cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.73n5tb2sn
title: Data from: Water availability and temperature induce changes in oxidative status during pregnancy in a viviparous lizard

description: Reproduction involves considerable reorganization in an organism’s
 physiology that incurs potential toxicity for cells (e.g., oxidative
 stress) and decrease in fitness. This framework has been the cornerstone
 of the so-called ‘oxidative cost of reproduction’, a theory that remains
 controversial and relatively overlooked in non-model ectotherms. Here, we
 used two complementary approaches in natural and controlled conditions to
 test whether altered access to climate conditions (water and temperature
 resources) alters oxidative status and mediates reproductive trade-offs in
 viviparous populations of the common lizard (Zootoca vivipara). First, we
 examined whether access to free standing water and differences in ambient
 temperature across 12 natural populations could be related with variation
 in oxidative status, reproductive effort and reproductive success. Second,
 we determined whether an experimental restriction to water triggers higher
 oxidative cost of reproduction and correlates with fitness measures
 (reproductive success, future survival rate and probability of future
 reproduction). Pregnant females exhibited higher sensitivity than males to
 natural or experimental limitations in temperature and water access. That
 is, in restricted environments, pregnant females with higher reproductive
 effort exhibited stronger oxidative damage despite enhanced non-enzymatic
 antioxidant capacity. Enhanced antioxidant defensive capacity in pregnant
 females was positively correlated with higher reproductive success,
 whereas elevated oxidative damage negatively correlated with offspring
 annual survival.  Altogether, our results revealed a
 context-dependent oxidative cost of reproduction that was concomitant with
 a conflict in water demand from offspring. These new insights should be
 critical for understanding ectotherm responses to heat waves and summer
 droughts that are increasing in frequency and duration.
DOI: 10.5061/dryad.hhmgqnkcg
title: Simulated pollinator declines intensify selection on floral traits that facilitate selfing and outcrossing in Impatiens capensis

description: PREMISE OF THE STUDY: Anthropogenic environmental change is causing
 pollinator populations to decline. These declines should intensify
 selection for floral traits that facilitate outcrossing by making plants
 more attractive to pollinators and/or for floral traits that facilitate
 selfing in the absence of pollinators. However, the effect of pollinator
 declines on selection on floral traits could be modified by other
 environmental factors such as herbivores.     
 METHODS: We studied the effect of simulated pollinator declines on
 selection on floral traits of Impatiens capensis, a mixed-mating species
 that produces both obligately selfing cleistogamous flowers and primarily
 outcrossing chasmogamous flowers. We measured directional selection
 differentials via seeds per plant on two traits that facilitate
 outcrossing (chasmogamous flower size and number) and one trait that
 facilitates selfing (cleistogamous flower number) in ambient, reduced
 pollinator access, and reduced pollinator access + increased foliar
 herbivory treatments. RESULTS: Reduced pollinator access intensified
 selection for larger chasmogamous flowers and more cleistogamous flowers.
 In contrast, increased herbivory did not affect selection on any floral
 trait.    CONCLUSIONS: Reduced pollinator access
 intensified selection for a trait that facilitates outcrossing, suggesting
 that even species such as I. capensis that can autonomously self-pollinate
 have the potential to respond to pollinator declines by evolving floral
 traits that reinforce interactions between plants and pollinators.
 However, reduced pollinator access also intensified selection for a trait
 that facilitates selfing, suggesting that I. capensis could adapt to
 pollinator declines by evolving floral traits that maintain the production
 of both selfed and outcrossed seeds.
DOI: 10.5061/dryad.p5hqbzkkt
title: Implementing large genomic SNP datasets in phylogenetic network reconstructions: a case study of particularly rapid radiations of cichlid fish

description: The Midas cichlids of
 the Amphilophus citrinellus spp. species complex from Nicaragua, are an extraordinary adaptive rapid radiation (&lt;24,000 years old; 13 described species). These cichlids are a very challenging group to infer its evolutionary history in phylogenetic analyses, due to the apparent prevalence of ILS, as well as past and current gene flow. Assuming solely a vertical transfer of genetic material from an ancestral lineage to new lineages is not appropriate in many cases of genes transferred horizontally in nature. Recently developed methods to infer phylogenetic networks under such circumstances might be able to circumvent these problems. These models accommodate not just incomplete lineage sorting, but also gene flow, under the multispecies network coalescent model (MSNC), processes that are at work in young, hybridizing, and/or rapidly diversifying lineages. There are currently only a few programs available that implement MSNC for estimating phylogenetic networks. Here, we present a novel way to incorporate single nucleotide polymorphism (SNP) data into the currently available PhyloNetworks program. Based on simulations, we demonstrate that SNPs can provide enough power to recover the true phylogenetic network. Moreover, our approach results in a faster algorithm compared to the original pipeline in PhyloNetworks, without losing power. We also applied our new approach to infer the phylogenetic network of Midas cichlid radiation. We implemented the most comprehensive genomic dataset to date (RADseq dataset of 679 individuals and &gt;37K SNPs from 19 ingroup lineages) and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation.
DOI: 10.5061/dryad.p2ngf1vm9
title: Relationship of total and calculated free 25-hydroxyvitamin D to biomarkers and metabolic indices in healthy children

description: ABSTRACT Context:  Vitamin D status is usually assessed by serum
 total 25-hydroxyvitamin D.  Whether free 25-hydroxyvitamin D
 measures better correlate with various clinical outcomes is unclear.
 Objective:  To identify correlations between total
 25-hydroxyvitamin D (t25-OHD), calculated and direct measures of free
 25-OHD, and to identify associations of these measures with other outcomes
 in children, across the 6 common GC haplotypes. Design:  Healthy
 urban-dwelling children underwent measurement of relevant variables.
 Setting: Academic medical center Participants: Healthy, urban-dwelling
 children, 6 months to 10 yrs old, predominantly of Hispanic background and
 representative of all common GC haplotypes. Intervention: None Main
 Outcome Measures: Total and free 25-OHD and 1,25(OH)2D, calcium,
 phosphate, PTH, glucose, insulin, aldosterone, and renin. Results: Mean
 t25-OHD [26.3±6.7ng/ml; 65.8±16.8nmol/L] were lowest in the GC2
 genotype.  Mean t1,25(OH)2D [57.6±16.5pg/ml; 143.9±41.3pmol/L],
 were lowest in GC1f/1f, GC1f/2, and GC2/2 groups. T25-OHD correlated
 strongly with circulating free 25-OHD (cf25-OHD) (r=0.89) and directly
 measured free 25-OHD (dmf25-OHD) (r=0.69). Cf25-OHD correlated with
 dmf25-OHD (r=0.69) (p&lt;0.001 for all).  t25-OHD inversely
 correlated with BMI (r=-0.191; p=0.006), skin reflectometry, and systolic
 blood pressure. T25-OHD correlated with fasting insulin and HOMA-IR,
 however significance for these correlations were not evident after
 adjustment for BMI. PTH inversely correlated with all measures of 25-OHD,
 but most strongly with t25-OHD. Conclusions:  Measure of
 circulating total and free 25-OHD are comparable measures of vitamin D
 status in heathy children. Correlations are similar with other outcome
 variables, however t25-OHD remains the strongest correlate of circulating
 PTH and other variables. These data argue against routine refinement of
 the t25-OHD measure using currently available assessments of free
 25-OHD.
DOI: 10.82294/dvnucwf66
title: Entrevistas semiestructuradas. Territorio: Cartagena. Sector: Cultura. Año: 2025

description: A partir de un proceso de acompañamiento situado, se recopilaron testimonios por medio de entrevistas semiestructuradas durante el año 2025, las cuales indagaron sobre 4 categorías que describían la práctica en educación artística de docentes, cultores, sabedores de la enseñanza del arte, que hacían parte de los programas de formación en educación artística y cultural del sector Cultura (educación informal) en la ciudad de Cartagena.
DOI: 10.5061/dryad.9ghx3ffd5
title: Data from: Strong dispersal limitation in post-fire regeneration of Baker cypress, a rare serotinous conifer

description: PREMISE:  Dispersal capacity primarily determines the spatial
 establishment patterns that drive range expansions and contractions in
 tree species. For Baker cypress (Hesperocyparis bakeri  [(Jeps.)
 Bartel]), seedling establishment relies predominantly on fire events due
 to its cone serotiny, shade intolerance, and small seeds requiring the
 optimal conditions of fire-exposed, mineral soil seedbeds. 
   METHODS:  This study quantified the density and
 spatial distribution of post-disturbance seedlings following the 2014
 Eiler fire in northern California and compared the observed recruitment to
 predictions from a mechanistic seed dispersal model.   
 RESULTS:  Post-fire recruitment was dense, averaging 11
 seedling/m  2  , and occurred primarily in the first
 year after fire. We estimated the mean descent velocity of the wingless
 seeds as around 4 m/sec, the highest value reported for any putatively
 wind-dispersed tree species. The rapid seed decent contributed to markedly
 constrained recruitment in space. Most seedlings (~81%) established within
 5 m of the parent tree, and 94% established within 10 m. The maximum
 observed dispersal distance was 48.5 m, and scaled linearly with canopy
 height. Distributions of modeled seed dispersal distance and observed
 seedling establishment in Baker cypress did not differ, demonstrating that
 wind disperses seeds a short distance due to the lack of a wing, and
 secondary dispersal appeared to be minimal at this recently burned
 site.    CONCLUSIONS:  If seed dispersal is
 solely reliant on wind, migration in response to rapid climate
 change will be impeded and potentially present difficulties in sustaining
 populations of this and other obligate seeder species with equally
 constrained dispersal.
description: We collected data on observed seedling establishment and modeled
 seed dispersal for 20 Baker cypress (Hesperocyparis bakeri) trees
 following the 2014 Eiler fire in a population located in northern
 California.
DOI: 10.5061/dryad.ttdz08kt6
title: Data from: A new mound-building biota from the lower Carboniferous of Alabama

description: A small (1.2 m) columnar carbonate mound in shaley strata equivalent to
 the Hartselle Sandstone (lower Serpukhovian) near Woodville in
 northeastern Alabama was built by a consortium of species unlike those of
 other Carboniferous mounds in the southeastern United States. The mound
 contains a new problematic microencruster, Aphralysia anfracta n. sp.,
 along with encrusting bryozoans (Fistulipora M'Coy, 1849),
 nonskeletal microbes, and other microencrusters, including Aphralysia
 capriorae Mamet and Roux 1975, in a carbonate mud matrix. Mound cavities
 are filled with three generations of carbonate and siliciclastic sediment.
 Other biotic constituents of the mound include oncoids, sponges (including
 Pileospongia Rigby et al., 1979), gastropods, crinoids, a tabulate coral,
 and coenobionts, including coccoid calcimicrobes. The mound biota,
 especially the microencrusters, is dramatically different from those of
 other Serpukhovian mounds that have been described from Alabama (made by
 various consortia of rugose corals, fenestrate bryozoa, crinoids, sponges,
 and nonskeletal microbes). Indeed, the Woodville mound extends the range
 of the lower Carboniferous encruster Aphralysia to North America.
description: These datasets consist of (1) sample site locations, (2)
 measurements of diameters, wall thickness, and shape characteristics of
 tubules of <em>Aphralysia anfracta</em>. These measurements
 were made on digital photographs of thin sections, at intersections of a
 superimposed grid, using a calibrated scale, (3) sample numbers, and (4)
 size
 measurements of
 <i>Aphralysia
 capriorae</i>
 vesicles in specimen GSA-M265, made as in dataset
 (2).
description: See README file and text of paper for further explanation.
DOI: 10.5061/dryad.3tx95x6bk
title: Data from: Regulators of an ancient polyphenism evolved through episodic protein divergence and parallel gene radiations

description: Polyphenism is a form of developmental plasticity that transduces
 environmental cues into discontinuous, often disparate phenotypes. In some
 cases, polyphenism has been attributed to facilitating morphological
 diversification and even the evolution of novel traits. However, this
 process is predicated on the origins
 and evolutionary maintenance of genetic mechanisms that
 specify alternate developmental networks. When and how regulatory loci
 arise and change, specifically before and throughout the history of a
 polyphenism, is little understood. Here, we establish a phylogenetic and
 comparative molecular context for two dynamically evolving
 genes, eud-1 and seud-1, which
 regulate polyphenism in the nematode Pristionchus pacificus. This
 species is dimorphic in its adult feeding-structures, allowing individuals
 to become microbivores or facultative predators depending on environment.
 Although polyphenism regulation is increasingly well understood
 in P. pacificus, the polyphenism is far older than this species
 and has diversified morphologically to enable an array of ecological
 functions across polyphenic lineages. To bring this taxonomic diversity
 into a comparative context, we reconstructed the histories
 of eud-1 and seud-1 relative to the
 origin and diversification of polyphenism, finding that homologs of both
 genes have undergone lineage-specific radiations across polyphenic taxa.
 Further, we detected signatures of episodic diversifying selection
 on eud-1, particularly in early diplogastrid lineages. Lastly,
 transgenic rescue experiments suggest that the gene’s product has
 functionally diverged from its ortholog’s in a non-polyphenic outgroup. In
 summary, we provide a comparative framework for the molecular components
 of a plasticity switch, enabling studies of how polyphenism, its
 regulation, and ultimately its targets evolve.
DOI: 10.5061/dryad.ttdz08kt7
title: Data from: Mountain Plover habitat selection and nest survival in relation to weather variability and spatial attributes of Black-tailed Prairie Dog disturbance

description: Habitat loss and altered disturbance regimes have led to declines in many
 species of grassland and sagebrush birds, including the imperiled Mountain
 Plover (Charadrius montanus). In certain parts of their range Mountain
 Plovers rely almost exclusively on Black-Tailed Prairie Dog (Cynomys
 ludovicianus) colonies as nesting habitat. Previous studies have examined
 Mountain Plover nest and brood survival on prairie dog colonies, but
 little is known about how colony size and shape influence these vital
 rates or patterns of habitat selection. We examined how 1) adult habitat
 utilization, 2) nest-site selection, and 3) nest success responded to a
 suite of local- and site-level variables on large prairie dog colony
 complexes in northeastern Wyoming. Abundance of adult Mountain Plovers was
 highest on points within older, “medium”-sized (100–500 ha) colonies with
 high cover of annual forbs and bare ground (5.8 birds/km2), but lower on
 extremely large (&gt;2000 ha) colonies (2.1 birds/km2). Nest sites
 were characterized by high proportions of annual forbs and bare ground and
 low cactus cover and vegetation height. Nest survival was higher for older
 nests, and nests with lower cactus cover, and decreased with increasing
 temperatures. Uncertainty was high for models of daily nest survival,
 potentially because of two competing sources of nest failure: nest
 depredation and nest abandonment or inviability of eggs. Drivers of these
 two sources of nest failure differed, with inclement weather and higher
 temperatures associated with nest abandonment or egg inviability. We
 highlight how prairie dogs alter vegetation structure and bare ground
 heterogeneously across the landscape, and how this in turn influences bird
 abundance and nest distribution at different temporal and spatial scales.
 Furthermore, our work reveals how partitioning the causes of nest failure
 during nest survival analyses enhances understanding of survival rate
 covariates.
DOI: 10.5061/dryad.stqjq2bzz
title: Among‐family variation in survival and gene expression uncovers adaptive genetic variation in a threatened fish

description: Variation in among‐family transcriptional responses to different
 environmental conditions can help to identify adaptive genetic variation,
 even prior to a selective event. Coupling differential gene expression
 with formal survival analyses allows for the disentanglement of treatment
 effects, required for understanding how individuals plastically respond to
 environmental stressors, from the adaptive genetic variation responsible
 for differential survival. We combined these two approaches to investigate
 responses to an emerging conservation issue, thiamine (vitamin B1)
 deficiency, in a threatened population of Atlantic salmon (Salmo salar).
 Thiamine is an essential vitamin that is increasingly limited in many
 ecosystems. In Lake Champlain, Atlantic salmon cannot acquire thiamine in
 sufficient quantities to support natural reproduction; fertilized eggs
 must be reared in hatcheries and treated with supplemental thiamine. We
 evaluated transcriptional responses (via RNA sequencing) to
 thiamine treatment across families and found 3,616 genes differentially
 expressed between control (no supplemental thiamine) and treatment
 individuals. Fewer genes changed expression equally across families (i.e.,
 additively) than exhibited genotype × environment
 interactions in response to thiamine. Differentially expressed genes were
 related to known physiological effects of thiamine deficiency, including
 oxidative stress, cardiovascular irregularities and neurological
 abnormalities. We also identified 1,446 putatively adaptive genes that
 were strongly associated with among‐family survival in the absence of
 thiamine treatment, many of which related to neurogenesis and visual
 perception. Our results highlight the utility of coupling RNA sequencing
 with formal survival analyses to identify candidate genes that underlie
 the among‐family variation in survival required for an adaptive response
 to natural selection.
description: Mortality counts taken for families spawned in 2016 and 2017.
 Censored data indicate that individuals were removed (alive) for other
 scientific studies, disease testing, or USFWS broodstock
 efforts. 
description: Data in 2017_survival_analysis_data_R.csv can be used as input
 for survival analysis in R (see survival_analysis.R at
DOI: 10.5061/dryad.wh70rxwj0
title: Fiber-tract localized diffusion coefficients highlight patterns of white matter disruption induced by proximity to glioma

description: Gliomas account for 26.5% of all primary central nervous system tumors.
 Recent studies have used diffusion tensor imaging (DTI) to extract white
 matter fibers and the diffusion coefficients derived from MR processing to
 provide useful, non-invasive insights into the extent of tumor invasion,
 axonal integrity, and gross differentiation of glioma from metastasis.
 Here, we extend this work by examining whether a tract-based analysis can
 improve non-invasive localization of tumor impact on white matter
 integrity. This study retrospectively analyzed preoperative magnetic
 resonance sequences highlighting contrast enhancement and DTI scans of 13
 subjects that were biopsy confirmed to have either high or low-grade
 glioma. We reconstructed the corticospinal tract and superior longitudinal
 fasciculus by applying atlas-based regions of interest to fibers derived
 from whole-brain deterministic streamline tractography. Within-subject
 comparison of hemispheric diffusion coefficients (e.g., fractional
 anisotropy and mean diffusivity) indicated higher levels of white matter
 degradation in the ipsilesional hemisphere. Novel application of
 along-tract analyses revealed that tracts traversing the tumor region
 showed significant white matter degradation compared to the contralesional
 hemisphere and ipsilesional tracts displaced by the tumor.
DOI: 10.5061/dryad.98sf7m0dw
title: Water availability drives above-ground biomass and bird richness in forest restoration plantings to achieve carbon and biodiversity co-benefits

description: To combat global warming and biodiversity loss we require effective forest
 restoration that encourages recovery of species diversity and ecosystem
 function to deliver essential ecosystem services, such as biomass
 accumulation. Further, understanding how and where to undertake
 restoration to achieve carbon sequestration and biodiversity conservation
 would provide an opportunity to finance ecosystem restoration under carbon
 markets. We surveyed 30 native mixed-species plantings in subtropical
 forests and woodlands in Australia, and used structural equation modelling
 to determine vegetation, soil and climate variables most likely driving
 above-ground biomass accrual and bird richness, and investigate the
 relationships between plant diversity, above-ground biomass accrual and
 bird diversity. We focussed on woodland and forest-dependent birds, and
 functional groups at risk of decline (insectivorous, understorey-nesting,
 and small-bodied birds). We found that mean moisture availability strongly
 limits above-ground biomass accrual and bird richness in restoration
 plantings, indicating potential synergies in choosing sites for carbon and
 biodiversity purposes. Counter to theory, woody plant richness was a poor
 direct predictor of above-ground biomass accrual, but was indirectly
 related via significant, positive effects of stand density. We also found
 no direct relationship between above-ground biomass accrual and bird
 richness, likely because of the strong effects of moisture availability on
 both variables. Instead, moisture availability and patch size strongly and
 positively influenced the richness of woodland and forest dependent birds.
 For understorey-nesting birds, however, shrub cover and patch size
 predicted richness. Stand age or area of native vegetation surrounding the
 patch did not influence bird richness. Our results suggest that in
 subtropical biomes, planting larger patches to higher densities, ideally
 using a diversity of trees and shrubs (characteristics of ecological
 plantings) in more mesic locations will enhance the provision of carbon
 and biodiversity co-benefits. Further, ecological plantings will aid the
 rapid recovery of woodland and forest bird richness, with comparable
 above-ground biomass accrual to less diverse forestry plantations.
description: Methods for collection of
 this data are available in Hagger, V, Wilson, K, England, JE and Dwyer, J
 (2019) Water availability drives above-ground biomass and bird richness in
 forest restoration plantings to achieve carbon and biodiversity
 co-benefits. Ecology and Evolution. In press.