cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4d79f7h
title: Data from: Testing the devil's impact on southern Baltic and North Sea basin whitefish (Coregonus spp.) diversity

description: Background: The diversity and phylogeny of whitefish of the genus
 Coregonus is complex, and includes many endemic species of high
 conservation concern. However, because of commercial importance of
 whitefish fisheries, stockings and translocations have occurred
 repeatedly, which challenges the identification of local populations as
 conservation units. This study analyses the phylogenetic relationships of
 15 contemporary and two historical populations of lake-resident and
 anadromous whitefish (Coregonus spp.) from the southern Baltic and North
 Sea basins. We elucidated the complex history of Lake Schaal (northern
 Germany) whitefish, for which a local tale suggests that the devil threw
 whitefish from the Central European Lake Constance into this lake. Studies
 from the early 20th century indeed suggested numerous stocking events for
 Lake Schaal from Lake Constance, from Estonian/Russian Lake Peipsi and
 from the anadromous whitefish of the Baltic Sea. Results: Analyses of 13
 microsatellite markers showed that Lake Constance whitefish are unrelated
 to any northern Germany whitefish population, including the contemporary
 whitefish population from Lake Schaal. Comparison with four historical
 specimens further showed that the native Lake Schaal whitefish (C.
 holsatus) vanished from the lake, but has survived as a non-native
 population in the north German Lake Drewitz. The whitefish currently
 occurring in Lake Schaal and three adjacent lakes are identified as C.
 maraenoides, introduced from Lake Peipsi. The contemporary anadromous
 whitefish populations from the Baltic (German and Finnish coast) and the
 German River Treene (North Sea basin, stocked from Danish River Vida)
 grouped together, but showed significant genetic differentiation. The 14
 historical specimens of C. oxyrinchus from Rivers Rhine and Schelde were
 assigned to several contemporary whitefish populations, but among them
 only one specimen was assigned to the contemporary River Treene
 population. Therefore, we do not support the view that the whitefish from
 River Vida/Treene are identical with the historical C. oxyrinchus.
 Conclusions: Our study demonstrates that lake and anadromous whitefish in
 the Baltic and North Sea basins reflect a complex phylogeography, which is
 further blurred by the effects of repeated stocking and translocations. To
 identify conservation units, the genetic identity of each population has
 to be scrutinized.
description: Raw Data of 13
 microsatellites of 17 Coregonus populations in Genetix
 formatRaw data of 13
 microsatellite loci; 343 individuals; 15 contemporary Coregonus
 populations; additional 18 individuals from 2 historical populations
 (museum material); lake-resident and anadromous whitefish populations of
 southern Baltic and North Sea basins; provided in Genetiix format;
 population names and geographic origin as in Table 1 of Mehner et al. BMC
 Evol BiolTotalDataset_13Mikrosats_17Pops_GENETIX_Dryad.gtx
DOI: 10.5061/dryad.4q730
title: Data from: Binocular combination of stimulus orientation

description: When two sine waves that differ slightly in orientation are presented to
 the two eyes separately, a single cyclopean sine wave is perceived.
 However, it is unclear how the brain calculates its orientation. Here, we
 used a signal detection rating method to estimate the perceived
 orientation when the two eyes were presented with Gabor patches that
 differed in both orientation and contrast. We found a nearly linear
 combination of orientation when both targets had the same contrast.
 However, the binocular percept shifted away from the linear prediction
 towards the orientation with the higher contrast, depending on both the
 base contrast and the contrast ratio. We found that stimuli that differ
 slightly in orientation are combined into a single percept, similarly for
 monocular and binocular presentation, with a bias that depends on the
 interocular contrast ratio. Our results are well fitted by gain-control
 models, and are consistent with a previous study that favoured the DSKL
 model that successfully predicts binocular phase and contrast combination
 and binocular contrast discrimination. In this model, the departures from
 linearity may be explained on the basis of mutual suppression and mutual
 enhancement, both of which are stronger under dichoptic than monocular
 conditions.
description: Perceived Orientation
 dataRaw perceived
 orientation data for each of 4 observers at different base contrasts and
 contrast ratios.
DOI: 10.5061/dryad.j555d
title: Data from: paco: implementing Procrustean Approach to Cophylogeny in R

description: 1. The concordance of evolutionary histories and extant species
 interactions provides a useful metric for addressing questions of how the
 structure of ecological communities is influenced by macro-evolutionary
 processes. 2. We introduce paco (v.0.3.1), an R package to perform
 Procrustean Approach to Cophylogeny. This method assesses the phylogenetic
 congruence, or evolutionary dependence, of two groups of interacting
 species using both ecological interaction networks and their phylogenetic
 history. 3. We demonstrate the functionality of paco through its
 application to empirical host-parasite and plant-pollinator communities 4.
 Although the package is intended to assess phylogenetic congruence between
 groups of interacting species, the method is also directly applicable to
 other scenarios that may show phylogenetic congruence including historical
 biogeography, molecular systematics, and cultural evolution.
description: Interaction data,
 phylogenies, and analysis code for pacoData on the Mendoza
 pollination network analysed with paco. Phylogenies of both plants and
 pollinators as well as their interaction network are included. There is
 also an R script for the analyses. Please note that the interaction
 network was originally published by Arroyo, M. T. K., Primack, R. B. &
 Armesto, J. J. (Community studies in pollination ecology in the high
 temperate Andes of central Chile. I. Pollination mechanisms and
 altitudinal variation, 1982). The version here has been cleaned to remove
 unidentified species and to confirm species names are
 correct.paco_appendix2.zip
DOI: 10.5061/dryad.85t2hr9
title: Data from: Incidence and risk factors of first-line antiretroviral treatment failure among human immunodeficiency virus-infected children in Amhara regional state, Ethiopia: a retrospective follow-up study

description: Objective: This study aimed to assess the incidence and risk factors of
 treatment failure among Human Immunodeficiency Virus (HIV)/Acquired
 Immunodeficiency Syndrome infected (AIDS) children who were on
 Antiretroviral Therapy (ART) in Amhara National Regional State, Ethiopia.
 Methods: A retrospective follow-up study was conducted from January 2010
 to March 2016. A total of 824 children under the age of 15 years who had
 started ART were included in the study. Data were collected from
 children’s medical chart and ART registration logbook using a standard
 checklist. A Weibull regression model was used to identify the risk
 factors for treatment failure. Adjusted Hazard Ratios with 95% confidence
 intervals were used to declare statistical significance. Results: The mean
 (±SD) age of the children was 6.4 ± 3.6 years with a median (IQR) follow
 up of 30.5 (IQR: 14.6, 51.4) months. Sixty-three children (7.7%,
 95%CI:5.8, 9.5) developed treatment failure. Seventeen (27.0%) of whom
 were immunological and 46 (73.0 %) clinical failures. The incidence rate
 of treatment failure was 22.1/10000 person-months. The cumulative
 probability of failure was 0.4 with 28562.5 person-month observations.
 Lack of disclosure [AHR=4. 4, 95%CI (1.8, 11.3)], opportunistic infections
 during initiation of ART [AHR= 2.3, 95% CI (1.3, 4.1)] and prolonged
 follow up [AHR = 0.06, 95% CI (0.02, 0.18)] were the main predictors of
 treatment failure. Conclusion: This study revealed that the incidence of
 treatment failure remains a significant public health concern in Ethiopia.
 Undisclosed HIV status to children, the presence of opportunistic
 infections during initiation of ART and prolonged follow up was found to
 be the main predictors of treatment failure. Hence, early detection of the
 treatment failures and further studies on viral monitor need to consider.
description: HIV_data_child
DOI: 10.5061/dryad.j6m2267
title: Data from: Estimating contributions of pelagic and benthic pathways to consumer production in coupled marine food webs

description: 1. Pelagic and benthic systems usually interact, but their dynamics and
 production rates differ. Such differences influence the distribution,
 reproductive cycles, growth rates, stability and productivity of the
 consumers they support. Consumer preferences for, and dependence on,
 pelagic or benthic production are governed by the availability of these
 sources of production and consumer life history, distribution, habitat,
 behavioural ecology, ontogenetic stage and morphology. 2. Diet studies may
 demonstrate the extent to which consumers feed on prey in pelagic or
 benthic environments. But they do not discriminate benthic production
 directly supported by phytoplankton from benthic production recycled
 through detrital pathways. The former will track the dynamics of
 phytoplankton production more closely than the latter. 3. We develop and
 apply a new analytical method that uses carbon (C) and sulfur (S) natural
 abundance stable isotope data to assess the relative contribution of
 pelagic and benthic pathways to fish consumer production. 4. For 13
 species of fish that dominate community biomass in the northern North Sea
 (estimated &gt;90% of total biomass), relative modal use of pelagic
 pathways ranged from &lt;25% to &gt;85%. Use of both C and S
 isotopes as opposed to just C reduced uncertainty in relative modal use
 estimates. Temporal comparisons of relative modal use of pelagic and
 benthic pathways revealed similar ranking of species dependency over four
 years, but annual variation in relative modal use within species was
 typically 10-40%. 5. For the total fish consumer biomass in the study
 region, the C and S method linked approximately 70% and 30% of biomass to
 pelagic and benthic pathways respectively. As well as providing a new
 method to define consumers’ links to pelagic and benthic pathways our
 results demonstrate that a substantial proportion of fish biomass, and by
 inference production, in the northern North Sea is supported by production
 that has passed through transformations on the seabed.
description: Sulphur stable isotope
 data for North Atlantic (North Sea) fishesSulphur stable isotope
 data were collected for the study of food webs and benthic-pelagic
 coupling in the North Sea. They comprise natural abundance stable isotope
 measurements of δ34S for 415 individuals from 15 species of fish sampled
 in 2006. Measurements of δ13C and δ15N for the same individuals were
 previously published by Jennings and Cogan (2015). A numeric code is
 included with the present data to allow the δ34S measurements to be
 matched to the δ13C and δ15N measurements by individual. Trophic level
 estimates for the same individuals, based on δ15N measurements, are
 provided in Supplementary Material supporting Jennings and van der Molen
 (2015). Please read the README file for information.SIA_S_North_Sea_fishes_20171129.csv
DOI: 10.5061/dryad.ss250
title: Data from: Social network structure in wintering golden-crowned sparrows is not correlated with kinship

description: Stable social organization in a wide variety of organisms has been linked
 to kinship, which can minimize conflict due to the indirect fitness
 benefits from cooperating with relatives. In birds, kin selection has been
 mostly studied in the context of reproduction or in species that are
 social year round. Many birds however are migratory, and the role of
 kinship in the winter societies of these species is virtually unexplored.
 In a previous study, we discovered striking social complexity and
 stability in a wintering population of migratory golden-crowned sparrows
 (Zonotrichia atricapilla) – individuals repeatedly form close associations
 with the same social partners, including across multiple winters. Here, we
 test the possibility that kinship might be involved in these close and
 stable social affiliations. We examine the relationship between kinship
 and social structure for two of the consecutive wintering seasons from the
 previous study. We found no evidence that social structure was influenced
 by kinship. Relatedness between most pairs of individuals was at most that
 of first cousins (and mostly far lower). Genetic networks based on
 relatedness do not correspond to the social networks, and Mantel tests
 revealed no relationship between kinship and pairwise interaction
 frequency. Kinship also failed to predict social structure in more
 fine-grained analyses, including analyses of each sex separately (in the
 event that sex-biased migration might limit kin selection to one sex), and
 separate analyses for each social community. The complex winter societies
 of golden-crowned sparrows appear to be based on cooperative benefits
 unrelated to kin selection.
description: Pair-wise relatedness
 values for 2009Pair-wise relatedness
 values for 2009Relatedness-2009.csvPairwise relatedness from 2010Relatedness-2010.csvSimple.ratio-2009Social values for 2009Simple.ratio-2010Social association values for 2010Microsatellite locus allelesContains alleles information for 14 loci for golden-crowned sparrows. These genetic data were used to estimate pair-wise relatednessMicrosatellite_alleles.csv
DOI: 10.5061/dryad.jh655f3
title: Data from: People making deontological judgments in the Trapdoor dilemma are perceived to be more prosocial in economic games than they actually are

description: Why do people make deontological decisions, although they often lead to
 overall unfavorable outcomes? One account is receiving considerable
 attention: deontological judgments may signal commitment to prosociality
 and thus may increase people’s chances of being selected as social
 partners–which carries obvious long-term benefits. Here we test this
 framework by experimentally exploring whether people making deontological
 judgments are expected to be more prosocial than those making
 consequentialist judgments and whether they are actually so. In line with
 previous studies, we identified deontological choices using the Trapdoor
 dilemma. Using economic games, we take two measures of general
 prosociality towards strangers: trustworthiness and altruism. Our results
 procure converging evidence for a perception gap according to which
 Trapdoor-deontologists are believed to be more trustworthy and more
 altruistic towards strangers than Trapdoor-consequentialists, but actually
 they are not so. These results show that deontological judgments are not
 universal, reliable signals of prosociality.
description: study1_and_2Data of the two studies reported in the manuscript.
DOI: 10.5061/dryad.df86m
title: Data from: Sperm morphology, adenosine triphosphate (ATP) concentration and swimming velocity: unexpected relationships in a passerine bird

description: The relationship between sperm energetics and sperm function is poorly
 known, but is central to our understanding of the evolution of sperm
 traits. The aim of this study was to examine how sperm morphology and ATP
 content affect sperm swimming velocity in the zebra finch Taeniopygia
 guttata. We exploited the high inter-male variation in this species and
 created extra experimental power by increasing the number of individuals
 with very long or short sperm through artificial selection. We found a
 pronounced quadratic relationship between total sperm length and swimming
 velocity, with velocity increasing with length up to a point, but
 declining in the very longest sperm. We also found an unexpected negative
 association between midpiece length and ATP content: sperm with a short
 midpiece generally contained the highest concentration of ATP. Low
 intracellular ATP is therefore unlikely to explain reduced swimming
 velocity among the very longest sperm (which tend to have a shorter
 midpiece).
description: ReadMe file for data
 files associated with the manuscript “Sperm morphology, ATP concentration
 and swimming velocity: unexpected relationships in a passerine
 bird”This readme file
 describes the data files accompanying the above
 publication.Experimental males
 summary dataThis data file contains
 all the data collected from each experimental male. Data include semen
 characteristics (e.g. sperm measurements) and morphological data (e.g.
 body weight).Microplate sample
 repeatabilityThis is the data file
 containing the data from experimental males used to test the repeatability
 of ATP content across triplicate wells. Descriptions of variables are
 included in the R code file “Sperm morphology, swimming velocity and ATP
 content.r”.R script for
 analysesThis file provides the
 code for the analyses carried out in the manuscript.Dryad script ATP MS
 29.7.16.R
DOI: 10.15468/dl.5esycf
title: Occurrence Download

description: A dataset containing 139 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((41.97432 14.47918,102.02568 14.47918,102.02568 38.52082,41.97432 38.52082,41.97432 14.47918))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Saara hardwickii"
 ]
}

 The dataset includes 139 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001098-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ft48k
title: Data from: Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species

description: Most evidence for hybrid swarm formation stemming from anthropogenic
 habitat disturbance comes from the breakdown of reproductive isolation
 between incipient species, or introgression between allopatric species
 following secondary contact. Human impacts on hybridization between
 divergent species that naturally occur in sympatry has received
 considerably less attention. Theory predicts that reinforcement should act
 to preserve reproductive isolation under such circumstances, potentially
 making reproductive barriers resistant to human habitat alteration. Using
 15 microsatellites we examined hybridization between sympatric populations
 of alewife (Alosa pseudoharengus) and blueback herring (A. aestivalis) to
 test whether the frequency of hybridization and pattern of introgression
 have been impacted by the construction of a dam that isolated formerly
 anadromous populations of both species in a landlocked freshwater
 reservoir. The frequency of hybridization and pattern of introgression
 differed markedly between anadromous and landlocked populations. The
 range-wide frequency of hybridization among anadromous populations was
 generally 0-8%, whereas all landlocked individuals were hybrids. Although
 neutral introgression was observed among anadromous hybrids, directional
 introgression leading to increased prevalence of alewife genotypes was
 detected among landlocked hybrids. We demonstrate that habitat alteration
 can lead to hybrid swarm formation between divergent species that
 naturally occur sympatrically, and provide empirical evidence that
 reinforcement does not always sustain reproductive isolation under such
 circumstances.
description: Admixed
 anadromousThis file contains
 multilocus data (15 microsatellite loci) for anadromous hybrid alewife and
 blueback herring (n=92) used in analysis of genomic
 clines.Admixed
 KerrThis file contains
 multilocus data (15 microsatellite loci) for landlocked (Kerr Reservoir)
 hybrid alewife and blueback herring (n=119) used in analysis of genomic
 clines.Parental
 ALEThis file contains
 multilocus data (15 microsatellite loci) for 100 purebred alewife
 specimens used in the simulation of hybrids (HYBRIDLAB v.1.0) and in the
 analysis of genomic clines by Hasselman et al. (2014).Parental
 BBHThis file contains
 multilocus data (15 microsatellite loci) for 100 purebred blueback herring
 specimens used in the simulation of hybrids (HYBRIDLAB v.1.0) and in the
 analysis of genomic clines by Hasselman et al. (2014).LociThis file contains locus
 information for the 15 microsatellite loci used in the analysis of genomic
 clines by Hasselman et al. (2014).
DOI: 10.5061/dryad.1g98m
title: Data from: Modelling the impact of curtailing antibiotic usage in food animals on antibiotic resistance in humans

description: Consumption of antibiotics in food animals is increasing worldwide and is
 approaching, if not already surpassing, the volume consumed by humans. It
 is often suggested that reducing the volume of antibiotics consumed by
 food animals could have public health benefits. Although this notion is
 widely regarded as intuitively obvious there is a lack of robust,
 quantitative evidence to either support or contradict the suggestion. As a
 first step towards addressing this knowledge gap, we develop a simple
 mathematical model for exploring the generic relationship between
 antibiotic consumption by food animals and levels of resistant bacterial
 infections in humans. We investigate the impact of restricting antibiotic
 consumption by animals and identify which model parameters most strongly
 determine that impact. Our results suggest that, for a wide range of
 scenarios, curtailing the volume of antibiotics consumed by food animals
 has, as a stand-alone measure, little impact on the level of resistance in
 humans. We also find that reducing the rate of transmission of resistance
 from animals to humans may be more effective than an equivalent reduction
 in the consumption of antibiotics in food animals. Moreover, the response
 to any intervention is strongly determined by the rate of transmission
 from humans to animals, an aspect which is rarely considered.
description: Mathematica notebook
 containing model and analysisMathemetica Notebook
 with the model description and analysis to create the Figures presented in
 the manuscript.ManuscriptCode.nbR Script for sensitivity analysisR script for the sensitivity analysis as described in the manuscriptManuscriptCode.R