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196 results for “mitochondrial phylogeny”
Phylogeny of "Philoceanus complex" seabird lice (Phthiraptera: Ischnocera) inferred from mitochondrial DNA sequences
<p>Data from "Phylogeny of “<em>Philoceanus </em>complex” seabird lice (Phthiraptera: Ischnocera) inferred from mitochondrial DNA sequences". See the file index.html for details. Data includes NEXUS files for sequences, tree files output by MrBayes and PAUP, and host-parasite association files for TreeMap.</p>
Figure 1 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 1. Circular map of Baltia butleri, Talbotia naganum, Pontia callidice, Pontia daplidice mitochondrial genome. COI, COII, and COIII refer to the cytochrome oxidase subunits; CytB refers to cytochrome B; ATP6 and ATP8 refer to subunits 6 and 8 of F0 ATPase; ND1-6 refers to the components of NADH dehydrogenase. The tRNAs locations are marked by the color blocks and labeled by the IUPAC-IUB single letter amino acid code. L1, L2, S1, and S2 denote tRNALeu (CUN), tRNALeu (UUR), tRNASer (AGN), and tRNASer (UCN), respectively. The non-underlined genes are transcribed on the majority strand whereas the underlined genes are transcribed on the minority strand.
Figure 16 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 16. Bayesian inference (BI) and Maximum likehood (ML) phylogenetic trees inferred from mitochondrial genomes of pierid family based on 22tRNA genes.
Figure 3 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 3. Relative Synonymous Codon Usage (RSCU) of the four pierid butterfly mitogenomes newly determined in this study.
Figure 15 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 15. Bayesian inference (BI) and Maximum likehood (ML) phylogenetic trees inferred from mitochondrial genomes of pierid family based on four datasets (13PCGs, 13PCGs+2rRNAs, 2rRNAs, 2rRNAs+22tRNAs).
Figure 5. Bayesian phylogeny, with species divergence age estimates reconstructed with BEAST using all the 26 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains
Figure 5. Bayesian phylogeny, with species divergence age estimates reconstructed with BEAST using all the 26 mitochondrial genomes generated in this study. The dataset was supplemented with Thyropygus sp. and Abacion magnum as outgroups, derived from GenBank. GenBank accession numbers are provided in parentheses. Blue bars indicate the 95% highest probability density intervals for node ages. Age estimation for lineage divergence was based on a general arthropod mitochondrial DNA substitution rate and should be considered with caution. *Thyropygus sp. (red font) is very likely to be a misidentification; for more information, see the Discussion.
Fig. 3 in Characterization of the mitochondrial genome of Tetrameres grusi and insights into the phylogeny of Spirurina
Fig. 3. Phylogenetic relationships of Tetrameres grusi with other 24 Spirurina species based on concatenated amino acid sequences of 12 PCGs analyzed by BI and ML using Bunostomum phlebotomum as outgroup. Posterior probability values are indicated.
Fig. 2 in Characterization of the mitochondrial genome of Tetrameres grusi and insights into the phylogeny of Spirurina
Fig. 2. Mitogenome arrangement in Tetrameres grusi compared with those in Spirurina nematodes. The circular mitogenomes were linearized at the 5′ end of cox1 gene for illustration purpose. Non-coding regions were not shown. Triangular markers of the same color represent the corresponding duplicated genes. The purple frames represent the duplicated gene fragments.
Fig. 1 in Characterization of the mitochondrial genome of Tetrameres grusi and insights into the phylogeny of Spirurina
Fig. 1. Gene map of the mitogenome of Tetrameres grusi. PCGs are colour-coded (cox: lavender; nad: yellow; atp: green; cyt: purple); rRNAs are in red; tRNAs are in dark blue. Abbreviations of PCGs are: atp6 for ATP synthase subunits 6, cox1–3 for cytochrome oxidase subunits 1–3, cytb for cytochrome b, nad1–6 and nad4L for NADH dehydrogenase subunits 1–6 and 4L, rrnL and rrnS for large and small rRNA subunits, 22 tRNAs are designated by the one-letter code for the corresponding amino acid, with numerals differentiating each of the two leucine and serine-specifying tRNAs (L1 and L2 for codon families CUN and UUR, respectively; S1 and S2 for codon families UCN and AGN, respectively), NCR refers to Noncoding region. All genes are transcribed in the clockwise direction.
Text-fig. 2. Phylogeography based on mitochondrial phylogeny showing several evolutionary lineages of Arvicola and the separation of the Italian lineage of Arvicola, currently A. italicus (lineage A1), from European and Euro-Asiatic groups. From Wust-Saucy (1998: fig. 27), modified. in Independent Water Vole (Mimomys Savini, Arvicola: Rodentia, Mammalia) Lineages In Italy And Central Europe
Text-fig. 2. Phylogeography based on mitochondrial phylogeny showing several evolutionary lineages of Arvicola and the separation of the Italian lineage of Arvicola, currently A. italicus (lineage A1), from European and Euro-Asiatic groups. From Wust-Saucy (1998: fig. 27), modified.
Figure 2. Phylogenetic relationships among the 29 in Molecular phylogeny and phylogeography of the Greek populations of the genus Orthometopon (Isopoda, Oniscidea) based on mitochondrial DNA sequences
Figure 2. Phylogenetic relationships among the 29 specimens of Orthometopon species. Individuals from two other terrestrial isopod species were used as outgroup taxa: Ligidium sp. and Armadillidium vulgare. Phylogenetic analyses, maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI), all produced trees with the same topology. Only the BI tree is presented here. Numbers above the branches indicate bootstrap values in the MP and ML analyses, respectively (MP/ML). Numbers below the branches indicate the posterior probabilities of the Bayesian analysis (BI).
Figure 1 in Molecular phylogeny and phylogeography of the Greek populations of the genus Orthometopon (Isopoda, Oniscidea) based on mitochondrial DNA sequences
Figure 1. Map showing the sampling localities of the 29 specimens used for the DNA analysis. The numbers correspond to those listed in Table 1.
Data from: Mitochondrial metagenomics reveals the ancient origin and phylodiversity of soil mites and provides a phylogeny of the Acari
<p>High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites from soils in an area of mixed forest and grassland in southern Iberia. Selected specimens representing the full morphological diversity were shotgun sequenced in bulk, followed by genome assembly of short reads from the mixture, which produced >100 mitochondrial genomes representing diverse acarine lineages. Phylogenetic analyses in combination with taxonomically limited mitogenomes available publicly resulted in plausible trees defining basal relationships of the Acari. Several critical nodes were supported by ancestral-state reconstructions of mitochondrial gene rearrangements. Molecular calibration placed the minimum age for the common ancestor of the superorder Acariformes, which includes most soil-dwelling mites, to the Cambrian-Ordovician (likely within 455–552 Mya), while the origin of the superorder Parasitiformes was placed later in the Carboniferous-Permian. Most family-level taxa within the Acariformes were dated to the Jurassic and Triassic. The ancient origin of Acariformes and the early diversification of major extant lineages linked to the soil are consistent with a pioneering role for mites in building the earliest terrestrial ecosystems.</p>
Figure 1. - Bayesian phylogeny of Euptychia based on one mitochondrial (COI) and one nuclear (EF1-a) gene. Posterior probabilities are listed above and bootstrap values below branches. A dash denotes bootstrap support lower than 50%. (Euptychiaattenboroughi is not included in the analysis – see text for details.)
Figure 1. - Bayesian phylogeny of Euptychia based on one mitochondrial (COI) and one nuclear (EF1-a) gene. Posterior probabilities are listed above and bootstrap values below branches. A dash denotes bootstrap support lower than 50%. (Euptychiaattenboroughi is not included in the analysis – see text for details.)
Figure 5 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 5. Predicted secondary structures of Pontia callidice and Pontia daplidice 22 tRNA genes.
Figure 10 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 10. Predicted secondary structure of Pontia callidice srRNA gene.
Figure 8 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 8. Predicted secondary structure of Talbotia naganum srRNA gene.
Figure 6 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 6. Predicted secondary structure of Baltia butleri srRNA gene.
Figure 4 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 4. Predicted secondary structures of Baltia butleri and Talbotia naganum 22 tRNA genes.
Figure 12 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets
Figure 12. Predicted secondary structure of Pontia daplidice srRNA gene.
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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.