cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2r732
title: Data from: Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis

description: The origin of the eukaryotic cell is considered one of the major
 evolutionary transitions in the history of life. Current evidence strongly
 supports a scenario of eukaryotic origin in which two prokaryotes, an
 archaebacterial host and an α-proteobacterium (the free-living ancestor of
 the mitochondrion), entered a stable symbiotic relationship. The
 establishment of this relationship was associated with a process of
 chimerization, whereby a large number of genes from the α-proteobacterial
 symbiont were transferred to the host nucleus. A general framework
 allowing the conceptualization of eukaryogenesis from a genomic
 perspective has long been lacking. Recent studies suggest that the origins
 of several archaebacterial phyla were coincident with massive imports of
 eubacterial genes. Although this does not indicate that these phyla
 originated through the same process that led to the origin of Eukaryota,
 it suggests that Archaebacteria might have had a general propensity to
 integrate into their genomes large amounts of eubacterial DNA. We suggest
 that this propensity provides a framework in which eukaryogenesis can be
 understood and studied in the light of archaebacterial ecology. We applied
 a recently developed supertree method to a genomic dataset composed of 392
 eubacterial and 51 archaebacterial genera to test whether large numbers of
 genes flowing from Eubacteria are indeed coincident with the origin of
 major archaebacterial clades. In addition, we identified two potential
 large-scale transfers of uncertain directionality at the base of the
 archaebacterial tree. Our results are consistent with previous findings
 and seem to indicate that eubacterial gene imports (particularly from
 δ-Proteobacteria, Clostridia and Actinobacteria) were an important factor
 in archaebacterial history. Archaebacteria seem to have long relied on
 Eubacteria as a source of genetic diversity, and while the precise
 mechanism that allowed these imports is unknown, we suggest that our
 results support the view that processes comparable to those through which
 eukaryotes emerged might have been common in archaebacterial history.
description: A set of input tree
 dataset inferred using RaxMl overlapping on 443 prokaryotic genera taxon
 set.This is a directory
 containing 5 input tree datasets in newick format. Prok_dataset: is
 composed of input trees overlapping on 443 prokaryotic genera taxon set.
 Prok_MinusRogue_dataset: The same as Prok dataset except the taxa that
 were identified as unstable by a concatabomination analysis have been
 pruned out. Eubac_dataset: Also a subset of Prok, this time with the
 archaebacterial taxon set pruned out. Eubac_MinusRogue_dataset: A subset
 of Eubac_dataset with the unstable taxa pruned out. Finally Arc_dataset:
 Another subset of Prok, this time with all the eubacterial taxon set
 pruned out.Archaebacteria_evolution_input_trees_dataset.tar.gz
DOI: 10.5061/dryad.v1v47
title: Data from: Unravelling the evolutionary history and future prospects of endemic species restricted to former glacial refugia

description: The contemporary distribution and genetic composition of biodiversity bear
 a signature of species’ evolutionary histories and the effects of past
 climatic oscillations. For many European species, the Mediterranean
 peninsulas of Iberia, Italy and the Balkans acted as glacial refugia and
 the source of range recolonization, and as a result, they contain
 disproportionately high levels of diversity. As these areas are
 particularly threatened by future climate change, it is important to
 understand how past climatic changes affected their biodiversity. We use
 an integrated approach, combining markers with different evolutionary
 rates and combining phylogenetic analysis with approximate Bayesian
 computation and species distribution modelling across temporal scales. We
 relate phylogeographic processes to patterns of genetic variation in
 Myotis escalerai, a bat species endemic to the Iberian Peninsula. We found
 a distinct population structure at the mitochondrial level with a strong
 geographic signature, indicating lineage divergence into separate glacial
 refugia within the Iberian refugium. However, microsatellite markers
 suggest higher levels of gene flow resulting in more limited structure at
 recent time frames. The evolutionary history of M. escalerai was shaped by
 the effects of climatic oscillations and changes in forest cover and
 composition, while its future is threatened by climatically induced range
 contractions and the role of ecological barriers due to competition
 interactions in restricting its distribution. This study warns that
 Mediterranean peninsulas, which provided refuge for European biodiversity
 during past glaciation events, may become a trap for limited dispersal and
 ecologically limited endemic species under future climate change,
 resulting in loss of entire lineages.
description: Razgour_etal15_M_escalerai_locations_MaxentMyotis escalerai location records used in the species distribution modelling.Razgour_etal15_M_escalerai_sequencesAligned mtDNA cytochrome b sequences for all Myotis escalerai individuals.Razgour_etal15_M_escalerai_MrBayes_inputNexus input file of collapsed Myotis escalerai haplotypes for MrBayes phylogenetic analysis.Razgour_etal15_M_escalerai_MrBayes_tree.conMrBayes tree file underlying the phylogeny for Myotis escalerai cytochrome b haplotypes.Razgour_etal15_Structure_allStructure input file for full Myotis escalerai microsatellite dataset.Razgour_etal15_Structure_no_relativesStructure input file for Myotis escalerai microsatellite dataset with relatives removed.Razgour_etal15_MolEcol_Structure_ResultsStructure results and individual assignments for Myotis escalerai full and no relatives microsatellite datasets.
DOI: 10.5061/dryad.90kj2
title: Data from: Normal vision can compensate for the loss of the circadian clock.

description: Circadian clocks are thought to be essential for timing the daily activity
 of animals, and consequently increase fitness. This view was recently
 challenged for clock-less fruit flies and mice that exhibited
 astonishingly normal activity rhythms under outdoor conditions.
 Compensatory mechanisms appear to enable even clock mutants to live a
 normal life in nature. Here, we show that gradual daily
 increases/decreases of light in the laboratory suffice to provoke normally
 timed sharp morning (M) and evening (E) activity peaks in clock-less
 flies. We also show that the compound eyes, but not Cryptochrome (CRY),
 mediate the precise timing of M and E peaks under natural-like conditions,
 as CRY-less flies do and eyeless flies do not show these sharp peaks
 independently of a functional clock. Nevertheless, the circadian clock
 appears critical for anticipating dusk, as well as for inhibiting sharp
 activity peaks during midnight. Clock-less flies only increase E activity
 after dusk and not before the beginning of dusk, and respond strongly to
 twilight exposure in the middle of the night. Furthermore, the circadian
 clock responds to natural-like light cycles, by slightly broadening
 Timeless (TIM) abundance in the clock neurons, and this effect is mediated
 by CRY.
description: Raw Data Schlichting et
 al
DOI: 10.5061/dryad.58q00
title: Data from: Pertussis immunity and epidemiology: mode and duration of vaccine-induced immunity

description: The resurgence of pertussis in some countries that maintain high
 vaccination coverage has drawn attention to gaps in our understanding of
 the epidemiological effects of pertussis vaccines. In particular, major
 questions surround the nature, degree and durability of vaccine
 protection. To address these questions, we used mechanistic transmission
 models to examine regional time series incidence data from Italy in the
 period immediately following the introduction of acellular pertussis (aP)
 vaccine. Our results concur with recent animal-challenge experiments
 wherein infections in aP-vaccinated individuals proved as transmissible as
 those in naive individuals but much less symptomatic. On the other hand,
 the data provide evidence for vaccine-driven reduction in susceptibility,
 which we quantify via a synthetic measure of vaccine impact. As to the
 precise nature of vaccine failure, the data do not allow us to distinguish
 between leakiness and waning of vaccine immunity, or some combination of
 these. Across the range of well-supported models, the nature and duration
 of vaccine protection, the age profile of incidence and the range of
 projected epidemiological futures differ substantially, underscoring the
 importance of the remaining unknowns. We identify key data gaps: sources
 of data that can supply the information needed to eliminate these
 remaining uncertainties.
description: Example workflow for
 parameter estimationThis archive contains a
 sample workflow for deriving the parameter sets to generate the plots in
 "Pertussis immunity and epidemiology: mode and duration of
 vaccine-induced immunity."Workflow.zipR Code for Plots in "Immunity and epidemiology: integrating theory and data for pertussis"This archive contains all of the required code to generate the figures and tables in the paper "Immunity and epidemiology: integrating theory and data for pertussis."FinalPlots.zip
DOI: 10.5061/dryad.tv380
title: Data from: Butterfly density and behaviour in uncut hay meadow strips: behavioral ecological consequences of an agri-environmental scheme

description: Sparing zones from mowing has been proposed, and applied, to improve local
 conditions for survival and reproduction of insects in hay meadows.
 However, little is known about the efficiency of refuge zones and the
 consequences for local populations. We studied population densities of
 butterflies before and after mowing in the refuge zone of 15 meadows in
 2009 and 2011. We also studied the behaviour of the meadow brown (Maniola
 jurtina) comparing nectar use, interactions and flights in the refuge zone
 before and after mowing. Densities of grassland butterflies in this zone
 doubled on average after mowing. The density of females of M. jurtina
 increased on average fourfold, while males showed a more modest increase.
 In line with the idea of increased scramble competition in the refuge zone
 after mowing, M. jurtina increased the time spent on nectar feeding, the
 preferred nectar source was visited more frequently, and females made more
 use of non-preferred nectar sources. Maniola jurtina did not interact more
 with conspecifics after mowing, but interactions lasted longer. Flight
 tracks did not change in linearity, but were faster and shorter after
 mowing. After mowing, only a part of the local grassland butterflies moved
 to the uncut refuge zone. The resulting concentration effect alters the
 time allocated to different activities, nectar use and movements. These
 aspects have been largely ignored for agri-environmental schemes and
 grassland management in nature reserves and raise questions about optimal
 quantities and quality of uncut refuge sites for efficient conservation of
 grassland arthropods in agricultural landscapes.
description: activity during transect
 countsCollected in the fiedl
 by Julie Lebeau.data JL et.
 al.activity_in_transects.pdftime allocated to feed
 during butterfly trackingsProportion of time
 allocated to feed during butterfly tracks.Collected in the field by Julie
 Lebeau.data
 JL et. al.feeding.pdfProportion of the
 feeding time that targeted Cj during butterfly trackingsCollected in the field
 by Julie Lebeaudata JL et.
 al.feeding_Cj.pdfFlight path observed
 during butterfly trackingsCollected by Julie
 Lebeaudata
 JL et.
 al.flight_path_analysis.pdfVisits on introduced
 potted plants recorded by camera recordersCollected by Julie
 Lebeau in the field.data JL et.
 al.flower_head_visitation.pdfInteractions during
 butterfly trackingsCollected in the field
 bu Julie Lebeau.data JL et.
 al.interacting.pdfNumber of activity
 changes during butterfly trackingsCollected by Julie
 Lebeau in the fielddata JL et.
 al.Nbr_activity°changes.pdfButterfly transect
 countsCollected by Julie
 Lebeau in the fielddata JL et.
 al.transects_counts.pdf
DOI: 10.5061/dryad.r3b5d
title: Data from: Initial colonization, community assembly, and ecosystem function: fungal colonist traits and litter biochemistry mediate decay rate

description: Priority effects are an important ecological force shaping biotic
 communities and ecosystem processes, in which the establishment of early
 colonists alters the colonization success of later-arriving organisms via
 competitive exclusion and habitat modification. However, we do not
 understand which biotic and abiotic conditions lead to strong priority
 effects and lasting historical contingencies. Using saprotrophic fungi in
 a model leaf decomposition system, we investigated whether compositional
 and functional consequences of initial colonization were dependent on
 initial colonizer traits, resource availability or a combination thereof.
 To test these ideas, we factorially manipulated leaf litter biochemistry
 and initial fungal colonist identity, quantifying subsequent community
 composition, using neutral genetic markers, and community functional
 characteristics, including enzyme potential and leaf decay rates. During
 the first 3 months, initial colonist respiration rate and physiological
 capacity to degrade plant detritus were significant determinants of fungal
 community composition and leaf decay, indicating that rapid growth and
 lignolytic potential of early colonists contributed to altered
 trajectories of community assembly. Further, initial colonization on oak
 leaves generated increasingly divergent trajectories of fungal community
 composition and enzyme potential, indicating stronger initial colonizer
 effects on energy-poor substrates. Together, these observations provide
 evidence that initial colonization effects, and subsequent consequences on
 litter decay, are dependent upon substrate biochemistry and physiological
 traits within a regional species pool. Because microbial decay of plant
 detritus is important to global C storage, our results demonstrate that
 understanding the mechanisms by which initial conditions alter priority
 effects during community assembly may be key to understanding the drivers
 of ecosystem-level processes.
description: 28S Sequence
 Alignment28S Sequence Alignments,
 one .fasta file for each harvest date28S_sequence_alignment.zip28S Tree File28S tree files, one file for each harvest data28S_tree_file.zip28S OTU tables28S OTUs tables, one file for each harvestCommunity Enzyme Dataenzyme_AH_all_harvests.txtCommunity Respiration AccumulationRespiration data was added weekly for the first 14 weeks of the experiment, and used for curve fittingAH_resp_accumulation_forcurvefitting.txtCommunity Ash-free massash_free_mass_AH_all_harvests.txt
DOI: 10.5061/dryad.vp18t
title: Data from: A comparison of breeding population estimators using nest and brood monitoring data

description: For many species, breeding population size is an important metric for
 assessing population status. A variety of simple methods are often used to
 estimate this metric for ground-nesting birds that nest in open habitats
 (e.g., beaches, riverine sandbars). The error and bias associated with
 estimates derived using these methods vary in relation to differing
 monitoring intensities and detection rates. However, these errors and
 biases are often difficult to obtain, poorly understood, and largely
 unreported. A method was developed to estimate the number of breeding
 pairs using counts of nests and broods from monitoring data where multiple
 surveys were made throughout a single breeding season (breeding pair
 estimator; BPE). The BPE method was compared to two commonly used
 estimation methods using simulated data from an individual-based model
 that allowed for the comparison of biases and accuracy. The BPE method
 underestimated the number of breeding pairs, but generally performed
 better than the other two commonly used methods when detection rates were
 low and monitoring frequency was high. As detection rates and time between
 surveys increased, the maximum nest and brood count method performs
 similar to the BPE. The BPE was compared to four commonly used methods to
 estimate breeding pairs for empirically derived data sets on the Platte
 River. Based on our simulated data, we expect our BPE to be closest to the
 true number of breeding pairs as compared to other methods. The methods
 tested resulted in substantially different estimates of the numbers of
 breeding pairs; however, coefficients from trend analyses were not
 statistically different. When data from multiple nest and brood surveys
 are available, the BPE appears to result in reasonably precise estimates
 of numbers of breeding pairs. Regardless of the estimation method,
 investigators are encouraged to acknowledge whether the method employed is
 likely to over- or underestimate breeding pairs. This study provides a
 means to recognize the potential biases in breeding pair estimates.
description: Breeding Pair Estimator
 SpreadsheetThis is a user-friendly
 spreadsheet that allows users the ability to obtain estimates of avian
 breeding pairs using the Breeding Pair Estimator (BPE). The associated
 'ReadMe' file is a tutorial with instructions for how to input
 data successfully into the BPE spreadsheet.Appendix S2 -
 Spreadsheet.xlsx
DOI: 10.5061/dryad.0m764
title: Data from: Diffusion tensor imaging in patients with glioblastoma multiforme using the supertoroidal model

description: Purpose: Diffusion Tensor Imaging (DTI) is a powerful imaging technique
 that has led to improvements in the diagnosis and prognosis of cerebral
 lesions and neurosurgical guidance for tumor resection. Traditional tensor
 modeling, however, has difficulties in differentiating tumor-infiltrated
 regions and peritumoral edema. Here, we describe the supertoroidal model,
 which incorporates an increase in surface genus and a continuum of
 toroidal shapes to improve upon the characterization of Glioblastoma
 multiforme (GBM). Materials and Methods: DTI brain datasets of 18
 individuals with GBM and 18 normal subjects were acquired using a 3T
 scanner. A supertoroidal model of the diffusion tensor and two new
 diffusion tensor invariants, one to evaluate diffusivity, the toroidal
 volume (TV), and one to evaluate anisotropy, the toroidal curvature (TC),
 were applied and evaluated in the characterization of GBM brain tumors. TV
 and TC were compared with the mean diffusivity (MD) and fractional
 anisotropy (FA) indices inside the tumor, surrounding edema, as well as
 contralateral to the lesions, in the white matter (WM) and gray matter
 (GM). Results: The supertoroidal model enhanced the borders between tumors
 and surrounding structures, refined the boundaries between WM and GM, and
 revealed the heterogeneity inherent to tumor-infiltrated tissue. Both MD
 and TV demonstrated high intensities in the tumor, with lower values in
 the surrounding edema, which in turn were higher than those of unaffected
 brain parenchyma. Both TC and FA were effective in revealing the
 structural degradation of WM tracts. Conclusions: Our findings indicate
 that the supertoroidal model enables effective tensor visualization as
 well as quantitative scalar maps that improve the understanding of the
 underlying tissue structure properties. Hence, this approach has the
 potential to enhance diagnosis, preoperative planning, and intraoperative
 image guidance during surgical management of brain lesions.
description: DataThese anonymized data
 include 18 control subjects and 18 patients with GBM in Analyze
 format.
DOI: 10.5061/dryad.817h6
title: Data from: Characterizing forest structure variations across an intact tropical peat dome using field samplings and airborne LiDAR

description: Tropical peat swamp forests (PSF) are one of the most carbon dense
 ecosystems on the globe and are experiencing substantial natural and
 anthropogenic disturbances. In this study we combined direct field
 sampling and airborne LiDAR to empirically quantify forest structure and
 aboveground live biomass (AGB) across a large, intact tropical peat dome
 in Northwestern Borneo. Moving up a 4m elevational gradient, we observed
 increasing stem density but decreasing canopy height, crown area and crown
 roughness. These findings were consistent with hypotheses that nutrient
 and hydrological dynamics co-influence forest structure and stature of the
 canopy individuals, leading to reduced productivity towards the dome
 interior. Gap frequency as a function of gap size followed a power law
 distribution with a shape factor (?) of 1.76 ± 0.06. Ground-based and
 dome-wide estimates of AGB were 217.7 ± 28.3 Mg C ha-1, and 222.4 ± 24.4
 Mg C ha-1, respectively, which were higher than previously reported AGB
 for PSF and tropical forests in general. However, dome-wide AGB estimates
 were based on height statistics and we found the coefficient of variation
 on canopy height was only 0.08, three times less than stem diameter
 measurements, suggesting LiDAR height metrics may not be a robust
 predictor of AGB in tall tropical forests with dense canopies. Our
 structural characterization of this ecosystem advances the understanding
 of the ecology of intact tropical peat domes and factors that influence
 biomass density and landscape-scale spatial variation. This ecological
 understanding is essential to improve estimates of forest carbon density
 and its spatial distribution in PSF and to effectively model the effects
 of disturbance and deforestation in these carbon dense ecosystems.
description: STEM LOCATIONS AND
 HEIGHTS IN ULU MENDARAMTHE STEM LOCATIONS AND
 HEIGHTS WERE EXTRACTED USING LOCAL MAXIMA FILTERING FROM A CANOPY HEIGHT
 MODEL AT 0.5M. THE CANOPY HEIGHT MODEL WAS PRODUCED USING SMALL FOOTPRINT
 AIRBORNE LIDAR DATA ACQUIRED IN 2010 OVER BRUNEI.md_stems.zipMendaram live tree survey 2014Csv contaning biometric data for live trees in Mendaram, Belait, Brunei.MENDARAM_LIVE_TREES_SURVEY_2014_Dryad.csv