Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
39
datasets available to search
ShareScore release 0.9.0
Dataset results
39 results for “molecular convergence”
Alignments from "Caecilian genomes reveal molecular basis of adaptation and convergent evolution of limblessness in vertebrates"
<p>Compressed file containing the alignments at both nucleotide and amino acid level for the manuscript "Caecilian genomes reveal molecular basis of adaptation and convergent evolution of limblessness in vertebrates" </p>
Data from: The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function
<p>An underexplored question in evolutionary genetics concerns the extent to which mutational bias in the production of genetic variation influences outcomes and pathways of adaptive molecular evolution. In the genomes of at least some vertebrate taxa, an important form of mutation bias involves changes at CpG dinucleotides: If the DNA nucleotide cytosine (C) is immediately 5' to guanine (G) on the same coding strand, and if the C is methylated, then C→T and G→A mutations occur at an elevated rate relative to mutations at non-CpG sites. Here we examine experimental data from case studies in which it has been possible to identify the causative substitutions that are responsible for adaptive changes in the functional properties of vertebrate hemoglobin (Hb). Specifically, we examine the molecular basis of convergent increases in Hb-O<sub>2</sub> affinity in high-altitude birds. Using a data set of experimentally verified, affinity-enhancing mutations in the Hbs of highland avian taxa, we tested whether causative changes are enriched for mutations at CpG dinucleotides relative to the frequency of CpG mutations among all possible missense mutations. The tests revealed that a disproportionate number of causative amino acid replacements were attributable to CpG mutations, demonstrating that mutation bias can influence outcomes of molecular adaptation.</p>
Estimates of molecular convergence reveal genes with intermediate pleiotropy underlying adaptive variation across teleost fish
<p>This dataset comprises raw sequence data, output of analyses, code used to reproduce the study, figures, and supplementary materials.</p> <p>Code and input files are in Datasets.zip</p> <p>Use the README to navigate this folder. </p> <p>Data to reproduce the CSUBST analysis are in the .tar.gz folder.</p> <p> </p> <p>For more information please check: </p> <p>https://github.com/agneeshbarua/Teleost_convergence</p>
Data from: The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function
Open the record for dataset details and reuse information.
A high-quality genome of the dobsonfly Neoneuromus ignobilis reveals molecular convergences in aquatic insects
<p><em>Neoneuromus ignobilis</em> is an archaic holometabolous aquatic predatory insect. However, a lack of genomic resources hinders the use of whole genome sequencing to explore their genetic basis and molecular mechanisms for adaptive evolution. Here, we provided a high-contiguity, chromosome-level genome assembly of <em>N</em>. <em>ignobilis</em> using high coverage nanopore reads and the Hi-C technique. The final assembly is 481.43 MB in size, containing 12 telomere-ended pseudochromosomes with only 23 gaps. We then compared 42 hexapod species genomes including six independent lineages comprising 11 aquatic insects, and found convergent expansions of long wavelength-sensitive and blue-sensitive opsins, thermal stress response TRP channels, and sulfotransferases in aquatic insects, which may be related to their aquatic adaptation. We also detected strong non-random signals of convergent amino acid substitutions in aquatic insects. Collectively, our comparative genomic analysis revealed the evidence of molecular convergences in aquatic insects during both gene family evolution and convergent amino acid substitutions.</p>
A high-quality genome of the dobsonfly Neoneuromus ignobilis reveals molecular convergences in aquatic insects
Open the record for dataset details and reuse information.
FIGURE 1 in Phylogenetic relationships in the genus Astropecten Gray (Paxillosida: Astropectinidae) on a global scale: molecular evidence for morphological convergence, species-complexes and possible cryptic speciation
FIGURE 1. Phylogeny of the genus Astropecten as suggested by Döderlein (1917) presenting the relationships of species and species groups relevant to this study.
Figure 6 in Morphology, morphogenesis, and molecular phylogeny of a new marine urostylid ciliate (Ciliophora, Stichotrichia) from the South China Sea, and a brief overview of the convergent evolution of the midventral pattern within the Spirotrichea
Figure 6. The maximum-likelihood (ML) tree inferred from the small subunit ribosomal RNA (SSU rRNA) gene sequences of 63 spirotrichous taxa, showing the position of Bergeriella ovata gen. et sp. nov. (boxed), and the phylogenetic relationships among the taxa possessing midventral cirral rows (i.e. urostylids s.l.; branches are depicted by thick lines, and species names are highlighted in bold text). Nodal support for branches in the ML, Bayesian inference (BI), and neighbour-joining (NJ) trees are marked in order. Bootstrap values lower than 50% and Bayesian posterior probabilities lower than 0.70 are replaced with hyphens. Clades with different topologies in the NJ tree relative to the ML and BI trees are indicated with asterisks. All branches are drawn to scale. The scale bar corresponds to five substitutions per 100 nucleotide positions. Phacodinium and Protocruzia were taken as out-group taxa.
Figure 3 in Morphology, morphogenesis, and molecular phylogeny of a new marine urostylid ciliate (Ciliophora, Stichotrichia) from the South China Sea, and a brief overview of the convergent evolution of the midventral pattern within the Spirotrichea
Figure 3. Ventral (A, C, E, G) and dorsal (B, D, F, H) views of Bergeriella ovata gen. et sp. nov. in morphogenesis (A–D) and regeneration (E–H), after impregnation with protargol. A, an early divider, showing the oral primordium (arrow) and fronto-ventral-transverse (FVT) anlagen (arrowhead) of the proter. The double arrowheads mark the anlagen for the nonmigratory row, which comes from the posteriormost FVT streak. B, the same specimen as shown in (A), showing the enlarged macronuclear nodules and the formation of the dorsal kinety anlagen (arrows). C, an individual at a late stage of division, with all cirri developed; note the structures that will respectively form the enlarged postoral ventral cirri (arrowheads) and the delicate left ventral cirri (arrows). The double arrowheads indicate the anlagen for the nonmigratory row. D, the differentiating marginal row (arrows) and dorsal kineties; note that the macronuclear nodules are separating. E, F, an early reorganizer, showing the oral primordium (arrow in E), FVT streak (arrowhead), nonmigratory row (double arrowheads) and dorsal kinety anlagen; the arrows in (F) indicate the anlagen for the right and left marginal rows, which are derived within the parental structure. G, H, a middle-stage reorganizer, with a further proliferation of kinetosomes, showing the first frontal cirrus (arrow in G) generated from the undulating membrane anlagen, the basal bodies developed from FVT streaks (arrowhead), the anlagen for the nonmigratory row (double arrowheads), and the anlagen for the right and left marginal rows (arrows in H). Abbreviations: DK, dorsal kineties; DKA, dorsal kinety anlagen. Scale bars: 40 Mm.
Figure 2 in Morphology, morphogenesis, and molecular phylogeny of a new marine urostylid ciliate (Ciliophora, Stichotrichia) from the South China Sea, and a brief overview of the convergent evolution of the midventral pattern within the Spirotrichea
Figure 2. Photomicrographs of Bergeriella ovata gen. et sp. nov. from life. A, ventral view of a specimen. B, C, ventral view of slender and fat forms; the arrow indicates the wide and bright oral field. D, lateral view. E, F, lateral (E) and dorsal (F) views, showing the distribution of the granules; the arrows mark the granule rows near the base of each marginal cirrus, the arrowheads point to the granule rows along with midventral rows, and the double arrowheads mark the granule bands in the gap between the somatic kineties. G, H, showing the cortical granules (arrows), the fibres associated with cirri (arrowheads), and a dorsal cilium (double arrowheads). I, focusing on the oral field; note the paroral membrane (arrowhead) and the endoral membrane (arrow). J, the cortical granules (arrow) near the base of marginal cirri. K, lateral view of the posterior portion; arrows point to the enlarged postoral ventral cirri. L, globular lipid droplets in the cytoplasm. Scale bars: 50 Mm.
Figure 1 in Morphology, morphogenesis, and molecular phylogeny of a new marine urostylid ciliate (Ciliophora, Stichotrichia) from the South China Sea, and a brief overview of the convergent evolution of the midventral pattern within the Spirotrichea
Figure 1. Bergeriella ovata gen. et sp. nov. drawn from life (A–C, E–F) and after impregnation with protargol (D, G–J). A, ventral view of a specimen. B, different body shapes. C, section of the ventral infraciliature, showing the fibres associated with the postoral ventral cirri (double arrowheads) and the obliquely arranged left ventral cirri (arrow). D, distribution of cortical granules (arrow) near the marginal cirri. E, F, distribution of the cortical granules on the ventral (E) and dorsal (F) sides; the arrow indicates the granules along the nonmigratory row, and the arrowheads point to the granular rows along the dorsal kineties. G, left lateral side view of the infraciliature. H–I, ventral (H) and dorsal (I) views of the infraciliature; note the enlarged postoral ventral cirri (dashed lines), the frontal cirri (dashed lines), and the three dorsal kineties (arrows). J, ventral view of an early divider; the arrow indicates the oral primordium of the proter, the arrowheads mark the old endoral membranes in dedifferentiation, and the double arrowhead points to the oral primordium of the opisthe. Abbreviations: AZM, adoral zone of membranelles; BC, buccal cirri; DK, dorsal kineties; EM, endoral membrane; FC, frontal cirri; LMR, left marginal row; LVR, left ventral rows; MVR, midventral rows; NMR, nonmigratory row; PM, paroral membrane; PVR, postoral ventral rows; RMR, right marginal row. Scale bars: 40 Mm (A–C, F–J); 15 Mm (E).
Figure 5 in Morphology, morphogenesis, and molecular phylogeny of a new marine urostylid ciliate (Ciliophora, Stichotrichia) from the South China Sea, and a brief overview of the convergent evolution of the midventral pattern within the Spirotrichea
Figure 5. Photomicrographs of regeneration in Bergeriella ovata gen. et sp. nov. after impregnation with protargol. A, B, ventral views of middle reorganizers, showing the oral primordium (arrow in A), fronto-ventral-transverse (FVT) anlagen (arrowheads), and the anlagen for the nonmigratory row (double arrowhead); the arrow in (B) points to the undulating membrane anlagen. C, a middle-stage reorganizer; the arrow marks the first frontal cirrus generated from the undulating membrane anlagen, and the arrowheads indicate the anlagen for the nonmigratory row. D, dorsal view of the same specimen, showing the anlagen for the left marginal row (arrow) and the dorsal kinety anlagen (arrowheads).
Figure 4 in Morphology, morphogenesis, and molecular phylogeny of a new marine urostylid ciliate (Ciliophora, Stichotrichia) from the South China Sea, and a brief overview of the convergent evolution of the midventral pattern within the Spirotrichea
Figure 4. Photomicrographs of Bergeriella ovata gen. et sp. nov. after impregnation with protargol. A, infraciliature of the ventral posterior portion, showing the nonmigratory row (arrow), the postoral (arrowheads), and the left ventral cirri (double arrowheads). B, infraciliature of an anterior portion, showing the frontal cirri (arrows), buccal cirri (arrowhead), and the undulating membranes (double arrowheads). C, left lateral view, showing the left ventral rows, and the left marginal row (arrow). D, dorsal kineties, in which kinetosomes become more densely spaced from left to right (arrows). E, dorsal view, showing the anterior portion of the nonmigratory row (arrowhead) and the right marginal row (arrow). F, nuclear apparatus, some with replication bands can be seen. G, H, ventral and dorsal views of an early stage divider, showing the undulating membrane anlagen (arrow in G), FVT anlagen (arrowheads), and the anlagen for the nonmigratory row, which come from the posteriormost FVT streak (double arrowheads) of the opisthe. The arrows in (H) indicate the dorsal kineties anlagen. I, early divider showing the appearance of the oral primordium (arrow) and the enlarged macronuclear nodules of the proter. J, separating ellipsoid macronuclear nodules. K, L, ventral views of a late-stage divider (same specimen), showing the developed cirri of the proter (K) and the opisthe (L); the arrows indicate the migrating postoral and left ventral cirri, and the arrowheads indicate the anlagen for the nonmigratory row. M, dorsal view of the same specimen shown in (K) and (L), showing the anlagen of the marginal rows (arrows) and the new dorsal kineties.
Molecular adaptation and convergent evolution of frugivory in Old World and New World fruit bats
<p>Repeated adaptations to the same dietary niche in different lineages are a hallmark in mammalian ecology. Molecular evolutionary analysis is powerful to dissect the evolutionary history of dietary adaptations based on the knowledge of gene functions. Here we used genome-wide analyses of molecular evolution to examine two lineages of bats that have independently evolved obligate frugivory: the Old World family Pteropodidae and the New World subfamily Stenodermatinae, although ancestral bats were insectivorous. We report novel genome sequences of two New World fruit bats (<i>Artibeus jamaicensis</i> and <i>Sturnira hondurensis</i>), which together provide a framework for comparisons with Old World fruit bats. Comparative genomics of 10 bat species, which have diverse diets across their phylogeny, revealed a number of convergent molecular signatures underlying evolutionary adaptations to obligate frugivory. We identified three subfamilies of olfactory receptor genes, losses of three bitter taste receptor genes, losses of two digestive enzyme genes, and convergent amino acid substitutions in several metabolic genes that are specifically linked to frugivory. This study provides an excellent model to explore molecular adaptations contributing to convergent evolution of obligate frugivory, and will facilitate future studies of ecological adaptations in mammals.</p>
Data from: Distinguishing between convergent evolution and violation of the molecular clock for three taxa
We give a non-technical introduction to convergence-divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of lineages after lineage-splitting but also allows for taxa to converge, i.e. become more similar over time. By examining the 3-taxon case in some detail we illustrate that phylogeneticists have been ``spoiled'' in the sense of not having to think about the structural parameters in their models by virtue of the strong assumption that evolution is tree-like. We show that there are not always good statistical reasons to prefer the usual class of tree-like models over more general convergence-divergence models. Specifically we show many 3-taxon data sets can be equally well explained by supposing violation of the molecular clock due to change in the rate of evolution along different edges, or by keeping the assumption of a constant rate of evolution but instead assuming that evolution is not a purely divergent process. Given the abundance of evidence that evolution is not strictly tree-like, our discussion is an illustration that as phylogeneticists we need to think clearly about the structural form of the models we use. For cases with four taxa we show that there will be far greater ability to distinguish models with convergence from non-clock-like tree models.
Exploring Conformational Landscapes and Binding Mechanisms of Convergent Evolition for the SARS-CoV-2 Spike Omicron Variant Complexes with the ACE2 Receptor Using AlphaFold2-Based Structural Ensembles and Molecular Dynamics Simulations
Open the record for dataset details and reuse information.
FIGURE 4 in Phylogenetic relationships in the genus Astropecten Gray (Paxillosida: Astropectinidae) on a global scale: molecular evidence for morphological convergence, species-complexes and possible cryptic speciation
FIGURE 4. Mediterranean and East Atlantic (see caption of Figure 3 for further explanations)
FIGURE 2 in Phylogenetic relationships in the genus Astropecten Gray (Paxillosida: Astropectinidae) on a global scale: molecular evidence for morphological convergence, species-complexes and possible cryptic speciation
FIGURE 2. Collection sites of Astropecten specimens and outgroup taxa.
Data from: Distinguishing between convergent evolution and violation of the molecular clock for three taxa
Open the record for dataset details and reuse information.
Molecular adaptation and convergent evolution of frugivory in Old World and New World fruit bats
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.