cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.43m76
title: Data from: Tree species composition, breeding systems, pollination and dispersal syndromes in three forest successional stages in a tropical dry forest in Mesoamerica

description: Tropical dry forests (TDF) in Mesoamerica are highly endangered by the
 expansion of human activities (e.g., agriculture and cattle ranching). In
 contrast, TDF in Costa Rica have experienced outstanding restoration due
 to changes in economic and conservation policies. Currently TDF landscapes
 in Costa Rica are a mosaic of different successional stages. Tree breeding
 systems and pollination and dispersal syndromes are key elements for
 understanding restoration processes in TDFs. In this study we describe and
 compare tree species composition and diversity in three TDF successional
 stages (early, intermediate and late) in Guanacaste, Costa Rica. We
 describe for the first time tree species breeding systems and pollination
 and dispersal syndromes for the largest and most significant TDF remnant
 in Mesoamerica. We set up nine plots, three per successional stage, and we
 measured and identified 1,072 trees from 96 species. Species richness and
 diversity indices were higher for the intermediate stage. Monoecy was the
 most common breeding system, as in other tropical life zones. Insects were
 the dominant pollinators, facilitated by the trees’ small inflorescences.
 Wind was found to be not only the next most influential pollinator, mainly
 in open and disturbed early forests, but also it was also a good seed
 dispersal agent. As TDF age increases so does the relevancy of birds and
 mammals as dispersers; the late stage therefore has more tree species with
 adaptations to these dispersers.
description: Database for Dryad costa
 rica curated
DOI: 10.5061/dryad.1194
title: Data from: How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles

description: The traditional view that species are held together through gene flow has
 been challenged by observations that migration is too restricted among
 populations of many species to prevent local divergence. However, only
 very low levels of gene flow are necessary to permit the spread of highly
 advantageous alleles, providing an alternative means by which
 low-migration species might be held together. We re-evaluate these
 arguments given the recent and wide availability of indirect estimates of
 gene flow. Our literature review of Fst values for a broad range of taxa
 suggests that gene flow in many taxa is considerably greater than
 suspected from earlier studies and often is sufficiently high to
 homogenize even neutral alleles. However, there are numerous species from
 essentially all organismal groups that lack sufficient gene flow to
 prevent divergence. Crude estimates on the strength of selection on
 phenotypic traits and effect sizes of quantitative trait loci (QTL)
 suggest that selection coefficients for leading QTL underlying phenotypic
 traits may be high enough to permit their rapid spread across populations.
 Thus, species may evolve collectively at major loci through the spread of
 favourable alleles, while simultaneously differentiating at other loci due
 to drift and local selection.
description: MorjanSupplementaryMaterial.docxSupplementary material for publication. Measures of population subdivision for fungi, bacteria, plants, and animals. Selection gradients and differentials for studies with experimentally enhanced phenotypic variation. Effects of quantitative trait loci for animal crosses.
DOI: 10.5061/dryad.1np06
title: Data from: Rapid range expansion is not restricted by inbreeding in a sexually cannibalistic spider

description: Few studies investigated whether rapid range expansion is associated with
 an individual's short-term fitness costs due to an increased risk of
 inbred mating at the front of expansion. In mating systems with low male
 mating rates both sexes share potential inbreeding costs and general
 mechanisms to avoid or reduce these costs are expected. The spider Argiope
 bruennichi expanded its range recently and we asked whether rapid
 settlement of new sites exposes individuals to a risk of inbreeding. We
 sampled four geographically separated subpopulations, genotyped
 individuals, arranged matings and monitored hatching success. Hatching
 success was lowest in egg-sacs derived from sibling pairs and highest in
 egg-sacs derived from among-population crosses, while within-population
 crosses were intermediate. This indicates that inbreeding might affect
 hatching success in the wild. Unlike expected, differential hatching
 success of within- and among-population crosses did not correlate with
 genetic distance of mating pairs. In contrast, we found high genetic
 diversity based on 16 microsatellite markers and a fragment of the
 mitochondrial COI gene in all populations. Our results suggest that even a
 very recent settlement secures the presence of genetically different
 mating partners. This leads to costs of inbreeding since the population is
 not inbred.
description: Sampling
 localitiesSampling localities of
 individuals from four geographically separated A. bruennichi
 populationsPrimer
 sequencesPrimers, which were used
 in the studyMitochondrial
 diversityMicrosatellite
 dataGenetic
 dataGenetic data including
 observed heterozygosity and genetic distance for the mating
 pairsBehavioural
 dataBehavioural data
 including mating behaviour and hatching success of the mating
 pairsCOI
 alignment
DOI: 10.5061/dryad.05j8s
title: Data from: Clarification of the use of the terms perigynium and utricle in Carex L. (Cyperaceae)

description: Despite previous efforts to unify the terminology for Cyperaceae, two
 different terms, perigynium and utricle, are in common use for the
 prophyllar bract enclosing the female flower of Carex. Use of these terms
 is divided largely on geographic lines (mainly North American versus
 European and other authors, respectively). The recent merging of Kobresia
 with Carex requires a single term to refer to both the open prophyll of
 Kobresia and the laterally closed one of Carex. However, even when authors
 use utricle for Carex species, these same authors do not refer to the open
 prophyll of Kobresia as a utricle. We show that perigynium was apparently
 coined earlier than utricle, at the end of the 18th century, but the term
 utricle became more widespread than perigynium by the 20th century.
 Neither of the two terms is unambiguous, as both have also been used for
 other structures in other plant groups. Given this background, we propose
 revised definitions of both terms based on two facts: 1) the greater
 semantic accuracy of perigynium to refer to both the prophylls of Carex
 and the former genus Kobresia; and 2) the greater spread, and thus social
 utility, of the term utricle. We also discuss the terminology used for the
 fertile prophylls of lower branching orders found in some Carex groups and
 recommend use of the terms cladoprophyll, tubular cladoprophyll, and
 utriculiform cladoprophyll.
description: SUPPLEMENTARY DATA
 1Terminology used to
 refer the prophyll in Carex s.l. in reference works, as well as another
 uses for the terms perigynium/utricle, listed by chronological
 order.Supp
 1_final.xls
DOI: 10.5061/dryad.h1t4h1m
title: Data from: Rates of population differentiation and speciation are decoupled in sea snakes

description: Comparative phylogeography can inform many macroevolutionary questions,
 such as whether species diversification is limited by rates of geographic
 population differentiation. We examined the link between population
 genetic structure and species diversification in the fully aquatic sea
 snakes (Hydrophiinae) by comparing mitochondrial phylogeography in 16
 species from two closely related clades that show contrasting
 diversification dynamics across northern Australia. Contrary to
 expectations from theory and several empirical studies, our results show
 that, at the geographic scale studied here, rates of population
 differentiation and speciation are not positively linked in sea snakes.
 The eight species sampled from the rapidly speciating Hydrophis clade have
 weak population differentiation that lacks geographic structure. In
 contrast, all eight sampled Aipysurus-Emydocephalus species show clear
 geographical patterns and many deep intraspecific splits, but have
 three-fold slower speciation rates. Alternative factors, such as
 ecological specialisation, species duration, and geographic range size,
 may underlie rapid speciation in sea snakes.
description: Nitschke_etal_BiolLettersMitochondrial cytochrome b alignment
DOI: 10.5061/dryad.7nf24
title: Data from: The causes of epistasis in genetic networks

description: Epistasis refers to the non-additive interactions between genes in
 determining phenotypes. Considerable efforts have shown that, even for a
 given organism, epistasis may vary both in intensity and sign. Recent
 comparative studies supported that the overall sign of epistasis switches
 from positive to negative as the complexity of an organism increases, and
 it has been hypothesized that this change shall be a consequence of the
 underlying gene network properties. Why should this be the case? What
 characteristics of genetic networks determine the sign of epistasis? Here
 we show, by evolving genetic networks that differ in their complexity and
 robustness against perturbations but that perform the same tasks, that
 robustness increased with complexity and that epistasis was positive for
 small non-robust networks but negative for large robust ones. Our results
 indicate that robustness and negative epistasis emerge as a consequence of
 the existence of redundant elements in regulatory structures of genetic
 networks and that the correlation between complexity and epistasis is a
 byproduct of such redundancy, allowing for the decoupling of epistasis
 from the underlying network complexity.
description: Figure 2-Association
 average connectivity and complexityAssociation between
 average degree connectivity and complexity.Figure 3-Association of
 complexity with epistasisAssociation between
 average epistasis and complexity in evolved genetic networks. File
 contains data for networks with feedback loops and for networks without
 feedback loops. In addition, two sets of smaller feedback loop-free
 networks (12 and 6 nodes) are included.Figure 4a-Association
 epistasis robustnessAssociation between
 epistasis and robustness for evolved networks with and without feedback
 loops.Figure 4b-Association
 complexity robustnessAssociation between
 complexity and robustness for evolved genetic networks with or without
 feedback loops.Figure 5a-Association
 degeneracy epistasisAssociation between
 degeneracy and epistasis for evolved genetic networks with and without
 feedback loops. Two small sets of networks without feedback loops of small
 size (12 and 6 nodes) are included. Data for feedback-loop containing
 mutated networks are also included.Figure 5b-Association
 redundancy epistasisAssociation between
 redundancy and epistasis for evolved genetic networks with and without
 feedback loops. Two small sets of networks without feedback loops of small
 size (12 and 6 nodes) are included. Data for feedback-loop containing
 mutated networks are also included.Figure 6-Association
 complexity degeneracyAssociation between
 complexity and degeneracy for evolved genetic networks with and without
 feedback loops.
DOI: 10.5061/dryad.85k8m
title: Data from: The meaning of melanin, carotenoid, and pterin pigments in the bluefin killifish, Lucania goodei

description: Male bluefin killifish (Lucania goodei) exhibit extensive color variation
 in their fins, but the utility of this variation has not yet been
 determined. We collected males from multiple populations and
 spectrophotometrically determined the pigment types responsible for fin
 coloration. We determined that the orange coloration in the caudal fin is
 caused by carotenoid pigmentation. In contrast, color in the anal fin is
 either pterin based (yellow and red) or structural (blue) with a melanic
 fin border. As these colors have different developmental origins, the
 potential for complex signaling is high. Therefore, we sought to determine
 whether behavior, reproductive success, or health correlated with
 pigmentation. Males with more melanin on the anal fin were more dominant
 and had higher spawning success. Male–male aggression was greater between
 males with similar-sized melanic borders, indicating that melanic markings
 function as badges of status between males. Caudal carotenoid pigmentation
 did not correlate with dominance, but this highly labile ornament was
 correlated with body condition, parasite infection, and spawning success,
 suggesting a role in intersexual selection by signaling health to
 potential mates. Similar results were found for caudal fin coloration
 using digital photography. Pterin pigmentation in the anal fin was not
 related to dominance but was related to overall spawning levels and
 parasite infection, suggesting that pterin pigmentation may also signal
 immune status. Thus, the coloration of male bluefin killifish provides
 multiple messages to multiple receivers through these 3 pigments (melanin,
 pterin, and carotenoid) that have distinct developmental origins.
description: Pigments_Johnson&Fuller_individualsThis file contains data on size, condition, coloration, dominance, and spawning for all of the males described in the paper by Johnson & Fuller. In this file, they are listed individually. See the README document for details on the definitions of the variables.Pigments_Johnson&Fuller_pairedThis file contains data on size, condition, coloration, dominance, and spawning for the males described in the paper by Johnson and Fuller. The data are listed here in a paired format where dominant and subdominant male data are listed in separate columns. See the README document for further details.
DOI: 10.5061/dryad.f6hc4rf
title: Data from: Cucumis omissus sp. nov. (Cucurbitaceae) from southern Arabia and Ethiopia and its phylogenetic position

description: The new species Cucumis omissus Thulin from Yemen, Oman and Ethiopia is
 described and illustrated. According to phylogenetic analyses based mainly
 on nuclear ribosomal ITS sequences and chloroplast trnG sequences, the new
 species is sister to C. hastatus in Somalia and Ethiopia. A map showing
 the distributions of both C. omissus and C. hastatus is provided and
 morphological differences between these two species are pointed out.
 Cucumis omissus has been confused with C. pustulatus and C. prophetarum in
 the literature and in herbaria, and morphological differences from these
 two species are provided as well. Oreosyce africana is nested within
 Cucumis in this, as well as in several previous studies. We clarify that
 when O. africana is treated as a Cucumis, its correct name is C.
 subsericeus.
description: Nucleotide
 datasetcombined-dataset.fastaMrBayes Consensus TreeMrBayes.consensus.tree.nexusRAxML bipartitions treeRAxML_bipartitions.tree.nexus
DOI: 10.5061/dryad.mk68f
title: Data from: Fine-grained adaptive divergence in an amphibian: genetic basis of phenotypic divergence and the role of non-random gene flow in restricting effective migration among wetlands

description: Adaptive ecological differentiation among sympatric populations is
 promoted by environmental heterogeneity, strong local selection and
 restricted gene flow. High gene flow, on the other hand, is expected to
 homogenize genetic variation among populations and therefore prevent local
 adaptation. Understanding how local adaptation can persist at the spatial
 scale at which gene flow occurs has remained an elusive goal, especially
 for wild vertebrate populations. Here, we explore the roles of natural
 selection and nonrandom gene flow (isolation by breeding time and habitat
 choice) in restricting effective migration among local populations and
 promoting generalized genetic barriers to neutral gene flow. We examined
 these processes in a network of 17 breeding ponds of the moor frog Rana
 arvalis, by combining environmental field data, a common garden experiment
 and data on variation in neutral microsatellite loci and in a thyroid
 hormone receptor (TRβ) gene putatively under selection. We illustrate the
 connection between genotype, phenotype and habitat variation and
 demonstrate that the strong differences in larval life history traits
 observed in the common garden experiment can result from adaptation to
 local pond characteristics. Remarkably, we found that haplotype variation
 in the TRβ gene contributes to variation in larval development time and
 growth rate, indicating that polymorphism in the TRβ gene is linked with
 the phenotypic variation among the environments. Genetic distance in
 neutral markers was correlated with differences in breeding time and
 environmental differences among the ponds, but not with geographical
 distance. These results demonstrate that while our study area did not
 exceed the scale of gene flow, ecological barriers constrained gene flow
 among contrasting habitats. Our results highlight the roles of strong
 selection and nonrandom gene flow created by phenological variation and,
 possibly, habitat preferences, which together maintain genetic and
 phenotypic divergence at a fine-grained spatial scale.
description: Phenotypic common garden
 dataPhenotypic common garden
 data, data of larval period, growth rate and mass at metamorphosis of the
 quantitative genetic laboratory experiments.Quantitative Genetic
 Data.txtFamily
 PhenotypesCommon garden phenotype
 results at the family level used in the phenotype-genotype
 analysesTRβ alignment
 sequencesTRβ alignment sequences
 in .fas format used in the phenotype-genotype analyses.allpops.fas.txt
DOI: 10.5061/dryad.6v0j9
title: Data from: Phosphate is a potential biomarker of disease severity and predicts adverse outcomes in acute kidney injury patients undergoing continuous renal replacement therapy

description: Hyperphosphatemia is associated with mortality in patients with chronic
 kidney disease, and is common in critically ill patients with acute kidney
 injury (AKI); however, its clinical implication in these patients is
 unknown. We conducted an observational study in 1144 patients (mean age,
 63.2 years; male, 705 [61.6%]) with AKI who received continuous renal
 replacement therapy (CRRT) between January 2009 and September 2016.
 Phosphate levels were measured before (0 h) and 24 h after CRRT
 initiation. We assessed disease severity using various clinical
 parameters. Phosphate at 0 h positively correlated with the Acute
 Physiology and Chronic Health Evaluation II (APACHE II; P &lt; 0.001)
 and Sequential Organ Failure Assessment (SOFA; P &lt; 0.001) scores,
 and inversely with mean arterial pressure (MAP; P = 0.02) and urine output
 (UO; P = 0.01). In a fully adjusted linear regression analysis for age,
 sex, Charlson comorbidity index (CCI), MAP, and estimated glomerular
 filtration rate (eGFR), higher 0 h phosphate level was significantly
 associated with high APACHE II (P &lt; 0.001) and SOFA (P = 0.04)
 scores, suggesting that phosphate represents disease severity. A
 multivariable Cox model also showed that hyperphosphatemia was
 significantly associated with increased 28-day (HR 1.05, 95% CI 1.02-1.08,
 P = 0.001) and 90-day (HR 1.05, 95% CI 1.02-1.08, P = 0.001) mortality.
 Furthermore, patients with increased phosphate level during 24 h were at
 higher risk of death than those with stable or decreased phosphate levels.
 Finally, c-statistics significantly increased when phosphate was added to
 a model that included age, sex, CCI, body mass index, eGFR, MAP,
 hemoglobin, serum albumin, C-reactive protein, and APACHE II score. This
 study shows that phosphate is a potential biomarker that can reflect
 disease severity and predict mortality in critically ill patients
 receiving CRRT.
description: CRRTstudy_1144patients1144 patients with acute kidney injury who received continuous renal replacement therapy (CRRT) were enrolled. Phosphate levels were measured before (0 h) and 24 h after CRRT initiation. We assessed disease severity using various clinical parameters.
DOI: 10.15468/dl.754q4b
title: Occurrence Download

description: A dataset containing 10455 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Lasionycteris noctivagans"
 ]
}

 The dataset includes 10455 records from 111 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000586-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7d65n
title: Data from: The REporting of studies Conducted using Observational Routinely-collected health Data (RECORD) statement: methods for arriving at consensus and developing reporting guidelines

description: Objective: Routinely collected health data, collected for administrative
 and clinical purposes, without specific a priori research questions, are
 increasingly used for observational, comparative effectiveness, health
 services research, and clinical trials. The rapid evolution and
 availability of routinely collected data for research has brought to light
 specific issues not addressed by existing reporting guidelines. The aim of
 the present project was to determine the priorities of stakeholders in
 order to guide the development of the REporting of studies Conducted using
 Observational Routinely-collected health Data (RECORD) statement. Methods:
 Two modified electronic Delphi surveys were sent to stakeholders. The
 first determined themes deemed important to include in the RECORD
 statement, and was analyzed using qualitative methods. The second
 determined quantitative prioritization of the themes based on
 categorization of manuscript headings. The surveys were followed by a
 meeting of RECORD working committee, and re-engagement with stakeholders
 via an online commentary period. Results: The qualitative survey (76
 responses of 123 surveys sent) generated 10 overarching themes and 13
 themes derived from existing STROBE categories. Highest-rated overall
 items for inclusion were: Disease/exposure identification algorithms;
 Characteristics of the population included in databases; and
 Characteristics of the data. In the quantitative survey (71 responses of
 135 sent), the importance assigned to each of the compiled themes varied
 depending on the manuscript section to which they were assigned. Following
 the working committee meeting, online ranking by stakeholders provided
 feedback and resulted in revision of the final checklist. Conclusions: The
 RECORD statement incorporated the suggestions provided by a large, diverse
 group of stakeholders to create a reporting checklist specific to
 observational research using routinely collected health data. Our findings
 point to unique aspects of studies conducted with routinely collected
 health data and the perceived need for better reporting of methodological
 issues.
description: Raw Data - Survey
 1Raw
 data from the first survey (qualitative themes)Raw Data - Survey
 2Raw
 Data from the second survey (quantitative ranking)