cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31157041.v1
title: Appendix

description: This section of the appendices systematically presents the complete empirical data and analytical framework that support the conclusions of this paper. The research follows a multidimensional and systematic investigative approach, examining five key levels: the foundational evidence from literature, tourists' individual characteristics, the social environment, physical attributes, and other supplementary factors. Together, these provide a comprehensive exploration of the mechanisms influencing tourist experiences in historic commercial districts. The appendices are interconnected and progressively structured, forming a complete chain of evidence from literature review to empirical validation. This aims to offer solid data support and detailed insights for understanding and optimizing the cultural-tourism integration and scene creation in historic districts.
DOI: 10.5061/dryad.t281k
title: Data from: Long-distance dispersal suppresses introgression of local alleles during range expansions

description: During range expansions, even low levels of interbreeding can lead to
 massive introgression of local alleles into an invader's genome.
 Nonetheless, this pattern is not always observed in human populations. For
 instance, European Americans in North America are barely introgressed by
 Amerindian genes in spite of known contact and admixture. With coalescent
 spatially explicit simulations, we examined the impact of long-distance
 dispersal (LDD) events on introgression of local alleles into the invading
 population using a set of different demographic scenarios applicable to a
 diverse range of natural populations and species. More specifically, we
 consider two distinct LDD models: one where LDD events originate in the
 range core and targets only the expansion front and a second one where LDD
 events can occur from any area to any other. We find that LDD generally
 prevents introgression, but that LDD events specifically targeting the
 expansion front are most efficient in suppressing introgression. This is
 likely due to the fact that LDD allows for the presence of a larger number
 of invader alleles at the wave front, where effective population size is
 thus increased and local introgressed alleles are rapidly outnumbered. We
 postulate that the documented settlement of pioneers directly on the wave
 front in North America has contributed to low levels of Amerindian
 admixture observed in European Americans and that this phenomenon may well
 explain the lack of introgression after a range expansion in natural
 populations without the need to evoke other mechanisms such as natural
 selection.
description: Inputs and executables
 for simulationsInputs and executables
 for simulationsinputs.zip
DOI: 10.5061/dryad.kv462
title: Data from: Trial-results reporting and academic medical centers.

description: To the Editor: Reporting of aggregate results helps mitigate disclosure
 biases affecting medical research. Although the reporting of summary
 results is currently mandated by the Food and Drug Administration
 Amendments Act of 2007 (FDAAA), published findings suggest underreporting.
 Two recent proposals are aimed at improving public reporting of aggregate
 results. These are a Notice of Proposed Rulemaking (NPRM) to expand FDAAA
 requirements to include the results of trials of unapproved products, and
 a draft policy requiring the results of all National Institutes of Health
 (NIH)-funded trials, including those not subject to the FDAAA.
description: Zarin_Tse_Ross_2015_NEJM_Figure_1-ReadMeFigure 1 data from Zarin, Tse, Ross (2015; NEJM)Zarin_Tse_Ross_2015_NEJM_Figure_1.csv
DOI: 10.5061/dryad.sj578
title: Data from: The state of European research in tropical biology

description: Global North research institutions have significantly contributed to the
 knowledge of tropical ecosystems, but their commitment to biological
 research in the tropics differs enormously between individual countries.
 We show that European nations that share a language, cultural affinities
 and/or retain social and political links with tropical countries (i.e.
 have an overseas history) make a larger contribution to tropical
 biological research. However, exceptions to this pattern demonstrate how
 science policy agendas can skew the capacity of countries to conduct
 biological research in the tropics. We conclude that some countries could
 make a far more important contribution to tropical biological knowledge,
 but for this to materialize, greater commitment by a country’s scientific
 community is needed, along with better financial and intellectual support
 from its public administrations.
description: Table
 S1Country to whose
 institutions authors of papers belonged (A); total scientific production
 in tropical biology as number of returns for the text string “_tropic*’in
 ISI WoS (B); total scientific production under the ISI WoS category of
 ‘ecology and environmental science’ (C); total research and development
 (R&D) personnel (D); relative production in tropical biology (E); and
 ratio between tropical biological scientific production and number of
 researchers (F). Relative production in tropical biology is calculated as
 (B) divided by (C). The ratio between tropical biology scientific
 production and number of researchers is calculated as (B) divided by (D).
 Results are ordered in decreasing order of number of tropical papers
 (B).
DOI: 10.5061/dryad.db3q9t0
title: Data from: Cascading effects of forested area and isolation on seed dispersal effectiveness of rodents on subtropical islands

description: 1. Habitat loss and fragmentation often leads to defaunation of
 large-bodied mammals, and their loss could trigger release from top-down
 control or food resource competition for small mammal seed dispersers,
 which in turn may affect the effectiveness of seed dispersal by altering
 the number of dispersed seeds or the manner in which they are dispersed.
 Although rodents are primary seed dispersers in habitat subjected to
 defaunation, changes in seed dispersal effectiveness of rodents along
 mammalian defaunation gradients, and empirical support for mechanisms
 underlying alteration of this ecological process, are unclear. 2. We
 assessed the direct and indirect effects of forested area and isolation on
 seed dispersal effectiveness of rodents on 21 study islands with varying
 levels of defaunation in the Thousand Island Lake, China. We used camera
 sampling, live traps, and semi-quantitative acorn counts to assess
 occurrence of large-bodied mammal species, relative abundance of small
 rodent species, and seed crop size, respectively. Seed dispersal,
 post-dispersal seed survival, seedling emergence, and seedling survival
 were estimated by tracking fates of tagged acorns and by planting acorns
 in exclosures. 3. Forested area had positive indirect effects on seed
 dispersal effectiveness through defaunation and rodent competition for
 acorns, whereas isolation had negative direct and weaker positive indirect
 effects on seed dispersal effectiveness mediated by loss of large-bodied
 mammals and rodent competition for acorns. Loss of large-bodied mammals
 negatively affected seed dispersal effectiveness indirectly by virtue of
 its impact on rodent competition for acorns. Seed dispersal effectiveness
 exhibited a unimodal relationship with intensity of rodent competition for
 acorns, peaking at intermediate levels. 4. Synthesis. Indirect effects of
 island attributes mediated by defaunation of large-bodied mammals on small
 or isolated islands appear to drive altered competition for food among
 rodents and decreased seed dispersal effectiveness. Altered interactions
 between acorns and their rodent consumers/dispersers can substantially
 affect oak population demography in the Thousand Island Lake system. More
 broadly our findings highlight the importance to the seed dispersal
 process of multiple interwoven effects between habitat fragmentation and
 defaunation of large-bodied mammals.
description: Seed dispersal
 effectiveness on islandsThis dataset included
 the islands mark(mark), defaunation index (D), rodent competition for
 acorns (CRA) and SDE on each study islands as well as islands
 attributessde.xlsx
DOI: 10.5061/dryad.dk73qp7
title: Data from: Functional connectivity and home range inferred at a microgeographic landscape genetics scale in a desert-dwelling rodent

description: Gene flow in animals is limited or facilitated by different features
 within the landscape matrix they inhabit. The landscape representation in
 landscape genetics (LG) is traditionally modeled as resistance surfaces
 (RS), where novel optimization approaches are needed for assigning
 resistance values that adequately avoid subjectivity. Also, desert
 ecosystems and mammals are scarcely represented in LG studies We addressed
 these issues by evaluating, at a microgeographic scale, the effect of
 landscape features on functional connectivity of the desert-dwelling
 Dipodomys merriami. We characterized genetic diversity and structure with
 microsatellites loci, estimated home ranges and movement of individuals
 using telemetry –one of the first with rodents–, generated a set of
 individual and composite environmental surfaces based on hypotheses of
 variables influencing movement, and assessed how these variables relate to
 individual-based gene flow. Genetic diversity and structure results
 evidenced a family-induced pattern driven by first-order related
 individuals, notably determining landscape genetic inferences. The
 vegetation cover and soil resistance optimized surface (NDVI) was the
 best-supported model and a significant predictor of individual genetic
 distance, followed by humidity and NDVI+humidity. Based on an accurate
 definition of thematic resolution we also showed that vegetation is better
 represented as continuously (versus categorically) distributed. Hence,
 with a non-subjective optimization framework for RS and telemetry, we were
 able to describe that vegetation cover, soil texture, and climatic
 variables influence D. merriami’s functional connectivity at a
 microgeographic scale, patterns we could further explain based on the home
 range, habitat use, and activity observed between sexes. We describe the
 relationship between environmental features and some aspects of D.
 merriami‘s behavior and physiology.
description: D. merriami
 genotypesMicrosatellites loci
 genotypes for the entire database (76 individuals)Flores-Manzanero_et_Dme-genotypes (76).csvFlores-Manzanero_et_DmeNR-genotypes(59)Microsatellites loci genotypes for the non-related individuals (59 )
DOI: 10.5061/dryad.g1t3680
title: Data from: Modelling landscape connectivity for greater horseshoe bat using an empirical quantification of resistance

description: 1. Habitat fragmentation and isolation as a result of human activities
 have been recognized as great threats to population viability. Evaluating
 landscape connectivity in order to identify and protect linkages has
 therefore become a key challenge in applied ecology and conservation. 2.
 One useful approach to evaluate connectivity is Least-Cost Path (LCP)
 analysis. However, several studies have highlighted importance of
 parameterization with empirical, biologically-relevant proxies of factors
 affecting movements, as well as the need to validate the LCP model with an
 independent dataset. 3. We used LCP analysis incorporating quantitative,
 empirical data about behaviour of the greater horseshoe bat Rhinolophus
 ferrumequinum to build up a model of functional connectivity in relation
 to landscape connecting features. We then validated the accumulated costs
 surface from the LCP model with two independent datasets; one at an
 individual level with radio tracking data and one at a population level
 with acoustic data. 4. When defining resistance, we found that the
 probability of bat presence in a hedgerow is higher when the distance
 between hedgerows is below 38 m, and decrease rapidly when gaps are larger
 than 50 m. The LCP model was validated by both datasets: the independent
 acoustic data showed that the probability of bat presence was
 significantly higher in areas with lower accumulated costs, and the radio
 tracking data showed that foraging was more likely in areas where
 accumulated costs were significantly lower. Synthesis and applications.
 Through our modelling approach, we recommend a maximum of 38m (and no more
 than 50m) between connecting features around colonies of greater horseshoe
 bats. Our quantitative study highlights the value of this framework for
 conservation: results are directly applicable in the field and the
 framework can be applied to other species sensitive to habitat loss,
 including other bats. Provided that it is parameterized with empirical,
 biologically-relevant data, this modelling approach can be used for
 restoring and evaluating green networks in agri-environmental schemes and
 management plans.20-Jun-2018
description: Pinaud2018_GapCrossingHorseshoeBat2016_ModellingAndValidationSynthesis of acoustic data (presence or absence of Greater Horseshoe Bat Rhinolophus ferrumequinum) for gap-crossing probability modelling and validation of the accumulated cost model. Data from the publication, Title: Modelling landscape connectivity for greater horseshoe bat using an empirical quantification of resistance, Authors: Pinaud, David; Claireau, Fabien; Leuchtmann, Maxime; Kerbiriou, Christian, Journal: Journal of Applied Ecology (2018)
DOI: 10.5061/dryad.pn7t4
title: Data from: microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate

description: Hagfish and lampreys are the only living representatives of the jawless
 vertebrates (agnathans), and compared with jawed vertebrates
 (gnathostomes), they provide insight into the embryology, genomics, and
 body plan of the ancestral vertebrate. However, this insight has been
 obscured by controversy over their interrelationships. Morphological
 cladistic analyses have identified lampreys and gnathostomes as closest
 relatives, whereas molecular phylogenetic studies recover a monophyletic
 Cyclostomata (hagfish and lampreys as closest relatives). Here, we show
 through deep sequencing of small RNA libraries, coupled with genomic
 surveys, that Cyclostomata is monophyletic: hagfish and lampreys share 4
 unique microRNA families, 15 unique paralogues of more primitive microRNA
 families, and 22 unique substitutions to the mature gene products.
 Reanalysis of morphological data reveals that support for cyclostome
 paraphyly was based largely on incorrect character coding, and a revised
 dataset is not decisive on the mono- vs. paraphyly of cyclostomes.
 Furthermore, we show fundamental conservation of microRNA expression
 patterns among lamprey, hagfish, and gnathostome organs, implying that the
 role of microRNAs within specific organs is coincident with their
 appearance within the genome and is conserved through time. Together,
 these data support the monophyly of cyclostomes and suggest that the last
 common ancestor of all living vertebrates was a more complex organism than
 conventionally accepted by comparative morphologists and developmental
 biologists.
description: Phenotype cladistic
 matrixCladistic matrix based
 on phenotypic charactersHLG_matrix_revision_submitted.txtmicroRNA cladistic character matrixCladistic character matrix for the repertoire of microRNAs in the taxa considered in the analysismiRNA_nexus.txt
DOI: 10.5061/dryad.50d1t3p
title: Data from: Predictive power of food web models based on body size decreases with trophic complexity

description: Food web models parameterized using body size show promise to predict
 trophic Interaction Strengths (IS) and abundance dynamics. However, this
 remains to be rigorously tested in food webs beyond simple trophic
 modules, where indirect and intraguild interactions could be important and
 driven by traits other than body size. We systematically varied predator
 body size, guild composition and richness in microcosm insect webs and
 compared experimental outcomes with predictions of IS from models with
 allometrically scaled parameters. Body size was a strong predictor of IS
 in simple modules (r2=0.92), but with increasing complexity the predictive
 power decreased, with model IS being consistently overestimated. We
 quantify the strength of observed trophic interaction modifications,
 partition this into density-mediated vs. behaviour-mediated indirect
 effects and show that model shortcomings in predicting IS is related to
 the size of behaviour-mediated effects. Our findings encourage development
 of dynamical food web models explicitly including and exploring indirect
 mechanisms.
description: Experimental data of
 microcosm food webExperimental data on
 number of individuals in different predator treatments of microcosm food
 web, used to analyze the predictive power of body size based ATN food web
 model.Jonssonetal_EL2018_Expdata.csv
DOI: 10.5061/dryad.cd1sf
title: Data from: Male courtship decisions are influenced by light environment and female receptivity

description: The appearance of animal colour signals depends jointly upon the ambient
 light spectrum and the signal's reflectance spectra. Light
 environment heterogeneity might, therefore, allow individuals to enhance
 their signal by signalling in an environment that increases signal
 efficacy. We tested this hypothesis by providing male guppies (Poecilia
 reticulata), a choice of three light environments in which to display
 their colour signal to females: green, lilac, and clear. We paired males
 with both receptive and non-receptive females to test whether female
 response might affect male behavioural decisions. Males preferred the
 clear environment in all trials and this environment also resulted in
 males having the highest average visual contrast. Sexual behaviour was
 influenced by complex interactions between female receptivity, light
 environment, and male colour pattern contrast. Males spent significantly
 more time in the environment in which their colour signal had the highest
 contrast, but only when paired with receptive females. Significant
 interactions between light environment and individual male colour
 components were also seen only in receptive trials. Our results suggest
 that males use light environment to enhance their colour pattern, but only
 in the presence of receptive females.
description: Data summary
 DryadSpreadsheet containing
 contrast measures and behavioural data.
DOI: 10.5061/dryad.b4s20
title: Data from: Cooperative breeding shapes post-fledging survival in an Afrotropical forest bird

description: While avian group living typically accrues multiple benefits, it is yet
 unknown how these benefits manifest post- fledging. Here, by using an
 indirect radio- telemetry approach, we found that cooperation increases
 fledgling survival in an Afrotropical forest bird. This result indicates
 the importance of considering the full breeding cycle in cooperative
 breeding research, which may ultimately lead to a better understanding of
 evolutionary drivers of cooperation.
description: CMR data juvenile Placid
 Greenbul - Van de Loock et al. 2017 Ecol&EvolResighting dataset of
 juvenile Placid greenbuls since fledging (day 1). Collected at Taita
 Hills, SE Kenya using an indirect radio-telemetry approach by tagging and
 relocating the breeding female.CMR data_Van de Loock et al.
 2017 Ecol&Evol.csvCovariate data juvenile
 Placid Greenbul - Van de Loock et al. 2017 Ecol&EvolCovariate data used in
 analysis on juvenile mortality of Placid greenbuls. Collected at Taita
 Hills, SE Kenya.Covariate data_Van de Loock et
 al. 2017 Ecol&Evol.csv
DOI: 10.5061/dryad.c699f
title: Data from: Ecological niche modeling for a cultivated plant species: a case study on taro (Colocasia esculenta) in Hawai‘i

description: Under the threat of ongoing and projected climate change, communities in
 the Pacific Islands face challenges of adapting culture and lifestyle to
 accommodate a changing landscape. Few models can effectively predict how
 biocultural livelihoods might be impacted. Here, we examine how
 environmental and anthropogenic factors influence an ecological niche
 model (ENM) for the realized niche of cultivated taro (Colocasia
 esculenta) in Hawai‘i. We created and tuned two sets of ENMs: one using
 only environmental variables, and one using both environmental and
 cultural characteristics of Hawa‘i. These models were projected under two
 different Intergovernmental Panel on Climate Change (IPCC) Representative
 Concentration Pathways (RCPs) for 2070. Models were selected and evaluated
 using average omission rate and area under the receiver operating
 characteristic curve (AUC). We compared optimal model predictions by
 comparing the percentage of taro plots predicted present and measured ENM
 overlap using Schoener’s D-statistic. The model including only
 environmental variables consisted of 19 Worldclim bioclimatic variables,
 in addition to slope, altitude, distance to perennial streams, soil
 evaporation, and soil moisture. The optimal model with environmental
 variables plus anthropogenic features also included a road density
 variable (which we assumed as a proxy for urbanization) and a variable
 indicating agricultural lands of importance to the State of Hawai‘i. The
 model including anthropogenic features performed better than the
 environment-only model based on omission rate, AUC, and review of spatial
 projections. The two models also differed in spatial projections for taro
 under anticipated future climate change. Our results demonstrate how ENMs
 including anthropogenic features can predict which areas might be best
 suited to plant cultivated species in the future, and how these areas
 could change under various climate projections. These predictions might
 inform biocultural conservation priorities and initiatives. In addition,
 we discuss the incongruences that arise when traditional ENM theory is
 applied to species whose distribution has been significantly impacted by
 human intervention, particularly at a local scale relevant to biocultural
 conservation initiatives.
description: Kodis_ENMScript_FinalThis code shows how to retrieve and prepare data for an ecological niche model and then use that data to tune and create a Maxent model with present and future projections.
DOI: 10.5061/dryad.11m00
title: Data from: Shrub encroachment can reverse desertification in semi-arid Mediterranean grasslands

description: The worldwide phenomenon of shrub encroachment in grass-dominated dryland
 ecosystems is commonly associated with desertification. Studies of the
 purported desertification effects associated with shrub encroachment are
 often restricted to relatively few study areas, and document a narrow
 range of possible impacts upon biota and ecosystem processes. We conducted
 a study in degraded Mediterranean grasslands dominated by Stipa
 tenacissima to simultaneously evaluate the effects of shrub encroachment
 on the structure and composition of multiple biotic community components,
 and on various indicators of ecosystem function. Shrub encroachment
 enhanced vascular plant richness, biomass of fungi, actinomycetes and
 other bacteria, and was linked with greater soil fertility and N
 mineralization rates. While shrub encroachment may be a widespread
 phenomenon in drylands, an interpretation that this is an expression of
 desertification is not universal. Our results suggest that shrub
 establishment may be an important step in the reversal of desertification
 processes in the Mediterranean region.
description: Environmental and soil
 data from encroached/unencroached Stipa tenacissima steppes from
 SpainEnvironmental
 (coordinates, elevation, slope, aspect, mean annual rainfall and
 temperature) and soil (pH, organic carbon, total nitrogen, total
 phosphorus, soil respiration, potassium and nitrogen mineralization)
 variables at the microsite and site scales for Stipa tenacissima
 grasslands with and without sprouting shrubs in a gradient from central to
 southern Spain.Ecol_Lett_2009.zip