cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.460rp51
title: Data from: Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test

description: Phylogenies inferred from independent data partitions usually differ from
 one another in topology despite the fact that they are drawn from the same
 set of organisms (Rodrigo et al., 1993). Some topological differences are
 due to sampling error or to the use of inappropriate phylogenetic models.
 These types of topological incongruence do not have their origin in
 genealogical discordance, i.e., differences between phylogenies underlying
 the respective data partitions (Baum et al., 1998). Incongruence that is
 not due to genealogical discordance can often be addressed by modifying
 the model used in phylogenetic reconstruction (Cunningham, 1997b), and
 combining data is an appropriate way of dealing with random topological
 differences that are attributable to sampling error. However, other
 topological differences, e.g., those arising from lineage sorting
 (Maddison, 1997; Avise, 2000) and hybridization (Dumolin-Lapègue et al.,
 1997; Rieseberg, 1997; McKinnon et al., 1999; Avise, 2000), reflect
 genealogical discordance between the data partitions.
description: DataHipp_et_al_PAUPfile.nex
DOI: 10.5061/dryad.d71n2
title: Data from: Sperm competition games: a general model for pre-copulatory male-male competition

description: Reproductive males face a trade-off between expenditure on pre-copulatory
 male-male competition – increasing the number of females that they secure
 as mates – and sperm competition – increasing their fertilisation success
 with those females. Previous sperm allocation models have focused on
 scramble competition in which males compete by searching for mates and the
 number of matings rises linearly with pre-copulatory expenditure. However,
 recent studies have emphasised contest competition involving
 pre-copulatory expenditure on armaments, where winning contests may be
 highly dependent on marginal increases in relative armament level. Here we
 develop a general model of sperm allocation that allows us to examine the
 effect of all forms of pre-copulatory competition on sperm allocation
 patterns. The model predicts that sperm allocation decreases if either the
 ‘mate-competition loading’, a, or the number of males competing for each
 mating, M, increases. Other predictions remain unchanged from previous
 models: (i) expenditure per ejaculate should increase and then decrease,
 and (ii) total post-copulatory expenditure should increase, as the level
 of sperm competition increases. A negative correlation between a and M is
 biologically plausible, and may buffer deviations from the previous
 models. There is some support for our predictions from comparative
 analyses across dung beetle species and frog populations.
description: Parker_et_al_2012Linear (mm) measures of the forearm, and weight (mg) of the body and testes of quacking frogs collected from 10 natural populations in Western Australia
DOI: 10.5061/dryad.h1m85
title: Data from: Top predators constrain mesopredator distributions

description: Top predators can suppress mesopredators by killing them, competing for
 resources and instilling fear, but it is unclear how suppression of
 mesopredators varies with the distribution and abundance of top predators
 at large spatial scales and among different ecological contexts. We
 suggest that suppression of mesopredators will be strongest where top
 predators occur at high densities over large areas. These conditions are
 more likely to occur in the core than on the margins of top predator
 ranges. We propose the Enemy Constraint Hypothesis, which predicts
 weakened top-down effects on mesopredators towards the edge of top
 predators’ ranges. Using bounty data from North America, Europe and
 Australia we show that the effects of top predators on mesopredators
 increase from the margin towards the core of their ranges, as predicted.
 Continuing global contraction of top predator ranges could promote further
 release of mesopredator populations, altering ecosystem structure and
 contributing to biodiversity loss.
description: Top predator and
 mesopredator bounty dataTop predator and
 mesopredator bounty data, with all datasets scaled (z-scores). File
 contains bounty data from three continents (sum of all data obtained).
 North America data is from Saskatchewan, Canada (1982-2011). Europe data
 is from Bulgaria and Serbia (2000-2009). Australia data is from Queensland
 and is split into two zones east and west (1950-1951).pred_edge_data_scaledData.csv
DOI: 10.5061/dryad.92bh000
title: Data from: A lateral flow immunochromatographic strip test for rapid detection of hexoestrol in fish samples

description: A lateral flow immunochromatographic test strip was developed for on-site
 rapid and sensitive detection of Hexoestrol (HES) residues in fish samples
 with colloidal gold labeled the anti-HES monoclonal antibody (mAb). The
 strip is composed of a sample pad, a conjugate reagent pad, an absorbent
 pad, and a test membrane containing a control line and a test line. The
 sensitivity (half inhibitory concentration, IC50) of the strip in the
 detection of fish extract samples was confirmed to be 1.86 μg/kg, and the
 limit detection (LOD) value was 0.62 μg/kg. For intra-assay and
 inter-assay reproducibility, recoveries of HES spiked samples were ranged
 from 86.3% to 92.3% and 85.8% to 93.4%, coefficients of variation were
 2.91-4.64% and 4.24-5.17% respectively. High-performance liquid
 chromatography (HPLC) was employed to confirm the performance of the
 strip. The strip test only took less than 10 minutes, and thus provides a
 repaid method for on-site detection of HES residues.
description: Experimental data of
 HESOriginal experimental
 data of HES
DOI: 10.5061/dryad.8566
title: Data from: Does a facultative mutualism limit species range expansion?

description: The availability and quality of mutualists beyond a species’ range edge
 may limit range expansion. With the legume Chamaecrista fasciculata, we
 asked to what extent the availability and quality of rhizobia beyond the
 range edge limits host range expansion. We tested the effect of rhizobia
 availability on plant growth by transplanting seed from three locations
 into five sites spanning C. fasciculata’s range (interior, at the northern
 and western range edges, and beyond the range edges), and inoculating half
 the seeds with rhizobia. We recorded growth of all surviving plants, and
 for the uninoculated plants, whether they had formed nodules or not. We
 isolated rhizobia from nodules collected on the uninoculated plants, and
 cross-inoculated seed from four populations (both range edge and interior
 populations) in the greenhouse to determine whether the quality of
 rhizobia differed between regions. We found that seeds transplanted beyond
 the range edge were less likely to be nodulated when they were not
 experimentally inoculated, and there was benefit to inoculation at all
 sites. In the greenhouse, the three inocula that formed nodules on plants,
 from the range interior, northern edge and beyond the northern edge, did
 not detectably differ in their effect on plant growth. These results
 suggest that low densities of suitable rhizobia beyond the range edge may
 limit range expansion of legume species.
description: field_inoculation_expt_2009Data from field experiment.greenhouse_inoculation_expt_2010
DOI: 10.5061/dryad.p4s53
title: Data from: No signs of inbreeding despite long-term isolation and habitat fragmentation in the critically endangered Montseny brook newt (Calotriton arnoldi)

description: Endemic species with restricted geographic ranges potentially suffer the
 highest risk of extinction. If these species are further fragmented into
 genetically isolated subpopulations, the risk of extinction is elevated.
 Habitat fragmentation is generally considered to have negative effects on
 species survival, despite some evidence for neutral or even positive
 effects. Typically, non-negative effects are ignored by conservation
 biology. The Montseny brook newt (Calotriton arnoldi) has one of the
 smallest distribution ranges of any European amphibian (8 km2) and is
 considered critically endangered by the International Union for
 Conservation of Nature. Here we apply molecular markers to analyze its
 population structure and find that habitat fragmentation owing to a
 natural barrier has resulted in strong genetic division of populations
 into two sectors, with no detectable migration between sites. Although
 effective population size estimates suggest low values for all
 populations, we found low levels of inbreeding and relatedness between
 individuals within populations. Moreover, C. arnoldi displays similar
 levels of genetic diversity to its sister species Calotriton asper, from
 which it separated around 1.5 million years ago and which has a much
 larger distribution range. Our extensive study shows that natural habitat
 fragmentation does not result in negative genetic effects, such as the
 loss of genetic diversity and inbreeding on an evolutionary timescale. We
 hypothesize that species in such conditions may evolve strategies (for
 example, special mating preferences) to mitigate the effects of small
 population sizes. However, it should be stressed that the influence of
 natural habitat fragmentation on an evolutionary timescale should not be
 conflated with anthropogenic habitat loss or degradation when considering
 conservation strategies.
description: Consequences of habitat
 fragmentationRaw
 dataRaw
 data.xlsx
DOI: 10.5061/dryad.ff6bd0pq
title: Data from: Oral contraceptive use is associated with prostate cancer: an ecologic study

description: INTRODUCTION: Recently there have been several studies suggesting that
 estrogen exposure may increase the risk of prostate cancer (PCa). In this
 report we examine associations between PCa incidence and mortality and
 population-based use of oral contraceptives (OC's). We hypothesized
 that OC's by-products may cause an environmental contamination
 leading to an increased low level estrogen exposure and therefore higher
 PCa incidence and mortality. METHODS: The hypothesis was studied in an
 ecologic study. We used data from the “international agency for research
 on cancer” (IACR) to retrieve age-standardized rates of prostate cancer in
 2007 and the “United Nations 2007 use of contraceptive report” to retrieve
 data on contraceptive use. We subsequently used a Pearson correlation and
 a multivariable linear regression to associate the percentage of women
 using OC's, intrauterine devices, condoms or vaginal barriers to the
 age standardized prostate cancer incidence and mortality. We performed
 these analyses by individual nation and by continent worldwide. RESULTS:
 OC's use was significantly associated with prostate cancer incidence
 and mortality in the individual nation world wide (r=0.61 and r=0.53,
 respectively p&lt;0.05 for all). PCa incidence was also associated
 with OC's use in Europe (r=0.545 p&lt;0.05) and by continent
 (r=0.522 p&lt;0.05). All other forms of contraceptives (i.e.
 intra-uterine devices, condoms or vaginal barriers) were not correlated
 with prostate cancer incidence or mortality. On multivariable analysis the
 correlation with OC was independent of nation’s wealth. CONCLUSION: In
 this hypothesis generating ecologic study we have demonstrated a
 significant association between OC's and PCa. We hypothesize that
 oral contraceptive effect may be mediated through environmental estrogen
 levels; this novel concept is worth further investigation.
description: whole_world_ocpExcel file containing data on all 160 countries available for analysis
DOI: 10.5061/dryad.16q12
title: Data from: The relationship between pond habitat depth and functional tadpole diversity in an agricultural landscape

description: One of the most important goals of biodiversity studies is to identify
 which characteristics of local habitats act as filters that determine the
 diversity of functional traits along environmental gradients. In this
 study, we investigated the relationship between the environmental
 variables of ponds and the functional trait diversity distribution of
 anuran tadpoles in an agricultural area in southeastern Brazil. Our
 results show that the functional trait diversity of frog tadpoles has a
 bell-curve-shaped relationship with the depths of ponds inserted in a
 pasture matrix. Because we are witnessing increasing human pressure on
 land use, simple acts (e.g. maintaining reproductive habitats with medium
 depth) can be the first steps towards preserving the diversity of
 Neotropical frog tadpole traits in agricultural landscapes.
description: all data used in the
 paperData available: i)
 presence and absence of tadpoles in the ponds; ii) tadpole traits; iii)
 characteristics of the ponds; and iv) geographic
 coordenates.
DOI: 10.5061/dryad.pk462
title: Data from: Body acceleration as indicator for walking economy in an ageing population

description: Background: In adults, walking economy declines with increasing age and
 negatively influences walking speed. This study aims at detecting
 determinants of walking economy from body acceleration during walking in
 an ageing population. Methods: 35 healthy elderly (18 males, age 51 to 83
 y, BMI 25.5±2.4 kg/m2) walked on a treadmill. Energy expenditure was
 measured with indirect calorimetry while body acceleration was sampled at
 60Hz with a tri-axial accelerometer (GT3X+, ActiGraph), positioned on the
 lower back. Walking economy was measured as lowest energy needed to
 displace one kilogram of body mass for one meter while walking (WCostmin,
 J/m/kg). Gait features were extracted from the acceleration signal and
 included in a model to predict WCostmin. Results: On average WCostmin was
 2.43±0.42 J/m/kg and correlated significantly with gait rate (r2 = 0.21,
 p&lt;0.01) and regularity along the frontal (anteroposterior) and
 lateral (mediolateral) axes (r2 = 0.16, p&lt;0.05 and r2 = 0.12,
 p&lt;0.05 respectively). Together, the three variables explained 46%
 of the inter-subject variance (p&lt;0.001) with a standard error of
 estimate of 0.30 J/m/kg. WCostmin and regularity along the frontal and
 lateral axes were related to age (WCostmin: r2 = 0.44, p&lt;0.001;
 regularity: r2 = 0.16, p&lt;0.05 and r2 = 0.12, p&lt;0.05
 respectively frontal and lateral). Conclusions: The age associated decline
 in walking economy is induced by the adoption of an increased gait rate
 and by irregular body acceleration in the horizontal plane.
description: Characteristics and
 prediction dataExcel file with subject
 characteristics and prediction dataRepository.xls
DOI: 10.5061/dryad.1jn88
title: Data from: A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus

description: Natural selection favors efficient expression of encoded proteins, but the
 causes, mechanisms, and fitness consequences of evolved coding changes
 remain an area of aggressive inquiry. We report a large-scale reversal in
 the relative translational accuracy of codons across 12 fly species in the
 Drosophila/Sophophora genus. Because the reversal involves pairs of codons
 that are read by the same genomically encoded tRNAs, we hypothesize, and
 show by direct measurement, that a tRNA anticodon modification from
 guanosine to queuosine has coevolved with these genomic changes. Queuosine
 modification is present in most organisms but its function remains
 unclear. Modification levels vary across developmental stages in D.
 melanogaster, and, consistent with a causal effect, genes maximally
 expressed at each stage display selection for codons that are most
 accurate given stage-specific queuosine modification levels. In a kinetic
 model, the known increased affinity of queuosine-modified tRNA for
 ribosomes increases the accuracy of cognate codons while reducing the
 accuracy of near-cognate codons. Levels of queuosine modification in D.
 melanogaster reflect bioavailability of the precursor queuine, which
 eukaryotes scavenge from the tRNAs of bacteria and absorb in the gut.
 These results reveal a strikingly direct mechanism by which recoding of
 entire genomes results from changes in utilization of a nutrient.
description: Drosophilid Akashi
 selection scoresA tar/bz2 file
 containing 22 files: 12 reporting Akashi selection scores over 12
 drosophilid species, 8 reporting Akashi selection scores over 6
 developmental stages plus two merged stages (embryo and adult), one
 reporting all-stage information, and one readme.txt
 file.drosophilid-akashi-selection-scores.tar.bz2
DOI: 10.5061/dryad.86b5m
title: Data from: Frequency-dependent selection on female morphs driven by pre-mating interactions with males

description: Species showing color polymorphisms—the presence of two or more
 genetically determined color morphs within a single population—are
 excellent systems for studying the selective forces driving the
 maintenance of genetic diversity. Despite a shortage of empirical
 evidence, it is often suggested that negative frequency-dependent mate
 preference by males (or diet choice by predators) results in fitness
 benefits for the rare female morph (or prey type). Moreover, most studies
 have focused on the male (or predator) behavior in these systems and
 largely overlooked the importance of female (or prey) resistance behavior.
 Here, we provide the first explicit test of the role of
 frequency-dependent and frequency-independent intersexual interactions in
 female polymorphic damselflies. We identify the stage of the mating
 sequence when frequency-dependent selection is likely to act by comparing
 indexes of male mate preference when the female has little (females
 presented on sticks), moderate (females in cages), and high (females free
 to fly in the field) ability to avoid male mating attempts.
 Frequency-dependent male preferences were found only in those experiments
 where females had little ability to resist male harassment, indicating
 that premating interactions most likely drive negative frequency-dependent
 selection in this system. In addition, by separating frequency-dependent
 male mating preference from the baseline frequency-independent component,
 we reconcile the seemingly contradictory results of previous studies and
 highlight the roles of both forms of selection in maintaining the
 polymorphism at a given equilibrium. We conclude that considering
 interactions among all players—here, males and females—is crucial to fully
 understanding the mechanisms underlying the maintenance of genetic
 polymorphisms in the wild.
description: Data Nehalennia
 ireneFull dataset for
 Nehalennia irene. Variables are explained in the text
 file.Dryad
 Bots et al. 2015 AmNat
 Nehalennia.xlsxData Ischnura
 elegansFull dataset for
 Ischnura elegans. Variables are explained in the text
 file.Dryad
 Bots et al. 2015 AmNat Ischnura.xlsx
DOI: 10.5061/dryad.8d987
title: Data from: Unexpected absence of genetic separation of a highly diverse population of hookworms from geographically isolated hosts

description: The high natal site fidelity of endangered Australian sea lions (Neophoca
 cinerea) along the southern Australian coast suggests that their
 maternally transmitted parasitic species, such as hookworms, will have
 restricted potential for dispersal. If this is the case, we would expect
 to find a hookworm haplotype structure corresponding to that of the host
 mtDNA haplotype structure; that is, restricted among geographically
 separated colonies. In this study, we used a fragment of the cytochrome c
 oxidase I mitochondrial DNA (mtDNA) gene to investigate the diversity of
 hookworms (Uncinaria sanguinis) in N. cinerea to assess the importance of
 host distribution and ecology on the evolutionary history of the parasite.
 High haplotype (h = 0.986) and nucleotide diversity (π = 0.013) were seen,
 with 45 unique hookworm mtDNA haplotypes across N. cinerea colonies; with
 most of the variation (78%) arising from variability within hookworms from
 individual colonies. This is supported by the low genetic differentiation
 co-efficient (GST = 0.007) and a high gene flow (Nm = 35.25) indicating a
 high migration rate between the populations of hookworms. The haplotype
 network demonstrated no clear distribution and delineation of haplotypes
 according to geographical location. Our data rejects the vicariance
 hypothesis; that female host natal site fidelity and the transmammary
 route of infection restrict hookworm gene flow between N. cinerea
 populations and highlights the value of studies of parasite diversity and
 dispersal to challenge our understanding of parasite and host ecology.
description: Unexpected absence of
 genetic separation of a highly diverse population of hookworms from
 geographically isolated hostsDRYAD.zip
DOI: 10.5061/dryad.7s403
title: Data from: Neonicotinoid insecticide travels through a soil food chain, disrupting biological control of non-target pests and decreasing soya bean yield

description: 1. Neonicotinoids are the most widely used insecticides world-wide, but
 their fate in the environment remains unclear, as does their potential to
 influence non-target species and the roles they play in agroecosystems. 2.
 We investigated in laboratory and field studies the influence of the
 neonicotinoid thiamethoxam, applied as a coating to soya bean seeds, on
 interactions among soya beans, non-target molluscan herbivores and their
 insect predators. 3. In the laboratory, the pest slug Deroceras
 reticulatum was unaffected by thiamethoxam, but transmitted the toxin to
 predaceous beetles (Chlaenius tricolor), impairing or killing &gt;60%.
 4. In the field, thiamethoxam-based seed treatments depressed
 activity–density of arthropod predators, thereby relaxing predation of
 slugs and reducing soya bean densities by 19% and yield by 5%. 5.
 Neonicotinoid residue analyses revealed that insecticide concentrations
 declined through the food chain, but levels in field-collected slugs (up
 to 500 ng g−1) were still high enough to harm insect predators. 6.
 Synthesis and applications. Our findings reveal a previously unconsidered
 ecological pathway through which neonicotinoid use can unintentionally
 reduce biological control and crop yield. Trophic transfer of
 neonicotinoids challenges the notion that seed-applied toxins precisely
 target herbivorous pests and highlights the need to consider predatory
 arthropods and soil communities in neonicotinoid risk assessment and
 stewardship.
description: Douglas_JAE_2014_Field-data-earlySee ReadMe fileDouglas_JAE_2014_Field-data-lateDouglas_JAE_2014_Insecticide-residuesDouglas_JAE_2014_Lab-plant-slugDouglas_JAE_2014_Lab-slug-beetle