cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j9390
title: Data from: Plant mutualisms with rhizosphere microbiota in introduced versus native ranges

description: The performance of introduced plants can be limited by the availability of
 soil mutualists outside their native range, but how interactions with
 mutualists differ between ranges is largely unknown. If mutualists are
 absent, incompatible or parasitic, plants may compensate by investing more
 in root biomass, adapting to be more selective or by maximizing the
 benefits associated with the mutualists available. We tested these
 hypotheses using seven non-agricultural species of Trifolium naturalized
 in New Zealand (NZ). We grew seeds from two native (Spain, UK) and one
 introduced (NZ) provenance of each species in glasshouse pots inoculated
 with rhizosphere microbiota collected from conspecifics in each region. We
 compared how plant biomass, degree of colonization by rhizobia and
 arbuscular mycorrhizal fungi (AMF), and the growth benefit associated with
 each mutualist differed between provenances (native and introduced
 populations) when grown with soil microbiota from each region. We also
 tested whether the growth benefit of colonization by mutualists was
 correlated with the extent to which alien plants were distributed in the
 introduced range. Rhizobia colonization was generally lower among
 introduced relative to native provenances. In NZ soils, 9% of all plants
 lacked rhizobia and 16% hosted parasitic nodules, whereas in native-range
 soils, there was no evidence of parasitism and all but one plant hosted
 rhizobia. Growth rates as a factor of rhizobia colonization were always
 highest when plants were grown in soil from their home range. Colonization
 by AMF was similar for all provenances in all soils but for four out of
 seven species grown in NZ soils, the level of AMF colonization was
 negatively correlated with growth rate. In general, introduced provenances
 did not compensate for lower growth rates or lower mutualist associations
 by decreasing shoot–root ratios. Synthesis. Despite differences between
 introduced and native provenances in their associations with soil
 mutualists and substantial evidence of parasitism in the introduced range,
 neither level of colonization by mutualists nor the growth benefit
 associated with colonization was correlated with the extent of species’
 distributions in the introduced range, suggesting mutualist associations
 are not predictive of invasion success for these species.
description: Shelby_et_al_Master_08.04.14pShelby_et_al_Mycorrhizae
DOI: 10.5061/dryad.qq877
title: Data from: The phylogenetic relationship of geographically separated “Flectonotus” (Anura: Hemiphractidae), as revealed by molecular, behavioral, and morphological data

description: Phylogenetic analyses of data derived from one mitochondrial gene and one
 nuclear gene show that the five species of small marsupial frogs currently
 recognized as Flectonotus are in fact two distinct and not closely related
 lineages. This conclusion is strongly supported by reproductive behavior
 and morphological characters. Thus, we recognize the genus Fritziana
 Mello-Leitão for the three species in southeastern Brazil and Flectonotus
 Miranda-Ribeiro for the two species in northern South America.
description: Multiple sequence
 alignmentNexus file containing
 multiple sequence alignment for phylogenetic analysis of Flectonotus and
 Fritziana, with character sets defined for mitochondrial 16S ribosomal RNA
 and proopiomelanocortin A (POMC) genes.Flectonotus_combined.nex
DOI: 10.5061/dryad.44ck7
title: Data from: New populations of the black-flanked rock-wallaby (Petrogale lateralis) from the Little Sandy Desert and Murchison, Western Australia

description: During two independent fauna surveys, rock-wallaby (Petrogale) scats were
 recorded from caves located outside the current known Petrogale
 distribution. Scats collected from Desert Queen Baths (Little Sandy
 Desert, Western Australia, 2012), and the Barr Smith Range (Murchison,
 Western Australia, 2015) were genetically analysed and a follow-up motion
 camera survey confirmed an extant rock-wallaby population at Desert Queen
 Baths. The combination of sampling techniques overcame the detection
 difficulties associated with rare and cryptic taxa, and together were
 important in establishing the presence of Petrogale lateralis from regions
 where the species has been poorly documented. At both locations, P.
 lateralis scats were recorded from deep caves situated close to permanent
 water, reflecting the species’ physiological constraints in the arid zone.
 These records represent significant range extensions of a highly
 threatened macropod.
description: MSRun73_DIRW_Control_BoneM5233_16S_UniqueSequencesMSRun73_WF15_01_1_Scat_16S_UniqueSequencesPetrogale_lateralis_16SPetrogale_lateralis_CRPetrogale_lateralis_CytB
DOI: 10.5061/dryad.1cc18
title: Data from: Experience-mediated plasticity in mate preferences: mating assurance in a variable environment

description: An individual’s prior experience of sexual signals can result in variation
 in mate preferences, with important consequences for the course of sexual
 selection. We test two hypotheses about the evolution of
 experience-mediated plasticity in mate preferences: mating assurance and
 mismating avoidance. We exposed female Enchenopa binotata treehoppers
 (Hemiptera: Membracidae) to treatments that varied their experience of
 signal frequency, the most divergent sexual signal trait in the E.
 binotata species complex. Treatments consisted of (1) signals matching the
 preferred frequency, (2-3) signals deviating either 100 Hz above or 100 Hz
 below the preferred frequency, and (4) no signals. Females experiencing
 preferred signals showed the greatest selectivity. However, experience had
 no effect on peak preference. These results support the hypothesis that
 selection has favored plasticity in mate preferences that ensures that
 mating takes place when preferred mates are rare or absent, while at the
 same time ensuring choice of preferred types when those are present. We
 consider how experience-mediated plasticity may influence selection on
 sexual advertisement signals, patterns of reproductive isolation, and the
 maintenance of genetic variation. We suggest that the plasticity we
 describe may increase the likelihood of successful colonization of a novel
 environment, where preferred mating types may be rare.
description: Lentago09indivdataCalculated from the individual response data. Measures of peak preference and selectivity for individual females. Width corresponds to tolerance. Average responsiveness corresponds to responsiveness. Coeff of variation squared refers to the strength of preference.Ptelea09indivdataLentPlast09responsedataxlsRaw response data collected in the lab. Female ID refers to the individual within treatment. Stimulus freq refers to the frequency of the stimulus. # responses refers to the number of times the female responded to a given stimulus frequency.ptelea09responsedataRaw response data collected in the lab. Female ID refers to the individual within treatment. Stimulus freq refers to the frequency of the stimulus. # responses refers to the number of times the female responded to a given stimulus frequency.
DOI: 10.5061/dryad.n4vp0
title: Data from: Bridging inter- and intraspecific trait evolution with a hierarchical Bayesian approach

description: The evolution of organisms is crucially dependent on the evolution of
 intraspecific variation. Its interactions with selective agents in the
 biotic and abiotic environments underlie many processes, such as
 intraspecific competition, resource partitioning and, eventually, species
 formation. Nevertheless, comparative models of trait evolution neither
 allow explicit testing of hypotheses related to the evolution of
 intraspecific variation nor do they simultaneously estimate rates of trait
 evolution by accounting for both trait mean and variance. Here, we present
 a model of phenotypic trait evolution using a hierarchical Bayesian
 approach that simultaneously incorporates interspecific and intraspecific
 variation. We assume that species-specific trait means evolve under a
 simple Brownian motion process, whereas species-specific trait variances
 are modeled with Brownian or Ornstein–Uhlenbeck processes. After
 evaluating the power of the method through simulations, we examine whether
 life-history traits impact evolution of intraspecific variation in the
 Eriogonoideae (buckwheat family, Polygonaceae). Our model is readily
 extendible to more complex scenarios of the evolution of inter- and
 intraspecific variation and presents a step toward more comprehensive
 comparative models for macroevolutionary studies.
description: Source code for the JIVE
 modelSet of R scripts to run
 the JIVE model described in the Kostikova et al
 manuscript.JIVE_source_code.zip
DOI: 10.5061/dryad.1c2d3
title: Data from: Friends and Family: a software program for identification of unrelated individuals from molecular marker data. And from: Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa

description: The identification of related and unrelated individuals from molecular
 marker data is often difficult, particularly when no pedigree information
 is available and the data set is large. High levels of relatedness or
 inbreeding can influence genotype frequencies and thus genetic marker
 evaluation, as well as the accurate inference of hidden genetic structure.
 Identification of related and unrelated individuals is also important in
 breeding programmes, to inform decisions about breeding pairs and
 translocations. We present Friends and Family, a Windows executable
 program with a graphical user interface that identifies unrelated
 individuals from a pairwise relatedness matrix or table generated in
 programs such as COANCESTRY and GenAlEx. Friends and Family outputs a list
 of samples that are all unrelated to each other, based on a user-defined
 relatedness cut-off value. This unrelated data set can be used in
 downstream analyses, such as marker evaluation or inference of genetic
 structure. The results can be compared to that of the full data set to
 determine the effect related individuals have on the analyses. We
 demonstrate one of the applications of the program: how the removal of
 related individuals altered the Hardy-Weinberg equilibrium test outcome
 for microsatellite markers in an empirical data set. Friends and Family
 can be obtained from https://github.com/DeondeJager/Friends-and-Family.
description: Friends&Family_genotypedata Friends&Family_genotypedata.csv Microsatellite genotype data of Cape buffalo (Syncerus caffer caffer) that was used in the analyses of the manuscript "Friends and Family: A software program for identification of unrelated individuals from molecular marker data".     <strong>Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa - Genotype data - PLOS ONE</strong>   PLOSONE_Buffalo_MicrosatelliteGenotypes_deJager_etal.csv Another file has been added to this dataset that includes the same microsatellite genotype data that was used in the PLOS ONE manuscript (title above). The only difference between this data set and the one used in the Friends and Family manuscript is that the population and sample names of the samples from national parks have been de-anonymozied in this dataset, so that it is possible to repeat the analyses in the PLOS ONE manuscript by knowing the exact origin of the national park samples.
DOI: 10.5061/dryad.hg7p0
title: Data from: No energetic benefits from sociality in tropical hibernation

description: Mammals generally profit from social thermoregulation, and the primary
 benefit of sociality during hibernation is thought to be the reduction of
 metabolic demands during periodic arousals. It has even been postulated
 that the energetic advantages during hibernation might have been the
 driver for the evolution of sociality in some mammal species. As the
 necessity to show arousals and the concurring energetic costs depend on
 the temperature regime in the hibernacula, we tested whether this is also
 a plausible scenario in tropical hibernators such as the Malagasy lemur
 Cheirogaleus medius, with comparatively high and often fluctuating
 temperature regimes in their hibernacula. To this end, we studied group
 composition and energy budgets (skin temperature patterns, metabolic rate)
 over three hibernation and activity seasons in a total of 53 free-ranging
 C. medius. Our results show that C. medius mostly occupied tree hollows
 solitarily during hibernation, contrary to the active season, and that the
 energetic savings were comparable for individuals hibernating socially in
 groups or solitarily (both about 74% compared to the resting metabolic
 rate of the active season). However, in larger groups hibernation patterns
 were less regular and synchronized and individual torpor-arousal cycles
 were more frequently interrupted by euthermic group members than in
 individuals hibernating solitarily or in pairs. We conclude that sociality
 during hibernation is not necessarily driven by energetic demands, and
 might even be energetically disadvantageous in tropical species (at least
 in larger groups). Other factors, like social coherence or ecological and
 behavioural constraints, may be of greater influence for the evolution of
 sociality under tropical conditions.
description: Analysis_Tb VO2
 DEEAnalysis of differences
 in body temperature and energy expenditure between solitarily and socially
 hibernating Cheirogaleus medius.arousal_frequency_allAnalysis of frequency of arousals of all analysed hibernating Cheirogaleus medius.arousal_frequency_socialAnalysis of frequency of arousals during hibernation in socially hibernating Cheirogaleus medius.group sizesGroup sizes of Cheirogaleus medius during hibernation.pair cohesivenessAnalysis on how often social pairs spend the daily resting phase or hibernation days together or in separate tree hollows.
DOI: 10.5061/dryad.6bt92
title: Data from: A unified anatomy ontology of the vertebrate skeletal system

description: The skeleton is of fundamental importance in research in comparative
 vertebrate morphology, paleontology, biomechanics, developmental biology,
 and systematics. Motivated by research questions that require
 computational access to and comparative reasoning across the diverse
 skeletal phenotypes of vertebrates, we developed a module of anatomical
 concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology
 (VSAO), to accommodate and unify the existing skeletal terminologies for
 the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies
 (teleost, amphibian) vertebrate anatomy ontologies. Previous differences
 between these terminologies prevented even simple queries across databases
 pertaining to vertebrate morphology. This module of upper-level and
 specific skeletal terms currently includes 223 defined terms and 179
 synonyms that integrate skeletal cells, tissues, biological processes,
 organs (skeletal elements such as bones and cartilages), and subdivisions
 of the skeletal system. The VSAO is designed to integrate with other
 ontologies, including the Common Anatomy Reference Ontology (CARO), Gene
 Ontology (GO), Uberon, and Cell Ontology (CL) and is freely available to
 the community to be updated with additional terms required for research.
 Its structure accommodates anatomical variation among vertebrate species
 in development, structure, and composition. Annotation of diverse
 vertebrate phenotypes with this ontology will enable novel inquiries
 across the full spectrum of phenotypic diversity.
description: VSAO Workshop Version
 (OBO format)This data file contains
 the workshop version of the Vertebrate Skeletal Anatomy Ontology described
 in Dahdul et al. (2012). It is a text file in OBO format
 (http://www.geneontology.org/GO.format.obo-1_2.shtml).VSAO-workshop.oboVSAO Revision 2012-11-6 (OBO format)This data file contains the version (2012-11-6) of the Vertebrate Skeletal Anatomy Ontology described in Dahdul et al. (2012). It is a text file in OBO format (http://www.geneontology.org/GO.format.obo-1_2.shtml).vsao.rev.2012-11-06.obo
DOI: 10.5061/dryad.dd64hf3
title: Data from: Sex-specific effects of outbreeding on offspring quality in pike (Esox lucius)

description: Intraspecific genetic admixture occurs when previously separated
 populations within a species start interbreeding, and it can have either
 positive, negative or netural effects on reproductive performance. There
 is currently little knowledge regarding what determines the outcome of
 admixture. We tested for effects of admixture on offspring quality in
 three subpopulations of pike (Esox lucius). Gametes were collected in the
 field, and eggs from each female were experimentally fertilized with milt
 from a male from each population (one ‘pure’ and two ‘admixed’
 treatments). Three offspring quality measures (hatching success, fry
 survival, and fry length) were determined and compared between (i) pure
 and admixed population combinations, and (ii) the sex-specific treatments
 within each admixed population combination (based on the origin of the
 male and female respectively). The results revealed that although there
 were no overall effects of admixture on offspring quality, the
 consequences for a given population combination could be sex-specific and
 thus differ depending on which of the parents originated from one or the
 other population. All offspring quality traits were influenced by both
 maternal ID and paternal ID. Sex- and individual-specific effects can have
 implications for dispersal behavior and gene flow between natural
 populations, and are important to consider in conservation efforts.
description: offspring.xlsxData obtained from a common garden admixture experiment with three subpopulations of anadromous pike (Esox lucius) from the Baltic Sea. In the experiment, gametes were stripped from ripe individuals from each of the three populations, and artificial fertilization utilized to create all possible pairwise population combinations (three pure and six admixed treatments). Three offspring quality traits was quantified (hatching success, fry survival, and fry length). Data on two out of the three offspring quality traits (hatching success and fry survival) is presented in this data file, and data on individual fry lengths can be found in the ‘fry.xlsx’ data file.180814_Admixture_unitinfo_Dryad.xlsxfry.xlsxData obtained from a common garden admixture experiment with three subpopulations of anadromous pike (Esox lucius) from the Baltic Sea. In the experiment, gametes were stripped from ripe individuals from each of the three populations, and artificial fertilization utilized to create all possible pairwise population combinations (three pure and six admixed treatments). Three offspring quality traits was quantified (hatching success, fry survival, and fry length). Data on individual fry lengths is presented in this data file, and data on the other two offspring quality traits (hatching success and fry survival) can be found in the ‘offspring.xlsx’ data file.180814_Admixture_lengths_Dryad.xlsx
DOI: 10.5061/dryad.619gd
title: Data from: Allometric scaling of long-distance seed dispersal by migratory birds

description: Migratory birds are often suggested to be important vectors for
 long-distance dispersal (LDD) of plant and animal propagules. The scale of
 such dispersal events (hundreds to thousands of kilometers) can influence
 landscape-level biological processes and species distributions. However,
 the few vector species studied and the lack of proper integration of their
 migratory movement in models of LDD has precluded the study of their
 potential as long-distance biotic dispersers. By means of a mechanistic
 model parameterized with empirical data, we first investigated the
 properties of seed dispersal curves generated by migratory birds and then
 analyzed the effect of bird size on model parameters and consequent seed
 dispersal patterns. Seed dispersal curves showed in most cases large and
 heavy tails, resulting in relatively frequent LDD (up to 3.5% of dispersal
 distances longer than 100 km). Bird size mediated trade-offs between bird
 movement and seed retention time that, in turn, determined seed dispersal
 patterns and the potential of each bird species as an LDD vector. Our
 modeling framework builds on a mechanistic understanding of seed dispersal
 by migratory birds and may thus be a useful tool to estimate the scale and
 frequency of bird-mediated, large-scale transport of native, invasive, and
 pathogenic organisms.
description: Banding_data_AmNat53974GRT_data_AmNat53974
DOI: 10.5061/dryad.cj910
title: Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria

description: Parasitism creates selection for resistance mechanisms in host populations
 and is hypothesized to promote increased host evolvability. However, the
 influence of these traits on host evolution when parasites are no longer
 present is unclear. We used experimental evolution and whole-genome
 sequencing of Escherichia coli to determine the effects of past and
 present exposure to parasitic viruses (phages) on the spread of mutator
 alleles, resistance and bacterial competitive fitness. We found that
 mutator alleles spread rapidly during adaptation to any of four different
 phage species, and this pattern was even more pronounced with multiple
 phages present simultaneously. However, hypermutability did not detectably
 accelerate adaptation in the absence of phages and recovery of fitness
 costs associated with resistance. Several lineages evolved phage
 resistance through elevated mucoidy, and during subsequent evolution in
 phage-free conditions they rapidly reverted to non-mucoid,
 phage-susceptible phenotypes. Genome sequencing revealed that this
 phenotypic reversion was achieved by additional genetic changes rather
 than by genotypic reversion of the initial resistance mutations. Insertion
 sequence (IS) elements played a key role in both the acquisition of
 resistance and adaptation in the absence of parasites; unlike single
 nucleotide polymorphisms (SNPs), IS insertions were not more frequent in
 mutator lineages. Our results provide a genetic explanation for rapid
 reversion of mucoidy, a phenotype observed in other bacterial species
 including human pathogens. Moreover, this demonstrates that the types of
 genetic change underlying adaptation to fitness costs, and consequently
 the impact of evolvability mechanisms such as increased point-mutation
 rates, depend critically on the mechanism of resistance.
description: Dryad
 entryIncludes phenotypic data
 files and genomic variant calls, plus a Readme.txt file with
 explanations