cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.80md2d10
title: Data from: Translocation of wild populations: conservation implications for the genetic diversity of the black-lipped pearl oyster Pinctada margaritifera

description: Translocation has been widely studied as a tool for conservation
 management to restore or enhance degraded populations. On the contrary few
 studies have been conducted on translocation for commercial purposes. In
 this study we evaluate the genetic consequences of translocation of wild
 individuals of Pinctada margaritifera on farmed and adjacent wild
 populations. We tested the hypotheses that translocations would induce
 high genetic heterogeneity in farmed populations and this heterogeneity
 would then leak into the adjacent wild populations. In fact, farmed
 samples exhibit high levels of heterogeneity and low pairwise relatedness
 compared to wild populations, highlighting the pooling of genetically
 divergent populations into farms. We also demonstrate that this
 heterogeneity is transmitted to adjacent wild populations as a result of
 interbreeding. Adjacent wild populations tend to have higher genetic
 diversity values and greater pairwise relatedness coefficient with farmed
 populations than wild populations. Overall pearl culture in French
 Polynesia promotes the mixing of unrelated individuals in farmed locations
 and reduces genetic divergence among geographically distant populations as
 well as among farmed and wild populations of a same lagoon. We also
 studied for the first time, a farmed population originating from spat
 collected in a lagoon where release of hatchery produced larvae occurred
 ten year ago and we were able to identify four distinct genetic groups.
 These groups contribute highly to reproduction and caused considerable
 genetic drift in the lagoon, suggesting that hatchery produced larvae are
 neither sustainable method for pearl culture nor for conserving the
 diversity of P. margaritifera in French Polynesia.
description: Genotype_Raw_DataFile: Genotype_Raw_data | Data collected by Lemer S.: sarah.lemer@gmail.com | Description of Data file | 1st column : individuals sampled in each populations. Individual names are composed of the 3 or 4 first letter of the sampled site followed by sample number. Population names are code as in Table 1 in the article. | 2nd to 21st column : individual genotype per locus. Alleles are reported for each locus in two columns. Locus are named as in Table A in the Supporting materials. | Alleles are reported in base pair. Missing data is indicated with the following sign '?'.
DOI: 10.5061/dryad.d08fb
title: Data from: The importance of factors controlling species abundance and distribution varies in native and non-native species.

description: How variation in factors controlling species abundance and distribution
 between native and non-native ranges compares to that within ranges
 remains poorly understood. We used a globally distributed ruderal,
 Centaurea solstitialis (Centaurea), to explore the possibility that the
 importance of those factors exhibits great variation between and within
 ranges. To test our hypothesis, we established seed addition experiments
 with soil disturbance (turnover and control) and biocide (fungicides,
 insecticide, and control) treatments in two regions within native (the
 Caucasus and south-western Turkey) and non-native (the western United
 States – US – and central Argentina) distributions. Also, we estimated the
 rate of vegetation recovery after disturbance (resilience) and related it
 to Centaurea density in experimental plots. Disturbance strongly increased
 Centaurea density in all regions. Density was similar between the native
 Caucasus and non-native Argentina and much greater in those regions than
 in the native Turkey and non-native US in biocide-free plots. Fungicides
 had positive effects on density in the US and negative ones in the
 Caucasus and Argentina, resulting in no differences between those three
 regions and greater density in the US than Turkey. Insecticide
 applications promoted Centaurea density in Turkey and Argentina, but
 inter-regional comparisons of density in treated plots were comparable to
 those in biocide-free plots. Overall, plants were smaller and less fecund
 in Turkey than the other regions, except the US. The greatest fungal
 attack was documented in Turkey, and herbivory was stronger there and in
 Argentina than in the Caucasus and US. The resilience of the local
 community explained a large proportion of variation in Centaurea density.
 These results support our hypothesis, and reveal that the speed at which
 competition is re-gained after disturbance may influence global variation
 in Centaurea abundance. Because many ruderals exhibit native and
 non-native distributions, our results are likely to be generalized to
 other systems.
description: Data from Hierro et al.
 2016 EcographyThis is an Excel file,
 where data from our study is organized in different
 sheets.
DOI: 10.5061/dryad.1j7g2k8
title: Data from: Rapid detection of cocaine using aptamer-based biosensor on an evanescent wave fibre platform

description: The rapid detection of cocaine has received considerable attention because
 of the instantaneous and adverse effects of cocaine overdose on human
 health. Aptamer-based biosensors for cocaine detection have been well
 established for research and application. However, reducing the analytic
 duration without deteriorating the sensitivity still remains as a
 challenge. Here, we proposed an aptamer-based evanescent wave fiber (EWF)
 biosensor to rapidly detect cocaine in a wide working range. At first, the
 aptamers were conjugated to complementary DNA with fluorescence tag and
 such conjugants were then immobilized on magnetic beads. After cocaine was
 introduced to compete against the aptamer-DNA conjugants, the released DNA
 in supernatant was detected on the EWF platform. The dynamic curves of EWF
 signals could be interpreted by the first order kinetics and saturation
 model. The semi-log calibration curve covered a working range of 10-5000
 μM of cocaine, and the limit of detection was approximately 10.5 μM. The
 duration of the full procedure was 990 s (16.5 min), and the detection
 interval was 390 s (6.5 min). The specified detection of cocaine was
 confirmed from four typical pharmaceutic agents. The analysis was repeated
 for 50 cycles without significant loss of sensitivity. Therefore, the
 aptamer-based EWF biosensor is a feasible solution to rapidly detect
 cocaine.
description: Excel of Raw data with
 figures embedded.aptamer-EWF-cocain-sensor-Excel-Figure.zip
DOI: 10.5061/dryad.6dr0475t
title: Data from: Species tree of a recent radiation: the subfamily Delphininae (Cetacea, Mammalia)

description: Lineages undergoing rapid radiations provide exceptional opportunities for
 studying speciation and adaptation, but also represent a challenge for
 molecular systematics because retention of ancestral polymorphisms and the
 occurrence of hybridization can obscure relationships among lineages.
 Dolphins in the subfamily Delphininae are one such case. Non-monophyly,
 rapid speciation events, and discordance between morphological and
 molecular characters have made the inference of phylogenetic relationships
 within this subfamily very difficult. Here we approach this problem by
 applying multiple methods intended to estimate species trees using a
 multi-gene dataset for the Delphininae (Sousa, Sotalia, Stenella,
 Tursiops, Delphinus and Lagenodelphis). Incongruent gene trees obtained
 indicate that incomplete lineage sorting and possibly hybridization are
 confounding the inference of species history in this group. Nonetheless,
 using coalescent-based methods, we have been able to extract an underlying
 species-tree signal from divergent histories of independent genes that
 supports relationships based on morphology. This is the first time a
 molecular study provides support for such relationships. This study
 further illustrates how methods of species-tree inference can be very
 sensitive both to the characteristics of the dataset and the evolutionary
 processes affecting the evolution of the group under study.
description: Amaraletal-DelphininaeSpeciesTree nexus fileNexus file for the concatenation of the 13 nuclear loci and 1 mitochondrial gene that were analyzed in order to estimate a species tree for the subfamily Delphininae.
DOI: 10.5061/dryad.2f6f2
title: Data from: A large new leanchoiliid from the Burgess Shale and the influence of inapplicable states on stem arthropod phylogeny

description: Characterized by atypical frontalmost appendages, leanchoiliids are early
 arthropods whose phylogenetic placement has been much debated.
 Morphological interpretations have differed, some of which concern
 critical characters such as the number of eyes and head appendages, but
 methodological approaches also have diverged. Here, we describe a new
 leanchoiliid, Yawunik kootenayi gen. et sp. nov., based on 42 specimens
 from the newly discovered Marble Canyon locality of the Burgess Shale
 (Kootenay National Park, British Columbia; middle Cambrian). This new
 morphotype demonstrates the presence of a four-segmented head in
 leanchoiliids, along with two small antero-median eyes in addition to
 lateral eyes. Yawunik is characterized by a 12-segmented trunk and a
 carinate, lanceolate telson adorned with minute spines. The ‘great
 appendages’ of the animal bear teeth on their two distal rami, which would
 have enhanced their ability to grasp prey. Attitudes of specimens,
 resulting from burial at multiple aspects of bedding, suggest the ‘great
 appendages’ were flexible and capable of antero-posterior rotation. We
 also discuss the nature of intersegmental tissues and filaments present
 within the ‘great appendages’. Our phylogenetic analyses extend the
 monophyly of leanchoiliids to include Haikoucaris and Yohoia in a new
 clade, the Cheiromorpha nom. nov. (within Heptopodomera nom. nov.). Other
 nodes are poorly resolved unless implied weights are used, and in this
 case, the topology is critically sensitive to the coding prerogative of
 inapplicable states (NAs). Both the traditional ‘Arachnomorpha’ hypothesis
 (NAs as additional states) and the more recently favoured ‘Artiopoda +
 Crustacea’ (NAs as uncertainties) were obtained using the same data set
 and outgroup. This result stresses, first, the historical importance of
 polarization over data content in scenarios of early arthropod evolution,
 and second, a pressing need to investigate the impacts of coding
 inapplicables, especially given the inflating effect of implied weights.
description: Character
 ListCharacters9-rev2.docCladistic MatrixMatrix.docMorphometric DataMEAS_TABLE-rev3.doc
DOI: 10.5061/dryad.85nn2
title: Data from: Hormesis results in trade-offs with immunity

description: Many have argued that we may be able to extend life and improve human
 health through hormesis, the beneficial effects of low-level toxins and
 other stressors. But, studies of hormesis in model systems have not yet
 established whether stress-induced benefits are cost free, artifacts of
 inbreeding, or come with deleterious side effects. Here, we provide
 evidence that hormesis results in trade-offs with immunity. We find that a
 single topical dose of dead spores of the entomopathogenic fungus,
 Metarhizium robertsii, increases the longevity of the fruit fly,
 Drosophila melanogaster, without significant decreases in fecundity. We
 find that hormetic benefits of pathogen challenge are greater in lines
 that lack key components of antifungal immunity (Dif and Turandot M). And,
 in outbred fly lines, we find that topical pathogen challenge enhances
 both survival and fecundity, but reduces ability to fight off live
 infections. The results provide evidence that hormesis is manifested by
 stress-induced trade-offs with immunity, not cost-free benefits or
 artifacts of inbreeding. Our findings illuminate mechanisms underlying
 pathogen-induced life-history trade-offs, and indicate that reduced immune
 function may be an ironic side effect of the “elixirs of life.”
description: Full Experimental
 DataThis Excel file contains
 all the data used for the accompanying manuscript. Each data set used for
 analysis or the production of figures are separated into individual
 worksheets, a plan to which is stated in the accompanying 'Read
 Me' document.
DOI: 10.5061/dryad.kq0n5
title: Data from: Genetic and morphological differentiation in Populus nigra L.: isolation by colonization or isolation by adaptation?

description: Identifying processes underlying the genetic and morphological differences
 among populations is a central question of evolutionary biology. Forest
 trees typically contain high levels of neutral genetic variation, and
 genetic differences are often correlated with geographic distance between
 populations [isolation by distance (IBD)] or are due to historic
 vicariance events [isolation by colonization (IBC)]. In contrast,
 morphological differences are largely due to local adaptation. Here, we
 examined genetic (microsatellite) and morphological (from a common garden
 experiment) variation in Populus nigra L., European black poplar,
 collected from 13 sites across western Europe and grown in a common garden
 in Belgium. Significant genetic differentiation was observed, with
 populations from France displaying greater admixture than the distinct
 Spanish and central European gene pools, consistent with previously
 described glacial refugia (IBC). Many quantitative traits displayed a
 bimodal distribution, approximately corresponding to small-leaf and
 large-leaf ecotypes. Examination of nine climatic variables revealed the
 sampling locations to have diverse climates, and although the correlation
 between morphological and climatic differences was significant, the
 pattern was not consistent with strict local adaptation. Partial Mantel
 tests based on multivariate summary statistics identified significant
 residual correlation in comparisons of small-leaf to large-leaf ecotypes,
 and within the small-leaf samples, but not within large-leaf ecotypes,
 indicating that variation within the small-leaf morphotype in particular
 may be adaptive. Some small-leaf populations experience climates very
 similar to those in large-leaf sites. We conclude that adaptive
 differentiation and persistent IBC acted in combination to produce the
 genetic and morphological patterns observed in P. nigra.
description: DeWoody P. nigra
 metadataMicrosatellite data
 associated with DeWoody, Trewin & Taylor, Genetic and morphological
 differentiation in Populus nigra L.: Isolation by colonization or
 isolation by adaptation?DeWoody et al Pnigra
 microsatellite data Dryad.csvDeWoody et al Pnigra
 morphological data DryadMorphological data from
 common garden experiment used in DeWoody, Trewin & Taylor, Genetic and
 morphological differentiation in Populus nigra L.: Isolation by
 colonization or isolation by adaptation?DeWoody et al Pnigra
 climate data DryadWorldClim climate data
 for Populus nigra sampling sites, plus the first three factors resulting
 from the multivariate analysis of such.
DOI: 10.5061/dryad.r76cm3bn
title: Data from: Interpreting the evolutionary regression: the interplay between observational and biological errors in phylogenetic comparative studies

description: Regressions of biological variables across species are rarely perfect.
 Usually there are residual deviations from the estimated model
 relationship, and such deviations commonly show a pattern of phylogenetic
 correlations indicating that they have biological causes. We discuss the
 origins and effects of phylogenetically correlated biological variation in
 regression studies. In particular, we discuss the interplay of biological
 deviations with deviations due to observational or measurement errors,
 which are also important in comparative studies based on estimated species
 means. We show how bias in estimated evolutionary regressions can arise
 from several sources, including phylogenetic inertia and either
 observational or biological error in the predictor variables. We show how
 all these biases can be estimated and corrected for in the presence of
 phylogenetic correlations. We present general formulas for incorporating
 measurement error in linear models with correlated data. We also show how
 alternative regression models, such as major-axis and reduced major-axis
 regression, which are often recommended when there is error in predictor
 variables, are strongly biased when there is biological variation in any
 part of the model. We argue that such methods should never be used to
 estimate evolutionary or allometric regression slopes.
description: HansenBartoszekSupplementaryA
DOI: 10.5061/dryad.6069g
title: Data from: Axial growth gradients across the postprotaspid ontogeny of the Silurian trilobite Aulacopleura koninckii

description: Recent morphometric analysis revealed a juvenile (meraspid) axial growth
 gradient in the trunk of the ~429 Myr old trilobite Aulacopleura koninckii
 that resulted from growth control based on positional specification, as is
 common among extant organisms. Here we explore axial growth gradients in
 the more anterior body region, the cephalon, and in the cephalon and trunk
 during subsequent development in the holaspid period. We detected an axial
 growth gradient in the cephalon in the meraspid period, flatter and
 opposite in direction to that of the trunk, which also persisted during
 the holaspid period. We also found an holaspid trunk growth gradient, with
 a different distribution of growth rates among segments than that of the
 meraspid period. These newly observed growth gradients are compatible with
 the mechanism of growth control inferred for the meraspid trunk. Thus, the
 same kind of growth control may have operated in both body regions and
 during the whole ontogeny of A. koninckii. This study, along with others
 on the same species that preceded it, show that morphometric analysis of
 appropriate data sets can address questions of high interest for
 evolutionary developmental biology using data from fossils. By revealing
 developmental features at deep nodes of the phylogenetic tree, these
 studies will elucidate both how developmental processes evolved and how
 they themselves affected the evolution of organismal body patterning.
description: Fusco et al. Appendices_
 Paleobiology 2016Supplementary
 information for Fusco et al. paper.
DOI: 10.5061/dryad.6cs91k3
title: Data from: Long-distance pollen and seed dispersal and inbreeding depression in Hymenaea stigonocarpa (Fabaceae: Caesalpinioideae) in the Brazilian savannah

description: Hymenaea stigonocarpa is a Neotropical tree that is economically important
 due to its high-quality wood; however, because it has been exploited
 extensively, it is currently considered threatened. Microsatellite loci
 were used to investigate the pollen and seed dispersal, mating patterns,
 spatial genetic structure (SGS), genetic diversity, and inbreeding
 depression in H. stigonocarpa adults, juveniles and open-pollinated seeds,
 which were sampled from isolated trees in a pasture and trees within a
 forest fragment in the Brazilian savannah. We found that the species
 presented a mixed mating system, with population and individual variations
 in the outcrossing rate (0.53–1.0). The studied populations were not
 genetically isolated due to pollen and seed flow between the studied
 populations and between the populations and individuals located outside of
 the study area. Pollen and seed dispersal occurred over long distances
 (&gt; 8 km); however, the dispersal patterns were isolated by
 distance, with a high frequency of mating occurring between near-neighbour
 trees and seeds dispersed near the parent trees. The correlated mating for
 individual seed trees was higher within than among fruits, indicating that
 fruits present a high proportion of full-sibs. Genetic diversity and SGS
 were similar among the populations, but offspring showed evidence of
 inbreeding, mainly originating from mating among related trees, which
 suggests inbreeding depression between the seed and adult stages. Selfing
 resulted in a higher inbreeding depression than mating among relatives, as
 assessed through survival and height. As the populations are not
 genetically isolated, both are important targets for in situ conservation
 to maintain their genetic diversity; for ex situ conservation, seeds can
 be collected from at least 78 trees in both populations separated by at
 least 250 m.
description: Microsatellite data for
 two Hymenaea stigonocarpa populationsData of Hymenaea
 stigonocarpa from two populations (adults, juveniles and seeds) have the
 individual number, spatial coordinates (UTM), diameter at breast height
 (dbh) or height of trees, and microsatellite multilocus genotype for 6
 loci.PA_PF_AD_JUV_SEEDS_15_05_2018.xls
DOI: 10.5061/dryad.5bg107j
title: Data from: Fitness costs of mating with preferred females in a scramble mating system

description: Little is known about the operation of male mate choice in systems with
 perceived high costs to male choosiness. Scramble mating systems are one
 type of system in which male choice is often considered too costly to be
 selected. However, in many scramble mating systems, there are also
 potentially high rewards of male choosiness, as females vary dramatically
 in reproductive output and males typically mate once per season and/or per
 lifetime. Using scramble-mating wood frogs (Rana sylvatica), we tested
 whether males gain fitness benefits by mating with preferred females. We
 conducted choice trials (one male presented simultaneously with two
 females) and permitted males to mate with their preferred or non-preferred
 female. Offspring of preferred and non-preferred females were reared in
 the laboratory and field, and we quantified various fitness-relevant
 parameters, including survivorship and growth rates. Across multiple
 parameters measured, matings with preferred females produced fewer and
 lower-quality offspring than did those with non-preferred females. Our
 results are inconsistent with the idea that mate choice confers benefits
 on the choosing sex. We instead propose that, in scramble systems, males
 will be more likely to amplex females that are easier to capture, which
 may correlate with lower quality but increases male likelihood of
 successfully mating. Such male choice may not favor increased fitness when
 the operational sex ratio is less biased toward males in scramble mating
 systems but is, instead, a bet-hedging tactic benefitting males when
 available females are limited.
description: Wood frog mating trials
 and offspring summary dataThis file contains data
 from wood frog mating trials (males divided into two treatments, to mate
 with preferred or non-preferred females) and includes summary data for the
 resulting offspring.Swierk_Langkilde_BEHECO_1.xlsxLaboratory-reared offspringThis file contains body size, date of metamorphosis, and parent morphology of all wood frog larvae that were reared in the laboratory.Swierk_Langkilde_BEHECO_2.xlsxField-reared offspringThis file contains the Gosner stages, sizes, and parent sizes of the wood frog larvae that were reared in field enclosures.Swierk_Langkilde_BEHECO_3.xlsx