cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.461g6
title: Data from: A new hierarchy of phylogenetic models consistent with heterogeneous substitution rates

description: When the process underlying DNA substitutions varies across evolutionary
 history, some standard Markov models underlying phylogenetic methods are
 mathematically inconsistent. The most prominent example is the general
 time-reversible model (GTR) together with some, but not all, of its
 submodels. To rectify this deficiency, nonhomogeneous Lie Markov models
 have been identified as the class of models that are consistent in the
 face of a changing process of DNA substitutions regardless of taxon
 sampling. Some well-known models in popular use are within this class, but
 are either overly simplistic (e.g., the Kimura two-parameter model) or
 overly complex (the general Markov model). On a diverse set of biological
 data sets, we test a hierarchy of Lie Markov models spanning the full
 range of parameter richness. Compared against the benchmark of the
 ever-popular GTR model, we find that as a whole the Lie Markov models
 perform well, with the best performing models having 8–10 parameters and
 the ability to recognize the distinction between purines and pyrimidines.
description: Read Me
 fileJava_SourceJava source files for the likelihood analysis using Lie Markov modelsLie Markov model analysis with MathematicaVarious analyses of the Lie Markov models: Fourier-Motzkin elimination, nesting, equilibrium base frequencies, time reversibility, embeddability.LieMarkov.nbPDF of Mathematica fileMathematica file LieMarkov.nb printed out in PDF format, to provide some accessibility to those without Mathematica.LieMarkov.pdfLikelihood analysis spreadsheetSpreadsheet taking output of test.sh and calculating AIC, BIC scores, ranking models, and formatting results for inclusion in the paper.likelihoods.odsRunable Java jar file for likelihood analysisSee ReadMe.txt for details. Requires library jar file (https://github.com/MichaelWoodhams/pal-mdw/releases) to run.LMM.jarShell script to run likelihood analysisTakes multiple days to run.test.shSupplementary tables and figuresSupplementary tables and figures in support of the main paper. Includes information repackaged from likelihoods.ods and LieMarkov.nb.supplementary_material.pdf
DOI: 10.5061/dryad.54sg8
title: Data from: An investigation of the therapeutic effects of statins with metformin on polycystic ovary syndrome: a meta-analysis of randomized controlled trials

description: Objectives: To investigate the therapeutic effects of statins with
 metformin on polycystic ovary syndrome (PCOS). Settings: Endocrinology
 department. Participants: MEDLINE, EMBASE and Cochrane Central Register of
 Controlled Trials were searched until October 2014. Studies comparing
 statins and placebo, as well as the combination of statins and metformin
 and metformin alone, were included in the analysis. Interventions: Data
 were independently extracted by two researchers; any convergence was
 resolved by a third reviewer. Primary and secondary outcome measures: The
 following properties were extracted from the qualified trials to identify
 the effects of statins: clinical variables, metabolic characteristics,
 hormone outcomes, sign of inflammation, glucose parameters and insulin
 outcomes. Results: Data from four trials comparing statin and metformin
 with metformin alone were analysed. The combination of statins and
 metformin decreases the levels of C reactive protein (standardised mean
 difference (SMD) −0.91; 95% CI −1.81 to −0.02; p=0.046), triglyceride (SMD
 −1.37; 95% CI −2.46 to −0.28; p=0.014), total cholesterol (SMD −1.28; 95%
 CI −1.59 to −0.97; p=0.000) and low-density lipoprotein (LDL) cholesterol
 (SMD −0.74; 95% CI −1.03 to −0.44; p=0.000). However, the combined therapy
 fails to reduce fasting insulin (SMD −0.92; 95% CI −2.07 to 0.24;
 p=0.120), homeostasis model assessment of insulin resistance (SMD −1.15;
 95% CI −3.36 to 1.06; p=0.309) and total testosterone (SMD −1.12; 95% CI
 −2.29 to 0.05; p=0.061). Analysis of the five trials comparing statin with
 placebo shows that statin monotherapy reduces LDL-cholesterol,
 triglyceride and total cholesterol. Conclusions: Combined statin and
 metformin therapy can improve lipid and inflammation parameters, but
 cannot effectively improve insulin sensitivity and reduce hyperandrogenism
 in women with PCOS. A large-scale randomised controlled study must be
 conducted to ascertain the long-term effects of the therapy.
description: table
 1Characteristics of
 included studiesfigureFigure1-flow
 chart;Figure 2-statin VS placebo;Figure 3-statin+metformin VS
 metformin
DOI: 10.5061/dryad.m0nh6
title: Data from: Drivers of climate change impacts on bird communities

description: 1. Climate change is reported to have caused widespread changes to
 species’ populations and ecological communities. Warming has been
 associated with population declines in long-distance migrants and habitat
 specialists, and increases in southerly distributed species. However, the
 specific climatic drivers behind these changes remain undescribed. 2. We
 analysed annual fluctuations in the abundance of 59 breeding bird species
 in England over 45 years to test the effect of monthly temperature and
 precipitation means upon population trends. 3. Strong positive
 correlations between population growth and both winter and breeding season
 temperature were identified for resident and short-distance migrants.
 Lagged correlations between population growth and summer temperature and
 precipitation identified for the first time a widespread negative impact
 of hot, dry summer weather. Resident populations appeared to increase
 following wet autumns. Populations of long-distance migrants were
 negatively affected by May temperature, consistent with a potential
 negative effect of phenological mismatch upon breeding success. There was
 evidence for some nonlinear relationships between monthly weather
 variables and population growth. 4. Habitat specialists and
 cold-associated species showed consistently more negative effects of
 higher temperatures than habitat generalists and southerly distributed
 species associated with warm temperatures. Results suggest that previously
 reported changes in community composition represent the accumulated
 effects of spring and summer warming. 5. Long-term population trends were
 more significantly correlated with species’ sensitivity to temperature
 than precipitation, suggesting that warming has had a greater impact on
 population trends than changes in precipitation. Months where there had
 been the greatest warming were the most influential drivers of long-term
 change. There was also evidence that species with the greatest sensitivity
 to extremes of precipitation have tended to decline. 6. Our results
 provide novel insights about the impact of climate change on bird
 communities. Significant lagged effects highlight the potential for
 altered species’ interactions to drive observed climate change impacts,
 although some community changes may have been driven by more immediate
 responses to warming. In England, resident and short-distance migrant
 populations have increased in response to climate change, but potentially
 at the expense of long-distance migrants, habitat specialists and
 cold-associated species.
description: Data for Pearce-Higgins
 et al. 2015Excel spreadsheet of
 population indices for England (1966-2011), monthly temperature and
 precipitation data, and species traits (migration strategy, species
 temperature index, species specialisation index)
DOI: 10.5061/dryad.2hb50
title: Data from: Rethinking refugia: tree topology, divergence dates, and demographic history trace the distribution of the endangered Plymouth gentian (Sabatia kennedyana) from the Pleistocene glaciation to present day

description: Premise of study: Molecular population genetics is a powerful tool to
 infer how species responded to past environmental change. In the northern
 hemisphere, interest is increasing in how species responded to changes in
 ice coverage and temperature during the last glaciation maximum (LGM,
 between 18000–21000 yr ago) with a common assumption that glacial refugia
 were located at the southern edge of a species range. Methods: We
 reconstructed the glacial and postglacial phylogeography of Sabatia
 kennedyana, a member of the Atlantic Coastal Plains Flora with a current
 distribution from Nova Scotia (NS) to South Carolina, using both cpDNA and
 nuclear markers. We also examined clinal variation in morphological
 traits, in particular relative investment in asexual vs sexual growth. Key
 results: We find strong evidence that the species did not reside in
 southern glacial refugia, but rather in primary glacial refugia off the
 exposed continental shelf extending from Cape Cod and that this area was
 responsible for the founding of modern populations across the range from
 Nova Scotia (NS) to the United States. Additionally, based on the finding
 of higher cpDNA diversity and older cpDNA lineages in NS, we propose that
 multiple founder events occurred in NS, while only a single lineage gave
 rise to current populations in the United States. Conclusions: By
 understanding how S. kennedyana responded to past shifts in climate and by
 identifying areas of high genetic diversity in the northern range edge, we
 discuss the potential response of the species to future climate change
 scenarios.
description: Alignment of the spacers
 between trnS and trnG and rpL20-5’rpS12 in 87 samples from Sabatia
 kennedyana, representing the northern (NS, Canada), central (MA, USA) and
 southern (NC, USA) range of the species.The spacers between trnS
 and trnG and rpL20-5’rpS12 were aligned with a consensus length of 1161 bp
 which was reduced to 812 bp after removing gaps and missing data. Among
 the 87 samples, 28 cpDNA haplotypes harbouring 38 informative sites were
 identified in 812 bp. Haplotype sequences were deposited in the GenBank
 database under accession numbers JX003130 –JX003186 for the rpL20-5’rpS12
 intergenic spacer and JX003187 – JX003245 for the trnS-trnG intergenic
 spacer.Appendix S3 -
 alignment.html
DOI: 10.5281/zenodo.18379586
title: Moure Neotropical Bees Cataogue

description: 2022 Version

Moure’s Catalog for Neotropical bee species.

Taxonomic information, published from 2011 to 2021.

The Brazilian fauna, which in the 2007 version consisted of 1678 species, now contains 1965 species, as follows: 121 belonging to Andreninae, 1031 to Apinae (of which 251 to Meliponini), 126 to Colletinae, 337 to Halictinae and 350 to Megachilinae.

Some new taxa were not cataloged in this version due to the impossibility of accessing the original content of the publication.

It is also important to warn that the information contained in the online versions of Moure’s catalog, for the most part, only refer to what is published in the literature. Thus, there is a large amount of unpublished information regarding taxonomic positioning, synonymy, existence of type material considered lost, etc., which are not being incorporated in the online versions.
DOI: 10.5061/dryad.7ht20
title: Data from: Batesian mimics influence the evolution of conspicuousness in an aposematic salamander

description: Conspicuousness, or having high contrast relative to the surrounding
 background, is a common feature of unpalatable species. Several hypotheses
 have been proposed to explain the occurrence of conspicuousness, and while
 most involve the role of conspicuousness as a direct signal of
 unpalatability to potential predators, one hypothesis suggests that
 exaggerated conspicuousness may evolve in unpalatable species to reduce
 predator confusion with palatable species (potential Batesian mimics).
 This hypothesis of antagonistic coevolution between palatable and
 unpalatable species hinges on the ‘cost of conspicuousness,’ in which
 conspicuousness increases the likelihood of predation more in palatable
 species than in unpalatable species. Under this mimicry scenario four
 patterns are expected: 1) mimics will more closely resemble local models
 than models from other localities, 2) there will be a positive
 relationship between mimic and model conspicuousness, 3) models will be
 more conspicuous in the presence of mimics, and 4) when models and mimics
 differ in conspicuousness, mimics will be less conspicuous than models. We
 tested these predictions in the salamander mimicry system involving
 Notophthalmus viridescens (model) and one color morph of Plethodon
 cinereus (mimic). All predictions were supported, indicating that
 selection for Batesian mimicry not only influences the evolution of
 mimics, but also the evolution of the models they resemble. These findings
 indicate that mimicry plays a large role in the evolution of model warning
 signals, particularly influencing the evolution of conspicuousness.
description: SalamanderSpectraJEB2015KraemerReflectance spectra from all salamanders in the study can be found in this file, as well as salamander conspicuousness as calculated for the main analyses.
DOI: 10.5061/dryad.p0372
title: Data from: Axl-regulating tumor suppressor miR-34a increased in ccRCC but not correlating with Axl mRNA or Axl protein levels

description: Background: High expression of the receptor tyrosine kinase Axl is
 associated with poor prognosis in patients with Renal Cell Carcinoma
 (RCC), the most common malignancy of the kidney. The miR-34a has been
 shown to directly regulate Axl in cancer cells. The miR-34a is a mediator
 of p53-dependent tumor suppression, and low expression of miR-34a has been
 associated with worse prognosis in several cancers. Our aim was to
 elucidate whether miR-34a or the other members of the miR-34 family
 (miR-34b/c) regulate Axl in RCC. Methodology and Results: Using western
 blot, flow cytometry, and RT-qPCR, we showed that Axl mRNA and protein are
 downregulated in 786-O cells by miR-34a and miR-34c but not by miR-34b. A
 luciferase reporter assay demonstrated direct interaction between the Axl
 3’ UTR and miR-34a and miR-34c. The levels of miR-34a/b/c were measured in
 tumor tissue in a cohort of 198 RCC patients, and the levels of miR-34a
 were found to be upregulated in clear cell RCC (ccRCC) tumors, but not
 associated with patient outcome. Neither of the miR-34 family members
 correlated with Axl mRNA, soluble Axl protein in serum, nor with
 immunohistochemistry of Axl in tumor tissue. In addition, we measured mRNA
 levels of a known miR-34a target, HNF4A, and found the HNF4A levels to be
 decreased in ccRCC tumors, but unexpectedly correlated positively rather
 than negatively with miR-34a. Conclusions: Although miR-34a and miR-34c
 can regulate Axl expression in vitro, our data indicates that the miR-34
 family members are not the primary regulators of Axl expression in RCC.
description: RCC data for
 DryadThis file conatins all
 the data files for the submission. The cohort data file is provided both
 as a SPSS file and as an excel file where varibales have been specifiec in
 the column headers. There is also a list file explaining sample lanes in
 the WB images. The file folder is compressed.Additional
 dataAdditional
 data.RCC
 data for Dryad - additional data.zip
DOI: 10.5061/dryad.fd862
title: Data from: Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks

description: An Illumina Infinium SNP genotyping array was constructed for European
 white oaks. Six individuals of Quercus petraea and Q. robur were
 considered for SNP discovery using both previously obtained Sanger
 sequences across 676 gene regions (1371 in vitro SNPs) and Roche 454
 technology sequences from 5112 contigs (6542 putative in silico SNPs). The
 7913 SNPs were genotyped across the six parental individuals, full-sib
 progenies (one within each species and two interspecific crosses between
 Q. petraea and Q. robur) and three natural populations from south-western
 France that included two additional interfertile white oak species (Q.
 pubescens and Q. pyrenaica). The genotyping success rate in mapping
 populations was 80.4% overall and 72.4% for polymorphic SNPs. In natural
 populations, these figures were lower (54.8% and 51.9%, respectively).
 Illumina genotype clusters with compression (shift of clusters on the
 normalized x-axis) were detected in ~25% of the successfully genotyped
 SNPs and may be due to the presence of paralogues. Compressed clusters
 were significantly more frequent for SNPs showing a priori incorrect
 Illumina genotypes, suggesting that they should be considered with caution
 or discarded. Altogether, these results show a high experimental error
 rate for the Infinium array (between 15% and 20% of SNPs potentially
 unreliable and 10% when excluding all compressed clusters), and
 recommendations are proposed when applying this type of high-throughput
 technique. Finally, results on diversity levels and shared polymorphisms
 across targeted white oaks and more distant species of the Quercus genus
 are discussed, and perspectives for future comparative studies are
 proposed.
description: 5112_fasta_in_silico_SNPs.tarFasta alignment files from which putative in silico SNPs have been extracted.
DOI: 10.5061/dryad.0q515
title: Data from: Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota)

description: Species recognition in lichen-forming fungi has been a challenge because
 of unsettled species concepts, few taxonomically relevant traits, and
 limitations of traditionally used morphological and chemical characters
 for identifying closely related species. Here we analyze species diversity
 in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in
 this group occur across diverse habitats from the boreal -arctic/alpine to
 the tropics, but their relationship to each other remains unexplored. In
 this study, we inferred the phylogeny of 18 species currently assigned to
 this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS,
 RPB1, MCM7, and TSR1. We assessed the circumscription of species-level
 lineages in Protoparmelia s. str. using two coalescent-based species
 delimitation methods – BP&P and spedeSTEM. Our results suggest the
 presence of a tropical and an extra-tropical lineage, and eleven
 previously unrecognized distinct species-level lineages in Protoparmelia
 s. str. Several cryptic lineages were discovered as compared to
 phenotype-based species delimitation. Many of the putative species are
 supported by geographic evidence.
description: Alignment-of-Protoparmelia-s.str_Concated-6-loci_2015Protoparmelia-s-sl_Concated-6-loci-Alignment_RPB1-MCM7-TSR1-NULSU-MTSSU-nrITS
DOI: 10.5061/dryad.tg0nq
title: Data from: Calibrating animal-borne proximity loggers

description: 1. Growing interest in the structure and dynamics of animal social
 networks has stimulated efforts to develop automated tracking technologies
 that can reliably record encounters in free-ranging subjects. A
 particularly promising approach is the use of animal-attached ‘proximity
 loggers’, which collect data on the incidence, duration and proximity of
 spatial associations through inter-logger radio communication. While
 proximity logging is based on a straightforward physical principle – the
 attenuation of propagating radio waves with distance – calibrating systems
 for field deployment is challenging, since most study species roam across
 complex, heterogeneous environments. 2. In this study, we calibrated a
 recently developed digital proximity-logging system (‘Encounternet’) for
 deployment on a wild population of New Caledonian crows Corvus
 moneduloides. Our principal objective was to establish a quantitative
 model that enables robust post hoc estimation of logger-to-logger (and,
 hence, crow-to-crow) distances from logger-recorded signal-strength
 values. To achieve an accurate description of the radio communication
 between crow-borne loggers, we conducted a calibration exercise that
 combines theoretical analyses, field experiments, statistical modelling,
 behavioural observations, and computer simulations. 3. We show that, using
 signal-strength information only, it is possible to assign crow encounters
 reliably to predefined distance classes, enabling powerful analyses of
 social dynamics. For example, raw data sets from field-deployed loggers
 can be filtered at the analysis stage to include predominantly encounters
 where crows would have come to within a few metres of each other, and
 could therefore have socially learned new behaviours through direct
 observation. One of the main challenges for improving data classification
 further is the fact that crows – like most other study species – associate
 across a wide variety of habitats and behavioural contexts, with different
 signal-attenuation properties. 4. Our study demonstrates that
 well-calibrated proximity-logging systems can be used to chart social
 associations of free-ranging animals over a range of biologically
 meaningful distances. At the same time, however, it highlights that
 considerable efforts are required to conduct study-specific system
 calibrations that adequately account for the biological and technological
 complexities of field deployments. Although we report results from a
 particular case study, the basic rationale of our multi-step calibration
 exercise applies to many other tracking systems and study species.
description: Data from field
 experimentsData collected during
 field experiments (relates to ‘Step 1’ in the published paper), to assess
 how signal strength is affected by inter-tag distance, as well as by a set
 of nuisance parameters (habitat type, tag height above ground, and
 relative antenna orientation).Rutz_etal_Dryad_dataset.csv
DOI: 10.5061/dryad.52hp1
title: Data from: Detecting hidden diversification shifts in models of trait-dependent speciation and extinction

description: The distribution of diversity can vary considerably from clade to clade.
 Attempts to understand these patterns often employ state-dependent
 speciation and extinction models to determine whether the evolution of a
 particular novel trait has increased speciation rates and/or decreased
 extinction rates. It is still unclear, however, whether these models are
 uncovering important drivers of diversification, or whether they are
 simply pointing to more complex patterns involving many unmeasured and
 co-distributed factors. Here we describe an extension to the popular
 state-dependent speciation and extinction models that specifically
 accounts for the presence of unmeasured factors that could impact
 diversification rates estimated for the states of any observed trait,
 addressing at least one major criticism of BiSSE (Binary State Speciation
 and Extinction) methods. Specifically, our model, which we refer to as
 HiSSE (Hidden State Speciation and Extinction), assumes that related to
 each observed state in the model are “hidden” states that exhibit
 potentially distinct diversification dynamics and transition rates than
 the observed states in isolation. We also demonstrate how our model can be
 used as character-independent diversification models that allow for a
 complex diversification process that is independent of the evolution of a
 character. Under rigorous simulation tests and when applied to empirical
 data, we find that HiSSE performs reasonably well, and can at least detect
 net diversification rate differences between observed and hidden states
 and detect when diversification rate differences do not correlate with the
 observed states. We discuss the remaining issues with state-dependent
 speciation and extinction models in general, and the important ways in
 which HiSSE provides a more nuanced understanding of trait-dependent
 diversification.
description: R scripts used in the
 manuscriptscripts.zipBeaulieuOMearaSupplementalMaterialsSupplemental Materials document