cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h443d
title: Data from: Experimental evolution of an emerging plant virus in host genotypes that differ in their susceptibility to infection

description: This study evaluates the extent to which genetic differences among host
 individuals from the same species conditions the evolution of a plant RNA
 virus. We performed a three-fold replicated evolution experiment in which
 Tobacco etch potyvirus isolate At17b (TEV-At17b), adapted to Arabidopsis
 thaliana ecotype Ler-0, was serially passaged in five genetically
 heterogeneous ecotypes of A. thaliana. After 15 passages we found that
 evolved viruses improved their fitness, showed higher infectivity and
 stronger virulence in their local host ecotypes. The genome of evolved
 lineages was sequenced and putative adaptive mutations identified.
 Host-driven convergent mutations have been identified. Evidences supported
 selection for increased translational efficiency. Next, we sought for the
 specificity of virus adaptation by infecting all five ecotypes with all 15
 evolved virus populations. We found that some ecotypes were more
 permissive to infection than others, and that some evolved virus isolates
 were more specialist/generalist than others. The bipartite network linking
 ecotypes with evolved viruses was significantly nested but not modular,
 suggesting that hard to infect ecotypes were infected by generalist
 viruses whereas easy to infect ecotypes were infected by all viruses, as
 predicted by a gene-for-gene model of infection.
description: Raw fitness
 dataFile contains three
 sheets. First sheet contains the raw fitness data (technical replicates of
 RT-qPCR per biological replicate). Second sheet contains the significance
 test for each fitness value corrected using FDR for multiple comparisons.
 Third sheet contains a summary of fitness data. Columns labels are
 self-explicative.
DOI: 10.5061/dryad.743
title: Data from: Testing for phylogenetic conflict among molecular data sets in the Tribe Triticeae (Gramineae)

description: Four molecular data sets are available for the diploid intersterile genera
 of the cereal grain tribe Triticeae, and there are numerous differences
 among the four published trees. All six pairwise combinations of data sets
 were examined using tree comparisons, the incongruence length difference
 test, the Wilcoxon signed ranks test, and a permutation test. We describe
 some advantages, disadvantages, and properties of the different comparison
 methods. Test results provide no evidence for significant differences in
 the phylogenetic signal among the three nuclear data sets, with the
 exception of the placement of a single taxon. The chloroplast DNA
 restriction site data, however, support a significantly different tree,
 and the differences probably reflect a separate evolutionary history of
 the chloroplast genome.
description: 5S Long (for 5S
 Short)5S Long and 5S
 Short5s Short and
 cpDNAcpDNA (for 5S
 Short)5S Short (for
 ITS)ITS (for 5S
 Short)ITS and 5S
 ShortcpDNA (for
 ITS)cpDNA and
 ITSITS (for
 cpDNA)5S Short (for 5S
 Long)5S Long (for
 cpDNA)5s Long and
 cpDNAcpDNA (for 5S
 Long)5S Long (for
 ITS)5S Long and
 ITSITS (for 5S
 Long)5S Short (for
 cpDNA)
DOI: 10.5061/dryad.b49n840
title: Data from: General trust impedes perception of self-reported primary psychopathy in thin slices of social interaction

description: Little is known about people’s ability to detect subclinical psychopathy
 from others’ quotidian social behavior, or about the correlates of
 variation in this ability. This study sought to address these questions
 using a thin slice personality judgment paradigm. We presented 108
 undergraduate judges (70.4% female) with 1.5 minute video thin slices of
 zero-acquaintance triadic conversations among other undergraduates
 (targets: n = 105, 57.1% female). Judges completed self-report measures of
 general trust, caution, and empathy. Target individuals had completed the
 Levenson Self-Report Psychopathy (LSRP) scale. Judges viewed the videos in
 one of three conditions: complete audio, silent, or audio from which
 semantic content had been removed using low-pass filtering. Using a novel
 other-rating version of the LSRP, judges’ ratings of targets’ primary
 psychopathy levels were significantly positively associated with targets’
 self-reports, but only in the complete audio condition. Judge general
 trust and target LSRP interacted, such that judges higher in general trust
 made less accurate judgments with respect to targets higher in primary and
 total psychopathy. Results are consistent with a scenario in which
 psychopathic traits are maintained in human populations by negative
 frequency dependent selection operating through the costs of detecting
 psychopathy in others.
description: Example of Stata Do-File
 running multi-level mixed effects modelThis file contains an
 example of the Stata Do-Files used to run the multi-level mixed effects
 regression models used in this paper. More details are found in the file
 itself. This script is not under any licensing
 agreement.Manson_et_al_Stata_Do-file_Example.txtData from Manson et al, "General Trust Impedes Perception..."Each row represents one combination of judge, target and psychopathy factor. Columns represent variables analyzed in this study.data_from_Manson_et_al_General-Trust-Impedes.csv
DOI: 10.5061/dryad.5fm00
title: Data from: A prioritised list of invasive alien species to assist the effective implementation of EU legislation

description: 1. Effective prevention and control of invasive species generally relies
 on a comprehensive, coherent and representative list of species that
 enables resources to be used optimally. European Union (EU) Regulation
 1143/2014 on invasive alien species (IAS) aims to control or eradicate
 priority species, and to manage pathways to prevent the introduction and
 establishment of new IAS; it applies to species considered of Union
 concern and subject to formal risk assessment. So far, 49 species have
 been listed but the criteria for selecting species for risk assessment
 have not been disclosed and were probably unsystematic. 2. We developed a
 simple method to systematically rank invasive alien species according to
 their maximum potential threat to biodiversity in the EU. We identified
 1323 species as potential candidates for listing, and evaluated them
 against their invasion stages and reported impacts, using information from
 databases and scientific literature. 3. 900 species fitted the criteria
 for listing according to IAS Regulation. We prioritised 207 species for
 urgent risk assessment, 59 by 2018 and 148 by 2020, based on their
 potential to permanently damage native species or ecosystems; another 336
 species were identified for a second phase (by 2025), to prevent or
 reverse their profound impacts on biodiversity; and a further 357 species
 for assessment by 2030. 4. Policy implications. We propose a systematic,
 proactive approach to selecting and prioritising invasive alien species
 for risk assessment to assist European Union policy implementation. We
 assess an unprecedented number of species with potential to harm EU
 biodiversity using simple methodology that we developed, and recommend
 which species should be considered for risk assessment in a ranked order
 of priority along the timeline 2018-2030, based on their maximum reported
 impact and their invasion history in Europe.
description: EU prioritised list of
 invasive alien speciesPrioritised list of
 invasive alien species in the European Union, according to the year when a
 risk assessment should be available, with an indication of the sources of
 information used for review. Contains 1323 species assessed for their
 potential inclusion in the EU list of invasive species of Union concern,
 based on their maximum reported impact (from databases and literature) and
 their invasion history in Europe.JPECarbonerasST2.xlsx
DOI: 10.5061/dryad.75030
title: Data from: Genetic architecture of survival and fitness-related traits in two populations of Atlantic salmon

description: The additive genetic effects of traits can be used to predict evolutionary
 trajectories, such as responses to selection. Non-additive genetic and
 maternal environmental effects can also change evolutionary trajectories
 and influence phenotypes, but these later effects have received less
 attention by researchers. We partitioned the phenotypic variance of
 survival and fitness-related traits into additive genetic, non- additive
 genetic, and maternal environmental effects using a full-factorial
 breeding design within two allopatric populations of Atlantic salmon
 (Salmo salar). Maternal environmental effects were large at early life
 stages, but decreased during development, with non-additive genetic
 effects being most significant at later juvenile stages (alevin and fry).
 Non- additive genetic effects were also, on average, larger than additive
 genetic effects. The populations, generally, did not differ in the trait
 values or inferred genetic architecture of the traits. Any differences
 between the populations for trait values could be explained by maternal
 environmental effects. We discuss if the similarities in architectures of
 these populations is the result of natural selection across a common
 juvenile environment.
description: Houde_heredityEarly life-history survival and fitness-related traits. Growing degree days information.
DOI: 10.5061/dryad.2v41qr7
title: Data from: Fitter frogs from polluted ponds: the complex impacts of human-altered environments

description: Human-modified habitats rarely yield outcomes that are aligned with
 conservation ideals. Landscapes that are subdivided by roads are no
 exception, precipitating negative impacts on populations due to
 fragmentation, pollution, and road kill. Although many populations in
 human modified habitats show evidence for local adaptation, rarely does
 environmental change yield outright benefits for populations of
 conservation interest. Contrary to expectations, we report surprising
 benefits experienced by amphibian populations breeding and dwelling in
 proximity to roads. We show that roadside populations of the wood frog,
 Rana sylvatica, exhibit better locomotor performance and higher measures
 of traits related to fitness compared with frogs from less disturbed
 environments located further away from roads. These results contrast
 previous evidence for maladaptation in roadside populations of wood frogs
 studied elsewhere. Our results indicate that altered habitats might not be
 unequivocally detrimental, and at times might contribute to metapopulation
 success. While the frequency of such beneficial outcomes remains unknown,
 their occurrence underscores the complexity of inferring consequences of
 environmental change.
description: Adult wood frog
 traitsJumping performance,
 adult size, and other morphometricsAdultWoodFrogTraits2014.xls
DOI: 10.5061/dryad.9f8q91q3
title: Data from: Cd36-deficient congenic strains show improved glucose tolerance and distinct shifts in metabolic and transcriptomic profiles

description: Deficiency of fatty acid translocase Cd36 has been shown to have a major
 role in the pathogenesis of metabolic syndrome in the spontaneously
 hypertensive rat (SHR). We have tested the hypothesis that the effects of
 Cd36 mutation on the features of metabolic syndrome are contextually
 dependent on genomic background. We have derived two new congenic strains
 by introgression of limited chromosome 4 regions of SHR origin, both
 including the defective Cd36 gene, into the genetic background of a highly
 inbred model of insulin resistance and dyslipidemia, polydactylous (PD)
 rat strain. We subjected standard diet-fed adult males of PD and the
 congenic PD.SHR4 strains to metabolic, morphometric and transcriptomic
 profiling. We observed significantly improved glucose tolerance and lower
 fasting insulin levels in PD.SHR4 congenics than in PD. One of the PD.SHR4
 strains showed lower triglyceride concentrations across major lipoprotein
 fractions combined with higher levels of low-density lipoprotein
 cholesterol compared with the PD progenitor. The hepatic transcriptome
 assessment revealed a network of genes differentially expressed between PD
 and PD.SHR4 with significant enrichment by members of the circadian
 rhythmicity pathway (Arntl (Bmal1), Clock, Nfil3, Per2 and Per3). In
 summary, the introduction of the chromosome 4 region of SHR origin
 including defective Cd36 into the PD genetic background resulted in
 disconnected shifts of metabolic profile along with distinct changes in
 hepatic transcriptome. The synthesis of the current results with those
 obtained in other Cd36-deficient strains indicates that the eventual
 metabolic effect of a deleterious mutation such as that of SHR-derived
 Cd36 is not absolute, but rather a function of complex interactions
 between environmental and genomic background, upon which it operates.
description: PDvsPD.SHR4_RTPCRRaw data and results for real-time PCR verification of microarray comparison of hepatic expression between PD and PD. SHR4 rat strains.PDvsPD.SHR4_metabprofileMetabolic and morphometric profile of PD and PD.SHR4 strains
DOI: 10.5061/dryad.h5nc8
title: Data from: An evaluation of rearing densities to improve growth and survival of hatchery spring Chinook salmon

description: We evaluated growth and survival of spring Chinook salmon (Oncorhynchus
 tshawytscha) reared at varying densities at Warm Springs National Fish
 Hatchery, Oregon. For three consecutive brood years, density treatments
 consisted of low, medium, and high groups in 57.8 m3 raceways with
 approximatly16,000, 24,000, and 32,000 fish/raceway, respectively. Fish
 were volitionally released in both the fall and spring to mimic the
 downstream migration timing of the endemic wild spring Chinook salmon
 stock. Just prior to the fall release, the rearing density estimate was
 4.24 kg/m3 for the low density group, 6.27 kg/m3 for the medium density
 group, and 8.42 kg/m3 for the high density group. Weight gain did not
 differ among density treatments (P = 0.72). A significant difference was
 found in median fork length (P &lt;0.001) for fish reared at different
 densities in the one year length was measured in the fall. Fish reared at
 high density exhibited the highest on-hatchery mortality rate during two
 brood years; however, differences in mortality rate among densities were
 not significant (P = 0.20). In one brood year, adult recovery rates
 appeared to support the hypothesis that lower initial densities improved
 post-release survival (P &lt; 0.001). All rearing densities utilized
 in this evaluation were relatively low and may partially explain why more
 differences were not readily apparent among density groups. In addition,
 the volitional release was a confounding factor in our study because we
 were unable to quantify the number of fish released in the fall. Even
 though the effects of initial rearing density on survival and growth were
 not clearly evident, high water temperatures observed each summer (22.8oC
 max) are a concern. Given current climate change predictions, hatcheries
 dependent on a surface water supply should regularly monitor water
 temperature and optimum rearing density may need adjustment.
description: On hatchery mortality
 during rearing density studyOn hatchery mortality of
 spring Chinook salmon during the rearing density evaluation at Warm
 Springs National Fish Hatchery from the start of the study in April
 through September just prior to fall release. Data stored in the Columbia
 River Information System maintained by the Columbia River Fisheries
 Program Office.OnHatcheryMortalityFigure3.xlsWeight gain by rearing densityFish weight (g) at start of study in April to prior to fall release in October by rearing density and brood year. Data from Columbia River Information System maintained at Columbia River Fisheries Program Office, Vancouver, WA.WeightGain.xlsForkLengthOctoberFork Length (mm) of spring Chinook salmon on 3 October 2002 (brood year 2001)ForkLengthMarchFork Length (mm) on 22 March 2004 (brood year 2002)
DOI: 10.5061/dryad.8635
title: Data from: Female ground tits prefer relatives as extra-pair partners: driven by kin-selection?

description: Socially monogamous female birds routinely mate with males outside the
 pair bond. Three alternative hypotheses consider genetic benefits as the
 major driver behind the female strategy. The inbreeding avoidance
 hypothesis predicts that females paired with closely related males should
 seek copulations with distantly related extra-pair partners to avoid
 fitness loss from inbreeding depression; the outbreeding avoidance
 hypothesis predicts the opposite; the kin-selection hypothesis suggests
 that regardless of social mate relatedness, females should give related
 males extra-pair fertilization opportunities to gain inclusive fitness if
 the costs from inbreeding are minor. We test these hypotheses with a
 facultative cooperative breeder, the ground tit (Parus humilis). Social
 pairs of ground tits formed randomly with respect to genetic relatedness.
 In both bi-parental and cooperative groups, a female’s engaging in
 extra-pair mating was independent of relatedness to her social mate;
 however, females preferred extra-pair sires to which they were more
 related than to their social mates. Moreover, females had higher
 relatedness with either their extra-group extra-pair sires in both
 bi-parental and cooperative groups, or within-group helper sires in
 cooperative groups, than expected by chance. When more than one potential
 extra-pair partner was available around a female’s nest, she tended to
 select a relative. There was no indication of fitness reduction from
 extra-pair mating, which occurred at an intermediate level of inbreeding.
 These data support the kin-selection hypothesis, although there might be
 alternative non-genetic reasons associated with the extra-pair mating
 preference. Our finding offers a new explanation for why female birds
 pursue extra-pair mating. It also may broaden our understanding of the
 role of kin-selection in the evolution of cooperative society.
description: Genotype dataset of
 ground tit for DryadThe dataset includes
 genotype information of all the ground tit individuals used in this
 paper.
DOI: 10.5061/dryad.523t1
title: Data from: The scaling of parasite biomass with host biomass in lake ecosystems: are parasites limited by host resources?

description: The standing crop biomass of different populations or trophic levels
 reflects patterns of energy flow through an ecosystem. The contribution of
 parasites to total biomass is often considered negligible; recent evidence
 suggests otherwise, although it comes from a narrow range of natural
 systems. Quantifying how local parasite biomass, whether that of a single
 species or an assemblage of species sharing the same host, varies across
 localities with host population biomass, is critical to determine what
 constrains parasite populations. We use an extensive dataset on all
 free-living and parasitic metazoan species from multiple sites in New
 Zealand lakes to measure parasite biomass and test how it covaries with
 host biomass. In all lakes, trematodes had the highest combined biomass
 among parasite taxa, ranging from about 0.01 to 0.25 g m−2, surpassing the
 biomass of minor free-living taxa. Unlike findings from other studies, the
 life stage contributing the most to total trematode biomass was the
 metacercarial stage in the second intermediate host, and not sporocysts or
 rediae within snail first intermediate hosts, possibly due to low
 prevalence and small snail sizes. For populations of single parasite
 species, we found no relationship between host and parasite biomass for
 either juvenile or adult nematodes. In contrast, all life stages of
 trematodes had local biomasses that correlated positively with those of
 their hosts. For assemblages of parasite species sharing the same host, we
 found strong relationships between local host population biomass and the
 total biomass of parasites supported. In these host–parasite biomass
 relationships, the scaling factor (slope in log-log space) suggests that
 parasites may not be making full use of available host resources. Host
 populations appear capable of supporting a little more parasite biomass,
 and may be open to expansion of existing parasites or invasion by new
 ones.
description: Mean Biomass of
 parasitic and free-living taxa from 4 lakesMean Biomass of all
 metazoan parasitic and free-living taxa from 4 lakes in New
 ZealandMean
 Biomass vs SD-spatial copy.xls
DOI: 10.5061/dryad.kv57r
title: Data from: Small RNAs from a big genome: the piRNA pathway and transposable elements in the salamander species Desmognathus fuscus

description: Most of the largest vertebrate genomes are found in salamanders, a clade
 of amphibians that includes 686 species. Salamander genomes range in size
 from 14 to 120 Gb, reflecting the accumulation of large numbers of
 transposable element (TE) sequences from all three TE classes. Although
 DNA loss rates are slow in salamanders relative to other vertebrates, high
 levels of TE insertion are also likely required to explain such high TE
 loads. Across the Tree of Life, novel TE insertions are suppressed by
 several pathways involving small RNA molecules. In most known animals, TE
 activity in the germline is primarily regulated by the Piwi-interacting
 RNA (piRNA) pathway. In this study, we test the hypothesis that
 salamanders’ unusually high TE loads reflect the loss of the ancestral
 piRNA-mediated TE-silencing machinery. We characterized the small RNA pool
 in the female and male adult gonads, testing for the presence of small RNA
 molecules that bear the characteristics of TE-targeting piRNAs. We also
 analyzed the amino acid sequences of piRNA pathway proteins from
 salamanders and other vertebrates, testing whether the overall patterns of
 sequence divergence are consistent with conserved pathway function across
 the vertebrate clade. Our results do not support the hypothesis of piRNA
 pathway loss; instead, they suggest that the piRNA pathway is expressed in
 salamanders. Given these results, we propose hypotheses to explain how the
 extraordinary TE loads in salamander genomes could have accumulated,
 despite the expression of TE-silencing machinery.
description: ASZ1.nex
 alignmentNexus file containing
 the trimmed alignment of amino acid sequences from salamanders and other
 vertebrates used to generate the phylogeny in the
 manuscript.Asz1.nexDdx4.nex alignmentDdx4.nexFKBP6.nex alignmentFKBP6.nexHen1.nex alignmentHen1.nexKIF17.nex alignmentKIF17.nexMov10l1.nex alignmentMov10l1.nexPiwil1.nex alignmentPiwil1.nexPiwil2.nex alignmentPiwil2.nexPld6.nex alignmentPld6.nexPrmt5.nex alignmentPrmt5.nexTdrd1.nex alignmentTdrd1.nexTdrkh.nex alignmentTdrkh.nexCryptobranchus pRNA proteinsAmino acid sequences for the 12 Cryptobranchus alleganiensis piRNA pathway proteins.Cryptobranchus_pRNA_proteins.txt