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235 results for “Evolutionary genomics”
FIG. 1 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations
FIG. 1.—Map of the Hawaiian Islands with collection sitesfor Hawaiian hoary bat tissues used inthis study. Sites with n> 1 are denoted with an asterisk.
FIG. 2 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations
FIG. 2.—PCA result plot showing clustering of individual bats from four Hawaiian Islands using 21,808,031 SNPs. Sample information included in supplementary table S4, Supplementary Material online.
FIG. 4 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations
FIG. 4.—SNAPP-based phylogenetic tree inference. (A) The maximum clade credibility or consensus tree, showing approximate divergence of hoary bats across the Hawaiian archipelago. The axis on the bottom of the figure corresponds to million years before present (Ma), using the emergence of Hawai'i (~0.43 Ma) as a calibration point (95% confidence intervals were given in square brackets). (B) The drawing of all sampled trees showing all ingroup nodes were supported by maximum posterior probabilities (1.00).
Data from: The spotted parrotfish genome provides evolutionary insight into the ecological adaptation of a keystone dietary specialist
<p>With over 600 valid species, the wrasses (family Labridae) are among the largest and most successful of the marine teleosts. They feature prominently on coral reefs where they are known not only for their impressive diversity in colouration and form, but also in their functional specialization and ability to occupy a wide variety of trophic guilds. Among the wrasses, the parrotfishes (tribe Scarini) display some one of the most dramatic examples of trophic specialization. Using abrasion-resistant biomineralized teeth, parrotfishes are able to mechanically extract protein-rich micro-photoautotrophs growing in and amongst reef carbonate material, a dietary niche that is inaccessible to most other teleost fishes. This ability to exploit an otherwise untapped trophic resource is thought to have played a role in the diversification and evolutionary success of the parrotfishes. In order to better understand the key evolutionary innovations leading to the success of these dietary specialists, we sequenced and analysed the genome of a representative species, the spotted parrotfish (<em>Cetoscarus ocellatus</em>). We find significant expansion, selection, and duplication within several detoxification gene families and a novel poly-glutamine expansion in the enamel protein ameloblastin, and we consider their evolutionary implications. Our genome provides a useful resource for comparative genomic studies investigating the evolutionary history of this highly specialized teleostean radiation.</p>
A Genome-Wide Evolutionary Simulation of the Transcription-Supercoiling Coupling: extended version
<p>Data set used for the Artificial Life journal paper <a href="https://direct.mit.edu/artl/article-abstract/28/4/440/112557/A-Genome-Wide-Evolutionary-Simulation-of-the"><em>A Genome-Wide Evolutionary Simulation of the Transcription-Supercoiling Coupling: extended version</em></a>. A preprint of the paper is also available <a href="https://hal.archives-ouvertes.fr/hal-03667822">here</a>.</p> <p>This data is also used in Chapter 4 of my <a href="https://gitlab.inria.fr/tgrohens/phd">PhD thesis</a>.</p>
Polymorphism-aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes
<p>Supplementary files of Polymorphism-aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes by Borges, Boussau, Höhna, Pereira and Kosiol<br> </p>
Figure 2 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 2 Comparisons and annotations of the official gene set (OGS) of Archegozetes longisetosus.a – Number of gene models of the mites compared to other mites, chelicerates and the fruit fly (Grbić et al., 2011; Cao et al., 2013; dos Santos et al., 2015; Gulia-Nuss et al., 2016; Schwager et al., 2017). b – Non-linear multidimensional scaling plot (NMDS) of clustered orthogroups based on the OGS or predicted proteins
Figure 3 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 3 Orthology comparison and phylogenetic placement of Archegozetes longisetosusamong other chelicerates. a – Maximum likelihood phylogeny based on concatenation of 1,121 orthologs showing the mites phylogenetic position within the Oribatida (all nodes have 100%
Figure 7 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 7 Horizontal gene transfer (HGT) and implications for the feeding biology of Archegozetes longisetosus. a – Blob-plot of the long- read genome assembly contigs plotting the read coverage against GC proportion [%]. Contigs are colored according to the taxonomic order
Figure 6 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 6 The sensory systems of Archegozetes longisetosusand phylogenetic analysis of selected photoreceptor and chemosensory genes. a – Scanning electron micrograph (SEM) showing the end of tarsus on Archegozetes′ first leg. Images shows normal setae, but also modified chemosensory setae, namely eupathidia, both paired (p) and single (s), as well as an omega-3 solenidium. SEM picture courtesy of Michael Heethoff. b – Phylogeny and classification of opsin genes across the Metazoa, including those of several Chelicerata. The tree was constructed using a maximum likelihood approach (LG+F+R4 model) and rooted with a jelly fish opsin. Archegozetes sequences are depicted in red, Drosophila in turquoise; branch length unit is substitutions per site. c – Maximum likelihood phylogeny of ionotropic receptors and ionotropic glutamate receptors (LG+F+R6 model) of Archegozetes (Along), Dinothrombium (Dt), Leptothrombidium (Ld), Tetranychus (Tu) and Drosophila (Dmel). IR25a/IR8a and antenna/1 st leg IRs contain genes with known chemosensory function in Drosophila. The tree was rooted to the middle point; Archegozetes sequences are depicted in red, Drosophila in turquoise; branch length unit is substitutions per site. Bootstrap values can be found in the supplementary Figure S13. d – Maximum likelihood phylogenetic tree of gustatory receptors (JTT+F+R6 model) of Archegozetes(Along), Ixodes (Is), Tropilaelaps (Tm), Metaseiulus (Mocc) and Drosophila (Dmel). The tree was rooted to the middle point; Archegozetessequences are depicted in red, Drosophila in turquoise; branch length unit is substitutions per site. Bootstrap values can be found in the supplementary Figure S14. e – Combined image of volume rendering (grey) and reconstructed nervous system of Archegozetesin dorsal view. Color-code corresponds to different parts of the nervous system, as depicted in the legend. The blue structure in the middle of the synganglion is the part of the esophagus which penetrates the synganglion. Scale bar: 200 µm. Image courtesy of Sebastian Schmelzle based
Figure 1 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 1 The mite, Archegozetes longisetosus, in its phylogenetic and natural environment. a – Species tree of selected oribatid mites of the family Trhypochthoniidae based on phylogenetic analyses and divergence time estimates (Heethoff et al., 2011b). b – Two adults and one tritonymph of Archegozeteson a piece of leaf litter. The algae growing on the leaf serves as a food source for the mites. c – Habitus of an adult mite based on a surface rendering of a µCT-scan reconstruction. Image courtesy of Sebastian Schmelzle. d – Hi-C interaction matrix maps of the nine Archegozeteschromosomes. The corrected contacts are indicated by the color scale on the right from red (high density) to blue (low density)
Figure 8 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 8 Reconstruction of the biosynthetic pathway leading to monoterpenes in Archegozetes longisetosus. a – Representative gas chro- matogram of the mite′ gland content; in order of retention time: 2-hydroxy-6-methyl-benzaldehyde (2,6-HMBD), neral (( Z)-3,7-dimethylocta- 2,6-dienal) neryl formate (( Z)-3,7-dimethyl-2,6-octadienyl formate), tridecane, 3-hydroxybenzene-1,2-dicarbaldehyde (γ-acaridial). Further alkanes/alkenes (pentadec-7-ene, pentadecane, heptadeca-6,9-diene, heptadec-8-ene, heptadecane) are not shown. Monoterpenes are marked
Figure 5 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 5 The genomic organization of the Hox genes and life-stage specific expression patters of developmental genes in Archegozetes longisetosus. a – Schematic of the genomic region enclosing the ArchegozetesHox cluster. The genomic organization of the Hox cluster is collinear,
Figure 4 in Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus
Figure 4 Comparison of repeat content estimations and transposable element (TE) landscape of Archegozetes longisetosus. a – Repetitive element categories of Archegozetes based on the results from RepeatModeler and MITETracker. LINE= long interspersed nuclear element, LTR= long terminal repeat. b – Comparison of total repetitive content among Archegozetes, other model chelicerates and the fly. All values are from the respective genome paper of the species, except for the fly. c – Repeat divergence plot showing TE activity through time for the major TE superfamilies of Archegozetes.Transposable elements with a low divergence from the consensus were recently active, while TEs diverging
Figure 2 in EVOLUTIONARY PATTERNS OF GENOME SIZE AND CHROMOSOME NUMBER VARIATION IN BEGONIACEAE
Figure 2. Genome sizes and chromosome numbers of 64 Begonia species and Hillebrandia sandwicensis. The sources of the data used to create this scatter plot are specified in Supplementary table 2. Species in the same sections are enclosed within an ellipse. Colours indicate the continent where each species is found. The Hillebrandia data point is labelled as 'Outgroup'.
Figure 1 in EVOLUTIONARY PATTERNS OF GENOME SIZE AND CHROMOSOME NUMBER VARIATION IN BEGONIACEAE
Figure 1. Variation in haploid chromosome number across the Begonia sections recognised by Moonlight et al. (2018) and their chromosome data. Boxes in the box plot are grouped by clade. The colours indicate the continent where these sections are found. Bar charts indicate the proportion of the section with known chromosome counts. Dots indicate sections with polyploid species or with species with known interspecific chromosome number variation (including B chromosomes). AC-C, Asian clade C; AC-D, Asian clade D; EDAB, early diverging Asian Begonia; FFAB, fleshy-fruited African Begonia; MB, Malagasy Begonia; NC1, Neotropical clade 1; NC2-i, Neotropical clade 2-i; NC2-ii, Neotropical clade 2-ii; NC2-iii, Neotropical clade 2-iii; SB, Socotran Begonia; SDAAB1, seasonally dry adapted African Begonia 1; SDAAB2, seasonally dry adapted African Begonia 2; YFAB, yellow-flowered African Begonia. * Unresolved or polyphyletic in the phylogeny of Moonlight et al. (2018).
FIGURE 5 in Tracking the evolutionary pathways among Brazilian Lebiasina species (Teleostei: Lebiasinidae): a chromosomal and genomic comparative investigation
FIGURE 5 | First Row: Mitotic chromosome spreads of Lebiasina minuta males after CGH— interspecific comparisons (A–D). Male-derived genomic probe of L. minuta (A); L. melanoguttata (B); L. bimaculata (C) hybridized against male metaphase plates of L. minuta (D). Second Row: Mitotic chromosome spreads of Lebiasina minuta males after CGH— intraspecific comparisons (E–H). DAPI image (E); Male-derived genomic probe of L. minuta (F); Female-derived genomic probe of L. minuta (G) hybridized against male metaphase plates of L. minuta (H). The common genomic regions of both compared karyomorphs are depicted in yellow. Scale bar = 5 µm.
FIGURE 4 in Tracking the evolutionary pathways among Brazilian Lebiasina species (Teleostei: Lebiasinidae): a chromosomal and genomic comparative investigation
FIGURE 4 | Whole chromosome painting (WCP) highlighting the first chromosome pair of Lebiasina minuta completely hybridized with the probe from the first chromosome pair of L. bimaculata.
FIGURE 6 in Tracking the evolutionary pathways among Brazilian Lebiasina species (Teleostei: Lebiasinidae): a chromosomal and genomic comparative investigation
FIGURE 6 | Representative idiograms of L. bimaculata (A); L. melanoguttata (B) and L. minuta (C) highlighting the distribution of the 18S (green) and 5S (red) rDNA sequences; (CGG)n microsatellite (blue) and C-positive heterochromatin (black): Data for L. bimaculata and L. melanoguttata are from Sassi et al. (2019).
FIGURE 3 in Tracking the evolutionary pathways among Brazilian Lebiasina species (Teleostei: Lebiasinidae): a chromosomal and genomic comparative investigation
FIGURE 3 | Metaphase chromosomes of Lebiasina minuta hybridized with microsatellite probes (A, B and C) and telomeric probes (D), using red signals. Scale bar = 5 µm.
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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.