cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.31zcrjdkb
title: Data From: A New Distinctive Species of Schizanthus (Solanaceae) and the Reinstatement of Schizanthus fallax

description: A new Schizanthus species from northern Chile is described and
 illustrated. Schizanthus nutantiflorus was discovered based on recent
 collections made during unusual rain events in the Atacama Desert in 2015.
 The new species is distinguished morphologically from other Schizanthus
 species from northern Chile by its short corolla tube, with a distinct
 upper lip arrangement and colour, having the longest lower lip, and
 downward-facing flowers. Additionally, the reinstatement of Schizanthus
 fallax is proposed. By using both nDNA and cpDNA, phylogenetic
 relationships among all species of Schizanthus were investigated.
 Molecular and field observations, as well as an exhaustive morphological
 revision of fresh material and herbarium specimens, supports the
 segregation of Schizanthus with short corolla tubes from northern Chile
 into three species. We propose that, in order to fully understand both the
 taxonomy and evolution of Schizanthus, an integrative framework
 encompassing molecular, ecological and morphological data should be
 carried out. Information on distribution, habitat, conservation status,
 besides taxonomic notes and illustrations are provided. In addition, an
 updated key for the species of Schizanthus from northern Chile is given.
description: The following dataset is the complete list of analysed specimens
 of Schizanthus. The revision was done by Javiera Chinga and Nicolás
 Lavandero.
description: <strong>Lavandero_et_al._2021_Schizanthus_specimens.csv </strong> A complete list of analyzed specimens of Schizanthus for the present study
DOI: 10.5061/dryad.51c59zw84
title: Deciphering voids in Dasycladales, the case of Dragastanella transylvanica, a new Lower Cretaceous triploporellacean genus from Romania

description: Dragastanella transylvanica n.gen. n.sp. is described. Its calcified
 skeleton contains numerous voids, partly related to the moulds of soft
 parts of the alga, but also to lack of calcification. Interpretation of
 these voids, especially their attribution to original structures (e.g.,
 primary lateral vs. reproductive organ), has important implications for
 the taxonomic position of the alga, even at family level. Examination of
 key sections that include the boundary between sterile and fertile parts
 of the alga excludes the occurrence of external reproductive organs.
 Unusual, paired pores in the outer part of the mineralized skeleton
 reflect an asymmetry within the whorl, excluding the presence of secondary
 laterals. The alga is characterized by a cylindrical to club-shaped
 thallus bearing only phloiophorous primary laterals arranged in whorls and
 flaring outwards, forming a cortex. Mineralized lenticular reproductive
 organs containing cysts set in the equatorial plane (Russoella-type
 gametophores) occur inside primary laterals (cladosporous arrangement of
 the reproductive organs). These characters support establishment of the
 new genus Dragastanella. The new species Dragastanella transylvanica
 resembles species previously referred to Zittelina (Zittelina hispanica
 and Zittelina massei) and Triploporella (Triploporella matesina and
 Triploporella carpatica). Except for Triploporella carpatica, whose
 mineralized skeleton does not permit confident attribution to either
 Triploporella or Dragastanella, the other species must be ascribed to
 Dragastanella. Therefore, the following new combinations are proposed:
 Dragastanella hispanica n. comb., Dragastanella massei n. comb.,
 Dragastanella matesina n. comb. Despite widely overlapping biometrical
 measurements, these species can be differentiated by the size and location
 of their reproductive organs, the pattern of calcification around the
 primary laterals, and relationships among structural parameters such as
 the size of laterals, number of laterals per whorl and distance between
 whorls.
description: Biometric measurements processed by excel.
DOI: 10.5061/dryad.rv15dv47s
title: Interactions between belowground traits and rhizosheath fungal and bacterial communities for phosphorus acquisition

description: 1. Plant-soil microbes interactions play a central role in plant nutrient
 acquisition and thus ecosystem functioning and nutrient availability in
 agroecosystems. Adjustments in root morphology, root exudation and
 associations with microorganisms such as arbuscular mychorrizal fungi are
 common for phosphorus acquisition. Yet how plant belowground functional
 traits interact with microbial communities for P-acquisition remains
 largely unknown, limiting our understanding of phosphorus availability in
 agroecosystems. 2. Interactions between belowground functional traits and
 rhizosheath soil microbial communities for P-acquisition were investigated
 across eight herbaceous species with contrasting root traits. Root
 morphological and physiological traits involved in P-acquisition were
 quantified simultaneously with PLFA (phospholipid fatty acid) and NLFA
 (neutral lipid fatty acid) microbial bioindicators. 3. Multiple
 correlations were observed between root morphology, root exudates and
 rhizosheath fungal and bacterial communities. Root exudates and in
 particular release of malate and malonate were strongly linked with
 indicators of Gram-negative bacteria, which were correlated with changes
 in rhizosheath soil P concentration and plant P content. 4. Our results
 suggest that root exudation of carboxylates may play an important role in
 plant-soil microorganism interactions for P-acquisition, underlining their
 likely role in shaping microbial communities. Incorporating these
 interactions in biogeochemical models would lead to better predicting
 power and understanding of P cycling and ecosystem functioning.
description: Michel-Pierre Faucon, David Houben and Anissa Lounès-Hadj
 Sahraoui helped define the experimental design. Hacène Meglouli and
 Nicolas Honvault carried out the experiment. Stéphane Firmin, Hans Lambers
 and Arnaud Coutu helped process and interpret the data. All authors
 contributed to the final version of the manuscript.
description: Missing values indicated by "NA"
DOI: 10.5061/dryad.2ngf1vhnc
title: Informed breeding dispersal following stochastic changes to patch quality in a pond-breeding amphibian

description: 1. The unidirectional movement of animals between breeding patches (i.e.,
 breeding dispersal) has profound implications for the ecological and
 evolutionary dynamics of spatially structured populations. In
 spatiotemporally variable environments, individuals are expected to adjust
 their dispersal decisions according to information gathered on the
 environmental and/or social cues that reflect the fitness prospects in a
 given breeding patch (i.e., informed dispersal). 2. A paucity of empirical
 work limits our understanding of the ability of animals to depart from low
 quality breeding patches and settle in high quality breeding patches. We
 examined the capacity of individuals to respond to stochastic changes in
 habitat quality via informed breeding dispersal in a pond-breeding
 amphibian. 3. We conducted a five-year (2015–2019) capture-recapture study
 of boreal toads Anaxyrus boreas boreas (n = 1100) that breed in beaver
 ponds in western Wyoming, USA. During early spring of 2017, an extreme
 flooding event destroyed several beaver dams and resulted in the loss of
 breeding habitat. We used multi-state models to investigate how temporal
 changes in pond characteristics influenced breeding dispersal, and
 determined whether movement decisions were in accordance with prospects
 for reproductive fitness. 4. Boreal toads more often departed from low
 quality breeding ponds (without successful metamorphosis) and settled in
 high quality breeding ponds (with successful metamorphosis). Movement
 decisions were context-dependent and associated with pond characteristics
 altered by beaver dam destruction. Individuals were more likely to depart
 from shallow ponds with high vegetation cover and settle in deep ponds
 with low vegetation cover. The probability of metamorphosis was related to
 the same environmental cues, suggesting that boreal toads assess the
 fitness prospects of a breeding patch and adjust movement decisions
 accordingly (i.e., informed breeding dispersal). 5. We demonstrate that
 stochastic variability in environmental conditions and habitat quality can
 underpin dispersal behavior in amphibians. Our study highlights the
 mechanistic linkages between habitat change, movement behavior, and
 prospects for reproductive performance, which is critical for
 understanding how wild animals respond to rapid environmental change.
description: Please refer to the README files associated with each dataset for
 information on how the data were collected and processed.
DOI: 10.5061/dryad.73n5tb2wx
title: Progressive neurochemical abnormalities in cognitive and motor subgroups of ALS: a prospective multicentre study

description: Objective: To evaluate progressive cerebral degeneration in amyotrophic
 lateral sclerosis (ALS) by assessing alterations in N-acetylaspartate
 (NAA) ratios in the motor and prefrontal cortex within clinical subgroups
 of ALS. Methods: Seventy-six ALS patients and 59 healthy controls were
 enrolled a prospective, longitudinal, multicenter study in the Canadian
 ALS Neuroimaging Consortium (CALSNIC). Participants underwent serial
 clinical evaluations and MRS at baseline, 4 and 8 months using a
 harmonized protocol across 5 centers. NAA ratios were quantified in the
 motor cortex and prefrontal cortex. Patients were stratified into
 subgroups based on disease progression rate, upper motor neuron (UMN)
 signs, and cognitive status. Linear mixed models were used for baseline
 and longitudinal comparisons of NAA metabolite ratios. Results: Patients
 with ALS had reduced NAA ratios in the motor cortex at baseline (P
 &lt; 0.001). Ratios were lower in those with more rapid disease
 progression and greater UMN signs (P &lt; 0.05). A longitudinal
 decline in NAA ratios was observed in the motor cortex in the rapid
 progressing (P &lt; 0.01) and high UMN burden (P &lt; 0.01)
 cohorts. The severity of UMN signs did not change significantly over time.
 NAA ratios were reduced in the prefrontal cortex only in cognitively
 impaired patients (P &lt; 0.05); prefrontal cortex metabolites did not
 change over time. Conclusions: Progressive degeneration of the motor
 cortex in ALS is associated with more aggressive clinical presentations
 These findings provide biological evidence of variable spatial and
 temporal cerebral degeneration linked to the disease heterogeneity of ALS.
 The use of standardized imaging protocols may have a role to play in
 clinical trials for patient selection or subgrouping. Classification of
 Evidence: This study provides Class II evidence that MRS NAA metabolite
 ratios of the motor cortex are associated with more rapid disease
 progression and greater UMN signs in patients with ALS.
DOI: 10.5068/d15q4c
title: Data from: Gentle topography increases vertical transport of coarse dust by orders of magnitude

description: The presence of coarse mineral dust in the atmosphere has been
 substantiated in several recent measurement campaigns, which include
 observations of particles up to and above 100 micrometer in diameter. Yet,
 atmospheric dust models either do not include particles larger than 20
 micrometer or severely underestimate their concentrations. One possibility
 for the underestimated concentrations is that models do not represent
 enhancements of particle transport due to subgrid-scale topography. Here,
 large-eddy simulations are used in combination with Lagrangian particle
 tracking to assess the impact of gentle two-dimensional topography with 50
 and 100 m elevation on the vertical transport of coarse dust in
 neutrally-stratified conditions. The presence of topography significantly
 increases the likelihood that 5 and 20 micrometer particles reach several
 hundred meters in altitude. Further, topography increases this likelihood
 by orders of magnitude for larger 60 micrometer particles. Three
 mechanisms are observed to contribute to the increased vertical transport:
 a strong upward mean flow region on the uphill side of the topography,
 ejection of particles downwind of the topography crest, and enhanced
 vertical dispersion in the wake of the crest. The compounding effects of
 these mechanisms provide a pathway for coarse dust emitted from the
 surface to reach elevations where they can be further transported into the
 free atmosphere by large-scale motions such as convective plumes. While
 these findings are motivated by mineral dust observations, they are
 generally applicable to other heavy aerosols such as pollen.
description: The dataset is a collection of computational results based on
 large-eddy simulation (LES) of the atmospheric boundary layer and
 Lagrangian tracking of coarse dust particles. Three simulations of the
 boundary layer are included: over flat terrain, over a small 50 m hill,
 and over a large 100 m hill. The LES was wall-modeled, and the
 two-dimensional hill was represented using immersed boundary
 methods. Coarse dust particles were released near the
 ground in the simulations and their trajectories were tracked based on the
 LES velocity fields. Three particle sizes - 5, 20, and 60 micrometer
 diameter - were released for each of the three LES topography cases, thus
 totaling nine scenarios. Further details regarding the methodology are
 available in the related article.
description: The data comprise processed statistics corresponding to the
 published results of the simulations. These include time-averages LES
 velocities and particle trajectory statistics. The data are organized as
 tab-separated values in text files, where the header rows provide relevant
 information. The figure number in each file name refers to the
 corresponding figure in the related article.
DOI: 10.5061/dryad.76hdr7swc
title: Comparison among the chloroplast genomes of five species of Chamaerhodos (Rosaceae: Potentilleae): phylogenetic implications

description: Chamaerhodos is a small genus with ca 7–8 species with a disjunct
 distribution in Asia and western North America. Due to limited
 sampling of species and genes in previous studies, little is known about
 the phylogenetic relationships among the species. Moreover, chloroplast
 genomic resources for Chamaerhodos have been limited. Herein, we conducted
 a comparative analysis of the complete chloroplast (cp)
 genomes of five Chamaerhodos species. The five
 cp genomes had a typical quadripartite structure with high conservation of
 gene content and gene order. These five cp genomes encoded an identical
 set of 129 genes, including 84 protein-coding genes, 37 tRNA genes and
 eight rRNA genes. Comparison of the boundaries between the IRs and single
 copy regions revealed only very slight boundary differences and the five
 cp genomes showed only little sequence divergence. Seven regions
 (trnR-UCU-atpA, trnS-GCU-
 trnG-UCC, TrnG-GCC-trnfM-CAU, trnL-UAA intron, trnH-GUG-psbA, trnF-GAA- ndhJ, matK-5′-trnK-UUU) were identified as excellent candidate markers. A total of 117, 108, 116, 117 and 118 perfect SSRs were detected in the cp genomes of Ch. altaica, Ch. canescens, Ch. erecta, Ch. sabulosa and Ch. trifida, respectively. A phylogenetic analysis support the monophyly of Chamaerhodos and place it as part of the Fragariinae clade sister to the clade of Dasiphora, Drymocallis and Potaninia. Within Chamaerhodos, Ch. canescens was inferred sister to a clade containing the other four species. The detailed characterization of the Chamaerhodos chloroplast genomes sets the foundation for further studies on the genus and its close relatives in the economically important Rosaceae.
description: Figure S1. MAUVE alignments of chloroplast genomes of five <i>Chamaerhodos</i> species. Table S1. The GenBank accession numbers of all the 41 chloroplast genome sequences used for phylogenetic analysis. Table S2. The nucleotide diversity (Pi) values of 264 homologous loci.
DOI: 10.5061/dryad.j9kd51cc7
title: Dual‐fluorescence imaging and automated trophallaxis detection for studying multi‐nutrient regulation in superorganisms

description: In the related manuscript, we present a dual-fluorescence imaging
 setup designed to track two food sources, each labeled with a
 different fluorophore, as they are disseminated throughout a freely
 behaving colony of individually tagged ants. Additionally, our image-based
 deep learning algorithm for automatic detection of ant trophallaxis events
 efficiently yields a detailed record of all food-transfer interactions.
 Using a series of calibration experiments, we demonstrate the reliability
 of our measurements. We then exemplify the capabilities of our new method
 by tracking food dissemination in a colony of Camponotus
 sanctus ants supplied with two nutritionally-distinct food
 sources. This dataset contains data and Matlab code related to: 1.
 Calibration and validation of the dual-fluorescence imaging technique 2.
 Training and employing a deep neural network for detecting trophallaxis 3.
 Sample data from a multinutrient feeding experiment
description: This data was collected using the experimental setup described in
 the manuscript. For further details, see README files
 within and related manuscript.
description: <strong>Dual fluorescence imaging:</strong>
 Data presented here was used to generate the figures in the
 related manuscript. <strong>Trophallaxis
 detection:</strong> We here provide our trained
 trophallaxis detection network and Matlab code for using it to
 detect trophallaxis in videos of <em>Camponotus
 sanctus</em> ants tagged with Bugtag (Robiotec) tags.
 One may modify the code to apply to videos of ants tracked with a
 different method (e.g. other tags, tracking of untagged ants), or to
 videos of untracked ants if the identity of ants is not important to
 one's needs. As the supplied network has been
 trained only on images of <i>C. sanctus</i> ants, it may be
 less optimal for detecting trophallaxis in other species. One may use the
 supplied network as a starting point for training detection of
 trophallaxis of other species. We supply code for transfer learning which
 was used for training our network. This code can be modified for
 retraining our network on additional training data. We
 also provide the library of annotated images used to train the
 trophallaxis detection network. One may use these images for training
 networks and classifiers other than the one we provide.
DOI: 10.5061/dryad.pk0p2ngn9
title: Extraordinarily rapid proliferation of cultured muscle satellite cells from migratory birds

description: Migratory birds experience bouts of muscle growth and depletion as they
 prepare for, and undertake prolonged flight. Our studies of migratory bird
 muscle physiology in vitro led to the discovery that sanderling (Calidris
 alba) muscle satellite cells proliferate more rapidly than other normal
 cell lines. Here we determined the proliferation rate of muscle satellite
 cells isolated from five migratory species (sanderling; ruff, Calidris
 pugnax; western sandpiper, Calidris mauri; yellow-rumped warbler,
 Setophaga coronata; Swainson’s thrush, Catharus ustulatus) from two
 families (shorebirds and songbirds) and with different migratory
 strategies. Ruff and sanderling satellite cells exhibited rapid
 proliferation, with population doubling times of 9.3±1.3 and 11.4±2.0 hrs
 whereas the remaining species’ cell doubling times were ≥24 hrs. The
 results indicate that the rapid proliferation of satellite cells is not
 associated with total migration distance but may be related to flight bout
 duration and interact with lifespan.
description: Cells were manually counted using a hemocytometer under a light
 microscope. 't' represents the number of hours after plating
 that cells were counted. 'sp' indicates the species and
 'id' indicates the individual identification name for each
 biological replicate. 'replicate' indicates the technical
 replicate on each row, counts were conducted in duplicate (A and B).
 'bFGF' indicates whether the basic fibroblast growth factor
 (bFGF) treatment was applied (Y) or not (N). 'count' indicates
 the total number of cell counted across 'squares_counted' number
 of squares on the hemocytometer. 'Dilution' indicates the
 dilution factor of the cell suspension added to the hemocytometer and
 'volume_ml' indicates the total volume of the cell
 suspension.
description: The associated .Rmd and .html files are matched source and
 knitted output files describing the analysis and visualization process
 used to produce the results in this manuscript. The comments and
 explanations are self contained with the data description above.
DOI: 10.5061/dryad.bzkh1898c
title: The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding the origin of domestic goat

description: The mammalian Y chromosome offers a unique perspective on the male
 reproduction and paternal evolutionary histories. However, further
 understanding of the Y chromosome biology for most mammals is hindered by
 the lack of a Y chromosome assembly. This study presents an integrated in
 silico strategy for identifying and assembling the goat Y-linked scaffolds
 using existing data. A total of 11.5 Mb Y-linked sequences were clustered
 into 33 scaffolds, and 187 protein-coding genes were annotated. We also
 identified high abundance of repetitive elements. A 5.84 Mb subset was
 further ordered into an assembly with the evidence from the goat
 Radiation-Hybrid map (RH map). The existing whole-genome re-sequencing
 data of 96 goats (worldwide distribution) were utilized to exploit the
 paternal relationships among bezoars and domestic goats. Goat paternal
 lineages were clearly divided into two clades (Y1 and Y2), predating the
 goat domestication. Demographic history analyses indicated that maternal
 lineages experienced a bottleneck effect around 2,000 YBP (years before
 present), after which goats belonging to the A haplogroup spread worldwide
 from the Near East. As opposed to this, paternal lineages experienced a
 population decline around the 10,000 YBP. The evidence from the Y
 chromosome suggests that male goats were not affected by the A haplogroup
 worldwide transmission, which implies sexually unbalanced contribution to
 the goat trade and population expansion in post-Neolithic period.