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FIGURE 11. Palaeoagraecia brunnea Ingrisch, 1998 in New additions to the Chinese Agraeciini Redtenbacher, 1891 (Orthoptera, Tettigoniidae: Conocephalinae) with report the complete mitochondrial genome of Palaeoagraecia brunnea Ingrisch, 1998
FIGURE 11. Palaeoagraecia brunnea Ingrisch, 1998. Female: A. head in frontal view; B–C. head and pronotum: B. dorsal view, C. lateral view; D. processes of thoraces in ventral view; E. apex of abdomen in lateral view; G. subgenital plate in ventral view; H. apices of ovipositor in lateral view.
FIGURE 8 in New additions to the Chinese Agraeciini Redtenbacher, 1891 (Orthoptera, Tettigoniidae: Conocephalinae) with report the complete mitochondrial genome of Palaeoagraecia brunnea Ingrisch, 1998
FIGURE 8. Liara (Liara) shii Liu & Bian sp. nov. Female: A. head, pronotum and tegmina in lateral view; B–C. apex of abdomen: B. lateral view, C. dorsal view; D. fore tibiae in dorsal view; E–F. genicular lobes of hind leg: E. external view, F. internal view.
FIGURE 7 in New additions to the Chinese Agraeciini Redtenbacher, 1891 (Orthoptera, Tettigoniidae: Conocephalinae) with report the complete mitochondrial genome of Palaeoagraecia brunnea Ingrisch, 1998
FIGURE 7. Liara (Liara) shii Liu & Bian sp. nov. Female: A. head in frontal view; B. fastigium verticis in frontal view; C. head and pronotum in dorsal view; D. head, pronotum and tegmina in dorsal view; E. head and thoraces in ventral view; F. subgenital plate in ventral view.
Figure 3 in What can the mitochondrial genome reveal about higher-level phylogeny of the molluscan class Cephalopoda?
Figure 3. Phylogeny derived from maximum likelihood analysis of 13 concatenated mitochondrial protein-coding genes, coded as amino acids, of 13 taxa (see Table 1) and from partial sequences of other taxa (see Table 3). Partial sequences are indicated by higher taxon names to distinguish them from those species for which the entire mitochondrial genome sequence was available. Bootstrap values generated from 100 replicates. Eight morphological characters are also mapped. Additional detail of characters 1, 2, 4-6, 8 can be found in Vecchione et al. (2000). Characters 2 and 7 are from Young et al. (2008). Hatched areas for Idiosepiidae in characters 2-4 and Sepiadariidae in character 4 indicate information was unavailable for the character in this taxon. The shell is absent in Sepiadariidae, indicated by white space. Abbreviations: w/o, without.
Figure 1 in What can the mitochondrial genome reveal about higher-level phylogeny of the molluscan class Cephalopoda?
Figure 1. Analyses of mitochondrial gene order data. Bootstrap values of 100 resulting from constraints on the model indicated by 100*. Posterior probabilities of 1 resulting from constraints on the model indicated by 1*. A, phylogeny recovered by Bayesian analysis in BADGER. Oegopsids excluded. B, phylogeny recovered by Bayesian analysis in BADGER. Duplicated genes excluded. C, topology recovered by breakpoint analysis in GRAPPA and MPME analysis of gene adjacency matrix. Resolution is restricted to that enforced by constraint tree. D, phylogeny derived from inversion distance analysis in GRAPPA.
Figure 1 in Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi)
Figure 1. Geographical regions of cypriniform fish distribution at the continental scale. The seven region scheme presented here [Africa (Af), South Asia (Sa), East Asia (Ea), Europe (Eu), Siberia (Sb), and western and eastern North America (Wn & En)] is a modification of the conventional Wallace's six region system (Berra, 2001). East Asia, Europe, and Siberia are subdivisions of the Palaearctic region, overlapping with each other. Western and eastern North America are subdivisions of the Nearctic region.
Figure 5. A in Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi)
Figure 5. A reconciled dispersal-vicariance analysis (DIVA; upper) and a simple parsimonious reconstruction (lower) inference of past ranges at the subfamilial level superimposed over divergence time estimates. Open rectangular bars stand for 95% confidence ranges of the divergence time estimates. The scale bar at the bottom represents the geological time scale according to Gradstein, Ogg & Smith (2004). Maps drawn from Smith, Smith & Funnel (1994) indicate onset (220 Mya) and completion (160 Mya) of the Pangaean breakup, and separation of the Indian land mass from Africa (130 Mya), which allowed marine permeation. Arrowheads indicate rifting margins; hatched pattern indicates area of black shale deposits (Olsen, 1997).
Figure 2. The maximum likelihood tree inferred from 14 594 in Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi)
Figure 2. The maximum likelihood tree inferred from 14 594 nucleotide sites of 60 Cypriniformes and six outgroups (lnL = -203 966.535). Numbers at each branch indicate the resampling the estimated log likelihood (RELL) local bootstrap probabilities. Asterisks indicate 100% local bootstrap support. Two major clades of Cyprinidae (A and B) correspond with those presented in Cavender & Coburn (1992).
Mitochondrial genome sequencing of marine leukemias reveals cancer contagion between clam species in the Seas of Southern Europe
<p>Clonally transmissible cancers are tumour lineages that are transmitted between individuals via the transfer of living cancer cells. In marine bivalves, leukemia-like transmissible cancers, called hemic neoplasias, have demonstrated the ability to infect individuals from different species. We performed whole-genome sequencing in eight <i>V. verrucosa</i> clams that were diagnosed with hemic neoplasia, from two sampling points located more than 1,000 nautical miles away in the Atlantic Ocean and the Mediterranean Sea Coasts of Spain. Mitochondrial genome sequencing of tumour tissues from neoplastic animals revealed the coexistence of haplotypes from two different clam species. Phylogenies estimated from mitochondrial and nuclear markers confirmed this leukemia originated in <i>C. gallina </i>(or a closely related taxa) and was later transmitted to <i>V. verrucosa</i>, in which it survived as a contagious cancer. The analysis of mitochondrial and nuclear gene sequences supports all the studied tumours belonging to a single neoplastic <i>C. gallina </i>lineage that spread in the Seas of Southern Europe.</p>
FIGURE 3 in The first mitochondrial genome of Creophilus Leach and Platydracus Thomson (Coleoptera: Staphylinidae: Staphylinini) and phylogenetic implications
FIGURE 3 Inferred secondary structures of 22 tRNAs of C. maxillosus. The red bases are anticodon. The tRNAs are labelled with the abbreviations of their corresponding amino acids according to the IUPAC-IUB code.
FIGURE 5 in The first mitochondrial genome of Creophilus Leach and Platydracus Thomson (Coleoptera: Staphylinidae: Staphylinini) and phylogenetic implications
FIGURE 5 Consensus trees built with different datasets under the respective best-fitting partitioning scheme and substitution model selected by AIC (see Table 2). (A) FP scheme of P1P2R matrix; (B) FP scheme of P12R matrix; (C) FP scheme of P2R matrix; (D) NP scheme of AA matrix (C60). The branch lengths are proportional to the number of nucleotide or amino acid substitutions. The species followed by an asterisk (*) are sequenced for this study. Coloured circles indicate bootstrap support. Nodes with 90–94 bootstrap values are labelled by red; 95–99 by yellow; 100 by blue. The expanded trees and trees built with alternative models can be found in the supplementary files at Zenodo (10.5281/zenodo.5847830).
FIGURE 2 in The first mitochondrial genome of Creophilus Leach and Platydracus Thomson (Coleoptera: Staphylinidae: Staphylinini) and phylogenetic implications
FIGURE 2 Relative synonymous codon usage (RSCU) of C. maxillosus and P. impotens. Codon families (in alphabetical order) are provided below the horizontal axis.
FIGURE 1 in The first mitochondrial genome of Creophilus Leach and Platydracus Thomson (Coleoptera: Staphylinidae: Staphylinini) and phylogenetic implications
FIGURE 1 Gene map of the mitochondrial genome of C. maxillosus and P. impotens. Genes outside the map are transcribed counterclockwise (reverse strand), whereas those inside are transcribed clockwise (forward strand). The outermost circle shows the gene features, sandy brown for rRNAs, salmon for tRNAs, and light sea green for PCGs. The innermost circle shows the GC content calculated in every 50-site window.
FIGURE 4 in The first mitochondrial genome of Creophilus Leach and Platydracus Thomson (Coleoptera: Staphylinidae: Staphylinini) and phylogenetic implications
FIGURE 4 Inferred secondary structures of 22 tRNAs of P. impotens. The red bases are anticodon. The tRNAs are labelled with the abbreviations of their corresponding amino acids according to the IUPAC-IUB code.
Deep-time reticulation and ancient mitochondrial genome capture during the radiation of Jamaican Anolis lizards (Squamata; Iguanidae)
<p>Gene flow and reticulation are increasingly recognized as important processes in the diversification of many taxonomic groups. With the increasing ease of collecting genomic data and the development of multispecies coalescent network approaches, such reticulations can be accounted for when inferring phylogeny and diversification. Caribbean <i>Anolis</i> lizards are a classic example of an adaptive radiation in which species have independently radiated on the islands of the Greater Antilles into the same ecomorph classes. Within the Jamaican radiation at least one species, <i>A. opalinus</i>, has been documented to be polyphyletic in its mitochondrial DNA, which could be the result of an ancient reticulation event or incomplete lineage sorting. Here we generate mtDNA and genotyping-by-sequencing (GBS) data and implement gene-tree, species-tree, and multispecies coalescent network methods to infer the diversification of this group. Our mtDNA gene-tree recovers the same relationships previously inferred for this group, which is strikingly different from the species-tree inferred from our GBS data. Posterior predictive simulations suggest that our genomic data violate commonly adopted assumptions of the multispecies coalescent model, so we use network approaches to infer phylogenetic relationships. The inferred network topology contains a reticulation event but does not explain the mtDNA polyphyly observed in this group, however coalescent simulations suggest that the observed mtDNA topology is likely the result of past introgression. How common a signature of gene flow and reticulation is across the radiation of <i>Anolis</i> is unknown; however, the reticulation events that we demonstrate here may have allowed for adaptive evolution, as has been suggested in other, more recent adaptive radiations.</p>
Data from: Historical mitochondrial genome introgression confounds species delimitation—evidence from phylogenetic inference in the Odorrana grahami species complex
<p>Species delimitation is essential to informing conservation policy and understanding ecological and evolutionary processes. Most of our recent gains in knowledge on animal diversity rely on morphological characteristics and mitochondrial (mt) DNA variation. Concordant results based on both have led to an unprecedented acceleration in the identification of new species and enriched the field of taxonomy. However, discordances are also found commonly between morphological and mtDNA evidence. This confounds species delimitation, especially when gene flow or mitochondrial genome introgression has occurred. Here we illustrate how mitochondrial genome introgression among species of the <em>Odorrana grahami </em>complex confounds species delimitation using the combined evidence of morphological characters, mitochondrial variation, and thousands of nuclear single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). Fifty-eight samples across the distribution of the <em>O. grahami </em>complex were included. The mtDNA matrilineal genealogy indicated two clades, with <em>O. grahami </em>and <em>O. junlianensis</em> clustered together. In contrast, all nuclear evidence including gene trees, species trees, and genetic structure analyses based on GBS data support three species with distinct genetic clusters. These three distinct genetic clusters also correspond to distinct morphological characters. They affirm the distinct taxonomic entities of both <em>O. grahami </em>and <em>O. junlianensis</em>, as well as a third clade distinct from either. Which species the third clade belongs to remains unclear and will require further testing. The nuclear genomic loci contradict the COI evidence, with indications of rampant historical mitochondrial genome introgression among the species of the <em>O. grahami</em> complex. These discordant signals previously confused species delimitation efforts in this group. Based on these findings, we recommend the integration of independent data, especially nuclear genomic evidence, in species delimitation so as to be robust against the pitfalls of mitochondrial introgression.</p>
Figure 3. Bayesian maximum clade credibility tree constructed from whole mitochondrial genome sequences, with a in Evolutionary history of Sundaland shrews (Eulipotyphla: Soricidae: Crocidura) with a focus on Borneo
Figure 3. Bayesian maximum clade credibility tree constructed from whole mitochondrial genome sequences, with a focus on Bornean Crocidura. Reconstructed with BEAST2. Dates are indicated on nodes and bar on bottom. Nodes used to calibrate the dating are marked with a black square. Uropsilus and Soricinae outgroups were included in the phylogenetic analysis for calibration purposes but removed from the figure for clarity. Since most nodes are highly supported (PP> 0.95), only less supported nodes (0.95 0.80) are marked with an orange circle. Colours on the vertical bar indicate geographical origin of sampled animals, and colors match the map. Samples from north of Kra are shown in grey.
FIGURE 3 in Seven new mitochondrial genomes of phytophagous scarab beetles (Coleoptera Scarabaeidae) and phylogenetic implications
FIGURE 3. Inferred secondary structure of tRNA-Ser1 (AGN) in seven new mitogenomes and tRNA-Val in the An. russiventris mitogenome.
FIGURE 5 in Seven new mitochondrial genomes of phytophagous scarab beetles (Coleoptera Scarabaeidae) and phylogenetic implications
FIGURE 5. Heterogeneous sequence divergence with nucleotides dataset and amino acids dataset of 13 PCGs of all taxa. The pairwise Aliscore scores are represented by colored squares. The scores range from -1, indicating full random similarity (dark blue), to +1, indicting non-random similarity (bright orange).
FIGURE 6 in Seven new mitochondrial genomes of phytophagous scarab beetles (Coleoptera Scarabaeidae) and phylogenetic implications
FIGURE 6. Phylogenetic tree produced using maximum likelihood (ML) and Bayesian (BI) methods based on the nucleotide sequences of 13 PCGs. The numbers on the left are Bayesian posterior probabilities (PP), and those on the right are maximum likelihood bootstrap values (BS). Asterisk indicates that this node is different in ML and BI.
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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.