cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7hs0n
title: Data from: Pleistocene climatic fluctuations drive isolation and secondary contact in the red diamond rattlesnake (Crotalus ruber) in Baja California

description: Aim: Many studies have investigated the phylogeographic history of species
 on the Baja California Peninsula, and they often show one or more genetic
 breaks that are spatially concordant among many taxa. These
 phylogeographic breaks are commonly attributed to vicariance as a result
 of geological or climatic changes, followed by secondary contact when
 barriers are no longer present. We use restriction-site associated DNA
 sequence data and a phylogeographic model selection approach to explicitly
 test the secondary contact hypothesis in the red diamond rattlesnake,
 Crotalus ruber. Location: Baja California and Southern California.
 Methods: We used phylogenetic and population clustering approaches to
 identify population structure. We then used coalescent methods to
 simultaneously estimate population parameters and test the fit of
 phylogeographic models to the data. We used ecological niche models to
 infer suitable habitat for C. ruber at the Last Glacial Maximum (LGM).
 Results: Crotalus ruber is composed of distinct northern and southern
 populations with a boundary near the town of Loreto in Baja California
 Sur. A model of isolation followed by secondary contact provides the best
 fit to the data, with both divergence and contact occurring in the
 Pleistocene. We also identify a genomic signature of northern range
 expansion in the northern population, consistent with LGM niche models
 showing that the northern-most portion of the range of C. ruber was not
 suitable habitat during the LGM. Main conclusions: We provide the first
 explicitly model-based test of the secondary contact model in Baja
 California and show that populations of C. ruber were isolated before
 coming back into contact near Loreto, a region that shows phylogeographic
 breaks for other taxa. Given the timing of divergence and contact, we
 suggest that climatic fluctuations have driven the observed
 phylogeographic structure observed in C. ruber and that they may have
 driven similar patterns in other taxa.
description: FSC2 input
 filesThis zip archive
 contains all necessary input to run FastSimCoal2 analyses performed. See
 the included readme file in the zip archive for further
 details.FSC2.zipAll other input filesThis zip archive contains the input files for all analyses other than FSC2, which are contained in a separate zip archive. See the readme included in the archive for further details on individual files.Input_files.zipR code for sPCA, DAPC, and Mantel testsThis file contains the R script used for DAPC, sPCA, and Mantel test analyses. Input files are contained in the input files zip archive separately available on Dryad.Harrington_et_al_JBio_R_code.R
DOI: 10.5061/dryad.kg5s5
title: Data from: De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii

description: Background: Propionibacterium freudenreichii is an industrially important
 bacterium granted the Generally Recognized as Safe (the GRAS) status, due
 to its long safe use in food bioprocesses. Despite the recognized role in
 the food industry and in the production of vitamin B12, as well as its
 documented health-promoting potential, P. freudenreichii remained poorly
 characterised at the genomic level. At present, only three complete genome
 sequences are available for the species. Results: We used the PacBio RS II
 sequencing platform to generate complete genomes of 20 P. freudenreichii
 strains and compared them in detail. Comparative analyses revealed both
 sequence conservation and genome organisational diversity among the
 strains. Assembly from long reads resulted in the discovery of additional
 circular elements: two putative conjugative plasmids and three active,
 lysogenic bacteriophages. It also permitted characterisation of the
 CRISPR-Cas systems. The use of the PacBio sequencing platform allowed
 identification of DNA modifications, which in turn allowed
 characterisation of the restriction-modification systems together with
 their recognition motifs. The observed genomic differences suggested
 strain variation in surface piliation and specific mucus binding, which
 were validated by experimental studies. The phenotypic characterisation
 displayed large diversity between the strains in ability to utilise a
 range of carbohydrates, to grow at unfavourable conditions and to form a
 biofilm. Conclusion: The complete genome sequencing allowed detailed
 characterisation of the industrially important species, P. freudenreichii
 by facilitating the discovery of previously unknown features. The results
 presented here lay a solid foundation for future genetic and functional
 genomic investigations of this actinobacterial species.
description: core_gene_alignmentThe Roary-generated core genome alignments of the 20 P. freudenreichii genomes. The file was the basis for the phylogenetic tree based on the core genome.Core genome alignment tree2_core_gene_alignment.treeaccessory genes treeTree calculated on the basis of presence/absence (binary) of accessory genes in the strains resulting from Roary analysis.2_accessory_binary_genes.fa.newickaccessory_binary_genesThe binary representation of accessory genes present (A) or absent (C) from the 20 P. freudenreichii genomes as determined by Roary analysis.
DOI: 10.5061/dryad.q2932
title: Data from: The genetic architecture of ecological adaptation: intraspecific variation in host plant use by the lepidopteran crop pest Chloridea virescens

description: Intraspecific variation in ecologically important traits is a cornerstone
 of Darwin’s theory of evolution by natural selection. The evolution and
 maintenance of this variation depends on genetic architecture, which in
 turn determines responses to natural selection. Some models suggest that
 traits with complex architectures are less likely to respond to selection
 than those with simple architectures, yet rapid divergence has been
 observed in such traits. The simultaneous evolutionary lability and
 genetic complexity of host plant use in the Lepidopteran subfamily
 Heliothinae suggest that architecture may not constrain ecological
 adaptation in this group. Here we investigate the response of Chloridea
 virescens, a generalist that feeds on diverse plant species, to selection
 for performance on a novel host, Physalis angulata (Solanaceae). P.
 angulata is the preferred host of Chloridea subflexa, a narrow specialist
 on the genus Physalis. In previous experiments, we found that the
 performance of C. subflexa on P. angulata depends on many loci of small
 effect distributed throughout the genome, but whether the same
 architecture would be involved in the generalist’s adoption of P. angulata
 was unknown. Here we report a rapid response to selection in C. virescens
 for performance on P. angulata, and establish that the genetic
 architecture of intraspecific variation is quite similar to that of the
 interspecific differences in terms of the number, distribution, and effect
 sizes of the QTL involved. We discuss the impact of genetic architecture
 on the ability of Heliothine moths to respond to varying ecological
 selection pressures.
description: Larval
 phenotypesPhenotypes of all larvae
 used in study.SupplementalFile2_Phenotypes.xlsxLinkage GroupsLinkage group mapping for the 3 backcross populations.100317_SupplementalFile3_LinkageGroups.xlsMarker GenotypesMarker genotypes for the 3 backcross families.SupplementalFile4_MarkerGenotypes.xlsx
DOI: 10.5061/dryad.2p4k0
title: Data from: 2D or Not 2D? Testing the utility of 2D vs. 3D landmark data in geometric morphometrics of the sculpin subfamily Oligocottinae (Pisces; Cottoidea)

description: We contrast 2D vs. 3D landmark‐based geometric morphometrics in the fish
 subfamily Oligocottinae by using 3D landmarks from CT‐generated models and
 comparing the morphospace of the 3D landmarks to one based on 2D landmarks
 from images. The 2D and 3D shape variables capture common patterns across
 taxa, such that the pairwise Procrustes distances among taxa correspond
 and the trends captured by principal component analysis are similar in the
 xy plane. We use the two sets of landmarks to test several
 ecomorphological hypotheses from the literature. Both 2D and 3D data
 reject the hypothesis that head shape correlates significantly with the
 depth at which a species is commonly found. However, in taxa where shape
 variation in the z‐axis is high, the 2D shape variables show sufficiently
 strong distortion to influence the outcome of the hypothesis tests
 regarding the relationship between mouth size and feeding ecology. Only
 the 3D data support previous studies which showed that large mouth sizes
 correlate positively with high percentages of elusive prey in the diet.
 When used to test for morphological divergence, 3D data show no evidence
 of divergence, while 2D data show that one clade of oligocottines has
 diverged from all others. This clade shows the greatest degree of z‐axis
 body depth within Oligocottinae, and we conclude that the inability of the
 2D approach to capture this lateral body depth causes the incongruence
 between 2D and 3D analyses.
description: Supplementary_Information_1_2Dv3D_RfolderA folder containing all pertinent data (landmark data, etc.) and an annotated R script that performs all operations conducted in R.2Dv3D_Rfolder.zip
DOI: 10.5061/dryad.73kq1
title: Data from: Too hard to swallow: a secret secondary defence of an aposematic insect

description: Anti-predator strategies are significant components of adaptation in prey
 species. Aposematic prey are expected to possess effective defences that
 have evolved simultaneously with their warning colours. This study tested
 the hypothesis of the defensive function and ecological significance of
 the hard body in aposematic Pachyrhynchus weevils pioneered by Alfred
 Russel Wallace nearly 150 years ago. We used predation trials with
 Japalura tree lizards to assess the survivorship of ‘hard’ (mature) vs.
 ‘soft’ (teneral) and ‘clawed’ (intact) vs. ‘clawless’ (surgically removed)
 weevils. The ecological significance of the weevil's hard body was
 evaluated by assessing the hardness of the weevils, the local prey
 insects, and the bite forces of the lizard populations. The existence of
 toxins or deterrents in the weevil was examined by gas chromatography-mass
 spectrometry (GC-MS). All ‘hard’ weevils were instantly spat out after
 being bitten once and survived attacks by the lizards. In contrast, the
 ‘soft’ weevils were chewed and subsequently swallowed. The results were
 the same regardless of the presence or absence of the weevil's tarsal
 claws. The hardness of ‘hard’ Pachyrhynchus weevils was significantly
 higher than the average hardness of other prey insects in the same habitat
 and the mean bite forces of the local lizards. The four candidate
 compounds of the weevil identified by GC-MS had no known toxic or
 repellent functions against vertebrates. These results reveal that the
 hardness of aposematic prey functions as an effective secondary defence,
 and they provide a framework for understanding the spatio-temporal
 interactions between vertebrate predators and aposematic insect prey.
description: activityGCMS reportr scriptdaily rhythm2daily rhythm2dayonlydatapachy.hardnesshardness.bodylength.remove.hard160710D-1160710D-2160710D-3160726A-1160726A-2160726A-3160805A-1160805A-2160805A-3160809-1160809-2160809-3161016A-1161016A-2161017-1161016A-3161017-2161017-3161018A-1161018A-2161018A-3161018B-1161018B-2161018B-3
DOI: 10.5061/dryad.4cb86
title: Data from: Intraspecific variation in cephalopod conchs changes during ontogeny: perspectives from three-dimensional morphometry of Nautilus pompilius

description: Intraspecific variation of organisms is of great importance to correctly
 carry out taxonomic work, which is a prerequisite for important
 disciplines in paleontology such as community paleoecology,
 biostratigraphy, and biogeography. However, intraspecific variation is
 rarely studied in ectocochleate cephalopods (ammonoids and nautiloids), in
 which an excessive number of taxa were established during the past
 centuries. Since intraspecific variation of fossilized organisms suffers
 from various biases (time averaging and taphonomy), an extant example is
 needed for actualistic comparison. We applied 3D morphometry to 93
 specimens of Nautilus pompilius from three different geographic
 populations. This dataset was used to examine the intraspecific variation
 throughout ontogeny in detail. Although there are slight differences
 between the populations as well as some measurement biases, a common
 pattern of intraspecific variation appears to be present. High variation
 appears early in ontogeny and then decreases gradually in the following
 ontogenetic stages. Subsequently, the variation shows an increase again
 before maturity until a sharp increase or decrease occurs towards the end
 of ontogeny. Comparison with intraspecific variation of ammonoids and
 belemnites illustrated that some groups have ontogenetic patterns of
 intraspecific variation, which are similar to that of N. pompilius. This
 implies that the above-mentioned ontogenetic pattern of intraspecific
 variation might be common in some major cephalopod clades.
description: Supplementary
 FigureMeasurement errors using
 a medical CT-scanner and high resolution CT scanner (Nikon XT H 225 ST).
 WER and WWI of Nautilus pompilius (PIM 7825) were measured in order to
 estimate measurement errors through ontogeny.Supplementary
 figure.tifSupplementary
 TableRaw data of the
 measurements.
DOI: 10.5061/dryad.9s68p
title: Data from: Transcript levels of orf288 are associated with the hau cytoplasmic male sterility system and altered nuclear gene expression in Brassica juncea

description: Cytoplasmic male sterility is primarily caused by chimeric genes located
 in the mitochondrial genomes. Previously, orf288 had been cloned as a
 CMS-associated gene in the hau CMS line. However, neither the specific
 abortive stage nor the molecular function of orf288 had been determined in
 hau CMS. To better understand the mechanism of hau CMS in Brassica, we
 further characterized the hau CMS line and found defective mitochondrial
 arrest during the development of archesporial cells during the L2 stage,
 leading to male sterility. Expression level of the orf288 transcript was
 higher in the male sterility line than in the restorer line, although no
 significant differences were apparent at the protein level. The toxicity
 region of ORF288 is located near the N-terminus and represses E. coli
 growth. However, transgenic expression of different portions of ORF288
 indicated that the region that causes male sterility resides between amino
 acids 73 and 288, which do not result in growth inhibition when expressed
 in E. coli. Transcriptome analysis revealed a wide range of genes involved
 in anther development and mitochondrial function that were differentially
 expressed in the hau CMS line. This study provides new insights into hau
 CMS mechanism by which orf288 affects Brassica juncea fertility.
description: Supplementary
 FiguresSupplementary Table
 S1Table
 S1.xlsSupplementary Table
 S2Table
 S2.xlsSupplementary Table
 S3Table
 S3.xlsxSupplementary Table
 S4Table
 S4.xlsSupplementary Table
 S5Table
 S5.xlsx
DOI: 10.5517/ccdc.csd.cc297c0y
title: CCDC 2122229: Experimental Crystal Structure Determination

description: Related Article: Amina Adala, Nadra Debbache, Tahar Sehili|2026|ChemPhotoChem|10|e202500228|doi:10.1002/cptc.202500228
description: Related Article: adala amina|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.1597
title: Data from: Mating patterns and determinants of individual reproductive success in brown trout (Salmo trutta) revealed by parentage analysis of an entire stream living population

description: Reproductive success and its determinants are difficult to infer for wild
 populations of species with no parental care where behavioral observations
 are difficult or impossible. In this study, we characterized the breeding
 system and provide estimates of individual reproductive success under
 natural conditions for a stream-resident, semi-isolated brown trout (Salmo
 trutta) population. We inferred parentage using a full probability
 Bayesian model that combines genetic (microsatellite) with phenotypic
 data. We had tried to exhaustively sample all individuals from a
 population, including large sib-ship families from three consecutive
 offspring cohorts. This allowed us to make inferences about the parental
 genotypes that had produced these families, and thus to augment the parent
 file with the inferred parental genotypes in cases where large families
 had unsampled parents. We observed both polygamous and monogamous matings
 and large reproductive skew for both sexes, but particularly so in males.
 We found no impact of individual neutral genetic variation or
 between-partners genetic similarity on reproductive success. Combining
 parentage analysis with sib-ship reconstruction allows for more precise
 inference on variance of family sizes and more definite statements on the
 determinants of reproductive success.
description: parentage
 dataThe genotype data from
 three consecutive seasons used in the parentage assignment analyses. The
 columns in the dataset are as follows: trout-the identity of the
 individual fish, function-description whether an individual is a potential
 parent or an offspring in each season, distance-the distance in meters
 from the mouth of the stream, present-whether an individual was observed
 in the focal spawning season (1) or not(0), the sex, age and length of the
 individuals, and the genotypes for 15 microsatellite
 loci.parentagedata.txt
DOI: 10.5061/dryad.g2fm2
title: Data from: Does fuel type influence the amount of charcoal produced in wildfires? Implications for the fossil record

description: Charcoal occurrence is extensively used as a tool for understanding
 wildfires over geological timescales. Yet, the fossil charcoal literature
 to date rarely considers that fire alone is capable of creating a bias in
 the abundance and nature of charcoal it creates, before it even becomes
 incorporated into the fossil record. In this study we have used
 state-of-the-art calorimetry to experimentally produce charcoal from
 twenty species that represent a range of surface fuels and growth habits,
 as a preliminary step towards assessing whether different fuel types (and
 plant organs) are equally likely to remain as charcoal post-fire. We
 observe that charcoal production appears to be species specific, and is
 related to the intrinsic physical and chemical properties of a given fuel.
 Our observations therefore suggest that some taxa are likely to be
 overrepresented in fossil charcoal assemblages(i.e. needle-shed conifers,
 tree ferns) and others poorly represented, or not preserved at all (i.e.
 broad shoot-shed conifers, weedy angiosperms, shrub angiosperms, some
 ferns). Our study highlights the complexity of charcoal production in
 modern fuels and we consider what a bias in charcoal production may mean
 for our understanding of palaeowildfires.
description: Hudspith et
 al_Table1Table 1. Summary of all
 taxa tested under ambient atmospheric oxygen conditions (21 vol. % pO2).
 Calorimetry test information along with an image analysis determined
 %charcoal left in the remaining ash/char residue post-burn are presented.
 Species are grouped according to growth habit.Hudspith et al Table
 2Table 2. Summary of the
 fifteen species tested under superambient atmospheric oxygen conditions
 (26 vol. % pO2). Calorimetry test information along with an image analysis
 determined %charcoal left in the remaining ash/char residue post-burn are
 presented. Species are grouped according to growth
 habit.Supplemental
 Fig1Figure 1. Podocarpus
 salignus dead foliage ash/char (Fig. 2E) illustrating the stages of image
 processing used to determine charcoal percentages. (A) Histogram values
 obtained for all pixel values in the 8 bit greyscale photograph. (B) Image
 manually thresholded to a greyscale value of 50 to highlight the charcoal
 in the image. (C) Default threshold applied to the whole image to separate
 the background from the ash/char sample and to derive a maximum ash
 greyscale value.
DOI: 10.5061/dryad.49g85
title: Data from: Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of South America

description: Much of the immense present day biological diversity of Neotropical
 rainforests originated from the Miocene onwards, a period of geological
 and ecological upheaval in South America. We assess the impact of the
 Andean orogeny, drainage of lake Pebas, and closure of the Panama Isthmus
 on two clades of tropical trees (Cremastosperma, c. 31 spp.; and
 Mosannona, c. 14 spp.; both Annonaceae). Phylogenetic inference revealed
 similar patterns of geographically restricted clades and molecular dating
 showed diversifications in the different areas occurred in parallel, with
 timing consistent with Andean vicariance and Central American
 geodispersal. Ecological niche modelling approaches show phylogenetically
 conserved niche differentiation, particularly within Cremastosperma. Niche
 similarity and recent common ancestry of Amazon and Guianan Mosannona
 species contrasts with dissimilar niches and more distant ancestry of
 Amazon, Venezuelan and Guianan species of Cremastosperma suggesting that
 this element of the similar patterns of disjunct distributions in the two
 genera is instead a biogeographic parallelism, with differing origins. The
 results provide further independent evidence for the importance of the
 Andean orogeny, the drainage of Lake Pebas, and the formation of links
 between South and Central America in the evolutionary history of
 Neotropical lowland rainforest trees.
description: Appendix_2DNA sequence matrices on which phylogenetic analyses were basedCollection coordinatesLatitude/longitude coordinates for collections of Cremastosperma and Mosannona (Annonaceae) species analysed for niche modelling.Collection_coordinates.zipEnvironmental layersEnvironmental layers used for niche modelling of Cremastosperma and Mosannona species.Appendix_4_environmental_layers.zip
DOI: 10.34894/l1ogei
title: Jedidiah Morse, The American Gazetteer (Boston 1797) [Transkribus PAGE format]

description: This dataset contains the digitalised text of Jedidiah Morse's &lt;em&gt;The American Gazetteer&lt;/em&gt; (Boston 1797). The text was digitalised using scans provided by the John Adams Library at the Boston Public Library (&lt;a href="https://archive.org/details/americangazettee00mors" target="_blank"&gt;Internet Archive&lt;/a&gt;) and the HTR software &lt;a href="http://www.transkribus.eu/" target="_blank"&gt;Transkribus&lt;/a&gt;.&lt;br&gt;&lt;br&gt;

This dataset contains the files in Transkribus PAGE/XML format.