cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18387349
title: Cosmological Application of Geometric Unification: Galactic Rotation Curves and Accelerated Expansion from Torsion-Gauge Field Coupling

description: .We present a cosmological application of the geometric unification framework developed in (1),where spacetime torsion is dynamically coupled to Standard Model gauge fields through a funda-mental algebraic constraint. This application provides a unified geometric explanation for two keyastrophysical phenomena: (1) flat galactic rotation curves without additional dark matter particles,and (2) the accelerated expansion of the Universe without cosmological constant. The mechanisminvolves the formation of chiral condensates in curved spacetime with torsion, leading to effective po-tentials that modify gravitational dynamics on both galactic and cosmological scales. All parametersare determined from first principles of the fundamental theory. We derive the modified Friedmann equations from the geometric constraint, solve for galactic rotation profiles, and demonstrate con-sistency with observational data from SPARC galaxies and Planck satellite. The model predictstestable signatures in CMB polarization and gravitational lensing statistics, providing observationaltests of the geometric unification framework.
DOI: 10.5061/dryad.qj552
title: Data from: Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses

description: Analyses of living and fossil taxa are crucial for understanding
 biodiversity through time. The total evidence method allows living and
 fossil taxa to be combined in phylogenies, using molecular data for living
 taxa and morphological data for living and fossil taxa. With this method,
 substantial overlap of coded anatomical characters among living and fossil
 taxa is vital for accurately inferring topology. However, although
 molecular data for living species are widely available, scientists
 generating morphological data mainly focus on fossils. Therefore, there
 are fewer coded anatomical characters in living taxa, even in well-studied
 groups such as mammals. We investigated the number of coded anatomical
 characters available in phylogenetic matrices for living mammals and how
 these were phylogenetically distributed across orders. Eleven of 28
 mammalian orders have less than 25% species with available characters;
 this has implications for the accurate placement of fossils, although the
 issue is less pronounced at higher taxonomic levels. In most orders,
 species with available characters are randomly distributed across the
 phylogeny, which may reduce the impact of the problem. We suggest that
 increased morphological data collection efforts for living taxa are needed
 to produce accurate total evidence phylogenies.
description: MatricesThis file contains the raw matrices analysed. For more informations on analysis them, please refer to: https://github.com/TGuillerme/Missing_living_mammals/ For any queries, please email me at: guillert@tcd.ie
DOI: 10.5061/dryad.4nb46
title: Data from: Microhabitat selection in the common lizard: implications of biotic interactions, age, sex, local processes, and model transferability among populations

description: Modeling species' habitat requirements are crucial to assess impacts
 of global change, for conservation efforts and to test mechanisms driving
 species presence. While the influence of abiotic factors has been widely
 examined, the importance of biotic factors and biotic interactions, and
 the potential implications of local processes are not well understood.
 Testing their importance requires additional knowledge and analyses at
 local habitat scale. Here, we recorded the locations of species presence
 at the microhabitat scale and measured abiotic and biotic parameters in
 three different common lizard (Zootoca vivipara) populations using a
 standardized sampling protocol. Thereafter, space use models and
 cross-evaluations among populations were run to infer local processes and
 estimate the importance of biotic parameters, biotic interactions, sex,
 and age. Biotic parameters explained more variation than abiotic
 parameters, and intraspecific interactions significantly predicted the
 spatial distribution. Significant differences among populations in the
 relationship between abiotic parameters and lizard distribution, and the
 greater model transferability within populations than between populations
 are in line with effects predicted by local adaptation and/or phenotypic
 plasticity. These results underline the importance of including biotic
 parameters and biotic interactions in space use models at the population
 level. There were significant differences in space use between sexes, and
 between adults and yearlings, the latter showing no association with the
 measured parameters. Consequently, predictive habitat models at the
 population level taking into account different sexes and age classes are
 required to understand a specie's ecological requirements and to
 allow for precise conservation strategies. Our study therefore stresses
 that future predictive habitat models at the population level and their
 transferability should take these parameters into account.
description: Population
 environmental, sociobiological and spatial parametersThis file contains data
 used for building Presence/absence models. Details of the analyses are
 provided in the main text under Presence/absence models in the Data
 Analysis section. Excel table with 4 sheets: i) Somport data; ii)
 Candanchú data; iii) Formigal data; iv) pooled data for the three
 populations.Population accuracy
 measuresThis file contains
 population accuracy measures derived from model transferability among
 model evaluation types. Details of the analyses are provided in the main
 text under Model Evaluation and Transferability of distribution models
 across populations in the Data Analysis section. Excel table with 5
 sheets: i) sensitivity values; ii) specificity values; iii) correct
 classification rate (CCR); iv) area under the ROC curve (AUC); v)
 prevalence.
DOI: 10.5061/dryad.4j7ss
title: Data from: Signalling with a cryptic trait: the regularity of barred plumage in common waxbills

description: Sexual signals often compromise camouflage, because of their
 conspicuousness. Pigmentation patterns, on the contrary, aid in
 camouflage. It was hypothesized that a particular type of pattern — barred
 plumage in birds, whereby pigmented bars extend across feathers — could
 simultaneously signal individual quality, because disruptions of these
 patterns should be perceptually salient at close range and help assess
 plumage condition. Here we show that common waxbills (Estrilda astrild),
 which have extensive barred plumage, have more regular patterns as adults
 than as juveniles, and that adult males have more regular patterns than
 females. Both these differences are indicative of sexual signalling in
 species with conventional sex roles. More regular barred plumage was
 related to better body condition in adult males. Colour ornamentation
 traits were also related to aspects of quality, either the same as barred
 plumage (body condition) or a different one (good feather development),
 supporting both the ‘redundant message’ and the ‘multiple message’
 hypotheses for the coexistence of multiple sexual signals. Although
 receiver responses to the regularity of barred plumage were not studied
 here, research on other species has shown barred plumage to mediate social
 interactions. We conclude that using barred plumage as a signal of quality
 helps circumvent the functional compromise between camouflage and
 communication.
description: DatasetMarques et al 2016 RSOS Dryad.xls
DOI: 10.5061/dryad.1131
title: Data from: Finding candidate genes under positive selection in non-model species: examples of genes involved in host specialization in pathogens

description: Numerous genes in diverse organisms have been shown to be under positive
 selection, especially genes involved in reproduction, adaptation to
 contrasting environments, hybrid inviability, and host-pathogen
 interactions. Looking for genes under positive selection in pathogens has
 been a priority in efforts to investigate coevolution dynamics and to
 develop vaccines or drugs. To elucidate the functions involved in host
 specialization, here we aimed at identifying candidate sequences that
 could have evolved under positive selection among closely related
 pathogens specialized on different hosts. For this goal, we sequenced ca.
 17,000-32,000 ESTs from each of four Microbotryum species, which are
 fungal pathogens responsible for anther smut disease on host plants in the
 Caryophyllaceae. Forty-two of the 372 predicted orthologous genes showed
 significant signal of positive selection, which represents a good number
 of candidate genes for further investigation. Sequencing 16 of these genes
 in 9 additional Microbotryum species confirmed that they have indeed been
 rapidly evolving in the pathogen species specialized on different hosts.
 The genes showing significant signals of positive selection were
 putatively involved in nutrient uptake from the host, secondary metabolite
 synthesis and secretion, respiration under stressful conditions and stress
 response, hyphal growth and differentiation, and regulation of expression
 by other genes. Many of these genes had transmembrane domains and may
 therefore also be involved in pathogen recognition by the host. Our
 approach thus revealed fruitful and should be feasible for many non-model
 organisms for which candidate genes for diversifying selection are needed.
description: Mviol_Dcarthusianorum_EST.fasta.zipEST (Expressed Sequence tags) of Microbotryum violaceum on D. carthusianorum.Mviol_Slatifolia_EST.fasta.zipEST (Expressed Sequence tags) of Microbotryum violaceum on S. LatifoliaMviol_Snutans_EST.fasta.zipEST (Expressed Sequence tags) of Microbotryum violaceum on S. nutansMviol_Svulgaris_EST.fasta.zipESTs of Microbotryum violaceum on S. vulgaris
DOI: 10.5061/dryad.j4j7q
title: Data from: Taxonomic quality of species descriptions varies over time and with the number of authors, but unevenly among parasitic taxa

description: Although concerns are being raised about a potential shortage of
 taxonomists and systematists, recent analyses suggest instead that the
 number of researchers involved in taxonomic descriptions is higher than
 ever and that the average number of new species described annually per
 taxonomist has declined in recent decades. Here, using nine metrics of
 taxonomic quality, such as the number of morphological traits measured,
 the number of separate line drawings included, and whether or not gene
 sequences are provided, we explore variation in taxonomic quality as a
 function of the number of authors and other potential determinants across
 2366 descriptions of parasitic helminths published in 1337 articles
 between 1980 and 2014. Taxonomic quality has generally increased over
 time, but unequally among different groups of helminths. For example, the
 number of scanning electron micrographs per description has risen
 significantly over time in cestodes and nematodes, but decreased for
 digeneans. For most metrics used, the greater the number of authors per
 species description, the higher its quality, suggesting not more
 taxonomists but more collaborations between taxonomists and experts from
 other fields to produce more comprehensive species characterizations.
 Re-descriptions of species were of higher quality than their original
 descriptions, and the improved quality correlated with the number of years
 elapsed between them. However, the extent of this improvement varied among
 helminth species with different host taxa. Overall, our findings provide a
 note of caution for anyone using trends in the number of species described
 per author to extrapolate the total number of extant species. They also
 reveal cultural differences among taxonomists working on different groups
 of parasites that can serve to identify areas for potential improvement.
description: Appendix 1_Supplementary
 MaterialContains additional
 methodological details, and additional results in the form of figures and
 tables.Taxonomic quality MAIN
 datasetDetailed taxonomic
 quality data for all 2366 descriptions of helminth
 species.Taxonomic quality
 REDESCRIPTION datasetDetailed taxonomic
 quality data for original descriptions and subsequent re-descriptions of
 574 helminth species.
DOI: 10.5061/dryad.3c7jb
title: Data from: Greater host breadth still not associated with increased diversification rate in the Nymphalidae – a response to Janz et al

description: In their technical comment, Janz et al. take issue with our recent study
 examining the association between host breadth and diversification rates
 in the brush footed butterflies (Lepidoptera: Nymphalidae) (Hamm and
 Fordyce 2015). Specifically, they are concerned that we misrepresent their
 “oscillation hypothesis” (OH) (Janz et al. 2016; Janz and Nylin 2008) and
 that one of our models was inadequate to test hypotheses regarding host
 breadth and diversification rate. Given our mutual interests in the
 macroevolutionary patterns of herbivorous insects, we appreciate the
 opportunity to respond to their concerns.
description: OH-reply-codeMain code file for Hamm and Fordyce 2016OH-reply-dataMain data file for Hamm and Fordyce 2016event_dataEvent data from the BAMM analysis used in Hamm and Fordyce 2015 and used for Hamm and Fordyce 2016.Janz_DataThe code and data file provided to us by Janz et al. (2016) and used for their response. Note, that one will need to adjust the sampling frequencies to reflect accurate proportions of specialists and herbivores.
DOI: 10.82209/hv44-a941
title: Performance of selected models for the recognition of 16 named entities in plasma physics research articles
DOI: 10.5061/dryad.41db8
title: Data from: Who directs group movement? Leader effort vs follower preference in stickleback fish of different personality

description: During collective movement, bolder individuals often emerge as leaders.
 Here, we investigate whether this reflects a greater propensity of bold
 individuals to initiate movement, or a preference for shy individuals to
 follow a bolder leader. We set up trios of stickleback fish comprising a
 focal individual who was either bold or shy, and one other individual of
 each personality. We then recorded the movements of all individuals in and
 out of cover in a foraging context to determine how assiduously the focal
 fish followed the movements of each other partner. We found that a shy
 focal fish preferred to follow a leader whose personality matched its own,
 but we did not detect such a difference in bold fish. Despite this
 preference, however, the greater propensity of bold individuals to
 initiate movements out of cover meant that they successfully led more
 joint trips. Thus, when offered a choice of leaders, sticklebacks prefer
 to follow individuals whose personality matches their own, but bolder
 individuals may, nevertheless, be able to impose their leadership, even
 among shy followers, simply through greater effort.
description: dataTimes of the fish moving
 out of cover ("M") and returning to cover
 ("W").
DOI: 10.5061/dryad.fh3h6
title: Data from: Inferring muscle functional roles of the ostrich pelvic limb during walking and running using computer optimization

description: Owing to their cursorial background, ostriches (Struthio camelus) walk and
 run with high metabolic economy, can reach very fast running speeds and
 quickly execute cutting manoeuvres. These capabilities are believed to be
 a result of their ability to coordinate muscles to take advantage of
 specialized passive limb structures. This study aimed to infer the
 functional roles of ostrich pelvic limb muscles during gait. Existing gait
 data were combined with a newly developed musculoskeletal model to
 generate simulations of ostrich walking and running that predict muscle
 excitations, force and mechanical work. Consistent with previous avian
 electromyography studies, predicted excitation patterns showed that
 individual muscles tended to be excited primarily during only stance or
 swing. Work and force estimates show that ostrich gaits are partially
 hip-driven with the bi-articular hip–knee muscles driving stance
 mechanics. Conversely, the knee extensors acted as brakes, absorbing
 energy. The digital extensors generated large amounts of both negative and
 positive mechanical work, with increased magnitudes during running,
 providing further evidence that ostriches make extensive use of tendinous
 elastic energy storage to improve economy. The simulations also highlight
 the need to carefully consider non-muscular soft tissues that may play a
 role in ostrich gait.
description: Models and Motion Files
 Used to Generate SimulationsPlease read the ReadMe
 file for detailed description of each file in the
 archiveModels and Motion
 Data.zip
DOI: 10.5061/dryad.s6f76
title: Data from: Microsatellite and major histocompatibility complex variation in an endangered rattlesnake, the Eastern Massasauga (Sistrurus catenatus)

description: Genetic diversity is fundamental to maintaining the long-term viability of
 populations, yet reduced genetic variation is often associated with small,
 isolated populations. To examine the relationship between demography and
 genetic variation, variation at hypervariable loci (e.g., microsatellite
 DNA loci) is often measured. However, these loci are selectively neutral
 (or near neutral) and may not accurately reflect genomewide variation.
 Variation at functional trait loci, such as the major histocompatibility
 complex (MHC), can provide a better assessment of adaptive genetic
 variation in fragmented populations. We compared patterns of
 microsatellite and MHC variation across three Eastern Massasauga
 (Sistrurus catenatus) populations representing a gradient of demographic
 histories to assess the relative roles of natural selection and genetic
 drift. Using 454 deep amplicon sequencing, we identified 24 putatively
 functional MHC IIB exon 2 alleles belonging to a minimum of six loci.
 Analysis of synonymous and nonsynonymous substitution rates provided
 evidence of historical positive selection at the nucleotide level, and
 Tajima's D provided support for balancing selection in each
 population. As predicted, estimates of microsatellite allelic richness,
 observed, heterozygosity, and expected heterozygosity varied among
 populations in a pattern qualitatively consistent with demographic history
 and abundance. While MHC allelic richness at the population and individual
 levels revealed similar trends, MHC nucleotide diversity was unexpectedly
 high in the smallest population. Overall, these results suggest that
 genetic variation in the Eastern Massasauga populations in Illinois has
 been shaped by multiple evolutionary mechanisms. Thus, conservation
 efforts should consider both neutral and functional genetic variation when
 managing captive and wild Eastern Massasauga populations.
description: DataArchive
DOI: 10.5061/dryad.b3d76
title: Data from: Competing influences on morphological modularity in biomechanical systems: a case study in mantis shrimp

description: [No abstract entered]
description: Andersonetal2016_Evo&Dev_dataZip file containing the raw tps and centroid size files used for morphometric analyses in the paper.
DOI: 10.5061/dryad.2ts15
title: Data from: Grouping substitution types into different relaxed molecular clocks

description: Different types of nucleotide substitutions experience different patterns
 of rate change over time. We propose clustering context-dependent (or
 context-independent) nucleotide substitution types according to how their
 rates change and then using the grouping for divergence time estimation.
 With our models, relative rates among types that are in the same group are
 fixed, whereas absolute rates of the types within a group change over time
 according to a shared relaxed molecular clock. We illustrate our procedure
 by analysing a 0.15 Mb intergenic region to infer divergence times
 relating eight primates. The different groupings of substitution types
 that we explore have little effect on the posterior means of divergence
 times, but the widths of the credibility intervals decrease as the number
 of groups increases.
description: 9speciesWe obtained sequence data of humans and 8 other primate species for a region that is orthologous to an intergenic part of human Chromosome 16 (hg19.chr16:60842337-61130970) according to the Multiz alignment of 100 vertebrates in the UCSC genome browser. CpG islands are masked by Repeatmasker.
DOI: 10.5061/dryad.8p5n5
title: Data from: Damming, lost connectivity and the historical role of anadromous fish in freshwater ecosystem dynamics

description: Recent research has demonstrated the important role that high-biomass
 species play in the transfer of energy and nutrients across habitat
 boundaries, as well as the ecosystem consequences of their loss. To
 contrast the historical and current biomass of historically abundant
 anadromous forage fish, we combined historical records of habitat loss
 from damming with contemporary freshwater productivity of alewives and
 diet data of freshwater predator fish. Significant declines in production
 occurred by 1850 in the northeastern United States, long before any direct
 abundance data were available, which would have had significant effects on
 freshwater prey resources for the numerous predators directly affected by
 the transfer of nutrients across the freshwater–marine nexus. Current
 freshwater systems operate at approximately 6.7% of historical capacity of
 anadromous alewife biomass and abundance. This provides an example of
 habitat-mediated changes in connectivity limiting nutrient flux and energy
 flow among populations and species that alter ecosystem function at
 multiple scales.
description: Southern New England
 Historical Dam DatabaseThis is a historical dam
 database created using historical maps, town history books, county history
 books, existing dam databases from other agencies (The Nature Conservancy,
 Charles River Watershed Association, Town of Plymouth, MA) and other
 historical documents. Access to historical documents on google books and
 archive.org was integral to compiling historical dams
 data.dams_final.xlsxMaine Dams Hall et al. 2011These are historical dams compiled by Hall et al. (2011). This data is also available at the Gulf of Maine Historical Ecology Research website: www.GOMHER.org.GOMHER_Maine dams_final_CHall copy.xls