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410 results for “Mitochondrial gene”
FIGURE 1. Maximum likelihood tree generated from three mitochondrial genes shows a in Disentangling vines: a study of morphological crypsis and genetic divergence in vine snakes (Squamata: Colubridae: Ahaetulla) with the description of five new species from Peninsular India
FIGURE 1. Maximum likelihood tree generated from three mitochondrial genes shows a number of new lineages (L1–L13) identified in our study. The lineages are marked with grey bars which represent the criteria used to delimit species boundaries, where three gene bPTP (P3), genetic p-distance (GD), morphological separation (M) and geographic isolation (G) are used to predict the number of putative lineages. The nodes below 70% parametric bootstrap support are indicated with asterisk (*). "+" indicates that the status of A. nasuta cf. isabellina needs further work (see Deepak et al. 2019).
Data from: Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota)
Mitochondrial genomes extracted from wild populations of Daucus carota have been used as a genetic resource by breeders of cultivated carrot, yet little is known concerning the extent of their diversity in nature. Of special interest is a SNP in the putative stop codon of the mitochondrial gene atp9 that has been associated previously with male-sterile and male-fertile phenotypic variants. In this study either sequence or PCR/RFLP genotypes were obtained from the mitochondrial genes atp1, atp9 and cox1 found in D. carota individuals collected from 24 populations in the eastern U.S. More than half of the 128 individuals surveyed had a CAA or AAA, rather than TAA, genotype at the position usually thought to function as an atp9 stop codon in this species. We also found no evidence for mitochondrial RNA editing (Cytosine to Uridine) of the CAA stop codon in either floral or leaf tissue. Evidence for intra-genic recombination, as opposed the more common inter-genic recombination in plant mitochondrial genomes, in our data set is presented. Indel and SNP variants elsewhere in atp9, and in the other two genes surveyed, were non-randomly associated with the three atp9 stop codon variants, though further analysis suggested that multi-locus genotypic diversity had been enhanced by recombination. Overall the mitochondrial genetic diversity was only modestly structured among populations with an Fst of 0.34.
Data from: Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary Ice Age events with inferred population expansions and dispersals in Japanese Apodemus
Background: Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely have promoted both rapid expansion events and interisland dispersal events. Results: We examined mitochondrial cytochrome b (Cytb) and control region (CR) gene sequences in two Japanese wood mouse species, Apodemus argenteus and A. speciosus, of temperate origin and found signs of rapid expansion in the population from Hokkaido, the northern island of Japan. Assuming that global warming after the last glacial period 7–10 thousand years before present (kyr BP) was associated with the expansion, the evolutionary rates (sites per million years, myr) of Cytb and CR were estimated as 11–16% and 22–32%, respectively, for A. argenteus, and 12–17% and 17–24%, respectively, for A. speciosus. Additionally, the significant signature of rapid expansion detected in the mtDNA sequences of A. speciosus from the remaining southern main islands, Honshu, Shikoku, and Kyushu, provided an estimated Cytb evolutionary rate of 3.1%/site/myr under the assumption of a postglacial population expansion event long ago, most probably at 130 kyr BP. Bayesian analyses using the higher evolutionary rate of 11–17%/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum. However, the slower evolutionary rate of 3.1%/site/myr would be reasonable for several divergence events that were associated with glacial periods older than 130 kyr BP. Conclusions: The faster and slower evolutionary rates of Cytb can account for divergences associated with the last and earlier glacial maxima, respectively, in the phylogenetic inference of murine rodents. The elevated evolutionary rate seemed to decline within 100,000 years.
Data from: Variation across mitochondrial gene trees provides evidence for systematic error: how much gene tree variation is biological?
The use of large genomic datasets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of biological versus methodological factors in explaining gene tree variation is a major unresolved question. Using mitochondrial genomes to control for biological causes of gene tree variation, we estimate the extent of gene tree discordance driven by systematic error and employ posterior prediction to highlight the role of model fit in producing this discordance. We find that the amount of discordance among mitochondrial gene trees is similar to the amount of discordance found in other studies that assume only biological causes of variation. This similarity suggests that the role of systematic error in generating gene tree variation is underappreciated and critical evaluation of fit between assumed models and the data used for inference is important for the resolution of unresolved phylogenetic questions.
Data from: Testing hypotheses of mitochondrial gene-tree paraphyly: unraveling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (P. musicus)
Species-level paraphyly inferred from mitochondrial gene trees is a prevalent phenomenon in taxonomy and systematics, but there are several potential causes that are not easily explained by currently used methods. The present study aims to test the underlying causes behind the observed paraphyly of Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) via statistical analyses of four mitochondrial (mtDNA) and nine nuclear (nuDNA) genes. Mitochondrial gene trees show paraphyly of P. ruficollis with respect to the Taiwan Scimitar Babbler (P. musicus), but nuclear genealogies support a sister-group relationship. Predictive coalescent simulations imply several hypothetical explanations, the most likely being mitochondrial capture of P. ruficollis by P. musicus for the observed cyto-nuclear incongruence. Further Approximate Bayesian Computation suggests a unidirectional introgression model with substantial level of gene flow from P. ruficollis to P. musicus during their initial divergence during the Late Pleistocene. This specific observation frames several potential causes for incongruent outcomes of mitochondrial and nuclear introgression in general, and on the whole, our results underscore the strength of multiple independent loci for species delimitation and importance of testing hypotheses that explain disparate causes of mitochondrial gene-tree paraphyly.
Data from: Ancient mitochondrial gene transfer between fungi and the orchids
The mitochondrial genomes (mitogenomes) of plants are known to incorporate and accumulate DNA from intra- and extracellular donors. Despite the intimate relationships formed between flowing plants (angiosperms) and fungi, lengthy fungal-like sequence has not been identified in angiosperm mitogenomes to date. Here we present multiple lines of evidence documenting horizontal gene transfer (HGT) between the mitogenomes of fungi and the ancestors of the orchids, plants that are obligate parasites of fungi during their early development. We show that the ancestor of the orchids acquired an approximately 270 bp fungal mitogenomic region containing three transfer RNA genes. We propose that the short HGT was later replaced by a second HGT event transferring more than 8 kb and 14 genes from a fungal mitogenome to that of the ancestor of the largest orchid subfamily, Epidendroideae. Our results represent the first evidence of genomic-scale HGT between fungal and angiosperm mitogenomes and demonstrate that the length intergenic spacer regions of angiosperm mitogenomes can effectively fossilize the genomic remains of ancient, non-plant organisms.
SUPPLEMENTARY FIGURE 2. Tree generated from the nucleotide sequence for the mitochondrial gene region, igr1–cox1 in A taxonomic revision of Anthothela (Octocorallia: Scleraxonia: Anthothelidae) and related genera, with the addition of new taxa, using morphological and molecular data
SUPPLEMENTARY FIGURE 2. Tree generated from the nucleotide sequence for the mitochondrial gene region, igr1–cox1 of Anthothela-like specimens. Bayesian posterior probabilities shown above branch, ML bootstrap values below branch; HKY+G (Bayesian results split freq = 0.0019, 10000000 gen, burnin=25000). (* indicates nodes present only in Bayesian analysis).
FIGURE 10. Bayesian inference phylogenetic reconstruction using the mitochondrial gene cox1 in Molecular delimitation of the seasonal killifishes of the Hypsolebias antenori species group (Cyprinodontiformes, Rivulidae), with description of two new species from the Caatinga coastal basins, northeastern Brazil
FIGURE 10. Bayesian inference phylogenetic reconstruction using the mitochondrial gene cox1 of the Hypsolebias antenori species-group. Vertical bars represent species complexes. Numbers next to nodes represent posterior probability values for the relevant nodes; values <0.5 are not shown.
FIGURE 5 in The phylogenetic status of Limnonectes liui (Yang, 1983) (Anura: Dicroglossidae based on mitochondrial genes and its taxonomic implications
FIGURE 5. Fifty percent majority-rule consensus phylogram resulting from Bayesian phylogenetic analysis of 1,696 aligned characters of the mitochondrial 16S ribosomal RNA gene and NADH dehydrogenase subunit 3 gene and its flanking regions from frogs of the genus Limnonectes. Numbers at nodes are Bayesian posterior probabilities ≥95% (left) and maximum likelihood bootstrap support values ≥ 70% on right, with lower support values denoted by "–". Numbers following terminals are localities presented in Figure 1. The scale bar represents 0.06 nucleotide substitutions per site.
FIGURE 2 in The phylogenetic status of Limnonectes liui (Yang, 1983) (Anura: Dicroglossidae based on mitochondrial genes and its taxonomic implications
FIGURE 2. Limnonectes liui in life (male) from Brown Mountain, Menghai County, Xishuangbanna Dai Nationality Autonomous Prefecture, Yunnan Province, China in (A) lateral, (B) ventral, (C) dorsal,
FIGURE 1 in The phylogenetic status of Limnonectes liui (Yang, 1983) (Anura: Dicroglossidae based on mitochondrial genes and its taxonomic implications
FIGURE 1. Geographic distributions of Limnonectes liui (stars) and Limnonectes limborgi (circles). The type locality of L. limborgi at "Tenasserim", Myanmar is near Site 21 and the type locality of L. liui at Menglun, Yunnan Province, China is near Site 1.
FIGURE 4 in The phylogenetic status of Limnonectes liui (Yang, 1983) (Anura: Dicroglossidae based on mitochondrial genes and its taxonomic implications
FIGURE 4. Male Limnonectes limborgi from Phou Dendin National Protected Area, Phongsaly District, Phongsaly Province, Laos [North Carolina Museum of Natural Sciences (NCSM) 86616] in (A) lateral view in life and (B) ventral and (C) dorsal views immediately prior to preservation.
FIGURE 3 in The phylogenetic status of Limnonectes liui (Yang, 1983) (Anura: Dicroglossidae based on mitochondrial genes and its taxonomic implications
FIGURE 3. Limnonectes liui in life (male) from Brown Mountain, Menghai County, Xishuangbanna Dai Nationality Autonomous Prefecture, Yunnan Province, China (A) dorsal hand, (B) palmar, (C) dorsal foot, and (D) plantar views in life, and (E) tongue and (F) maxillary and vomerine teeth views in preservative.
FIGURE 4 in The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders
FIGURE 4. Comparison diagram of mitochondrial gene arrangement patterns of nine millipede species. One-letter codes corresponding to the amino acids of the tRNAs are used. Diagram is adapted and modified from Brewer et al. (2013).
FIGURE 2 in The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders
FIGURE 2. Potential stem and loop structures of the junctional sequences of (A) COI-COII, (B) ATP8-ATP6, (C) ND6- Cytb, (D) ND4L-ND4, and (E) ATP6-COIII, and (F) a non-coding region in the mitochondrial genome of Anaulaciulus koreanus (Verhoeff, 1937). The anticodon sequences are boxed, and termination codons or incomplete termination codons are drawn with an underline or side-line. The number of nucleotide sequences in each loop is shown.
FIGURE 1 in The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders
FIGURE 1. The mitochondrial genome structures of Anaulaciulus koreanus (Verhoeff, 1937). The direction of transcription for each gene is shown by an arrow. The hatch-marked area is a large non-coding region.
FIGURE 3 in The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders
FIGURE 3. Putative secondary structures of the 22 tRNAs observed from the mitochondrial genome of Anaulaciulus koreanus (Verhoeff, 1937)
Supplementary material 1 from: Yuhui X, Lijun Z, Yue H, Xiaoqi W, Chen Z, Huilun Z, Ruoran W, Da P, Hongying S (2017) Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order (Brachyura, Potamidae). ZooKeys 705: 41-60. https://doi.org/10.3897/zookeys.705.11852
Figure S1 : Explanation note: Comparisons of the consensus sequence and variable sites in the entire mNCR for Sinopotamon yaanense, S. yangtsekiense and S. xiushuiense. The conserved central domain is grey shaded, and the extended termination associated sequences (ETAS) is underlined.
Figure 7 in Molecular characterisation of leeches (Clitellata, Annelida) based on the mitochondrial cytochrome oxidase I (COI) gene region for Turkish fauna
Figure 7. Bayesian tree analysis of the COI (629 positions) data set of Hirudo species, with MrBayes v. 3.2.7.
Figure 8 in Molecular characterisation of leeches (Clitellata, Annelida) based on the mitochondrial cytochrome oxidase I (COI) gene region for Turkish fauna
Figure 8. Maximum likelihood phylogeny for Limnatis species based on COI sequences. Bootstrap values are shown for 1000 replicates.
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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.