cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5m582
title: Data from: The role of livestock intensification and landscape structure in maintaining tropical biodiversity

description: 1. As tropical cattle ranching continues to expand, successful
 conservation will require an improved understanding of the relative
 impacts of different livestock systems and landscape structure on
 biodiversity. Here, we provide the first empirical and multi-scale
 assessment of the relative effects of livestock intensification and
 landscape structure on biodiversity in the threatened tropical dry forests
 of Mesoamerica. 2. We used a dataset of dung beetles (169 372 individuals
 from 33 species) collected from twenty 1-km2 landscapes, ranging from
 zero-yielding forest sites to high-yield cattle ranches and maize farms,
 to investigate the relative effect of livestock intensification (net
 cattle production; macrocyclic lactone use; annual dung production) and
 landscape structure (landscape composition and configuration) at multiple
 spatial scales on different attributes of dung beetle communities using a
 multi-model averaging approach. 3. Dung beetle species richness, biomass
 and composition were more strongly related to landscape structure than to
 livestock intensification. 4. Forest cover was the best predictor of dung
 beetle assemblages, being positively related to species diversity and
 biomass across multiple spatial scales. The use of macrocyclic lactones
 was strong and negatively related to dung beetle communities at the local
 scale. 5. Synthesis and applications: Maximizing forest protection through
 a ‘land sparing’ strategy is therefore likely to be the best strategy for
 reducing the negative impacts of cattle farming on Neotropical dung beetle
 communities. However, increasing or maintaining yields whilst reducing
 agrochemical inputs will be important for conserving on-farm biodiversity
 and the ecosystem services that dung beetles provide in
 livestock-dominated landscapes.31-May-2017
description: The role of livestock
 intensification and landscape structure in maintaining tropical
 biodiversityIncluded original data
 information (collected in the field, analyzed with satellite imagery and
 statistical modeling. We also shows a description of abbrevations
 mentioned in Alvarado et al. (2017) JAEData_Alvarado et
 al_JAE.xlsx
DOI: 10.5061/dryad.rg155q32
title: Data from: Insects on plants: explaining the paradox of low diversity within specialist herbivore guilds

description: Classical niche theory explains the coexistence of species through their
 exploitation of different resources. Assemblages of herbivores coexisting
 on a particular plant species are thus expected to be dominated by species
 from host-specific guilds with narrow, coexistence-facilitating niches,
 rather than by species from generalist guilds. Exactly the opposite
 pattern is observed for folivores feeding on trees in New Guinea. The
 least specialized mobile chewers were most species-rich, followed by the
 moderately specialized semi-concealed and exposed chewers. The highly
 specialized miners and mesophyll suckers were the least species-rich
 guilds. The Poisson distribution of herbivore species richness among plant
 species in specialized guilds and the absence of a negative correlation
 between species richness in different guilds on the same plant species
 suggest that these guilds are not saturated with species. We show that
 herbivore assemblages are enriched with generalists because they are more
 completely sampled from regional species pools. The herbivore diversity
 increases as a power function of plant diversity, and the rate of increase
 is inversely related to their host-specificity. The relative species
 diversity among guilds is thus scale-dependent, as the importance of
 specialized guilds increases with plant diversity. Specialized insect
 guilds may therefore comprise a larger component of overall diversity in
 the tropics (where they are also poorly known taxonomically) than in the
 temperate zone, which has lower plant diversity.
description: NovotnyEtAl2011DryadDataThis is the plant x herbivore data matrix for 38 woody plant species from a lowland rainforest in Papua New Guinea and their folivorous insect herbivores. The herbivores were sampled from 1,500 m2 of foliage area for each plant species. The matrix includes the number of individuals of each herbivore species on each plant species, except for singleton records (i.e., combinations of a particular herbivore species feeding on a particular plant species supported by only a single individual) which were excluded. All records in the matrix are feeding records, verified either by rearing of larvae or no-choice feeding experiments for adults. Each herbivore species is denoted by a species code, identified as far as possible, and assigned to its feeding guild. The number of individuals (ni.) and the number of host plant species (pi) are reported for each species. These are original data obtained by research in the field. This data set is associated with the paper Insects on Plants: Explaining the Paradox of Low Diversity within Specialist Herbivore Guilds by V. Novotny, S. E. Miller, J. Hrcek, L. Baje, Y. Basset, O. T. Lewis, A. J. A. Stewart and G. D. Weiblen published in the American Naturalist. This paper includes the definition of each herbivore guild, phylogeny of the plant species, and the information on the depositories of the plant and insect vouchers documenting the data.
DOI: 10.5061/dryad.7cj42
title: Data from: Rates of fitness decline and rebound suggest pervasive epistasis

description: Unraveling the factors that determine the rate of adaptation is a major
 question in evolutionary biology. One key parameter is the effect of a new
 mutation on fitness, which invariably depends on the environment and
 genetic background. The fate of a mutation also depends on population
 size, which determines the amount of drift it will experience. Here, we
 manipulate both population size and genotype composition and follow
 adaptation of 23 distinct Escherichia coli genotypes. These have
 previously accumulated mutations under intense genetic drift and encompass
 a substantial fitness variation. A simple rule is uncovered: the net
 fitness change is negatively correlated with the fitness of the genotype
 in which new mutations appear—a signature of epistasis. We find that
 Fisher's geometrical model can account for the observed patterns of
 fitness change and infer the parameters of this model that best fit the
 data, using Approximate Bayesian Computation. We estimate a genomic
 mutation rate of 0.01 per generation for fitness altering mutations,
 albeit with a large confidence interval, a mean fitness effect of
 mutations of −0.01, and an effective number of traits nine in mutS− E.
 coli. This framework can be extended to confront a broader range of models
 with data and test different classes of fitness landscape models.
description: Data from: Rates of
 fitness decline and rebound suggest pervasive epistasisThe data relative of
 Figures 1 and 2, collected by experimental competitive fitness assays in
 laboratory rich mediumPerfeitoSousaBataillonGordoData.rtf
DOI: 10.5061/dryad.q49p6d8
title: Data from: Factors associated with first- versus second-generation long-acting antipsychotics prescribed under ordinary clinical practice in Italy

description: Background. For many years, long-acting intramuscular (LAI) antipsychotics
 have been prescribed predominantly to chronic and severe patients, as a
 last resort when other treatments failed. Recently, a broader and earlier
 use of LAIs, particularly second-generation LAIs, has been emphasized. To
 date, few studies attempted to frame how this change in prescribing took
 place in real-world practice. Therefore, this study aimed to describe the
 clinical features of patients prescribed with LAIs, and to explore
 possible prescribing differences between first- and second-generations
 LAIs under ordinary clinical practice in Italy. Methods. The STAR Network
 "Depot" Study is an observational, longitudinal, multicenter
 study involving 35 centers in Italy. In the cross-sectional phase,
 patients prescribed with LAIs were consecutively recruited and assessed
 over a period of 12 months. Descriptive statistics and multivariable
 logistic regression analyses were employed. Results. Of the 451 recruited
 patients, 61% were males. The level of social and working functioning was
 heterogeneous, as was the severity of disease. Seventy-two per cent of the
 patients had a diagnosis of the schizophrenia spectrum. Seventy per cent
 was prescribed with second-generation antipsychotic (SGA) LAIs (mostly
 paliperidone, aripiprazole and risperidone). Compared to first-generation
 antipsychotic (FGA) LAIs, patients prescribed with SGA LAIs were more
 often younger; employed; with a diagnosis of the schizophrenia spectrum or
 bipolar disorder; with higher levels of affective symptoms; with fewer LAI
 prescriptions in the past. Discussion. LAIs' prescribing practices
 appear to be more flexible as compared to the past, although this change
 is mostly restricted to SGA LAIs.
description: database STAR network
 depot studyThis dataset reports
 socio-demographic and clinical data from a cohort of 451 patients
 beginning a long-acting antipsychotic medication. Patients were recruited
 in 35 Italian Community Psychiatric Services between December 2015 and May
 2017. All variables and codes are explained in a legend within the excel
 file, with the exception of some masked variables.
DOI: 10.5061/dryad.44bm6
title: Data from: The relative contribution of species richness and species composition to ecosystem functioning

description: The influence of species diversity on ecosystem functioning has been the
 subject of many experiments and remains a key question for ecology and
 conservation biology. However, the fact that diversity cannot be
 manipulated without affecting species composition makes this quest
 methodologically challenging. We used partial Mantel tests to evaluate the
 relative importance of diversity and of composition on biomass production.
 Here, we applied partial Mantel tests (controlling for the other variable)
 on two datasets, the Jena (2002–2008) and the Grandcour (2008–2009)
 Experiment. In both experiments, plots were sown with different numbers of
 species to unravel mechanisms underlying the biodiversity-ecosystem
 functioning relationships. Contrary to Jena, plots were not mowed nor
 weeded in Grandcour, allowing external species to establish. Based on the
 diversity–ecosystem functioning and competition theories, we tested two
 predictions: 1) the contribution of composition should increase with time;
 2) the contribution of composition should be more important in non-weeded
 than in controlled systems. We found support for the second hypothesis,
 but not for the first. On the contrary, the contribution of species
 richness became markedly more important few years after the start of the
 Jena Experiment. This result can be interpreted as species
 complementarity, rather than intraspecific competition, being the driving
 force in this system. Finally, we explored to what extent the estimated
 relative importance of both factors could vary when measured on different
 spatial scales of the experiment (in our case, increasing the number of
 plots included in the analyses). We found a strong effect of scale,
 suggesting that comparisons between studies, and more generally the
 extrapolation of results from experiments to natural situations, should be
 made with caution.
description: Grandcour Wildflower
 strip vegetation dataThe first datasheet
 contains the metadata explaining the abbreviations in the main datasheet.
 It contains information about species richness, above-ground biomass and
 species cover, that was visually estimated.BB_all_4_SimilMatrices_Dryad.xlsx
DOI: 10.5061/dryad.86n98
title: Data from: Prey state shapes the effects of temporal variation in predation risk

description: The ecological impacts of predation risk are influenced by how prey
 allocate foraging effort across periods of safety and danger. Foraging
 decisions depend on current danger, but also on the larger temporal,
 spatial or energetic context in which prey manage their risks of predation
 and starvation. Using a rocky intertidal food chain, we examined the
 responses of starved and fed prey (Nucella lapillus dogwhelks) to
 different temporal patterns of risk from predatory crabs (Carcinus
 maenas). Prey foraging activity declined during periods of danger, but as
 dangerous periods became longer, prey state altered the magnitude of risk
 effects on prey foraging and growth, with likely consequences for
 community structure (trait-mediated indirect effects on basal resources,
 Mytilus edulis mussels), prey fitness and trophic energy transfer. Because
 risk is inherently variable over time and space, our results suggest that
 non-consumptive predator effects may be most pronounced in productive
 systems where prey can build energy reserves during periods of safety and
 then burn these reserves as ‘trophic heat’ during extended periods of
 danger. Understanding the interaction between behavioural (energy gain)
 and physiological (energy use) responses to risk may illuminate the
 context dependency of trait-mediated trophic cascades and help explain
 variation in food chain length.
description: All
 datamatassa&trussell_1-7.zip contains 7 consecutively numbered csv files which contain all of the data presented in the manuscript and its appendicesmatassa&trussell_1-7.zip
DOI: 10.5061/dryad.j5c2j
title: Data from: Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny.

description: Classically, the mitochondrial genome is sequenced by a series of
 amplicons using conserved PCR primers. Here we show how shot-gun
 transcriptome sequencing can be used to obtain the complete set of
 protein-coding genes from the mtDNA of four passerine bird species. With
 these sequences, we address the still unresolved basal Passerida
 relationships (Aves: Passeriformes). Our analysis suggests a new
 hypothesis for the basal relationships of Passerida, namely a clade
 grouping Sylvioidea and Passeroidea, with Paridae and Muscicapidae as
 successive sister groups to this clade. This study demonstrates the
 usefulness of next-generation sequencing transcriptome sequencing for
 obtaining new mtDNA genomes.
description: Aligned and unaligned
 sequences use for phylogenetics analysesThe gene folder contains
 three type of files : 1) The *.fst files are unaligned nucleotides
 sequences 2) The *.mafft.fst are aligned amino-acid sequences 3) The
 *_base.fst are aligned nucleotides sequences corvusBrachyrhynchos,
 parusCaeruleus, manacusVitellinus, ficedulaHypoleuca sequences were
 obtained from brain transcriptome sequencing (see Nabholz B, Jarvis ED,
 Ellegren H. 2010. Obtaining mtDNA genomes from next-generation
 transcriptome sequencing: a case study on the basal Passerida (Aves:
 Passeriformes) phylogeny. Mol. Phylogenet. Evol.
 57:466–470)gene.zip
DOI: 10.5061/dryad.3c2hm
title: Data from: Feeding ecology and habitat preferences of top predators from two Miocene carnivore-rich assemblages

description: Carnivoran-rich fossil sites are uncommon in the fossil record and,
 accordingly, provide valuable opportunities to study predators from
 vantages that are rarely applied to ancient faunas. Through stable
 isotopes of carbon and a Bayesian mixing model, we analyze time-successive
 (nearly contemporaneous), late Miocene carnivoran populations from two
 fossil sites (Batallones-1 and Batallones-3) from central Spain. Stable
 isotopes of carbon in tooth enamel provide a reliable and direct
 methodology to track ancient diets. These two carnivoran-dominated fossil
 sites display differences in the composition and abundance of the
 carnivoran species, with some species present at both sites and some
 present only in one site. This disparity has been interpreted as the
 consequence of habitat differences between Batallones-1, the older site,
 and Batallones-3, the younger site. However, carbon isotope values of
 carnivore and herbivore tooth enamel suggest a common habitat of C3
 woodland originally present at both sites. The differences in the
 carnivoran faunas may be rather the consequence of the dynamics of species
 entrance and exit from the Madrid Basin during the time elapsed between
 Batallones-1 and Batallones-3 and changes in population densities due to
 biotic factors. We infer higher levels of interspecific competition in
 Batallones-3 than in Batallones -1, because of the larger number of
 similar-sized, sympatric predators, the clear overlap in their δ13C values
 (except for the amphicyonid Magericyon anceps), and similarity of their
 preferred prey: the hipparionine horses. Finally, carbon stable isotopic
 composition of Indarctos arctoides teeth implies that this ursid was a
 carnivorous omnivore rather than a herbivorous omnivore. This work
 demonstrates the insights that stable isotopes can provide in
 characterizing the feeding ecology and trophic interactions of ancient
 carnivoran taxa.
description: Supplementary Table
 1Supplementary Table
 2Supplementary Table
 3
DOI: 10.5061/dryad.m75g2
title: Data from: Lincoln estimates of mallard (Anas platyrhynchos) abundance in North America

description: Estimates of range-wide abundance, harvest, and harvest rate are
 fundamental for sound inferences about the role of exploitation in the
 dynamics of free-ranging wildlife populations, but reliability of existing
 survey methods for abundance estimation is rarely assessed using
 alternative approaches. North American mallard populations have been
 surveyed each spring since 1955 using internationally coordinated aerial
 surveys, but population size can also be estimated with Lincoln's
 method using banding and harvest data. We estimated late summer population
 size of adult and juvenile male and female mallards in western,
 midcontinent, and eastern North America using Lincoln's method of
 dividing (i) total estimated harvest, H, by estimated harvest rate, h,
 calculated as (ii) direct band recovery rate, f, divided by the (iii) band
 reporting rate, p. Our goal was to compare estimates based on
 Lincoln's method with traditional estimates based on aerial surveys.
 Lincoln estimates of adult males and females alive in the period
 June–September were 4.0 (range: 2.5–5.9), 1.8 (range: 0.6–3.0), and 1.8
 (range: 1.3–2.7) times larger than respective aerial survey estimates for
 the western, midcontinent, and eastern mallard populations, and the two
 population estimates were only modestly correlated with each other
 (western: r = 0.70, 1993–2011; midcontinent: r = 0.54, 1961–2011; eastern:
 r = 0.50, 1993–2011). Higher Lincoln estimates are predictable given that
 the geographic scope of inference from Lincoln estimates is the entire
 population range, whereas sampling frames for aerial surveys are
 incomplete. Although each estimation method has a number of important
 potential biases, our review suggests that underestimation of total
 population size by aerial surveys is the most likely explanation. In
 addition to providing measures of total abundance, Lincoln's method
 provides estimates of fecundity and population sex ratio and could be used
 in integrated population models to provide greater insights about
 population dynamics and management of North American mallards and most
 other harvested species.
description: Data from Lincoln
 estimates of mallard abundance in North AmericaMicrosoft Excel *.xlsx
 file
DOI: 10.5061/dryad.kk65m
title: Data from: The static allometry of sexual and non-sexual traits in vervet monkeys

description: Sexual traits vary tremendously in static allometry. This variation may be
 explained in part by body size-related differences in the strength of
 selection. We tested this hypothesis in two populations of vervet monkeys,
 using estimates of the level of condition dependence for different
 morphological traits as a proxy for body size-related variation in the
 strength of selection. In support of the hypothesis, we found that the
 steepness of allometric slopes increased with the level of condition
 dependence. One trait of particular interest, the penis, had shallow
 allometric slopes and low levels of condition dependence, in agreement
 with one of the most consistent patterns yet detected in the study of
 allometry, namely that of genitalia exhibiting shallow allometries.
description: Rodriguez etal BJLS
 vervet allometry dataComplete data set from
 which allometry was characterizedRodriguez et al BJLS
 vervet allometry trait typesAllometric slopes and
 condition dependence values by trait category
DOI: 10.5061/dryad.232ss
title: Data from: Grazing exclusion unleashes competitive plant responses in Iberian Atlantic mountain grasslands

description: Questions: Does the absence of equalizing mechanisms after cessation of
 grazing unleash strong aboveground competitors to create large patches in
 the community? Do these competitive intraspecific aggregations displace
 and exclude other species, thereby reducing species diversity? Location:
 Atlantic grasslands in the Aralar Natural Park, Basque Country, Northern
 Iberian Peninsula. Methods: Large herbivores were experimentally excluded
 from three sites (50 m × 50 m exclusion fences) during nine years in a
 productive semi-natural grassland system with long history of grazing,
 using adjacent grazed plots as experimental controls. Sampling was carried
 out by placing systematically one hundred quadrats (0.5 m × 0.5 m) in each
 of the six plots. Floristic composition and abundance, as well as eight
 hydrological and chemical soil properties, were measured in each quadrat.
 The spatial structures created by competitive species were analysed using
 Redundancy analysis in conjunction with Moran's Eigenvector Maps, and
 soil variables were simultaneously included in the analyses, thus
 disentangling the structures likely created by niche effects. Competitive
 exclusion was further determined using linear regressions between species
 richness and abundance of competitive species. Results: Grazing exclusion
 unleashed competitive species such as Festuca rubra and Agrostis
 capillaris, which became dominant in the exclusion plots and created large
 spatial patches. Furthermore, a negative linear relationship, consistent
 across exclusion plots, was observed between species richness and
 abundance of competitive species, indicating that strong aboveground
 competitors outcompeted other species when herbivores were excluded.
 However, the outcome of grazing exclusion across sites depended to some
 extent on local environmental conditions (niche effects). Conclusions:
 This work confirms that the powerful equalizing mechanism of disturbance
 by herbivores is crucial for species co-existence in productive
 grasslands. However, important differences observed in environmental
 effects across sites suggest that, even in highly productive grasslands,
 plant traits and local environmental characteristics (niche effects) do
 matter for species co-existence.
description: Aralar.datasetFine-scale floristic composition and soil descriptors in three sites of Aralar Natural Park (northern Iberian Peninsula).