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477 results for “Evolution: molecular”
Data from: "Rapid molecular evolution of Spiroplasma symbionts of Drosophila"
<p>This repository contains data and information to reproduce the findings reported in the paper.</p> <p>File descriptions:</p> <ul> <li>OTU_sequences.fasta – all <em>Spiroplasma</em> sequences that contained an <a href="https://pfam.xfam.org/family/OTU">OTU domain</a> as predicted by <a href="https://www.ebi.ac.uk/Tools/pfa/pfamscan/">PfamScan</a></li> <li>OTU_alignments.fasta – alignment of OTU domains performed using <a href="https://mafft.cbrc.jp/alignment/software/">Mafft</a></li> <li>RIP_sequences.fasta – all <em>Spiroplasma</em> sequences that contained an <a href="https://pfam.xfam.org/family/RIP">RIP domain</a> as predicted by <a href="https://www.ebi.ac.uk/Tools/pfa/pfamscan/">PfamScan</a></li> <li>RIP_alignments.fasta – alignment of RIP domains performed using the <a href="http://hmmer.org/">HMMER package</a></li> <li>Spiroplasma_supermatrix.fasta – Fasta alignment of concatenated single copy <em>Spiroplasma</em> loci conserved across the investigated strains. Loci that showed signs of recombination were not included</li> <li>Spiroplasma_partitions.txt – Lists the loci that make up the <em>Spiroplasma</em> supermatrix</li> <li>Spiroplasma_partitioning.scheme.txt – Partitioning scheme employed in our Maximum Likelihood analysis of the supermatrix. This was the best fitting partitioning scheme as determined with <a href="http://www.iqtree.org/">IQ-TREE</a></li> <li>Protocol_1.pdf – Chloroform–Ethanol protocol used for extracting <em>Spiroplasma</em> DNA for <em>s</em>Hy-Tx</li> </ul>
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>
Figure 2 in The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review
Figure 2. Polyploidy scenario suggested by and reproduced from Bonnaud et al. (2004). Updated diploid chromosome numbers (see Table 2) for the various branches are now Nautiloidea 52; Octopoda 56–60; Sepiolida 74; Sepiida 48–112; Myopsida 86–92 (?22-?172).
Figure 6 in The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review
Figure 6. Relationships among Sepiida. (A) Consensus tree based on 12S rRNA, 16S rRNA, cytochrome oxidase subunit II (Bonnaud et al. 2006); (B) maximum likelihood tree of cytochrome oxidase subunit I, cytochrome b and ND5 combined (Yoshida et al. 2010); (C) whole evidence approach using four to ten genes (Lindgren et al. 2012). Trees redrawn from original sources.
Figure 7 in The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review
Figure 7. Relationships within Onychoteuthidae. (A) Neighbour-joining tree based on 16S ribosomal RNA (Bonnaud et al. 1998); (B) maximum likelihood tree of five genes (see text) combined (Lindgren 2010); (C) maximum likelihood tree based on whole evidence approach using four to ten genes (Lindgren et al. 2012). All trees redrawn from original sources. Nomenclature uses systematic revision of Bolstad (2010).
Data from: Natural selection and repeated patterns of molecular evolution following allopatric divergence
Background: Geographic speciation is a major force in generating biodiversity. However, how genomes diverge over time after geographic isolation has halted gene flow has remained unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) from transcriptomes in 20 allopatric species/variety pairs from diverse angiosperm clades. Sixteen of these pairs reflect the well-known eastern Asia – eastern North America floristic disjunction; these species have been isolated for different lengths of time, from the Miocene to Pleistocene. Results: Molecular evolutionary analyses revealed that >90% of the genes examined are under purifying selection and <10% are under positive selection, and this pattern was observed for all taxon pairs, despite differences in divergence time. The divergence level at synonymous sites shared by most POGs in each taxon pair predicts the divergence time between the species/varieties. Divergence time estimates were positively correlated with abundance of genes under moderate purifying selection, but negatively correlated with abundance of genes under strong purifying selection. We identified 200 genes under strong positive selection across the species pairs, with 14 shared by 10-15 pairs and one shared by all taxon pairs. An additional 15 loci annotated to biological processes responding to various stimuli were present in 1-3 pairs.Conclusions: Our results suggest a common "most genes conserved–few genes adaptive" genomic architecture for the taxon pairs, which may be a key for maintaining a balance between the ability to conserve ancestral functions and the ability to evolve new features beneficial for new adaptations. As geographic isolation proceeds through time, the evolutionary trajectory of some genes changed from strong purifying selection to more relaxed selection. The allopatric divergence of these taxon pairs involved both neutral and adaptive evolution of functional genes.
Data for: Faster rates of molecular sequence evolution in reproduction-related genes and in species with hypodermic sperm morphologies
<p>This repository contains a record of analysis scripts and sequence alignments used for the analyses presented in the manuscript.</p> <p>Some of the R scripts depend on supplementary tables associated with the manuscript.</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>
Dataset for Bate (2022): Dust coagulation during the early stages of star formation: molecular cloud collapse and first hydrostatic core evolution
<p>This data set contains 12 smoothed particle hydrodynamics (SPH) dump files that were used to produce some of the figures in the journal paper:</p> <p>Bate, Matthew. R., 2022, Monthly Notices of the Royal Astronomical Society, accepted 13 May 2022</p> <p>Each of the SPH dump files is from a different calculation of the early stages of star formation: the gravitational collapse of a molecular cloud core, including dust coagulation. Each SPH dump file gives the state of the SPH calculation when the maximum temperature reached 1500 K, except for the beta=0.05 cases which give the state when the maximum hydrogen number density reaches 10^{14} cm^{-3}. The calculations were each performed using 3 million SPH particles and differed by their initial rotation rate, which was parameterised by beta=0, 0.0025, 0.005, 0.01, 0.02, and 0.05 (the magnitude of the ratio of the rotational and gravitational potential energies). Dump files from calculations that include and exclude envelope turbulence are provided (both are used for Figure B1). The dump files associated with each calculation are:</p> <p>beta=0: B1M0123 (does not include envelope turbulence)<br> beta=0.0025: B1M2123 (does not include envelope turbulence)<br> beta=0.005: B1M5123 (does not include envelope turbulence)<br> beta=0.01: B1M1128 (does not include envelope turbulence)<br> beta=0.02: B1M2126 (does not include envelope turbulence)<br> beta=0.05: B1M5109_b05_NoEnvTurb (does not include envelope turbulence)</p> <p>beta=0.0: B1M0123_b0_EnvTurb<br> beta=0.0025: B1M2177_b0025_EnvTurb<br> beta=0.005: B1M5209_b005_EnvTurb<br> beta=0.01: B1M1219_b01_EnvTurb<br> beta=0.02: B1M2221_b02_EnvTurb<br> beta=0.05: B1M5321_b05_EnvTurb</p> <p>The SPH dump files are Fortran binary files written in big endian format and generated by the sphNG code (Benz 1990; Bate 1995; Bate & Keto 2015). They can be read, visualised, and manipulated using the free, publicly available SPLASH visualisation code (which reads sphNG dump files), written by Daniel J. Price, that can be downloaded from: </p> <p>http://users.monash.edu.au/~dprice/splash/ </p> <p>The SPLASH configuration files used to produce Figs. 10,11,12,and B1 in Bate (2022) are included with this dataset in a gzipped tar file.</p> <p> </p>
Fig. 3 in Molecular and cytogenetic analyses of cryptic species within the Synbranchus marmoratus Bloch, 1795 (Synbranchiformes: Synbranchidae) grouping: species delimitations, karyotypic evolution and intraspecific diversification
Fig. 3. Representative ideograms of the analyzed karyomorphs of Synbranchus marmoratus showing the heterochromatic blocks, as determined by C-banding, and hybridization patterns of ribosomal sites.
Fig. 1. A in Molecular and cytogenetic analyses of cryptic species within the Synbranchus marmoratus Bloch, 1795 (Synbranchiformes: Synbranchidae) grouping: species delimitations, karyotypic evolution and intraspecific diversification
Fig. 1. A map showing the Synbranchus marmoratus specimen collection sites. Numbers indicate the sample locality, whereas symbols represent the karyomorphs found at each locality.
Fig. 4. A in Molecular and cytogenetic analyses of cryptic species within the Synbranchus marmoratus Bloch, 1795 (Synbranchiformes: Synbranchidae) grouping: species delimitations, karyotypic evolution and intraspecific diversification
Fig. 4. A dendrogram representing the relationship between the sampled Synbranchus marmoratus specimens based on the mitochondrial 16S, COI and Cyt B genes. The colors represent each of the characterized karyomorphs, and the groups (IA, IB, IC, ID and II) used as references are shown on the right side. Bootstrap support (>50%) are given above the branches. Diploid numbers of the samples are given along the branches. 2n=46* Diploid number of Ophisternon aenigmaticum (Nirchio et al., 2011).
Fig. 6 in Evolution and systematics of Green Bush-crickets (Orthoptera: Tettigoniidae: Tettigonia) in the Western Palaearctic: testing concordance between molecular, acoustic, and morphological data
Fig. 6 Comparison of the duty cycle in the songs of the T. armeniaca complex and T. caudata (left panel) and the Tettigonia viridissima group (right panel)
Fig. 2 in Evolution and systematics of Green Bush-crickets (Orthoptera: Tettigoniidae: Tettigonia) in the Western Palaearctic: testing concordance between molecular, acoustic, and morphological data
Fig. 2 Oscillograms of the song of the Tettigonia viridissima group (1–9) and T. cantans (10) recorded at two speeds: 1 T. cf. longealata (MO: Ajabo, T = 20 °C), 2 T. cf. vaucheriana (MO: N Fes, T = 20 °C), 3 T. cf. vaucheriana (MO: Bouchfaa W of Taza, T = 21 °C), 4 T. cf. vaucheriana (MO: Tilougguite Pass, T = 23 °C), 5 T. cf. vaucheriana and cf. longealata (MO: El Kebab, T = 25 °C), 6 T. cf. vaucheriana (MO: El Kebab, T = 28–30 °C), 7 T. cf. viridissima (MO: S Aïn Zora, T = 22 °C), 8 T. cf. viridissima (MO: S Aïn Zora, T = 25 °C), 9 T. viridissima (BG: Sofia, T = 27 °C), and 10 T. cantans (IT: Val Malene; from Massa et al. 2012, T = 15 °C)). Scale bar for A is 10 s and for B 2 s
Fig. 5 in Evolution and systematics of Green Bush-crickets (Orthoptera: Tettigoniidae: Tettigonia) in the Western Palaearctic: testing concordance between molecular, acoustic, and morphological data
Fig. 5 Appearance of some taxa of Western Palaearctic Tettigonia (relative size proportions between photos not retained). a T. cantans, male, Germany, Gunzenhausen; b T. cantans, female, Germany, Gunzenhausen; c T. uvarovi Ebner, 1946—male, holotype, Siberia (NHMW), lateral view; d same, dorsal view; e T. caudata, male, Bulgaria, Russe district, Byala; f T. acutipennis Ebner, 1946—male, holotype, "Kleinasien 1914 | Marasch, Tölg. | coll. R. Ebner" (NHMW), dorsal view; g same, lateral view; h T. armeniaca, male, Armenia, Djermuk; i T. armeniaca, male, Turkey, Ispir; j T. viridissima morphotype of longealata, male, Morocco, El Kebab; k T. viridissima morphotype of longealata, female, Morocco, El Kebab; l T. viridissima morphotype of vaucheriana, male, Morocco, El Kebab; and m T. viridissima, male and female in copula, Bulgaria, Haskovo district, Kostilkovo village
Fig. 4 in Evolution and systematics of Green Bush-crickets (Orthoptera: Tettigoniidae: Tettigonia) in the Western Palaearctic: testing concordance between molecular, acoustic, and morphological data
Fig. 4 Phylogenetic tree of the genus Tettigonia based on BI analysis of concatenated COI-ITS1-ITS2 sequences. BI posterior probability (PP) values are shown near resolved branches (only support values above 0.50). Species groups, as defined by genetic and morpho-acoustic data, are distinctly shaded, and the respective branches are marked with an open circle and a capital letter as follows: "A"—T. viridissima group, "B"—T. caudata group, and "C"—T. cantans group. Haplotype codes correspond to Table 1 in the Supplement, followed by morphological identification. Squares on the right side of names correspond to relative wing length: filled squares short wings and open squares long wings;
Fig. 7 in Evolution and systematics of Green Bush-crickets (Orthoptera: Tettigoniidae: Tettigonia) in the Western Palaearctic: testing concordance between molecular, acoustic, and morphological data
Fig. 7 Relationship between the duration of chirps and inter-chirp intervals in T. caudata and the Tettigonia armeniaca complex. Green triangles mark recordings from Ispir, Turkey, where monosyllabic, disyllabic, and polysyllabic songs of T. armeniaca were recorded, as well as a song of T. caudata (Color figure online)
Fig. 4 in Molecular characterization of Babesia peircei and Babesia ugwidiensis provides insight into the evolution and host specificity of avian piroplasmids
Fig. 4. Geographic distribution of the phylogenetic groups of avian piroplasmids (based on the 18S rRNA gene). Map prepared based on information provided in Criado et al. (2006), Yabsley et al. (2006, 2009), Jefferies et al. (2008), Paparini et al. (2014), Quillfeldt et al. (2014), Martínez et al. (2015), Montero et al. (2016) and Chavatte et al. (2017).
Fig. 2 in Molecular characterization of Babesia peircei and Babesia ugwidiensis provides insight into the evolution and host specificity of avian piroplasmids
Fig. 2. Maximum likelihood phylogenetic tree of the ITS-1 (445 bp) and ITS-2 regions sequences (290 bp) of select avian-infecting Babesia lineages. Sequences identified in this study are emphasized in red, and those of other avian-infecting lineages are shown in blue. For each sequence, the following information is provided: morphospecies (individual identification or Genbank code) host species. Branch lengths are drawn proportionally to evolutionary distance (scale bar shown corresponds to both trees). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
Fig. 3 in Molecular characterization of Babesia peircei and Babesia ugwidiensis provides insight into the evolution and host specificity of avian piroplasmids
Fig. 3. Distribution of the phylogenetic groups of avian piroplasmids (based on the 18S rRNA gene) in relation to the phylogeny of avian orders (based on multiple nuclear genes). Avian orders investigated in this study are shown in red, and other avian orders known to host piroplasmids are shown in blue. Avian phylogeny was adapted from Yuri et al. (2013). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
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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.