cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r32p3
title: Data from: A Palaeozoic stem-group to mite harvestmen revealed through integration of phylogenetics and development

description: Successfully placing fossils in phylogenies is integral to understanding
 the tree of life. Crown-group Paleozoic members of the arachnid order
 Opiliones are indicative of ancient origins and one of the earliest
 arthropod terrestrialization events. Opiliones epitomize morphological
 stasis, and all known fossils have been placed within the four extant
 suborders. Here we report a Carboniferous harvestman species, Hastocularis
 argusgen. nov., sp. nov., reconstructed with microtomography (microCT).
 Phylogenetic analysis recovers this species, and the Devonian Eophalangium
 sheari, as members of an extinct harvestman clade. We establish the
 suborder Tetrophthalmi subordo nov., which bore four eyes, to accommodate
 H. argus and E. sheari, the latter previously considered to be a
 phalangid. Furthermore, embryonic gene expression in the extant species
 Phalangium opilio demonstrates vestiges of lateral eye tubercles. These
 lateral eyes are lost in all crown-group Phalangida, but are observed in
 both our fossil and outgroup chelicerate orders. These data independently
 corroborate the diagnosis of two eye pairs in the fossil and demonstrate
 retention of eyes of separate evolutionary origins in modern harvestmen.
 The discovery of Tetrophthalmi alters molecular divergence time estimates,
 supporting Carboniferous rather than Devonian diversification for extant
 suborders and directly impacting inferences of terrestrialization history
 and biogeography. Multidisciplinary approaches integrating fossil and
 neontological data increase confidence in phylogenies and elucidate
 evolutionary history.
description: File S1, related to
 Figure 1.A zipped VAXML model of
 the whole body, and anterior of Hastocularis argus
 scan.Garwood_et_al_2014_-_Supplementary_File_S1.zipFile S2, related to Figure 3.Alignments corresponding to total evidence phylogenetic analysis and molecular dating analysis in Figure 3.Garwood_et_al_2014_-_Supplementary_File_S2.zipMovie S1, related to Figure 1.A video showing the two scans of Hastocularis argus conducted for this study.Garwood_et_al_2014_-_Supplementary_Movie_S1.avi
DOI: 10.5061/dryad.mc04d
title: Data from: Fine-scale genetic structure due to adaptive divergence among microhabitats

description: It has been suggested that adaptive evolution on ecological timescales
 shapes communities. However, adaptation among environments relies on
 isolation or large selection coefficients that exceed migration effects.
 This reliance is tempered if adaptation is polygenic—does not depend on
 one allele completely replacing another but instead requires small allele
 frequency changes at many loci. Thus, whether individuals can evolve
 adaptation to fine-scale habitat variation (for example, microhabitats) is
 not resolved. Here we analyze the genetic divergence of the teleost fish,
 Fundulus heteroclitus, among microhabitats that are &lt;200 m apart in
 three separate saltmarshes using 4741 single-nucleotide polymorphisms
 (SNPs). Among these SNPs, 1.3–2.3% have large and highly significant
 differences among microhabitats (mean FST=0.15; false discovery rate less
 than or equal to1%). The divergence among microhabitats for these outlier
 SNPs is larger than that among populations, exceeds neutral expectation
 and indicates surprising population structure among microhabitats. Thus,
 we suggest that polygenic selection is surprisingly effective in altering
 allele frequencies among many different SNPs that share similar biological
 functions in response to environmental and ecological differences over
 very small geographic distances. We acknowledge the evolutionary
 difficulty of large genetic divergence among well-connected habitats.
 Therefore, these studies are only the first step to discern whether
 natural selection is responsible and capable of effecting genetic
 divergence on such a fine scale.
description: Unfiltered
 HapmapThis file contains the
 raw, unfiltered hapmap from GBS. Individuals are identified as: MB -
 Mantoloking Basin, MC - Mantoloking Creek, MP - Mantoloking Pond, RB -
 Rutgers Basin, RC - Rutgers Creek, RP - Rutgers Pond, SB - Stone Harbor
 Basin, SC - Stone Harbor Creek, SP - Stone Harbor PondGBS_unfiltered_all.hmp.txtFinal HapmapHapmap of SNPs used in final analyses. SNPs have been filtered to include 30% of all taxa, 80% of all sites, and a 5% minimum allele frequency. SNPs in significant LD (p &lt; 0.01) have also been removed. Individuals are identified as: MB - Mantoloking Basin, MC - Mantoloking Creek, MP - Mantoloking Pond, RB - Rutgers Basin, RC - Rutgers Creek, RP - Rutgers Pond, SB - Stone Harbor Basin, SC - Stone Harbor Creek, SP - Stone Harbor PondDNW_thinned_4741.hmp.txtFiltered HapmapHapmap of SNPs after initial filtering. SNPs have been filtered to include 30% of all taxa, 80% of all sites. Individuals are identified as: MB - Mantoloking Basin, MC - Mantoloking Creek, MP - Mantoloking Pond, RB - Rutgers Basin, RC - Rutgers Creek, RP - Rutgers Pond, SB - Stone Harbor Basin, SC - Stone Harbor Creek, SP - Stone Harbor Pondfiltered80_30.hmp.txt
DOI: 10.5061/dryad.f9k77
title: Data from: Novel Fibonacci and non-Fibonacci structure in the sunflower: results of a citizen science experiment

description: This citizen science study evaluates the occurrence of Fibonacci structure
 in the spirals of sunflower (Helianthus annuus) seedheads. This phenomenon
 has competing biomathematical explanations, and our core premise is that
 observation of both Fibonacci and non-Fibonacci structure is informative
 for challenging such models. We collected data on 657 sunflowers. In our
 most reliable data subset, we evaluated 768 clockwise or anticlockwise
 parastichy numbers of which 565 were Fibonacci numbers, and a further 67
 had Fibonacci structure of a predefined type. We also found more complex
 Fibonacci structures not previously reported in sunflowers. This is the
 third, and largest, study in the literature, although the first with
 explicit and independently checkable inclusion and analysis criteria and
 fully accessible data. This study systematically reports for the first
 time, to the best of our knowledge, seedheads without Fibonacci structure.
 Some of these are approximately Fibonacci, and we found in particular that
 parastichy numbers equal to one less than a Fibonacci number were present
 significantly more often than those one more than a Fibonacci number. An
 unexpected further result of this study was the existence of quasi-regular
 heads, in which no parastichy number could be definitively assigned.
description: Annotated seedhead
 imagesZip file containing
 multiple Powerpoint files, each containing images of sunflower heads with
 parastichies overlaid and countedJS annotations for
 MSF007_CountdataSummary of parastichy
 counts made by author when photoreviewing images in associated Powerpoint
 fileMSF007_SunflowerData_20151020_anonymisedSunflower data as uploaded to project website by the public and anonymized.MOSIpaperPE Sweave sourceSource code used to generate all figures, tables and text of the paper. In combination with the spreadsheets, can be compiled using R and standard libraries to create a tex file. The tex file can be compiled to PDF using pdflatex and standard packages.MOSIpaperPE.Rnw
DOI: 10.5061/dryad.d19j0
title: Data from: Morphological identification and single-cell genomics of marine diplonemids

description: Recent global surveys of marine biodiversity have revealed that a group of
 organisms known as “marine diplonemids” constitutes one of the most
 abundant and diverse planktonic lineages [1]. Though discovered over a
 decade ago [2 and 3], their potential importance was unrecognized, and our
 knowledge remains restricted to a single gene amplified from environmental
 DNA, the 18S rRNA gene (small subunit [SSU]). Here, we use single-cell
 genomics (SCG) and microscopy to characterize ten marine diplonemids,
 isolated from a range of depths in the eastern North Pacific Ocean.
 Phylogenetic analysis confirms that the isolates reflect the entire range
 of marine diplonemid diversity, and comparisons to environmental SSU
 surveys show that sequences from the isolates range from rare to
 superabundant, including the single most common marine diplonemid known.
 SCG generated a total of ∼915 Mbp of assembled sequence across all ten
 cells and ∼4,000 protein-coding genes with homologs in the Kyoto
 Encyclopedia of Genes and Genomes (KEGG) orthology database, distributed
 across categories expected for heterotrophic protists. Models of highly
 conserved genes indicate a high density of non-canonical introns, lacking
 conventional GT-AG splice sites. Mapping metagenomic datasets [4] to SCG
 assemblies reveals virtually no overlap, suggesting that nuclear genomic
 diversity is too great for representative SCG data to provide meaningful
 phylogenetic context to metagenomic datasets. This work provides an entry
 point to the future identification, isolation, and cultivation of these
 elusive yet ecologically important cells. The high density of
 nonconventional introns, however, also portends difficulty in generating
 accurate gene models and highlights the need for the establishment of
 stable cultures and transcriptomic analyses.
description: Single-cell genomic
 scaffolds from 10 'wild-caught' marine
 diplonemidsFASTA format single-cell
 genomic scaffolds of 10 marine diplonemid (protist) cells are presented.
 Scaffolds were generated with the SPAdes assembler; contaminating
 sequences were removed, as described in the publication. Each FASTA file
 is derived from a single cell. Cells are referred to by the numbers used
 in the publication (i.e., cells 3, 13, 21, 27, 37, 47, 1sb, 4sb, 9sb,
 21sb) as no species names exist.marine_diplonemid_SAGs.zipFigure S1 (related to Figure 1). Taxon-annotated GC plots demonstrate the effectiveness of our decontamination procedure.Plots were generated using blobtools (https://github.com/DRL/blobtools) for each SCG assembly before and after decontamination using the megablast/blastx protocol described in Experimental Procedures. Plots are based on megablast queries of the NCBI nt database according to taxonomic Order.FigS1.pdf
DOI: 10.5061/dryad.80442
title: Data from: The multivariate association between genomewide DNA methylation and climate across the range of Arabidopsis thaliana

description: Epigenetic changes can occur due to extracellular environmental
 conditions. Consequently, epigenetic mechanisms can play an intermediate
 role to translate environmental signals to intracellular changes. Such a
 role might be particularly important in plants, which often show strong
 local adaptation and have the potential for heritable epigenetic states.
 However, little is currently known about the role of epigenetic variation
 in the ecological mechanisms of adaptation. Here, we used multivariate
 redundancy analyses to examine genomewide associations between DNA
 methylation polymorphisms and climate variation in two independent panels
 of Arabidopsis accessions, including 122 Eurasian accessions as well as in
 a regional panel of 148 accessions in Sweden. At the single-nucleotide
 methylation level, climate and space (geographic spatial structure)
 explain small yet significant amount of variation in both panels. On the
 other hand, when viewed in a context of genomic clusters of methylated and
 unmethylated cytosines, climate and space variables explain much greater
 amounts of variation in DNA methylation than those explained by variation
 at the single-nucleotide level. We found that the single-nucleotide
 methylation polymorphisms with the strongest associations with climate
 were enriched in transposable elements and in potentially RNA-directed
 methylation contexts. When viewed in the context of genomic clusters,
 variation of DNA methylation at different sequence contexts exhibit
 distinctive segregation along different axes of variation in the
 redundancy analyses. Genomewide methylation showed much stronger
 associations with climate within the regional panel (Sweden) compared to
 the global (Eurasia). Together, these findings indicate that genetic and
 epigenetic variation across the genome may play a role in response to
 climate conditions and local adaptation.
description: Arabidopsis epigenome
 and climate datasetsEpigenome and genetic
 maps for Eurasian and Swedish Arabidopsis accessions. Also included are
 climate variables at these accession sites as well as R scripts to conduct
 RDA analyses.Arabidopsis_epigenome_climate.tar.gz
DOI: 10.5061/dryad.353q5
title: Data from: Analysis of phylogenomic tree space resolves relationships among marsupial families

description: A fundamental challenge in resolving evolutionary relationships across the
 Tree of Life is to account for heterogeneity in the evolutionary signal
 across loci. Studies of marsupial mammals have demonstrated that this
 heterogeneity can be substantial, leaving considerable uncertainty in the
 evolutionary timescale and relationships within the group. Using
 simulations and a new phylogenomic data set comprising nucleotide
 sequences of 1550 loci from 18 of the 22 extant marsupial families, we
 demonstrate the power of a method for identifying clusters of loci that
 support different phylogenetic trees. We find two distinct clusters of
 loci, each providing an estimate of the species tree that matches
 previously proposed resolutions of the marsupial phylogeny. We also
 identify a well supported placement for the enigmatic marsupial moles
 (Notoryctes) that contradicts previous molecular estimates but is
 consistent with morphological evidence. The pattern of gene-tree variation
 across tree-space is characterized by changes in information content, GC
 content, substitution-model adequacy, and signatures of purifying
 selection in the data. In a simulation study, we show that incomplete
 lineage sorting can explain the division of loci into the two
 tree-topology clusters, as found in our phylogenomic analysis of
 marsupials. We also demonstrate the potential benefits of minimizing
 uncertainty from phylogenetic conflict for molecular dating. Our analyses
 reveal that Australasian marsupials appeared in the early Paleocene,
 whereas the diversification of present-day families occurred primarily
 during the late Eocene and early Oligocene. Our methods provide an
 intuitive framework for improving the accuracy and precision of
 phylogenetic inference and molecular dating using genome-scale data.
description: Marsupial family
 phylogneomics analyses resultsAnalyses results for
 each data set, including phylogenetic and dating analyses. For access to
 target sequences and code used to process the sequencing reads, please see
 the Bioinformatics directory at
 https://github.com/duchene/marsupial_family_phylogenomics (linked
 below).marsupial_family_phylogneomics_analyses_results.zipMarsupial family phylogenomics target sequences and code.The directory 'Bioinformatics' contains the target sequences and code used to process the sequencing reads.
DOI: 10.5061/dryad.278q9
title: Data from: Adaptive evolution of a derived radius morphology in manakins (Aves, Pipridae) to support acrobatic display behavior

description: The morphology of the avian skeleton is often studied in the context of
 adaptations for powered flight. The effects of other evolutionary forces,
 such as sexual selection, on avian skeletal design are unclear, even
 though birds produce diverse behaviors that undoubtedly require a variety
 of osteological modifications. Here, we investigate this issue in a family
 of passerine birds called manakins (Pipridae), which have evolved
 physically unusual and elaborate courtship displays. We report that, in
 species within the genus Manacus, the shaft of the radius is heavily
 flattened and shows substantial solidification. Past work anecdotally
 notes this morphology and attributes it to the species' ability to
 hit their wings together above their heads to produce loud mechanical
 sonations. Our results show that this feature is unique to Manacus
 compared to the other species in our study, including a variety of taxa
 that produce other sonations through alternate wing mechanisms. At the
 same time, our data reveal striking similarities across species in total
 radius volume and solidification. Together, this suggests that supposedly
 adaptive alterations in radial morphology occur within a conserved
 framework of a set radius volume and solidness, which in turn is likely
 determined by natural selection. Further allometric analyses imply that
 the radius is less constrained by body size and the structural demands
 that underlie powered flight, compared to other forelimb bones that are
 mostly unmodified across taxa. These results are consistent with the idea
 that the radius is more susceptible to selective modification by sexual
 selection. Overall, this study provides some of the first insight into the
 osteological evolution of passerine birds, as well as the way in which
 opposing selective forces can shape skeletal design in these species.
description: Pmentalis_HighResolutionScansReplaceHigh Resolution CT scans of Pipra mentalisPmentalis.HighResolutionScans.zipMvitellinus_HighResolutionScansReplaceHigh Resolution CT scans of Manacus vitellinusMvitellinus.HighResolutionScans.zipMcandei_HighResolutionScansReplaceHigh Resolution CT scans of Manacus candeiMcandei.HighResolutionScans.zipCotinga_HighResolutionScansReplaceHigh Resolution CT scans of Cotinga cayanaCotinga.HighResolutionScans.zipCleuchorrhea_HighResolutionScansReplaceHigh Resolution CT scans of Corapipo leucorrhoaCleuchorrhea.HighResolutionScans.zipClanceolata_HighResolutionScansReplaceHigh Resolution CT scans of Chiroxiphia lanceolataClanceolata.HighResolutionScans.zip
DOI: 10.5061/dryad.m8j17
title: Data from: High suckling rates and acoustic crypsis of humpback whale neonates maximise potential for mother–calf energy transfer

description: 1. The migration of humpback whales to and from their breeding grounds
 results in a short, critical time period during which neonatal calves must
 acquire sufficient energy via suckling from their fasting mothers to
 survive the long return journey. 2. Understanding neonate suckling
 behaviour is critical for understanding the energetics and evolution of
 humpback whale migratory behaviour and for informing conservation efforts,
 but despite its importance, very little is known about the details, rate
 and behavioural context of this critical energy transfer. 3. To address
 this pertinent data gap on calf suckling behaviour, we deployed
 multi-sensor Dtags on eight humpback whale calves and two mothers allowing
 us to analyse detailed suckling and acoustic behaviour for a total of 68·8
 h. 4. Suckling dives were performed 20·7 ± 7% of the total tagging time
 with the mothers either resting at the surface or at depth with the calves
 hanging motionless with roll and pitch angles close to zero. 5.
 Vocalisations between mother and calf, which included very weak tonal and
 grunting sounds, were produced more frequently during active dives than
 suckling dives, suggesting that mechanical stimuli rather than acoustic
 cues are used to initiate nursing. 6. Use of mechanical cues for
 initiating suckling and low level vocalisations with an active space of
 &lt;100 m indicate a strong selection pressure for acoustic crypsis.
 7. Such inconspicuous behaviour likely reduces the risk of exposure to
 eavesdropping predators and male humpback whale escorts that may disrupt
 the high proportion of time spent nursing and resting, and hence
 ultimately compromise calf fitness. 8. The small active space of the weak
 calls between mother and calf is very sensitive to increases in ambient
 noise from human encroachment thereby increasing the risk of mother–calf
 separation.
description: Readme file for the DTG
 filesDtag files
 mn238mn238.zipDtag files mn238bmn238b.zipDtag files mn239amn239a.zipDtag files mn239bmn239b.zipDtag files mn241amn241a.zipDtag files mn242amn242a.zipDtag files mn243amn243a.zipDtag files mn246bmn246b.zipDtag files mn247amn247a.zipDtag files mn247bmn247b.zip
DOI: 10.5061/dryad.hh42t4j
title: Data from: Mechanical incompatibility caused by modifications of multiple male genital structures using genomic introgression in Drosophila

description: Mechanical incompatibility of male and female genitalia is common in
 animals with internal fertilization. However, our knowledge regarding the
 precise mechanisms is limited. One key question regards the susceptibility
 of the match between male and female genitalia to morphological
 modification. To address this issue, we generated six different
 second-chromosome introgression lines possessing partially Drosophila
 mauritiana-like genital morphology in multiple structures in D. simulans
 background. Three of the six introgression males showed elevated mobility
 at some stages during copulation with D. simulans females; this was
 assumed to be an indication of genital mismatch. Notably, one of the
 introgression males with D. mauritiana-like enlarged anal plates showed
 occasional leakage of adhesive ejaculate on the body surface when mated
 with pure D. simulans females, suggesting apparent structural
 incompatibility in genital coupling. These observations suggested that
 both sexual and natural selection shape the anal plate morphology,
 highlighting the role of this structure as an important component of
 mechanical isolation. Partial replacement (introgression) by a sibling
 species genome can induce perturbations in genital coupling mechanics,
 suggesting that genital compatibility can be susceptible to subtle genomic
 changes at the early stages of divergence in these species.
description: 1.0_Discription_of_dissection_images1.1_Summary2.0_Discription_of_coupling_pairs2.1_Duration2.2_MobilityII.2P-1II.2P-2II.2P-3II.2P-3aII.2P-3bII.2P-3cII.2P-4II.2P-5II.2P-7mauWw501w501xII2P1_1w501xII2P1_2w501xII2P1_3w501xII2P1_4w501xII2P1_5w501xII2P2_1w501xII2P2_2w501xII2P2_3w501xII2P2_4w501xII2P3_1w501xII2P3_2w501xII2P3_3w501xII2P3_4w501xII2P3_5w501xII2P3_6w501xII2P3_7w501xII2P4_1w501xII2P4_2w501xII2P4_3w501xII2P4_4w501xII2P5_1w501xII2P5_2w501xII2P5_3w501xII2P5_4w501xII2P7_1w501xII2P7_2w501xII2P7_3w501xII2P7_4w501xII2P7_5w501xmauW_1w501xmauW_2w501xw501_1w501xw501_2w501xw501_3w501xw501_4