cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q343c
title: Data from: Domestication genomics of the open-pollinated scarlet runner bean (Phaseolus coccineus L.)

description: The runner bean is a legume species from Mesoamerica closely related to
 common bean (Phaseolus vulgaris). It is a perennial species, but it is
 usually cultivated in small-scale agriculture as an annual crop for its
 dry seeds and edible immature pods. Unlike the common bean, P. coccineus
 has received little attention from a genetic standpoint. In this work we
 aim to (1) provide information about the domestication history and
 domestication events of P. coccineus; (2) examine the distribution and
 level of genetic diversity in wild and cultivated Mexican populations of
 this species; and, (3) identify candidate loci to natural and artificial
 selection. For this, we generated genotyping by sequencing data (42,548
 SNPs) from 242 individuals of P. coccineus and the domesticated forms of
 the closely related species P. vulgaris (20) and P. dumosus (35). Eight
 genetic clusters were detected, of which half corresponds to wild
 populations and the rest to domesticated plants. The cultivated
 populations conform a monophyletic clade, suggesting that only one
 domestication event occurred in Mexico, and that it took place around
 populations of the Trans-Mexican Volcanic Belt. No difference between wild
 and domesticated levels of genetic diversity was detected and effective
 population sizes are relatively high, supporting a weak genetic bottleneck
 during domestication. Most populations presented an excess of
 heterozygotes, probably due to inbreeding depression. One population of P.
 coccineus subsp. striatus had the greatest excess and seems to be
 genetically isolated despite being geographically close to other wild
 populations. Contrasting with previous studies, we did not find evidence
 of recent gene flow between wild and cultivated populations. Based on
 outlier detection methods, we identified 24 domestication-related SNPs, 13
 related to cultivar diversification and eight under natural selection. Few
 of these SNPs fell within annotated loci, but the annotated
 domestication-related SNPs are highly expressed in flowers and pods. Our
 results contribute to the understanding of the domestication history of P.
 coccineus, and highlight how the genetic signatures of domestication can
 be substantially different between closely related species.
description: Scripts and data of
 Phaseolus coccineus population genomicsScript for genomic
 population analyses of wild and cultivated populations of Scarlet Runner
 Bean (Phaseolus coccineus). Please consult README file for detail
 information.repo_data.tar.gz
DOI: 10.7910/dvn/1as45t
title: Nine centuries of floods in the Moselle river basin (12th–21st centuries): The documentary database on floods

description: The data correspond to the article “Neuf siècles d’inondations dans le bassin versant de la Moselle (XIIe–XXIe siècles) : la base de données documentaires sur les inondations” (“Nine centuries of floods in the Moselle river basin (12th–21st centuries): The documentary database on floods”). This dataset brings together 947 documentary sources reporting hydrological information related to floods in the Moselle River and its tributaries. The database was compiled as part of the “XXXXX” research project, which aims to reconstruct a chronology of floods and droughts in the Moselle basin since the High Middle Ages, using instrumental, documentary, and sedimentary archives. It is a multidisciplinary project involving geographers, hydrologists, historians, and geochemists. Flood events are classified according to an intensity index ranging from 0 to 3.
description: This dataset is released under the Creative Commons CC0 Public Domain Dedication. The data were collected and analyzed within the framework of the "XXXXX" research project, which aims to reconstruct the chronology of floods in the Moselle River basin since the Central Middle Ages. The associated article presents a reconstruction of flood events over the past nine centuries, in terms of seasonality, cause and intensity, based on this database. The dataset is freely available for reuse in hydrological and historical research.
DOI: 10.5061/dryad.06c67
title: Data from: Genetic diversity, population structure and ancestral origin of Australian wheat

description: Since the introduction of wheat into Australia by the First Fleet
 settlers, germplasm from different geographical origins has been used to
 adapt wheat to the Australian climate through selection and breeding. In
 this paper, we used 482 cultivars, representing the breeding history of
 bread wheat in Australia since 1840, to characterize their diversity and
 population structure and to define the geographical ancestral background
 of Australian wheat germplasm. This was achieved by comparing them to a
 global wheat collection using in-silico chromosome painting based on SNP
 genotyping. The global collection involved 2,335 wheat accessions which
 was divided into 23 different geographical subpopulations. However, the
 whole set was reduced to 1,544 accessions to increase the differentiation
 and decrease the admixture among different global subpopulations to
 increase the power of the painting analysis. Our analysis revealed that
 the structure of Australian wheat germplasm and its geographic ancestors
 have changed significantly through time, especially after the Green
 Revolution. Before 1920, breeders used cultivars from around the world,
 but mainly Europe and Africa, to select potential cultivars that could
 tolerate Australian growing conditions. Between 1921 and 1970, a
 dependence on African wheat germplasm became more prevalent. Since 1970, a
 heavy reliance on International Maize and Wheat Improvement Center
 (CIMMYT) germplasm has persisted. Combining the results from linkage
 disequilibrium, population structure and in-silico painting revealed that
 the dependence on CIMMYT materials has varied among different Australian
 Sstates, has shrunken the germplasm effective population size and produced
 larger linkage disequilibrium blocks. This study documents the
 evolutionary history of wheat breeding in Australia and provides an
 understanding for how the wheat genome has been adapted to local growing
 conditions. This information provides a guide for industry to assist with
 maintaining genetic diversity for long-term selection gains and to plan
 future breeding programs.
description: Joukhadar2017Genotype calls for 8194 SNPs in 2026 Australian and worldwide bread wheat accessions
DOI: 10.5061/dryad.77r93d5
title: Data from: Evolution at two time frames: polymorphisms from an ancient singular divergence event fuel contemporary parallel evolution

description: When environments change, populations may adapt surprisingly fast,
 repeatedly and even at microgeographic scales. There is increasing
 evidence that such cases of rapid parallel evolution are fueled by
 standing genetic variation, but the source of this genetic variation
 remains poorly understood. In the saltmarsh beetle Pogonus chalceus,
 short-winged ‘tidal’ and long-winged ‘seasonal’ ecotypes have diverged in
 response to contrasting hydrological regimes and can be repeatedly found
 along the Atlantic European coast. By analyzing genomic variation across
 the beetles’ distribution, we reveal that alleles selected in the tidal
 ecotype are spread across the genome and evolved during a singular and,
 likely, geographically isolated divergence event, within the last 190 Kya.
 Due to subsequent admixture, the ancient and differentially selected
 alleles are currently polymorphic in most populations across its range,
 which could potentially allow for the fast evolution of one ecotype from a
 small number of random individuals, as low as 5 to 15, from a population
 of the other ecotype. Our results suggest that cases of fast parallel
 ecological divergence can be the result of evolution at two different time
 frames: divergence in the past, followed by repeated selection on the same
 divergently evolved alleles after admixture. These findings highlight the
 importance of an ancient and, likely, allopatric divergence event for
 driving the rate and direction of contemporary fast evolution under gene
 flow. This mechanism is potentially driven by periods of geographic
 isolation imposed by large-scale environmental changes such as glacial
 cycles.
description: snps.rad1200bp.rb_phased.filtered.final.noLG.nodupResults of SNP calling by GATK, presented in Variance Call Format (VCF)bayenv_outputResults of the BayEnv2 analysisBEL_bayescanResults of the BayeScan analysis of population pair BeFRA_bayescanResults of the BayeScan analysis of population pair FrPOR_bayescanResults of the BayeScan analysis of population pair PoSPA_bayescanResults of the BayeScan analysis of population pair SpdadiResultsResults of the dadi analysisPogo_stats.40ind.Be.nodupRADtag sequence statistics of population pair BePogo_stats.40ind.Fr.nodupRADtag sequence statistics of population pair frPogo_stats.40ind.Po.nodupRADtag sequence statistics of population pair PoPogo_stats.40ind.Sp.nodupRADtag sequence statistics of population pair Sp
DOI: 10.5061/dryad.24fb2
title: Data from: Late Pleistocene origin of the entire circumarctic range of the arctic-alpine plant Kalmia procumbens

description: The circumarctic ranges of arctic-alpine plants are thought to have been
 established in the late Pliocene/early Pleistocene, when the modern arctic
 tundra was formed in response to climate cooling. Previous findings of
 range-wide genetic structure in arctic-alpine plants have been thought to
 support this hypothesis, but few studies have explicitly addressed the
 temporal framework of the genetic structure. Here, we estimated the
 demographic history of the genetic structure in the circumarctic Kalmia
 procumbens using sequences of multiple nuclear loci and examined whether
 its genetic structure reflects prolonged isolation throughout the
 Pleistocene. Both Bayesian clustering and phylogenetic analyses revealed
 genetic distinction between alpine and arctic regions, whereas detailed
 groupings were somewhat discordant between the analyses. By assuming a
 population grouping based on the phylogenetic analyses, which likely
 reflects a deeper intraspecific divergence, we conducted model-based
 analyses and demonstrated that the intraspecific genetic divergence in K.
 procumbens likely originated during the last glacial period. Thus, there
 is no need to postulate range separation throughout the Pleistocene to
 explain the current genetic structure in this species. This study
 demonstrates that range-wide genetic structure in arctic-alpine plants
 does not necessarily result from the late Pliocene/early Pleistocene
 origin of their circumarctic ranges, and emphasizes the importance of a
 temporal framework of the current genetic structure for understanding the
 biogeographic history of the arctic flora.
description: Data-Ikeda-Mol_Ecol
DOI: 10.5061/dryad.sm282vt
title: Data from: Hypothesis: a plastically-produced phenotype predicts host specialization and can precede subsequent mutations in bacteriophage

description: The role of phenotypic plasticity in the evolution of new traits is
 controversial due to a lack of direct evidence. Phage host range becomes
 plastic in the presence of restriction-modification (R-M) systems in their
 hosts. I modeled the evolution of phage host range in the presence of R-M
 systems. The model makes two main predictions. The first prediction is
 that the offspring of the first phage to gain a new methylation pattern by
 infecting a new host make up a disproportionate fraction of the subsequent
 specialist population, indicating that the plastically produced phenotype
 is highly predictive of evolutionary outcome. The second prediction is
 that the first phage to gain this pattern is not always genetically
 distinct from other phages in the population. Taken together, these
 results suggest that plasticity could play a causal role on par with
 mutation during the evolution of phage host range. This uniquely tractable
 system could enable the first direct test of “plasticity first” evolution.
description: Code to generate
 figuresThis contains the output
 of the ABM and the code used to generate the figures in the manuscript.
 The output files are defined based on code in the phage-abm.zip
 file.generate-figures.zipAgent based model codeThis is the code that defines the agent based model. See also https://github.com/csmaxwell/phage-abmphage-abm.zip
DOI: 10.5061/dryad.2js00
title: Data from: Less favorable climates constrain demographic strategies in plants

description: Correlative species distribution models are based on the observed
 relationship between species’ occurrence and macroclimate or other
 environmental variables. In climates predicted less favourable populations
 are expected to decline, and in favourable climates they are expected to
 persist. However, little comparative empirical support exists for a
 relationship between predicted climate suitability and population
 performance. We found that the performance of 93 populations of 34 plant
 species worldwide – as measured by in situ population growth rate, its
 temporal variation and extinction risk – was not correlated with climate
 suitability. However, correlations of demographic processes underpinning
 population performance with climate suitability indicated both resistance
 and vulnerability pathways of population responses to climate: in less
 suitable climates, plants experienced greater retrogression (resistance
 pathway) and greater variability in some demographic rates (vulnerability
 pathway). While a range of demographic strategies occur within species’
 climatic niches, demographic strategies are more constrained in climates
 predicted to be less suitable.
description: Supporting
 InformationFile (1) COMPADRE Plant
 Matrix Database version 3.0.0 downloaded on July 21, 2014; File (2) Data
 spreadsheet with population-level demographic metrics and climate
 suitability values (calculated using the R codes appended here); File (3)
 R scripts for demographic metric calculations, Species Distribution Models
 and statistical analyses; File (4) Projected maps based on the Species
 Distribution Models for species in this study.Csergo et al
 ELE.zip
DOI: 10.5061/dryad.28sb6
title: Data from: The fungus that came in from the cold: dry rot’s pre-adapted ability to invade buildings

description: Many organisms benefit from being pre-adapted to niches shaped by human
 activity, and have successfully invaded man-made habitats. One such
 species is the dry rot fungus Serpula lacrymans, which has a wide
 distribution in buildings in temperate and boreal regions, where it
 decomposes coniferous construction wood. Comparative genomic analyses and
 growth experiments using this species and its wild relatives revealed that
 S. lacrymans evolved a very effective brown rot decay compared to its wild
 relatives, enabling an extremely rapid decay in buildings under suitable
 conditions. Adaptations in intracellular transport machineries promoting
 hyphal growth, and nutrient and water transport may explain why it is has
 become a successful invader of timber in houses. Further, we demonstrate
 that S. lacrymans has poor combative ability in our experimental setup,
 compared to other brown rot fungi. In sheltered indoor conditions, the dry
 rot fungus may have limited encounters with other wood decay fungi
 compared to its wild relatives. Overall, our analyses indicate that the
 dry rot fungus is an ecological specialist with poor combative ability
 against other fungi.
description: Gene predictions of
 Serpula lacrymans var. shastensis SHA17-1Gene predictions for the
 assemblies published in BioProject PRJNA412961Sshas_SHA17-1_maker_genes.gff3Gene predictions of Serpula lacrymans var. lacrymans SL200Gene predictions for the assemblies published in BioProject PRJNA412961Slac_SL200_maker_genes.gff3Gene predictions of Serpula himantioides MUCL38935Gene predictions for the assemblies published at JGI https://genome.jgi.doe.gov/Serla_varsha1/Serla_varsha1.info.htmlShim_MUCL38935_maker_genes.gff3Alignments of one-to-one orthologs used for selection screen (FASTA format)alignments_selection_screen.zipClustering membership of each proteinClustering membership of each protein in the above genomes. Proteins not included in the cluster map are singletonscluster_geneID_map.txtREADME
DOI: 10.5061/dryad.bk827
title: Data from: Angiosperm phylogeny based on 18S/26S rDNA sequence data: constructing a large dataset using next-generation sequence data

description: The utility of 18S and 26S in broad phylogenetic analyses has been much
 maligned due in large part to the low signal in both genes. However, few
 analyses have employed complete 26S rDNA sequences over a broad range of
 taxa, and most alignments of the two genes are done de novo, without
 taking into account the secondary structure of the two rRNA genes. Here we
 mine next-generation sequence data to compile large matrices (429 taxa) of
 complete 18S + 26S gene sequences, and we compare both de novo alignment
 methods with curated alignments done by eye that take into account
 secondary structure and hard-to-align regions (profile alignments). The
 combined 18S + 26S topology is overall very similar to recently published
 gene trees for the angiosperms based on three or more genes. Overall
 support for the backbone or framework of the combined tree is low
 (bootstrap support below 50%). Few major clades have bootstrap support
 above 50%. Most well-supported clades are tip clades (families and orders
 sensu APG III 2009). Importantly, the 18S + 26S rDNA topology is
 consistent with current estimates of relationships: the basalmost
 angiosperms are recovered (Amborellaceae, Nymphaeales, Austrobaileyales),
 as are most major clades, including Mesangiospermae, eudicots
 (Eudicotyledoneae sensu Cantino et al. 2007), core eudicots (Gunneridae
 sensu Cantino et al. 2007), rosids (Rosidae sensu Cantino et al. 2007),
 asterids (Asteridae sensu Cantino et al. 2007), and Caryophyllales. Most
 clades recognized at the ordinal level (sensu APG III 2009) are also
 recovered. However, there are also some unusual placements in the 18S +
 26S topology, but none of these receives bootstrap support above 50%. The
 profile and de novo alignments gave very similar topologies. 18S + 26S
 trees remain useful sources of data in large combined analyses. This is
 the first time a large data set of complete 26S gene sequences has been
 employed at this scale; this gene in particular proved to be useful
 phylogenetically. Targeted sequencing of 18S/26S rDNA is not advocated
 here, but given that these regions provide useful phylogenetic information
 and are abundant in next-generation sequencing runs, we suggest that the
 data be used rather than discarded.
description: 26S_profile26S_de novo18S_profile18S_de novo18S_26S_conc_strict_profile18S_26S_conc_strict_de novo18S_26S_conc_full_profile18S_26S_conc_full_de novo
DOI: 10.5061/dryad.s8c2c
title: Data from: Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea

description: To test the hypothesis that different drivers shape the diversity and
 biogeography of the total and active bacterial community, we examined the
 bacterial community composition along two transects, one from the inner
 Pearl River estuary to the open waters of the South China Sea (SCS) and
 the other from the Luzon Strait to the SCS basin, using 454 pyrosequencing
 of the 16S rRNA and 16S rRNA gene (V1-3 regions) and thereby,
 characterizing the active and total bacterial community, respectively. The
 diversity and biogeographic patterns differed substantially between the
 active and total bacterial communities. Although the composition of both,
 the total and active bacterial community was strongly correlated with
 environmental factors and weakly correlated with geographic distance, the
 active bacterial community displayed higher environmental sensitivity than
 the total community and particularly, a greater distance effect largely
 caused by the active assemblage from deep waters. The 16S rRNA versus rDNA
 relationships indicated that the active bacteria were low in relative
 abundance in the SCS. This might be due to a high competition between
 active bacterial taxa as indicated by our community network models. Based
 on these analyses, we speculate that high competition could cause some
 dispersal limitation of the active bacterial community resulting in a
 distinct distance-decay relationship. Altogether, our results indicated
 that the biogeographic distribution of bacteria in the SCS is the result
 of both environmental control and distance-decay.
description: Environmental
 dataMID#-SampleMID numbers corresponding to the samples. These MID numbers were used in the analysis input files.R input filesR input files for Mantel and Partial Mantel testsCANOCO input filesCANOCO input files for community CCA analysisGENE-E input filesGENE-E input files for heatmapsNetwork input filesNetwork input files for network analysisOTU tablesThe OTU tables produced from MOTHURMOTHUR input filesMOTHUR input files for DNA and RNA sequences analysis
DOI: 10.5061/dryad.j702j
title: Data from: Dealing with AFLP genotyping errors to reveal genetic structure in Plukenetia volubilis (Euphorbiaceae) in the Peruvian Amazon

description: An analysis of the population structure and genetic diversity for any
 organism often depends on one or more molecular marker techniques.
 Nonetheless, these techniques are not absolutely reliable because of
 various sources of errors arising during the genotyping process. Thus, a
 complex analysis of genotyping error was carried out with the AFLP method
 in 169 samples of the oil seed plant Plukenetia volubilis L. from small
 isolated subpopulations in the Peruvian Amazon. Samples were collected in
 nine localities from the region of San Martin. Analysis was done in eight
 datasets with a genotyping error from 0 to 5%. Using eleven primer
 combinations, 102 to 275 markers were obtained according to the dataset.
 It was found that it is only possible to obtain the most reliable and
 robust results through a multiple-level filtering process. Genotyping
 error and software set up influence both the estimation of population
 structure and genetic diversity, where in our case population number (K)
 varied between 2 - 9 depending on the dataset and statistical method used.
 Surprisingly, discrepancies in K number were caused more by statistical
 approaches than by genotyping errors themselves. However, for estimation
 of genetic diversity, the degree of genotyping error was critical because
 descriptive parameters (He, FST, PLP 5%) varied substantially (by at least
 25%). Due to low gene flow, P. volubilis mostly consists of small isolated
 subpopulations (ΦPT = 0.252-0.323) with some degree of admixture given by
 socio-economic connectivity among the sites; a direct link between the
 genetic and geographic distances was not confirmed. The study illustrates
 the successful application of AFLP to infer genetic structure in non-model
 plants.
description: plukenetia-AFLP-JVRaw data in *.fsa format together with intermediate and final datasets. Final datasets may be directly used for many statistical analyses.