cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.84t05
title: Data from: Bioclimatic, ecological, and phenotypic intermediacy and high genetic admixture in a natural hybrid of octoploid strawberries

description: PREMISE OF THE STUDY: Hybrid zones provide ‘natural laboratories’ for
 understanding the processes of selection, reinforcement and speciation. We
 sought to gain insight into the degree of introgression and the extent of
 ecological/phenotypic intermediacy in the natural hybrid strawberry,
 Fragaria × ananassa subsp. cuneifolia. METHODS: We used whole plastome
 sequencing to identify parental species-specific (Fragaria chiloensis and
 F. virginiana) chloroplast SNPs, and combined the use of these with
 nuclear microsatellite markers to genetically characterize the hybrid
 zone. We assessed the potential role of selection in the observed
 geographic patterns by bioclimatically characterizing the niche of the
 hybrid populations and phenotypically characterizing hybrid individuals of
 known genomic constitution. KEY RESULTS: Significant admixture and little
 overall maternal bias in chloroplast or nuclear genomes suggest a high
 degree of inter-fertility among the parental and hybrid species and point
 to a long history of backcrossing and genetic mixing in the hybrid zone.
 Even though hybrids were phenotypically intermediate to the parental
 species there was still a discernible fingerprint of the parental genotype
 within hybrid individuals. Thus, while the pattern of introgression
 observed suggests geographic limitations to gene flow, it may be
 reinforced by selection for specific parental traits in the
 bioclimatically-intermediate habitat occupied by the hybrid. CONCLUSION:
 This work uncovered the genetic complexity underlying the hybrid zone of
 the wild relatives of the cultivated strawberry. It lays the foundation
 for experimental dissection of the causes of genomic introgression and
 nuclear-cytoplasmic disassociation, and understanding other parts of the
 Fragaria evolutionary history.
description: cunei_HZ_morphometric_data_12Feb2012cuneiHZ_genotypedata_10Feb2012
DOI: 10.15468/dl.acrymn
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lycianthes sprucei",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 96 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000947-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.s69g4
title: Data from: Phenotypic variation and covariation indicate high evolvability of acoustic communication in crickets

description: Studying the genetic architecture of sexual traits provides insight into
 the rate and direction at which traits can respond to selection. Traits
 associated with few loci and limited genetic and phenotypic constraints
 tend to evolve at high rates typically observed for secondary sexual
 characters. Here, we examined the genetic architecture of song traits and
 female song preferences in the field crickets Gryllus rubens and G.
 texensis. Song and preference data were collected from both species and
 interspecific F1 and F2 hybrids. We first analysed phenotypic variation to
 examine interspecific differentiation and trait distributions in parental
 and hybrid generations. Then, the relative contribution of additive and
 additive-dominance variation was estimated. Finally, phenotypic
 variance-covariance (P) matrices were estimated to evaluate the
 multivariate phenotype available for selection. Song traits and
 preferences had unimodal trait distributions and hybrid offspring were
 intermediate with respect to the parents. We uncovered additive and
 dominance variation in song traits and preferences. For two song traits we
 found evidence for X-linked inheritance. On one hand, the observed genetic
 architecture does not suggest rapid divergence, although sex-linkage may
 have allowed for somewhat higher evolutionary rates. On the other hand, P
 matrices revealed that multivariate variation in song traits aligned with
 major dimensions in song preferences, suggesting a strong selection
 response. We also found strong covariance between the main traits that are
 sexually selected and traits that are not directly selected by females,
 providing an explanation for the striking multivariate divergence in male
 calling songs despite limited divergence in female preferences.
description: RubTex_RawData_FinalRaw data for G. rubens, G. texensis, and hybrid F1 (reciprocal crosses separate) and F2 (combined) males (song recordings) and females (phonotactic scores).
DOI: 10.5061/dryad.4gg88
title: Data from: Macronutrient balance mediates the growth of sexually selected weapons but not genitalia in male broad-horned beetles

description: Condition is defined as the pool of resources available to an individual
 that can be allocated to fitness-enhancing traits. Consequently, condition
 could influence developmental trade-offs if any occur. Although many
 studies have manipulated diet to demonstrate condition-dependent trait
 expression, few studies have determined the contribution of specific
 nutrients to condition or trade-offs. We used nutritional geometry to
 quantify the effects of dietary protein and carbohydrate content on larval
 performance and the development of adult morphology including body size as
 well as a primary and secondary sexually selected trait in male
 broad-horned beetles, Gnatocerus cornutus. We found that offspring
 survival, development rate and morphological traits were highly affected
 by dietary carbohydrate content and to a lesser extent by protein content
 and that all traits were maximized at a protein-to-carbohydrate ratio
 around 1:2. The absolute size of a secondary sexual character, the
 mandibles, had a heightened response to the increased availability and
 ratio of both macronutrients. Male genitalia, in contrast, were relatively
 insensitive to the increased availability of macronutrients. Overall,
 while nutrition influenced trait expression, the nutritional requirements
 of development rate and morphological traits were largely the same and
 resource acquisition seems to implement only weak trade-offs in this
 species. This finding contrasts with some resource constraint predictions,
 as beetles seem able to simultaneously meet the nutritional requirements
 of most traits.
description: House et al.
 ConditionData-Survival&Development&MorphologicalDataSheet 1 includes survival (0 = died, 1 = survived), development time and body size. Diet is a number from 1 - 24, Plate number is a number from 1 - 96. The %P and %C is the percentage P and C in that diet. Sheet 2 includes the morphometric data - body size, mean eye area, mandible size & genital size. As before, Diet is a number from 1 - 24, Plate number is a number from 1 - 71. The %P and %C is the percentage P and C in that diet. Please refer to the manuscript for information explaining why some diets aren't represented in the morphological data and the 'plate' effect.House et al. ConditionDataSurvival&Development.xlsx
DOI: 10.5061/dryad.20k62r83
title: Data from: Sexual, fecundity, and viability selection on flower size and number in a sexually dimorphic plant

description: The evolution of sexual dimorphism will depend on how sexual, fecundity
 and viability selection act within each sex, with the different forms of
 selection potentially operating in opposing directions. We examined
 selection in the dioecious plant Silene latifolia using planted arrays of
 selection lines that differed in flower size (small vs. large). In this
 species a flower size/number tradeoff exists within each sex, and males
 produce smaller and more numerous flowers than females. Moreover, floral
 traits are genetically correlated with leaf physiology. Sexual selection
 favoring males in the small-flower line occurred via greater overlap in
 the timing of flower output between males from this line and females.
 Fecundity selection favored males with high flower production, as siring
 success was proportionate to pollen production. Viability selection
 opposed sexual selection, favoring males from the large-flower line. In
 females, fecundity and viability selection operated in the same direction,
 favoring those from the large-flower line via greater seed production and
 survival. These results concur with the pattern of floral sexual
 dimorphism. Together with previous results they suggest that the outcome
 of the different forms of selection will be environmentally dependent, and
 therefore help to explain variation among populations in sexually
 dimorphic traits.
description: Flower counts
 2004Flower counts taken in
 the field during the reproductive period of 2004.flower counts
 2005Flower counts taken in
 the field during the reproductive period of 2005.Fruit and seed
 dataData on fruit and seed
 production by the females in the field.Individual
 dataData on a variety of
 traits for all plants in the field.Siring success and male
 floweringThe number of flowers
 produced by males and siring success based on genotyping of seeds produced
 during the same time period.
DOI: 10.5061/dryad.k17j5
title: Data from: Large brains, small guts: the expensive tissue hypothesis supported within anurans

description: Brain size differs substantially among species and several hypotheses have
 been proposed to explain the evolution of brain size. Because the brain is
 among the most energetically expensive organs in the vertebrate body,
 trade-offs have been hypothesized to exert constraints on brain size
 evolution. Prominently, the expensive-tissue hypothesis (ETH) proposes
 that reducing the size of another expensive organ, such as the gut, should
 compensate for the cost of a large brain. But energetic constraints may
 also drive covariation between the brain and other costly traits such as
 body maintenance, locomotion or reproduction, as formulated in the energy
 trade-off hypothesis. To date, these hypotheses have mainly been tested in
 homoeothermic animals and within the ectothermic animals, primarily in
 fishes. Here, we undertake a comparative test of the interplay between
 energetic limitations and brain size evolution within amphibians. After
 controlling for phylogenetic relationships and body size, we find a
 negative correlation between brain mass and the length of the digestive
 tract within 30 species of anurans. We further find that the evolution of
 large brain size is accompanied by an increase in female reproductive
 investment into egg size. Our results suggest that the evolution of brain
 size follows general patterns across vertebrate clades.
description: Data of larger brains,
 small gutsData of larger
 brain.xls
DOI: 10.5061/dryad.6m0f6870
title: Data from: Negative frequency-dependent selection of sexually antagonistic alleles in Myodes glareolus

description: Sexually antagonistic genetic variation, where optimal values of traits
 are sex-dependent, is known to slow the loss of genetic variance
 associated with directional selection on fitness-related traits. However,
 sexual antagonism alone is not sufficient to maintain variation
 indefinitely. Selection of rare forms within the sexes can help to
 conserve genotypic diversity. We combined theoretical models and a field
 experiment with Myodes glareolus to show that negative frequency-dependent
 selection on male dominance maintains variation in sexually antagonistic
 alleles. In our experiment, high-dominance male bank voles were found to
 have low-fecundity sisters, and vice versa. These results show that
 investigations of sexually antagonistic traits should take into account
 the effects of social interactions on the interplay between ecology and
 evolution, and that investigations of genetic variation should not be
 conducted solely under laboratory conditions.
description: Mokkonen_etal_empirical_dataData collected from the field experiment and used to generate statistics presented in article. Mf: high-dominance males with low-fecundity sisters, mF: low-dominance males with high-fecundity sisters.
DOI: 10.5061/dryad.7j3g5
title: Data from: Distance, flow, and PCR inhibition: eDNA dynamics in two headwater steams

description: Environmental DNA (eDNA) detection has emerged as a powerful tool for
 monitoring aquatic organisms, but much remains unknown about the dynamics
 of aquatic eDNA over a range of environmental conditions. DNA
 concentrations in streams and rivers will depend not only on the
 equilibrium between DNA entering the water and DNA leaving the system
 through degradation, but also on downstream transport. To improve
 understanding of the dynamics of eDNA concentration in lotic systems, we
 introduced caged trout into fishless headwater streams and took eDNA
 samples at evenly spaced downstream intervals. This was repeated 18 times
 from mid-summer through autumn, over flows ranging from approximately 1 to
 96 L/sec. We used qPCR to relate DNA copy number to distance from source
 for each sampling event. We found that regardless of flow, there were
 detectable levels of DNA at 239.5 m. The main effect of flow on eDNA
 counts was in opposite directions in the two streams. At the lowest flows,
 eDNA counts were highest close to the source and quickly trailed off over
 distance. At the highest flows, DNA counts were relatively low both near
 and far from the source. Biomass was positively related to eDNA copy
 number in both streams. A combination of cell settling, turbulence, and
 dilution effects is likely responsible for our observations. Additionally,
 during high leaf deposition periods, the presence of inhibitors resulted
 in no amplification for high copy number samples in the absence of an
 inhibition-releasing strategy, demonstrating the necessity to carefully
 consider inhibition in eDNA analysis.
description: eDNA
 DataExcel file containing
 raw eDNA data.
DOI: 10.5061/dryad.1n50q
title: Data from: Axial myopia is associated with visual field prognosis of primary open-angle glaucoma

description: Purpose: To identify whether myopia was associated with the visual field
 (VF) progression of primary open-angle glaucoma (POAG). Methods: A total
 of 270 eyes of 270 POAG followed up for more than 3 years with ≥9 reliable
 VFs by Octopus perimetry were retrospectively reviewed. Myopia was divided
 into: mild myopia (-2.99 diopter [D], 0), moderate myopia (-5.99, 3.00 D),
 marked myopia (-9.00, -6.00 D) and non-myopia (0 D or more). An annual
 change in the mean defect (MD) slope &gt;0.22 dB/y and 0.30 dB/y was
 defined as fast progression, respectively. Logistic regression was
 performed to determine prognostic factors for VF progression. Results: For
 the cutoff threshold at 0.22 dB/y, logistic regression showed that
 vertical cup-to-disk ratio (VCDR; p = 0.004) and the extent of myopia (p =
 0.002) were statistically significant. When logistic regression was
 repeated after excluding the extent of myopia, axial length (AL; p =
 0.008, odds ratio [OR] = 0.796) reached significance, as did VCDR (p =
 0.001). Compared to eyes with AL≤23 mm, the OR values were 0.334 (p =
 0.059), 0.309 (p = 0.044), 0.266 (p = 0.019), 0.260 (p = 0.018),
 respectively, for 23 26 mm. The significance of vertical cup-to-disk ratio
 of (p = 0.004) and the extent of myopia (p = 0.008) did not change for the
 cutoff threshold at 0.30dB/y. Conclusions: VCDR and myopia were associated
 with VF prognosis of POAG. Axial myopia may be a protective factor against
 VF progression.
description: data_Axial myopia and VF
 progressionWe collected the
 original data at Eye and Ear, Nose and Throat Hospital of Fudan
 University, Shanghai, China. eye: "1"=left, "2"=right;
 gender: "1"=male, "2"=female; SE = spherical
 equivalent; BCVA(logMAR) = logarithm of the minimum angle of resolution of
 best-corrected visual acuity; CCT = central corneal thickness; VCDR =
 vertical cup-to-disk ratio; MD = mean defect; IOP = intraocular pressure;
 AXL = axial length; GAXL = grouping by axial length;diagnosis:
 "1" = high tension glaucoma, "2" = normal tension
 glaucoma; GSE = grouping by spherical equivalent; FastPro(0.22) =
 fast/slow progression at the cutoff threshold 0.22; FastPro(0.30) =
 fast/slow progression at the cutoff threshold 0.30.Data from Axial Myopia is
 asscoiated with Visual Field Prognosis of Primary Open-angle
 Glaucoma.xls
DOI: 10.5061/dryad.v61m2
title: Data from: Status of the mountain ungulate prey of the endangered snow leopard Panthera uncia in the Tost Local Protected Area, South Gobi, Mongolia

description: The availability of wild prey is a critical predictor of carnivore
 density. However, few conservation programmes have focused on the
 estimation and monitoring of wild ungulate populations and their trends,
 especially in the remote mountains of Central Asia. We conducted
 double-observer surveys to estimate the populations of ibex Capra sibirica
 and argali Ovis ammon in the mountainous regions of Tost Local Protected
 Area, South Gobi province, Mongolia, which is being considered for
 designation as a Nature Reserve. We also conducted demographic surveys of
 the more abundant ibex to examine their sex-ratio and the survival of
 young during 2012–2013. The estimated ibex population remained stable in
 2012 and 2013 and the estimated argali population increased from 108 in
 2012 to 230 in 2013. The biomass of wild ungulates was c. 6% that of
 livestock. Mortality in young ibex appeared to increase after weaning, at
 the age of 12 months. We estimated the population of wild ungulates was
 sufficient to support 14–18 adult snow leopards Panthera uncia. The adult
 snow leopard population in our study area during 2012–2013, estimated
 independently using camera-trap-based mark–recapture methods, was 12–14.
 Based on our results we identify the Tost Local Protected Area as an
 important habitat for the conservation of these ungulates and their
 predator, the Endangered snow leopard, and recommend elevation of its
 status to a Nature Reserve.
description: Double-observer data
 used to estimate population of Ibex and Argali in Tost Local Protected
 Area in South Gobi Mongolia in 2012-2013Contains the sighting
 and detection history for all the surveys conductedData for Editor
 Oryx.zip
DOI: 10.5061/dryad.f1h1t
title: Data from: Estimating abundance of an open population with an N-mixture model using auxiliary data on animal movements

description: Accurate assessment of abundance forms a central challenge in population
 ecology and wildlife management. Many statistical techniques have been
 developed to estimate population sizes because populations change over
 time and space, and to correct for the bias resulting from animals that
 are present in a study area but not observed. The mobility of individuals
 makes it difficult to design sampling procedures that account for movement
 into and out of areas with fixed jurisdictional boundaries. Aerial surveys
 are the gold standard used to obtain data of large mobile species in
 geographic regions with harsh terrain, but these surveys can be
 prohibitively expensive and dangerous. Estimating abundance with ground
 based census methods have practical advantages, but it can be difficult to
 simultaneously account for temporary emigration and observer error to
 avoid biased results. Contemporary research in population ecology
 increasingly relies on telemetry observations of the states and locations
 of individuals to gain insight on vital rates, animal movements, and
 population abundance. Analytical models that use observations of movements
 to improve estimates of abundance have not been developed. Here we build
 upon existing multi-state mark recapture methods using a hierarchical
 N-mixture model with multiple sources of data, including telemetry data on
 locations of individuals, to improve estimates of population sizes. We
 used a state-space approach to model animal movements to approximate the
 number of marked animals present within the study area at any observation
 period, thereby accounting for a frequently changing number of marked
 individuals. We illustrate the approach using data on a population of elk
 (Cervus elaphus nelsoni) in Northern Colorado, USA. We demonstrate
 substantial improvement compared to existing abundance estimation methods
 and corroborate our results from the ground based surveys with estimates
 from aerial surveys during the same seasons. We develop a hierarchical
 Bayesian N-mixture model using multiple sources of data on abundance,
 movement and survival to estimate the population size of a mobile species
 that uses remote conservation areas. The model improves accuracy of
 inference relative to previous methods for estimating abundance of open
 populations.
description: Ketz_et_al_2018_RMNP_Data.zipThe zipped folder contains all data used for the analysis, including 12 comma separated value files, that are to be used with the R code provided in the supplemental materials DataS1 and DataS2.
DOI: 10.5061/dryad.ff852
title: Data from: Multilocus phylogeographic assessment of the California Mountain Kingsnake (Lampropeltis zonata) suggests alternative patterns of diversification for the California Floristic Province

description: Phylogeographic inference can determine the timing of population
 divergence, historical demographic processes, patterns of migration, and
 when extended to multiple species, the history of communities. Single
 locus analyses can mislead interpretations of the evolutionary history of
 taxa and comparative analyses. It is therefore important to revisit
 previous single-locus phylogeographic studies, particularly those that
 have been used to propose general patterns for regional biotas and the
 processes responsible for generating inferred patterns. Here we employ a
 multilocus statistical approach to re-examine the phylogeography of
 Lampropeltis zonata. Using nonparametic and Bayesian species delimitation,
 we determined that there are two well supported species within L. zonata.
 Ecological niche modeling supports the delimitation of these taxa,
 suggesting that the two species inhabit distinct climatic environments.
 Gene flow between the two taxa is low, and appears to occur
 unidirectionally. Further, our data suggest that gene flow was mediated by
 females, a rare pattern in snakes. In contrast to previous analyses, we
 determined that the divergence between the two lineages occurred in the
 late Pliocene (ca. 2.07 ma). Spatially and temporally, the divergence of
 these lineages is associated with the inundation of central California by
 the Monterey Bay. The effective population sizes of the two species appear
 to have been unaffected by Pleistocene glaciation. Our increased sampling
 of loci for L. zonata, combined with previously published multi-locus
 analyses of other sympatric species, suggest that previous conclusions
 reached by comparative phylogeographic studies conducted within the
 California Floristic Province should be reassessed.
description: 2CL8 phased nexus
 fileAnonymous nuclear locus
 collected for L. zonata.2CL8_ZONATA_PHASED.nexCL4 phased nexus filePhased nexus file for anonymous locus CL4, Lampropeltis zonataCL4_ZONATA_PHASED.nexND4 nexus fileAligned ND4 locus originally from Rodríguez-Robles JA, DeNardo DF, Staub RE (1999) Phylogeography of the California mountain kingsnake, Lampropeltis zonata (Colubridae). Molecular Ecology 8, 1923-1934.ND4.nex