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196 results for “mitochondrial phylogeny”
Alignments used for the phylogenies in "Caryophylliids (Anthozoa, Scleractinia) have a mitochondrial gene rearrangement: lesson learned from mitochondrial and nuclear phylogenomics"
<p>"mitochondrial_caryotree.phy": concatenated alignment of mitochondrial data in phylip format; "mitochondrial_caryotree.partitions.txt": indication of start/stop positions of each partition in the mitochondrial data alignment; "nuclear_caryotree_55taxa-50p.phylip": alignment of nuclear exons and ultraconserved elements in phylip format.</p>
Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets
<p>Angiosperms dominate the Earth's ecosystems and provide most of the basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by the APG IV classification. However, the phylogenetic relationships of angiosperms remain unclear, as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available <em>de novo</em> genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear, plastid, and mitochondrial genomes of the same species with compatible datasets. The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type. However, there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined. We discuss ways to address these inconsistencies, which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life. The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons. These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation. </p>
Comparative Mitochondrial Genomics of selected Noctuoid Moths (Lepidoptera: Noctuoidea) with implications for their Phylogeny
<p>In this study, I sequenced and annotated the complete mitochondrial genome sequences of 19 species that belong to the superfamily Noctuoidea viz. <em>Actinotia polyodon, Episparis tortuosalis, Ercheia cyllaria, Eudocima salaminia, Hulodes caranea, Hypospila bolinoides, Ischyja manlia, Lygephila dorsigera, Mecodina praecipua, Mocis undata, Odontodes seranensis, Ophiusa tirhaca, Oraesia emarginata, Pandesma quenavadi, Polydesma boarmoides, Psimada quadripennis, Rusicada privata, Trigonodes hyppasia </em>and<em> Xanthodes albago</em>. In addition to this, I performed the analysis of their genetic compositions as well as their molecular characterization in order to provide molecular insights into their taxonomic and phylogenetic implications. Based on the data and those obtained from the NCBI database, I examined the phylogenetic relationships among the species of the superfamily Noctuoidea.</p>
Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets
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Data from: Mitochondrial metagenomics reveals the ancient origin and phylodiversity of soil mites and provides a phylogeny of the Acari
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Data from the article "The mitochondrial phylogeny of land plants shows support for Setaphyta under non-stationary substitution models"
<p>Data from the article:</p> <p>"The mitochondrial phylogeny of land plants shows support for Setaphyta under non-stationary substitution models"</p> <p>Filipe de Sousa, Peter Civáň, João Brazão, Peter G. Foster, Cymon J. Cox</p> <p> </p> <p>These data are divided in four folders:</p> <p>* 1_36_gene_nt_alignments_&_trees - contains 36 single gene nucleotide alignments and the corresponding trees inferred from a MCMC analysis on the program p4</p> <p>* 2_36_gene_aa_alignments_&_trees - contains 36 single gene amino acid alignments and the corresponding trees inferred from a MCMC analysis on the program p4</p> <p>* 3_concatenated_alignments_&_trees - contains the nucleotide, codon-degenerate and amino acid alignments of 36 concatenated genes and the corresponding trees inferred from MCMC analyses on the programs p4 and phylobayes with composition homogeneous, tree-heterogeneous and site-heterogeneous models; trees correspond to figures S1-S7 on the online supplemental file.</p> <p>* 4_concatenated_ML_trees - contains the ML trees from the analyses of the concatenated datasets (nucleotide, codon degenerate and amino acid).</p> <p> </p> <p> </p> <p> </p>
FIGURE 10 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 10. Austinixa felipensis; male, cw 12.3 mm (ULLZ 5556); from San Felipe, Baja California, Mexico. A, carapace, chelipeds, and right ambulatory appendages, dorsal; B, carapace frontal region, from anterior; C. third maxilliped, external; D, right chela, internal; E, right cheliped, external; F, left cheliped internal; G, left cheliped external; H, right pereopod 2, dorsal; I, right pereopod 3, dorsal; J, right pereopod 4, dorsal; K, right pereopod 5, dorsal. Scale bars = 2.0 mm.
FIGURE 12 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 12. Austinixa artankeri sp. nov.; A, male, cw 8.9 mm, Panama Caribbean (UF 18950, photograph from A. Anker); B, ovigerous female, cw 6.8 mm, Panama Caribbean (ULLZ 13336); C, female, Panama Caribbean (ULLZ 13334). Austinixa roblesi sp. nov.; D, male, cw 9.2 mm, Belize (ULLZ 12114); E, ovigerous female, cw 7.8 mm, Panama Caribbean (ULLZ 13335); F, ovigerous female, cw 11.1 mm, Belize (ULLZ 12114). Austinixa cuestai sp. nov.; G, male, cw 7.7 mm, Panama Pacific (USNM1552956); H, male, cw 11.1 mm, Panama Pacific (USNM 1552956); I, female, cw 8.5 mm, Panama Pacific (USNM 1552957); J, ovigerous female, cw 10.7 mm, Panama Pacific (USNM 1552958) (photographs from J. Scioli).
FIGURE 8 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 8. Austinixa roblesi sp. nov.; A, B, D–G, male paratype, cw 9.0 mm (USNM 1558340); C, H, I, male holotype, cw 9.9 mm (USNM 1558341); both from Dangriga, Belize. A, carapace, chelipeds, and right ambulatory appendages, dorsal; B, carapace frontal region, from anterior; C. third maxilliped, external; D, right chela, internal, setae not shown; E, right pereopod 4, dorsal; F, right pereopod 5, dorsal; G, male pleon; H, left first gonopod tip, pleonal surface; I left first gonopod tip, sternal surface. Scale bars = 1.0 mm.
FIGURE 4 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 4. Austinixa artankeri sp. nov.; male holotype, cw 7.6 mm (USNM 1558334), Bocas del Toro, Caribbean coast of Panama. A, carapace and right appendages, dorsal; B, carapace frontal region, from anterior; C, left third maxilliped, external; D, right chela, internal; E, right pereopod 2, dorsal; F, right pereopod 3, dorsal; G, right pereopod 4, dorsal; H, right pereopod 4 setae not shown, dorsal; I, right pereopod 4, ventral; J. right pereopod 5, dorsal. Scale bars = 1.0 mm.
FIGURE 7 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 7. Austinixa cuestai sp. nov.; A–C, male paratype, cw 8.3 mm (ULLZ 5566); D–F ovigerous female paratype, cw 8.3 mm (ULLZ 5566); both from Nagualapa, Pacific coast of Nicaragua. A, male pleon; B, left first gonopod, sternal surface; C, left first gonopod tip, pleonal surface; D, right cheliped, internal; E, right cheliped, external; F, female pleon. Scale bars = 1.0 mm (A, B, D–F), 0.5 mm (C).
FIGURE 11 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 11. Austinixa felipensis; A–C, male, cw 12.3 mm (ULLZ 5556); D–F, female cw 10.6 mm, both from San Felipe, Baja California, Mexico. A, male pleon; B, right first gonopod, sternal surface; C, right first gonopod tip, pleonal surface; D, left chela, external; E, left chela, internal. Scale bars = 1.0 mm (A, B, D–F), 0.5 mm (C).
FIGURE 9 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 9. Austinixa roblesi sp. nov.; A–D, ovigerous female paratype, cw 9.8 mm (USNM 1558340); E, ovigerous female paratype, cw 9.4 mm (ULLZ 12115); F, female paratype, cw 6.6 mm (ULLZ 13143); all from Dangriga, Belize. A, carapace, dorsal; B, enlarged right side of carapace, dorsal; C, carapace frontal region, from anterior; D, right chela, internal; E, left chela, dorsal, F, female pleon. Scale bars = 1.5 mm (A), 1.0 mm (B–F).
FIGURE 5 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 5. Austinixa artankeri sp. nov.; A, male paratype, cw 7.3 mm (UF 18916); B, male paratype, cw 8.5 mm (ULLZ 13732); C, D, male paratype, cw 6.2 mm (ULLZ 13731); E, ovigerous female paratype, cw 8.5 mm (UF 18928); F, female paratype, cw 8.8 mm (UF 18950); G, ovigerous female paratype, cw 9.0 mm (USNM 1558331); H, ovigerous female paratype, cw 5.8 mm (ULLZ 13644), all from Bocas del Toro, Caribbean coast of Panama. A, right chela, internal, setae not shown; B, male pleon; C, D, left first gonopod, pleonal surface, entire and enlarged tip; E, right chela, internal, setae not shown; left chela, internal, setae not shown. Scale bars = 1.0 mm (A, B, E–H), 0.5 mm (C), 0.25 mm (D).
FIGURE 3 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 3. Distribution of the species of Austinixa Heard & Manning, 1997. In most cases, latitudinal ranges are shown. For A. cristata, the latitudinal range shown corresponds to the distribution on the Atlantic coast only. Specific locations are shown for records of A. cristata in the Gulf of Mexico, as well as for A. bragantina and three undescribed species (symbols as shown in legend). Only A. bragantina and A. leptodactyla were not included in the present phylogenetic analyses.
FIGURE 2 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 2. Phylogeny of Pinnotheroidea, with emphasis on Austinixa Heard & Manning, 1997, inferred from Maximum Likelihood analysis of concatenated 1415 bp sequence of mitochondrial 16S/tRNA-Leu/NADH1 complex (705 bp), the mitochondrial 12S rRNA gene (293 bp) and nuclear histone 3 subunit (328 bp). Maximum Likelihood (ML) bootstrap, Bayesian (BAY) posterior probabilities and maximum parsimony (MP) bootstrap values are shown, in order ML/BAY/MP. "–" indicates a value lower than 50%. When all three values are the same, only one number is shown. If values are lower than 50% for all three, no number is shown. Letters and collection accession numbers follow the species name, to distinguish geographic origin and samples (see Material and methods for abbreviations). Modified from Palacios Theil et al. (2016) and generic assignments of some species of Pinnixa updated according to Palacios Theil & Felder (2020)
FIGURE 1 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 1. Consensus tree for Austinixa Heard & Manning, 1997, inferred from Maximum Likelihood analysis of 821 bp sequence of mitochondrial 16S/tRNA-Leu/NADH1 gene complex. Bootstrap values higher than 50% indicated at internal nodes. Letters and collection accession numbers follow the species name, to distinguish geographic origin and samples (see Material and methods for abbreviations).
Mitochondrial DNA sequence phylogeny of Daucus
We explored the phylogenetic utility of mitochondrial DNA sequences in Daucus and compared the results with prior phylogenetic results using the same 36 accessions of Daucus (and two additional outgroups) with plastid DNA sequences and with other nuclear results. As in the plastid study we used Illumina HiSeq sequencer to obtain resequencing data of the same accessions of Daucus and outgroups, and analyzed the data with maximum parsimony and maximum likelihood. We obtained data from 47 of 71 total mitochondrial genes but only 17 of these 47 genes recovered major clades that were common in prior plastid and nuclear studies. Our phylogenetic trees of the concatenated data set of 47 genes were moderately resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. There are areas of hard incongruence with phylogenies using plastid and nuclear data. In agreement with other studies, we conclude that mitochondrial sequences are generally poor phylogenetic markers, at least at the genus level, despite their utility in some other studies.
Data from: Molecular phylogeny of the Taeniapterini (Diptera: Micropezidae) using nuclear and mitochondrial DNA, with a reclassification of the genus Taeniaptera Macquart
DNA molecular data are used to generate a phylogeny for the micropezid subfamily Taeniapterinae. Thirty-two taeniapterine species were sampled, including 10 of the 20 New World genera recognized by Steyskal, as well as one genus formerly treated as a synonym of Poecilotylus Hennig (Hemichaeta Steyskal). Five species from the Micropezinae were included as outgroups. A total DNA dataset of 4705 bp, including mitochondrial genes (12S and cytochrome c oxidase I (COI)) and nuclear coding genes (wingless and CAD), was analysed using maximum parsimony and Bayesian inference. The genus Taeniaptera Macquart was found to be non-monophyletic with respect to the remainder of the Taeniapterini analysed here. Taeniaptera is restricted to the Taeniaptera trivittata Macquart species group, Mitromyia Cresson is resurrected to contain the Taeniaptera grata (Wulp) species group, and Paragrallomyia Hendel is resurrected to contain most species previously considered Taeniaptera. Poecilotylus is recognized as a paraphyletic group awaiting further research.
Data from: Biogeography and evolution of body size and life history of African frogs: phylogeny of squeakers (Arthroleptis) and long-fingered frogs (Cardioglossa) estimated from mitochondrial data
The evolutionary history of living African amphibians remains poorly understood. This study estimates the phylogeny within the frog genera Arthroleptis and Cardioglossa using approximately 2400 bases of mtDNA sequence data (12S, tRNA-Valine, and 16S genes) from half of the described species. Analyses are conducted using parsimony, maximum likelihood, and Bayesian methods. The effect of alignment on phylogeny estimation is explored by separately analyzing alignments generated with different gap costs and a consensus alignment. The consensus alignment results in species paraphyly, low nodal support, and incongruence with the results based on other alignments, which produced largely similar results. Most nodes in the phylogeny are highly supported, yet several topologies are inconsistent with previous hypotheses. The monophyly of Cardioglossa and of miniature species previously assigned to Schoutedenella was further examined using Templeton and Shimodaira–Hasegawa tests. Cardioglossa monophyly is rejected and C. aureoli is transferred to Arthroleptis. These tests do not reject Schoutedenella monophyly, but this hypothesis receives no support from non-parametric bootstrapping or Bayesian posterior probabilities. This phylogeny provides a framework for reconstructing historical biogeography and analyzing the evolution of body size and life history. Direct development and miniaturization appear at the base of Arthroleptis phylogeny concomitant with a range expansion from Central Africa to throughout most of sub-Saharan Africa.
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