cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g1t69
title: Data from: Tradeoffs, spatial heterogeneity, and the maintenance of microbial diversity

description: Specialization and concomitant tradeoffs are assumed to underlie the
 non-neutral coexistence of lineages. Tradeoffs across heterogeneous
 environments can promote diversity by preventing competitive exclusion.
 However, the importance of tradeoffs in maintaining diversity in natural
 microbial assemblages is unclear, as tradeoffs are frequently not detected
 in artificial evolution experiments. Stressful conditions associated with
 patches of heavy-metal enriched serpentine soils provide excellent
 opportunities for examining how heterogeneity may foster genetic
 diversity. Using a spatially-replicated design, we demonstrate that
 rhizobium bacteria symbiotic with legumes inhabiting contrasting
 serpentine and non-serpentine soils exhibit a tradeoff between a
 genotype’s nickel tolerance and its ability to replicate rapidly.
 Furthermore, we detected adaptive divergence in rhizobial assemblages
 across soil type heterogeneity at multiple sites, suggesting that this
 tradeoff may promote the coexistence of phenotypically distinct bacterial
 lineages. Tradeoffs and adaptive divergence may be important factors
 maintaining the tremendous diversity within natural assemblages of
 bacteria.
description: TableS2Collection information, fitness, Genbank Accession, and closest 16S match in Genbank for each rhizobium isolate (.xls format in Microsoft Excel)
DOI: 10.5061/dryad.s587t
title: Data from: Cats in the forest: predicting habitat adaptations from humerus morphometry in extant and fossil Felidae (Carnivora)

description: Mammalian carnivores are rarely incorporated in paleoenvironmental
 reconstructions, largely because of their rarity within the fossil record.
 However, multivariate statistical modeling can be successfully used to
 quantify specific anatomical features as environmental predictors. Here we
 explore morphological variability of the humerus in a closely related
 group of predators (Felidae) to investigate the relationship between
 morphometric descriptors and habitat categories. We analyze linear
 measurements of the humerus in three different morphometric combinations
 (log-transformed, size-free, and ratio), and explore four distinct ways of
 categorizing habitat adaptations. Open, Mixed, and Closed categories are
 defined according to criteria based on traditional descriptions of
 species, distributions, and biome occupancy. Extensive exploratory work is
 presented using linear discriminant analyses and several fossils are
 included to provide paleoecological reconstructions. We found no
 significant differences in the predictive power of distinct morphometric
 descriptors or habitat criteria, although sample splitting into small and
 large cat guilds greatly improves the stability of the models. Significant
 insights emerge for three long-canine cats: Smilodon populator,
 Paramachairodus orientalis, and Dinofelis sp. from Olduvai Gorge (East
 Africa). S. populator and P. orientalis are both predicted to have been
 closed-habitat adapted taxa. The false “sabertooth” Dinofelis sp. from
 Olduvai Gorge is predicted to be adapted to mixed habitat. The application
 of felid humerus ecomorphology to the carnivoran record of Olduvai Gorge
 shows that the older stratigraphic levels (Bed I, 1.99–1.79 Ma) included a
 broader range of environments than Beds II or V, where there is an
 abundance of cats adapted to open environments.
description: Meloro_etal_Paleobiology_Supplementary_R2
DOI: 10.5061/dryad.tg20p4k
title: Data from: Variations in ramet performance and the dynamics of an alpine evergreen herb, Gentiana nipponica, in different snowmelt conditions

description: Premise of the study: Variation in demographic parameters reflects the
 life-history strategies of plants in response to specific environments. We
 aimed to investigate the intraspecific variation in life-history traits of
 a clonal alpine herb, Gentiana nipponica, in various snowmelt conditions.
 Methods: Individual ramets within genets accumulate leaves for 7-9 years
 without shedding, and die after reproduction. We tested the physiological
 function of accumulated leaves for reproduction and monitored the ramet
 demography in early, intermediate, and late snowmelt populations over 3
 years. Then, we simulated ramet dynamics using the demographic parameters.
 Key results: Old leaves had a carbon storage function, and the initiation
 of reproduction depended on the amount of ramet leaves. Growth and
 reproductive performance were highest in the population with an
 intermediate snowmelt period. The early snowmelt population showed short
 persistence periods due to restricted growth and high mortality of the
 ramets. The late snowmelt populations showed slow growth, but high
 survival rate of the ramets, in which the ramet size at reproduction was
 smallest and fruit formation was often suppressed by the short growing
 period. Conclusions: Limiting factors dictating the distribution of G.
 nipponica differed between the early and late snowmelt habitats. High
 mortality and restricted growth, because of the harsh environment,
 determine the distribution limit toward earlier snowmelt locations. In
 contrast, late snowmelt strongly limited fecundity because of the short
 period for fruit maturation. The difference in snowmelt time provides a
 clear gradient of selective forces that may promote local adaptation among
 neighboring populations. If you would like your personal information to be
 removed from the database, please contact the publication office.
description: physiological_leaf_function and_ramet_demography_Kawai&KudoRamet demographic date over tree years and Physiological function of accumulated leaves
DOI: 10.5061/dryad.s5b62
title: Data from: Sex-specific weight loss mediates sexual size dimorphism in Drosophila melanogaster

description: The selective pressures leading to the evolution of Sexual Size Dimorphism
 (SSD) have been well studied in many organisms, yet, the underlying
 developmental mechanisms are poorly understood. By generating a complete
 growth profile by sex in Drosophila melanogaster, we describe the
 sex-specific pattern of growth responsible for SSD. Growth rate and
 critical size for pupariation significantly contributed to adult SSD,
 whereas duration of growth did not. Surprisingly, SSD at peak larval mass
 was twice that of the uneclosed adult SSD with weight loss between peak
 larval mass and pupariation playing an important role in generating the
 final SSD. Our finding that weight loss is an important regulator of SSD
 adds additional complexity to our understanding of how body size is
 regulated in different sexes. Collectively, these data allow for the
 elucidation of the molecular-genetic mechanisms that generate SSD, an
 important component of understanding how SSD evolves.
description: R
 analysisThis folder contains the
 R script file used in the analyses, including all referenced data as
 individual csv files.ssd critical
 sizegrowth rate
 data
DOI: 10.5061/dryad.2593t
title: Data from: Patterns of genetic diversity and differentiation in resistance gene clusters of two hybridizing European Populus species

description: Resistance genes (R-genes) are essential for long-lived organisms such as
 forest trees, which are exposed to diverse herbivores and pathogens. In
 short-lived model species, R-genes have been shown to be involved in
 species isolation. Here, we studied more than 400 trees from two natural
 hybrid zones of the European Populus species Populus alba and Populus
 tremula for microsatellite markers located in three R-gene clusters,
 including one cluster situated in the incipient sex chromosome region. The
 results indicate that all three R-gene clusters present extensive linkage
 disequilibrium (LD). Outlier tests suggest balancing selection as a
 potential driver of R-gene diversity, but divergent selection was also
 detected. Nucleotide-binding site leucine-rich repeat (NBS-LRR) type
 R-gene clusters exhibit low species differentiation and appear to be
 affected by shared selection pressures between species, recurrent
 interspecific gene flow, or both. Our results are consistent with a role
 for R-gene clusters in the evolution of chromosome XIX, recently put
 forward as an incipient sex chromosome in Populus.
description: 45Markers_HungaryMicrosatellite information for Tisza river hybrid zone. Read the README file for informations45Markers_ItalyMicrosatellite information for Ticino river hybrid zone. Read the README file for informations
DOI: 10.5061/dryad.s2np7
title: Data from: Environmental levels of oestrogenic and antiandrogenic compounds feminize digit ratios in male rats and their unexposed male progeny

description: Digit length ratios, especially the second-to-fourth digit ratio (2D :
 4D), are associated with various pathological and behavioural conditions
 in many species including humans and are dependent upon prenatal androgen
 to oestrogen balance. It is unknown whether digit ratios are modified by
 environmental exposure to ubiquitous endocrine disruptors. We studied the
 effect on adult male Wistar rat digit ratios of a gestational exposure to
 the oestrogenic and antiandrogenic compounds bisphenol A (BPA), genistein
 and vinclozolin, in low doses, and in combination with investigating in
 parallel a possible sexual dimorphism of this trait. We also investigated
 the effects on the male progeny not exposed during gestation. X-rays were
 taken of the left and right forepaws, and 2D–5D proximal to distal phalanx
 distances were measured by a standardized procedure based on
 semi-automatic image analysis. We provide evidence that there is a sexual
 dimorphism of digit ratios in the Wistar rat, and we found that BPA alone
 or in combination with genistein and vinclozolin significantly feminized
 digit ratios in male rats. Intriguingly, significant feminization of digit
 ratios was also found in the unexposed male progeny of males that had been
 exposed to compound mixtures. In conclusion, prenatal environmental levels
 of endocrine-active substances permanently disrupt digit ratios. Digit
 ratio measurement in adults is thus a promising biomarker of prenatal
 exposure to low-dose endocrine disruptors in rodents, with potential
 implications for future studies in humans.
description: Auger et al F1 digit
 length and ratio input fileAll basic measurements
 on digit length and ratio according to exposures conditions; from semi
 automatic image analysis of forepaw X-rays.Auger et al F2 digit
 length and ratio input fileAll basic measurements
 on digit length and ratio in the progeny according to exposures conditions
 in fathers; from semi automatic image analysis of forepaw X-rays in the
 second unexposed generation sired by exposed fathers and unexposed
 mothers.Auger et al F1 2D4D vs
 AGD input file2D to 4D digit ratio
 measured by semi-automatic image analysis vs relative anogenital distance
 (AGD) measured by a standardized method according to exposure conditions
 in the F1 generationAuger et al F2 2D4D vs
 AGD input file2D to 4D digit ratio
 measured by semi-automatic image analysis vs relative anogenital distance
 (AGD) measured by a standardized method according to exposure conditions
 in the F2 unexposed generation sired by exposed fathers and unexposed
 mothers
DOI: 10.5061/dryad.q91bt
title: Data from: Phenotypic plasticity of mate recognition systems prevents sexual interference between two sympatric leaf beetle species

description: Maladaptive sexual interactions among heterospecific individuals (sexual
 interference) can prevent the coexistence of animal species. Thus, the
 avoidance of sexual interference by divergence of mate recognition systems
 is crucial for a stable coexistence in sympatry. Mate recognition systems
 are thought to be under tight genetic control. However, we demonstrate
 that mate recognition systems of two closely related sympatric leaf beetle
 species show a high level of host-induced phenotypic plasticity. Mate
 choice in the mustard leaf beetles, Phaedon cochleariae and P. armoraciae,
 is mediated by cuticular hydrocarbons (CHCs). Divergent host plant use
 causes a divergence of CHC phenotypes, whereas similar host use leads to
 their convergence. Consequently, both species exhibit significant
 behavioral isolation when they feed on alternative host species, but mate
 randomly when using a common host. Thus, sexual interference between these
 syntopic leaf beetles is prevented by host-induced phenotypic plasticity
 rather than by genotypic divergence of mate recognition systems.
description: Cuticular hydrocarbon
 phenotypes of indivudual Phaedon beetlesRelative composition of
 cuticular hydrocarbons (% total peak area) of individual 21-d-old beetles
 of Phaedon cochleariae and P. armoraciae. Beetles were either reared on
 their native host plant species or on Brassica rapa ssp.
 pekinensis.Otte et al 2016
 Evolution.xlsx
DOI: 10.5061/dryad.g92d1
title: Data from: Repeatable and heritable behavioural variation in a wild cooperative breeder

description: Quantifying consistent differences in behaviour among individuals is vital
 to understanding the ecological and evolutionary significance of animal
 personality. To quantify personality, the phenotypic variation of a
 behavioural trait is partitioned to assess how it varies among
 individuals, which is also known as repeatability. If pedigree data are
 available, the phenotypic variation can then be further partitioned to
 estimate the additive genetic variance and heritability. Assessing the
 repeatability and heritability of personality traits therefore allows for
 a better understanding of what natural selection can act upon, enabling
 evolution. In a natural population of facultative cooperatively breeding
 Seychelles warbler (Acrocephalus sechellensis) on Cousin Island, a lack of
 breeding vacancies forces individuals into different life-history
 strategies, and these differences in reproductive state could generate
 behavioural differences among individuals in the population. We used this
 population to estimate the repeatability of 4 behavioural traits (novel
 environment exploration, novel object exploration, obstinacy/struggle
 rate, and escape response), and narrow-sense heritability (of behavior,
 h2B; behavior minus observer variance; and personality), and evolvability,
 of the repeatable behavioural traits. We also tested for an
 among-individual correlation between the repeatable traits. We found that,
 compared to estimates in other study species, the exploratory behaviours
 were moderately repeatable (0.23–0.37), there was a positive
 among-individual correlation (0.51) between novel environment and novel
 object exploration, and that novel environment exploration was moderately
 heritable (0.17; h2B was low as it includes observer variance). This study
 further clarifies the additive genetic variance available for selection to
 act upon in this cooperatively breeding bird.
description: Data for analysis of
 personality in the Seychelles warblerEach sheet contains the
 data for each personality trait.Edwards et al. 2017_Behav
 Eco_data.xlsx
DOI: 10.5061/dryad.sd1dt
title: Data from: Population structure, genetic variation and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance

description: Low temperature is one of the abiotic stresses seriously affecting the
 growth of perennial ryegrass (Lolium perenne L. Understanding the genetic
 control of freezing tolerance would aid in the development of cultivars of
 perennial ryegrass with improved adaptation to frost. A total number of 80
 individuals (24 of High frost [HF]; 29 of Low frost [LF] and 27 of
 Unselected [US]) from the second generation of the two divergently
 selected populations and an unselected control population were genotyped
 using 278 genome-wide SNPs derived from Lolium perenne L. transcriptome
 sequence. Our studies showed that the HF and LF populations are very
 divergent after selection for freezing tolerance, whereas the HF and US
 populations are more similar. Linkage disequilibrium (LD) decay varied
 across the seven chromosomes and the conspicuous pattern of LD between the
 HF and LF population confirmed their divergence in freezing tolerance.
 Furthermore, two Fst outlier methods; finite island model (fdist) by
 LOSITAN and hierarchical structure model using ARLEQUIN detected six loci
 under directional selection. These outlier loci are most probably linked
 to genes involved in freezing tolerance, cold adaptation and abiotic
 stress and might be the potential marker resources for breeding perennial
 ryegrass cultivars with improved freezing tolerance.
description: Frost_278_SNPs_Genotyping_Rawdata_Kovi_et_al_2015_frontiers_PlantscienceTwo hundred and seventy-eight Lolium perenne genic SNP markers distributed across the seven linkage groups [LG1 (37); LG2 (57); LG3 (32); LG4 (40); LG5 (39); LG6 (37); and LG7 (36)] were genotyped using Sequenom MassARRAY iPLEX platform. The 'Genotype' column indicates the population labels used during the analyses. For each SNP marker, one column with a unique label (i.e. marker name) indicate the two alleles. Missing data are labelled '0'.Frost_genotype_filtering_231SNPs_Kovi_et_al_frontiers_PlantscienceTwo hundred and thirty one SNPs were obtained for data analysis after removing eleven SNPs which failed in genotyping and twenty-seven SNPs with missing data &gt; 5% from the initial genotyping dataset. Of the remaining 231 SNPs, 181 SNPs (78.3%), 162 SNPs (70.1%), and 180 SNPs (77.9 %) were polymorphic across the HF (High frost), LF (Low frost) and US (Unselected) populations, respectively. Missing data is represented as "0".Frost_genotype_filtering_231SNPs_Kovi_et_al_2015_Frontiers_Plantscience.odsfrost_structure_excludinghomozygous_outlierSNPs_linkedmarkers_Kovi_et_al_2015_frontiers_PlantscienceStructure input file, after discarding 94 SNP markers closely linked with a minimum distance of 2 cM and 32 outlier SNP markers from the analysis. In total, 105 SNP markers were used to estimate the population structure using linkage model.frost_Kovi_et_al_2015_frontiers_PlantScienceArlequin input file
DOI: 10.5061/dryad.94j0f
title: Data from: Within-female plasticity in sex allocation is associated with a behavioral polyphenism in house wrens

description: Sex allocation theory assumes individual plasticity in maternal
 strategies, but few studies have investigated within-individual changes
 across environments. In house wrens, differences between nests in the
 degree of hatching synchrony of eggs represent a behavioural polyphenism
 in females, and its expression varies with seasonal changes in the
 environment. Between-nest differences in hatching asynchrony also create
 different environments for offspring, and sons are more strongly affected
 than daughters by sibling competition when hatching occurs asynchronously
 over several days. Here, we examined variation in hatching asynchrony and
 sex allocation, and its consequences for offspring fitness. The number and
 condition of fledglings declined seasonally, and the frequency of
 asynchronous hatching increased. In broods hatched asynchronously, sons,
 which are over-represented in the earlier-laid eggs, were in better
 condition than daughters, which are over-represented in the later-laid
 eggs. Nonetheless, asynchronous broods were more productive later within
 seasons. The proportion of sons in asynchronous broods increased
 seasonally, whereas there was a seasonal increase in the production of
 daughters by mothers hatching their eggs synchronously, which was
 characterized by within-female changes in offspring sex and not by
 sex-biased mortality. As adults, sons from asynchronous broods were in
 better condition and produced more broods of their own than males from
 synchronous broods, and both males and females from asynchronous broods
 had higher lifetime reproductive success than those from synchronous
 broods. In conclusion, hatching patterns are under maternal control,
 representing distinct strategies for allocating offspring within broods,
 and are associated with offspring sex ratios and differences in offspring
 reproductive success.
description: NESTSYOUNGEGGS
DOI: 10.5061/dryad.rf500
title: Data from: Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)

description: Background: Whole genome duplication plays a central role in plant
 evolution. There are two main classes of polyploid formation:
 autopolyploids which arise within one species by doubling of similar
 homologous genomes; in contrast, allopolyploidy (hybrid polyploidy) arise
 via hybridization and subsequent doubling of nonhomologous (homoeologous)
 genomes. The distinction between polyploid origins can be made using gene
 phylogenies, if alleles from each genome can be correctly retrieved. We
 examined whether two closely related tetraploid Mediterranean shrubs
 (Medicago arborea and M. strasseri) have an allopolyploid origin - a
 question that has remained unsolved despite substantial previous research.
 We sequenced and analyzed ten low-copy nuclear genes from these and
 related species, phasing all alleles. To test the efficacy of allele
 phasing on the ability to recover the evolutionary origin of polyploids,
 we compared these results to analyses using unphased sequences. Results:
 In eight of the gene trees the alleles inferred from the tetraploids
 formed two clades, in a non-sister relationship. Each of these clades was
 more closely related to alleles sampled from other species of Medicago, a
 pattern typical of allopolyploids. However, we also observed that alleles
 from one of the remaining genes formed two clades that were sister to one
 another, as is expected for autopolyploids. Trees inferred from unphased
 sequences were very different, with the tetraploids often placed in poorly
 supported and different positions compared to results obtained using
 phased alleles. Conclusions: The complex phylogenetic history of M.
 arborea and M. strasseri is explained predominantly by shared
 allotetraploidy. We also observed that an increase in woodiness is
 correlated with polyploidy in this group of species and present a new
 possibility that woodiness could be a transgressive phenotype. Correctly
 phased homoeologues are likely to be critical for inferring the hybrid
 origin of allopolyploid species, when most genes retain more than one
 homoeologue. Ignoring homoeologous variation by merging the homoeologues
 can obscure the signal of hybrid polyploid origins and produce inaccurate
 results.
description: Alignments_allopolyploid_arboreaAlignments after allele phasing and RDP (Recombination detection program) testing. Alignments from majority consensus sequences.Alignments for dryad.zipArborea_alleles_Alignments_before_RDPAlignments after phasing. Original files.Alignments before RDP.zip