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196 results for “mitochondrial phylogeny”
Data from: Phylogeny and biogeography of Poecilia (Cyprinodontiformes: Poeciliinae) across Central and South America based on mitochondrial and nuclear DNA markers
Poeciliids are a diverse group of small Neotropical fishes, and despite considerable research attention as models in ecology and evolutionary biology, our understanding of their biogeographic and phylogenetic relationships is still limited. We investigated the phylogenetic relationships of South and Central American Poecilia, by examining 2395 base pairs of mitochondrial DNA (ATPase 8/6, COI) and nuclear DNA (S7) for 18 species across six subgenera. Fifty-eight novel sequences were acquired from newly collected specimens and 20 sequences were obtained from previously published material. Analyses of concatenated and partitioned mitochondrial DNA and nuclear DNA sets resulted in a well-supported phylogeny that resolved several monophyletic groups corresponding to previously hypothesized subgenera and species complexes.
Data from: Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny
BACKGROUND: Tunicates represent a key metazoan group as the sister-group of vertebrates within chordates. The six complete mitochondrial genomes available so far for tunicates have revealed distinctive features. Extensive gene rearrangements and particularly high evolutionary rates have been evidenced with regard to other chordates. This peculiar evolutionary dynamics has hampered the reconstruction of tunicate phylogenetic relationships within chordates based on mitogenomic data. RESULTS: In order to further understand the atypical evolutionary dynamics of the mitochondrial genome of tunicates, we determined the complete sequence of the solitary ascidian Herdmania momus. This genome from a stolidobranch ascidian presents the typical tunicate gene content with 13 protein-coding genes, 2 rRNAs and 24 tRNAs which are all encoded on the same strand. However, it also presents a novel gene arrangement, highlighting the extreme plasticity of gene order observed in tunicate mitochondrial genomes. Probabilistic phylogenetic inferences were conducted on the concatenation of the 13 mitochondrial protein-coding genes from representatives of major metazoan phyla. We show that whereas standard homogeneous amino acid models support an artefactual sister position of tunicates relative to all other bilaterians, the CAT and CAT+BP site- and time-heterogeneous mixture models place tunicates as the sister-group of vertebrates within monophyletic chordates. Moreover, the reference phylogeny indicates that tunicate mitochondrial genomes have experienced a drastic acceleration in their evolutionary rate that equally affects protein-coding and ribosomal-RNA genes. CONCLUSION: This is the first mitogenomic study supporting the new chordate phylogeny revealed by recent phylogenomic analyses. It illustrates the beneficial effects of an increased taxon sampling coupled with the use of more realistic amino acid substitution models for the reconstruction of animal phylogeny.
FIGURE 4 in Nuclear markers support the mitochondrial phylogeny of Vipera ursinii – renardi complex (Squamata: Viperidae) and species status for the Greek meadow viper
FIGURE 4. Species tree of the Vipera ursinii–renardi complex (with V. berus as outgroup) as inferred in *BEAST based on two mitochondrial and three nuclear loci (A); species-tree cloudogram of the complex based on 27 000 post-burn-in trees resulting from 3 runs of *BEAST, each producing 10,000 trees from which 10% was discarded as burn-in. Higher colour densities represent higher levels of certainty. Maximum clade credibility tree is superimposed upon the cloudogram in bold violet (B). Values of posterior probabilities are given. This figure is published in colour in the online version, the colours of the branches correspond with the colour of mitochondrial lineages in Fig. 2A.
FIGURE 1 in Nuclear markers support the mitochondrial phylogeny of Vipera ursinii – renardi complex (Squamata: Viperidae) and species status for the Greek meadow viper
FIGURE 1. Sampled localities inside the approximate distribution area of Vipera ursinii–renardi complex in Europe. Circles indicate sampling localities of Vipera ursinii–renardi complex, and triangles show the sampling of outgroup taxa. A diamond indicates the type locality of Vipera graeca stat. nov. This figure is published in colour in the online version, the colour of the patches corresponds to the colour of mitochondrial lineages in Fig. 2A.
FIGURE 2 in Nuclear markers support the mitochondrial phylogeny of Vipera ursinii – renardi complex (Squamata: Viperidae) and species status for the Greek meadow viper
FIGURE 2. (A) Current mitochondrial Bayesian phylogenetic hypothesis of Vipera ursinii–renardi complex based on CYT B dataset of Ferchaud et al. (2012) and Zinenko et al. (2015); (B) Phylogenetic reconstruction of the concatenated dataset (mtDNA+nDNA genes) obtained in MrBayes/Maximum likelihood (see Table 1). Sequences of Vipera berus (Vbbe-HU, Vbbo-AL, Vbni-RO) included as outgroup are not shown. Bayesian posterior probabilities/bootstrap pseudoreplicates are shown at nodes; (C) SplitsTree phylogenetic network (Huson & Bryant 2006) of the dataset for five mitochondrial and nuclear loci sequenced in the present study using the neighbornet algorithm. Asterisks in Fig. 2C indicate both phased sequences in one branch. Numbers along the edges are the bootstrap support values from 1000 replicates. The scale bar indicates one substitution per one hundred nucleotide positions. Taxon names of the phylogenetic network correspond with the Table 1. Inset shows a male Greek Meadow Viper from Dhëmbel Mountains, Albania.
FIGURE 3 in Nuclear markers support the mitochondrial phylogeny of Vipera ursinii – renardi complex (Squamata: Viperidae) and species status for the Greek meadow viper
FIGURE 3. Nuclear allele networks of the three analysed nuclear loci. Circle sizes are proportional to the number of samples/ sequences, small black circles indicate hypothetical haplotypes (alleles). This figure is published in colour in the online version, the colour of the circles in the network corresponds to the colour of mitochondrial lineages in Fig. 2A.
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 6 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 6. Chronogram of Fulgoroidea estimated using the Bayesian phylogenetic by MCMCTREE in paml. Time units are in millions of years. Estimated divergence times are shown near nodes.
Figure 5 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 5. BI analysis (PhyloBayes) based on PCG12R–ATP8. Numerals at nodes are Bayesian posterior probabilities (PP). '–' indicates different clades.
Figure 1 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 1. Sliding window analysis. The red curve shows the value of nucleotide diversity (Pi). Pi value of each PCG is shown below the arrows.
Figure 4 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 4. BI analysis (MrBayes) based on PCG12R–ATP8. Numerals at nodes are Bayesian posterior probabilities (PP). '–' indicates different clades.
Figure 2 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 2. Genetic distance (on average) and ratio of non-synonymous (Ka) to synonymous (Ks) substitution rates.
Figure 3 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 3. ML analysis based on PCG12R–ATP8. Numerals at nodes are bootstrap values (BS). '–' indicates different clades.
FIGURE 2. Molecular phylogeny estimated using IQTREE2 in A cautionary note on synonymization based on mitochondrial data in Orthoptera: a comment of Hochkirch et al. 2023
FIGURE 2. Molecular phylogeny estimated using IQTREE2 (Minh et al. 2020) and the complete mitochondrial genome showing the paraphyly of the species within the genus Omocestus and Gomphocerrippus. Node supports are ultra-fast bootstrap supports. The code to the right of the species name indicates SRA accession number. All data are from Hawlitschek et al. 2022 except Omocestus haemorrhoidalis accession SRR21022974. Abbreviation: O. = Omocestus, P. = Pseudochorthippus and G. = Gomphocerrippus.
FIGURE 1. Molecular phylogeny estimated using IQTREE2 in A cautionary note on synonymization based on mitochondrial data in Orthoptera: a comment of Hochkirch et al. 2023
FIGURE 1. Molecular phylogeny estimated using IQTREE2 (Minh et al. 2020) and ITS2 loci. Colours represent species according to Supplementary Table 1 of Hochkirch et al. 2023. Dotted lines indicate species not supported by the phylogenetic estima.
Fig. 3 in A phylogeny of Sericini with particular reference to Chinese species using mitochondrial and ribosomal DNA (Coleoptera: Scarabaeidae)
Fig. 3 Projections of phylogenetic relationships of selected Sericina clades into geographical space, illustrating the spatial within clade divergence between Himalayan and Chinese lowland species. a Sericina subclade 2 (Fig. 2), the North American clade is not shown, b detail of
Fig. 3 in Phylogeny of Cidaroida (Echinodermata: Echinoidea) based on mitochondrial and nuclear markers
Fig. 3 Optimal tree obtained under ML (LogL 0 –5,265.11487) with PHYML 3.0 for the 28 S and COI genes concatenated under a GTR + gamma model. Bootstrap frequencies (1,000 replicates) are indicated below nodes. We also report, to the right of the nodes, bootstrap
Fig. 4 in Phylogeny of Cidaroida (Echinodermata: Echinoidea) based on mitochondrial and nuclear markers
Fig. 4 Strict consensus of the two optimal trees (L 01,060) obtained under maximum parsimony with TNT for the 28 S and COI genes concatenated. Bootstrap frequencies (1,000 replicates) are indicated below nodes
Fig. 2 in Phylogeny of Cidaroida (Echinodermata: Echinoidea) based on mitochondrial and nuclear markers
Fig. 2 Optimal tree obtained under ML (LogL 0 –3,825.12487) with PHYML 3.0 for the mitochondrial cytochrome c oxydase subunit I gene (COI) under a GTR + I + gamma model. Bootstrap frequencies (1,000 replicates) are indicated below nodes
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