cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fj4f2
title: Data from: Long-term impacts of variable retention harvesting on ground-layer plant communities in Pinus resinosa forests

description: Concerns about loss of biodiversity and structural complexity in managed
 forests have recently increased and led to the development of new
 management strategies focused on restoring or maintaining ecosystem
 functions while also providing wood outputs. Variable Retention Harvest
 (VRH) systems, in which mature overstorey trees are retained in various
 spatial arrangements across harvested areas, represent one potential
 approach to this problem. However, long-term evaluations of the
 effectiveness of this strategy at sustaining plant community composition
 are needed as this strategy is increasingly applied in managed forest
 landscapes throughout the world. The forest ground layer plays a central
 role in forest ecosystem functioning and we evaluated the long-term (11+
 year) dynamics in ground-layer plant communities in response to VRH study
 in Pinus resinosa Aiton. forests. This large-scale, manipulative study
 included four overstorey (control, small gap-aggregated, large
 gap-aggregated and dispersed) and two understorey (ambient and reduced
 shrubs) treatments replicated four times in 16 ha stands. Changes in
 ground-layer community composition were apparent 11 years following
 harvest, regardless of live-tree retention pattern. Richness and diversity
 increased and were driven by introduction and colonization of ruderal
 species, while forest interior species continued to persist across
 treatments. All life-forms responded positively to harvest with the
 exception of moss and clubmoss species. The lack of effect of spatial
 pattern of retention on ground-layer plant communities was likely related
 to the presence of a dense and persistent shrub layer, a result of decades
 of fire suppression. In particular, the greatest responses to overstorey
 retention pattern occurred in areas receiving shrub reduction treatments,
 indicating this recalcitrant layer likely filtered response to retention
 pattern. Synthesis and applications. Overall, this work highlights
 flexibility in choosing a Variable Retention Harvest (VRH) approach when
 sustaining ground-layer plant community diversity and composition are
 goals, but altered disturbance regimes (e.g. fire suppression, timber
 harvesting) that have facilitated the presence or formation of
 recalcitrant understories, need to be considered. The legacy effects of
 historical land use and alterations to natural disturbance regimes on the
 understorey in northern temperate forests are of equal, if not greater
 importance to overstorey retention patterns, in eliciting desired
 responses to VRH and need to be more carefully considered in future
 applications of this method.
description: Long-term impacts of
 variable retention harvesting on ground-layer plant communities in Pinus
 resinosa forests. Roberts, D'Amato, Kern, Palik.
DOI: 10.5061/dryad.1838
title: Data from: Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes

description: The 30 living species of armadillos, anteaters, and sloths (Mammalia:
 Xenarthra) represent one of the three major clades of placentals.
 Armadillos (Cingulata: Dasypodidae) are the earliest and most speciose
 xenarthran lineage with 21 described species. The question of their tricky
 phylogeny was here studied by adding two mitochondrial genes (NADH
 dehydrogenase subunit 1 [ND1] and 12S ribosomal RNA [12S rRNA]) to the
 three protein-coding nuclear genes (α2B adrenergic receptor [ADRA2B],
 breast cancer susceptibility exon 11 [BRCA1], and von Willebrand factor
 exon 28 [VWF]) yielding a total of 6869 aligned nucleotide sites for
 thirteen xenarthran species. The two mitochondrial genes were
 characterized by marked excesses of transitions over transversions—with a
 strong bias toward CT transitions for the 12S rRNA—and exhibited two- to
 fivefold faster evolutionary rates than the fastest nuclear gene (ADRA2B).
 Maximum likelihood and Bayesian phylogenetic analyses supported the
 monophyly of Dasypodinae, Tolypeutinae, and Euphractinae, with the latter
 two armadillo subfamilies strongly clustering together. Conflicting
 branching points between individual genes involved relationships within
 the subfamilies Tolypeutinae and Euphractinae. Owing to a greater number
 of informative sites, the overall concatenation favored the mitochondrial
 topology with the classical grouping of Cabassous and Priodontes within
 Tolypeutinae, and a close relationship between Euphractus and
 Chaetophractus within Euphractinae. However, low statistical support
 values associated with almost equal distributions of apomorphies among
 alternatives suggested that two parallel events of rapid speciation
 occurred within these two armadillo subfamilies.
description: Delsuc2003MolPhyloGenetEvol.nexDelsuc2003MolPhyloGenetEvol.tredelsuc2003molphylogenetevolphy.tre
DOI: 10.5061/dryad.hn4tn
title: Data from: Contrasting reproductive strategies of triploid hybrid males in vertebrate mating systems

description: The scarcity of parthenogenetic vertebrates is often attributed to their
 ‘inferior’ mode of clonal reproduction, which restricts them to
 self-reproduce their own genotype lineage and leaves little evolutionary
 potential with regard to speciation and evolution of sexual reproduction.
 Here, we show that for some taxa such uniformity does not hold. By using
 hybridogenetic water frogs (Pelophylax esculentus) as a model system, we
 demonstrate that triploid hybrid males from two geographic regions exhibit
 very different reproductive modes. With an integrative data set combining
 field studies, crossing experiments, flow cytometry and microsatellite
 analyses, we found that triploid hybrids from Central Europe are rare,
 occur in male sex only and form diploid gametes of a single clonal
 lineage. In contrast, triploid hybrids from North Western Europe are
 widespread, occur in both sexes and produce recombined haploid gametes.
 These differences translate into contrasting reproductive roles between
 regions. In Central Europe, triploid hybrid males sexually parasitize
 diploid hybrids and just perpetuate their own genotype – which is the
 usual pattern in parthenogens. In North Western Europe, on the other hand,
 the triploid males are gamete donors for diploid hybrids, thereby
 stabilizing the mixed 2n-3n hybrid populations. By demonstrating these
 contrasting roles in male reproduction, we draw attention to a new
 significant evolutionary potential for animals with non-sexual
 reproduction, namely reproductive plasticity.
description: DNA microsatelitte
 allele data setDNA microsatelitte data
 file for the 16 loci used in the study (RlCA5 and Res16 were not used for
 any of the analyses). (txt tabulated format)PruvostEtAlJEBSupp1.txt
DOI: 10.5061/dryad.jf6ht
title: Data from: Theropod forelimb design and evolution

description: We examined the relationship between forelimb design and function across
 the 230-million-year history of theropod evolution. Forelimb disparity was
 assessed by plotting the relative contributions of the three main limb
 elements on a ternary diagram. Theropods were divided into five functional
 groups: predatory, reduced, flying, wing-propelled diving, and flighdess.
 Forelimbs which maintained their primitive function, predation, are
 similarly proportioned, but non-avian theropods with highly reduced
 forelimbs have relatively longer humeri. Despite the dramatically
 different forces imparted by the evolution of flight, forelimb proportions
 of basal birds are only slighdy different from those of their non-avian
 relatives. An increase in disparity accompanied the subsequent radiation
 of birds. Each transition to flightlessness has been accompanied by an
 increase in relative humeral length, which results from relatively short
 distal limb elements. We introduce theoretical predictions based on five
 biomechanical and developmental factors that may have influenced the
 evolution of theropod limb proportions.
description: Neornithes Limb
 MeasurementsTab-delimited text file
 with Neornithine limb measurements. Sources are given in the
 file.Neornithes_Limb_Measurements.txtNon-Neornithes Limb MeasurementsTab-delimited text file with non-Neornithine limb measurements. Sources are given in the file.Non-Neornithes_Limb_Measurements.txt
DOI: 10.5061/dryad.6fq63
title: Data from: Divergent habitat use of two urban lizard species

description: Faunal responses to anthropogenic habitat modification represent an
 important aspect of global change. In Puerto Rico, two species of arboreal
 lizard, Anolis cristatellus and A. stratulus, are commonly encountered in
 urban areas, yet seem to use the urban habitat in different ways. In this
 study, we quantified differences in habitat use between these two species
 in an urban setting. For each species, we measured habitat use and
 preference, and the niche space of each taxon, with respect to manmade
 features of the urban environment. To measure niche space of these species
 in an urban environment, we collected data from a total of six urban sites
 across four different municipalities on the island of Puerto Rico. We
 quantified relative abundance of both species, their habitat use, and the
 available habitat in the environment to measure both microhabitat
 preference in an urban setting, as well as niche partitioning between the
 two different lizards. Overall, we found that the two species utilize
 different portions of the urban habitat. Anolis stratulus tends to use
 more “natural” portions of the urban environment (i.e., trees and other
 cultivated vegetation), whereas A. cristatellus more frequently uses
 anthropogenic structures. We also found that aspects of habitat
 discrimination in urban areas mirror a pattern measured in prior studies
 for forested sites in which A. stratulus was found to perch higher than A.
 cristatellus and preferred lower temperatures and greater canopy cover. In
 our study, we found that the multivariate niche space occupied by A.
 stratulus did not differ from the available niche space in natural
 portions of the urban environment and in turn represented a subset of the
 niche space occupied by A. cristatellus. The unique niche space occupied
 by A. cristatellus corresponds to manmade aspects of the urban environment
 generally not utilized by A. stratulus. Our results demonstrate that some
 species are merely tolerant of urbanization while others utilize urban
 habitats in novel ways. This finding has implications for long-term
 persistence in urban habitats and suggests that loss of natural habitat
 elements may lead to nonrandom species extirpations as urbanization
 intensifies.
description: Winchell_etal_urbanhabitatuse_JEE17Habitat data from Winchell et al. "Divergent Habitat Use of Two Urban Lizard Species".
DOI: 10.5061/dryad.5fm52
title: Data from: Quantifying individual heterogeneity and its influence on life-history trajectories: different methods for different questions and contexts

description: Heterogeneity among individuals influences the life-history trajectories
 we observe at the population level because viability selection, selective
 immigration and emigration processes, and ontogeny change the proportion
 of individuals with specific trait values with increasing age. Here, we
 review the two main approaches that have been proposed to account for
 these processes in life-history trajectories, contrasting how they
 quantify ontogeny and selection, and proposing ways to overcome some of
 their limitations. Nearly all existing approaches to model individual
 heterogeneity assume either a single normal distribution or a priori known
 groups of individuals. Ontogenetic processes, however, can vary across
 individuals through variation in life-history tactics. We show the
 usefulness of describing ontogenetic processes by modelling trajectories
 with a mixture model that focuses on heterogeneity in life-history
 tactics. Additionally, most methods examine individual heterogeneity in a
 single trait, ignoring potential correlations among multiple traits caused
 by latent common sources of individual heterogeneity. We illustrate the
 value of using a joint modelling approach to assess the presence of a
 shared latent correlation and its influence on life-history trajectories.
 We contrast the strengths and limitations of different methods for
 different research questions, and we exemplify the differences among
 methods using empirical data from long-term studies of ungulates.
description: all_datasetsSee readme file
DOI: 10.15468/dl.nzqzcy
title: Occurrence Download

description: A dataset containing 581 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Potentilla nivea"
 ]
}

 The dataset includes 581 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000894-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6rn29
title: Data from: Slowing them down will make them lose: a role for attine ant crop fungus in defending pupae against infections?

description: Fungus-growing ants (Attini) have evolved an obligate dependency upon a
 basidiomycete fungus that they cultivate as their food. Less well known is
 that the crop fungus is also used by many attine species to cover their
 eggs, larvae and pupae. The adaptive functional significance of this brood
 covering is poorly understood. One hypothesis to account for this
 behaviour is that it is part of the pathogen protection portfolio when
 many thousands of sister workers live in close proximity and larvae and
 pupae are not protected by cells, as in bees and wasps, and are immobile.
 We performed behavioural observations on brood covering in the
 leaf-cutting ant Acromyrmex echinatior and we experimentally manipulated
 mycelial cover on pupae and exposed them to the entomopathogenic fungus
 Metarhizium brunneum to test for a role in pathogen resistance. Our
 results show that active mycelial brood covering by workers is a
 behaviourally plastic trait that varies temporally, and across life stages
 and castes. The presence of a fungal cover on the pupae reduced the rate
 at which conidia appeared and the percentage of pupal surface that
 produced pathogen spores, compared to pupae that had fungal cover
 experimentally removed or naturally had no mycelial cover. Infected pupae
 with mycelium had higher survival rates than infected pupae without the
 cover, although this depended upon the time at which adult sister workers
 were allowed to interact with pupae. Finally, workers employed higher
 rates of metapleural gland grooming to infected pupae without mycelium
 than to infected pupae with mycelium. Our results imply that mycelial
 brood covering may play a significant role in suppressing the growth and
 subsequent spread of disease, thus adding a novel layer of protection to
 their defence portfolio.
description: Raw
 dataThe file contains raw
 data from the behavioural and fungal exposure experiments. Each worksheet
 is labelled with the corresponding experiment and more information about
 the raw data is given at the top of each worksheet.Armitage et al raw data for
 Dryad.xlsx
DOI: 10.5061/dryad.76670
title: Data from: Patterns of local adaptation in space and time among soil bacteria

description: Our understanding of microbial biogeography has been governed by the
 dictum “Everything is everywhere, but the environment selects.” In other
 words, the distribution of microbes is thought to occur in a regime of
 extensive dispersal and strong selection, generating local adaptation.
 However, direct tests of these assumptions are rare. Here, we investigate
 the extent of local adaptation in space and time of a collection of
 soil-derived microbial isolates, most belonging to the genus Pseudomonas,
 across a growing season from a deciduous forest in western Quebec, Canada,
 using a reciprocal transplant design. Average performance of all clones
 varied substantially in both space and time, in line with the expectation
 of strong selection in both dimensions. The behavior of
 genotype-by-environment variance in fitness and its components,
 responsiveness and inconsistency, in space and through time suggests that
 the strength of divergent selection increases as sites become more distant
 from each other in both dimensions. However, divergent selection was not
 strong enough to maintain different specialized types across the
 environments studied, which suggests that Pseudomonas and their close
 relatives are not locally adapted to the prevailing conditions of growth.
description: Supplemental Table 1:
 Haplotype of IsolatesSupp_Table1.docxSupp_Table2Supplemental Table 2: Average ODs of negative control wells and fraction of control wells with an OD &gt; 0.1 for each 96 well plate assessed.Supp_Table3: Model fitting: detailed modelsSupp_Table3.xlsxSupp_Table4Supplemental Table 4: Coefficients for each haplotype-by-spatial distance interaction, the corresponding p-value and the significance level
DOI: 10.5061/dryad.0cq3rm5
title: Data from: A four-questions perspective on public information use in sticklebacks (Gasterosteidae)

description: Whether learning primarily reflects general processes or species-specific
 challenges is a longstanding matter of dispute. Here we present a
 comprehensive analysis of public information use (PI-use) in sticklebacks
 (Gasterosteidae). PI-use is a form of social learning by which animals are
 able to assess the relative quality of resources, here prey patches, by
 observing the behaviour of others. PI-use was highly species-specific with
 only two of the assayed species, Pungitius spp. and their closest relative
 Culaea inconstans showing evidence of PI-use. We saw no effects of
 ontogenetic experience upon PI-use in P. pungitius. Experiments with live
 demonstrators and animated fish revealed that heightened activity and
 feeding strikes by foraging conspecifics are important cues in the
 transmission of PI. Finally, PI-use was the only form of learning in which
 P. pungitius and another stickleback, Gasterosteus aculeatus differed.
 PI-use in sticklebacks is species-specific and may represent an
 ‘ecological specialisation’ for social foraging. Whether this reflects
 selection on perception, attentional or cognitive processes remains to be
 determined.
description: Data from Webster et al.
 PI-use 4Qs approach RSOSData from the article:
 'A Four-Questions Perspective on Public Information Use in
 Sticklebacks (Gasterosteidae)' by Webster et al.
DOI: 10.15468/dl.t7atta
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Deprea parviflora",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 28 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000895-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1rk60
title: Data from: Quantifying crowd size with mobile phone and Twitter data

description: Being able to infer the number of people in a specific area is of extreme
 importance for the avoidance of crowd disasters and to facilitate
 emergency evacuations. Here, using a football stadium and an airport as
 case studies, we present evidence of a strong relationship between the
 number of people in restricted areas and activity recorded by mobile phone
 providers and the online service Twitter. Our findings suggest that data
 generated through our interactions with mobile phone networks and the
 Internet may allow us to gain valuable measurements of the current state
 of society.
description: Datasets for Quantifying
 Crowd Size for Mobile Phone and Twitter DataData.zip
DOI: 10.5061/dryad.t6v47p1
title: Data from: Pollinator-mediated mechanisms for increased reproductive success in early flowering plants

description: Mating activities change within a season in many animal and plant
 populations. In plants, selection towards early flowering is commonly
 observed. Pollinator-mediated selection is hypothesized to be a pervasive
 evolutionary force acting directionally on flowering time. However,
 pollinator-mediated mechanisms have rarely been tested in realistic field
 conditions, especially in perennial plants visited by a diversity of
 generalist insect pollinators. We examined pollinator visitation in eight
 Echinacea angustifolia populations in western Minnesota, USA, to gauge the
 potential for pollinator-mediated selection. Echinacea is a common prairie
 perennial that persists in isolated remnant populations. Echinacea is
 self-incompatible and is pollinated by a diversity of generalist solitary
 bees. A previous study found that early flowering Echinacea plants have
 higher seed set and their reproduction is less pollen-limited than late
 flowering plants. Twelve times throughout a flowering season, we
 quantified pollinator visitation rates and pollinator community
 composition. In three sites, we also estimated the quality of pollinator
 visits by examining the composition of pollinators’ pollen loads brought
 to Echinacea plants. We found that three aspects of pollination
 dramatically decreased over the course of the flowering season. (1)
 Pollinators visited early flowering plants more frequently than late
 flowering plants. (2) The pollinator community was also less diverse late
 in the flowering season and became dominated by a single species of small
 bee, Augochlorella aurata. (3) Pollinators visiting Echinacea late in the
 season carried proportionally less conspecific pollen compared to
 pollinators visiting Echinacea early in the flowering season.
 Understanding within-season dynamics of pollination helps predict the
 prevalence of inbreeding, phenological assortative mating, and
 reproductive failure, especially in fragmented plant populations.
description: IsonPrescottEtAl_Data&ScriptsThis folder includes 4 data files, 3 metadata files, and 4 R scripts.