cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hn390
title: Data from: Within-family parent-offspring co-adaptation in a wild bird: on static traits, behavioural reaction norms and sex differences

description: Parental care, a central component of reproduction in a wide range of
 animal species, often involves elaborate behavioural interactions between
 parents and their offspring. Due to the reciprocal nature of these
 interactions, it has been hypothesized that parental and offspring
 behaviours (e.g. parental food provisioning and offspring begging) are not
 only target but also agent of selection. These traits are therefore
 expected to co-evolve, ultimately leading to co-adaptation of parent and
 offspring behaviours within families. However, empirical data on such
 parent-offspring co-adaptation are limited, particularly for wild
 populations. Furthermore, mean levels of behaviour (as measured in
 previous studies) may not adequately describe the dynamic nature of the
 reciprocal interplay between parents and their offspring, and instead
 rather the behavioural reaction norms for provisioning and begging may be
 co-adapted. We applied a large-scale cross-fostering study over 3
 consecutive breeding seasons to investigate whether provisioning behaviour
 of wild blue tit (Cyanistes caeruleus) parents co-varies with the begging
 behaviour of their genetic, cross-fostered offspring. We simultaneously
 analysed parent and offspring behaviours, both as static traits (mean
 levels) and behavioural reaction norms (offspring begging as a function of
 food deprivation and parental provisioning as a function of short-term
 experimental changes in brood size). Neither maternal nor paternal
 provisioning rates co-varied with the begging intensity of their genetic
 offspring when analysed as mean levels of behaviour. However, the slopes
 of the reaction norms for provisioning and begging were negatively
 correlated between male, but not female, parents and their genetic
 offspring. Thus, fathers that change their provisioning rate strongly with
 brood size sire offspring whose level of begging only weakly increases
 with hunger, and vice versa. The observed co-variation suggests the
 existence of sex-specific optima for parent-offspring trait combinations.
 Thus, our study not only highlights the importance of a behavioural
 reaction norm approach when investigating parent-offspring interactions,
 but also stresses the relevance of considering parents as separate units,
 at least for biparental species.
description: Coadaptation
 dataData description can be
 found in the ReadMe file.Coadaptation_Data.xlsx
DOI: 10.5061/dryad.387n8
title: Data from: Serum copeptin and neuron specific enolase are markers of neonatal distress and long-term neurodevelopmental outcome

description: The objective of this study was to evaluate the early changes in serial
 serum levels of copeptin and neuron-specific enolase (NSE) in neonates
 diagnosed with birth asphyxia, and to determine whether these biomarkers
 measured in the first 168 hours after birth are predictive of long-term
 neurodevelopmental outcome. Copeptin and NSE levels were measured from
 serum samples collected 6, 12, 24, 48, 72, and 168 hours after birth from
 75 term neonates diagnosed with hypoxic-ischemic encephalopathy (HIE) and
 treated with therapeutic hypothermia for 72 hours. In addition, serum
 copeptin levels after birth were measured from 10 HIE diagnosed neonates,
 who were randomized to the normothermic arm of the TOBY cohort. All
 neonates underwent neurodevelopmental assessment using the Bayley Scales
 of Infant and Toddler Development-II at two years of age. Copeptin levels
 were highest at 6 hours after birth and steadily decreased, whereas the
 highest NSE levels were measured at 24 hours after birth. The biomarker
 levels correlated with blood-gas parameters (base excess, pH and lactate)
 at 6 and 12 hours after birth. Copeptin and NSE levels in the early
 postnatal period were significantly higher in neonates with poor outcome
 compared to those with favorable outcome at two years of age. Furthermore,
 in the TOBY cohort, copeptin levels were significantly lower in
 hypothermic compared to normothermic neonates. To conclude, copeptin and
 NSE measured in the early postnatal period are potential prognostic
 biomarkers of long-term neurodevelopmental outcome in term neonates
 diagnosed with HIE and treated with therapeutic hypothermia.
description: Minimal data
 setMinimal data set for
 2017 PLOS ONE article "Serum copeptin and neuron specific enolase are
 markers of neonatal distress and long-term neurodevelopmental
 outcome".minimal data
 set.xlsx
DOI: 10.5061/dryad.pd45719
title: Data from: Genetic pedigree analysis of the pilot breeding program for the rediscovered Galapagos giant tortoise from Floreana island

description: An aim of many captive breeding programs is to increase population sizes
 for reintroduction and establishment of self-sustaining wild populations.
 Genetic analyses play a critical role in these programs: monitoring
 genetic variation, identifying the origin of individuals, and assigning
 parentage to track family sizes. Here we use genetic pedigree analyses to
 examine three seasons of a pilot breeding program for the Floreana island
 Galapagos giant tortoise, C. niger, that had been declared extinct for
 ~150 years until individuals with mixed ancestry were recently discovered.
 We determined that eight of nine founding individuals were assigned
 parentage to at least one of 130 offspring produced, though there was
 considerable reproductive skew. In addition, we observed that genetic
 diversity of the progeny was lower than that of the founders. Despite the
 observed reproductive skew, we did not see evidence for assortative mating
 based on relatedness, but there was a trend towards reduced fitness when
 more related individuals bred. Finally, we found that the majority of
 progeny had ancestry assigned to the Floreana species (mean±SE =
 0.51±0.02), though individual estimates varied. The success of these pilot
 seasons bodes well for a larger breeding program to help restore the
 previously extinct tortoise from Floreana island. Future efforts should
 continue to monitor for reproductive skew and assortative mating in order
 to maintain allelic diversity. We would also recommend forming smaller
 breeding groups and rotating individuals among them to prevent long-term
 reproductive skew among pairs.
description: Breeders and Progeny
 Microsatellite GenotypesIndividual genotypes for
 12 di-nucleotide microsatellites used for pedigree construction and
 calculation of of genetic diversity. There is one row per individual with
 marker names indicated in row 1. The first column contains the individual
 ID and each subsequent column has an allele score. Missing alleles are
 indicated by "-9".Miller_et_al_Genotypes_for_Dryad.xlsx
DOI: 10.5061/dryad.f4r5574
title: Data from: Experimental measurement of the growth costs and benefits of clonal integration of Zoysia japonica in habitats with various N/P ratios

description: A small number of previous studies investigating the potential advantages
 of clonal integration, have focused on the measurement of the costs and
 benefits of clonal integration at various N/P ratios. Clonal plants
 adaptively respond to abiotic stress but to date little is known about at
 what level clonal integration is beneficial or costly at various
 conditions. To study the costs and benefits of clonal integration on the
 clonal growth of Zoysia japonica, the studied species was grown under
 three ratios of N:P (N:P≈7, 14:1 and 21:1), and four types of stolon
 severing treatments (connected stolon CS, light severing LS, moderate
 severing MS, serious severing SS) were implemented. The results showed
 that Z. japonica performed best at a low ratio of N:P (N:P≈7:1). Under the
 stolons connected CS, the growth of primary A-ramets, multiple-nodes and
 stolons benefited by clonal integration; however, the growth of primary
 B-ramets on the primary stolons, A and B ramet significantly declined (p
 &lt; 0.05). Under moderate stolon severing treatment MS7:1 (N:P≈7),
 the clonal integration showed most cost effective compared to all other
 treatments. On the whole, with increasing stolon severing intensity, the
 cost of clonal integration increased and the clonal growth of Z. japonica
 declined significantly. The pattern of biomass allocation may be useful
 for Z. japonica to adapt to the various environments, and clonal
 integration plays a significant role under adverse environmental
 conditions.
description: NJB
 1795
DOI: 10.5061/dryad.h359g
title: Data from: Infanticide as a male reproductive strategy has a nutritive risk effect in brown bears

description: Behavioral strategies to reduce predation can incur costs (i.e. risk
 effects). A common strategy to avoid predation is spatiotemporal avoidance
 of predators, in which prey typically trade optimal resources for safety.
 Analogous with predator-prey theory, risk effects should also arise in
 species with sexually selected infanticide (SSI), in which females with
 dependent offspring avoid infanticidal males. In brown bears (Ursus
 arctos), SSI is common and explains spatiotemporal segregation among
 reproductive classes. Here, we show that females with cubs-of-the-year had
 lower quality diets than conspecifics during the SSI high-risk period, the
 mating season. After the mating season, their diets were of similar
 quality to diets of their conspecifics. Our results suggest a nutritive
 risk effect of SSI, in which females with cubs-of-the-year alter their
 resource selection and trade optimal resources for offspring safety. We
 suggest that risk effects can be widespread among species with SSI, and
 that these risk effects can add to the female costs of reproduction.
description: ESM_data_ssi_risk_effectsFecal crude fiber (fiber) and protein content (% dry matter) in brown bear feces collected during the mating (1) and postmating (3) season of 2010 in central Sweden. 'repro' indicates the reproductive status (AM = adult males, FWC = females with cubs-of-the-year, AF = lone adult female). Age indicates the age (years) of the each individual bear. 'fieldtime' and 'oventime' indicate the time (hours) that samples were exposed in the field and the oven, respectively. 'densiometer' indicates the canopy cover at the location where each sample was collected.
DOI: 10.5061/dryad.qj163
title: Data from: Towards a mechanistic understanding of vulnerability to hook-and-line fishing: boldness as the basic target of angling-induced selection

description: In passively operated fishing gear, boldness-related behaviors should
 fundamentally affect the vulnerability of individual fish and thus be
 under fisheries selection. To test this hypothesis, we used juvenile
 common-garden reared carp (Cyprinus carpio) within a narrow size-range to
 investigate the mechanistic basis of behavioral selection caused by
 angling. We focused on one key personality trait (i.e., boldness),
 measured in groups within ponds, two morphological traits (body-shape and
 head-shape), and one life-history trait (juvenile growth capacity) and
 studied mean standardized selection gradients caused by angling. Carp
 behavior was highly repeatable within ponds. In the short-term, over seven
 days of fishing, total length, not boldness, was the main predictor of
 angling vulnerability. However, after 20 days of fishing, boldness turned
 out to be the main trait under selection, followed by juvenile growth
 rate, while morphological traits were only weakly related to angling
 vulnerability. In addition, we found juvenile growth rate to be moderately
 correlated with boldness. Hence, direct selection on boldness will also
 induce indirect selection on juvenile growth and vice versa, but given
 that the two traits are not perfectly correlated, independent evolution of
 both traits is also possible. Our study is among the first to
 mechanistically reveal that energy-acquisition related behaviors, and not
 growth rate per se, are key factors determining the probability of
 capture, and hence behavioral traits appear to be the prime targets of
 angling selection. We predict an evolutionary response towards increased
 shyness in intensively angling-exploited fish stocks, possibly causing the
 emergence of a timidity-syndrome.
description: KlefothEtAl_data
DOI: 10.5061/dryad.20k7j
title: Data from: Positive epistasis drives the acquisition of multidrug resistance.

description: The evolution of multiple antibiotic resistance is an increasing global
 problem. Resistance mutations are known to impair fitness, and the
 evolution of resistance to multiple drugs depends both on their costs
 individually and on how they interact—epistasis. Information on the level
 of epistasis between antibiotic resistance mutations is of key importance
 to understanding epistasis amongst deleterious alleles, a key theoretical
 question, and to improving public health measures. Here we show that in an
 antibiotic-free environment the cost of multiple resistance is smaller
 than expected, a signature of pervasive positive epistasis among alleles
 that confer resistance to antibiotics. Competition assays reveal that the
 cost of resistance to a given antibiotic is dependent on the presence of
 resistance alleles for other antibiotics. Surprisingly we find that a
 significant fraction of resistant mutations can be beneficial in certain
 resistant genetic backgrounds, that some double resistances entail no
 measurable cost, and that some allelic combinations are hotspots for rapid
 compensation. These results provide additional insight as to why
 multi-resistant bacteria are so prevalent and reveal an extra layer of
 complexity on epistatic patterns previously unrecognized, since it is
 hidden in genome-wide studies of genetic interactions using gene
 knockouts.
description: Trindade et al Fitness
 DataSingle- and
 double-fitness data
DOI: 10.5061/dryad.bb5hr
title: Data from: Monoallelic loss of the imprinted gene Grb10 promotes tumor formation in irradiated Nf1+/- mice

description: Imprinted genes are expressed from only one parental allele and
 heterozygous loss involving the expressed allele is sufficient to produce
 complete loss of protein expression. Genetic alterations are common in
 tumorigenesis but the role of imprinted genes in this process is not well
 understood. In earlier work we mutagenized mice heterozygous for the
 Neurofibromatosis I tumor suppressor gene (NF1) to model
 radiotherapy-associated second malignant neoplasms that arise in
 irradiated NF1 patients. Expression analysis of tumor cell lines
 established from our mouse models identified Grb10 expression as widely
 absent. Grb10 is an imprinted gene and polymorphism analysis of cell lines
 and primary tumors demonstrates that the expressed allele is commonly lost
 in diverse Nf1 mutant tumors arising in our mouse models. We performed
 functional studies to test whether Grb10 restoration or loss alter
 fundamental features of the tumor growth. Restoring Grb10 in Nf1 mutant
 tumors decreases proliferation, decreases soft agar colony formation and
 downregulates Ras signaling. Conversely, Grb10 silencing in untransformed
 mouse embryo fibroblasts significantly increased cell proliferation and
 increased Ras-GTP levels. Expression of a constitutively activated MEK
 rescued tumor cells from Grb10-mediated reduction in colony formation.
 These studies reveal that Grb10 loss can occur during in vivo
 tumorigenesis, with a functional consequence in untransformed primary
 cells. In tumors, Grb10 loss independently promotes Ras pathway
 hyperactivation, which promotes hyperproliferation, an early feature of
 tumor development. In the context of a robust Nf1 mutant mouse model of
 cancer this work identifies a novel role for an imprinted gene in
 tumorigenesis.
description: Grb10 sequence
 dataThis file contains Grb10
 exomic sequences from tumors described in the
 manuscript.
DOI: 10.5061/dryad.v7817
title: Data from: Measuring asymmetry in time-stamped phylogenies

description: Previous work has shown that asymmetry in viral phylogenies may be
 indicative of heterogeneity in transmission, for example due to acute HIV
 infection or the presence of ‘core groups’ with higher contact rates.
 Hence, evidence of asymmetry may provide clues to underlying population
 structure, even when direct information on, for example, stage of
 infection or contact rates, are missing. However, current tests of
 phylogenetic asymmetry (a) suffer from false positives when the tips of
 the phylogeny are sampled at different times and (b) only test for global
 asymmetry, and hence suffer from false negatives when asymmetry is
 localised to part of a phylogeny. We present a simple permutation-based
 approach for testing for asymmetry in a phylogeny, where we compare the
 observed phylogeny with random phylogenies with the same sampling and
 coalescence times, to reduce the false positive rate. We also demonstrate
 how profiles of measures of asymmetry calculated over a range of
 evolutionary times in the phylogeny can be used to identify local
 asymmetry. In combination with different metrics of asymmetry, this
 combined approach offers detailed insights of how phylogenies
 reconstructed from real viral datasets may deviate from the simplistic
 assumptions of commonly used coalescent and birth-death process models.
description: Trees in newick
 formatThis is a .zip file
 containing the within-host HIV, H5N1 influenza and ebola virus trees in
 Newick format which were analysed in the paper. Many thanks to Andrew
 Rambaut (University of Edinburgh) for providing the ebola phylogeny. Data
 originally from: 1) Within-host HIV (P83_HIV.nwk) Frost SDW, Wrin T, Smith
 DM, Kosakovsky Pond SL, Liu Y, et al. (2005) Neutralizing antibody
 responses drive the evolution of human immunodeficiency virus type 1
 envelope during recent HIV infection. Proc Natl Acad Sci USA 102: 18514-9
 2) H5N1 influenza (H5N1_flu.nwk) Wallace RG, HoDac H, Lathrop RH, Fitch WM
 (2007) A statistical phylogeography of influenza A H5N1. Proc Natl Acad
 Sci USA 104: 4473-4478. 3) Ebola Virus (Ebola.nwk) Gire SK, Goba A,
 Andersen KG, Sealfon RSG, Park DJ, et al. (2014) Genomic surveillance
 elucidates Ebola virus origin and transmission during the 2014 outbreak.
 Science 345: 1369-1372.Trees.ziptreeImbalanceAn R package containing the functions used for detecting asymmetry as described in the paper.R script for analysis of treesR script used in the analysis of the HIV, influenza and ebola trees, and to produce figures 4, 6 and 7. Requires the ape, cluster, phylobase and adephylo packages in addition to the treeImbalance package included in this repository.example-analysis-script.R
DOI: 10.5061/dryad.d437289
title: Data from: Thick eggshells of brood parasitic cowbirds protect their eggs and damage host eggs during laying

description: Brood parasites lay thick-shelled eggs and numerous hypotheses have been
 proposed to explain the significance of this trait. We examined whether
 thick eggshells protect the parasite egg during laying events. We used
 eggs of the parasitic shiny cowbird (Molothrus bonariensis) and its hosts,
 the house wren (Troglodytes aedon) and chalk-browed mockingbird (Mimus
 saturninus) in South America and the eggs of the parasitic brown-headed
 cowbird (M. ater) and its hosts the house wren and red-winged blackbird
 (Agelaius phoeniceus) in North America. We experimentally dropped parasite
 eggs onto host eggs to simulate laying by the parasite, parasite eggs onto
 parasite eggs to simulate multiple parasitism, host eggs onto parasite
 eggs to simulate hosts laying from the height cowbirds lay, and stirred
 eggs to simulate jostling that may occur when cowbirds and hosts interact
 during laying events. We found that cowbird eggs were significantly less
 likely to be damaged than host eggs when they were laid onto a host egg
 and when host and cowbird eggs were laid onto them. There was minimal
 damage to eggs during jostling experiments, thereby failing to support the
 hypothesis that thick eggshells provide protection when eggs are jostled.
 These findings support the hypotheses that thick eggshells resist damage
 when laid from an elevated position, when additional cowbird eggs are laid
 onto them in multiply parasitized nests, and these eggs also damage host
 eggs when laid.
description: data_Dryad_lopezetal
DOI: 10.15468/dl.p6dnv6
title: Occurrence Download

description: A dataset containing 369 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Conostephium pendulum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 369 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001246-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sj138
title: Data from: Females can solve the problem of low signal reliability by assessing multiple male traits

description: Male signals that provide information to females about mating benefits are
 often of low reliability. It is thus not clear why females often express
 strong signal preferences. We tested the hypothesis that females can
 distinguish between males with preferred signals that provide lower and
 higher quality direct benefits. In the field cricket, Gryllus lineaticeps,
 females usually prefer higher male chirp rates, but chirp rate is
 positively correlated with the fecundity benefits females will receive
 from males only for males that have experienced low quality diets. We
 paired females with muted males that were maintained on low or high
 nutrition diets, during the interactions we broadcast a replacement high
 chirp rate, and we observed whether females mated with the assigned male.
 Females were more likely to mate when paired with low nutrition males.
 These results suggest that females have evolved assessment mechanisms that
 allow them distinguish between males with preferred signals that provide
 high quality benefits (low nutrition males with high chirp rates) and
 males with preferred signals that provide low quality benefits (high
 nutrition males with high chirp rates).
description: Female
 ResponsesData on females
 responses to low and high nutrition males in the presence of high chirp
 rate calling song.