cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.72b792p
title: Data from: Time explains regional richness patterns within clades more often than diversification rates or area

description: Most groups of organisms occur in multiple regions, and have different
 numbers of species in different regions. These richness patterns are
 directly explained by speciation, extinction, and dispersal. Thus,
 regional richness patterns may be explained by differences in when regions
 were colonized (more time-for-speciation in regions colonized earlier),
 how often they were colonized, or differences in diversification rates
 (speciation – extinction) among regions (with diversification rates
 potentially influenced by area, climate, and/or many other variables). Few
 studies have tested all three factors, and most that did examined them
 only in individual clades. Here, we analyze a diverse set of 15 clades of
 plants and animals to test the causes of regional species richness
 patterns within clades. We find that time was the sole variable
 significantly explaining richness patterns in the best-fit models for most
 clades (10/15), whereas time combined with other factors explained
 richness in all others. Time was the most important factor explaining
 richness in 13 of 15 clades, and explained 72% of the variance in species
 richness among regions across all 15 clades (on average). Surprisingly,
 time was increasingly important in older and larger clades. In contrast,
 the area of the regions was relatively unimportant for explaining these
 regional richness patterns. A systematic review yielded 15 other relevant
 studies, which also overwhelmingly supported time over diversification
 rates (13 to 1, with one study supporting both diversification rates and
 time). Overall, our results suggest that colonization time is a major
 factor explaining regional-scale richness patterns within clades (e.g.,
 families). 
description: Online Appendix
 ATrees used in
 biogeographic analysesOnline Appendix
 BEstimates of richness,
 ages, and diversification rates for each colonization event for each
 region in each cladeOnline Appendix
 CData
 for each region for all 15 cladesOnline Appendix
 DTables
 D1–D14.
DOI: 10.5061/dryad.06g12
title: Data from: An eco-epidemiological study of Morbilli-related paramyxovirus infection in Madagascar bats reveals host-switching as the dominant macro-evolutionary mechanism

description: An eco-epidemiological investigation was carried out on Madagascar bat
 communities to better understand the evolutionary mechanisms and
 environmental factors that affect virus transmission among bat species in
 closely related members of the genus Morbillivirus, currently referred to
 as Unclassified Morbilli-related paramyxoviruses (UMRVs). A total of 947
 bats were investigated originating from 52 capture sites (22 caves, 18
 buildings, and 12 outdoor sites) distributed over different bioclimatic
 zones of the island. Using RT-PCR targeting the L-polymerase gene of the
 Paramyxoviridae family, we found that 10.5% of sampled bats were infected,
 representing six out of seven families and 15 out of 31 species analyzed.
 Univariate analysis indicates that both abiotic and biotic factors may
 promote viral infection. Using generalized linear modeling of UMRV
 infection overlaid on biotic and abiotic variables, we demonstrate that
 sympatric occurrence of bats is a major factor for virus transmission.
 Phylogenetic analyses revealed that all paramyxoviruses infecting Malagasy
 bats are UMRVs and showed little host specificity. Analyses using the
 maximum parsimony reconciliation tool CoRe-PA, indicate that
 host-switching, rather than co-speciation, is the dominant
 macro-evolutionary mechanism of UMRVs among Malagasy bats.
description: Database Malagasy
 batsDescription of bats
 collected in MadagascarBat paramyxoviruses
 database.xls
DOI: 10.5061/dryad.p3q6c
title: Data from: Proteomic evidence of a paedomorphic evolutionary process within a marine snail species: a strategy for adapting to extreme ecological conditions?

description: The exposed and sheltered ecotypes of the marine snail Littorina saxatilis
 from European rocky shores are considered a key model system to study
 adaptation and ecological speciation. Previous studies showed that two
 ecotypes (RB and SU) of this species in NW Spain have differently adapted
 to different shore levels and microhabitats. In order to understand how
 this divergent adaptive process has been accomplished, we followed a
 quantitative proteomic approach to investigate the proteome variation in a
 number of different biological factors, i.e. ecotype, ontogeny and their
 interactions. This approach allowed testing the hypothesis that one of the
 ecotypes has evolved by paedomorphosis, and also whether or not the
 molecular mechanisms related to ecotype differentiation are set up in
 early developmental stages. Additionally the identification of some
 candidate proteins by mass spectrometry provides some functional insights
 about these evolutionary processes. Results from this study provided
 evidence of higher ontogenetic differentiation at proteome level in the RB
 (metamorphic) than in SU (paedomorphic) ecotype that point to the
 possibility of juvenile stage retention in this latter ecotype. The level
 of protein expression (proteome) differences between ecotypes maintained
 nearly constant from late embryonic stages to adulthood, although some
 proteins involved in these changes considerably differed in embryonic
 compared to other ontogenetic stages. Paedomorphosis may be the
 evolutionary response of the SU ecotype of solving the trade-off during
 sexually immaturity that is caused by the evolution of small size arising
 from adaptation to the wave exposed habitat. Some potential candidate
 genes of adaptation related to energetic metabolism have been identified,
 providing a promising baseline for future functional analyses.
description: 2-DE spot
 volumes_Proteomic data LittorinaNormalised and
 log10-transformed data obtained from two-dimensional electrophoresis
 (2-DE) image analyses by using SameSpots v3.3 software (Nonlinear Dynamics
 Ltd). 2-DE gels were silver stained.
DOI: 10.5061/dryad.rk3gn
title: Data from: Experimental evolution of insect immune memory versus pathogen resistance

description: Under strong pathogen pressure, insects often evolve resistance to
 infection. Many insects are also protected via immune memory (‘immune
 priming’), whereby sub-lethal exposure to a pathogen enhances survival
 after secondary infection. Theory predicts that immune memory should
 evolve when the pathogen is highly virulent, or when pathogen exposure is
 relatively rare. However, there are no empirical tests of these
 hypotheses, and the adaptive benefits of immune memory relative to direct
 resistance against a pathogen are poorly understood. To determine the
 selective pressures and ecological conditions that shape immune evolution,
 we imposed strong pathogen selection on flour beetle (Tribolium castaneum)
 populations, infecting them with Bacillus thuringiensis (Bt) for 11
 generations. Populations injected first with heat-killed and then live Bt
 each generation evolved high basal resistance against multiple Bt strains.
 In contrast, populations injected only with a high dose of live Bt evolved
 a less effective but strain-specific priming response. Control populations
 injected with heat-killed Bt did not evolve priming; and in the ancestor,
 priming was effective only against a low Bt dose. Intriguingly, one
 replicate population first evolved priming and subsequently evolved basal
 resistance, suggesting the potential for dynamic evolution of different
 immune strategies. Our work is the first report showing that pathogens can
 select for rapid modulation of insect priming ability, allowing hosts to
 evolve divergent immune strategies (generalized resistance vs. specific
 immune memory) with potentially distinct mechanisms.
description: Survival
 dataThis file contains raw
 survival data for all the analysis, including post-infection mortality
 across generations; priming and resistance at generation 8 and 11 and
 priming in PI lines against a high infection doseDryad
 data_final.xlsx
DOI: 10.5061/dryad.fn4nf
title: Data from: Generalized spatial mark-resight models with an application to grizzly bears

description: 1. The high cost associated with capture-recapture studies presents a
 major challenge when monitoring and managing wildlife populations.
 Recently-developed spatial mark-resight (SMR) models were proposed as a
 cost-effective alternative because they only require a single marking
 event. However, existing SMR models ignore the marking process and make
 the tenuous assumption that marked and unmarked populations have the same
 encounter probabilities. This assumption will be violated in most
 situations because the marking process results in different spatial
 distributions of marked and unmarked animals. 2. We developed a
 generalized SMR model that includes sub-models for the marking and
 resighting processes, thereby relaxing the assumption that marked and
 unmarked populations have the same spatial distributions and encounter
 probabilities. 3. Our simulation study demonstrated that conventional SMR
 models produce biased density estimates with low credible interval
 coverage when marked and unmarked animals had differing spatial
 distributions. In contrast, generalized SMR models produced unbiased
 density estimates with correct credible interval coverage in all
 scenarios. 4. We applied our SMR model to grizzly bear (Ursus arctos) data
 where the marking process occurred along a transportation route through
 Banff and Yoho National Parks, Canada. Twenty-two grizzly bears were
 trapped, fitted with radio-collars, and then detected along with unmarked
 bears on 214 remote cameras. Closed population density estimates
 (posterior median + 1 SD) averaged from 2012 to 2014 were much lower for
 conventional SMR models (7.4 + 1.0 bears per 1,000 km2) than for
 generalized SMR models (12.4 + 1.5). When compared to previous DNA-based
 estimates, conventional SMR estimates erroneously suggested a 51% decline
 in density. Conversely, generalized SMR estimates were similar to previous
 estimates, indicating that the grizzly bear population was relatively
 stable. 5. Synthesis and application. Conventional SMR models that ignore
 the marking process should only be used when marked and unmarked animals
 share the same spatial distribution, such as when a subset of the
 population has natural marks. Generalized SMR models that include the
 marking process are much more widely applicable. They represent a
 promising new approach for reducing the costs of studies aimed at
 understanding spatial and temporal variation in density.24-May-2017
description: Grizzly Bear Generalized
 Spatial Mark-Resight Scripts and DataGeneralized SMR Scripts and
 Data.zip
DOI: 10.5061/dryad.78fm3
title: Data from: Exposure to Mycobacterium tuberculosis during flexible bronchoscopy in patients with unexpected pulmonary tuberculosis

description: Objective: Recent guidelines recommend the use by healthcare personnel of
 a fit-tested N95 particulate respirator or higher-grade respiratory
 precaution in a patient undergoing bronchoscopy when pulmonary
 tuberculosis (PTB) is suspected. However, PTB may be unexpectedly
 diagnosed in this setting and therefore not evaluated, resulting in the
 unexpected exposure to Mycobacterium tuberculosis (MTB) of healthcare
 workers in the bronchoscopy suite. Here, we examined the incidence of
 unexpected exposure to MTB during flexible bronchoscopy and determined the
 exposure-related factors. Methods: Between 2011 and 2013, a retrospective
 study was conducted to evaluate unexpected diagnoses of PTB in the
 bronchoscopy suite. During the study period, 1650 consecutive patients for
 whom previous CT scans were available and who underwent bronchoscopy for
 respiratory disease other than PTB were included. The results of bronchial
 washing, bronchoalveolar lavage, and post-bronchoscopic sputum were
 reviewed. Results: PTB was unexpectedly diagnosed in 76 patients (4.6%).
 The presence of anthracofibrosis [odds ratio (OR), 3.878; 95% confidence
 interval (CI), 1.291–11.650; P = 0.016), bronchiectasis (OR, 1.974; 95%
 CI, 1.095–3.557; P = 0.024), or atelectasis (OR, 1.740; 95% CI,
 1.010–2.903; P = 0.046) as seen on chest CT scan was independently
 associated with unexpected PTB. Patients with both anthracofibrosis and
 atelectasis were at much higher risk of unexpected PTB (OR, 4.606; 95% CI,
 1.383–15.342; P = 0.013). Conclusions: The risk of MTB exposure by
 healthcare personnel in the bronchoscopy suite due to patients with
 undiagnosed PTB has been underestimated. Therefore, in geographic regions
 with an intermediate PTB prevalence, such as South Korea (97/100,000
 persons per year), higher-grade respiratory precaution, such as a
 fit-tested N95 particulate respirator, should be considered to prevent
 occupational exposure to MTB during routine bronchoscopy, especially in
 patients with CT-confirmed anthracofibrosis, bronchiectasis, or
 atelectasis.
description: Suspected to have
 PTBSuspected to have
 respiratory diseases other than PTB
DOI: 10.5061/dryad.tj7pp1b
title: Data from: Effectiveness of camera traps for quantifying daytime and nighttime visitation by vertebrate pollinators

description: 1. Identification of pollen vectors is a fundamental objective of
 pollination biology. The foraging and social behavior of these pollinators
 has profound effects on plant mating, making quantification of their
 behaviour critical for understanding the ecological and evolutionary
 consequences of different pollinators for the plants they visit. However,
 accurate quantification of visitation may be problematic, especially for
 shy animals and/or when the temporal and spatial scale of observation
 desired is large. Sophisticated heat- and movement-triggered motion-sensor
 cameras (‘camera trapping’) provide new, underutilized tools to address
 these challenges. However, to date there has been no rigorous evaluation
 of the sampling considerations needed for using camera trapping in
 pollination research. 2. We measured the effectiveness of camera trapping
 for identifying vertebrate visitors and quantifying their visitation rates
 and foraging behaviour on Banksia menziesii (Proteaceae). Multiple still
 cameras (Reconyx HC 500) and a video camera (Little Acorn LTL5210A) were
 deployed. 3. From 2,753 recorded visits by vertebrates, we identified five
 species of nectarivorous honeyeater (Meliphagidae) and the honey possum
 (Tarsipedidae), with significant variation in the species composition of
 visitors among inflorescences. Species of floral visitor showed
 significant variation in their time of peak activity, duration of visits,
 and numbers of flowers probed per visit. Where multiple cameras were
 deployed on individual inflorescences, effectiveness of individual still
 cameras varied from 15% to 86% of all recorded visits. Methodological
 issues and solutions, and the future uses of camera traps in pollination
 biology, are discussed. 4. Conclusions and wider implications:
 Motion-triggered cameras are promising tools for the quantification of
 vertebrate visitation and some aspects of behaviour on flowers. However,
 researchers need to be mindful of the variation in effectiveness of
 individual camera traps in detecting animals. Pollinator studies using
 camera traps are in their infancy, and the full potential of this
 developing technology is yet to be realized.
description: Camera_trapping_data for
 graphs_FINALSummary data for
 figures
DOI: 10.5061/dryad.nh8c7
title: Data from: Beyond climate: convergence in fast evolving sclerophylls in Cape and Australian Rhamnaceae predates the mediterranean climate

description: Morphological convergence in mediterranean-type ecosystems (MTEs) has long
 been interpreted as adaptation to climatic similarities among the five
 MTEs of the world. Here, we challenge this model using the globally
 distributed Rhamnaceae. We collected functional trait data (specific leaf
 area, leaf area, spinescence, leaf phenology, growth form and leaf margin
 type) and biome data to test for trait convergence in MTEs, for models of
 trait evolution and ancestral state reconstruction and for the effect of
 traits on speciation and extinction rates, using a phylogenetic framework.
 We show that leaf functional traits evolve to three optima, which
 correspond to (a) the edaphically specialized Australian and Cape MTEs
 (AC), (b) the mediterranean-type climates, but edaphically normal Chile,
 California and Mediterranean Basin (CCM), and (c) the non-mediterranean
 habitats. We find that Rhamnaceae in CCM are predominantly characterized
 by non-sclerophylly, the ancestral state in Rhamnaceae, and Rhamnaceae in
 AC by sclerophylly. These leaf character syndromes have evolved prior to
 mediterranean climates in MTEs, thereby failing to be adaptive to this
 selective regime. However, sclerophylly evolved contemporaneously with the
 transitions to AC, and may therefore be an adaptation to nutrient-poor
 soils. The evolution of sclerophylly has contributed to increased
 diversification rates of Pomaderreae in Australia and Phyliceae in the
 Cape, by reducing extinction rates and thereby facilitating evolutionary
 persistence. The historical relatively stable conditions in AC are
 consistent with this persistence hypothesis. Synthesis. In this study we
 integrate the fields of macroevolution and ecology and show that low
 extinction rates may not only account for the ecological, but also for the
 floristic dominance of sclerophylly in the hyperdiverse Australian and
 Cape mediterranean-type ecosystems.
description: BEAST MCC tree
 Rhamnaceae Onstein et alFor details also see
 Onstein et al. 2015 Evolution DOI: 10.1111/evo.12605. BEAST MCC tree based
 on sequence data for species of Rhamnaceae and outgroup taxa collected
 from GenBank (www.ncbi.nlm.nih.gov) (513 accessions) and generated by
 ourselves (379 accessions), for six chloroplast markers (matK gene 1593
 base pairs (bp), trnL-F genes and intergenic spacer 1232 bp, rbcL gene
 1425 bp, psbA gene and psbA-trnH intergenic spacer 775 bp, ndhF gene 2163
 bp, rpl16 gene and intron 1344 bp) and one nuclear marker (ITS gene 952
 bp). The best fit model for the chloroplast and ITS markers were
 identified with the Bayesian Information Criterion (BIC) implemented in
 PartitionFinder v 1.0.1, as follows: GTR + G + I for the linked
 chloroplast markers, and SYM + G + I for the ITS marker. We used the
 uncorrelated lognormal relaxed clock and a yule tree prior available in
 BEAST v.1.7.5. The MCC tree is based on the 10250 subsampled
 trees.
DOI: 10.5061/dryad.qc580
title: Data from: Latest Carboniferous (late Gzhelian) fusulinids from Timor Leste and their paleobiogeographic affinities

description: An uppermost Gzhelian bioherm discovered in the central highlands of Timor
 Leste contains abundant foraminifera belonging to 17 genera.
 Representatives of the families Biseriamminidae, Biwaellidae, Bradyinidae,
 Cornuspiridae, Lasiodiscidae, Palaeotextulariidae, Pseudotaxidae,
 Ozawainellidae, Schubertellidae, Schwagerinidae, Staffellidae and
 Textrataxidae are present, including 21 species referred to known types
 and 12 species left in open nomenclature. Two new Schwagerina species are
 described: Schwagerina timorensis new species, and Schwagerina
 maubissensis new species. The assemblage belongs to the uppermost Gzhelian
 Schwagerina robusta–Ultradaixina bosbytauensis Zone although a possible
 lowest Asselian correlation cannot be excluded (the name Ultradaixina is
 controversial and sometimes synonymized as Bosbytauella. The case to
 resolve this issue has been submitted to the Bulletin of Zoological
 Nomenclature). The bioherm is the oldest carbonate unit so far recorded
 from the Maubisse Formation and the oldest sedimentary unit
 biostratigraphically dated in Timor. This discovery has implications for
 the latest Carboniferous–earliest Permian climate history of Timor that
 lay in the northern part of the north-south East Gondwana rift system
 along which the western margin of Australia later developed. The highest
 peak in fusulinid diversity within the Pennsylvanian–Cisuralian interval
 and a major marine transgression documented in many regions in Northern
 Pangaea took place during the latest Gzhelian to earliest Asselian and
 evidence for this is now extended to southern Pangaea. Cluster analysis,
 using the Jaccard similarity index at species level, of late Gzhelian
 fusulinids from 16 regions has been performed. This shows that the Timor
 fauna is most closely related to faunas from South China and the
 Changning-Menlian region of Yunnan (China). The assemblages here are
 distinct from those of three biogeographic regions (Arctic, Uralo-Asian
 and Irano-Taurids) recognized within the Tropical belt.
description: Supplement_genera and
 speciesMatrixesSupplemental_data.pdf
DOI: 10.15468/dl.7n2vt7
title: Occurrence Download

description: A dataset containing 1291 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Clarkia pulchella",
 "Year 1981-2026"
 ]
}

 The dataset includes 1291 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000573-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.r4jq1
title: Data from: Rook, but not jackdaw, post-conflict third-party affiliation reduces aggression for aggressors

description: Post-conflict (PC) affiliation refers to positive social interactions that
 occur after fights. Although this behavior has been widely studied, its
 functions are rarely tested. We examine a potential function of PC
 third-party affiliation (affiliation between former opponents and
 bystanders) in rooks and jackdaws by investigating the hypothesis that
 conflicts lead to further aggression and that PC third-party affiliation
 increases to reduce such aggression. The results show that PC affiliation
 reduces PC aggression for rook aggressors who were less likely to receive
 aggression after conflicts when they were affiliating with another vs.
 when they were alone. The opposite result was found for victims of both
 species who received more aggression after conflicts, and this aggression
 was not reduced by the act of affiliating. Finally, for jackdaw
 aggressors, the amount of aggression received after conflicts was not
 influenced by whether the individual was affiliating or alone, indicating
 that PC third-party affiliation may serve a function that we did not
 examine. These findings highlight the importance of investigating
 functional differences in PC affiliative behavior according to the role
 played in the conflict.
description: DataPrediction1JackdawTable1Model1DataPrediction1JackdawTable1Model2DataPrediction1JackdawTable2Model1DataPrediction1JackdawTable2Model2DataPrediction1RookTable1Model1DataPrediction1RookTable1Model2DataPrediction1RookTable2Model1DataPrediction1RookTable2Model2DataPrediction3JackdawTable3DataPrediction3RookTable3DataPrediction4JackdawTable4DataPrediction4RookTable4