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452 results for “Mitogenomics”
Fig. 4 in The complete mitogenome of Argas vulgaris (Filippova, 1961) and its phylogenetic status in subgenus Argas (Acari: Argasidae)
Fig. 4. Phylogenetic tree of Argas species based on the COI gene contained in the mitochondrial genome. Numbers at the nodes are bootstrap values of the ML analysis. The GenBank accession numbers are listed after the species names.
Linked collectors and determiners for: Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species.
Natural history specimen data linked to collectors and determiners held within, "Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/532758c6-a328-4d53-82f5-592d22419678">https://bionomia.net/dataset/532758c6-a328-4d53-82f5-592d22419678</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/532758c6-a328-4d53-82f5-592d22419678">https://gbif.org/dataset/532758c6-a328-4d53-82f5-592d22419678</a>. Formatted as a Frictionless Data package.
Figure S1 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure S1. Map of the Gigantometra gigas mitogenome using Sanger method (GenBank accession number: MF177288). Genes in the outer circle indicate the direction of transcription of the majority strand (J-strand), and those in the inner circle indicate that of the minority strand (N-strand). The GC content, GC skew+, and GC skew- are separately shown in the circle.
Figure 6 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure 6. Two examples of the heteroplasmic sites in Sanger sequencing which correspond to the differently sequenced sites. Panels A and B indicate the sites at which the second-peak is obviously higher than the third-peak and fourth-peak, and the base state of the second-peak can be obtained by at least one result of HTS. The different fluorescence densities of base situated at np 1923 in the cox1 are shown in the panel A, and the panel B shows the nucleotides with amino acids at np 1923 in the results of Sanger and HTS methods. The nucleotides are C in the results of HTS sequencing, while the corresponding nucleotides are T in the results of Sanger method in both positions, and the different nucleotides lead not to the amino acids changed. Panels C and D indicate the site at the unobvious second-peak, which is slightly higher than the third-peak and fourth-peak, and the base state of the second-peak can also be obtained by at least one result of HTS. Panel C shows the unobvious second-peak at np 7125, and the nucleotide and amino acid of the site in the results of Sanger and HTS methods are shown in panel D. The amino acids are listed using single-letter amino acid abbreviations.
Figure 4. Intraspecific pairwise K2P in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure 4. Intraspecific pairwise K2P distance of G. gigas based on barcode fragment size of cox1 (Sanger). The red boxplot shows the genetic distances of individuals in all three collecting sites, and the boxplots (blue, green, and yellow) separately show the distances of individuals within each place (HNYG, HNDL, and VIET). The pink boxplot shows the distances of the corresponding cox1 sequences obtained by the two sequencing methods. Abbreviation: HNYG—Yinggeling Nature Reserve, Hainan; HNDL— Diaoluoshan Nature Reserve, Hainan; VIET—northern Vietnam.
Figure S5 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure S5. The coverage of short fragments at each position in the assembly results of HTS. The three results of HTS method were separately used as reference sequences to be mapped back onto the corresponding HTS scaffolds, and the mitochondrial genes were shown below the corresponding coverage. The scale bar had an indicator at the mean coverage level and the coverage for each nucleotide position was indicated by the height of the blue line.
Figure 3 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure 3. The different nucleotides in the ITS-1 and ITS-2 regions are shown. The result shows the different nucleotides at nucleotide position np 1897 (G nucleotide and T nucleotide) and np 2790 (C nucleotide and T nucleotide) obtained by Sanger and HTS methods.
Figure 1. Gigantometra gigas. A. Female, dorsal view. B. Male, dorsal view. C in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure 1. Gigantometra gigas. A. Female, dorsal view. B. Male, dorsal view. C. The narrow distribution of G. gigas.
Figure 4 in Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand Callaeidae (Aves: Passerida)
Figure 4. Palaeogeographical reconstructions of New Zealand. Land is shaded in green, coastal areas in light yellow, shallow sea in light blue, and deep sea in dark blue. Inset shows present-day map of New Zealand: (1) the Wanganui Basin; (2) the Kuripapango Strait; (3) the Ruataniwha Strait; and (4) the Manawatu Strait. Row A maps are adapted from GNS Science reconstructions based on the studies by King et al. (1999) and King (2000). Row B maps are adapted from the work of Trewick & Bland (2012) and are focused on the area outlined in red on the present-day inset. Row C maps are adapted from the study by Bunce et al. (2009); the ~20 Mya map shows the entire landmass, and subsequent ones are focused on the area outlined in the black bounding box. Background grey shading denotes changing geological periods.
Figure 2 in Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand Callaeidae (Aves: Passerida)
Figure 2. RAXML tree of Callaeidae mitogenomes, excluding the control region, showing different relationships and bootstrap support between Callaeidae (shaded green), Notiomystis cincta, Petroica spp. and Poodytes punctatus. Bootstrap support is shown at nodes.
Figure 3 in Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand Callaeidae (Aves: Passerida)
Figure 3. BEAST chronogram of Callaeidae and 17 other passerines, based on a relaxed lognormal clock and fossil calibrations from the studies by Oliveros et al. (2019) and Scofield et al. (2017). Time scale is in millions of years. Mean divergence dates are shown in black at nodes; bars represent posterior probability intervals. Bayesian posterior probability is one unless specified by a red asterisk.
FIG. 4 in First report of complete mitogenome for an Itarinae species (Orthoptera, Grylloidea) with phylogenetic analysis
FIG. 4. — Phylogeny of the superfamily Grylloidea with Bayesian inference (BI) and maximum likelihood (ML) based on PCGs + rRNA + tRNA matrix. The numbers on each node are Bayesian posterior probabilities (BPP, left) and ML bootstrap support values (MLB, right) respectively.
FIG. 3 in First report of complete mitogenome for an Itarinae species (Orthoptera, Grylloidea) with phylogenetic analysis
FIG. 3. — Predicted secondary structures of 22 tRNAs in Itara minor Chopard, 1925. Dash (–) represents Watson-Crick bonds and dot (•) represents trans Watson- Crick GU bonds.
Figure 5 in Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution
Figure 5. Molecular clades of A. mellifera mapped onto the first two PCA axes of morphometric ACMO space, redrawn afer Fig. 10.8 in Ref.8. Individual bees are identified to subspecies by the numeric color codes, and re-grouped to genetic clades as in Fig. 3, with additional color variants for Sub-Saharan taxa. Ruttner's four groups [African (A), European (C [Continental]), Mellifera (M), and Asian (O [Oriental]] correspond roughly to the four quadrants, clockwise from the upper lef as A, M, C, and O. Ŀe Levantine/Nilotic/Arabian clade overlays the Sub-Saharan clade, including local variants. Ŀe Asia Minor A. m. caucasia clade is distributed along the M → O axis, and is bisected by its Southeast European sister clade A. m. ligustica. Ŀe Afro-European Mediterranean clade overlies all three, as well as the basal A. m. mellifera clade.
Figure 2 in Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution
Figure 2. Schematic maximum parsimony analysis of phylogenetic relationships among mtDNA genome sequences of 66 individual A. mellifera honey bees from 22 subspecies. Rooting as indicated by Fig. 1. Numbers above branches are inferred numbers of nucleotide substitutions; numbers in bold below branches are percent support in 3000 bootstrap replicates, with SPR branching swapping. Ŀe tree shown is one of nine minimum length trees that differ only by rearrangements at unresolved nodes. Sequences in the Sub-Saharan clade that make that subspecies paraphyletic are tagged in Roman font, as are two sequences referred to A. m. scutellata that are outside that clade. An additional 12 sequences from the Arabian series that are identical to the four shown are not included. Sequences curated as A. m. mellifera in GenBank15 are re-assigned their proper names in parentheses (J. M. Fuller, pers. comm). Subspecies represented by single sequences are indicated by (*). Named phylogeographic clades discussed in the text are indicated in color. Ŀe complete MP tree with GenBank accession numbers is given in Supplementary Fig. S1, along with those for Maximum Likelihood and Neighbor Joining methods (Supplementary Figs. S2 and S3, respectively).
Figure 6 in Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution
Figure 6. Comparison of Boardman et al.11 and Tihelka et al.20 meta-analyses with Fig. 2. Ŀe base phylogram is a Maximum Parsimony analysis calculated as in Fig. 2, with the addition of two problematic sequences mentioned in the text, KY926882 and KY926883, attributed to A. m. syriaca and A. m. intermissa, respectively. Ŀe 17 sequences used by Boardman et al. are marked "B" and the 16 sequences used by Tihelka et al. "T", with the 11 sequences common to both sets "TB". Note the anomalous pairwise placements of two sequences attributed to KY026882 and KY926883 with respect to their nominal sister subspecies (* and *, respectively).
Figure 1 in Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution
Figure 1. Maximum Parsimony analysis of phylogenetic relationships among mtDNA genomes sequences of nine species of Apis honey bees. (a) Ŀe tree is rooted with a bumblebee Bombus ignitus as outgroup. A. m. mellifera (KY926884) is the basal-most member of that species and the alignment reference. Numbers above branches are inferred numbers of nucleotide substitutions; numbers in bold below branches are percent support in 3000 bootstrap replicates. Identical branching order and substantially similar bootstrap support are given by Maximum Likelihood and Neighbor Joining methods. (b) As above, with removal of Bombus and addition of key subspecies of A. mellifera (cf. Fig. 2).
Figure 4 in Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution
Figure 4. An mtDNA-based molecular clock for within- and among-subspecies divergences of A. mellifera. Sequences are coded as in Fig. 2: only one representative each of A. m. scutellata and A. m. capensis is included (n = 37). Divergence times are calculated from a linearized ML model with A. m. mellifera sequences as the designated outgroup (cf. Supplementary Fig. S2). Ŀe clock is calibrated from the mean linearized nucleotide subs/site distances to each node (Relative Time) at 0.0115 subs/site/Myr (see text for sample calculation). See Supplementary Fig. S4 for the clock of A. mellifera within Apis, with Bombus as the designated outgroup.
Figure 3 in Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution
Figure 3. Phylogeographic evolution in context of geographic distribution2 of subspecies of A. mellifera as inferred from mitogenomic data. Numbered symbols indicate five clades described in the text and in Fig. 2. Dark and light green circles indicate respectively subspecies in the Southeast European and Asia Minor clades included within the Eurasian superclade. Blue symbols indicate the Levantine (circles), Nilotic (squares), and Arabian (A. m. jemenitica) (diamonds) clades. Light and dark purple circles indicate independent A. m. simensis and A. m. unicolor lineages, respectively. Light orange symbols indicate subspecies in the Mediterranean clade. Red circles indicate the paraphyletic assemblage of A. m. scutellata and A. m. capensis, including A. m. adansonii (light red) and A. m. monticola (brown). Base map modified from [https://commons. wikimedia.org/wiki/File:BlankMap-World.svg].
Analyses of the redlegged earth mite mitogenome (Halotydeus destructor: Tucker)
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