cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1261
title: Data from: Temporal variation in the genetic structure of a drone congregation area: An insight into the population dynamics of wild African honeybees (Apis mellifera scutellata)

description: The mating system of the honeybee (Apis mellifera) has been regarded as
 one of the most panmictic in the animal kingdom, with thousands of males
 aggregating in drone congregation areas (DCAs) that virgin queens visit to
 mate with tens of partners. Although males from many colonies gather at
 such congregations, the temporal changes in the colonies contributing
 drones remain unknown. Yet, changes in the DCAs' genetic structure
 will ultimately determine population gene flow and effective population
 size. By repeatedly sampling drones from an African DCA over a period of
 three years, we studied the temporal changes in the genetic structure of a
 wild honeybee population. Using three sets of tightly linked
 microsatellite markers, we were able to reconstruct individual queen
 genotypes with a high accuracy, follow them through time and estimate
 their rate of replacement. The number of queens contributing drones to the
 DCA varied from 12 to 72 and was correlated with temperature and rainfall.
 We found that more than 80% of these queens were replaced by mostly
 unrelated ones in successive eight months sampling intervals, which
 resulted in a clear temporal genetic differentiation of the DCA. Our
 results suggest that the frequent long range migration of colonies without
 nest-site fidelity is the main driver of this high queen turnover. DCAs of
 African honeybees should thus be regarded as extremely dynamic systems
 which together with migration boost the effective population size and
 maintain a high genetic diversity in the population.
description: Fig.
 S1Figure
 S1.tifTable
 S1Table
 S2Arlequin input file
 containing the multilocus genotype of 510 Apis mellifera scutellata drones
 collected at a single DCA over a period of 3 years. The 12 loci employed
 for genotyping are shown in the first line. The collection date of each
 sample is given as Ma, No, Ap, Se and De, referring to March 2004,
 November 2004, April 2007, September 2007 and December 2007,
 respectively.
DOI: 10.5061/dryad.4r668
title: Data from: The importance of delineating networks by activity type in bottlenose dolphins (Tursiops truncatus) in Cedar Key, Florida

description: Network analysis has proved to be a valuable tool for studying the
 behavioural patterns of complex social animals. Often such studies either
 do not distinguish between different behavioural states of the organisms
 or simply focus attention on a single behavioural state to the exclusion
 of all others. In either of these approaches it is impossible to ascertain
 how the behavioural patterns of individuals depend on the type of activity
 they are engaged in. Here we report on a network-based analysis of the
 behavioural associations in a population of bottlenose dolphins (Tursiops
 truncatus) in Cedar Key, Florida. We consider three distinct behavioural
 states—socializing, travelling and foraging—and analyse the association
 networks corresponding to each activity. Moreover, in constructing the
 different activity networks we do not simply record a spatial association
 between two individuals as being either present or absent, but rather
 quantify the degree of any association, thus allowing us to construct
 weighted networks describing each activity. The results of these weighted
 activity networks indicate that networks can reveal detailed patterns of
 bottlenose dolphins at the population level; dolphins socialize in large
 groups with preferential associations; travel in small groups with
 preferential associates; and spread out to forage in very small, weakly
 connected groups. There is some overlap in the socialize and travel
 networks but little overlap between the forage and other networks. This
 indicates that the social bonds maintained in other activities are less
 important as they forage on dispersed, solitary prey. The overall network,
 not sorted by activity, does not accurately represent any of these
 patterns.
description: Overall
 NetworkOverall Network with a
 threshold of three sightings.all.gmlAll Dolphin SightingsRaw data of all of the dolphin sightings for all networks.all_orig.csvanalysePerforms basic network analysis on the specified networks and prints the results to the screen. The analysis includes the calculation of the community structure overlap between network pairs and the calculation of basic network metrics for each network.csv2gmlConstructs a network from the sightings data using the specified value for threshold. The resulting network is saved as a GML file.ForageForage Network, constructed with a threshold value of three sightings.forage.gmlForage OriginalOriginal data on the forage sightings.forage_orig.csvgraph_permutationsA module for performing randomisation tests on networks in order to test the statistical significance of network metrics.SocialiseSocialise Network constructed using a threshold value of three sightings.socialise.gmlSocialise OriginalAll of the original sightings for the Socialise Network.socialise_orig.csvTravelTravel Network constructed using a threshold value of three sightings.travel.gmltravel_origAll of the sightings for the Travel Network.
DOI: 10.5061/dryad.6qk05
title: Data from: Are patients with cancer with sepsis and bacteraemia at a higher risk of mortality? A retrospective chart review of patients presenting to a tertiary care centre in Lebanon

description: Objective: Most sepsis studies have looked at the general population. The
 aim of this study is to report on the characteristics, treatment and
 hospital mortality of patients with cancer diagnosed with sepsis or septic
 shock. Setting: A single-centre retrospective study at a tertiary care
 centre looking at patients with cancer who presented to our tertiary
 hospital with sepsis, septic shock or bacteraemia between 2010 and 2015.
 Participants: 176 patients with cancer were compared with 176 cancer-free
 controls. Primary and secondary outcomes: The primary outcome of this
 study was the in hospital mortality in both cohorts. Secondary outcomes
 included patient demographics, emergency department (ED) vital signs and
 parameters of resuscitation along with laboratory work. Results: A total
 of 352 patients were analysed. The mean age at presentation for the cancer
 group was 65.39±15.04 years, whereas the mean age for the control group
 was 74.68±14.04 years (p&lt;0.001). In the cancer cohort the
 respiratory system was the most common site of infection (37.5%) followed
 by the urinary system (26.7%), while in the cancer-free arm, the urinary
 system was the most common site of infection (40.9%). intravenous fluid
 replacement for the first 24 hours was higher in the cancer cohort. ED,
 intensive care unit and general practice unit length of stay were
 comparable in both the groups. 95 (54%) patients with cancer died compared
 with 75 (42.6%) in the cancer-free group. The 28-day hospital mortality in
 the cancer cohort was 87 (49.4%) vs 46 (26.1%) in the cancer-free cohort
 (p=0.009). Patients with cancer had a 2.320 (CI 95% 1.225 to 4.395,
 p=0.010) odds of dying compared with patients without cancer in the
 setting of sepsis. Conclusions: This is the first study looking at an
 in-depth analysis of sepsis in the specific oncology population. Despite
 aggressive care, patients with cancer have higher hospital mortality than
 their cancer-free counterparts while adjusting for all other variables.
description: Oncology data_30 Jan
 2017Excel sheet containing
 the control and cases for the oncology including demographics and
 bacteriology
DOI: 10.5061/dryad.m8446
title: Data from: Disentangling the effect of competition, CO2 and climate on intrinsic water-use efficiency and tree growth

description: 1. Climate change scenarios forecast rising temperatures for the
 Mediterranean region, which could enhance vulnerability to drought stress
 in forest ecosystems. The long-term effects of climate forcing on tree
 performance can be, however, modulated by other environmental factors,
 such as competition and rising atmospheric CO2 concentrations. 2. We
 assessed the concomitant effect of competition, climate and CO2
 concentrations on the tree-ring δ13C-derived intrinsic water-use
 efficiency (iWUE) and basal area increments (BAI) of species with
 different drought tolerance: two Mediterranean deciduous species (Quercus
 faginea Lam. and Quercus pyrenaica Willd.) and one conifer (Pinus
 sylvestris L.). Additionally, given that competition may be managed to
 mitigate the effect of increasing drought stress, we further examined the
 influence of this variable on iWUE and growth using data compiled from the
 literature, providing the first review on the response of iWUE to
 competition. 3. Competition had no significant effect on iWUE in any of
 the three species studied, whereas, as expected, growth rates were
 significantly higher under low competition levels. This was consistent
 with the literature review, which showed that shifts in iWUE with
 competition changes are rare; supporting the hypothesis that leaf-level
 gas exchange tends to be a homeostatic trait. In the long term, the three
 species exhibited a significant increasing trend in iWUE due to the
 combined effect of increased CO2 concentration, climate and age. Growth,
 however, was mostly affected by competition and climate and in most cases
 was not enhanced as a result of the increase in iWUE. 4. Synthesis.
 Regardless of their functional response to drought, trees respond to
 reduced competition through structural shifts such as increased radial
 growth rather than leaf-level gas exchange adjustments. CO2 and climate
 are, therefore, the main drivers of iWUE variability, rather than
 competition. Thus, if temperature-induced drought becomes limiting,
 reducing competition for resources may not offset the detrimental effect
 of increasing drought stress on tree physiology and growth decline may
 occur without a CO2 fertilization effect.
description: Fernández-de-Uña et al
 JEcol DatasetAnnual CO2 partial
 pressure, basal area increment and plot basal area data per treatment
 (control vs. thinning) for Pinus sylvestris (two sites), Quercus faginea
 (one site) and Quercus pyrenaica (two sites)
DOI: 10.5061/dryad.02jk0
title: Data from: The evolution of parental cooperation in birds

description: Parents in many animal species care for their offspring. In some species,
 males care more; in other species, females care more; in still other
 species, the contribution of the sexes is equal. However, we do not know
 what explains these differences among species. Using the most
 comprehensive analyses of parental care to date, here we show that parents
 cooperate more when sexual selection is not intense and the adult sex
 ratio of males to females is not strongly skewed. However, the degree of
 parental cooperation is unrelated to harshness and predictability of the
 ambient environment during the breeding season. Our work therefore
 suggests that several types of parental care may coexist in a given set of
 ambient environment.
description: PNAS_dataPNAS_data_climatic
DOI: 10.5061/dryad.6j777
title: Data from: Climate, not Aboriginal landscape burning, controlled the historical demography and distribution of fire-sensitive conifer populations across Australia

description: Climate and fire are the key environmental factors that shape the
 distribution and demography of plant populations in Australia. Because of
 limited palaeoecological records in this arid continent, however, it is
 unclear as to which factor impacted vegetation more strongly, and what
 were the roles of fire regime changes owing to human activity and
 megafaunal extinction (since ca 50 kya). To address these questions, we
 analysed historical genetic, demographic and distributional changes in a
 widespread conifer species complex that paradoxically grows in fire-prone
 regions, yet is very sensitive to fire. Genetic demographic analysis
 showed that the arid populations experienced strong bottlenecks,
 consistent with range contractions during the Last Glacial Maximum (ca 20
 kya) predicted by species distribution models. In southern temperate
 regions, the population sizes were estimated to have been mostly stable,
 followed by some expansion coinciding with climate amelioration at the end
 of the last glacial period. By contrast, in the flammable tropical
 savannahs, where fire risk is the highest, demographic analysis failed to
 detect significant population bottlenecks. Collectively, these results
 suggest that the impact of climate change overwhelmed any modifications to
 fire regimes by Aboriginal landscape burning and megafaunal extinction, a
 finding that probably also applies to other fire-prone vegetation across
 Australia.
description: Callitris_nSSR_genotypeThe microsatellite genotype data of Callitris columellaris species complex (Cupressaceae), analysed in the MS (RSPB-2013-2182).
DOI: 10.5061/dryad.rf452
title: Data from: Herbivore-induced DNA demethylation changes floral signalling and attractiveness to pollinators in Brassica rapa

description: Plants have to fine-tune their signals to optimise the trade-off between
 herbivore deterrence and pollinator attraction. An important mechanism in
 mediating plant-insect interactions is the regulation of gene expression
 via DNA methylation. However, the effect of herbivore-induced DNA
 methylation changes on pollinator-relevant plant signalling has not been
 systematically investigated. Here, we assessed the impact of foliar
 herbivory on DNA methylation and floral traits in the model crop plant
 Brassica rapa. Methylation-sensitive amplified fragment length
 polymorphism (MSAP) analysis showed that leaf damage by the caterpillar
 Pieris brassicae was associated with genome-wide methylation changes in
 both leaves and flowers of B. rapa as well as a downturn in flower number,
 morphology and scent. A comparison to plants with jasmonic acid-induced
 defence showed similar demethylation patterns in leaves, but both the
 floral methylome and phenotype differed significantly from P. brassicae
 infested plants. Standardised genome-wide demethylation with 5-azacytidine
 in five different B. rapa full-sib groups further resulted in a
 genotype-specific downturn of floral morphology and scent, which
 significantly reduced the attractiveness of the plants to the pollinator
 bee Bombus terrestris. These results suggest that DNA methylation plays an
 important role in adjusting plant signalling in response to changing
 insect communities.
description: Brassica rapa herbivory
 phenotype and MSAP profilesPhenotypic data
 (morphological traits and floral volatiles) and MSAP profiles of Brassica
 rapa R-o-18 plants under herbivore (Pieris brassicae) and methyl jasmonate
 treatment.Brassica_rapa_R-o-18_herbivory.xlsxBrassica rapa 5-azacytidine phenotype and assayPhenotypic data (morphological traits and floral volatiles) and results of a two-choice assay with the pollinator Bombus terrestris of Brassica rapa rapid-cycling plants under 5-azacytidine treatment.Brassica_rapa_fc_azacytidine.xlsx
DOI: 10.5061/dryad.6jg7g
title: Data from: The genetic architecture of local adaptation and reproductive isolation in sympatry within the Mimulus guttatus species complex

description: The genetic architecture of local adaptation has been of central interest
 to evolutionary biologists since the modern synthesis. In addition to
 classic theory on the effect size of adaptive mutations by Fisher, Kimura
 and Orr, recent theory addresses the genetic architecture of local
 adaptation in the face of ongoing gene flow. This theory predicts that
 with substantial gene flow between populations local adaptation should
 proceed primarily through mutations of large effect or tightly linked
 clusters of smaller effect loci. In this study, we investigate the genetic
 architecture of divergence in flowering time, mating system-related
 traits, and leaf shape between Mimulus laciniatus and a sympatric
 population of its close relative M. guttatus. These three traits are
 probably involved in M. laciniatus’ adaptation to a dry, exposed granite
 outcrop environment. Flowering time and mating system differences are also
 reproductive isolating barriers making them ‘magic traits’. Phenotypic
 hybrids in this population provide evidence of recent gene flow. Using
 next-generation sequencing, we generate dense SNP markers across the
 genome and map quantitative trait loci (QTLs) involved in flowering time,
 flower size and leaf shape. We find that interspecific divergence in all
 three traits is due to few QTL of large effect including a highly
 pleiotropic QTL on chromosome 8. This QTL region contains the pleiotropic
 candidate gene TCP4 and is involved in ecologically important phenotypes
 in other Mimulus species. Our results are consistent with theory,
 indicating that local adaptation and reproductive isolation with gene flow
 should be due to few loci with large and pleiotropic effects.
description: F2 Genotype Phenotype
 matrixThis is a matrix of
 genotype and phenotype information in .csv file format with F2 genotype
 called as heterozygotes (H) and homozygotes (A = M. guttatus, B = M.
 laciniatus) at each SNP marker. Each row is a SNP marker and each column
 is an individual. Phenotypes are described in the top 6 columns. This file
 is formatted to be input into Rqtl.SHLxSHG_75bp.qtl_corrected.csvMSG_Genotype_Parse_FerrisMSA custom perl script used to call F2 genotypes in sliding windows of 75 SNPs.
DOI: 10.5061/dryad.7455b
title: Data from: A Bayesian method for the joint estimation of outcrossing rate and inbreeding depression

description: The population outcrossing rate (t) and adult inbreeding coefficient (F)
 are key parameters in mating system evolution. The magnitude of inbreeding
 depression as expressed in the field can be estimated given t and F via
 the method of Ritland (1990). For a given total sample size, the optimal
 design for the joint estimation of t and F requires sampling large numbers
 of families (100-400) with fewer offspring (1-4) per family.
 Unfortunately, the standard inference procedure (MLTR) yields
 significantly biased estimates for t and F when family sizes are small and
 maternal genotypes are unknown (a common occurrence when sampling natural
 populations). Here, we present a Bayesian method implemented in the
 program BORICE that effectively estimates t and F when family sizes are
 small and maternal genotype information is lacking. BORICE should enable
 wider use of the Ritland approach for field-based estimates of inbreeding
 depression. As proof of concept, we estimate t and F in a natural
 population of Mimulus guttatus. In addition, we describe how individual
 maternal inbreeding histories inferred by BORICE may prove useful in
 studies of inbreeding and its consequences.
description: 1. Simulation Data for
 Table 1Please see the Read Me
 file associated with this data deposit.2. MLTR Bias Simulations
 File 1Please see the Read Me
 file included with this data deposit.3. MLTR Bias Simulations
 File 2Please see the Read Me
 file included with this data deposit.4. BORICE
 simulationsPlease see the Read Me
 file associated with this data deposit.5. BORICE correlated
 matings simulationsPlease see the Read Me
 file associated with this data deposit.6. BORICE null alleles
 simulationsPlease see the Read Me
 file associated with this data deposit.7. BORICE variable
 outcrossing rate simulationsPlease see the READ ME
 file associated with this data deposit.8. t & F no mom
 databasePlease see the READ ME
 file associated with this data deposit.9. Table 2 F
 dataPlease see the READ ME
 file associated with this data deposit.10. Table 2 t
 dataPlease see the READ ME
 file associated with this data deposit.
DOI: 10.5061/dryad.64r0j
title: Data from: Rediscovery of the enigmatic fungus-farming ant "Mycetosoritis" asper Mayr (Hymenoptera: Formicidae): Implications for taxonomy, phylogeny, and the evolution of agriculture in ants

description: We report the rediscovery of the exceedingly rarely collected and
 enigmatic fungus-farming ant species Mycetosoritis asper. Since the
 description of the type specimen in 1887, only four additional specimens
 are known to have been added to the world's insect collections. Its
 biology is entirely unknown and its phylogenetic position within the
 fungus-farming ants has remained puzzling due to its aberrant morphology.
 In 2014 we excavated and collected twenty-one colonies of M. asper in the
 Floresta Nacional de Chapecó in Santa Catarina, Brazil. We describe here
 for the first time the male and larva of the species and complement the
 previous descriptions of both the queen and the worker. We describe, also
 for the first time, M. asper biology, nest architecture, and colony
 demographics, and identify its fungal cultivar. Molecular phylogenetic
 analyses indicate that both M. asper and M. clorindae are members of the
 genus Cyphomyrmex, which we show to be paraphyletic as currently defined.
 More precisely, M. asper is a member of the Cyphomyrmex strigatus group,
 which we also show to be paraphyletic with respect to the genus
 Mycetophylax. Based on these results, and in the interest of taxonomic
 stability, we transfer the species M. asper, M. clorindae, and all members
 of the C. strigatus group to the genus Mycetophylax, the oldest available
 name for this clade. Based on ITS sequence data, Mycetophylax asper
 practices lower agriculture, cultivating a fungal species that belongs to
 lower-attine fungal Clade 2, subclade F.
description: Combined Mesquite data
 file (alignment and tree)SosaCalvo_combined.nex