cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tc6r3
title: Data from: Toward translating near-infrared spectroscopy oxygen saturation data for the non-invasive prediction of spatial and temporal hemodynamics during exercise

description: Image-based computational fluid dynamics (CFD) studies conducted at rest
 have shown that atherosclerotic plaque in the thoracic aorta (TA)
 correlates with adverse wall shear stress (WSS), but there is a paucity of
 such data under elevated flow conditions. We developed a pedaling exercise
 protocol to obtain phase contrast magnetic resonance imaging (PC-MRI)
 blood flow measurements in the TA and brachiocephalic arteries during
 three-tiered supine pedaling at 130, 150, and 170 % of resting heart rate
 (HR), and relate these measurements to non-invasive tissue oxygen
 saturation [Formula: see text] acquired by near-infrared spectroscopy
 (NIRS) while conducting the same protocol. Local quantification of WSS
 indices by CFD revealed low time-averaged WSS on the outer curvature of
 the ascending aorta and the inner curvature of the descending aorta (dAo)
 that progressively increased with exercise, but that remained low on the
 anterior surface of brachiocephalic arteries. High oscillatory WSS
 observed on the inner curvature of the aorta persisted during exercise as
 well. Results suggest locally continuous exposure to potentially
 deleterious indices of WSS despite benefits of exercise. Linear
 relationships between flow distributions and tissue oxygen extraction
 calculated from [Formula: see text] were found between the left common
 carotid versus cerebral tissue [Formula: see text] and the dAo versus leg
 tissue [Formula: see text]. A resulting six-step procedure is presented to
 use NIRS data as a surrogate for exercise PC-MRI when setting boundary
 conditions for future CFD studies of the TA under simulated exercise
 conditions. Relationships and ensemble-averaged PC-MRI inflow waveforms
 are provided in an online repository for this purpose.
description: Use of NIRS data as
 boundary conditions for CFD simulations (PMID27376865)This Excel file contains
 the following 4 worksheets that allow researchers to confirm, extend and
 apply the findings from PMID 27376865: Worksheet 1 - Windkessel parameters
 from Table 1 of the paper; Worksheet 2 - A blood flow distribution
 calculator that uses NIRS data as input; Worksheet 3 - Ensemble-averaged
 (n=6) blood flow waveforms in the ascending aorta under resting blood flow
 conditions and three levels of exercise; Worksheet 4 - A waveform creator
 that automatically generates ascending aortic blood flow waveforms during
 rest and exercise using cardiac output and heart rate data from any
 patient.DryadRespository_PMID27376865.xls
DOI: 10.5061/dryad.53vg0
title: Data from: Interaction specificity between leaf-cutting ants and vertically transmitted Pseudonocardia bacteria

description: Background: The obligate mutualism between fungus-growing ants and
 microbial symbionts offers excellent opportunities to study the
 specificity and stability of multi-species interactions. In addition to
 cultivating fungus gardens, these ants have domesticated actinomycete
 bacteria to defend gardens against the fungal parasite Escovopsis and
 possibly other pathogens. Panamanian Acromyrmex echinatior leaf-cutting
 ants primarily associate with actinomycetes of the genus Pseudonocardia.
 Colonies are inoculated with one of two vertically transmitted phylotypes
 (Ps1 or Ps2), and maintain the same phylotype over their lifetime. We
 performed a cross-fostering experiment to test whether co-adaptations
 between ants and bacterial phylotypes have evolved, and how this affects
 bacterial growth and ant prophylactic behavior after infection with
 Escovopsis. Results: We show that Pseudonocardia readily colonized ants
 irrespective of their colony of origin, but that the Ps2 phylotype, which
 was previously shown to be better able to maintain its monocultural
 integrity after workers became foragers than Ps1, reached a higher final
 cover when grown on its native host than on alternative hosts. The
 frequencies of major grooming and weeding behaviors co-varied with
 symbiont/host combinations, showing that ant behavior also was affected
 when cuticular actinomycete phylotypes were swapped. Conclusion: These
 results show that the interactions between leaf-cutting ants and
 Pseudonocardia bear signatures of mutual co-adaptation within a single ant
 population.
description: Bacterial cover
 dataBacterial cover of A.
 echinatior ants scored from 0-12. Each ant is identified by an ID and the
 host and donor colony noted. Each treatment was replicated and each sub
 colony harboured 4 ants. Bacterial cover was scored on day 1, 4, 8, 12 and
 16 after eclosion, at the time of experimental infection with Escovopsis
 and 2 weeks post infection. From these scores the logistic growth rate was
 estimated and subsequently this rate was Box-Cox transformed. Some
 subcolonies were excluded from the analysis due to garden
 loss.Behaviour
 dataBehaviours performed by
 cross-fostered A. echinatior ants following experimental Escovopsis
 infection. For each sub-colony the frequency of behaviours performed by
 all individuals is noted, together with the proportion of time spent on
 each and the first four principal components following PCA. Some
 sub-colonies were excluded from the analysis due to garden
 loss.
DOI: 10.5061/dryad.r0d1j88
title: Data from: Let the most motivated win: resource value components affect contest outcome in a parasitoid wasp

description: Studying physical contests for indivisible resources is a major theme in
 behavioral ecology. Intensity (aggressiveness) and outcome of such
 contests may be influenced by individual abilities to gain and keep the
 resource (Resource Holding Potential, RHP), but also by the value they
 place in the resource (Resource Value, RV). Contestants can assess
 resource quality directly (objective RV) or estimate it according to their
 physiological status and their experience (subjective RV). In some
 parasitoid species, adult females fight for hosts on which they lay eggs
 and feed. Here, we studied contests between two females of the solitary
 parasitoid Eupelmus vuilleti when exploiting simultaneously a host: a
 fourth instar larva or a pupa of the cowpea seed beetle Callosobruchus
 maculatus. We first demonstrated that fourth instar larvae represent a
 resource of higher objective RV because offspring that developed on such
 hosts were heavier. We then showed that both objective (host quality) and
 subjective (initial egg load and habitat quality) RV did not influence
 oviposition decisions, but interacted to affect aggressiveness and
 contests outcome. Females won more frequently when they had more mature
 eggs than their opponent, but this effect was less pronounced when
 fighting for a high quality host. In addition, females from high-quality
 habitat were more aggressive and more frequently won contests over low
 quality hosts, while females from low quality habitat were more aggressive
 and more frequently won contests over high quality hosts. This experiment
 thus highlights the complex relationships existing between key factors
 that affect animals’ conflict resolution.
description: Mathiron_et_al_2018_resource_value_contest_wasp_data_filesThis xlm file contains all the data required to reproduce analyses reported in the associated paper.Mathironetal_2018_datafiles.xml
DOI: 10.5061/dryad.69sg2
title: Data from: Carbon content of tree tissues: a synthesis

description: Assessing the potential for forest carbon (C) capture and storage requires
 accurate assessments of C in live tree tissues. In the vast majority of
 local, regional, and global assessments, C content has been assumed to be
 50% of tree biomass; however, recent studies indicate that this assumption
 is not accurate, with substantial variation in C content among tree
 species as well as among tissue types. Here we conduct a comprehensive
 literature review to present a global synthesis of C content in tissues of
 live trees. We found a total of 253 species-specific stem wood C content
 records owing to 31 studies, and an additional 34 records of species with
 C content values of other tissues in addition to stem wood. Stem wood C
 content varied significantly as a function of biome (tropical,
 subtropical/ Mediterranean, temperate/ boreal) and species type (conifer,
 angiosperm). Conifer species exhibited greater wood C content than
 angiosperm species (50.8 ± 0.7% (95% C.I.) vs. 47.7 ± 0.3%, respectively),
 a trend that was consistent among all biomes. Although studies have
 documented differences in C content among plant tissues, interspecific
 differences in stem wood appear to be of greater importance overall: among
 species, stem wood C content explained 37, 76, 48, 81, and 63%
 respectively of the variation in bark, branch, twig, coarse root, and fine
 root C content values, respectively. In each case, these intraspecific
 patterns approximated 1:1 linear relationships. Most published stem wood C
 content values (and all values for other tree tissues) are based on dried
 wood samples, and so neglect volatile C constituents that constitute on
 average 1.3 – 2.5% of total C in live wood. Capturing this volatile C
 fraction is an important methodological consideration for future studies.
 Our review, and associated data compilation, provides empirically
 supported wood C fractions that can be easily incorporated into forest C
 accounting, and may correct systematic errors of ~1.6 – 5.8% in forest C
 assessments.
description: Thomas_and_Martin_Dryad_global_wood_carbon_database
DOI: 10.5061/dryad.8h6k1
title: Data from: Model-based analysis supports interglacial refugia over long-dispersal events in the diversification of two South American cactus species

description: Pilosocereus machrisii and P. aurisetus are cactus species within the P.
 aurisetus complex, a group of eight cacti that are restricted to rocky
 habitats within the Neotropical savannas of eastern South America.
 Previous studies have suggested that diversification within this complex
 was driven by distributional fragmentation, isolation leading to
 allopatric differentiation, and secondary contact among divergent
 lineages. These events have been associated with Quaternary climatic
 cycles, leading to the hypothesis that the xerophytic vegetation patches
 which presently harbor these populations operate as refugia during the
 current interglacial. However, owing to limitations of the standard
 phylogeographic approaches used in these studies, this hypothesis was not
 explicitly tested. Here we use Approximate Bayesian Computation to refine
 the previous inferences and test the role of different events in the
 diversification of two species within P. aurisetus group. We used
 molecular data from chloroplast DNA and simple sequence repeats loci of P.
 machrisii and P. aurisetus, the two species with broadest distribution in
 the complex, in order to test if the diversification in each species was
 driven mostly by vicariance or by long-dispersal events. We found that
 both species were affected primarily by vicariance, with a refuge model as
 the most likely scenario for P. aurisetus and a soft vicariance scenario
 most probable for P. machrisii. These results emphasize the importance of
 distributional fragmentation in these species, and add support to the
 hypothesis of long-term isolation in interglacial refugia previously
 proposed for the P. aurisetus species complex diversification.
description: Perezetal_2016_Pilosocereus_SSRdataSSR data from populations of Pilosocereus aurisetus and P. machrisii species (Cactaceae)Perez_etal_2016_Pilosocereus.xlsxrunms_PaurA python script to draw values for the parameters tau, theta, ancient migration, current migration, bottleneck and population expansion. This file contains the 7 models tested in this study and outputs the ms' simulation results for both cpDNA and SSR markers in the species P. aurisetus.runms_PmacA python script to draw values for the parameters tau, theta, ancient migration, current migration, bottleneck and population expansion. This file contains the 7 models tested in this study and outputs the ms' simulation results for both cpDNA and SSR markers in the species P. machrisii.runPPC_PaurRetrieve parameter values from the parameter estimates of the selected in the P. aurisetus dataset and use them to simulate new data to perform PPC analysis.runPPC_PmacRetrieve parameter values from the parameter estimates of the selected in the P. machrisii dataset and use them to simulate new data to perform PPC analysis.microsat2arpA python script that converts the microsatellite data from ms' accessory program microsat to the arlequin format.
DOI: 10.5061/dryad.t24pq
title: Data from: Epidemiological implications of host biodiversity and vector biology: key insights from simple models

description: Models used to investigate the relationship between biodiversity change
 and vector-borne disease risk often do not explicitly include the vector;
 they instead rely on a frequency-dependent transmission function to
 represent vector dynamics. However, differences between classes of vector
 (e.g., ticks and insects) can cause discrepancies in epidemiological
 responses to environmental change. Using a pair of disease models
 (mosquito- and tick-borne), we simulated substitutive and additive
 biodiversity change (where noncompetent hosts replaced or were added to
 competent hosts, respectively), while considering different relationships
 between vector and host densities. We found important differences between
 classes of vector, including an increased likelihood of amplified disease
 risk under additive biodiversity change in mosquito models, driven by
 higher vector biting rates. We also draw attention to more general
 phenomena, such as a negative relationship between initial infection
 prevalence in vectors and likelihood of dilution, and the potential for a
 rise in density of infected vectors to occur simultaneously with a decline
 in proportion of infected hosts. This has important implications; the
 density of infected vectors is the most valid metric for primarily
 zoonotic infections, while the proportion of infected hosts is more
 relevant for infections where humans are a primary host.
description: Dobson & Auld AmNat
 codeAll code (in R),
 including graphing. Tinn-R file, but should open in Notepad, Wordpad,
 etc..
DOI: 10.5061/dryad.0v6f8
title: Data from: A tapetal ablation transgene induces stable male-sterility and slows field growth in Populus

description: The field performance of genetic containment technologies–considered
 important for certain uses of transgenic trees in forestry–is poorly
 known. We tested the efficiency of a barnase gene driven by the TA29
 tapetum-dominant promoter for influencing growth rate and inducing male
 sterility in a field trial of transgenic hybrid poplar (Populus
 tremula × Populus tremuloides). When the growth of 18 transgenic insertion
 events with the sterility transgene were compared to non-transgenic
 controls after two growing seasons, they grew 40 % more slowly in stem
 volume, and all but one transgenic event grew significantly more slowly
 than the control. In contrast, when we compared the growth of transgenic
 trees containing four kinds of β-glucuronidase (GUS) reporter gene
 constructs to non-transgenic trees—all of which had been produced using
 the same transformation method and poplar clone and grown at the same
 field site—there were no statistically significant differences in growth
 after three growing seasons. In 2 years where gross pollen release from
 catkins was monitored and found to be abundant in the control, no pollen
 was visible in the transgenic trees; microscopy suggested the cause was
 tapetal collapse and revealed the presence of a very few normal-sized
 pollen grains of unknown viability. In two additional years when viable,
 well-formed pollen was microscopically documented in controls, and no
 pollen could be observed in any transgenic trees. We conclude that this
 construct resulted in robust and possibly complete male sterility that was
 stable over 4 years in the field.
description: Growth data of the trees
 involved in the barnase sterility trialSterility_VolumeIndex.xlsxGrowth data of the trees involved in the reporter trialReporter_VolumeIndex.xlsxCatkin length, weight, and angle dataThe length, weight, and angle of catkins from the trees in the sterility trial were measured and compared to that of non-transgenic controls.Catkin_length_weight.xlsxPollen count and viability data for the trees in the barnase sterility trialPollen_count.xlsxR programming codeProgramming code for R used when comparing the growth data of the sterility and reporter trees to the data of the non-transgenic controlsR code.txt
DOI: 10.5061/dryad.5c88j
title: Data from: Genotypic variation in a foundation tree (Populus tremula L.) explains community structure of associated epiphytes

description: Community genetics hypothesizes that within a foundation species the
 genotype of an individual significantly influences the assemblage of
 dependent organisms. To assess whether these intra-specific genetic
 effects are ecologically important, it is required to compare their impact
 on dependent organisms with that attributable to environmental variation
 experienced over relevant spatial scales. We assessed bark epiphytes on 27
 aspen (Populus tremula L.) genotypes grown in a randomized experimental
 array at two contrasting sites spanning the environmental conditions from
 which the aspen genotypes were collected. We found that variation in aspen
 genotype significantly influenced bark epiphyte community composition, and
 to the same degree as environmental variation between the test sites. We
 conclude that maintaining genotypic diversity of foundation species may be
 crucial for conservation of associated biodiversity.
description: Aspen epiphytes
 Davies_et_al (1)Frequency of occurrence
 of epiphyte species on clones of aspen replicated in blocks at two sites.
 Data are from 5 cm x 25 cm quadrats divided into sub-quadrats of 5 cm x 5
 cm, each with 1 cm x 1 cm subunits. Quadrats were place at cardinal points
 on the bole at a height of 1.3 m..raw_data_Davies_et_al
 (1).xlsx
DOI: 10.5061/dryad.3tk7g
title: Data from: Contrasting impacts of land use change on phylogenetic and functional diversity of tropical forest birds

description: 1.Biodiversity conservation strategies increasingly target maintaining
 evolutionary history and the resilience of ecosystem function, not just
 species richness (SR). This has led to the emergence of two metrics
 commonly proposed as tools for decision making: phylogenetic diversity
 (PD) and functional diversity (FD). Yet the extent to which they are
 interchangeable remains poorly understood. 2.We explore shifts in and
 relationships between FD and PD of bird communities across a disturbance
 gradient in Borneo, from old-growth tropical forest to oil palm
 plantation. 3.We show a marked decline in PD, and an increase in
 phylogenetic mean nearest taxon distance (MNTD) from forest to oil palm,
 in line with declining SR across the gradient. However, phylogenetic mean
 pairwise distance (MPD) is constrained by forest logging more than by
 conversion to oil palm, taking account of SR. 4.The decline in FD across
 the gradient is less severe than in PD, with all metrics indicating
 relatively high trait diversity in oil palm despite low SR, although
 functional redundancy is much reduced. Accounting for SR, levels of
 functional over- or under-dispersion of bird communities are strongly
 coupled to habitat disturbance level rather than to any equivalent
 phylogenetic metric. 5.Policy Implications. We suggest that while
 phylogenetic diversity (PD) is an improvement on species richness as a
 proxy for functional diversity (FD), conservation decisions based on PD
 alone cannot reliably safeguard maximal FD. Thus, PD and FD are related
 but still complementary. Priority setting exercises should use these
 metrics in combination to identify conservation targets.
description: Trait
 MatrixTrait matrix used in
 calculation of our functional diversity indices.Chapman_trait_matrix.csvCommunity matrixCommunity matrix used in the calculation of our functional diversity indices.Chapman_community_matrix.csv
DOI: 10.5061/dryad.dg715
title: Data from: Organismal responses to habitat change: herbivore performance, climate, and leaf traits in regenerating tropical dry forests

description: 1. The ecological effects of large-scale climate change have received much
 attention, but the effects of the more acute form of climate change that
 results from local habitat alteration have been less explored. When forest
 is fragmented, cut, thinned, cleared or otherwise altered in structure,
 local climates and microclimates change. Such changes can affect
 herbivores both directly (e.g., through changes in body temperature) and
 indirectly (e.g., through changes in host plant traits). 2. We advance an
 eco-physiological framework to understand the effects of changing forests
 on herbivorous insects. We hypothesize that if tropical forest
 caterpillars are climate and resource specialists, then they should have
 reduced performance outside of mature forest conditions. 3. We tested this
 hypothesis with a field experiment contrasting the performance of
 Rothschildia lebeau (Saturniidae) caterpillars feeding on the host plant
 Casearia nitida (Salicaceae) in two different aged and structured tropical
 dry forests in Area de Conservación Guanacaste, Costa Rica. 4. Compared to
 more mature closed-canopy forest, in younger secondary forest we found
 that: (1) ambient conditions were hotter, drier, and more variable; (2)
 caterpillar growth and development were reduced; and (3) leaves were
 tougher, thicker, and drier. Further, caterpillar growth and survival were
 negatively correlated with these leaf traits, suggesting indirect
 host-mediated effects of climate on herbivores. 5. Based on the available
 evidence, and relative to mature forest, we conclude that reduced
 herbivore performance in young secondary forest could have been driven by
 changes in climate, leaf traits (which were likely climate induced), or
 both. However, additional studies will be needed to provide more direct
 evidence of cause-and-effect and to disentangle the relative influence of
 these factors on herbivore performance in this system.
description: Climate and leaf
 temperature dataThis Excel file contains
 climate and leaf temperature data collected in the field at two principal
 study sites representative of two different habitats, relatively mature
 (&gt; 80 yrs) and relatively young (&lt; 50 yrs) tropical dry forest, in
 the Area de Conservación Guanacaste, Costa Rica. These data were collected
 during the same time period at the same sites and on the same trees as the
 caterpillar performance and leaf trait data. See article for further
 details.Caterpillar performance
 dataThis Excel file contains
 the results of the field experiment on caterpillar performance. Note that
 data on caterpillar mass were collected only twice during the experiment,
 on the first and last collection dates for each family. See article for
 further details.Caterpillar
 performance.xlsxLeaf trait
 dataThis Excel file contains
 data on the suite of leaf traits measured for each tree used in the
 caterpillar performance experiment. See article for further
 details.Leaf
 traits.xlsx