cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v77cn
title: Data from: Inhibition of histone deacetylases facilitates extinction and attenuates reinstatement of nicotine self-administration in rats

description: Chromatin remodelling is integral to the formation of long-term memories.
 Recent evidence suggests that histone modification may play a role in the
 persistence of memories associated with drug use. The present series of
 experiments aimed to examine the effect of histone deacetylase (HDAC)
 inhibition on the extinction and reinstatement of nicotine
 self-administration. Rats were trained to intravenously self-administer
 nicotine for 12 days on a fixed-ratio 1 schedule. In Experiment 1,
 responding was then extinguished through removal of nicotine and
 response-contingent cues. After each extinction session, the HDAC
 inhibitor, sodium butyrate (NaB), was administered immediately, or six
 hours after each session. In Experiment 2, response-contingent cues
 remained available across extinction to increase rates of responding
 during this phase, and NaB was administered immediately after the session.
 Finally, in Experiment 3, the effect of NaB treatment on extinction of
 responding for sucrose pellets was assessed. Across all experiments
 reinstatement to the cue and/or the reward itself was then tested. In the
 first experiment, treatment with NaB significantly attenuated nicotine and
 nicotine + cue reinstatement when administered immediately, but not six
 hours after each extinction session. When administered after
 cue-extinction (Expt. 2), NaB treatment specifically facilitated the rate
 of extinction across sessions, indicating that HDAC inhibition enhanced
 consolidation of the extinction memory. In contrast, there was no effect
 of NaB on the extinction and reinstatement of sucrose-seeking (Expt. 3),
 indicating that the observed effects are specific to a drug context. These
 results provide the first demonstration that HDAC inhibition facilitates
 the extinction of responding for an intravenously self-administered drug
 of abuse and further highlight the potential of HDAC inhibitors in the
 treatment of drug addiction.
description: Self-administration,
 extinction and reinstatement data from all experimentsThis file contains the
 self-administration, extinction and reinstatement data collected from all
 three experiments. It includes active and inactive responses, locomotor
 activity and rewards obtained.PLoS ONE_MS
 Data.xlsx
DOI: 10.5061/dryad.n4d73sg
title: Data from: Predictable gene expression related to behavioral variation in parenting

description: Differential gene expression has been associated with transitions between
 behavioral states for a wide variety of organisms and behaviors.
 Heterochrony, genetic toolkits, and predictable pathways underlying
 behavioral transitions have been hypothesized to explain the relationship
 between transcription and behavioral changes. Less studied is how
 variation in transcription is related to variation within a behavior, and
 if the genes that are associated with this variation are predictable. Here
 we adopt an evolutionary systems biology perspective to address two
 hypotheses relating differential expression to changes within and between
 behavior. We predicted fewer genes will be associated with variation
 within a behavior than with transitions between states, and the genes
 underlying variation within a behavior will represent a narrower set of
 biological functions. We tested for associations with parenting variation
 within a state with a set of genes known a priori to be differentially
 expressed between parenting states in the burying beetle Nicrophorus
 vespilloides. As predicted, we found that far fewer genes are
 differentially expressed related to variation within parenting. Moreover,
 these were not randomly distributed among categories or pathways in the
 gene set we tested and primarily involved genes associated with
 neurotransmission. We suggest that this means candidate genes will be
 easier to identify for associations within a behavior, as descriptions of
 behavioral state may include more than a single phenotype.
description: Gene expression during
 parental provisioning directly to offspring in a burying
 beetleGene expression for
 multiple genes defined a-priori as associated with parental care. This
 file contains expression in high-caring and low-caring
 females.Benowitz_BEHECO-2018-0478.R2.xlsx
DOI: 10.5061/dryad.77g469g
title: Data from: Crowding induces entropically-driven changes to DNA dynamics that depend on crowder structure and ionic conditions

description: Macromolecular crowding plays a principal role in a wide range of
 biological processes including gene expression, chromosomal compaction,
 and viral infection. However, the impact that crowding has on the dynamics
 of nucleic acids remains a topic of debate.  To address this
 problem, we use single-molecule fluorescence microscopy and custom
 particle-tracking algorithms to investigate the impact of varying
 macromolecular crowding conditions on the transport and conformational
 dynamics of large DNA molecules. Specifically, we measure the mean-squared
 center-of-mass displacements, as well as the conformational size, shape,
 and fluctuations, of individual 115 kbp DNA molecules diffusing through
 various in vitro solutions of crowding polymers. We determine the role of
 crowder structure and concentration, as well as ionic conditions, on the
 diffusion and configurational dynamics of DNA. We find that branched,
 compact crowders (10 kDa PEG, 420 kDa Ficoll) drive DNA to compact,
 whereas linear, flexible crowders (10 kDa, 500 kDa dextran) cause DNA to
 elongate. Interestingly, the extent to which DNA mobility is reduced by
 increasing crowder concentrations appears largely insensitive to crowder
 structure (branched vs linear), despite the highly different
 configurations DNA assumes in each case. We also characterize the role of
 ionic conditions on crowding-induced DNA dynamics. We show that both DNA
 diffusion and conformational size exhibit an emergent non-monotonic
 dependence on salt concentration that is not seen in the absence of
 crowders.
description: Figure 1
 DataData displayed in Figure
 1 of manuscriptFigure 2
 DataData displayed in Figure
 2 of manuscriptFigure 3
 DataData displayed in Figure
 3 of manuscriptFigure 4
 DataData displayed in Figure
 4 of manuscript
DOI: 10.5061/dryad.86523
title: Data from: Sexual selection on skeletal shape in Carnivora

description: Lifetime reproductive success of males is often dependent upon the ability
 to physically compete for mates. However, species variation in social
 structure leads to differences in the relative importance of intraspecific
 aggression. Here we present a large comparative data set on sexual
 dimorphism in skeletal shape in Carnivora to test the hypotheses that
 carnivorans exhibit sexual dimorphism in skeletal anatomy that is
 reflective of greater specialization for physical aggression in males
 relative to females and that this dimorphism is associated with the
 intensity of sexual selection. We tested these hypotheses using a set of
 functional indices predicted to improve aggressive performance. Our
 results indicate that skeletal shape dimorphism is widespread within our
 sample. Functional traits thought to enhance aggressive performance are
 more pronounced in males. Phylogenetic model selection suggests that the
 evolution of this dimorphism is driven by sexual selection, with the
 best-fitting model indicating greater dimorphism in polygynous versus
 non-polygynous species. Skeletal shape dimorphism is correlated with body
 size dimorphism, a common indicator of the intensity of male-male
 competition, but not with mean body size. These results represent the
 first evidence of sexual dimorphism in the primary locomotor system of a
 large sample of mammals.
description: Morris_2016_Evolution_Carnivora_indices_dataValues for all functional indices and geometric means for all specimens used in the analysis.Morris_2016_Evolution_Carnivora_species_infoBody mass and life history trait infomation for all species used in correlational analysis and phylogenetic model selection analysis.
DOI: 10.5061/dryad.785sc
title: Data from: Ecological causes and consequences of intratropical migration in temperate-breeding migratory birds

description: New discoveries from direct tracking of temperate-breeding passerines show
 that intratropical migration (ITM) occurs in a growing number of species,
 which has important implications for understanding their evolution of
 migration, population dynamics, and conservation needs. Our large sample
 size ([Formula: see text]) for purple martins (Progne subis subis) tracked
 with geolocators to winter sites in Brazil, combined with geolocator
 deployments at breeding colonies across North America, allowed us to test
 hypotheses for ITM, something which has not yet been possible to do for
 other species. ITM in purple martins was not obligate; only 44% of
 individuals exhibited ITM, and movements were not coordinated in time or
 space. We found no evidence to support the resource hypothesis; rainfall
 and temperature experienced by individual birds during their last 2 weeks
 at their first roost site were similar to conditions at their second roost
 site after ITM. Birds generally migrated away from the heavily forested
 northwestern Amazon to less forested regions to the south and east. ITM in
 this aerial insectivore appears to support the competition-avoidance
 hypothesis and may be triggered by increasing local density in the core
 wintering region. Full life cycle models and migratory networks will need
 to incorporate ITM to properly address seasonal carryover effects and
 identify which wintering regions are most important for conservation.
description: Purple Martin
 Intratropical Migration Data - Stutchbury et alTiming of migration and
 location of wintering roosts for Purple Martins tracked by deploying
 geolocator tracking devices at multiple breeding colonies in North
 America
DOI: 10.5061/dryad.mm36n
title: Data from: Feather bacterial load shapes the trade-off between preening and immunity in pigeons

description: Background: Complex communities of bacteria inhabit the feathers of all
 birds. Under normal conditions, individuals maintain a healthy state by
 defending themselves against these potential invaders by preening. The
 immune system is only triggered when bacteria gain access into the body.
 Preening is, however, costly and may trade-off with investment in the
 immune system. To shed light on how birds balance the trade-off between
 immunity and preen secretions when facing high or low feather bacterial
 load, we experimentally manipulated feather bacteria load of feral pigeons
 (Columba livia), and investigated the effects on immune defenses. Results:
 Birds facing high feather bacterial load had lower immune response to PHA
 skin-swelling test (a measure of induced pro-inflammatory capacity) than
 controls, while birds facing low feather bacterial load had higher blood
 bacterial killing ability (a measure of the capacity to eliminate
 bacterial pathogens) than controls. No other components of the immune
 system (i.e., hemagglutination and hemolysis capacity of plasma, primary
 and secondary responses to KLH and quantity of blood parasites) were found
 to be affected by feather bacterial load. Conclusion: Pigeons had
 previously been shown to adjust preening to feather bacterial load. The
 decrease in the energetically costly inflammatory response of birds
 experiencing high bacterial load suggests a trade-off between investment
 in preen secretion and immunity and reinforces the idea that feather
 microbiota may have a strong impact on the ecology and evolution of the
 avian host.
description: Data from: Feather
 bacterial load shapes the trade-off between preening and immunity in
 pigeonsData
 DRYAD.xls
DOI: 10.5061/dryad.24kj1
title: Data from: Experimental evolution to increase the efficacy of the entomopathogenic fungus Beauveria bassiana against malaria mosquitoes: effects on mycelial growth and virulence

description: Entomopathogenic fungi such as Beauveria bassiana are currently considered
 as a potential control agent for malaria mosquitoes. The success of such
 strategies depends among others on the efficacy of the fungus to kill its
 hosts. As B. bassiana can use various resources for growth and
 reproduction, increasing the dependency on mosquitoes as a nutritional
 source may be instrumental for reaching this goal. Passage of
 entomopathogenic fungi through an insect host has been shown to increase
 its virulence. We evaluated the virulence, fungal outgrowth, mycelial
 growth rate, and sporulation rate of two B. bassiana isolates (Bb1520 and
 Bb8028) that underwent 10 consecutive selection cycles through malaria
 mosquitoes (Anopheles coluzzii) using an experimental evolution approach.
 This cycling resulted in an altered capacity of evolved B. Bassiana
 lineages to grow on different substrates while maintaining the ability to
 kill insects. Notably, however, there were no significant changes in
 virulence or speed of outgrowth when comparing the evolved lineages
 against their un-evolved ancestors. These results suggest that fungal
 growth and sporulation evolved through successive and exclusive use of an
 insect host as a nutritional resource. We discuss the results in the light
 of biocontrol and provide suggestions to increase fungal virulence.
description: Raw_Data_ExpEvo_Valero-Jimenez_etalFile containing all raw data generated and analysed in this study.
DOI: 10.5061/dryad.j611s56r
title: Data from: Is recombination a problem for species-tree analyses?

description: As the field of phylogenetics transitions into phylogenomics it has
 spurred a shift in the general paradigm for data analysis whereby specific
 dataset attributes can now be considered in a model-based framework. Much
 effort has been put in to modeling the effects of nucleotide substitution
 within a genealogy (i.e., modeling mutations; Felsenstein 2005) and the
 sorting genes between lineages (i.e., coalescence; Knowles and Kubatko
 2010), both of which are inherent properties of all species histories.
 Improvements in accuracy of species-tree estimation related to using
 models that account for these two sources of uncertainty have been well
 documented (Carstens and Knowles 2007; Edwards et al. 2007; Kubatko and
 Degnan 2007), but these are clearly not the only sources of gene tree
 species-tree discordance. As the field transitions towards using
 multilocus data, the role of other inherent dataset properties that may be
 sources of uncertainty, such as intralocus recombination needs to be
 examined and quantified. As all species-tree methods in current use rely
 on the simplifying assumption that recombination occurs between but not
 within loci, ignoring the presence of recombination represents a
 widespread and ubiquitous violation of species-tree models. Recombination
 within a locus may be a greater problem for species-tree methodologies
 than for concatenation because species-tree methods more accurately model
 the patterns arising from coalescent stochasticity. Concatenation assumes
 all genes share a common underlying tree, a model violated by most
 multilocus data (Knowles and Carstens 2007; Cranston 2010; Linnen 2010;
 Wiens et al. 2010). Relative to the presence of such a gross model
 violation, errors introduced by within-locus recombination are likely to
 be minor for datasets analyzed by concatenation. Coalescent methods for
 species-tree estimation explicitly model each gene tree separately, making
 the relative contribution of recombination to the uncertainty of the
 estimated species tree greater. Challenges posed by recombination may also
 be greatest for species-tree methods that rely on estimating parameters
 related to the scaled mutation rate (Liu 2008; Liu et al. 2008; Heled and
 Drummond 2010) because recombination-introduced heterogeneity may
 interfere with branch length estimates. Lastly, recombination may interact
 with other aspects of the speciation history, such as time to divergence,
 population size, and the length of time between speciation events, and
 sampling effort (McCormack et al. 2009). For example, recombination events
 occurring in recently speciated groups may not have accumulated a
 sufficient number of mutations for the effects to be problematic (see Fig.
 1).
description: species_trees10 species trees used in data simulationLanier&Knowles_supplementaryMaterial2Supplementary online figure demonstrating the robustness of STEM to the presence of recombination in a dataset
DOI: 10.5061/dryad.rb14v
title: Data from: Ecological release lead to novel otogenetic diet shift in kokanee (Oncoryhnchus nerka)

description: We investigate adaptive resource polymorphism in kokanee (Oncorhynchus
 nerka) from Jo-Jo Lake, Alaska by determining whether previously observed
 niche expansion occurs at the population or individual level. Utilizing
 morphological, genetic, and stable isotope techniques, we found no
 evidence of discrete trophic morphotypes as previously described, but
 instead found evidence for an ontogenetic diet shift. Carbon and nitrogen
 isotope data indicate a 40% decrease in the proportion of benthic feeding
 and an increase of 1 trophic position over the size and age ranges of
 adult kokanee, corresponding to a diet shift from consumption of
 macroinvertebrates in smaller individuals to piscivory in larger
 individuals. This novel piscivory in kokanee may result from predatory and
 competitive freedom resulting from the lack of limnetic predators in Jo-Jo
 Lake. Piscivorous feeding despite a phenotype-environment mismatch has
 resulted in large, piscivorous kokanee having up to 70% of their gill
 rakers damaged. Observed reductions in gill raker number relative to the
 putative ancestral population are convergent with expectations for
 piscivorous fishes, despite a presumed lack of standing genetic variation
 for piscivory in the sockeye salmon-kokanee species complex. Jo-Jo Lake
 kokanee are a distinctive example of adaptation in salmonids in response
 to ecological release. This unusual population highlights the importance
 of phenotypic plasticity in response to competition in shaping the
 adaptive landscape and altering evolutionary trajectories.
description: Shedd_et_al_2015_GenepopThis is the Genepop file for "Ecological release lead to novel otogenetic diet shift in kokanee (Oncoryhnchus nerka)". The file contains 482 individuals genotyped at 14 microsatellite loci. The name of each sample includes the putative diet class based on stomach content analysis (Nonpiscivore, Piscivore, and Unknown), the year collected, and the individual identification number(s).Shedd_et_al_2015_StableIsotopeThis file contains carbon and nitrogen stable isotope data for all aquatic samples analyzed in this study. Note that only samples collected in 2011 where analyzed for stable isotopes.Shedd_et_al_2015_StomachContentsThis file contains the % of total weight stomach content data for the 64 kokanee stomachs collected in 2011. Column headings for each diet category are found in the caption for Figure 1.Shedd_et_al_2015_GillRakerThis file contains gill raker data for 161 kokanee.Shedd_et_al_2015_GeometricMorphometricsThis file contains geometric morphometric data on the relative warps for 124 kokanee.
DOI: 10.5061/dryad.8621
title: Data from: Microsatellite loci for dreissenid mussels (Mollusca: Bivalvia: Dreissenidae) and relatives: markers for assessing exotic and native populations

description: We developed and tested 14 new polymorphic microsatellite loci for
 dreissenid mussels, including the two species that have invaded many
 freshwater habitats in Eurasia and North America, where they cause serious
 industrial fouling damage and ecological alterations. These new loci will
 aid our understanding of their genetic patterns in invasive populations as
 well as throughout their native Ponto-Caspian distributions. Eight new
 loci for the zebra mussel Dreissena polymorpha and six for the quagga
 mussel D. rostriformis bugensis were compared with new results from six
 previously published loci to generate a robust molecular toolkit for
 dreissenid mussels and their relatives. Taxa tested include D. polymorpha
 , D. r. bugensis , D. r. grimmi , D. stankovici , the “living fossil”
 Congeria kusceri , and the dark false mussel Mytilopsis leucophaeata (the
 latter also is invasive). Overall, most of the 24 zebra mussel (N=583) and
 13 quagga mussel (N=269) population samples conformed to Hardy-Weinberg
 equilibrium expectations for the new loci following Bonferroni correction.
 The 11 loci (eight new, three previously published) evaluated for D.
 polymorpha averaged 35.1 alleles and 0.72 mean observed heterozygosity per
 locus, and 25.3 and 0.75 for the nine loci (six new, three previously
 published) developed for D. r. bugensis . All but three of these loci
 successfully amplified the other species of Dreissena , and all but one
 also amplified Congeria and Mytilopsis . All species and populations
 tested were significantly divergent using the microsatellite data, with
 neighbor-joining trees reflecting their evolutionary relationships; our
 results reveal broad utility for resolving their biogeographic,
 evolutionary, population, and ecological patterns.
description: Dreissena primer data
 filesThis file contains the
 raw data for the paper, as well as genepop and microchecker input and
 output files. File formats include excel, genepop, and microchecker. This
 is compressed in a .zip file.
DOI: 10.5061/dryad.tm80k
title: Data from: Bias in tree searches and its consequences for measuring group supports

description: When doing a bootstrap analysis with a single tree saved per
 pseudoreplicate, biased search algorithms may influence support values
 more than actual properties of the data set. Two methods commonly used for
 finding phylogenetic trees consist of randomizing the input order of
 species in multiple addition sequences followed by branch swapping, or
 using random trees as the starting point for branch swapping. The
 randomness inherent to such methods is assumed to eliminate any consistent
 preferences for some trees or unsupported groups of taxa, but both methods
 can be significantly biased. In the case of trees created by sequentially
 adding taxa, a bias may occur even if every addition sequence is
 equiprobable, and if one of the equally optimal positions for each
 terminal to add to the tree is selected equiprobably. In the case of
 branch swapping, the bias can happen even when branch swapping
 equiprobably selects any of the trees of better score in the
 SPR-neighborhood or TBR-neighborhood. Consequently, when the data set is
 ambiguous, both random-addition sequences and branch swapping from random
 trees may (a) find some of the optimal trees much more frequently than
 others, and (b) find some groups with a frequency that differs from their
 frequency among all optimal trees. When the data set defines a single
 optimal tree, the groups present in that tree may have a different
 probability of being found by a search, even if supported by equal amounts
 of evidence. This may happen in both parsimony and maximum-likelihood
 analyses, and even in small data sets without incongruence.
description: Supplementary_Material_Search_biasC code and Windows executables, to calculate bias for wagner trees and branch-swapping starting from random trees.