cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.11p757m0
title: Data from: Does hybridization drive the transition to asexuality in diploid Boechera?

description: Gametophytic apomixis is a common form of asexual reproduction in plants.
 Virtually all gametophytic apomicts are polyploids, and some view
 polyploidy as a prerequisite for the transition to apomixis. However, any
 causal link between apomixis and polyploidy is complicated by the fact
 that most apomictic polyploids are allopolyploids, leading some to
 speculate that hybridization, rather than polyploidy, enables apomixis.
 Diploid apomixis presents a rare opportunity to isolate the role of
 hybridization, and a number of diploid apomicts have been documented in
 the genus Boechera (Brassicaceae). Here we present the results of a
 microsatellite study of 1393 morphologically and geographically diverse
 diploid individuals, evaluating the hypothesis that diploid Boechera
 apomicts are hybrids. This genus-wide dataset was made possible by the
 applicability of a core set of microsatellite loci in 69 of the 70 diploid
 Boechera species and by our ability to successfully genotype herbarium
 specimens of widely varying ages. With few exceptions, diploid apomicts
 exhibited markedly high levels of heterozygosity resulting from the
 combination of disparate genomes. This strongly suggests that most
 apomictic diploid Boechera lineages are of hybrid origin, and that the
 genomic consequences of hybridization allow for the transition to
 gametophytic apomixis in this genus.
description: 96-well_extractionThe associated file describes a plant DNA extraction protocol modified for deep-welled tubes in 96-well racks.1393_diploids_dataSample information for the 1393 diploids analyzed in this study.
DOI: 10.5061/dryad.f3g87s82
title: Data from: Phylogeny and taxonomy of an enigmatic sterile lichen

description: Crustose, asexually reproducing taxa represent a large component of lichen
 biodiversity that is often overlooked and underestimated; as a result,
 remarkable potential remains for discovery of new species in this
 neglected, polyphyletic group. For this study, ITS and mtSSU rDNA
 sequences were analyzed in conjunction with chemical and anatomical data
 to understand the systematic placement of an enigmatic, sterile lichen.
 This species, despite references in the literature, and being known for
 over half a decade, has remained undescribed due to our inability to
 integrate it into a higher-level taxonomic framework using morphology
 alone. Here we demonstrate the utility of a systematic methodology that
 combines molecular and non-molecular characters to place and circumscribe
 species of asexually reproducing lichens that are typically sterile. Based
 on our analyses, the new species, Caloplaca reptans, shows phylogenetic
 and morphological affinities to a broad group of Caloplaca species with
 gray thalli, including the type species of the genus, C. cerina. This
 study highlights that the family Teloschistaceae is morphologically more
 diverse than previously understood, and contains elements that cannot
 easily be placed in known 'species groups.'
description: Hodkinson_and_Lendemer_reptans_Perl_scriptsThis zip archive contains two Perl scripts for processing FASTA files exported from GenBank. The Perl script 'fasta_from_NCBI_editor.pl' creates a fasta file with names that can be easily used for downstream applications (e.g., 'Genus_species_GBAcc_GI'). The 'create_data_table_from_NCBI_fasta.pl' script automatically creates a data table with all species identifications, GenBank Accession numbers and GenInfo Identifiers for the exported sequences.Hodkinson_and_Lendemer_reptans_2_genesThis zip archive contains all of the input and output files associated with phylogenetic analyses run on the two-gene data set assembled for the associated publication.Hodkinson_and_Lendemer_reptans_ITS_onlyThis zip archive contains all of the input and output files associated with phylogenetic analyses run on the ITS-only data set assembled for the associated publication.
DOI: 10.5061/dryad.4jh2t893
title: Data from: Genetic diversity of wild grapevine populations in Spain and their genetic relationships with cultivated grapevines

description: The wild grapevine, Vitis vinifera L. ssp sylvestris (Gmelin) Hegi,
 considered as the ancestor of the cultivated grapevine, is native from
 Eurasia. In Spain natural populations of Vitis vinifera ssp sylvestris can
 still be found along river banks. In this work we have performed a wide
 search of wild grapevine populations in Spain and characterized the amount
 and distribution of their genetic diversity using 25 nuclear SSR loci. We
 have also analyzed the possible coexistence in the natural habitat of wild
 grapevines with naturalized grapevine cultivars and rootstocks. In this
 way, phenotypic and genetic analyses identified 19% of the collected
 samples as derived from cultivated genotypes, being either naturalized
 cultivars or hybrid genotypes derived from spontaneous crosses between
 wild and cultivated grapevines. The genetic diversity of wild grapevine
 populations was similar than that observed in the cultivated group. The
 molecular analysis showed that cultivated and wild germplasm are
 genetically divergent with low level of introgression. Using a model-based
 approach implemented in the software STRUCTURE we identified four genetic
 groups, with two of them fundamentally represented among cultivated
 genotypes and two among wild accessions. The analyses of genetic
 relationships among wild and cultivated grapevines could suggest a genetic
 contribution of wild accessions from Spain to current western cultivars.
description: Supplementary
 Information Table S3Genotype of wild
 accessions from SpainSupplementary
 Information Table S4Genotype of cultivated
 grapevine from Spain
DOI: 10.5061/dryad.3mv8v434
title: Data from: Tracking earthworm communities from soil DNA

description: Earthworms are known for their important role within the functioning of an
 ecosystem, and their diversity can be used as an indicator of ecosystem
 health. To date, earthworm diversity has been investigated through
 conventional extraction methods such as handsorting, soil washing or the
 application of a mustard solution. Such techniques are time-consuming and
 often difficult to apply. We showed that combining DNA metabarcoding and
 next generation sequencing facilitates the identification of earthworm
 species from soil samples. The first step of our experiments was to create
 a reference database of mitochondrial DNA (mtDNA) 16S gene for 14
 earthworm species found in the French Alps. Using this database, we
 designed two new primer pairs targeting very short and informative DNA
 sequences (about 30 bp and 70 bp) that allow unambiguous species
 identification. Finally, we analyzed extracellular DNA taken from soil
 samples in two localities (two plots per locality, eight samples per
 plot). The two short metabarcode regions led to the identification of a
 total of eight earthworm species. The earthworm communities identified by
 the DNA-based approach appeared to be well-differentiated between the two
 localities, and are consistent with results derived from inventories
 collected using the handsorting method. The possibility of assessing
 earthworm communities from hundreds or even thousands of localities
 through the use of extracellular soil DNA will undoubtedly stimulate
 further ecological research on these organisms. Using the same DNA
 extracts, our study also illustrates the potential of environmental DNA as
 a tool to assess the diversity of other soil-dwelling animal taxa.
description: MEC-11-1215_sequence_data_bcFasta file containing all unique sequences produced with the ewB/ewC primersMEC-11-1215_sequence_data_deFasta file containing all unique sequences produced with the ewD/ewe primersMEC-11-1215_filtered_data_bcText file showing the filtered data produced by primers ewB/ewC.MEC-11-1215_filtered_data_deText file showing the filtered data produced by primers ewD/ewE.
DOI: 10.5061/dryad.n5k77dd4
title: Data from: Systematics of snow voles (Chionomys, Arvicolinae) revisited

description: To elucidate the evolutionary history of snow voles, genus Chionomys, we
 studied the phylogeography of Chionomys nivalis across its range and
 investigated its relationships with two congeneric species, C. gud and C.
 roberti, using independent molecular markers. Analyses were based on
 mitochondrial (~940 bp cyt b) and Y-chromosomal (~2020 bp from three
 introns) genetic variation. Our data provide conclusive evidence for a
 Caucasian and Middle Eastern origin for the three species and a subsequent
 westward expansion of C. nivalis. In addition, we discuss the taxonomic
 status of the genus Chionomys in relation to the genus Microtus.
description: 1_README2_SupplementaryTables3_Cytochrome_b_for_Arvicolinae4_Nuclear_genes5_Cytochrome_b_for_Chionomys6_Y-Chromosome_for_Chionomys7_UTY11_for_Chionomys8_DBY7_for_Chionomys9_DBY14_for_Chionomys
DOI: 10.5061/dryad.d24sb3h8
title: Data from: Graptoloid diversity and disparity became decoupled during the Ordovician mass extinction

description: The morphological study of extinct taxa allows for analysis of a diverse
 set of macroevolutionary hypotheses, including testing for change in the
 magnitude of morphological divergence, extinction selectivity on form, and
 the ecological context of radiations. Late Ordovician graptoloids
 experienced a phylogenetic bottleneck at the Hirnantian mass extinction
 (~445 Ma), when a major clade of graptoloids was driven to extinction
 while another clade simultaneously radiated. In this study, we developed a
 dataset of 49 ecologically-relevant characters for 183 species with which
 we tested two main hypotheses: (a) could the biased survival of one
 graptoloid clade over another have resulted from morphological selectivity
 alone and (b) are the temporal patterns of morphological disparity and
 innovation during the recovery consistent with an interpretation as an
 adaptive radiation resulting from ecological release? We find that a
 general model of morphological selectivity has a low probability of
 producing the observed pattern of taxonomic selectivity. Selectivity on
 non-morphological variation, such as geographic range or different
 physiological tolerances, is more likely the cause. Contrary to
 predictions from theory on adaptive radiations and ecological speciation,
 changes in disparity and species richness are uncoupled. We also find that
 the early recovery is unexpectedly characterized by relatively low
 morphological disparity and innovation, despite also being an interval of
 elevated speciation. As it is necessary to invoke factors other than
 ecology to explain the graptoloid recovery, more complex models may be
 needed to explain recovery dynamics after mass extinctions.
description: data_unc-rem_11-15-11Data File for Input into Ranalysis_for_pub_11-24-11R Script for all analyses in publicationSupp_data_table_for_Dryad 11-15-11Raw Data Filedistmat_11-15-11Taxon-by-Taxon Distance matrix
DOI: 10.5281/zenodo.18391762
title: Dataset to the article "Development of PTSD-like symptoms in susceptible individuals correspond to alterations in gut microbiome and integrity in a rat model"

description: This dataset was generated for a manuscript currently under peer review:

This dataset was generated for a manuscript currently under peer review:

Authors: Csilla Lea Fazekas1,2,3$, Krisztina Bánrévi1$, Pedro Correia1,2,3, Bibiána Török1,2,3, Adrienn Szabó1,2,3, Peter Karailiev4, Manon Bellardie1, Eszter Sipos1, Ferenczi Szilamér1, Anita Bufa5, Kitti Mintál2, Zoltán S. Zádori6, Daniela Jezova4$ and Dóra Zelena1,2, $*

Title: Development of PTSD-like symptoms in susceptible individuals correspond to alterations in gut microbiome and integrity in a rat model

Submitted to Microbiome

The dataset corresponds to the experiments and analyses described in the manuscript and will be updated with the article DOI upon publication.

Description:This dataset contains experimental and analytical data generated in a rat model of post-traumatic stress disorder (PTSD) based on footshock trauma. Male Long Evans rats (14–18 weeks old) were divided into control (non-shocked), resilient, and vulnerable groups based on behavioral z-scores derived from anxiety, fear, and sociability tests. Behavioral classification and grouping details are described in a previously published study (doi: 10.1080/10253890.2020.1795121).

Data types included:



Behavioral data



z-score classification data for group assignment


Physiological and tissue data



Small intestine length


Histology data (ileum)



Quantitative measurements of villi height and thickness


Microbiome data



Processed taxonomic tables


Metabolomics data



Short-chain fatty acid (SCFA) concentrations measured from feces and plasma


Gene expression data (qPCR)



mRNA levels for ileum and PFC

Genes measured include: Muc2, Reg3β, CAMP, DEF5α, TLR-4, TNFα, IL-1β, IL-10, ZO-1, Occludin, Claudin-1/8/11/12.

Primers listed in Table 1 of the manuscript



Metadata and processing notes:



Raw data are organized into an Excel file, each row containg all the data from a single animasl, while column heading containing teh type of measurement in the given column. 

Statistical analysis was performed using StatSoft STATISTICA 13.4; Levene’s test, one-way ANOVA, repeated measures ANOVA, Fisher LSD post hoc tests, and Pearson correlations were used as appropriate. The mean ±SEM values are in Supplementary Tables as well as represented on Figures. 


Access restricted for peer review purposes. Data available to reviewers via private link.
DOI: 10.5281/zenodo.18391761
title: Dataset to the article "Development of PTSD-like symptoms in susceptible individuals correspond to alterations in gut microbiome and integrity in a rat model"

description: This dataset was generated for a manuscript currently under peer review:

This dataset was generated for a manuscript currently under peer review:

Authors: Csilla Lea Fazekas1,2,3$, Krisztina Bánrévi1$, Pedro Correia1,2,3, Bibiána Török1,2,3, Adrienn Szabó1,2,3, Peter Karailiev4, Manon Bellardie1, Eszter Sipos1, Ferenczi Szilamér1, Anita Bufa5, Kitti Mintál2, Zoltán S. Zádori6, Daniela Jezova4$ and Dóra Zelena1,2, $*

Title: Development of PTSD-like symptoms in susceptible individuals correspond to alterations in gut microbiome and integrity in a rat model

Submitted to Microbiome

The dataset corresponds to the experiments and analyses described in the manuscript and will be updated with the article DOI upon publication.

Description:This dataset contains experimental and analytical data generated in a rat model of post-traumatic stress disorder (PTSD) based on footshock trauma. Male Long Evans rats (14–18 weeks old) were divided into control (non-shocked), resilient, and vulnerable groups based on behavioral z-scores derived from anxiety, fear, and sociability tests. Behavioral classification and grouping details are described in a previously published study (doi: 10.1080/10253890.2020.1795121).

Data types included:



Behavioral data



z-score classification data for group assignment


Physiological and tissue data



Small intestine length


Histology data (ileum)



Quantitative measurements of villi height and thickness


Microbiome data



Processed taxonomic tables


Metabolomics data



Short-chain fatty acid (SCFA) concentrations measured from feces and plasma


Gene expression data (qPCR)



mRNA levels for ileum and PFC

Genes measured include: Muc2, Reg3β, CAMP, DEF5α, TLR-4, TNFα, IL-1β, IL-10, ZO-1, Occludin, Claudin-1/8/11/12.

Primers listed in Table 1 of the manuscript



Metadata and processing notes:



Raw data are organized into an Excel file, each row containg all the data from a single animasl, while column heading containing teh type of measurement in the given column. 

Statistical analysis was performed using StatSoft STATISTICA 13.4; Levene’s test, one-way ANOVA, repeated measures ANOVA, Fisher LSD post hoc tests, and Pearson correlations were used as appropriate. The mean ±SEM values are in Supplementary Tables as well as represented on Figures. 


Access restricted for peer review purposes. Data available to reviewers via private link.
DOI: 10.5061/dryad.qq106tm4
title: Data from: Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales)

description: Although temporal calibration is widely recognized as critical for
 obtaining accurate divergence-time estimates using molecular dating
 methods, few studies have evaluated the variation resulting from different
 calibration strategies. Depending on the information available,
 researchers have often used primary calibrations from the fossil record or
 secondary calibrations from previous molecular dating studies. In analyses
 of flowering plants, primary calibration data can be obtained from macro-
 and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g.,
 pollen). Fossil data can vary substantially in accuracy and precision,
 presenting a difficult choice when selecting appropriate calibrations.
 Here, we test the impact of eight plausible calibration scenarios for
 Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly
 rich and well-studied fossil record. To do so, we reviewed the
 phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus
 and other Fagales, and we identified minimum age constraints for up to 18
 nodes of the phylogeny of Fagales. Molecular dating analyses were
 conducted for each scenario using maximum likelihood (RAxML + r8s) and
 Bayesian (BEAST) approaches on sequence data from six regions of the
 chloroplast and nuclear genomes. Using either ingroup or outgroup
 constraints, or both, led to similar age estimates, except near strongly
 influential calibration nodes. Using ‘early but risky’ fossil constraints
 in addition to ‘safe but late’ constraints, or using assumptions of
 vicariance instead of fossil constraints, led to older age estimates. In
 contrast, using secondary calibration points yielded drastically younger
 age estimates. This empirical study highlights the critical influence of
 calibration on molecular dating analyses. Even in a best-case situation,
 with many thoroughly vetted fossils available, substantial uncertainties
 can remain in the estimates of divergence times. For example, our
 estimates for the crown-group age of Nothofagus varied from 13 to 113 Ma
 across our full range of calibration scenarios. We suggest that increased
 background research should be made at all stages of the calibration
 process to reduce errors wherever possible, from verifying the
 geochronological data on the fossils to critical re-assessment of their
 phylogenetic position.
description: WG32ms_AlignmentAlignment in NEXUS formatWG32ms_RAxMLphylogramRAxML tree (NEXUS format)WG32ms_SAppendices-v13Supplementary material: online-only appendices (Appendices S1-S6)WG32ms_SFigures-v13Supplementary material: online-only figures (Figures S0-S42)
DOI: 10.5061/dryad.2jc763qt
title: Data from: Miocene dispersal drives island radiations in the palm tribe Trachycarpeae (Arecaceae)

description: The study of three island groups of the palm tribe Trachycarpeae
 (Arecaceae/Palmae) permits both the analysis of each independent radiation
 and comparisons across the tribe to address general processes that drive
 island diversification. Phylogenetic relationships of Trachycarpeae were
 inferred from three plastid and three low-copy nuclear genes. The
 incongruent topological position of Brahea in CISP5 was hypothesized to be
 caused by duplication event and was addressed using uninode coding. The
 resulting phylogenetic trees were well-resolved and the genera were all
 highly-supported except for Johannesteijsmannia and Serenoa. Divergence
 time analysis estimated the stem of the tribe to be ca. 86 Ma ca. and the
 crown to be 38 Ma, indicating that significant extinction may have
 occurred along this branch. Historical biogeographic analysis suggested
 that Trachycarpeae are of southern North American, Central American, or
 Caribbean origin and supports previous hypotheses of a Laurasian origin.
 The biogeography and disjunctions within the tribe were interpreted with
 respect to divergence times, the fossil record, and geological factors
 such as the formation of the Greater Antilles - Aves Ridge, the Bering,
 and the North Atlantic land bridges, tectonic movement in Southeast Asia,
 climatic shifts between the Eocene and Pliocene, and volcanism in the
 Pacific basin. In considering the three major island radiations within
 Trachycarpeae, Miocene dispersal appears to have been the driving force in
 allopatric speciation and is highlighted here as an emerging pattern
 across the tree of life.
description: simul_PhoFixedSimultaneous concatenated datasetBacon et al_OnlineAppendix1Online Appendix 1Supp Fig 1Supplemental Figure 1Supp Fig 2Supplemental Figure 2Supp Fig 3Supplemental Figure 3Supp Fig 4Supplemental Figure 4Supp Fig 5_newSupplemental Figure 5Supp Fig 6_newSupplemental Figure 6
DOI: 10.21223/p3/rwimfo
title: Dataset for: Participatory Varietal Selection of 16 late blight resistant clones (B1C5) in the localities of Yanamayo and Patacancha in Cusco, Peru

description: The Mother and Baby (M&B) trial methodology was adapted by CIP for Participatory Variety Selection (PVS) through decentralized evaluation networks and multi-year evaluations in potato growing areas in the Andean region. The M&B trial design encourages active participation of farmers through the application of treatments through systematic evaluations and selections of treatments in their own plots called "Baby trials" (i.e. farmer managed trials) and in fields with an experimental design called "Mother trials" (i.e. researcher managed trials). Objective: Analyze characteristics, attributes and preferences that men and women have when selecting a new potato variety at the phase of flowering and harvesting. A M&B trial was performed to evaluate 16 clones of the population B1C5 with late blight resistance at the localities of Yanamayo and Patacancha, in Ollantaytambo province, in Cusco department, Peru. The trial design was a Randomized Complete Block Design (RCBD) with 3 replicates for Mother trials and 3 replicates for Baby trials during 2009-2010. In this experiment characteristics of plant (size, type of foliage), yield, quality, and pest and disease resistance during flowering and harvesting were evaluated. The number of participants was 10 at flowering and 10 at harvesting (men=5 and women=5).
DOI: 10.5061/dryad.q1v14ns0
title: Data from: Apparent signal of competition limits diversification after ecological transitions from marine to freshwater habitats

description: Adaptive radiations are typically triggered when a lineage encounters a
 significant range of open niche space (ecological opportunity), stemming
 from i) colonization of new areas, ii) extinction of competitors, or iii)
 key innovations. The most well-known of these is the colonization of new
 areas, either through geographic dispersal or the invasion of a novel
 ecological habitats. One aspect of ecological opportunity that has rarely
 been studied, however, is whether the existence of potential competitors
 may act to limit evolutionary diversification in newly colonized adaptive
 zones. Here, we show that in multiple geographically independent
 reinvasions of freshwaters by marine Sea Catfishes (Ariidae), rates of
 diversification (estimated as a function of morphological disparity and
 cladogenesis) have been constrained by pre-existing high diversity
 freshwater lineages. Only one region (Australia-New Guinea), characterized
 by an otherwise-depauperate freshwater fauna, has an ariid invasion gained
 any substantial traction. This is true at both regional and community
 scales, suggesting that competitive constraints may be an important factor
 for adaptive radiation.
description: BEAST file including
 sequence alignment, model parameters, and priors.BEAST_file_Ariidae.xmlMorphologic matrix for 118 species and 30 variables (log-transformed morphometric data and square-root-transformed meristic data)Morphologic_data.xlsx