cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pd6mn
title: Data from: Levels of 8-oxodG predict hepatobiliary-pathology in Opisthorchis viverrini endemic settings in Thailand

description: Opisthorchis viverrini is distinct among helminth infections as it drives
 a chronic inflammatory response in the intrahepatic bile duct that
 progresses from advanced periductal fibrosis (APF) to cholangiocarcinoma
 (CCA). Extensive research shows that oxidative stress (OS) plays a
 critical role in the transition from chronic O. viverrini infection to
 CCA. OS also results in the excision of a modified DNA lesion (8-oxodG)
 into urine, the levels of which can be detected by immunoassay. Herein, we
 measured concentrations of urine 8-oxodG by immunoassay from the following
 four groups in the Khon Kaen Cancer Cohort study: (1) O. viverrini
 negative individuals, (2) O. viverrini positive individuals with no APF as
 determined by abdominal ultrasound, (3) O. viverrini positive individuals
 with APF as determined by abdominal ultrasound, and (4) O. viverrini
 induced cases of CCA. A logistic regression model was used to evaluate the
 utility of creatinine-adjusted urinary 8-oxodG among these groups, along
 with demographic, behavioral, and immunological risk factors. Receiver
 operating characteristic (ROC) curve analysis was used to evaluate the
 predictive accuracy of urinary 8-oxodG for APF and CCA. Elevated
 concentrations of 8-oxodG in urine positively associated with APF and CCA
 in a strongly dose-dependent manner. Urinary 8-oxodG concentrations also
 accurately predicted whether an individual presented with APF or CCA
 compared to O. viverrini infected individuals without these pathologies.
 In conclusion, urinary 8-oxodG is a robust ‘candidate’ biomarker of the
 progression of APF and CCA from chronic opisthorchiasis, which is
 indicative of the critical role that OS plays in both of these advanced
 hepatobiliary pathologies. The findings also confirm our previous
 observations that severe liver pathology occurs early and asymptomatically
 in residents of O. viverrini endemic regions, where individuals are
 infected for years (often decades) with this food-borne pathogen. These
 findings also contribute to an expanding literature on 8-oxodG in an
 easily accessible bodily fluid (e.g., urine) as a biomarker in the
 multistage process of inflammation, fibrogenesis, and infection-induced
 cancer.
description: demographic,
 parasitologic, and biomarker dataThe data set includes
 the demographic, parasitologic, and biomarker variable values from 182
 participants from an O. viverrini endemic area of Khon Kean Province in
 Thailand._8oxodG.csv
DOI: 10.5061/dryad.bj20f
title: Data from: Long-term effect of social interactions on behavioral plasticity and lifetime mating success

description: Behavioral traits often change over an individual’s lifetime. Experience,
 physiological senescence, and age-dependent differences in optimal
 behavior can, in theory, all cause longitudinal behavioral changes. Yet
 most studies of behavioral plasticity and selection on behavior focus on
 short-term population-level responses to social factors such as
 conspecific density or sex ratio. Longer-term effects of social
 interactions on individual behavior have rarely been tested. Here we
 tested these effects by exposing male water striders (Hemiptera: Gerridae)
 to two different social conditions throughout their lifetime; we call
 these the nonsocial and social treatments. We then measured each male’s
 lifetime mating success and individual behavioral plasticity by observing
 four different behaviors (exploring a novel environment, dispersal
 ability, sex-recognition sensitivity, and tendency to remount a resistant
 female after being dislodged) every 2 weeks. The social environment
 influenced individual variation in behavioral plasticity as well as
 population-level behavioral plasticity. Moreover, when we calculated
 linear selection gradients of individual behavioral traits and their
 plasticities on lifetime mating success, male remounting tendency and
 individual plasticity in exploration ability were likely to be the most
 important factors explaining variation in male lifetime mating success. In
 conclusion, the variation in social interactions throughout an
 individual’s lifetime contributes to the individual variation in
 behavioral plasticity, which can significantly affect a male’s lifetime
 fitness.
description: DataSocial: Social
 treatments (L: non-social treatment, H: social treatment); relative fit:
 Relative fitness; R: Attempt to remount; D: Dispersal ability; S: Sex
 recognition sensitivity; E: Exploration in a new environment; The number
 indicates the age.Amnat_Data.xlsx
DOI: 10.15468/dl.a73843
title: Occurrence Download

description: A dataset containing 163 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemitomes congestum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 163 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001311-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g1vc4
title: Data from: Intraspecific divergence and convergence of floral tube length in specialized pollination interactions

description: Floral tubes are often thought to be a consequence of adaptive
 specialization towards pollinator morphology. We explore floral tube
 length evolution within Tritoniopsis revoluta (Iridaceae), a species with
 considerable geographical tube length variation. We ask whether tube
 lengths of T. revoluta populations are associated with pollinator
 proboscis lengths, whether floral divergence occurs in the presence of
 different pollinators and whether floral convergence occurs between
 distantly related populations pollinated by the same pollinator. Finally,
 we ask whether tube length evolution is directional. Shifts between
 morphologically different pollinators were always associated with shifts
 in floral morphology, even when populations were very closely related.
 Distantly related populations had similar tube lengths when they were
 pollinated by the same pollinator. Shifts in tube length tended to be from
 short to long, although reversals were not infrequent. After correcting
 for the population-level phylogeny, there was a strong positive, linear
 relationship between floral tube length and pollinator proboscis length,
 suggesting that plants are functionally specialized on different
 pollinators at different sites. However, because tube length evolution in
 this system can be a bidirectional process, specialization to the local
 pollinator fauna is unlikely to result in evolutionary or ecological
 dead-ends such as canalization or range limitation.
description: tube and tongue lengths
 of plants and pollinatorsThis data contains tube
 lengths of Tritoniopsis revoluta populations and the tongue lengths of
 their pollinators at each site. It also contains the relative abundances
 of different pollinator species at each sitedryad
 database.xlsx
DOI: 10.5061/dryad.8612
title: Data from: Scavenging: how carnivores and carrion structure communities

description: Recent advances in the ecology of food webs underscore the importance of
 detritus and indirect predator–prey effects. However, most research
 considers detritus as an invariable pool and predation as the only
 interaction between carnivores and prey. Carrion consumption, scavenging,
 is a type of detrital feeding that should have widespread consequences for
 the structure and stability of food webs. Providing access to high-quality
 resources, facultative scavenging is a ubiquitous and phylogenetically
 widespread strategy. In this review, we argue that scavenging is
 underestimated by 16-fold in food-web research, producing inflated
 predation rates and underestimated indirect effects. Furthermore, more
 energy is generally transferred per link via scavenging than predation.
 Thus, future food-web research should consider scavenging, especially in
 light of how major global changes can affect scavengers.
description: ScavengingFoodWebs_2009REVFood web characteristics (number of links, number of types of links, numbers of predators, scavengers, estimated scavengers etc.).scavengingR code for analysis in Wilson & Wolkovich 2011 TREE paper that goes with csv datafile.
DOI: 10.5061/dryad.448sc26
title: Data from: Population structure leads to male-biased population sex ratios under environmental sex determination

description: Spatial structure has been shown to favor female-biased sex allocation,
 but current theory fails to explain male biases seen in many taxa,
 particularly those with environmental sex determination (ESD). We present
 a theory and accompanying individual-based simulation model that
 demonstrates how population structure leads to male-biased population sex
 ratios under ESD. Our simulations agree with earlier work showing that the
 high productivity of female-producing habitats creates a net influx of
 sex-determining alleles into male-producing habitats, causing larger sex
 ratio biases and lower productivity in male-producing environments (Harts
 et al. 2014). In contrast to previous findings, we show that male-biasing
 habitats disproportionately impact the global sex ratio, resulting in
 stable male-biased population sex ratios under ESD. The failure to detect
 a male bias in earlier work can be attributed to small subpopulation sizes
 leading to local mate competition, a condition unlikely to be met in most
 ESD systems. Simulations revealed that consistent male biases are expected
 over a wide range of population structures, environmental conditions, and
 genetic architectures of sex determination, with male excesses as large as
 30 percent under some conditions. Given the ubiquity of genetic structure
 in natural populations, we predict that modest, enduring male biased
 allocation should be common in ESD species, a pattern consistent with
 reviews of ESD sex ratios.
description: ESDSexRatioCode
DOI: 10.5061/dryad.842nm
title: Data from: Individual recognition through olfactory - auditory matching in lemurs

description: Individual recognition can be facilitated by creating representations of
 familiar individuals, whereby information from signals in multiple sensory
 modalities become linked. Many vertebrate species use auditory–visual
 matching to recognize familiar conspecifics and heterospecifics, but we
 currently do not know whether representations of familiar individuals
 incorporate information from other modalities. Ring-tailed lemurs (Lemur
 catta) are highly visual, but also communicate via scents and
 vocalizations. To investigate the role of olfactory signals in
 multisensory recognition, we tested whether lemurs can recognize familiar
 individuals through matching scents and vocalizations. We presented lemurs
 with female scents that were paired with the contact call either of the
 female whose scent was presented or of another familiar female from the
 same social group. When the scent and the vocalization came from the same
 individual versus from different individuals, females showed greater
 interest in the scents, and males showed greater interest in both the
 scents and the vocalizations, suggesting that lemurs can recognize
 familiar females via olfactory–auditory matching. Because identity signals
 in lemur scents and vocalizations are produced by different effectors and
 often encountered at different times (uncoupled in space and time), this
 matching suggests lemurs form multisensory representations through a newly
 recognized sensory integration underlying individual recognition.
description: Olfactory - auditory
 recognition in lemursKulahci et al. ProcRSocB 2014
 data.xlsx
DOI: 10.5061/dryad.65610
title: Data from: Genetic diversity and population structure of Mesoamerican jaguars (Panthera onca): implications for conservation and management

description: Mesoamerican jaguars (Panthera onca) have been extirpated from over 77% of
 their historic range, inhabiting fragmented landscapes at potentially
 reduced population sizes. Maintaining and restoring genetic diversity and
 connectivity across human-altered landscapes has become a major
 conservation priority; nonetheless large-scale genetic monitoring of
 natural populations is rare. This is the first regional conservation
 genetic study of jaguars to primarily use fecal samples collected in the
 wild across five Mesoamerican countries: Belize, Costa Rica, Guatemala,
 Honduras, and Mexico. We genotyped 445 jaguar fecal samples and examined
 patterns of genetic diversity and connectivity among 115 individual
 jaguars using data from 12 microsatellite loci. Overall, moderate levels
 of genetic variation were detected (NA = 4.50 ± 1.05, AR = 3.43 ± 0.22, HE
 = 0.59 ± 0.04), with Mexico having the lowest genetic diversity, followed
 by Honduras, Guatemala, Belize, and Costa Rica. Population-based gene flow
 measures (FST = 0.09 to 0.15, Dest = 0.09 to 0.21), principal component
 analysis, and Bayesian clustering applied in a hierarchical framework
 revealed significant genetic structure in Mesoamerican jaguars, roughly
 grouping individuals into four genetic clusters with varying levels of
 admixture. Gene flow was highest among Selva Maya jaguars (northern
 Guatemala and central Belize), whereas genetic differentiation among all
 other sampling sites was moderate. Genetic subdivision was most pronounced
 between Selva Maya and Honduran jaguars, suggesting limited jaguar
 movement between these close geographic regions and ultimately refuting
 the hypothesis of contemporary panmixia. To maintain a critical linkage
 for jaguars dispersing through the Mesoamerican landscape and ensure
 long-term viability of this near threatened species, we recommend
 continued management and maintenance of jaguar corridors. The baseline
 genetic data provided by this study underscores the importance of
 understanding levels of genetic diversity and connectivity to making
 informed management and conservation decisions with the goal to maintain
 functional connectivity across the region.
description: STRUCTURE - Mesoamerican
 Jaguars - Wultsch et al. 2016STRUCTURE file for the
 manuscript "Genetic diversity and population structure of
 Mesoamerican jaguars (Panthera onca): implications for conservation and
 management ". The file includes microsatellite genotype data for
 jaguars studied across five Mesoamerican countries.Wultsch et
 al_Structure_MAJags.str
DOI: 10.5061/dryad.r4mk47p
title: Data from: Landscape history confounds the ability of the NDVI to detect fine-scale variation in grassland communities

description: 1. The NDVI is a remotely-sensed vegetation index that is frequently used
 in ecological studies. There is, however, a lack of studies that evaluate
 the ability of the NDVI to detect fine-scale variation in grassland plant
 community composition and species richness. Ellenberg indicators
 characterize the environmental preferences of plant species – and
 community-mean Ellenberg values have been used to explore the
 environmental drivers of community assembly. 2. We used variation
 partitioning to test the ability of satellite-based NDVI to explain
 community-mean Ellenberg nutrient (mN) and moisture (mF) indices, and the
 richness of habitat-specialist species in dry grasslands of different
 ages. The grasslands represent a gradient of decreasing soil nutrient
 status. 3. If community composition is determined by the responses of
 individual species to the underlying environmental conditions and if, at
 the same time, community composition determines the optical
 characteristics of the vegetation canopy, then positive relationships
 between the NDVI and mN and mF are expected. Many grassland specialists
 are intolerant of nutrient-rich soils. If specialist richness is
 negatively related to soil-nutrient levels, then a negative association
 between the NDVI and specialist richness is expected. However, because
 grassland community composition is not only influenced by abiotic
 variables but also by other spatial and temporal drivers, we included
 spatial variables and grassland age in the statistical analyses. 4. The
 NDVI explained the majority of the variation in mF, and also contributed
 to a substantial proportion of the variation in mN. However, variation in
 specialist richness and the lowest values of mN were explained by
 grassland age and spatial variables – but were poorly explained by the
 NDVI. 5. Synthesis and applications. The NDVI showed a good ability to
 detect variation in plant community composition, and should provide a
 valuable tool for assessing fine-scale environmental variation in
 grasslands or for monitoring changes in grassland habitat properties.
 However, because the concentration of grassland specialists not only
 depends on environmental variables but also on the age and spatial context
 of the grasslands, the NDVI is unlikely to allow the identification of
 grasslands with high numbers of specialist species.
description: Grassland site data used
 in the analysesd.csvDCA scoresDCA_scores.zip
DOI: 10.5061/dryad.22s3p
title: Data from: Hybrid crosses and the genetic basis of interspecific divergence in lifespan in Pristionchus nematodes

description: Characterizing the genetic basis of among-species variation in lifespan is
 a major goal of evolutionary gerontology research, but the very feature
 that defines separate species—the inability to interbreed—makes achieving
 this goal impractical, if not impossible, for most taxa. Pristionchus
 nematodes provide an intriguing system for tackling this problem, as
 female lifespan varies among species that can be crossed to form viable
 (though infertile) hybrids. By conducting reciprocal crosses among three
 species—two dioecious (long-lived P. exspectatus and short-lived P.
 arcanus) and one androdioecious (short-lived P. pacificus)—we found that
 female lifespan was long for all hybrids, consistent with the hypothesis
 that the relatively short lifespans seen for P. pacificus hermaphrodites
 and P. arcanus females are caused by independent, recessive alleles that
 are masked in hybrid genomes. Cross direction had a small effect on
 survivorship for crosses involving P. exspectatus, indicating that
 nuclear-mitochondrial interactions may also influence Pristionchus
 longevity. Our findings suggest that long lifespan in P. exspectatus
 reflects the realization of an ancestral potential for extended longevity
 in the P. pacificus species complex. This work demonstrates the utility of
 interspecific hybrids for ageing research and provides a foundation for
 future work on the genetic architecture of interspecific lifespan
 variation.
description: JEB-2016-00542 - Dryad
 Data FileAn R script file (.R
 extension) containing survival time data for various Pristionchus
 nematodes. Data are provided as R objects and as CSV data tables. Comments
 are included to define the data columns within each
 object.
DOI: 10.5061/dryad.7652s
title: Data from: An examination of the accuracy of a sequential PCR and sequencing test used to detect the incursion of an invasive species: the case of the red fox in Tasmania

description: 1. Polymerase Chain Reaction (PCR) diagnostic tests are increasingly
 applied to the identification of wildlife. Yet rigorous verification is
 rare and the estimation of test accuracy (the probability that true
 positive and true negative samples are correctly identified – test
 sensitivity and specificity, respectively), particularly in combination
 with sequencing, is uncommon. This is important because PCR-based tests
 are prone to contamination in sampling and the laboratory. 2. Here, we use
 an experimental case–control approach to estimate the sensitivity and
 specificity of a sequential PCR-based wildlife detection test used to
 identify incursions of red foxes into Tasmania from predator faeces
 (scats). 3. Our results show that the sensitivity of the fox test is high
 (~94%) for the PCR-based test on its own, but this decreases to ~84% when
 combined with the DNA sequencing step. In contrast, the specificity
 increases from ~96% in the PCR only test to ~99.6% after inclusion of the
 DNA sequencing step. 4. The intense public scrutiny of the fox eradication
 program in Tasmania, has undoubtedly influenced the application of a
 sequential PCR test that maximises specificity at the expense of
 sensitivity and so increases the risk that scats containing fox DNA would
 not be detected. This could lead to the establishment of foxes in Tasmania
 as a consequence. 5. Synthesis and applications. Importantly, the
 estimation of the sensitivity and specificity of sequential tests enables
 decisions about the risk associated with mistaken identification (i.e.
 false negatives vs false positives) to be quantified for decision makers.
 The cost of false negative errors should be balanced against the costs of
 false positive errors, which could include the expenditure incurred in the
 application of unnecessary management actions were foxes not in fact
 present. Understanding the risks and costs associated with both false
 negative and false positive errors is therefore a key component to the
 decision making process for the management of the Tasmanian fox incursion.
description: PCR_DNA_test_results
DOI: 10.5061/dryad.8073
title: Data from: On the origin of a domesticated species: identifying the parent population of Russian silver foxes (Vulpes vulpes)

description: The foxes at Novosibirsk, Russia, are the only population of domesticated
 foxes in the world. These domesticated foxes originated from farm-bred
 silver foxes (Vulpes vulpes), whose genetic source is unknown. In the
 present study, we examined the origin of the domesticated strain of foxes
 and two other farm-bred fox populations (aggressive and unselected)
 maintained in Novosibirsk. To identify the phylogenetic origin of these
 populations we sequenced two regions of mitochondrial DNA, cytochrome b
 and d-loop, from 24 Novosibirsk foxes (eight foxes from each population)
 and compared them with corresponding sequences of native red foxes from
 Europe, Asia, Alaska and Western Canada, Eastern Canada, and the Western
 Mountains of the USA. We identified seven cytochrome b–d-loop haplotypes
 in Novosibirsk populations, four of which were previously observed in
 Eastern Canada. The three remaining haplotypes differed by one or two base
 change from the most common haplotype in Eastern Canada. ΦST analysis
 showed significant differentiation between Novosibirsk populations and red
 fox populations from all geographic regions except Eastern Canada. No
 haplotypes of Eurasian origin were identified in the Novosibirsk
 populations. These results are consistent with historical records
 indicating that the original breeding stock of farm-bred foxes originated
 from Prince Edward Island, Canada. Mitochondrial DNA data together with
 historical records indicate two stages in the selection of domesticated
 foxes: the first includes captive breeding for approximately 50 years with
 unconscious selection for behaviour; the second corresponds to &gt; 50
 years of additional intensive selection for tame behaviour.
description: Silver_fox_dataset_DRYADmtDNA sequences for 3 breeding lines of russian silver foxes