cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tv45802
title: Data from: Urban versus forest ecotypes are not explained by divergent reproductive selection

description: Increasing urbanisation offers a unique opportunity to study adaptive
 responses to rapid environmental change. Numerous studies have
 demonstrated phenotypic divergence between urban and rural organisms.
 However, comparing the direction and magnitude of natural selection
 between these environments has rarely been attempted. Using seven years of
 nest-box breeding monitoring of great tits (Parus major) in the city of
 Montpellier and in a nearby oak forest, we find phenotypic divergence in
 four morphological and two life-history traits between urban and forest
 birds. We then measure reproductive selection on these traits, and compare
 selection between the habitats. Urban birds had significantly smaller
 morphological features than their rural counterparts, with shorter tarsus,
 lower body mass and smaller wing and tail lengths relative to their
 overall body size. While urban female tarsus length was under stabilising
 selection, and forest males show positive selection for tarsus length and
 negative selection for body mass, selection gradients were significantly
 divergent between habitats only for body mass. Urban great tits also had
 earlier laying dates and smaller clutches. Surprisingly, we found
 selection for earlier laying date in the forest but not in the city.
 Conversely, we detected no linear selection on clutch size in the forest,
 but positive selection on clutch size in the urban habitat. Overall, these
 results do not support the hypothesis that contemporary reproductive
 selection explains differences in morphology and life history between
 urban and forest breeding great tits. We discuss how further experimental
 approaches will help confirm whether the observed divergence is
 maladaptive while identifying the environmental drivers behind it.
description: morpho_data_openlife history traits datalht_data_open.xlsx
DOI: 10.5061/dryad.9bp88
title: Data from: The genetics of phenotypic plasticity. XII. Temporal and spatial heterogeneity

description: In order to understand empirical patterns of phenotypic plasticity, we
 need to explore the complexities of environmental heterogeneity and how it
 interacts with cue reliability. I consider both temporal and spatial
 variation separately and in combination, the timing of temporal variation
 relative to development , the timing of movement relative to selection,
 and two different patterns of movement: stepping-stone and island.
 Among-generation temporal heterogeneity favors plasticity, while
 within-generation heterogeneity can result in cue unreliability. In
 general, spatial variation more strongly favors plasticity than temporal
 variation, and island migration more strongly favors plasticity than
 stepping-stone migration. Negative correlations among environments between
 the time of development and selection can result in seemingly maladaptive
 reaction norms. The effects of higher dispersal rates depends on the life
 history stage when dispersal occurs and the pattern of environmental
 heterogeneity. Thus, patterns of environmental heterogeneity can be
 complex and can interact in unforeseen ways to affect cue reliability.
 Proper interpretation of patterns of trait plasticity require
 consideration of the ecology and biology of the organism. More information
 on actual cue reliability and the ecological and developmental context of
 trait plasticity is needed.
description: Scheiner - Plasticity
 XII computer codeFortran 77 source
 code
DOI: 10.5061/dryad.m1v40
title: Data from: Genome-wide analysis of colonization history and concomitant selection in Arabidopsis lyrata

description: The high climatic variability in the past hundred thousand years has
 affected the demographic and adaptive processes in many species,
 especially in boreal and temperate regions undergoing glacial cycles. This
 has also influenced the patterns of genome-wide nucleotide variation, but
 the details of these effects are largely unknown. Here we study the
 patterns of genome-wide variation to infer colonization history and
 patterns of selection of the perennial herb species Arabidopsis lyrata, in
 locally adapted populations from different parts of its distribution range
 (Germany, UK, Norway, Sweden, and USA) representing different
 environmental conditions. Using site frequency spectra based demographic
 modelling we found strong reduction in the effective population size of
 the species in general within the past 100 000 years, with more pronounced
 effects in the colonizing populations. We further found that the
 northwestern European A. lyrata populations (UK and Scandinavian) are more
 closely related to each other than with the Central European populations,
 and coalescent based population split modelling suggests that western
 European and Scandinavian populations became isolated relatively recently
 after the glacial retreat. We also highlighted loci showing evidence for
 local selection associated with the Scandinavian colonization. The results
 presented here give new insights into post-glacial Scandinavian
 colonization history and its genome-wide effects.
description: STAPLER_pipelineA zip archive containing input file for STAPLER pipeline toolData processing pipelineA zip archive containing pipeline scripts for mapping data processingData_processing_pipeline.zipStairwayplot_pipelinesA zip archive containing files for Stairwayplot analysisANGSD_pipelinesA zip archive containing pipelines for population genetics analyses with ANGSDfastsimcoal2_modelsA zip archive containing fastsimcoal2 model and prior specification filesadmixture_pipeline_REVISIONA file containing commands to run ADMIXTURE analysisNGSadmix pipelineA file containing commands for NGSadmix analysisngsadmix_pipeline_REVISION.txtTHIN_table_2A script for thinning ANGSD genotype outputangsd2fsc_multipop_04A script for generating grid script to run multiple instances of fatsimcoal2 simultaneously from ANGSD input SFScorrect_sfsA script for correcting SFS using the method described in the original paperREADMEa README file
DOI: 10.5061/dryad.br5df
title: Data from: Phenotypic traits and resource quality as factors affecting male reproductive success in a toadfish

description: A male’s reproductive success often depends on both his phenotypic quality
 and the quality of the resources he controls. An important and
 longstanding challenge for evolutionary biologists has been to disentangle
 these two often-correlated factors. Here, we present a large multi-year,
 multi-population field study along with complementary laboratory
 experiments aimed at disentangling the effects of male quality and nest
 quality in driving male reproductive success in the plainfin midshipman
 fish, Porichthys notatus. We investigate how these factors are linked to
 reproductive success using a number of different reproductive success
 components, including female attraction, cuckolder male attraction, egg
 acquisition, and rearing success. We show in the field that both male size
 and nest size are important correlates of reproductive success in this
 paternal care-giving species, but also that nest size can impose a limit
 on reproductive success regardless of the quality of the male nest owner.
 Females in the laboratory prefer large males when nest size is held
 constant, but females show no detectable preference for larger nests when
 nest size is varied and male size is held constant. We also explore a
 suite of additional male and nest traits – including male body condition,
 sonic organ investment, nest species richness, and nest density. Our
 results highlight how male and resource quality are multivariate concepts
 that incorporate information from the male phenotype, the ecological
 environment, and even the social environment and shape mating systems by
 influencing an animal’s choice of mating partners and nesting sites.
description: Bose et al. 2018 1 &
 3 field dataBose et al. 2018 Study 2
 Female Choice (male size)Bose et al. 2018 Study 2
 Female Choice (nest size)Bose et al. 2018 Study 2
 Male Choice (nest enclosure)Bose et al. 2018 Study 2
 Male Choice (nest size)
DOI: 10.5061/dryad.18tb602
title: Data from: Demographic senescence in the aquatic plant Lemna gibba L. (Araceae)

description: Senescence is progressive, age-related bodily deterioration, accompanied
 at the population level by declines in average survival and fecundity
 (i.e., ‘demographic senescence’). Demographic senescence of plants has
 been investigated in only a few species, including small, floating
 macrophytes in the genus Lemna (family Araceae, subfamily Lemnoideae – the
 ‘duckweeds’). Unlike most plant species, Lemna ramets exhibit determinate
 growth, potentially rendering them more likely to experience demographic
 senescence. Here, our objective was to investigate senescence in a Lemna
 species not previously studied in this context, L. gibba L., toward the
 long-term goal of conducting cross-species comparative analyses. In a
 longitudinal lab study, we investigated a cohort of 334 individual L.
 gibba fronds, whose survival and reproduction we followed daily from birth
 (defined by the date a focal frond detached from its parent) to death
 (defined by the date a focal frond’s last daughter detached). We fit
 survival data to exponential, Weibull, Gompertz, and logistic models, the
 first of which represents ‘no senescence’. The logistic model was found to
 have the greatest support (AICC weight &gt;0.99), indicating strong
 age-related declines in survival. We fit reproduction data using a
 generalized estimating equation approach, which showed a significant
 age-related decline in the predicted probability of daily reproduction –
 from 0.61 at age 3 days to 0.23 at age 52 days (i.e., after excluding the
 first two days of reproduction data to account for the initial,
 pre-reproductive phase of the L. gibba lifecycle). These age-related
 declines provide strong evidence that L. gibba does exhibit demographic
 senescence, consistent with evidence from congeneric species.
description: Gibba - Data
 (Raw)Lemna_gibba_R_codeAnnotated R code to recreate analyses and figures.
DOI: 10.5061/dryad.8573
title: Data from: Hybrid origin of Audubon's warbler

description: Several animal species have recently been shown to have hybrid origins,
 but no avian examples have been documented with molecular evidence. We
 investigate whether the Audubon's warbler, one of four visually
 distinct species in the yellow-rumped warbler (Dendroica coronata)
 complex, may have originated through hybridization between two other
 species in this group, the myrtle warbler and black-fronted warbler.
 Analysis of nuclear AFLP and sequence markers shows that Audubon's
 warblers are genetically intermediate, and carry a mixture of alleles
 otherwise found only in one or the other of their putative parental
 species. Audubon's warblers also carry two deeply divergent
 mitochondrial DNA lineages, each shared with only one putative parental
 form. Broad clines between Audubon's and black-fronted warblers in
 AFLP markers call into question the validity of these two forms as full
 species; nevertheless, our results suggest that the Audubon’s warbler
 likely originated through hybridization between two long-diverged species.
 It is likely that more cases of avian species of hybrid origin will be
 revealed by surveys of variation in nuclear DNA and other traits.
description: AFLP data for four
 species of yellow-rumped warblersAFLP data collected by
 polyacrylamide gel electrophoresis on a LiCor 4300 analyzer, and scored
 manually using Saga software. Samples were collected during the breeding
 season throughout the range of the species complex in 2001-2007; all
 individuals in the AFLP dataset are male.AFLPBrelsfordetal2011.csv
DOI: 10.5061/dryad.m7n7f
title: Data from: The coexistence of generalist and specialist clonal lineages in natural populations of the Irish Famine pathogen Phytophthora infestans explains local adaptation to potato and tomato

description: Phytophthora infestans, causing late blight on Solanaceae, is a serious
 threat to potato and tomato crops worldwide. P. infestans populations
 sampled on either potato or tomato differ in genotypes and pathogenicity,
 suggesting niche exclusion in the field. We hypothesized that such niche
 separation can reflect differential host exploitation by different P.
 infestans genotypes. We thus compared genotypes and phenotypes in 21
 isolates sampled on potato (n = 11) or tomato (n = 10). Typing at 12
 microsatellite loci assigned potato isolates to the 13_A2, 6_A1 and 1_A1
 lineages, and tomato isolates to the 23_A1, 2_A1 and unclassified
 multi-locus genotypes. Cross-inoculations on potato and tomato leaflets
 showed that all isolates were pathogenic on both hosts. However: tomato
 isolates performed much better on tomato than did potato isolates, which
 performed better on potato than did tomato isolates, thus revealing a
 clear pattern of local adaptation. Potato isolates were significantly
 fitter on potato than on tomato, and are best described as
 potato-specialists; tomato isolates appear to be generalists, with similar
 pathogenicity on both hosts. Niche separation in the field may thus result
 mainly from the large fitness gap on tomato between generalists and
 unadapted potato-specialists, while the small, but significant fitness
 difference on potato between both types of isolates may prevent population
 invasion by generalists. Extreme specialization to potato seems very
 costly relative to performance loss on the alternative host. This study
 therefore shows that local adaptation and niche separation, commonly
 expected to involve and generate specialists, can occur with generalists.
description: Phytophthora infestans
 genotypes21 isolates of
 Phytophthora infestans were genotyped at 12 microsatellite loci: D13,
 PinfSSR8, PinfSSR4, PinfSSR11, PinfSSR6a, PinfSSR3, Pi4B, Pi70, Pi63,
 Pi04, G11 and PinfSSR2. Binary data indicate presence (1) or absence (0)
 of alleles.Phytophthora infestans
 phenotypes21 isolates of
 Phytophthora infestans were phenotyped on detached leaflets of the potato
 cultivar Bintje and the tomato cultivar Marmande. The following traits
 were measured on 6 replicate leaflets: latency, lesion size (lesion
 length/width) and number of sporangia produced per lesion. The experiment
 was repeated twice.
DOI: 10.5061/dryad.0g1f2
title: Data from: Artificial selection sheds light on developmental mechanisms of limb elongation

description: Species diversity in limb lengths and proportions is thought to have
 evolved adaptively in the context of locomotor and habitat specialization,
 but the heritable cellular processes that drove this evolution within
 species are poorly understood. In this study, we take a novel
 “micro-evo-devo” approach, using artificial selection on relative limb
 length to amplify phenotypic variation in a population of mice, known as
 Longshanks, to examine the cellular mechanisms of postnatal limb
 development that contribute to intraspecific limb length variation.
 Cross-sectional growth data indicate that differences in bone length
 between Longshanks and random-bred controls are not due to prolonged
 growth, but to accelerated growth rates. Histomorphometric and cell
 proliferation assays on proximal tibial growth plates show that
 Longshanks’ increased limb bone length is associated with an increased
 number of proliferative chondrocytes. In contrast, we find no differences
 in other growth plate cellular features known to underlie interspecific
 differences in limb bone size and shape, such as the rates of chondrocyte
 proliferation or the size and number of hypertrophic cells in the growth
 plate. These data suggest that small differences among individuals in the
 number of proliferating chondrocytes are a potentially important
 determinant of selectable intraspecific variation in individual limb bone
 lengths, independent of body size.
description: Marchini and Rolian -
 Longshanks Growth Raw DataRaw data for mechanisms
 of comparative limb elongation in wildtype and artificially selected mice.
 Contains three sheets (Gompertz growth data, histomorphometric data, BrDU
 assay data)
DOI: 10.5061/dryad.532s2
title: Data from: Incubation temperature influences survival in a small passerine bird

description: In birds parental incubation behaviour is an important factor shaping the
 environmental conditions under which the embryos develop, and sub-optimal
 incubation temperatures are known to negatively affect early growth and
 development. It is less well known if variation in incubation temperature
 can impose life-long differences in individual performance and survival.
 In the present study we investigated the effects of incubation temperature
 on long-term survival in a small passerine bird. Using our captive
 population of the zebra finch Taeniopygia guttata we artificially
 incubated eggs at three biologically relevant temperatures (35.9, 37.0 and
 37.9°C) for two-thirds of the incubation period and then monitored
 individual lifespan of the hatched chicks for two and a half years. We
 found that individuals from eggs incubated under the lowest temperature
 exhibited significantly lower long-term survival compared to those which
 had been incubated at the highest temperature. Our results show that
 incubation temperature in birds, and thus parental incubation behaviour,
 play an important role in shaping the life-history trajectories of
 offspring.
description: Data from: Incubation
 temperature influences survival in a small passerine
 birdDescription is given in
 the file.Supporting
 data.xls
DOI: 10.5061/dryad.b3h4q
title: Data from: Density triggers maternal hormones that increase adaptive offspring growth in a wild mammal

description: [No abstract entered]
description: Spruce cone and squirrel
 density dataData used to investigate
 how previous year spruce cones and food-supplementation affected red
 squirrel density. All data collected in Kluane, Yukon,
 Canada.Spruce cone and density
 data.csvTable S2 Results -
 neonate mass and growth rateData used for results
 shown in Table 2. Only neonate mass and offspring growth data. All data
 collected in Kluane, Yukon, Canada.Table S2 - neonate mass and
 growth rate.csvTable S2-S3
 ResultsData for results shown
 in Table S2 and S3. All data collected in Kluane, Yukon,
 Canada.Table
 S2-S3.csvTable S4
 resultsData use for Results
 shown in Table S4. All data collected in Kluane, Yukon,
 Canada.FCM
 data dryad.csvTable S5
 ResultsData for results shown
 in Table S5. All data collected in Kluane, Yukon,
 Canada.Table S6 Results -
 neonate mass and growth rateData used for results
 shown in Table S6 (neonate mass and offspring growth rate). All data
 collected in Kluane, Yukon, Canada.Table S6-S7 Results -
 litter size and sex ratioData used for results
 shown in Table S6 (litter size) and S7 (litter sex ratio). All data
 collected in Kluane, Yukon, Canada.Effects of GC
 manipulation on offspring growth -individual treatmentsData used to show how
 offspring growth rates were affected by each treatment (Fig. S2). All data
 collected in Kluane, Yukon, Canada.raw growth rates gc
 manip.csvEffects of GC
 manipulation on fecal cortisol metabolitesEffects of GC
 manipulation on fecal cortisol metabolite levels in pregnant females (Fig.
 S1). All data collected in Kluane, Yukon, Canada.gc manip fcm
 data.csvFecal cortisol
 metrabolite levels in playback experimentFecal cortisol
 metabolite levels in female squirrels prior to being exposed to the
 playback treatments (Fig. S3). All data collected in Kluane, Yukon,
 Canada.before.playback.fcm.data.csvTable S4 - playback fecal cortisol metabolite dataContains data for Table 4 about how the playback experiment affected fecal cortisol metabolite levels. Data collected in Kluane, Yukon, Canada.Table S4 - playback FCM data.csv
DOI: 10.5061/dryad.qc264m2
title: Data from: Assessment of plasma proteomics biomarker’s ability to distinguish benign from malignant lung nodules

description: Background: Lung nodules are a diagnostic challenge, with an estimated
 yearly incidence of 1.6 million in the United States. This study evaluated
 the accuracy of an integrated proteomic classifier in identifying benign
 nodules in patients with a pretest probability of cancer (pCA) ≤ 50%.
 Methods: A prospective, multicenter observational trial of 685 patients
 with 8- to 30-mm lung nodules was conducted. Multiple reaction monitoring
 mass spectrometry was used to measure the relative abundance of two plasma
 proteins, LG3BP and C163A. Results were integrated with a clinical risk
 prediction model to identify likely benign nodules. Sensitivity,
 specificity, and negative predictive value were calculated. Estimates of
 potential changes in invasive testing had the integrated classifier
 results been available and acted on were made. Results: A subgroup of 178
 patients with a clinician-assessed pCA ≤ 50% had a 16% prevalence of lung
 cancer. The integrated classifier demonstrated a sensitivity of 97% (CI,
 82-100), a specificity of 44% (CI, 36-52), and a negative predictive value
 of 98% (CI, 92-100) in distinguishing benign from malignant nodules. The
 classifier performed better than PET, validated lung nodule risk models,
 and physician cancer probability estimates (P &lt; .001). If the
 integrated classifier results were used to direct care, 40% fewer
 procedures would be performed on benign nodules, and 3% of malignant
 nodules would be misclassified. Conclusions: When used in patients with
 lung nodules with a pCA ≤ 50%, the integrated classifier accurately
 identifies benign lung nodules with good performance characteristics. If
 used in clinical practice, invasive procedures could be reduced by
 diverting benign nodules to surveillance. Trial Registry:
 ClinicalTrials.gov; No.: NCT01752114; URL: www.clinicaltrials.gov).
description: Data File Supporting
 PublicationData
 Flatfile.xlsx