cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2rr59
title: Data from: Matching genetics with oceanography: directional gene flow in a Mediterranean fish species

description: Genetic connectivity and geographic fragmentation are two opposing
 mechanisms determining the population structure of species. While the
 first homogenizes the genetic background across populations the second one
 allows their differentiation. Therefore, knowledge of processes affecting
 dispersal of marine organisms is crucial to understand their genetic
 distribution patterns and for the effective management of their
 populations. In this study, we use genetic analyses of eleven
 microsatellites in combination with oceanographic satellite and dispersal
 simulation data to determine distribution patterns for Serranus cabrilla,
 a ubiquitous demersal broadcast spawner, in the Mediterranean Sea.
 Pairwise population FST values ranged between −0.003 and 0.135. Two
 genetically distinct clusters were identified, with a clear division
 located between the oceanographic discontinuities at the Ibiza Channel
 (IC) and the Almeria-Oran Front (AOF), revealing an admixed population in
 between. The Balearic Front (BF) also appeared to dictate population
 structure. Directional gene flow on the Spanish coast was observed as S.
 cabrilla dispersed from west to east over the AOF, from north to south on
 the IC and from south of the IC towards the Balearic Islands. Correlations
 between genetic and oceanographic data were highly significant. Seasonal
 changes in current patterns and the relationship between ocean circulation
 patterns and spawning season may also play an important role in population
 structure around oceanographic fronts.
description: DRYAD
 DATAMicrosatellite data for
 11 microsatellites for Serranus cabrilla at the 13 locations. Two columns
 per microsatellite.
DOI: 10.5061/dryad.62cr1q22
title: Data from: Development of conserved microsatellite markers of high cross-species utility in bat species (Vespertilionidae, Chiroptera, Mammalia)

description: Comparative ecological and behavioural studies of the widespread and
 diverse Vespertilionidae, which comprise almost 400 of the 1,100 bat
 species, have been limited by the availability of markers. The potential
 of new methods for developing conserved microsatellite markers which
 possess enhanced cross-species utility has recently been illustrated in
 studies of birds. We have applied these methods to develop enhanced
 microsatellite markers for vespertilionid bats, in particular for the
 genus Myotis (103 species). We compared published bat microsatellites with
 their homologs in the genome sequence of the little brown bat, Myotis
 lucifugus to create consensus sequences which were used to design
 candidate primer sets. Primer sets were then tested for amplification and
 polymorphism in 22 species of bat from nine of the largest families
 (including 11 Vespertilionidae). Of 46 loci tested, 33 were polymorphic,
 on average, for each of seven Myotis species tested, 20 in each of four
 non-Myotis vespertilionid species, and two in 11 non-vespertilionid
 species.
description: Jan et al MER Genotype
 dataMicrosatellite genotypes
 for loci and species included in the polymorphism tests
DOI: 10.5061/dryad.fv3cb
title: Data from: Correlated responses to clonal selection in populations of Daphnia pulicaria: mechanisms of genetic correlation and the creative power of sex

description: Genetic correlations among traits alter evolutionary trajectories due to
 indirect selection. Pleiotropy, chance linkage, and selection can all lead
 to genetic correlations, but have different consequences for phenotypic
 evolution. We sought to assess the mechanisms contributing to correlations
 with size at maturity in the cyclic parthenogen Daphnia pulicaria. We
 selected on size in each of four populations that differ in the frequency
 of sex, and evaluated correlated responses in a life table. Size at
 advanced adulthood, reproductive output, and adult growth rate clearly
 showed greater responses in high sex populations, with a similar pattern
 in neonate size and r. This pattern is expected only when trait
 correlations are favored by selection and the frequency of sex favors the
 creation and demographic expansion of highly fit clones. Juvenile growth
 and age at maturity did not diverge consistently. The inter-clutch
 interval appeared to respond more strongly in low sex populations, but
 this was not statistically significant. Our data support the hypothesis
 that correlated selection is the strongest driver of genetic correlations,
 and suggest that in organisms with both sexual and asexual reproduction,
 adaptation can be enhanced by recombination.
description: Correlated responses to
 clonal selection in populations of Daphnia pulicariaData from a life table
 of 79 clones of Daphnia pulicaria. Clone means are provided, as clone was
 the primary unit of replication.CRCTS
 dryad.xls
DOI: 10.5061/dryad.7968
title: Data from: Vertebrate host protective immunity drives genetic diversity and antigenic polymorphism in Schistosoma mansoni

description: Schistosomes are gonochoric blood parasites with a complex life cycle
 responsible for a disease of considerable medical and veterinary
 importance in tropical and subtropical regions. Understanding the
 evolution of schistosome genetic diversity is clearly of fundamental
 importance to interpreting schistosomiasis epidemiology and disease
 transmission patterns of this parasite. In this paper we have the putative
 role of the host immune system in the selection of male genetic diversity.
 We demonstrated the link between genetic dissimilarity and the protective
 effect among male worms. We then compared the proteomes of three male
 clones with different genotypes and differing by their capacity to protect
 against reinfection. The identified differences correspond mainly to
 antigens known or supposed to be involved in the induction of protective
 immunity. These results underline the role played by host immune system in
 the selection of schistosome genetic diversity that is linked to antigenic
 diversity. We discuss the evolutionary consequences in the context of
 schistosome infection.
description: Qualitative protein
 identifications in a comparative screen among A10, A35 and A4 S. mansoni
 adult clonesFor each spot, the
 name(s) of protein(s) identified, species and database accession numbers,
 peptide number and MASCOT score are reported. *: signal anchor and signal
 peptide (SP) were predicted using SignalP 3.0.Qualitative.xlsQuantitative protein identifications in a comparative screen among A10, A35 and A4 S. mansoni adult clonesFor each spot, the name(s) of protein(s) identified, species and database accession numbers, peptide number and MASCOT score are reported. ND: not done, NS: not significant. *: signal anchor and signal peptide (SP) were predicted using SignalP 3.0.Quantitative.xls
DOI: 10.5061/dryad.688nk
title: Data from: Stage-specific plasticity in ovary size is regulated by insulin/insulin-like growth factor and ecdysone signalling in Drosophila

description: Animals from flies to humans adjust their development in response to
 environmental conditions through a series of developmental checkpoints,
 which alter the sensitivity of organs to environmental perturbation.
 Despite their importance, we know little about the molecular mechanisms
 through which this change in sensitivity occurs. Here we identify two
 phases of sensitivity to larval nutrition that contribute to plasticity in
 ovariole number, an important determinant of fecundity, in Drosophila
 melanogaster. These two phases of sensitivity are separated by the
 developmental checkpoint called “critical weight”; poor nutrition has
 greater effects on ovariole number in larvae before critical weight than
 after. We find that this switch in sensitivity results from distinct
 developmental processes. In precritical weight larvae, poor nutrition
 delays the onset of terminal filament cell differentiation, the starting
 point for ovariole development, and strongly suppresses the rate of
 terminal filament addition and the rate of increase in ovary volume.
 Conversely, in postcritical weight larvae, poor nutrition affects only the
 rate of increase in ovary volume. Our results further indicate that two
 hormonal pathways, the insulin/insulin-like growth factor and the
 ecdysone-signaling pathways, modulate the timing and rates of all three
 developmental processes. The change in sensitivity in the ovary results
 from changes in the relative contribution of each pathway to the rates of
 terminal filament addition and increase in ovary volume before and after
 critical weight. Our work deepens our understanding of how hormones act to
 modify the sensitivity of organs to environmental conditions, thereby
 affecting their plasticity.
description: Data&ScriptsAll data and R scripts for the analysis of the rate of terminal filament addition and ovary volume.
DOI: 10.5061/dryad.16m53
title: Data from: Potential of environmental DNA to evaluate Northern pike (Esox lucius) eradication efforts: an experimental test and case study

description: Determining the success of invasive species eradication efforts is
 challenging because populations at very low abundance are difficult to
 detect. Environmental DNA (eDNA) sampling has recently emerged as a
 powerful tool for detecting rare aquatic animals; however, detectable
 fragments of DNA can persist over time despite absence of the targeted
 taxa and can therefore complicate eDNA sampling after an eradication
 event. This complication is a large concern for fish eradication efforts
 in lakes since killed fish can sink to the bottom and slowly decay. DNA
 released from these carcasses may remain detectable for long periods.
 Here, we evaluated the efficacy of eDNA sampling to detect invasive
 Northern pike (Esox lucius) following piscicide eradication efforts in
 southcentral Alaskan lakes. We used field observations and experiments to
 test the sensitivity of our Northern pike eDNA assay and to evaluate the
 persistence of detectable DNA emitted from Northern pike carcasses. We
 then used eDNA sampling and traditional sampling (i.e., gillnets) to test
 for presence of Northern pike in four lakes subjected to a
 piscicide-treatment designed to eradicate this species. We found that our
 assay could detect an abundant, free-roaming population of Northern pike
 and could also detect low-densities of Northern pike held in cages. For
 these caged Northern pike, probability of detection decreased with
 distance from the cage. We then stocked three lakes with Northern pike
 carcasses and collected eDNA samples 7, 35 and 70 days post-stocking. We
 detected DNA at 7 and 35 days, but not at 70 days. Finally, we collected
 eDNA samples ~ 230 days after four lakes were subjected to
 piscicide-treatments and detected Northern pike DNA in 3 of 179 samples,
 with a single detection at each of three lakes, though we did not catch
 any Northern pike in gillnets. Taken together, we found that eDNA can help
 to inform eradication efforts if used in conjunction with multiple lines
 of inquiry and sampling is delayed long enough to allow full degradation
 of DNA in the water.
description: Raw_dataQuantification cycle values and scores for Northern pike DNA in water samples collected at multiple lakes across time.
DOI: 10.5061/dryad.m543580
title: Data from: Drivers of vegetative dormancy across herbaceous perennial plant species

description: Vegetative dormancy, that is the temporary absence of aboveground growth
 for ≥ 1 year, is paradoxical, because plants cannot photosynthesise or
 flower during dormant periods. We test ecological and evolutionary
 hypotheses for its widespread persistence. We show that dormancy has
 evolved numerous times. Most species displaying dormancy exhibit
 life‐history costs of sprouting, and of dormancy. Short‐lived and
 mycoheterotrophic species have higher proportions of dormant plants than
 long‐lived species and species with other nutritional modes. Foliage loss
 is associated with higher future dormancy levels, suggesting that carbon
 limitation promotes dormancy. Maximum dormancy duration is shorter under
 higher precipitation and at higher latitudes, the latter suggesting an
 important role for competition or herbivory. Study length affects
 estimates of some demographic parameters. Our results identify life
 historical and environmental drivers of dormancy. We also highlight the
 evolutionary importance of the little understood costs of sprouting and
 growth, latitudinal stress gradients and mixed nutritional modes.
description: Main data file and
 legendThis Excel file includes
 two spreadsheets. The first, labelled "Data file", includes the
 data needed to run the main mixed modeling in our paper. The second,
 labelled "Legend", describes the variables. Please note that
 commas and ambiguous punctuation have been avoided so that the files can
 be exported as CSV files. Also, please note that, due to conservation
 concerns and legal requirements, population locations have been withheld.
 Instead, we present the latitude and longitude of populations, both
 rounded to the nearest 5 degrees.meta.dorm.final.xlsx
DOI: 10.5061/dryad.g1nq02r
title: Data from: Revisiting protein aggregation as pathogenic in sporadic Parkinson’s and Alzheimer’s diseases

description: The gold standard for a definitive diagnosis of Parkinson’s disease (PD)
 is the pathologic finding of aggregated alpha-synuclein into Lewy bodies
 and for Alzheimer’s disease (AD) aggregated amyloid into plaques and
 hyperphosphorylated tau into tangles. Implicit in this
 clinico-pathologic-based nosology is the assumption that pathological
 protein aggregation at autopsy reflect pathogenesis at disease onset.
 While these aggregates may in exceptional cases be on a causal pathway in
 humans (e.g., aggregated alpha-synuclein in SNCA gene multiplication or
 aggregated -amyloid in APP mutations), their near universality at
 postmortem in sporadic PD and AD suggests they may alternatively represent
 common outcomes from upstream mechanisms or compensatory responses to
 cellular stress in order to delay cell death. These three conceptual
 frameworks of protein aggregation (pathogenic, epiphenomenon, protective)
 are difficult to resolve because of the inability to probe brain tissue in
 real time. Whereas animal models, in which neither PD nor AD occur in
 natural states, consistently support a pathogenic role of protein
 aggregation, indirect evidence from human studies does not. We hypothesize
 that (1) current biomarkers of protein aggregates may be relevant to
 common pathology but not to subgroup pathogenesis, and (2)
 disease-modifying treatments targeting oligomers or fibrils might be
 futile or deleterious because these proteins are epiphenomena or
 protective in the human brain under molecular stress. Future
 precision-medicine efforts for molecular targeting of neurodegenerative
 diseases may require analyses not anchored on current clinico-pathologic
 criteria but instead on biological signals generated from large
 deeply-phenotyped aging populations or from smaller but well-defined
 genetic-molecular cohorts.
description: Table
 e-1Search
 strategyTable
 e-2Characteristics of
 Supporting and Opposing Studies summarized in Table 1eReferences
DOI: 10.5061/dryad.pg46f
title: Data from: Identifying heterogeneity in rates of morphological evolution: discrete character change in the evolution of lungfish (Sarcopterygii; Dipnoi)

description: Quantifying rates of morphological evolution is important in many
 macroevolutionary studies, and critical when assessing possible adaptive
 radiations and episodes of punctuated equilibrium in the fossil record.
 However, studies of morphological rates of change have lagged behind those
 on taxonomic diversification, and most authors have focused on continuous
 characters and quantifying patterns of morphological rates over time.
 Here, we provide a phylogenetic approach, using discrete characters and
 three statistical tests to determine points on a cladogram (branches or
 entire clades) that are characterized by significantly high or low rates
 of change. These methods include a randomization and likelihood ratio
 tests that pinpoint either branches or clades that have significantly
 higher or lower rates than the pooled rate of the remainder of the tree.
 As a test case for these methods we analyze a discrete character dataset
 of lungfish, which have long been regarded as having an apparent slow down
 in rates since the Devonian. We find that morphological rates are highly
 heterogeneous across the phylogeny and recover a general pattern of
 decreasing rates along the phylogenetic backbone towards living taxa, from
 the Devonian until the present. Compared with previous work, we are able
 to report a more nuanced picture of lungfish evolution using these new
 methods.
description: Code and
 dataR
 code and data as MS Excel worksheets that were used for the
 analyses.Archive.zip
DOI: 10.5061/dryad.585t1
title: Data from: A comparative study on genetic effects of artificial and natural habitat fragmentation on Loropetalum chinense (Hamamelidaceae) in Southeast China

description: Elucidating the demographic and landscape features that determine the
 genetic effects of habitat fragmentation has become fundamental to
 research in conservation and evolutionary biology. Land-bridge islands
 provide ideal study areas for investigating the genetic effects of habitat
 fragmentation at different temporal and spatial scales. In this context,
 we compared patterns of nuclear microsatellite variation between insular
 populations of a shrub of evergreen broad-leaved forest, Loropetalum
 chinense, from the artificially created Thousand-Island Lake (TIL) and the
 Holocene-dated Zhoushan Archipelago of Southeast China. Populations from
 the TIL region harboured higher levels of genetic diversity than those
 from the Zhoushan Archipelago, but these differences were not significant.
 There was no correlation between genetic diversity and most island
 features, excepting a negative effect of mainland–island distance on
 allelic richness and expected heterozygosity in the Zhoushan Archipelago.
 In general, levels of gene flow among island populations were moderate to
 high, and tests of alternative models of population history strongly
 favoured a gene flow-drift model over a pure drift model in each region.
 In sum, our results showed no obvious genetic effects of habitat
 fragmentation due to recent (artificial) or past (natural) island
 formation. Rather, they highlight the importance of gene flow (most likely
 via seed) in maintaining genetic variation and preventing inter-population
 differentiation in the face of habitat ‘insularization’ at different
 temporal and spatial scales.
description: Loropetalum chinense
 microsatellite
DOI: 10.5061/dryad.0n5f66n
title: Data from: Spondyloarthritis in the Democratic Republic of the Congo: a prospective hospital-based study

description: Abstract Objectives: To determine the spectrum of SpA in outpatients with
 rheumatic complaints attending two rheumatology practices in the
 Democratic Republic of Congo. Design: A descriptive prospective
 multicenter outpatient study. Setting: The present study analyzed 6 months
 data (from December 1st, 2012 till May 31st, 2013). Participants: 984
 consecutive outpatients were studied. Interventions: none Primary and
 secondary outcome measures: A clinical diagnosis of SpA was made and
 several classification criteria were applied afterwards. Sacroiliac joint
 radiographic lesions were scored with the modified New York criteria.
 BASDAI and BASFI were evaluated in axial SpA. The primary end point was
 the prevalence of SpA and the secondary endpoints were the spectrum of SpA
 and its subtypes. Results: One hundred and five patients (10.7%) were
 diagnosed among 984 consecutive outpatients with a sex ratio (male to
 female) of 1.4. The average age at disease onset was 41.3±12.4 years.
 Non-radiographical axial spondyloarthritis was the most frequent subtype
 (5.0%) followed by reactive arthritis (4.3%). Other subtypes were:
 ankylosing spondylitis (1.0%), psoriatic arthritis (0.1%), SAPHO syndrome
 (0.1%) and IBD associated arthritis (0.1%). Mean BASDAI and BASFI in axial
 SpA were 42.7/100 and 46.4/100 respectively. Peripheral enthesitis was
 found in 43% of SpA patients and uveitis (10.4%) was the most frequent
 extra-articular manifestation. We did not detect any family history.
 Median erythrocyte sedimentation rate and C reactive protein were
 37(range: 7-110) mm/h and 22 (range: 4-48) mg/l respectively. Conclusions:
 This hospital-based study suggests a substantial occurrence of some
 subtypes of SpA in central Africa. A population-based study is needed.
description: Different subtypes of
 Spondyloarthritis in the University Hospital of Kinshasa and Provincial
 General Hospital of KinshasaDemographic and clinical
 features of patients with axial SpondyloarthritisNouvelle base de données
 sur validation critères SpA VERSION 1
DOI: 10.15468/dl.jc9pa5
title: Occurrence Download

description: A dataset containing 60639 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Corbicula fluminea"
 ]
}

 The dataset includes 60639 records from 339 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000918-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k6r4v
title: Data from: Convergent reversion to single mating in a wasp social parasite

description: While eusociality arose in species with single-mating females, multiple
 mating by queens has evolved repeatedly across the social ants, bees, and
 wasps. Understanding the benefits and costs of multiple mating of queens
 is important because polyandry results in reduced relatedness between
 siblings, reducing kin-selected benefits of helping while also selecting
 for secondary social traits that reduce intracolony conflict. The leading
 hypothesis for the benefits of polyandry in social insects emphasizes
 advantages of a genetically diverse workforce. Workerless social parasite
 species (inquilines) provide a unique opportunity to test this hypothesis,
 since they are derived from social ancestors but do not produce workers of
 their own. Such parasites are thus predicted to evolve single mating
 because they would experience the costs of multiple mating but not the
 benefits if such benefits accrue through the production of a genetically
 diverse group of workers. Here we show that the workerless social parasite
 Dolichovespula arctica, a derived parasite of wasps, has reverted to
 obligate single mating from a facultatively polyandrous ancestor,
 mirroring a similar reversion from obligate polyandry to approximate
 monandry in a social parasite of fungus-farming ants. This finding and a
 comparison with two other cases where inquilinism did not induce reversal
 to monandry support the hypothesis that facultative polyandry can be
 costly and may be maintained by benefits of a genetically diverse
 workforce.
description: Microsatellite and
 comparative dataThis file contains all
 microsatellite genotype data, as well as comparative data and the list of
 accession numbers for sequences used in this study.DATA_FOR_DRYAD.xlsx