cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t1g1jwszq
title: Data from: Resident microbial communities inhibit growth and antibiotic resistance evolution of Escherichia coli in human gut microbiome samples

description: Countering the rise of antibiotic resistant pathogens requires improved
 understanding of how resistance emerges and spreads in individual species,
 which are often embedded in complex microbial communities such as the
 human gut microbiome. Interactions with other microorganisms in such
 communities might suppress growth and resistance evolution of individual
 species (e.g. via resource competition), but could also potentially
 accelerate resistance evolution via horizontal transfer of resistance
 genes. It remains unclear how these different effects balance out, partly
 because it is difficult to observe them directly. Here, we used a gut
 microcosm approach to quantify the effect of three human gut microbiome
 communities on growth and resistance evolution of a focal strain
 of Escherichia coli. We found the resident microbial communities
 not only suppressed growth and colonization by focal E. coli,
 they also prevented it from evolving antibiotic resistance upon exposure
 to a beta-lactam antibiotic. With samples from all three human donors, our
 focal E. colistrain only evolved antibiotic resistance in the
 absence of the resident microbial community, even though we found
 resistance genes, including a highly effective resistance plasmid, in
 resident microbial communities. We identified physical constraints on
 plasmid transfer that can explain why our focal strain failed to acquire
 some of these beneficial resistance genes, and we found some chromosomal
 resistance mutations were only beneficial in the absence of the resident
 microbiota. This suggests, depending on in situgene transfer
 dynamics, interactions with resident microbiota can inhibit antibiotic
 resistance evolution of individual species.
DOI: 10.5061/dryad.h9w0vt4fd
title: Half-Dose Fulvestrant plus Anastrozole as a First-Line Treatment for Hormone Receptor-Positive Metastatic Breast Cancer: A Cost-Effectiveness Analysis

description: Abstract Objective The S0226 trial demonstrated that the combination of
 half-dose fulvestrant (FUL) and anastrozole (ANA) (F&A) caused a
 significant improvement in overall survival (OS) versus ANA monotherapy
 for first-line treatment of postmenopausal women with hormone
 receptor-positive metastatic breast cancer (PMW-MBC[HR+]). The objective
 of this study was to evaluate the cost-effectiveness of F&A in the
 first-line treatment for PMW-MBC(HR+) in China. Design We constructed a
 Markov model over a life-time horizon. The clinical outcomes and utility
 data were obtained from published literature. Cost data were obtained from
 official Chinese websites. Sensitivity analyses were performed to test
 result uncertainty. Setting Chinese health care system perspective.
 Population A hypothetical cohort of adult patients presenting with
 PMW-MBC(HR+). Interventions F&A compared with full-dose FUL and
 ANA monotherapy. Main outcome measures The main outcome of this study was
 the incremental cost-effectiveness ratio (ICER) and quality-adjusted
 life-years (QALY). Results ANA was estimated to have the lowest cost and
 minimum life years (LYs). The ICER of F&A versus ANA was
 $15,665.891/QALY with incremental cost and QALY of $12,401.120 and 0.792,
 respectively, which was less than the willingness-to-pay (WTP) of
 $29,383/QALY. Compared with F&A, FUL yielded a higher cost and a
 shorter lifetime; hence, it was identified as a dominated strategy. The
 univariate sensitivity analysis indicated the price of FUL was the most
 influential factor in our study. The probability that F&A was
 cost-effective at a threshold of $29,383/QALY in China was 86.5%.
 Conclusion F&A is a cost-effective alternative to FUL and ANA
 monotherapy for the first-line treatment of PMW-MBC(HR+) in China.
 F&A is a promising first-line treatment for PMW-MBC(HR+), and more
 research is needed to evaluate the economy of using F&A in other
 countries.
description: Methods available in manuscript.
DOI: 10.5061/dryad.jq2bvq86c
title: Temporal variation in maternal nest choice and its consequences for lizard embryos

description: Microhabitat choice of nest sites is an important maternal effect that
 influences the survival and development of embryos in oviparous species.
 Embryos of many species display a high degree of plasticity in response to
 developmental environments, which places maternal nesting behavior under
 strong selective pressure, particularly in temporally-changing
 environments. Nesting behavior varies widely across taxa that exhibit
 diverse reproductive strategies. The brown anole (Anolis sagrei), for
 example, lays one egg every 7-10 days across an extended reproductive
 season from April to October. This aspect of their reproduction provides
 an opportunity to examine temporal shifts in nesting behavior and its
 consequences on egg survival and offspring development under
 seasonally-changing climatic conditions. We conducted a two-part study to
 quantify temporal variation in maternal nesting behavior and its effect on
 development of A. sagrei embryos. First, we measured nest
 microenvironments over the nesting season. Second, we “planted” eggs
 across the landscape at our field site to examine the influence of nest
 conditions on egg survival and hatchling phenotypes. We also incubated
 eggs inside chambers in the field to decouple effects of nest moisture
 from those of other environmental variables (e.g., temperature).Females
 chose nest sites with higher moisture and lower temperatures relative to
 what was generally available across the landscape during the nesting
 season. In addition, eggs exposed to relatively cool temperatures had
 higher hatching success, and high nest moisture increased egg survival and
 body condition of hatchlings. Overall, we provide evidence in the field
 that maternal nesting behavior facilitates offspring survival.
DOI: 10.5061/dryad.0vt4b8gvz
title: Data from: Species richness and patterns of overdispersion, clustering and randomness shape phylogenetic and functional diversity-area relationships in habitat islands

description: Aim: To evaluate how the area of ​habitat island systems influences
 multiple facets of diversity.  Location: Southern
 Brazil.  Taxon: Birds.  Methods: Using an Information
 Theoretic approach, we compared the fit of 20 diversity–area relationship
 (DARs) models in three habitat island systems. We tested for the best-fit
 model, model-family, shape, and presence/absence of an asymptote. We used
 species richness (SR), Faith's phylogenetic diversity (PD) and
 Faith's functional diversity (FD) to assess species–area (SARs),
 phylogenetic (PDARs) and functional diversity–area relationships (FDARs).
 We controlled for the effect of SR in PD and FD via null models to assess
 PDARs and FDARs independently of SR and to explore the influence of
 phylogenetic and functional randomness, clustering and
 overdispersion.  Results: PDARs and FDARs built with PD and FD
 resembled SARs and were all best fitted by convex or sigmoidal, upwards
 oriented, non-asymptotic models. Controlling for SR in diversity indices
 produced flat or downwards-oriented, weak PDARs and FDARs, which were best
 fitted by convex, non-asymptotic models or the linear model. Taxonomic
 diversity accumulated faster with area than functional diversity, which
 accumulated faster than phylogenetic diversity. Randomness and clustering
 patterns prevailed in shaping PDARs and FDARs relative to
 overdispersion.  Main conclusions: Controlling for SR in
 PD and FD affects DARs patterns and the strength of the relationships.
 Irrespective of this influence of SR, a few simple models of the power and
 exponential model-families best fit DARs. Model parameters reveal
 differences in the response of each facet of diversity to increases in
 area, highlighting the complementary nature of DARs. When considered
 independently of SR, both PDAR and FDAR patterns largely reflect the broad
 variation of phylogenetic and functional diversity in small islands. It is
 therefore likely that the ecological processes that promote phylogenetic
 and functional overdispersion and clustering operate at contrasting
 spatial scales.
description: Spreadsheet contains 3 tabs: Grassland island system, Bulrush
 island system, Washout island system SR - species
 richness<br> PD - Faith's Phylogenetic Diversity
 Index<br> PD.SES - standardized effect size of PD<br> FD -
 Faith's Functional Diversity Index<br> FD.SES - standardized
 effect size of FD *SES values cannot be calculated for
 islands containing a single species
DOI: 10.5061/dryad.nvx0k6dp0
title: Elucidating mechanisms of invasion success: effects of parasite removal on growth and survival rates of invasive and native frogs

description: 1. Identifying the mechanisms underlying biological invasions can inform
 the management of invasive species. The enemy release hypothesis (ERH)
 suggests that invasive species have a competitive advantage in their
 introduced range because they leave behind many of their predators and
 parasites from their native range, allowing them to shift resources from
 defenses to growth, reproduction, and dispersal. Many studies have
 demonstrated that invasive species have fewer parasites than their native
 counterparts, but few studies have tested whether the loss of these
 natural enemies appears to be a primary driver of the invasion process. 2.
 To test the ERH, we conducted a mark-recapture study in which we used an
 anthelmintic drug to successfully reduce parasitic worms in invasive Cuban
 treefrogs (Osteopilus septentrionalis) and native treefrogs (Hyla spp.) at
 half of 12 wetlands, marking nearly 4,200 frogs. If the ERH is supported,
 we would expect that treating for parasitic worms would have a greater
 benefit to native than invasive hosts. 3. Growth and survival rates of
 invasive and native treefrogs responded similarly to the anthelmintic
 treatment, suggesting that the Cuban treefrog’s release from parasitic
 worms does not appear to significantly contribute to its invasiveness in
 established areas. Instead, it appears that the overall faster rates of
 growth and maturation, higher survival rates, and larger body sizes of
 Cuban treefrogs that we observed may contribute to their expansion and
 proliferation. 4. Synthesis and applications. Although Cuban treefrogs
 have a lower diversity of parasitic worms in their invasive than native
 range, this does not appear to significantly contribute to their invasion
 success in areas where they have been established for more than 20 years.
 This suggests that any manipulation of parasites in invasive or native
 hosts would not be an effective method of controlling Cuban treefrogs or
 reducing their impacts. Further research into other hypotheses is needed
 to explain the Cuban treefrog’s success and help guide management actions
 to reduce their spread and negative impacts. Our study demonstrates that
 enemy release may not be a primary driver of invasiveness, highlighting
 the need for more experimental tests of the enemy release hypothesis to
 examine its generality.
description: Metadata are included in the Excel workbook.
DOI: 10.5061/dryad.k0p2ngf51
title: SNP datasets obtained with ddRADseq from four contact zones between Podarcis carbonelli and four other Podarcis species

description: We used double digestion restriction site associated DNA (ddRAD)
 sequencing to discover SNPs in samples from four contact zones between
 Podarcis carbonelli and four other Podarcis species. We
 obtained a panel of SNPs for each for each contact zone and
 reference populations and a dataset of diagnostic SNPs between
 reference populations for each contact zone but excluding private alleles
 from references, i.e. excluding alleles that are not present in the
 populations of contact. The final datasets (complete and
 diagnostic) were obtained after removing loci with depth coverage
 &lt;8, missing data &gt;20% and removing individuals with more
 than 35% of missing data. Across complete and diagnostic datasets, mean
 coverage by individuals ranged from 28 to 47 and by loci from 28 to 44.
 The analysis of replicate samples (about 6% of samples were replicated,
 i.e. were amplified and sequenced in independent libraries and SNP calling
 was performed independently) showed high levels (&gt;99%) of
 multilocus genotype replicability.
description: Samples were collected between spring and autumn of 2013 in four
 contact zones between <i>P. carbonelli</i> and one of four
 other <i>Podarcis </i>species (<i>P. bocagei</i>,
 <i>P. virescens</i>, <i>P. guadarramae
 lusitanicus</i> and <i>Podarcis vaucheri</i>). We
 colected 115 specimens in the contact zone between <i>P. bocagei
 </i>and <i>P. carbonelli,</i> 61 between <i>P.
 virescens</i> and <i>P.
 carbonelli,</i> 77 between <i>P. guadarramae
 lusitanicus</i> and <i>P. carbonelli
 </i>and<i> </i>69 between <i>P. vaucheri</i>
 and <i>P. carbonelli</i>. In all contact zones the sampling
 scheme aimed at capturing all the individuals encountered, avoiding bias
 towards species, sex or age. We used 19 <i>P.
 bocagei</i>, 7 <i>P. virescens</i>, 18 <i>P. g.
 lusitanicus</i>, 9 <i>P. vaucheri</i> and 33 <i>P.
 carbonelli</i> samples from nearby populations outside the contact
 zones as reference. We obtained SNP datasets from ddRAD sequencing by
 preparing two libraries (both include more samples thatn the samples
 described here) with following the same protocol and sequenced on both
 Illumina<sup>®</sup>  HiSeq 2000 and HiSeq 1500. 
 Individual raw reads were demultiplexed using the process_radtags module
 of Stacks version 2.2 (Catchen <em>et al.</em>, 2013). SNP
 calling was performed using
 the Stacks pipeline, following Rochette and Catchen (2017)
 recomandations, by running consecutivelly ustacks (build loci), cstacks
 (create a catalogue of loci), sstacks (match individual samples against
 the catalogue), tsv2bam (transpose data) and gstacks (align each read to a
 locus and call SNPs) units. SNP filtering was done with populations unit
 from Stacks, VCFtools 0.1.15 (Danecek <em>et al.</em>, 2011)
 and a custom Python script (available at https://github.com/catpinho/filter_RADseq_data).
DOI: 10.5061/dryad.j6q573n9j
title: Plant-pollinator networks for three subseasons and six years from Villavicencio Nature Reserve

description: The R dataset consists of the bipartite plant-pollinator interaction
 matrices (bipartite.networks) for 18 subseas (3 subseasons per 6
 years), 18 subseasonal dependence matrices (directed.networks), and the
 plant species (plant.id) and pollinator species (pollinator.id)
 identification codes. The code used for the analyses (miele-JAE.R) is also
 provided.
description: <strong>Study site and data
 collection</strong> Data come from a previously
 published study describing a plant-pollinator network from pollinator
 visits to flowers in a dryland ecosystem (Chacoff et al., 2018, Ecology
 99: 21-28). Data collection was conducted in sites lying at the lowlands
 of Villavicencio Nature Reserve, Mendoza, Argentina.
 Data were collected weekly during three months during the
 flowering season (Austral spring and early summer, September-December)
 between 2006 and 2011. Pollinator visits to flowers were recorded in two
 1-ha sites separated by ca. 5 km, with two additional 1-ha sites sampled
 in only in 2006. Data from these sites were combined into a single network
 to improve sampling completeness of species and interactions occurring in
 the region. Pollinator visits to flowers were recorded between 7:00 and
 14:00 in 5-min observation periods, a representative portion of the daily
 activity period of pollinators in our study sites. The data include 59
 plant species, 196 flower visiting insect species, and 28015 interaction
 events (flower visits) involving 1050 different pairs of interacting
 species. Plant abundance was estimated based on the density of flowers of
 each plant species, as flowers are the relevant plant structure for this
 interaction type. Flower abundance was estimated during the flowering
 season of all study years using fixed quadradts/transects. Several rare
 plant species were absent from our fixed quadrats and transects but
 present elsewhere in our study site; for those species we assigned an
 abundance of one flower, the minimum we could have detected with our
 sampling method. We aggregated the data by pooling the
 number of visits of any pollinator to any plant into three subseasons of
 approximately equal length throughout the flowering season of each year
 (before November 1st, after November 30th and in between). Such level of
 aggregation allowed us to consider seasonal dynamics at a temporal grain
 that was not too fine nor too coarse to allow a reasonable seasonal
 representation of network structure. For any subseason, we built a
 plant-pollinator <em>dependence network</em>
 <em>D</em>, a directed weighted network representing the
 relative dependences among plant and pollinator species.
DOI: 10.6071/m39q2v
title: Snow depth, air temperature, humidity, soil moisture and temperature, and solar radiation data from the basin-scale wireless-sensor network in American River Hydrologic Observatory (ARHO)

description: Snow depth, air temperature, humidity, soil moisture and temperature, and
 solar radiation are measured by a basin-scale wireless-sensor network in
 the American River Hydrologic Observatory (ARHO). The wireless-sensor
 network is deployed across the upper, snow-covered areas of the American
 River basin from 1510 to 2723 m elevation on the western slope of the
 Sierra Nevada in California. The network comprises 13 sensor clusters
 (Schneiders, Echo Peak, MT Lincoln, Caples Lake, Alpha, Duncan Peak, Van
 Vleck, Dolly Rice, Onion Creek, Robbs Saddle, Talbot Camp, Owens Camp,
 Bear Trap) at different elevations. Each cluster comprises 10 wirelessly
 connected sensor nodes strategically placed with distinct elevation,
 canopy cover, slope, and aspect within a 1 km2 area. These 130 spatially
 distributed sensor nodes measure snow depth, air temperature, relative
 humidity, soil moisture and temperature, and solar radiation at 15-minute
 intervals. Raw data (level 0) have been processed to level 1 (QA/QC) and
 level 2 (gap-filled, derived, model-ready). Time period: water year 2014
 through water year 2017.
description: The wireless sensor network provides continuous observations with
 a high spatial and high temporal resolution by sensor nodes connected via
 Metronome systems (http://metronomesystems.com/). Each sensor node is
 equipped with an ultrasonic snow-depth sensor (Judd Ultrasonic Depth
 Sensor, http://juddcom.com/) and a temperature/relative humidity sensor
 (Sensirion SHT-15,
 https://www.sensirion.com/en/environmental-sensors/humidity-sensors/digital-humidity-sensors-for-accurate-measurements/). Soil volumetric water content and soil temperature (Decagon GS3, https://www.metergroup.com/environment/articles/meter-legacy-soil-moisture-sensors/) are measured at depths of 30 and 60 cm by nodes in five clusters. Solar radiation is measured by upward-pointing Hukseflux-LP02 pyranometers (https://www.hukseflux.com/products/solar-radiation-sensors/pyranometers/lp02-pyranometer) at nine clusters. The data processing procedure is described in Bales et al. (2018, https://doi.org/10.5194/essd-2018-69).
description: Time zone: Pacific Standard Time (PST). Level
 0: raw data from datalogger. Level 1: QA/QC data at
 15-min intervals. Level 2: gap-filled data at 15-min
 intervals; and model-ready derived hourly and daily data.
 Spatial Information of sensor nodes of the wireless sensor
 network is in the directory “Gis_sensor”. Figures of
 all sensor data are placed in the directory “Data_plots”.
 Photos for each cluster are placed in the directory
 “Site_photos”. Please see README.md for additional
 information.
DOI: 10.5061/dryad.z8w9ghx82
title: Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish

description: The establishment of reproductive barriers between populations can fuel
 the evolution of new species. A genetic framework for this process posits
 that "incompatible" interactions between genes can evolve that
 result in reduced survival or reproduction in hybrids. However, progress
 has been slow in identifying individual genes that underlie hybrid
 incompatibilities. Here, we use a combination of approaches to map the
 genes that drive the development of an incompatibility that
 causes melanoma in swordtail fish hybrids. One of the genes
 involved in this incompatibility also causes melanoma in hybrids between
 distantly related species. Moreover, this melanoma reduces survival in the
 wild, likely due to progressive degradation of the fin. This work
 identifies genes underlying a vertebrate hybrid incompatibility and
 provides a glimpse into the action of these genes in natural hybrid
 populations.
DOI: 10.5061/dryad.b2rbnzsb5
title: The influence of feeding behaviour and temperature on the capacity of mosquitoes to transmit malaria

description: Insecticide-treated bed nets reduce malaria transmission by limiting
 contact between mosquito vectors and human hosts when mosquitoes feed
 during the night. However, malaria vectors can also feed in the early
 evening and in the morning when people are not protected. Here, we
 explored how timing of blood feeding interacts with environmental
 temperature to influence the capacity of Anopheles mosquitoes to transmit
 the human malaria parasite, Plasmodium falciparum. In laboratory
 experiments, we found no effect of biting time itself on the proportion of
 mosquitoes that became infectious (vector competence) at constant
 temperature. However, when mosquitoes were maintained under more realistic
 fluctuating temperatures there was a significant increase in competence
 for mosquitoes feeding in the evening (18:00h), and a significant
 reduction in competence for those feeding in the morning (06:00h),
 relative to those feeding at midnight (00:00h). These effects appear to be
 due to thermal sensitivity of malaria parasites during the initial stages
 of parasite development within the mosquito, and the fact that mosquitoes
 feeding in the evening experience cooling temperatures during the night,
 whereas mosquitoes feeding in the morning quickly experience warming
 temperatures that are inhibitory to parasite establishment. A transmission
 dynamics model illustrates that such differences in competence could have
 important implications for malaria prevalence, the extent of transmission
 that persists in the presence of bed nets, and the epidemiological impact
 of behavioural resistance.  These results indicate the
 interaction of temperature and feeding behaviour could be a major
 ecological determinant of the vectorial capacity of malaria mosquitoes.
description: Laboratory experiment data