cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m5f7b44
title: Data from: Kin discrimination and outer membrane exchange in Myxococcus xanthus: a comparative analysis among natural isolates

description: Genetically similar cells of the soil bacterium Myxococcus xanthus
 cooperate at multiple social behaviours, including motility and
 multicellular development. Another social interaction in this species is
 outer-membrane exchange (OME), a behaviour of unknown primary benefit in
 which cells displaying closely related variants of the outer-membrane
 protein TraA transiently fuse and exchange membrane contents. Functionally
 incompatible TraA variants do not mediate OME, which led to the proposal
 that TraA incompatibilities determine patterns of intercellular
 cooperation in nature, but how this might occur remains unclear. Using
 natural isolates from a centimetre-scale patch of soil, we analyse
 patterns of TraA diversity and ask whether relatedness at TraA is causally
 related to patterns of kin discrimination in the form of both
 colony-merger incompatibilities (CMIs) and inter-strain antagonisms. A
 large proportion of predicted TraA functional diversity documented among
 global isolates is contained within the cm-scale population. We find
 evidence of balancing selection on the PA14-portion of TraA and extensive
 transfer of traA alleles across genomic backgrounds. CMIs are shown to be
 common among strains identical at TraA, suggesting that CMI kin
 discrimination is not generally caused by TraA dissimilarity. Finally, it
 has been proposed that inter-strain antagonisms might be caused by
 OME-mediated toxin transfer. However, we find that most strain pairs
 exhibiting strong antagonisms are predicted to be incapable of OME due to
 TraA dissimilarity. Overall, our results suggest that documented patterns
 of kin discrimination in a defined natural population of M. xanthus are
 not causally related to the degree of TraA relatedness among interactants.
description: Data from: Variation in
 the outer-membrane exchange protein TraA does not explain patterns of
 inter-colony kin discrimination among local natural strains of Myxococcus
 xanthusMOLECOL-WIELGOSS-DRYAD-updated.zip
DOI: 10.5061/dryad.9nq2kc4
title: Data from: Novel acridine-based thiosemicarbazones as “turn-on” chemosensors for selective recognition of fluoride anion: a spectroscopic and theoretical study

description: New thiosemicarbazide linked acridines 3a-c were prepared and investigated
 as chemosensors for the detection of biologically and environmentally
 important anions. The compounds 3a-c were found selective for fluoride
 (Fˉ) with no affinity for other anions i.e. ˉOAc, Brˉ, Iˉ, HSO4ˉ, SO4ˉ2,
 PO4ˉ3, ClO3ˉ, ClO4ˉ, CNˉ, and SCNˉ. Further, upon the gradual addition of
 fluoride anion (Fˉ) source (TBAF), a well-defined change in color of
 solution of probes 3a-c was observed. The anion sensing process was
 studied in detailed via UV-Vis absorption, fluorescence and 1H NMR
 experiments. Moreover, during the synthesis of acridine probes 3a-c nickel
 fluoride (NiF2), a rarely explored transition metal fluoride salt was used
 as catalyst. Theoretical studies via density functional theory (DFT) were
 also carried out to further investigate the sensing and anion (Fˉ)
 selectivity pattern of these probes.
description: NMR
 dataNMR data can be viewed
 in Bruker TopSpin SoftwareRSOS_ESM.rar
DOI: 10.5061/dryad.tg35c95
title: Data from: Phylogenetic analysis and a review of the history of the accidental phytoplankter, Phaeodactylum tricornutum Bohlin (Bacillariophyta)

description: The diatom Phaeodactylum tricornutum has been used as a model for cell
 biologists and ecologists for over a century. We have incorporated several
 new raphid pennates into a three gene phylogenetic dataset (SSU, rbcL,
 psbC), and recover Gomphonemopsis sp. as sister to P. tricornutum with
 100% BS support. This is the first time a close relative has been
 identified for P. tricornutum with robust statistical support. We test and
 reject a succession of hypotheses for other relatives. Our molecular data
 are statistically significantly incongruent with placement of either or
 both species among the Cymbellales, an order of diatoms with which both
 have been associated. We believe that further resolution of the
 phylogenetic position of P. tricornutum will rely more on increased taxon
 sampling than increased genetic sampling. Gomphonemopsis is a benthic
 diatom, and its phylogenetic relationship with P. tricornutum is congruent
 with the hypothesis that P. tricornutum is a benthic diatom with specific
 adaptations that lead to active recruitment into the plankton. We
 hypothesize that other benthic diatoms are likely to have similar
 adaptations and are not merely passively recruited into the plankton.
description: Phaeodactylum.actualAligned data matrix including Phaeodactylum and the closely related Gomphonemopsis. Nuclear SSU columns 1-1527, plastid rbcL 1528-2877, plastid psbC 2878-3926.
DOI: 10.5061/dryad.142jn5t
title: Data from: Evolution of morphological integration in the skull of Carnivora (Mammalia): changes in Canidae lead to increased evolutionary potential of facial traits

description: Morphological integration refers to the fact that different phenotypic
 traits of organisms are not fully independent from each other, and tend to
 covary to different degrees. The covariation among traits is thought to
 reflect properties of the species' genetic architecture and thus can
 have an impact on evolutionary responses. Furthermore, if morphological
 integration changes along the history of a group, inferences of past
 selection regimes might be problematic. Here we evaluated the stability
 and evolution of the morphological integration of skull traits in
 Carnivora by using evolutionary simulations and phylogenetic comparative
 methods. Our results show that carnivoran species are able to respond to
 natural selection in a very similar way. Our comparative analyses show
 that the phylogenetic signal for pattern of integration is lower than that
 observed for morphology (trait averages), and that integration was stable
 throughout the evolution of the group. That notwithstanding, Canidae
 differed from other families by having higher integration, evolvability,
 flexibility and allometric coefficients on the facial region. These
 changes might have allowed canids to rapidly adapt to different food
 sources, helping to explain not only the phenotypic diversification of the
 family, but also why humans were able to generate such a great diversity
 of dog breeds through artificial selection.
description: Phenotypic
 covariancesIndividual species
 phenotypic covariance matrices. Zip file containing 145 CSV
 format-tables.Supplementary_Data_A_Ps.zipAlign cytochrome b sequencesAlign cytochrome b sequences used to estimate branch-lengths.Supplementary_Data_B_cytb.fastaPhylogenetic hypothesis for CarnivoraCarnivora Cladogram used in analyses. Three in Newick format with no branch-lengths.Supplementary_Data_C_tree.txtLDA scores for CarnivoraLinear Discriminant Scores for the averages phenotypes for each taxa. LDA scores were used to calculate mahalanobis distances and were used as input in comparative analyses.Supplementary_Data_D_LDAscores.csvRandom Skewers TableFull Random Skewers table of pairwise comparisons.Values below the diagonal are observed values and the ones above the diagonal are corrected values. The diagonal contain the matrix repeatabilities.Supplementary_Data_E_RS_tab.xlsx
DOI: 10.5061/dryad.550mc88
title: Data from: The bacterium Pseudomonas aeruginosa senses and gradually responds to inter-specific competition for iron

description: Phenotypic plasticity in response to competition is a well-described
 phenomenon in higher organisms. Here, we show that also bacteria have the
 ability to sense the presence of competitors and mount fine-tuned
 responses to match prevailing levels of competition. In our experiments,
 we studied inter-specific competition for iron between the bacterium
 Pseudomonas aeruginosa (PA) and its competitor Burkholderia cenocepacia
 (BC). We focused on the ability of PA to phenotypically adjust the
 production of pyoverdine, an iron-scavenging siderophore. We found that PA
 up-regulates pyoverdine production early on during competition under
 condition of low iron availability. This plastic upregulation was
 fine-tuned in response to the level of competition imposed by BC, and
 seems to confer a relative fitness benefit to PA in the form of an earlier
 initiation of growth. At later time points, however, PA showed reduced
 growth in mixed compared to monoculture, suggesting that competitive
 responses are costly. Altogether, our results demonstrate that phenotypic
 plasticity in siderophore production plays an important role in
 inter-specific competition for iron. Upregulating siderophore production
 may be a powerful strategy to lock iron away from competing species, and
 to reserve this nutrient for strain members possessing the compatible
 receptor for uptake.
description: Leinweber_etal_Evolution_2018_rawdataThis file contains all the raw data used in Leinweber et al. (2018) The bacterium Pseudomonas aeruginosa senses and gradually responds to inter-specific competition for iron. Evolution. DOI: 10.1111/evo.13491. Please consult sheet 1 for an overview and description of the individual data sets.
DOI: 10.5061/dryad.np7332q
title: Data from: Incomplete lineage sorting impacts the inference of macroevolutionary regimes from molecular phylogenies when concatenation is employed: an analysis based on Cetacea

description: Interest in methods that estimate speciation and extinction rates from
 molecular phylogenies has increased over the last decade. The application
 of such methods requires reliable estimates of tree topology and node
 ages, which are frequently obtained using standard phylogenetic inference
 combining concatenated loci and molecular dating. However, this practice
 disregards population-level processes that generate gene tree/species tree
 discordance. We evaluated the impact of employing concatenation and
 coalescent-based phylogeny inference in recovering the correct
 macroevolutionary regime using simulated data based on the
 well-established diversification rate shift of delphinids in Cetacea. We
 found that under scenarios of strong incomplete lineage sorting,
 macroevolutionary analysis of phylogenies inferred by concatenating loci
 failed to recover the delphinid diversification shift, while the
 coalescent-based tree consistently retrieved the correct rate regime. We
 suggest that ignoring microevolutionary processes reduces the power of
 methods that estimate macroevolutionary regimes from molecular data.
description: Simulation
 dataDirectories contain the
 analyses results for replicates in each effective population size
 (Ne).dryad.zip
DOI: 10.5061/dryad.qm01v75
title: Data from: Dietary challenges differentially affect activity and sleep/wake behavior in mus musculus: isolating independent associations with diet/energy balance and body weight

description: Background and Aims: Associated with numerous metabolic and behavioral
 abnormalities, obesity is classified by metrics reliant on body weight
 (such as body mass index). However, overnutrition is the common cause of
 obesity, and may independently contribute to these obesity-related
 abnormalities. Here, we use dietary challenges to parse apart the relative
 influence of diet and/or energy balance from body weight on various
 metabolic and behavioral outcomes. Materials and Methods: Seventy male
 mice (mus musculus) were subjected to the diet switch feeding paradigm,
 generating groups with various body weights and energetic imbalances.
 Spontaneous activity patterns, blood metabolite levels, and unbiased gene
 expression of the nutrient-sensing ventral hypothalamus (using
 RNA-sequencing) were measured, and these metrics were compared using
 standardized multivariate linear regression models. Results: Spontaneous
 activity patterns were negatively related to body weight (p&lt;0.0001)
 but not diet/energy balance (p=0.63). Both body weight and diet/energy
 balance predicted circulating glucose and insulin levels, while body
 weight alone predicted plasma leptin levels. Regarding gene expression
 within the ventral hypothalamus, only two genes responded to diet/energy
 balance (neuropeptide y [npy] and agouti-related peptide [agrp]), while
 others were related only to body weight. Conclusions: Collectively, these
 results demonstrate that individual components of obesity—specifically
 obesogenic diets/energy imbalance and elevated body mass—can have
 independent effects on metabolic and behavioral outcomes. This work
 highlights the shortcomings of using body mass-based indices to assess
 metabolic health, and identifies novel associations between blood
 biomarkers, neural gene expression, and animal behavior following dietary
 challenges.
description: PerronIJ_PLOS_RawDataZip file containing 6 files and 2 folders (with 4 files and 9 files).
DOI: 10.5061/dryad.2v160c9
title: Data from: A spatial genetics approach to inform vector control of tsetse flies (Glossina fuscipes fuscipes) in Northern Uganda

description: Tsetse flies (genus Glossina) are the only vector for the parasitic
 trypanosomes responsible for sleeping sickness and nagana across
 sub-Saharan Africa. In Uganda, the tsetse fly Glossina fuscipes fuscipes
 is responsible for transmission of the parasite in 90% of sleeping
 sickness cases, and co-occurrence of both forms of human-infective
 trypanosomes makes vector control a priority. We use population genetic
 data from 38 samples from northern Uganda in a novel methodological
 pipeline that integrates genetic data, remotely sensed environmental data,
 and hundreds of field-survey observations. This methodological pipeline
 identifies isolated habitat by first identifying environmental parameters
 correlated with genetic differentiation, second, predicting spatial
 connectivity using field-survey observations and the most predictive
 environmental parameter(s), and third, overlaying the connectivity surface
 onto a habitat suitability map. Results from this pipeline indicated that
 net photosynthesis was the strongest predictor of genetic differentiation
 in G. f. fuscipes in northern Uganda. The resulting connectivity surface
 identified a large area of well-connected habitat in northwestern Uganda,
 and twenty-four isolated patches on the northeastern margin of the G. f.
 fuscipes distribution. We tested this novel methodological pipeline by
 completing an ad hoc sample and genetic screen of G. f. fuscipes samples
 from a model-predicted isolated patch, and evaluated whether the ad hoc
 sample was in fact as genetically isolated as predicted. Results indicated
 that genetic isolation of the ad hoc sample was as genetically isolated as
 predicted, with differentiation well above estimates made in samples from
 within well-connected habitat separated by similar geographic distances.
 This work has important practical implications for the control of tsetse
 and other disease vectors, because it provides a way to identify isolated
 populations where it will be safer and easier to implement vector control
 and that should be prioritized as study sites during the development and
 improvement of vector control methods.
description: Saarmanetal2018_Gff_RasterLayersThis is a zipped folder that contains the connectivity surface and final habitat suitability map in "ascii" raster/ArcGIS format, as well as an R script (see README file) that displays an example of how to load and visualize the included raster files.
DOI: 10.5061/dryad.1j5h875
title: Data from: Journeys through discrete-character morphospace: synthesising phylogeny, tempo, and disparity

description: Palaeontologists have long employed discrete categorical data to capture
 morphological variation in fossil species, using the resulting
 character-taxon matrices to measure evolutionary tempo, infer phylogenies,
 and capture morphological disparity. However, to date these have been seen
 as separate approaches despite a common goal of understanding
 morphological evolution over deep time. Here I argue that there are clear
 advantages to considering these three lines of enquiry in a single space:
 the phylomorphospace. Conceptually these high-dimensional spaces capture
 how a phylogenetic tree explores morphospace and allow us to consider
 important process questions around evolutionary rates, constraints,
 convergence, and directional trends. Currently the literature contains
 fundamentally different approaches used to generate such spaces, with no
 direct comparison between them despite the differing evolutionary
 histories they imply. Here I directly compare five different
 phylomorphospace approaches, three with direct literature equivalents and
 two that are novel. I use a single empirical case study of coelurosaurian
 theropod dinosaurs (152 taxa, 853 characters) to show that under many
 analyses the literature-derived approaches tend to reflect introduced
 phylogenetic – rather than the intended morphological – signal. The two
 novel approaches, which produce limited ancestral state estimates prior to
 ordination, are able to minimise this phylogenetic signal and thus exhibit
 more realistic amounts of phylogenetic signal, rate heterogeneity, and
 convergent evolution. Palaeontologists are interested in the diversity and
 tempo of evolutionary change along the branches of the tree of life, but
 these are typically treated as separate numerical analyses. Here I argue
 for a statistical technique that allows us to treat these aspects of
 evolution simultaneously, allowing a more complete understanding of how
 evolution has explored the possibilities of physical form. Specifically, I
 compare five different approaches, two novel to this study, showing that
 the three pre-existing approaches may contain biases that stem from a
 different signal (evolutionary relationships) than we intend to capture
 (the exploration of physical form).
description: CodeAndDataZip files containing all R code and data used.
DOI: 10.5061/dryad.b323d8m
title: Data from: Genetic diversity of melon aphids Aphis gossypii associated with landscape features

description: Despite increasing evidence that landscape features strongly influence the
 abundance and dispersal of insect populations, landscape composition has
 seldom been explicitly linked to genetic structure. We conducted a genetic
 study of the melon aphid, Aphis gossypii, in two counties of Beijing,
 China during spring migration using samples from watermelon. We performed
 aphid genetic analysis using restriction-site-associated DNA-sequencing
 (2b-RAD) and investigated the relationship between land cover and the
 genetic diversity. The percentage area of land cover (cropland, vegetable,
 orchard, grassland, woodland) was quantified in each particular scale
 (ranging from 0.5 km to 3 km) and was used as a predictor variable in our
 generalized linear models. We found a moderate level of genetic
 differentiation among 9 sampled populations. Geographic distance and
 genetic distance were not significantly associated, indicating that
 geographic location was not a barrier to migration. These 9 populations
 could be clustered depending on their level of genetic diversity (high and
 low). The genetic diversity (Shannon’s information index) was positively
 correlated with grassland at the spatial scales of 1 and 2 km and
 negatively with orchard and vegetable at 0.5 and 1 km. Genetic diversity
 was best predicted by the grassland + orchard + vegetable model at a
 spatial scale of 1 km. Based on the method of relative weights, orchard
 land had the greatest relative importance, followed by grassland and
 vegetable land, in that order. This study contributes to our understanding
 of the genetic variation of aphids in agricultural landscapes.
description: SNP genotypes of Aphis
 gossypii from nine locations in BeijingThe file refers to the
 result of genotyping. A total of 90 aphids were genotyped for SNP loci.
 2b-RAD sequencing and genotyping was outsourced to Shanghai OE Biotech Ltd
 (Shanghai, China). SNPs were determined and genotypes were called using a
 maximum-likelihood statistical model implemented in software Stacks v1.32
 (Catchen et al. 2011).OE2015H1099-SNP-genotypes.xlsxSNP data of Aphis gossypii in GenALEx formatSNP data in GenALEx format. The SNP loci have been selected by setting the coverage at 95% in MEGA 7. The results analyzed by GenALEx are also shown in this file.cover95Alloneline.xlsxGenotype of Aphis gossypiiMEGA format file for selecting SNP loci and further analysis of genetic diversity of Aphis gossypii.Genotype of melon aphids.mdsx
DOI: 10.5061/dryad.s114355
title: Data from: Vitellogenin-like A–associated shifts in social cue responsiveness regulate behavioral task specialization in an ant

description: Division of labor and task specialization explain the success of human and
 insect societies. Social insect colonies are characterized by division of
 labor with workers specializing on brood care early and foraging later in
 life. Theory posits that this task switching requires shifts in
 responsiveness to task-related cues, yet experimental evidence is weak.
 Here we show that a Vitellogenin (Vg) ortholog identified in a RNAseq
 study on the ant Temnothorax longispinosus is involved in this process:
 Using phylogenetic analyses of Vg and Vg-like genes, we firstly show that
 this candidate gene does not cluster with the intensively studied honey
 bee Vg, but falls into a separate Vg-like A cluster. Secondly, an
 experimental knockdown of Vg-like A in the fat body caused a reduction in
 brood care and an increase in nestmate care in young ant workers. Nestmate
 care is normally exhibited by older workers. We demonstrate experimentally
 that this task switch is at least partly based on Vg-like-A-associated
 shifts in responsiveness from brood to worker cues. We thus reveal a novel
 mechanism leading to early behavioral maturation via changes in social cue
 responsiveness mediated by Vg-like A and associated pathways, which
 proximately play a role in regulating division of labor.
description: Data from: Kohlmeier et
 al. Age polyethism experimentThe datafile contains
 raw data of the age polyethism experiment in which we manipulated age
 structure of colonies.Age polyethism experiment raw
 data.txtLongterm knock down raw
 dataThis datafile contains
 the raw data of the behavioral observations after a longterm knockdown of
 Vg-like APreference test raw
 dataRaw data of the
 experiment in which the responsiveness of young and old workers to brood
 and adult worker CHC's was testedPreference_test.txtShortterm knock down raw dataThis data file contains the raw data of the behavioral observations after a shortterm knockdown of Vg-like ALight dark testRaw data of the light/dark testBroodcare test raw dataThis data file contains the raw data of the individualized brood care test to disentangle the effects of worker and larva treatmentBroodcare test.txtOvary measurementsThis data file contains the ovary measurements of queens and brood carersOvaries.txtqPCR raw dataThis data file contain all qPCR raw dataAlignmentAlignment of all Vg and Vg-like sequences used to contruct phylogenetic treeFINAL ALIGNMENT.clustalVg_Vg-like_sequencesFasta file containing all sequnces used to contruct phylogenetic treeCHC_analysisThis datafile contains the results of the CHC analysis of brood carers and foragers from Vg-like A knockdown or control colonies