cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.63q3283
title: Data from: Common noctules exploit low levels of the aerosphere

description: Aerial habitats present a challenge to find food across a large potential
 search volume, particularly for insectivorous bats that rely on
 echolocation calls with limited detection range and may forage at heights
 over 1000 m. To understand how bats use vertical space, we tracked one to
 five foraging flights of eight common noctules (Nyctalus noctula). Bats
 were tracked for their full foraging session (87.27 ± 24 mins) using
 high-resolution atmospheric pressure radio transmitters that allowed us to
 calculate height and wingbeat frequency. Bats used diverse flight
 strategies, but generally flew lower than 40 m, with scouting flights to
 100 m and a maximum of 300 m. We found no influence of weather on height
 and high-altitude ascents were not preceded by an increase in foraging
 effort. Wingbeat frequency was independent from climbing or descending
 flight, and bats skipped wingbeats or glided in 10% of all observations.
 Wingbeat frequency was positively related to capture mass, and wingbeat
 frequency was positively related to time of night, indicating an effect of
 load increase over a foraging bout. Overall, individuals used a wide range
 of airspace including altitudes that put them at increased risk from
 human-made structures. Further work is needed to test the context of these
 flight decisions, particularly as individuals migrate throughout Europe.
description: Weather annotated
 foraging dataFlight heights and
 wingbeat frequency are derived from atmospheric pressure radio
 transmitters. Weather data were collected from the German weather service,
 Deutscher Wetterdienst (DWD), and interpolated to the timestamps of the
 observed altitude data. Additional movement data are available at the
 Movebank Data Repository: doi:10.5441/001/1.7t4b97qf. Please see the
 README for data definitions.Noctule Altitude foraging pub
 data.csvData
 README.txt
DOI: 10.5061/dryad.t3q8b
title: Data from: Temporal patterns of diversification across global cichlid biodiversity (Acanthomorpha: Cichlidae)

description: The contrasting distribution of species diversity across the major
 lineages of cichlids makes them an ideal group for investigating
 macroevolutionary processes. In this study, we investigate whether
 different rates of diversification may explain the disparity in species
 richness across cichlid lineages globally. We present the most
 taxonomically robust time-calibrated hypothesis of cichlid evolutionary
 relationships to date. We then utilize this temporal framework to
 investigate whether both species-rich and depauperate lineages are
 associated with rapid shifts in diversification rates and if exceptional
 species richness can be explained by clade age alone. A single significant
 rapid rate shift increase is detected within the evolutionary history of
 the African subfamily Pseudocrenilabrinae, which includes the
 haplochromins of the East African Great Lakes. Several lineages from the
 subfamilies Pseudocrenilabrinae (Australotilapiini, Oreochromini) and
 Cichlinae (Heroini) exhibit exceptional species richness given their clade
 age, a net rate of diversification, and relative rates of extinction,
 indicating that clade age alone is not a sufficient explanation for their
 increased diversity. Our results indicate that the Neotropical Cichlinae
 includes lineages that have not experienced a significant rapid burst in
 diversification when compared to certain African lineages (rift lake).
 Neotropical cichlids have remained comparatively understudied with regard
 to macroevolutionary patterns relative to African lineages, and our
 results indicate that of Neotropical lineages, the tribe Heroini may have
 an elevated rate of diversification in contrast to other Neotropical
 cichlids. These findings provide insight into our understanding of the
 diversification patterns across taxonomically disparate lineages in this
 diverse clade of freshwater fishes and one of the most species-rich
 families of vertebrates.
description: Cichlidae_4genessequences of four genes across all four subfamilies of cichlid fishesCichlid_4genes_Medusa_Bayes_30Apr2013.txtMorphological data_CichlidaeMorphological data matrix from Supplemental InformationSouthAmericanCichlid.nex
DOI: 10.5061/dryad.2rg12
title: Data from: Limitations of climate data for inferring species boundaries: insights from speckled rattlesnakes

description: Phenotypes, DNA, and measures of ecological differences are widely used in
 species delimitation. Although rarely defined in such studies, ecological
 divergence is almost always approximated using multivariate climatic data
 associated with sets of specimens (i.e., the “climatic niche”); the
 justification for this approach is that species-specific climatic
 envelopes act as surrogates for physiological tolerances. Using identical
 statistical procedures, we evaluated the usefulness and validity of the
 climate-as-proxy assumption by comparing performance of genetic (nDNA SNPs
 and mitochondrial DNA), phenotypic, and climatic data for objective
 species delimitation in the speckled rattlesnake (Crotalus mitchellii)
 complex. Ordination and clustering patterns were largely congruent among
 intrinsic (heritable) traits (nDNA, mtDNA, phenotype), and discordance is
 explained by biological processes (e.g., ontogeny, hybridization). In
 contrast, climatic data did not produce biologically meaningful clusters
 that were congruent with any intrinsic dataset, but rather corresponded to
 regional differences in atmospheric circulation and climate, indicating an
 absence of inherent taxonomic signal in these data. Surrogating climate
 for physiological tolerances adds artificial weight to evidence of species
 boundaries, as these data are irrelevant for that purpose. Based on the
 evidence from congruent clustering of intrinsic datasets, we recommend
 that three subspecies of C. mitchellii be recognized as species: C.
 angelensis, C. mitchellii, and C. Pyrrhus.
description: Dstat_Tests_fastaFasta files for four-taxon Patterson's D-statistics used in Meik et al., 'Limitations of climate data for inferring species boundaries: insights from speckled rattlesnakes.' .fasta files.Morph_datasetMorphological dataset used in Meik et al., 'Limitations of climate data for inferring species boundaries: insights from speckled rattlesnakes.' See Supplemental Information for metadata (character abbreviations). .csv filemtDNA_590_bp_ATPase_alignmentmtDNA alignment for a fragment of ATPase 8 and 6 (590 bp), used in Meik et al. 'Limitations of climate data for inferring species boundaries: insights from speckled rattlesnakes.' .fasta filenucDNA_1826_SNPsAlignment of 1826 SNPs used for STRUCTURE analysis in Meik et al., 'Limitations of climate data for inferring species boundaries: insights from speckled rattlesnakes.' .stru filenucDNA_2318_SNP_alignmentAlignment of 2318 SNPs used in phylogenetic analysis of rattlesnake relationships in Meik et al. 'Limitations of climate data for inferring species boundaries: insights from speckled rattlesnakes.' phylipnucDNA_SNAPP_alignmentAlignment of SNPs used for species tree analysis (SNAPP) in Meik et al. 'Limitations of climate data for inferring species boundaries: insights from speckled rattlesnakes.' .nex file
DOI: 10.5061/dryad.7809km8
title: Data from: Reconstructing the evolution of giant extinct kangaroos: comparing the utility of DNA, morphology, and total evidence

description: Combined “total evidence” analysis of molecular and morphological data
 offers the opportunity to objectively merge fossils into the tree of life,
 and challenges the primacy of solely DNA based phylogenetic and dating
 inference, even among modern taxa. To investigate the relative utility of
 DNA, morphology, and total evidence for evolutionary inference, we
 sequenced the first near-complete mitochondrial genomes from extinct
 Australian megafauna: a 40-50 thousand year old giant short-faced kangaroo
 (Simosthenurus occidentalis) and giant wallaby (Protemnodon anak). We
 analysed the ancient DNA and fossil data alongside comparable data from
 extant species to infer phylogeny, divergence times, and ancestral body
 mass among macropods (kangaroos and wallabies). Our results confirm a
 close relationship between Protemnodon and the iconic kangaroo genus
 complex “Macropus”, and unite the giant Simothenurus with the hare-sized
 Lagostrophus fasciatus (banded hare-wallaby), suggesting that the latter
 is the closest living link to the once diverse sthenurine kangaroo
 radiation. We find that large body size evolved multiple times among
 kangaroos, coincident with expansion of open woodland habitats beginning
 in the Late Miocene. In addition, our results suggest that morphological
 data mislead macropod phylogeny reconstruction and in turn can distort
 total evidence estimation of divergence dates. However, a novel result
 with potentially broad application is that the accuracy and precision of
 reconstructing ancestral body mass was improved by tracing body mass on
 morphological branch lengths. This is likely due to positive allometric
 correlation between morphological and body size variation – a relationship
 that may be masked or even misleadingly inverted with the temporal or
 molecular branch lengths that typically underpin ancestral body size
 reconstruction. Our study supports complementary roles for DNA and
 morphology in evolutionary inference, and opens a new window into the
 evolution of Australia’s unique marsupial fauna.
description: PhylogenyThis folder contains matrices used for the phylogenetic analyses and resulting trees.DatingSupplementary Material_review_Manu
DOI: 10.5061/dryad.rc628
title: Data from: Molecular phylogeny of an ancient rodent family (Aplodontiidae)

description: The family Aplodontiidae contains a single, monotypic extant genus,
 Aplodontia (mountain beaver), which was 1st described by Rafinesque in
 1817. Phylogenetic studies have shown that it is the sister lineage to
 squirrels. Aplodontia rufa is endemic to the Pacific Northwest and ranges
 from central California to British Columbia. Currently, 7 described
 subspecies are recognized based on morphological taxonomic studies. In
 this study, mitochondrial and nuclear genes were sequenced to infer
 molecular phylogenies of A. rufa. One of the goals of this study was to
 test the current taxonomic hypothesis based on morphology with molecular
 data. Another goal was to incorporate geographic information to elucidate
 distributions of major clades. Our results support the previously held
 subspecies designations based on morphological taxonomy, with 1 main
 exception: we determined that within A. rufa, the subspecies A. rufa
 rainieri and A. rufa rufa north of the Columbia River represent a single
 lineage and should revert to the name A. rufa olympica. Although we
 revised geographic boundaries for some groups (A. r. rufa, A. r. olympica,
 A. r. pacifica), only the conservation status and management of A. r.
 olympica (previously 2 subspecies) in Canada may be affected. Our findings
 support the continued conservation efforts for the isolated and endangered
 lineages present in coastal California.
description: all
 nuc.TXTBEAST input file:GHR
 nuclear DNA sequencescytb prior root stdev
 mean CABEAST inout file:
 Mitochondrial DNA cytochrome b sequencesAppendix 1 cytb 1050bp
 080612Haplotype Table whole
 cytochrome b sequencesAppendix 2 cytb 450bp
 080612Haplotype table partial
 cytochrome bAppendix 3 CR
 080612Haplotype table control
 region mitochondrial DNAAppendix 4 GHR
 080612Haplotype table nuclear
 DNA GHR sequences
DOI: 10.5061/dryad.8m405
title: Data from: Exploring foraging decisions in a social primate using discrete choice models

description: There is a growing appreciation of the multiple social and nonsocial
 factors influencing the foraging behavior of social animals, but little
 understanding of how these factors depend on habitat characteristics or
 individual traits. This partly reflects the difficulties inherent in using
 conventional statistical techniques to analyze multi-factor, multi-context
 foraging decisions. Discrete choice models provide a way to do so, and we
 demonstrate this by using them to investigate patch preference in a wild
 population of social foragers (chacma baboons, Papio ursinus). Data were
 collected from 29 adults across two social groups encompassing 683
 foraging decisions over a six-month period, and the results interpreted
 using an information theoretic approach. Baboon foraging decisions were
 influenced by multiple nonsocial and social factors, and were often
 contingent on the characteristics of the habitat or individual.
 Differences in decision-making between habitats were consistent with
 changes in interference competition costs but not changes in social
 foraging benefits. Individual differences in decision-making were
 suggestive of a trade-off between dominance rank and social capital. Our
 findings emphasize that taking a multi-factor, multi-context approach is
 important to fully understand animal decision-making. We also demonstrate
 how discrete choice models can be used to achieve this.
description: Baboon foraging decision
 dataRaw data used in the
 analysis. See ReadMe file for details.Marshalletal2012data.csvPatch preference models 95% confidence setsThis supplement (1) briefly outlines the model averaging process used to calculate the final models presented in the paper, and (2) tabulates the 95% confidence sets of the candidate models used in each of these averaging processes.Patch preference models 95 percent confidence sets.doc
DOI: 10.5061/dryad.16830
title: Data from: Community analysis of microbial sharing and specialization in a Costa Rican ant–plant–hemipteran symbiosis

description: Ants have long been renowned for their intimate mutualisms with
 trophobionts and plants and more recently appreciated for their widespread
 and diverse interactions with microbes. An open question in symbiosis
 research is the extent to which environmental influence, including the
 exchange of microbes between interacting macroorganisms, affects the
 composition and function of symbiotic microbial communities. Here we
 approached this question by investigating symbiosis within symbiosis.
 Ant–plant–hemipteran symbioses are hallmarks of tropical ecosystems that
 produce persistent close contact among the macroorganism partners, which
 then have substantial opportunity to exchange symbiotic microbes. We used
 metabarcoding and quantitative PCR to examine community structure of both
 bacteria and fungi in a Neotropical ant–plant–scale-insect symbiosis. Both
 phloem-feeding scale insects and honeydew-feeding ants make use of
 microbial symbionts to subsist on phloem-derived diets of suboptimal
 nutritional quality. Among the insects examined here, Cephalotes ants and
 pseudococcid scale insects had the most specialized bacterial symbionts,
 whereas Azteca ants appeared to consume or associate with more fungi than
 bacteria, and coccid scale insects were associated with unusually diverse
 bacterial communities. Despite these differences, we also identified
 apparent sharing of microbes among the macro-partners. How microbial
 exchanges affect the consumer-resource interactions that shape the
 evolution of ant–plant–hemipteran symbioses is an exciting question that
 awaits further research.
description: Pringle&Moreau_Data&CodeCode, OTU tables, taxonomy, and FASTA sequences associated to the paper.Pringle_and_Moreau_Data_and_Code.zip
DOI: 10.7910/dvn/kibr6j
title: A First-Principles Benchmark of TD-DFT Functionals for the Photoabsorption of Camphorquinone: Validating a Quantum-Chemical Protocol for Dental Photoinitiator Design

description: This dataset supports the study “A First-Principles Benchmark of TD-DFT Functionals for the Photoabsorption of Camphorquinone: Validating a Quantum-Chemical Protocol for Dental Photoinitiator Design.” The work presents a systematic first-principles evaluation of commonly used time-dependent density functional theory (TD-DFT) functionals for modeling the primary photoabsorption of camphorquinone, a clinically established dental photoinitiator.

The dataset includes all computational inputs and outputs required to reproduce the reported results, including optimized ground-state geometries, TD-DFT excitation calculations, and associated analysis files. Ground-state optimization was performed using density functional theory with the B3LYP functional and a 6-31G(d) basis set under an implicit polarizable continuum model representing a resin-relevant dielectric environment (ε = 4.0). Vertical electronic excitations were subsequently computed using TD-DFT with B3LYP, PBE0, CAM-B3LYP, and ωB97XD functionals under consistent methodological conditions.

Benchmarking focuses on the lowest optically allowed singlet excitation of camphorquinone, with computed absorption maxima compared directly against the experimentally established peak near 468 nm. Natural Transition Orbital (NTO) data are provided to support assignment of the excitation character as a localized carbonyl-centered n(O) → π*(C=O) transition. The dataset is intended to facilitate transparency, reproducibility, and critical evaluation of functional performance for this system.

All files are provided to enable independent verification, methodological comparison, and reuse in future mechanistic studies or in silico screening of related carbonyl-based photoinitiators. The scope of the data is explicitly limited to vertical excitation benchmarking under an implicit solvent model and does not imply general functional transferability beyond the studied system.
DOI: 10.5061/dryad.n2cj3
title: Data from: Temporal dynamics of linkage disequilibrium in two populations of bighorn sheep

description: Linkage disequilibrium (LD) is the nonrandom association of alleles at two
 markers. Patterns of LD have biological implications as well as practical
 ones when designing association studies or conservation programs aimed at
 identifying the genetic basis of fitness differences within and among
 populations. However, the temporal dynamics of LD in wild populations has
 received little empirical attention. In this study, we examined the
 overall extent of LD, the effect of sample size on the accuracy and
 precision of LD estimates, and the temporal dynamics of LD in two
 populations of bighorn sheep (Ovis canadensis) with different demographic
 histories. Using over 200 microsatellite loci, we assessed two metrics of
 multi-allelic LD, D′, and χ′2. We found that both populations exhibited
 high levels of LD, although the extent was much shorter in a native
 population than one that was founded via translocation, experienced a
 prolonged bottleneck post founding, followed by recent admixture. In
 addition, we observed significant variation in LD in relation to the
 sample size used, with small sample sizes leading to depressed estimates
 of the extent of LD but inflated estimates of background levels of LD. In
 contrast, there was not much variation in LD among yearly cross-sections
 within either population once sample size was accounted for. Lack of
 pronounced interannual variability suggests that researchers may not have
 to worry about interannual variation when estimating LD in a population
 and can instead focus on obtaining the largest sample size possible.
description: RM_DataMicrosatellite genotypes for the Ram Mountain population.NBR_DataMicrosatellite genotypes for the National Bison Range population.
DOI: 10.5061/dryad.6n70v4b
title: Data from: Axial symptoms predict mortality in patients with Parkinson disease with subthalamic stimulation

description: Objective: To characterize how disease progression is associated with
 mortality in a large cohort of PD patients with long-term follow-up after
 STN-DBS. Methods: Motor and cognitive disabilities were assessed before,
 and 1, 2, 5 and 10 years after STN-DBS in 143 consecutive PD patients. We
 measured motor symptoms Off and On levodopa and STN-DBS, and recorded
 causes of death. We used linear mixed-models to characterize symptom
 progression, including interactions between treatment conditions and time
 to determine how treatments changed efficacy. We used joint models to link
 progression to mortality. Results: Median observation time was 12 years
 after surgery, during which akinesia, rigidity and axial symptoms
 worsened, with mean increases of 8.8 (SD 6.5), 1.8 (3.1) and 5.4 (4.1)
 points from year 1 to 10 after surgery (On dopamine/On STN-DBS),
 respectively. Responses to dopaminergic medication and STN-DBS were
 attenuated with time, but remained effective for all except axial
 symptoms, for which both treatments and their combination were predicted
 to be ineffective 20 years after surgery. Cognitive status significantly
 declined. Forty-one patients died with a median time to death of 9 years
 after surgery. The current level of axial disability was the only symptom
 that significantly predicted death (HR=4.30 [SE 1.50] per unit of
 square-root transformed axial score). Conclusions: We quantified long-term
 symptom progression and attenuation of dopaminergic medication and STN-DBS
 treatment efficacy in PD patients, and linked symptom progression to
 mortality. Axial disability significantly predicts individual risk of
 death after surgery, which may be useful for planning therapeutic
 strategies in PD.
description: Additional
 dataFigures 1-2, Tables
 1-4Lau_et_al_AdditionalData.pdf
DOI: 10.5061/dryad.939
title: Data from: Evidence that Egfr contributes to cryptic genetic variation for photoreceptor determination in natural populations of Drosophila melanogaster

description: One objective of quantitative genetics is to identify the nucleotide
 variants within genes that contribute to phenotypic variation and
 susceptibility [1]. In an evolutionary context, this means characterizing
 the molecular polymorphisms that modify the penetrance and expressivity of
 perturbed traits. A survey of association between 267 SNPs in almost 11 kb
 of the D. melanogaster Egfr and the degree of eye roughening due to a
 gain-of-function EgfrE1 allele crossed into 210 isogenic wild-type lines
 provides evidence that a handful of synonymous substitutions supply
 cryptic variation for photoreceptor determination. Ten sites exceed
 Bonferroni threshold for association in two sets of crosses to different
 EgfrE1 backgrounds including a particularly significant cluster of sites
 in tight linkage disequilibrium toward the 3′ end of the coding region.
 Epistatic interaction of this cluster with one other site enhances the
 expressivity of this haplotype. Replication of the strongest associations
 with an independent sample of 302 phenotypically extreme individuals
 derived from 1000 crosses of EgfrE1 to freshly trapped males was achieved
 using modified case-control and transmission-disequilibrium tests. A
 tendency for the rarer alleles to have more disrupted eye development
 suggests that mutation-selection balance is a possible mechanism
 contributing to maintaining cryptic variation for Egfr.
description: SNP Genotypes and Eye
 PhenotypesSNPeye.xlsCase-Control and TDTCaseTDT.xlsEnhanced MethodsDPBG_EnhMethods.pdfSupplementary Tables 1-3DPBG_SupplTables.pdf