cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7d2hm
title: Data from: Contrasting patterns of genome-wide polymorphism in the native and invasive range of the marine mollusk Crepidula fornicata

description: Selection processes are believed to be an important evolutionary driver
 behind the successful establishment of non-indigenous species, however
 evidence is still scarce. Genome-scans have often identified loci with
 atypical patterns of genetic differentiation (i.e. outliers) indicative of
 selection processes. Using microsatellite- and AFLP-based genome-scans, we
 looked for evidence of post-introduction selection in the mollusk
 Crepidula fornicata, native from the northwestern Atlantic and introduced
 in the northeastern Atlantic and northeastern Pacific during the 19th and
 20th centuries. We examined 683 individuals from 7 native and 15
 introduced populations spanning the latitudinal introduction and native
 ranges of the species. Our results showed the high genetic diversity in
 all populations with little genetic structure between the two ranges, a
 pattern typical of marine invaders. Analyzing 344 loci, no outliers were
 detected between introduced and native populations or within introduced
 populations. The genomic sampling may have been insufficient to reveal
 selection especially if it acts on traits determined by a few genes. Eight
 outliers were however identified within the native range, underlining a
 genetic singularity congruent with a well-known biogeographic break along
 the Florida. Our results call into question the relevance of AFLP
 genome-scans in detecting adaptation on the time-scale of biological
 invasions: genome-scans often reveal long-term adaptation involving
 numerous genes throughout the genome but seem less effective in detecting
 recent adaptation from pre-existing variation on polygenic traits. This
 study advocates other methods to detect selection effects during
 biological invasions – on phenotypic traits, although genome-scans may
 remain useful for elucidating introduction histories.
description: MEC-12-0950
DOI: 10.5061/dryad.88rb5
title: Data from: Once-daily long-acting beta-agonists for chronic obstructive pulmonary disease: an indirect comparison of olodaterol and indacaterol

description: Purpose: In the absence of head-to-head clinical trials comparing the
 once-daily, long-acting beta2-agonists olodaterol and indacaterol for the
 treatment of chronic obstructive pulmonary disease (COPD), an indirect
 treatment comparison by systematic review and synthesis of the available
 clinical evidence was conducted. Methods: A systematic literature review
 of randomized, controlled clinical trials in patients with COPD was
 performed to evaluate the efficacy and safety of olodaterol and
 indacaterol. Network meta-analysis and adjusted indirect comparison
 methods were employed to evaluate treatment efficacy, using outcomes based
 on trough forced expiratory volume in 1 second (FEV1), Transition Dyspnea
 Index, St George’s Respiratory Questionnaire total score and response,
 rescue medication use, and proportion of patients with exacerbations.
 Results: Eighteen trials were identified for meta-analysis (eight,
 olodaterol; ten, indacaterol). Olodaterol trials included patients of all
 severities, whilst indacaterol trials excluded patients with very severe
 COPD. Concomitant maintenance bronchodilator use was allowed in most
 olodaterol trials, but not in indacaterol trials. When similarly designed
 trials/data were analyzed for change from baseline in trough FEV1
 (liters), the following mean differences (95% confidence interval) were
 observed: trials excluding concomitant bronchodilator: indacaterol 75 mcg
 versus olodaterol 5 mcg, –0.005 (–0.077 to 0.067), and indacaterol 150 mcg
 versus olodaterol 5 mcg, 0.020 (–0.036 to 0.077); trials with concomitant
 tiotropium: indacaterol 150 mcg versus olodaterol 5 mcg, 0.000 (–0.043 to
 0.042). In sensitivity analyses of the full network, results for change
 from baseline in trough FEV1 favored indacaterol, but this dataset
 suffered from trial design heterogeneity. For the other endpoints
 investigated, no statistically significant differences were found when
 analyzed in the full network. Conclusion: When compared under similar
 trial conditions, olodaterol and indacaterol have similar efficacy in
 patients with COPD. This research highlights the importance of considering
 the concomitant COPD medication when evaluating treatment effects in COPD.
description: Supplemental Material:
 Once-daily long-acting beta-agonists for chronic obstructive pulmonary
 disease: an indirect comparison of olodaterol and
 indacaterolIndirect Comparison of
 Olodaterol and Indacaterol. Supplemental Material: Roskell et al. Int J
 Chron Obstruct Pulmon Dis. 2014.MTC_Olodaterol_Manuscript_Supplement.pdf
DOI: 10.5061/dryad.m2dk7
title: Data from: Neandertal and Denisovan DNA from Pleistocene sediments

description: Although a rich record of Pleistocene human-associated archaeological
 assemblages exists, the scarcity of hominin fossils often impedes the
 understanding of which hominins occupied a site. Using targeted enrichment
 of mitochondrial DNA we show that cave sediments represent a rich source
 of ancient mammalian DNA that often includes traces of hominin DNA, even
 at sites and in layers where no hominin remains have been discovered. By
 automation-assisted screening of numerous sediment samples we detect
 Neandertal DNA in eight archaeological layers from four caves in Eurasia.
 In Denisova Cave we retrieved Denisovan DNA in a Middle Pleistocene layer
 near the bottom of the stratigraphy. Our work opens the possibility to
 detect the presence of hominin groups at sites and in areas where no
 skeletal remains are found.
description: Multiple sequence
 alignment filesThis submission contains
 multiple sequence alignment files used for phylogenetic reconstructions.
 Sequences reconstructed from sediments are denominated by the site and
 layer of origin. The comparative data (identical in all files) is
 identified by the name of the individual and the accession code of its
 mtDNA sequence.MSA_sedimentDNA.zip
DOI: 10.5061/dryad.7t3d30c
title: Data from: Reef fish functional traits evolve fastest at trophic extremes

description: Trophic ecology is thought to exert a profound influence on biodiversity,
 but the specifics of the process are rarely examined at large spatial and
 evolutionary scales. We investigate how trophic position and diet breadth
 influence functional trait evolution in one of the most species-rich and
 complex vertebrate assemblages, coral reef fishes, within a large-scale
 phylogenetic framework. We show that, in contrast with established theory,
 functional traits evolve fastest in trophic specialists with narrow diet
 breadths at both very low and high trophic positions. Top trophic level
 specialists exhibit the most functional diversity, while omnivorous taxa
 with intermediate trophic positions and wide diet breadth have the least
 functional diversity. Our results reveal the importance of trophic
 position in shaping evolutionary dynamics while simultaneously
 highlighting the incredible trophic and functional diversity present in
 coral reef fish assemblages.
description: NEE_borstein_SupplementalFilesSupplemental R scripts and data files used to perform analyses in Borstein et al., 2018 " Reef fish functional traits evolve fastest at trophic extremes".NEE_borstein_dryad.zip
DOI: 10.5061/dryad.8bn8p
title: Data from: Characterizing vocal repertoires - hard vs. soft classification approaches

description: To understand the proximate and ultimate causes that shape acoustic
 communication in animals, objective characterizations of the vocal
 repertoire of a given species are critical, as they provide the foundation
 for comparative analyses among individuals, populations and taxa. Progress
 in this field has been hampered by a lack of standard in methodology,
 however. One problem is that researchers may settle on different variables
 to characterize the calls, which may impact on the classification of
 calls. More important, there is no agreement how to best characterize the
 overall structure of the repertoire in terms of the amount of gradation
 within and between call types. Here, we address these challenges by
 examining 912 calls recorded from wild chacma baboons (Papio ursinus). We
 extracted 118 acoustic variables from spectrograms, from which we
 constructed different sets of acoustic features, containing 9, 38, and 118
 variables; as well 19 factors derived from principal component analysis.
 We compared and validated the resulting classifications of k-means and
 hierarchical clustering. Datasets with a higher number of acoustic
 features lead to better clustering results than datasets with only a few
 features. The use of factors in the cluster analysis resulted in an
 extremely poor resolution of emerging call types. Another important
 finding is that none of the applied clustering methods gave strong support
 to a specific cluster solution. Instead, the cluster analysis revealed
 that within distinct call types, subtypes may exist. Because hard
 clustering methods are not well suited to capture such gradation within
 call types, we applied a fuzzy clustering algorithm. We found that this
 algorithm provides a detailed and quantitative description of the
 gradation within and between chacma baboon call types. In conclusion, we
 suggest that fuzzy clustering should be used in future studies to analyze
 the graded structure of vocal repertoires. Moreover, the use of factor
 analyses to reduce the number of acoustic variables should be discouraged.
description: Dataset Chacma Baboon
 Vocal RepertoireParameterized dataset of
 chacma baboon vocal repertoire. Calls have been fast Fourier transformed
 into their frequency-time domain using Avisoft SASLab Pro. Acoustic
 features have been extracted with LMA 2012.
DOI: 10.5061/dryad.s5r8q
title: Data from: A degradation debt? large-scale shifts in community composition and loss of biomass in a tropical forest fragment after 40 years of isolation

description: Habitat loss and fragmentation are among the biggest threats to tropical
 biodiversity and associated ecosystem services. We examined forest
 dynamics in a mid-elevation 365-ha fragment in southern Costa Rica. The
 fragment was isolated in the mid-1970s and belongs to the Las Cruces
 Biological Station. A 2.25-ha permanent plot was established in the center
 of the old-growth forest (&gt;400 m to nearest edge boundary) and all
 plants &gt;5 cm DBH were censused, mapped, and identified to species
 in two surveys taken ~5–6 years apart (&gt;3,000 stems/survey).
 Although the reserve maintains high species richness (&gt;200 spp.),
 with many rare species represented by only one individual, we document a
 strong shift in composition with a two-fold increase in the number of
 soft-wooded pioneer individuals. The dominant late-successional understory
 tree species, Chrysochlamys glauca (Clusiaceae), and most species in the
 Lauraceae, declined dramatically. Turnover was high: 22.9% of stems in the
 first survey were lost, and 27.8% of stems in the second survey
 represented new recruits. Mean tree diameter decreased significantly and
 there was a 10% decrease in overall biomass. Such alteration has been
 documented previously but only in smaller fragments or within ~100 m of an
 edge boundary. Further penetration into this fragment was perhaps driven
 by a progressive invasion of disturbance-adapted species into the
 fragment’s core over time; the loss of once-dominant late successional
 species could be a contributing factor. The pattern found is of particular
 concern given that such fragments represent a substantial portion of
 today’s remaining tropical habitat; further studies in similar-sized
 fragments that have been isolated for similar prolonged periods are called
 for.
description: FDP inventory for
 DryadWoody plant inventories
 from first and second survey of the Las Cruces Biological Station forest
 dynamics plot.FDP grid topography for
 DryadX, Y coordinates and
 elevation relative to an arbitrary starting point, for all corners of the
 10 m x 10 m grid demarking the LCBS forest dynamics plot. In addition,
 change in elevation and steepness (degrees) between adjacent grid
 points.
DOI: 10.5061/dryad.9n859
title: Data from: Patterns and thresholds of grazing-induced changes in community structure and ecosystem functioning: species-level responses and the critical role of species traits

description: Overgrazing has resulted in widespread decline in biodiversity and
 ecosystem functioning in grasslands worldwide in recent decades. However,
 few studies have examined the patterns and thresholds of grazing-induced
 changes in community structure and ecosystem functioning along a grazing
 gradient and based on species-level responses and plant functional traits.
 To identify the thresholds of grazing intensity at both species and
 community levels, we conducted a grazing manipulation experiment with
 seven levels of grazing intensity (0–9 sheep ha-1) and two topographies
 (flat versus slope) in a typical steppe. Four plant functional traits were
 measured, including specific leaf area (SLA), plant height, leaf nitrogen
 content (LNC) and stem: leaf ratio (SLR). The threshold of grazing
 intensity that significantly altered community composition was at 3.75
 sheep ha-1 for the flat system and 3.0 sheep ha-1 for the slope system.
 For both flat and slope systems, the threshold grazing intensity for
 changes in primary productivity was at 3.0 sheep ha-1, beyond which the
 productivity decreased substantially. At species level, the abundances of
 common species, most of which are perennial grasses, declined at moderate
 grazing intensities (3.0–4.5 sheep ha-1). The abundances of most rare
 species, which are perennial forbs, declined at low grazing intensities
 (1.5–3.0 sheep ha-1). Specific leaf area and leaf nitrogen content are
 good predictors of species-level responses to grazing. Low SLA and high
 LNC species are negatively affected by high grazing intensity, while high
 SLA and low LNC species are little affected by grazing. The negative
 effect of grazing intensity on species abundance was greater in the slope
 system than in the flat system. Synthesis and applications. Our results
 indicate that the structural and functioning thresholds of grazing
 intensity depend on plant traits and species composition, which is
 mediated by topographic location. These findings, integrating plant
 functional traits and threshold approaches, have important implications
 for determining sustainable grazing intensity in grassland management and
 biodiversity conservation in semi-arid regions.
description: Data from: Patterns and
 thresholds of grazing-induced changes in community structure and ecosystem
 functioning: species-level responses and the critical role of species
 traitsSpecies abundance,
 aboveground net primary production (ANPP) and plant functional traits data
 used in the analyses are included in this file. Species abundance is the
 number of individuals of each species in each 1m × 1m quadrat. Plant
 functional traits include specific leaf area, plant height, stem to leaf
 biomass ratio, and leaf nitrogen content. For each trait, the mean trait
 value was the average of 30 individuals of each
 species.Species abundance and
 functional trait_2016-09-25.xlsx
DOI: 10.5061/dryad.1425c
title: Data from: Social learning and the replication process: an experimental investigation

description: Human cultural traits typically result from a gradual process that has
 been described as analogous to biological evolution. This observation has
 led pioneering scholars to draw inspiration from population genetics to
 develop a rigorous and successful theoretical framework of cultural
 evolution. Social learning, the mechanism allowing information to be
 transmitted between individuals, has thus been described as a simple
 replication mechanism. Although useful, the extent to which this
 idealization appropriately describes the actual social learning events has
 not been carefully assessed. Here, we used a specifically developed
 computer task to evaluate (i) the extent to which social learning leads to
 the replication of an observed behaviour and (ii) the consequences it has
 for fitness landscape exploration. Our results show that social learning
 does not lead to a dichotomous choice between disregarding and replicating
 social information. Rather, it appeared that individuals combine and
 transform information coming from multiple sources to produce new
 solutions. As a consequence, landscape exploration was promoted by the use
 of social information. These results invite us to rethink the way social
 learning is commonly modelled and could question the validity of
 predictions coming from models considering this process as replicative.
description: SocialLearningAndTheReplicationProcess_DataSocial_Learning_and_the_Replication_Process.xlsx
DOI: 10.5061/dryad.66598
title: Data from: Lungfish diversity in Romer’s Gap: reaction to the end-Devonian extinction

description: Romer's Gap, the interval following the end-Devonian extinction
 event, has been described as a post-extinction trough for vertebrates. It
 is a time roughly equivalent to the Tournaisian stage of the early
 Carboniferous and has been characterized by a lull in diversity of
 survivors. Lungfish typified this description. One species was known from
 one locality. Recently, a diverse collection of lungfish tooth plates,
 representing seven new forms, was recovered from new Tournaisian
 vertebrate localities in northern Britain. They display a range of
 previously unknown morphologies, with tooth shape and wear patterns not
 seen in other post-Devonian forms. A comparison of tooth ridge number and
 tooth ridge angle in lungfishes from the Famennian, Tournaisian and Visean
 reveals marked differences between late Devonian and early Carboniferous
 taxa. The most common tooth plate shape in the Famennian is absent from
 our sample of Tournaisian taxa. Two completely new shapes have evolved,
 one with a relatively low tooth ridge angle, no greater than 40°, in which
 most of the tooth ridges are essentially parallel, and the other with a
 much higher tooth ridge angle of up to 180° where the tooth ridges are
 highly divergent. This high level of morphological diversity over a narrow
 time period suggests that, following the end-Devonian extinction, gaps in
 ecospace left by the extinction of major groups of fishes were exploited
 by a previously unrecorded radiation of lungfishes. Whilst taxonomic
 diversity of lungfishes declined following the end-Devonian extinction,
 recovery and diversification among tooth-plated forms was rapid, and
 morphological disparity among these forms subsequently increased. Contrary
 to previous assumptions, morphological disparity among lungfish did not
 decline until much later in the Carboniferous.
description: Lungfish diversity in
 Romer's Gap supplementary materialPrincipal component
 analysis of lungfish tooth plates and tooth ridge angle
 analysis
DOI: 10.5061/dryad.0n94k1s
title: Data from: Combined measurements of prey availability explain habitat selection in foraging seabirds

description: Understanding links between habitat characteristics and foraging
 efficiency help to predict how environmental change could influence
 populations of top-predators. This study examines whether measurements of
 prey (clupeids) availability varied over stratification gradients, and
 determined if any of those measurements coincided with aggregations of
 foraging seabirds (common guillemot Uria aalge, Manx shearwater Puffinus
 puffinus) in the Celtic Sea, UK. The probability of encountering foraging
 seabirds was highest around fronts between mixed and stratified water.
 Prey were denser and shallower in mixed water, and encounters with prey
 most frequent in stratified water. Therefore, no single measurement of
 increased prey availability coincided with the location of fronts.
 However, when considered in combination, overall prey availability was
 highest in these areas. These results show that top-predators may select
 foraging habitats by trading-off several elements of prey availability. By
 showing that top-predators select areas where prey are switching between
 behaviours, these results also identify a mechanism that could explain the
 wider importance of edge habitats for these taxa. As offshore developments
 (e.g. marine renewable energy installations) change patterns of
 stratification, their construction may have consequences on the foraging
 efficiency of seabirds.
description: MERP_Apr16_CTS_SeabirdEnvironment_UTM30NSeabird, Prey and Environmental data.
DOI: 10.5061/dryad.h3390h5
title: Data from: Drivers of phylogenetic assemblage structure of the Furnariides, a widespread clade of lowland Neotropical birds

description: Species co-occurrence in local assemblages is shaped by different
 processes at different spatial and temporal scales. Here we focus on
 historical explanations and examine the phylogenetic structure of local
 assemblages of the Furnariides clade (Aves: Passeriformes), assessing the
 influence of diversification rates on the assembly and species
 co-occurrence within those assemblages. Using 120 local assemblages across
 Bolivia and Argentina and a nearly complete phylogeny for the clade, we
 analyzed assemblage phylogenetic structure applying a recently developed
 model (DAMOCLES) accounting for the historical processes of speciation,
 colonization and local extinction. We also evaluated how diversification
 rates determine species co-occurrence. We found that the assembly of
 Furnariides assemblages can largely be explained by speciation,
 colonization and local extinction without invoking current local species
 interactions. Phylogenetic structure of open habitat assemblages mainly
 showed clustering, characterized by faster rates of colonization and local
 extinction than in forest habitats, whereas forest habitat assemblages
 were congruent with the model’s equal rates expectation, thus highlighting
 the influence of habitat preferences on assembly and co-occurrence
 patterns. Our results suggest that historical processes are sufficient to
 explain local assemblage phylogenetic structure, while there is little
 evidence for species ecological interactions in avian assemblage diversity
 and composition.
description: Furnariides MCC
 treeMCC phylogenetic tree
 for the Furnariides infraorderAppendix_S3.Furnariides_divTime_MCC.nexTable S1This dataset is a presence-absence or incidence matrix for the 120 assemblages used in this study.Table_S1.xlsxTable S2Furnariides local assemblages obtained from the literature.Table_S2_From_bibliographic_sources.pdfTable S3GenBank Accession numbers of the sequences included in the Furnariides phylogenyTable_S3_GenBankAccesions.pdf