cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bnzs7h48m
title: Phenotypic integration in feliform carnivores: covariation patterns and disparity in hypercarnivores versus generalists

description: The skeleton is a complex arrangement of anatomical structures that covary
 to various degrees depending on both intrinsic and extrinsic factors.
 Among the Feliformia, many species are characterized by predator
 lifestyles providing a unique opportunity to investigate the impact of
 highly specialised hypercarnivorous diet on phenotypic integration and
 shape diversity. To do so, we compared the shape of the skull, mandible,
 humerus, and femur of species in relation to their feeding strategies
 (hypercarnivorous versus generalist species) and prey preference
 (predators of small versus large prey) using three-dimensional geometric
 morphometric techniques. Our results highlight different degrees of
 morphological integration in the Feliformia depending on the functional
 implication of the anatomical structure, with an overall higher
 covariation of structures in hypercarnivorous species. The skull and the
 forelimb are not integrated in generalist species whereas they are in
 hypercarnivores. These results can potentially be explained by the
 different feeding strategies of these species. Contrary to our
 expectations, hypercarnivores display a higher disparity for the skull
 than generalist species. This is probably due to the fact that a
 specialisation toward high-meat diet could be achieved through various
 phenotypes. Finally, humeri and femora display shape variations depending
 on relative prey size preference. Large species feeding on large prey tend
 to have robust long bones due to higher biomechanical constraints.
DOI: 10.15468/dl.m9kbm5
title: Occurrence Download

description: A dataset containing 2434 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Prosopium coulterii",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2434 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002603-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.573n5tb5p
title: One-Year Outcome After Endovascular Treatment for Acute Basilar Artery Occlusion

description: Objective: To report the results of clinical follow-up at one year among
 patients in the BASILAR registry, a prospective registry that
 consecutively enrolled stroke patients with acute basilar artery occlusion
 from 47 comprehensive stroke centers in China between January 2014 and May
 2019. Methods: Patients in the BASILAR study received either conventional
 treatment or endovascular treatment. We assessed clinical outcomes in
 patients one year after enrolment into the BASILAR registry. The primary
 outcome was the modified Rankin scale score at one year, assessed as a
 common odds ratio using ordinal logistic regression shift analysis
 adjusted for pre-specified prognostic factors. Secondary outcomes included
 the modified Rankin scale-based outcome group at one year (0 to 1
 [excellent outcome], 0 to 2 [good outcome], or 0 to 3 [favorable outcome])
 and death from any cause. Results: Of the 829 patients enrolled in the
 original BASILAR study, one-year data were available for 785 patients
 (94.7%). The distribution of outcomes on the modified Rankin scale favored
 endovascular treatment over conventional treatment (adjusted common odds
 ratio, 4.50; 95% confidence interval, 2.81 to 7.29; P &lt; 0.001). The
 cumulative one-year mortality rate was 54.6% in the endovascular treatment
 group versus 83.5% in the conventional treatment group (adjusted hazard
 ratio, 4.36; 95% confidence interval, 2.69 to 7.29; P &lt; 0.001).
 Conclusions: The beneficial effect of endovascular treatment on functional
 outcome at one year in patients with acute basilar artery occlusion is
 similar to that reported at 90 days in the original study. Clinical trial
 identifiers Numbers: ChiCTR-180001475
DOI: 10.5061/dryad.cvdncjt2t
title: Carbohydrate depletion in roots impedes phosphorus nutrition of forest trees

description: The aim of the study was to determine the effect of belowground
 plant-derived carbohydrates on P uptake, P concentrations and enzymes
 activities related to P mobilization in roots, ectomycorrhizas and soil
 and on the abundances of P-related genes in soil bacteria. We report data
 from a girdling experiment in two temperate beech forest with contrasting
 soil phosphorus concentrations. We used soil cores and the fractions of
 the organic layer and mineral topsoil separately one and eight weeks after
 the girdling treatment. We collected bulk soil, rhizosphere and root. We
 provide data on soil for pH, water extractable organic carbon mineral
 elements in soil, and soil enzyme activities. Enzyme activities are shown
 for the bulk soil and the rhizosphere We provide data for microbial P,
 microbial biomass, gene abundances of P-related genes for soil bacteria,
 and phospholipid fatty acids. We provide data on root biomass,
 carbohydrates, total P, soluble, other root mineral nutrients, and
 phopphatase and enzyme activities. The data set further contain 33P
 labelling data for P uptake into roots.
description: Girdling plots were installed in beech (F. sylvatica L.) forests
 in two areas that differ in soil properties: Bad Brückenau (BBR), a high-P
 (HP) and Luess (LUE), a low-P (LP) site. For this study, three plots were
 installed in the HP and four in the LP forests in May 2017 (HP: 12.05, LP:
 05.05). Each plot had an area of 4 m² and was separated from the forest
 floor by a 0.25 m deep trench. Each plot was divided by a lawn edge into
 two equal subplots.
DOI: 10.5061/dryad.fj6q573sg
title: Using genomic prediction to detect microevolutionary change of a quantitative trait

description: Detecting microevolutionary responses to natural selection by observing
 temporal changes in individual breeding values is challenging. The
 collection of suitable datasets can take many years and disentangling the
 contributions of the environment and genetics to phenotypic change is not
 trivial. Furthermore, pedigree-based methods of obtaining individual
 breeding values have known biases. Here, we apply a genomic prediction
 approach to estimate breeding values of adult weight in a 35-year dataset
 of Soay sheep (Ovis aries). Comparisons are made with a traditional
 pedigree-based approach. During the study period adult body weight
 decreased, but the underlying genetic component of body weight increased,
 at a rate that is unlikely to be attributable to genetic drift. Thus
 cryptic microevolution of greater adult body weight has probably occurred.
 Genomic and pedigree-based approaches gave largely consistent results.
 Thus, using genomic prediction to study microevolution in wild populations
 can remove the requirement for pedigree data, potentially opening up new
 study systems for similar research.
description: The data includes a combination of field data and genomic and
 pedigree-derived estimated breeding values (GEBVs/PEBVs) of weight,
 collected from a wild population of Soay sheep (Ovis aries).
 R code to reproduce the results in the paper is also
 included.
description: There are no missing data, although users are encouraged to
 contact the authors for further information about the biology of the study
 system.
DOI: 10.5061/dryad.bcc2fqz9v
title: Data from: Changes in soil pH and their dependence on the species of cereals and strategies for sustainable agriculture

description: The acidity of the environment is one of the key elements determining
 proper conditions for crop cultivation. Inappropriate environmental
 conditions may contribute to numerous changes in plant raw materials. New
 strategies introduced in agriculture bring with them some uncertainties
 associated with the adaptation of plants to the soil. Currently, in the EU
 market, a gradual replacement of conventional strategies in favour of
 organic ones is observed. The change in fertilization strategy may lead to
 the emergence of new soil conditions in cultivation. Soil pH and humus
 content determine the phenomenon of soil fertility as well as soil
 physical, chemical, and biological properties. Rational and effective
 management of nutrients is related to the assessment of the content of
 available nutrients in the soil, as well as to the agronomic assessment of
 the soil class. This type of treatment is key in the planning of crops
 rotation. The study aimed to evaluate soil pH after combine harvesting, in
 wheat, rye, and barley crops cultivation according to two agricultural
 strategies, viz. ecological and conventional.  In the course of
 the study mature soil was sampled. The research was carried out on pH
 meter CP 411 combined with an EPS-1 pH electrode. The obtained soil pH
 results varied according to the type of cereal grown. Statistical analysis
 of variance with the significance level of 0.05 showed no significant
 difference regardless of the implemented agricultural strategy. It is
 recommended once every 4 years to perform laboratory examination of soil
 pH for fertilization advice.
description: The samples were collected directly on the field in 30 samples
 and pH was measured in the labolatory according to standards.
DOI: 10.5061/dryad.12jm63xwd
title: Exposing distinct subcortical components of the auditory brainstem response evoked by continuous naturalistic speech

description: Speech processing is built upon encoding by the auditory nerve and
 brainstem, yet we know very little about how these processes unfold in
 specific subcortical structures. These structures are deep and respond
 quickly, making them difficult to study during ongoing speech. Recent
 techniques begin to address this problem, but yield temporally broad
 responses with consequently ambiguous neural origins. Here we describe a
 method that pairs re-synthesized 'peaky' speech with
 deconvolution analysis of EEG recordings. We show that in adults with
 normal hearing, the method quickly yields robust responses whose component
 waves reflect activity from distinct subcortical structures spanning
 auditory nerve to rostral brainstem. We further demonstrate the
 versatility of peaky speech by simultaneously measuring bilateral and
 ear-specific responses across different frequency bands, and discuss
 important practical considerations such as talker choice. The peaky speech
 method holds promise as a tool for investigating speech encoding and
 processing, and for clinical applications.
description: Methods information is provided in the manuscript as well as the
 README and accompanying files to the datasets.
description: All necessary information is provided in the manuscript, a README
 file for the entire dataset, as well as README and sidecar files in the
 datasets.
DOI: 10.5061/dryad.dbrv15f04
title: Three-dimensional surface models of hand bones (individual 15-06)

description: Objectives: Cuncaicha, a rockshelter site in the southern Peruvian Andes,
 has yielded archaeological evidence for human occupation at high elevation
 (4480 masl) during the Terminal Pleistocene (12,500 to 11,200 cal BP),
 Early Holocene (9500-9000 cal BP), and later periods. One of the excavated
 human burials (Feature 15-06), corresponding to a middle-aged female dated
 to ~8500 cal BP, exhibits skeletal osteoarthritic lesions previously
 proposed to reflect habitual loading and specialized crafting labor. Three
 small tools found in association with this burial are hypothesized to be
 associated with precise manual dexterity. Materials and Methods: Here, we
 tested this functional hypothesis through the application of a novel
 multivariate methodology for the three-dimensional analysis of muscle
 attachment surfaces (entheses). This original approach has been recently
 validated on both lifelong-documented anthropological samples as well as
 experimental studies in non-human laboratory samples. Additionally, we
 analyzed the three-dimensional entheseal shape and resulting moment arms
 for muscle opponens pollicis. Results: Results show that Cuncaicha
 individual 15-06 shows a distinctive entheseal pattern associated with
 habitual precision grasping via thumb-index finger coordination, which is
 shared exclusively with documented long-term precision workers from recent
 historical collections. The separate geometric morphometric analysis
 revealed that the individual’s opponens pollicis enthesis presents a
 highly projecting morphology, which was found to strongly correlate with
 long joint moment arms (a fundamental component of force-producing
 capacity), closely resembling the form of Paleolithic hunter-gatherers
 from diverse geo-chronological contexts of Eurasia and North Africa.
 Discussion: Overall, our findings provide the first bio-cultural evidence
 to confirm that the lifestyle of some of the earliest Andean inhabitants
 relied on habitual and forceful precision grasping tasks.
description: Three-dimensional surface models were developed using a
 Breuckmann Smartscan scanner (Hexagon Inc.).
description: For calculating entheseal 3D form (size and shape) and performing
 multivariate analyses using different entheses, please refer to the
 detailed information of the manuscript itself.
DOI: 10.5061/dryad.2rbnzs7m9
title: Data for Concordance-based approaches in phylogenomics

description: Gene tree conflict is common and finding methods to analyze and alleviate
 the negative effects that conflict has on species tree analysis is a
 crucial part of phylogenomics. This study aims to expand the discussion of
 inferring species trees and molecular branch lengths when conflict is
 present. Conflict is typically examined in two ways: inferring its
 prevalence, and inferring the influence of the individual genes (how
 strongly one gene supports any given topology compared to an alternative
 topology). Here, we examine a procedure for incorporating both conflict
 and the influence of genes in order to infer evolutionary relationships.
 All supported relationships in the gene trees are analyzed and the
 likelihood of the genes constrained to these relationships is summed to
 provide a likelihood for the relationship. Consensus tree assembly is
 conducted based on the sum of likelihoods for a given relationship and
 choosing relationships based on the most likely relationship assuming it
 does not conflict with a relationship that has a higher likelihood score.
 If it is not possible for all most likely relationships to be combined
 into a single bifurcating tree then multiple trees are produced and a
 consensus tree with a polytomy is created. This procedure allows for more
 influential genes to have greater influence on an inferred relationship,
 does not assume conflict has arisen from any one source, and does not
 force the dataset to produce a single bifurcating tree. Using this
 approach on three empirical datasets, we examine and discuss the
 relationship between influence and prevalence of gene tree conflict. We
 find that in one of the datasets, assembling a bifurcating consensus tree
 solely composed of the most likely relationships is impossible. To account
 for conflict in molecular rate analysis we also introduce a
 concordance-based approach to the summary and estimation of branch lengths
 suitable for downstream comparative analyses. We demonstrate through
 simulation that even under high levels of stochastic conflict, the mean
 and median of the concordant rates recapitulate the true molecular rate
 better than using a supermatrix approach. Using a large phylogenomic
 dataset, we examine rate heterogeneity across concordant genes with a
 focus on the branch subtending crown angiosperms. Notably, we find highly
 variable rates of evolution along the branch subtending crown angiosperms.
 The approaches outlined here have several limitations,­ but they also
 represent some alternative methods for harnessing the complexity of
 phylogenomic datasets and enrich our inferences of both species’
 relationships and evolutionary processes.
DOI: 10.5061/dryad.73n5tb2vw
title: Data from: An analysis of travel reports of the Finnish botanical expeditions to Russian Lapland (Murmansk Region and Northern Karelia) in 1861 and 1863

description: Finnish botanical expeditions, which were made to Russian Lapland
 (present-day Murmansk Region and northern Karelia, Russia) in 1861 and
 1863, published travel reports with preliminary information, which
 contained numerous floristic novelties and phytogeographical observations
 but have been overlooked in present-day studies. Two reports appeared in
 print, by Gustav Selin on the expedition made in 1861, and by Nils Isak
 Fellman on the expedition made in 1863. We analysed mentions of vascular
 plant species published in these travel reports in order to trace and
 evaluate first records and localities of rare and legally protected
 species on the basis of herbarium vouchers kept at H. In spite of high
 self-claims, Selin actually reported 9 species new to present-day Murmansk
 Region and 1 species new to Republic of Karelia, and 4 species of vascular
 plants that are currently under legal protection in Murmansk Region,
 whereas Fellman reported 11 species new to Murmansk Region and 5 species
 new to Karelia, with 34 species under legal protection in Murmansk Region.
 First records of alien plants were 7 species from Selin and 4 species from
 Fellman. These numbers brought the contemporary floristic knowledge in
 Russian Lapland to 504 species of native plants (50% of the current total)
 and 54 species of alien plants (11% of the current total). Fellman’s
 report included the first phytogeographical observations from the Kola
 Peninsula, with the first botanical limits observed, and the first
 descriptions of key botanical territories which are currently under strict
 protection. This study contributes to botanical history, plant protection
 and management of plant invasions in Murmansk Region.
description: The dataset is based on the specimens kept at the Museum of
 Natural History, University of Helsinki.
DOI: 10.5061/dryad.hx3ffbgck
title: The perfect storm: Gene tree estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant ancient angiosperm clade, Malpighiales

description: The genomic revolution offers renewed hope of resolving rapid radiations
 in the Tree of Life. The development of the multispecies coalescent (MSC)
 model and  improved gene tree estimation methods can better
 accommodate gene tree heterogeneity caused by incomplete lineage sorting
 (ILS) and gene tree estimation error stemming from the short internal
 branches. However, the relative influence of these factors in species tree
 inference is not well understood. Using anchored hybrid enrichment, we
 generated a data set including 423 single-copy loci from 64 taxa
 representing 39 families to infer the species tree of the flowering plant
 order Malpighiales. This order includes nine of the top ten most unstable
 nodes in angiosperms, which have been hypothesized to arise from the rapid
 radiation during the Cretaceous. Here, we show that coalescent-based
 methods do not resolve the backbone of Malpighiales and concatenation
 methods yield inconsistent estimations, providing evidence that gene tree
 heterogeneity is high in this clade. Despite high levels of ILS and gene
 tree estimation error, our simulations demonstrate that these two factors
 alone are insufficient to explain the lack of resolution in this order. To
 explore this further, we examined triplet frequencies among empirical gene
 trees and discovered some of them deviated significantly from those
 attributed to ILS and estimation error, suggesting gene flow as an
 additional and previously unappreciated phenomenon promoting gene tree
 variation in Malpighiales. Finally, we applied a novel method to quantify
 the relative contribution of these three primary sources of gene tree
 heterogeneity and demonstrated that ILS, gene tree estimation error, and
 gene flow contributed to 15%, 52%, and 32% of the variation, respectively.
 Together, our results suggest that a perfect storm of factors likely
 influence this lack of resolution, and further indicate that recalcitrant
 phylogenetic relationships like the backbone of Malpighiales may be better
 represented as phylogenetic networks. Thus, reducing such groups solely to
 existing models that adhere strictly to bifurcating trees greatly
 oversimplifies reality, and obscures our ability to more clearly discern
 the process of evolution.
description: Supplementary materials for Cai et al., including supplementary
 notes, figures, and tables. Sequence alignment, gene trees, and species
 trees are also included.
DOI: 10.5061/dryad.jwstqjq79
title: A new phylogenetic hypothesis for Cereinae (Cactaceae) points to a monophyletic subtribe

description: Cereinae comprises 14 genera distributed in Neotropical dry forest
 formations such as in the Caatingas of Northeastern  or in rocky
 outcrops in the north of Southeastern Brazil. Historically, the taxonomy
 of the group has been very controversial, especially regarding generic
 circumscriptions, and phylogenetic relationships within the group are
 still poorly understood. To investigate the delimitation of the subtribe
 and infra-subtribal relationships, we performed a phylogenetic analysis
 including 50 taxa representing 13 genera using one nuclear (PhyC) and four
 cpDNA (petL-psbE, trnL-trnT, trnS-trnG, and rpl16) regions. Our results
 show a monophyletic Cereinae with high support in Bayesian, maximum
 parsimony, and maximum likelihood analyses based on combined matrices.
 Although our results expand the knowledge of generic relationships, we
 emphasize the need for further molecular phylogenetic studies combined
 with ecological evidence to clarify relationships at the more inclusive
 nodes of the subtribe.