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62 results for “Mitochondrial and nuclear markers”
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).
Data from: Population genetic structure and intraspecific genetic distance of Periplaneta americana (Blattodea: Blattidae) based on mitochondrial and nuclear DNA markers
<p>The American cockroach (<i>Periplaneta americana</i>) is a globally invasive pest that can cause significant economic loss and threaten human health. Although it is abundant and lives in close proximity to humans, few studies have investigated the genetic diversity of <i>P. americana</i>. Our study analyzed 1053 <i>P. americana</i> and other <i>Periplaneta</i> species' samples from different locations in China and the USA. A traditional tree-based method using 17 unique mitochondrial COI haplotypes of <i>P. americana</i> and 20 haplotypes of the other <i>Periplaneta</i> species accurately identified <i>P. americana</i> with a barcoding threshold of 5.1%. To identify the population genetic structure of <i>P. americana,</i> we investigated <i>wingless</i> gene and pooled them with obtained mtDNA data for a combined analysis. Although the genetic diversity of the USA group was relatively higher than the China group, the number of haplotypes and alleles of both groups was small. Molecular variance (AMOVA), intraspecific phylogeny, and haplotype networks indicated that <i>P. americana</i> had very little global genetic differentiation. The weak geographic genetic structure might reflect the human-mediated dispersal of <i>P. americana</i>. Despite no apparent phylogeographic assignment of mtDNA and nuclear lineages was observed in both BI trees, the integrated COI sequence data identified four distinct <i>P. americana</i> haplotype groups, showing four ancient maternal lineages of <i>P. americana</i> in China and the USA.</p>
Data from: Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard
Historical factors, current population size, population connectivity and selective processes at linked loci contribute to shaping contemporary patterns of neutral genetic diversity. It is now widely acknowledged that nuclear and mitochondrial markers react differently to current demography as well as to past history, so the use of both types of markers is often advocated to gain insight on both historical and contemporary processes. We used 12 microsatellite loci genotyped in 13 populations of a mountain lizard (Iberolacerta bonnali) to test if the historical scenario favoured by a previous mitochondrial study was also supported by nuclear markers and thereby evaluated the consequences of post-glacial range movements on nuclear diversity. Congruent signals of recent history were revealed by nuclear and mitochondrial markers using an Approximate Bayesian Computation approach but contemporary patterns of mtDNA and nuclear DNA diversity were radically different. Although dispersal in this species is probably highly restricted at all spatial scales, colonisation abilities have been historically good, suggesting capability for reestablishment of locally extinct populations except in fully disconnected habitats.
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.
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 Molecular phylogenetic analysis of subfamilial placement of Haplotropis Saussure, 1888 (Orthoptera: Pamphagidae) based on mitochondrial and nuclear DNA markers
FIGURE 3. Phylogenetic tree based on the nucleotide sequences of ITS2 region of Pamphagidae. Support values shown as: SH-aLRT support/ ultrafast bootstrap (probability> 80/90 considered significant). The brackets on the right side show subfamily and family clusters.
FIGURE 2 in Molecular phylogenetic analysis of subfamilial placement of Haplotropis Saussure, 1888 (Orthoptera: Pamphagidae) based on mitochondrial and nuclear DNA markers
FIGURE 2. Phylogenetic tree based on the nucleotide sequences of COII mitochondrial gene of Pamphagidae. Support values shown as: SH-aLRT support/ ultrafast bootstrap (probability> 80/90 considered significant). The brackets on the right side show subfamily and family clusters.
FIGURE 1 in Molecular phylogenetic analysis of subfamilial placement of Haplotropis Saussure, 1888 (Orthoptera: Pamphagidae) based on mitochondrial and nuclear DNA markers
FIGURE 1. Phylogenetic tree, based on the nucleotide sequences of COI mitochondrial gene of Pamphagidae. Support values shown as: SH-aLRT support/ultrafast bootstrap (probability> 80/90 considered significant). The brackets on the right side show subfamily and family clusters.
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
Figure 5 in Evolutionary relationships among American mud crabs (Crustacea: Decapoda: Brachyura: Xanthoidea) inferred from nuclear and mitochondrial markers, with comments on adult morphology
Figure 5. Ventral view of the anterior portion of the thoracic sternum. A, Panopeus herbstii (ULLZ 8457); B, Rhithropanopeus harrisii (ULLZ 3995); C, Pseudorhombila quadridentata (ULLZ 9326); D, Chacellus filiformis (ULLZ 12296). Lines in A indicate the length and width dimensions of the anterior portion of the thoracic sternum.
Figure 4 in Evolutionary relationships among American mud crabs (Crustacea: Decapoda: Brachyura: Xanthoidea) inferred from nuclear and mitochondrial markers, with comments on adult morphology
Figure 4. Apex of the first gonopod (first male pleopod). A, Pseudorhombila quadridentata (ULLZ 9326); B, Chacellus filiformis (ULLZ 12296); C, Panopeus herbstii (ULLZ 8457); D, Rhithropanopeus harrisii (ULLZ 3995). Arrows and lines indicate measurements taken for preliminary morphometric analyses of sternal proportions.
Figure 3 in Evolutionary relationships among American mud crabs (Crustacea: Decapoda: Brachyura: Xanthoidea) inferred from nuclear and mitochondrial markers, with comments on adult morphology
Figure 3. Stylized drawing of the dactylus of the 5th pereopod. A, typical American xanthid; B, typical panopeid; C, typical pseudorhombilid. Arrow indicates distinct, subterminal, calcareous tooth.
Figure 1 in Evolutionary relationships among American mud crabs (Crustacea: Decapoda: Brachyura: Xanthoidea) inferred from nuclear and mitochondrial markers, with comments on adult morphology
Figure 1. Phylogenetic relationships among selected representatives of Xanthoidea sensu Ng et al., 2008 inferred by ML analysis of 2788 bp of a concatenated 12S, 16S, COI, 18S, ENO and H3 dataset. Confidence values are 1000 bootstrap ML values followed by Bayesian posterior probabilities. Values below 50 are indicated by '–'. Brackets and associated names represent the primary clades discussed.
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