cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8902n
title: Data from: A phylogenetic, biogeographic, and taxonomic study of all extant species of Anolis (Squamata; Iguanidae)

description: Anolis lizards (anoles) are textbook study organisms in evolution and
 ecology. Although several topics in evolutionary biology have been
 elucidated by the study of anoles, progress in some areas has been
 hampered by limited phylogenetic information on this group. Here we
 present a phylogenetic analysis of all 379 extant species of Anolis, with
 new phylogenetic data for 139 species including new DNA data for 101
 species. We use the resulting estimates as a basis for defining anole
 clade names under the principles of phylogenetic nomenclature and to
 examine the biogeographic history of anoles. Our new taxonomic treatment
 achieves the supposed advantages of recent subdivisions of anoles that
 employed ranked Linnaean–based nomenclature while avoiding the pitfalls of
 those approaches regarding artificial constraints imposed by ranks. Our
 biogeographic analyses demonstrate complexity in the dispersal history of
 anoles, including multiple crossings of the Isthmus of Panama, two
 invasions of the Caribbean, single invasions to Jamaica and Cuba, and a
 single evolutionary dispersal from the Caribbean to the mainland that
 resulted in substantial anole diversity. Our comprehensive phylogenetic
 estimate of anoles should prove useful for rigorous testing of many
 comparative evolutionary hypotheses.
description: FigS1mapFigS2lnlFigS3mccCaribFigS4mccMnlndFigS5mrcCaribFigS6mrcMnlndFigS7timetree
DOI: 10.5061/dryad.9c250
title: Data from: Mapping the four-horned locus and testing the polled locus in three Chinese sheep breeds

description: Four-horned sheep are an ideal animal model for illuminating the genetic
 basis of horn development. The objective of this study was to locate the
 genetic region responsible for the four-horned phenotype and to verify a
 previously reported polled locus in three Chinese breeds. A genome-wide
 association study (GWAS) was performed using 34 two-horned and 32
 four-horned sheep from three Chinese indigenous breeds: Altay, Mongolian
 and Sishui Fur sheep. The top two significant single nucleotide
 polymorphisms (SNPs) associated with the four-horned phenotype were both
 located in a region spanning positions 132.6 to 132.7 Mb on sheep
 chromosome 2. Similar locations for the four-horned trait were previously
 identified in Jacob, Navajo-Churro, Damara and Sishui Fur sheep,
 suggesting a common genetic component underlying the four-horned
 phenotype. The two identified SNPs were both downstream of the metaxin 2
 (MTX2) gene and the HOXD gene cluster. For the top
 SNP—OAR2:g.132619300G&gt;A—the strong associations of the AA and AG
 genotypes with the four-horned phenotype and the GG genotype with the
 two-horned phenotype indicated the dominant inheritance of the four-horned
 trait. No significant SNPs for the polled phenotype were identified in the
 GWAS analysis, and a PCR analysis for the detection of the 1.8-kb
 insertion associated with polled sheep in other breeds failed to verify
 the association with polledness in the three Chinese breeds. This study
 supports the hypothesis that two different loci are responsible for horn
 existence and number. This study contributes to the understanding of the
 molecular regulation of horn development and enriches the knowledge of
 qualitative traits in domestic animals.
description: Mapping the four-horned
 locus in sheepSample identification,
 sample locations and population cluster membership for all
 individuals.96 Chinese
 sheep.xlsxMAP file:
 96_ChineseSheepSingle nucleotide
 polymorphism (SNP) raw data files with 54241 loci for 43 Altay sheep, 30
 Mongolian sheep and 22 Sishui Fur sheep from China in
 PLINK-format.96_ChineseSheep.mapPED file: 96_ChineseSheepSingle nucleotide polymorphism (SNP) raw data files with 54241 loci for 43 Altay sheep, 30 Mongolian sheep and 22 Sishui Fur sheep from China in PLINK-format.96_ChineseSheep.ped
DOI: 10.5061/dryad.29h6k
title: Data from: Is asexual reproduction an evolutionary dead-end in lichens?

description: Classical hypotheses in lichenology predict pairs of species in which
 sexual lineages are ancestral and long-lived evolutionarily and that these
 give rise to derived, evolutionarily transient asexual lineages. Extensive
 phylogenetic information generated over the last 20 years regarding
 relationships within and among various groups of lichens makes possible an
 investigation of polarity and lability in reproductive mode across diverse
 clades. To test the long-held hypothesis of asexual reproduction as an
 evolutionary dead end in lichens, existing phylogenetic data from 23
 studies were utilized to reconstruct gains and losses of sexual and
 asexual reproduction in a model-based statistical framework. Summed across
 all studies, between 26–44 origins of asexual reproduction from sexual
 ancestors (forward transitions) and 14–25 origins of sexual reproduction
 from asexual ancestors (reverse transitions) were identified. However, the
 higher number of gains of asexual reproduction was concentrated in a
 relatively low number of clades (e.g. Dirina). The greater number of
 forward compared to reverse transitions is consistent with dogma in both
 lichenology and evolutionary biology, but nonetheless this study documents
 numerous reverse transitions, suggesting that asexual lineages represent a
 source for evolutionary innovation.
description: BiatoraT68835.nexCaloplacaT20723.nexCladoniaDirina130805_4komb_Dirina_206.nexFlavoparmeliaT63498_ET modified_Mesquite.nexFulgensiaT49479.nexLecaniaT972.nexLecanora53taxabayes18dec.nexLethariaT27653.nexLobariellalobariella_ITS_new.treMelanohaleaT50986_ET modified_Mesquite.nexMiriquidicaConcat_6locus_SinghEtAl_2015.treMontaneliaT76977.nexParmotremaProtoparmeliaConcat_6locus_SinghEtAl_2015.trePuncteliaT90392.nexXanthomendozaT66987.nexAustroparmelinacombined_min3_max2_ex_2.mb.con.nexBulbothrixcombined_min3_max2_ex_2.mb.con.nexFuscopannariaT68563.nexHypogymniaT73442.nexPannariaT68563.nexParmelinacombined_min3_max2_ex_2.mb.con.nex
DOI: 10.5061/dryad.h1v2g
title: Data from: Factors related to building loss due to wildfires in the conterminous United States

description: Wildfire is globally an important ecological disturbance affecting
 biochemical cycles, and vegetation composition, but also puts people and
 their homes at risk. Suppressing wildfires has detrimental ecological
 effects and can promote larger and more intense wildfires when fuels
 accumulate, which increases the threat to buildings in the Wildland Urban
 Interface (WUI). Yet, when wildfires occur, typically only a small
 proportion of the buildings within the fire perimeter are lost, and the
 question is what determines which buildings burn. Our goal was to examine
 which factors are related to building loss when a wildfire occurs
 throughout the United States. We were particularly interested in the
 relative roles of vegetation, topography, and the spatial arrangement of
 buildings, and how their respective roles vary among ecoregions. We
 analyzed all fires that occurred within the conterminous U.S. from 2000 to
 2010 and digitized which buildings were lost and which survived according
 to Google Earth historical imagery. We modeled the occurrence as well as
 the percentage of buildings lost within clusters using logistic and linear
 regression. Overall, variables related to topography and the spatial
 arrangement of buildings were more frequently present in the best 20
 regression models than vegetation-related variables. In other words,
 specific locations in the landscape have a higher fire risk, and certain
 development patterns can exacerbate that risk. Fire policies and
 prevention efforts focused on vegetation management are important, but
 insufficient to solve current wildfire problems. Furthermore, the factors
 associated with building loss varied considerably among ecoregions
 suggesting that fire policy applied uniformly across the US will not work
 equally well in all regions and that efforts to adapt communities to
 wildfires must be regionally tailored.
description: US Burned Buildings data
 packageIt contains a copy of
 the main data files exactly as used for this paper, as well as other
 accompanying files. Contains all the digitized burned and survived
 buildings that were within fire perimeters that occurred between 2000 and
 2010 in the conterminous U.S.USBurnedBuildings.rar
DOI: 10.5061/dryad.8ch1b
title: Data from: Three-dimensional simulation for fast forward flight of a calliope hummingbird

description: We present a computational study of flapping-wing aerodynamics of a
 calliope hummingbird (Selasphorus calliope) during fast forward flight.
 Three-dimensional wing kinematics were incorporated into the model by
 extracting time-dependent wing position from high-speed videos of the bird
 flying in a wind tunnel at 8.3 m s−1. The advance ratio, i.e. the ratio
 between flight speed and average wingtip speed, is around one. An
 immersed-boundary method was used to simulate flow around the wings and
 bird body. The result shows that both downstroke and upstroke in a
 wingbeat cycle produce significant thrust for the bird to overcome drag on
 the body, and such thrust production comes at price of negative lift
 induced during upstroke. This feature might be shared with bats, while
 being distinct from insects and other birds, including closely related
 swifts.
description: Data
 sourceThis TAR ball contains
 all matlab figures with the data source embedded.Data.tar
DOI: 10.5061/dryad.jk680
title: Data from: Investigating genomic and phenotypic parallelism between piscivorous and planktivorous lake trout (Salvelinus namaycush) ecotypes by means of RADseq and morphometrics analyses

description: Repeated adaptive ecological diversification has commonly been reported in
 fish and has often been associated with trophic niche diversity. The main
 goal of this study was to investigate the extent of parallelism in the
 genomic and phenotypic divergence between piscivorous and planktivorous
 lake trout ecotypes from Laurentian Shield lakes, Canada. This was
 achieved by documenting the extent of morphological differentiation using
 geometric morphometrics and linear measurements as well as the pattern of
 genomic divergence by means of RADseq genotyping (3925 filtered SNPs) in
 12 lakes. Our results indicate that the two ecotypes evolved distinct body
 shape and several linear measurements in parallel. Neutral genetic
 differentiation was pronounced between all isolated populations (Mean FST
 = 0.433), indicating no or very limited migration and pronounced genetic
 drift. Significant genetic differentiation also suggested partial
 reproductive isolation between ecotypes in the two lakes where they are
 found in sympatry. Combining different outlier detection methods, we
 identified 48 SNPs putatively under divergent selection between ecotypes,
 among which 10 could be annotated and related to functions such as
 developmental processes and ionic regulation. Finally, our results
 indicate that parallel morphological divergence is accompanied by both
 parallel and nonparallel genomic divergence, which is associated with the
 use of different trophic niches between ecotypes. The results are also
 discussed in the context of management and conservation of this highly
 exploited species throughout northern North America.
description: genepop_all_snpsGenotypes data (all loci) for S. namaycush individuals in Genepop format.genepop_pot_selected_snpsGenotypes data (48 potentially selected loci, intersection of Bayenv2 and LFMM results) for S. namaycush individuals in Genepop format.population_mapIndividual's population membership (by population (or lake) or sympatric ecotype).population_map_ecotypeIndividual's ecotype membership (by population (or lake) or sympatric ecotype).geometric_morphometricsGeometric morphometrics data in TPS format.infos_tpsInformation (ecotype and sex) for geometric morphometrics analyses.measurementsGill rakers and linear measurements data.ReadMeInformation about the files.read_me.txt
DOI: 10.5061/dryad.820j2
title: Data from: A new method for reconstructing brain morphology: applying the brain-neurocranial spatial relationship in an extant lungfish to a fossil endocast

description: Lungfish first appeared in the geological record over 410 million years
 ago and are the closest living group of fish to the tetrapods.
 Palaeoneurological investigations into the group show that unlike numerous
 other fishes—but more similar to those in tetrapods—lungfish appear to
 have had a close fit between the brain and the cranial cavity that housed
 it. As such, researchers can use the endocast of fossil taxa (an internal
 cast of the cranial cavity) both as a source of morphological data but
 also to aid in developing functional and phylogenetic implications about
 the group. Using fossil endocast data from a three-dimensional-preserved
 Late Devonian lungfish from the Gogo Formation, Rhinodipterus, and the
 brain-neurocranial relationship in the extant Australian lungfish,
 Neoceratodus, we herein present the first virtually reconstructed brain of
 a fossil lungfish. Computed tomographic data and a newly developed
 ‘brain-warping’ method are used in conjunction with our own distance map
 software tool to both analyse and present the data. The brain
 reconstruction is adequate, but we envisage that its accuracy and wider
 application in other taxonomic groups will grow with increasing
 availability of tomographic datasets.
description: parameters_BSpline_for_SICode used for landmark registration and elastic deformation of volumesR_kimberleyensis_Endocast_001Rhinodipterus endocast STL fileNeoceratodus_Endocast_STLNeoceratodus endocast STL fileNeoceratodus_Brain_STLNeoceratodus brain STL file
DOI: 10.5061/dryad.s84v4
title: Data from: Using big data to assess prescribing patterns in Greece: the case of chronic obstructive pulmonary disease

description: Introduction: Chronic Obstructive Pulmonary Disease (COPD) is one of the
 top leading causes of death and disability, and its management is focused
 on reducing risk factors, relieving symptoms, and preventing
 exacerbations. The study aim was to describe COPD prescribing patterns in
 Greece by using existing health administrative data for outpatients.
 Methods: This is a retrospective cross-sectional study based on
 prescriptions collected by the largest social insurance fund, during the
 first and last trimester of 2012. Selection criteria were the prescription
 of specific active substances and a COPD diagnosis. Extracted information
 included active substance, strength, pharmaceutical form and number of
 packages prescribed, diagnosis, time of dispensing, as well as
 insurees' age, gender, percentage of co-payment and social security
 unique number. Statistical analysis included descriptive statistics and
 logistic regression. Results: 174,357 patients received medicines for COPD
 during the study period. Patients were almost equally distributed between
 male and female, and age above 55 years was strongly correlated with COPD.
 Most patients received a long-acting beta agonist plus inhaled
 corticosteroid combination (LABA +ICS), followed by long-acting muscarinic
 agonist (LAMA). 63% patients belonging in the 35-54 age received LABA+ICS.
 LAMA was prescribed more frequently among males and was strongly
 correlated with COPD. Conclusion: The study provides big data analysis of
 Greek COPD prescribing patterns. It highlights the need for appropriate
 COPD classification in primary care illustrating the role of electronic
 prescribing in ensuring appropriate prescribing. Moreover, it indicates
 possible gender differences in treatment response or disease severity, and
 the impact of statutory co-payments on prescribing.
description: Data base of EOPYY
 insurees' COPD prescriptionsData base of
 prescriptions collected by the largest social insurance fund, EOPYY during
 the first and last trimester of 2012. Extracted information included
 active substance, strength, pharmaceutical form and number of packages
 prescribed, diagnosis, time of dispensing, as well as insurees’ age,
 gender, percentage of co-payment and social security unique
 number.Eoppy_Plos_One
 (1).rar
DOI: 10.5061/dryad.3p27r
title: Data from:Spatio-temporal networks: reachability, centrality and robustness

description: Recent advances in spatial and temporal networks have enabled researchers
 to more-accurately describe many real-world systems such as urban
 transport networks. In this paper, we study the response of real-world
 spatio-temporal networks to random error and systematic attack, taking a
 unified view of their spatial and temporal performance. We propose a model
 of spatio-temporal paths in time-varying spatially embedded networks which
 captures the property that, as in many real-world systems, interaction
 between nodes is non-instantaneous and governed by the space in which they
 are embedded. Through numerical experiments on three real-world urban
 transport systems, we study the effect of node failure on a network's
 topological, temporal and spatial structure. We also demonstrate the
 broader applicability of this framework to three other classes of network.
 To identify weaknesses specific to the behaviour of a spatio-temporal
 system, we introduce centrality measures that evaluate the importance of a
 node as a structural bridge and its role in supporting spatio-temporally
 efficient flows through the network. This exposes the complex nature of
 fragility in a spatio-temporal system, showing that there is a variety of
 failure modes when a network is subject to systematic attacks.
description: FAA Flights
 Spatio-Temporal NetworkA spatio-temporal
 network of US domestic flights. This is a spatially embedded time-varying
 public transport network. The network represents actual flights among 299
 US airports over 10 days.flightsFAA.tar.gzParis Metro Spatio-Temporal NetworkA spatio-temporal network of the Paris Metro. This is a spatially embedded time-varying public transport network. The network represents timetabled Metro journeys for two days.paris.tar.gzNew York Subway Spatio-Temporal NetworkA spatio-temporal network of the New York Subway. This is a spatially embedded time-varying public transport network. The network represents timetabled subway journeys for two days.newyork.tar.gzLondon Underground Spatio-Temporal NetworkA spatio-temporal network of the London Underground. This is a spatially embedded time-varying public transport network. The network represents timetabled journeys for two days. Files are available at figshare at https://dx.doi.org/10.6084/m9.figshare.1452948.v1 - Please see files "underground_coords.csv.gz" and "underground_stnet.csv.gz" specifically.
DOI: 10.5061/dryad.dp3js
title: Data from: Novel approaches for phylogenetic inference from morphological data and total-evidence dating in squamate reptiles (lizards, snakes, and amphisbaenians)

description: Here, I combine previously underutilized models and priors to perform more
 biologically-realistic phylogenetic inference from morphological data,
 with an example from squamate reptiles. When coding morphological
 characters, it is often possible to denote ordered states with explicit
 reference to observed or hypothetical ancestral conditions. Using this
 logic, we can integrate across character-state labels and estimate
 meaningful rates of forward and backwards transitions from plesiomorphy to
 apomorphy. I refer to this approach as MkA, for 'asymmetric.'
 The MkA model incorporates the biological reality of limited reversal for
 many phylogenetically informative characters, and significantly increases
 likelihoods in the empirical datasets. Despite this, the phylogeny of
 Squamata remains contentious. Total-evidence analyses using combined
 morphological and molecular data and the MkA approach tend towards recent
 consensus estimates supporting a nested Iguania. However, support for this
 topology is not unambiguous across datasets or analyses, and no mechanism
 has been proposed to explain the widespread incongruence between
 partitions, or the hidden support for various topologies in those
 partitions. Furthermore, different morphological datasets produced by
 different authors contain both different characters and different states
 for the same or similar characters, resulting in drastically different
 placements for many important fossil lineages. Effort is needed to
 standardize ontology for morphology, resolve incongruence, and estimate a
 robust phylogeny. The MkA approach provides a preliminary avenue for
 investigating morphological evolution while accounting for temporal
 evidence and asymmetry in character-state changes.
description: SquamataAll included files are described in README.txt file attached.READMEContains descriptions of all data and results files, along with software used, and links to source code.
DOI: 10.5061/dryad.16n4q
title: Data from: The small nuclear genomes of Selaginella are associated with a low rate of genome size evolution

description: The haploid nuclear genome size (1C DNA) of vascular land plants varies
 over several orders of magnitude. Much of this observed diversity in
 genome size is due to the proliferation and deletion of transposable
 elements. To date, all vascular land plant lineages with extremely small
 nuclear genomes represent recently derived states, having ancestors with
 much larger genome sizes. The Selaginellaceae represent an ancient lineage
 with extremely small genomes. It is unclear how small nuclear genomes
 evolved in Selaginella. We compared the rates of nuclear genome size
 evolution in Selaginella and major vascular plant clades in a comparative
 phylogenetic framework. For the analyses, we collected 29 new flow
 cytometry estimates of haploid genome size in Selaginella to augment
 publicly available data. Selaginella possess some of the smallest known
 haploid nuclear genome sizes, as well as the lowest rate of genome size
 evolution observed across all vascular land plants included in our
 analyses. Additionally, our analyses provide strong support for a history
 of haploid nuclear genome size stasis in Selaginella. Our results indicate
 that Selaginella, similar to other early diverging lineages of vascular
 land plants, has relatively low rates of genome size evolution. Further,
 our analyses highlight that a rapid transition to a small genome size is
 only one route to an extremely small genome.
description: final.alnchronogram