, and hence patterns of genetic structure, in
 agricultural pest voles. Ten populations of fossorial water vole, Arvicola
 scherman, located in a bocage landscape in Atlantic NW Spain were studied
 using DNA microsatellite markers and a graph-based model. The results
 showed a strong isolation-by-distance pattern with a strong and
 significant genetic correlation at smaller geographic scales, while
 genetic differentiation at larger geographic scales indicated a
 hierarchical pattern of up to eight genetic clusters. A
 metapopulation-type structure was observed, immersed in a landscape with a
 low proportion of suitable habitats. Matrix scale rather than matrix
 heterogeneity per se may have an important effect upon determining gene
 flow, acting as a demographic sink. The identification of sub-populations,
 considered to be independent management units, allows the establishment of
 feasible population control efforts in this area. These insights support
 the use of agro-ecological tools aimed at recreating enclosed field
 systems when planning integrated managements for controlling
 patch-dependent species such as grassland voles.
description: <i>G</i><i>raph-based landscape
 model</i>: Habitat patches were represented by polygons
 of soil occupancy with a 5 m<sup>2</sup> resolution, extracted
 from the Land Cover and Use Information System of Spain and analysed in a
 vector-based geographic information system (GIS). Soil-occupancy polygons
 were classified into nine categories: meadows, fruit orchards, pastures or
 grasslands, annual crops, shrubs, eucalyptus plantations, deciduous
 woodlots, settlements and roads and bodies of water.
 <i>Microsatellite genotyping: </i>PCR-amplification
 of 12 microsatellite loci was carried out in two multiplex panels: panel
 1: AV3, AV8, AV11, AV15, AT2 and AT24; and panel 2: AV12, AV14, AV13P,
 AT9, AT13 and AT22 (Stewart <i>et al</i>. 1999; Berthier
 <i>et al</i>. 2004, 2005). AV13 reverse microsatellite primer
 was labelled with a "pig-tail" to increase the accuracy of
 genotyping. Forward primers were labelled using FAM, NED, PET and VIC
 fluorochromes.
DOI: 10.5061/dryad.dncjsxm1c
title: Data from: Landscape genetics reveals contrasting patterns of connectivity in two newt species (Lissotriton montandoni and L. vulgaris)

description: Ecologically distinct species may respond to landscape changes in
 different ways. In addition to basic ecological data, the extent of the
 geographic range has been successfully used as an indicator of species
 sensitivity to anthropogenic landscapes, with widespread species usually
 found to be less sensitive compared to range-restricted species. In this
 study, we investigate connectivity patterns of two closely related but
 ecologically distinct newt species – the range-restricted, Lissotriton
 montandoni and the widespread, L. vulgaris – using genomic data, a highly
 replicated setting (six geographic regions per species), and tools from
 landscape genetics. Our results show the importance of forest for
 connectivity in both species, but at the same time suggest differential
 use of forested habitat, with L. montandoni and L. vulgaris showing the
 highest connectivity at forest-core and forest-edges, respectively.
 Anthropogenic landscapes (i.e., higher crop- or urban-cover) increased
 resistance in both species, but the effect was one to three orders of
 magnitude stronger in L. montandoni than in L. vulgaris. This result is
 consistent with a view of L. vulgaris as an ecological generalist. Even
 so, currently, the negative impact of anthropogenic landscapes is mainly
 seen in connectivity among L. vulgaris populations, which show
 significantly stronger isolation and lower effective sizes relative to L.
 montandoni. Overall, this study emphasizes how habitat destruction is
 compromising genetic connectivity not only in endemic, range-restricted
 species of conservation concern but also in widespread generalist species,
 despite their comparatively lower sensitivity to anthropogenic landscape
 changes.
description: See associated publication for details.
description: <em><strong>R_scripts_newts_connectivity</strong></em> This folder includes R scripts used for replicated <em>ResistanceGA</em> analyses, model transferability and visualization of results. Includes input necessary to run analyses: 1) Fst matrices; 2) Population coordinates; and 3) Rasters from landscape variables. For more details see associated publication and README file. <em><strong>Landscape_genetics_dataset</strong></em> Genomic data used for landscape genetic analyses in .vcf and .ped format (and associated .map). For more details see associated publication and README file. <em><strong>Ne_dataset</strong></em> Genomic data used for effective population size analyses in .vcf and .ped format (and associated .map). For more details see associated publication and README file.
DOI: 10.5061/dryad.5qfttdz72
title: Seasonal elevational patterns and the underlying mechanisms of avian diversity and community structure on the eastern slope of Mt. Gongga

description: This dataset contains bird survey data (Appedenix 2) and bird trait data
 (Appedenix 1) in the paper: “He et al. (2022) Seasonal elevational
 patterns and the underlying mechanisms of avian diversity and community
 structure on the eastern slope of Mt. Gongga. Diversity and
 Distributions”. Main results of the paper are that TD, PD and FD
 showed similar hump-shaped elevational patterns in both seasons. In the
 breeding season, TD, PD and FD for small-ranged species, were highly
 correlated with climatic factors (mean daily temperature, seasonal
 temperature range) and vegetation factors (enhanced vegetation index),
 while large-ranged species were correlated with spatial factors
 (mid-domain effect). In the non-breeding season, TD, PD and FD for all
 species groupings were positively correlated with climate factors. For
 small-ranged species in both seasons, community structure was more
 overdispersed at low and high elevations, and more clustered at middle
 elevations. For large-ranged species, community structure differed between
 seasons, showing a general trend toward clustering as elevations increase
 in the breeding season and trends toward overdispersion and/or evenness as
 elevations increase in the non-breeding season.
DOI: 10.5061/dryad.5qfttdz73
title: Abundance data of anuran species in forest fragments

description: Understanding the effects of random versus niche-based processes on
 biodiversity patterns is a central theme in ecology, and an important tool
 for predicting effects of habitat loss and fragmentation on biodiversity.
 We investigated the predictive power of random processes to explain
 species richness and species dissimilarity of amphibian assemblages in a
 fragmented tropical landscape of the Atlantic Forest of South America. We
 analyzed a large database of amphibian abundance and occupancy, sampled in
 21 forest fragments ranging in size from 1.9 to 619 ha. We compared
 observed species richness and species dissimilarity with the outcomes of
 two null (random placement) models: 1- the traditional Coleman’s
 area-based model and 2 – an abundance-based model (based on the number of
 individuals observed in each fragment). We applied these models for all
 species combined, and separately for forest‐dependent and
 habitat-generalist species. The abundance-based model fitted the observed
 species richness data better than the area-based model for all species,
 forest-dependent species, and generalist species. The area-based and the
 abundance-based models were also able to significantly explain species
 dissimilarity for all species and for generalists, but not for
 forest-dependent species. The traditional area-based model assigned too
 many individuals to large fragments, thus failing to accurately explain
 species richness within patches across the landscape. Although niche-based
 processes may be important to structuring the regional pool of species in
 fragmented landscapes, our results suggest that part of the variation in
 species richness and species dissimilarity can be successfully explained
 by random placement models, especially for generalist species. Evaluating
 which factors cause variation in the number of individuals among patches
 should be a focus in future studies aiming to understand biodiversity
 patterns in fragmented landscapes.
description: All species.xlsx file contains the area of each fragment (F1-F21)
 and the abundance of all frog species (N = 37) per fragment.<br>
 Forest-dependent species.xlsx file contains the area of each fragment
 (F1-F21) and the abundance of forest-dependent species (N = 14) per
 fragment.<br> Habitat-generalist species.xlsx file contains the area
 of each fragment (F1-F21) and the abundance of habitat-generalist species
 (N = 23) per fragment.
DOI: 10.25625/czcjcr
title: Meta data for "Neurodegenerative disease of the brain: a survey of interdisciplinary approaches"

description: This article is a comprehensive interdisciplinary review and as such does not contain original data.