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401 results for “Nuclear Genes”
Figure 7. Neighbour-nets generated using SplitsTree4 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Figure 7. Neighbour-nets generated using SplitsTree4 from the three mtDNA gene fragments studied (16S, 12S, and COI) in shrimps from the genera Lysmata, Exhippolysmata, and Merguia. Species pertaining to the different monophyletic clades previously revealed by the combined analyses of the three mtDNA gene fragments are highlighted with different colours, as in Figure 3. Abbreviations: LA, Lysmata ankeri; LABP, Lysmata cf. vittata; LAM, Lysmata amboinensis; LARG, Lysmata argentopuctata; LBA, Lysmata bahia; LBO, Lysmata boggessi; LCA, Lysmata californica; LD, Lysmata debelius; LGA, Lysmata galapagensis; LGB, Lysmata grabhami; LGR, Lysmata gracilirostris; LH, Lysmata hochi; LHO, Lysmata holthuisi; LI, Lysmata intermedia; LIM2, Lysmata cf. intermedia; LK, Lysmata kuekenthali; LM, Lysmata moorei; LN, Lysmata nayaritensis; LNI, Lysmata nilita; LO, Lysmata olavoi; LP, Lysmata pederseni; LRA, Lysmata rafa; LSET, Lysmata seticaudata; LT, Lysmata cf. ternatensis; LV, Lysmata vittata; LU, Lysmata udoi; LWEF, Lysmata wurdemanni EFL; LWG, Lysmata wurdemanni TX; LWWF, Lysmata wurdemanni WFL; EXO, Exhippolysmata oplophoroides; EXE, Exhippolysmata ensirostris; MO, Merguia oligodon; MR, Merguia rhizophorae; and NSP, Nikoides sp.
Figure 3 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Figure 3. Tree topology resulting from the combined analysis of the three mtDNA gene fragments studied (16S, 12S, and COI) for shrimps from the genus Lysmata (29 taxa), Exhippolysmata (two taxa), Merguia (two taxa), and one out-group (Nikoides sp.), under maximum likelihood (ML). Numbers above or below the branches represent the bootstrap values obtained from the maximum likelihood (ML) analysis in TREEFINDER and posterior probabilities from the Bayesian inference (BI) analysis in MrBayes (ML/BI). The general topology of the trees obtained from ML and BI analyses was the same.
Figure 1 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Figure 1. Amino acid usage analysis (mean amino acid count per sequence) for COI reference sequences (from selected species of crustaceans: Macrobrachium rosenbergii, Exopalaemon caricaudinata, Halocaridina rubra, and Cherax destructor), for COI orthologous sequences obtained from shrimps from the genus Lysmata, and for COI-like cloned sequences from Lysmata seticaudata. The error bars in each graph represent the highest and lowest amino acid counts per sequence in the three data sets. Amino acid determination and naming follows the invertebrate mitochondrial translation code, and was performed in MEGA 5.
Figure 2 in Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea: Lysmata, Exhippolysmata, and Merguia)
Figure 2. Tree topologies resulting from the analysis of COI-like cloned sequences from Lysmata seticaudata and mtDNA COI gene fragments for shrimps from the genus Lysmata (29 taxa), Exhippolysmata (two taxa), Merguia (two taxa), and one out-group (Nikoides sp.), under maximum likelihood (ML) and Bayesian inference (BI). Numbers above or below the branches represent the bootstrap values obtained from the ML analysis in TREEFINDER, and posterior probabilities from the BI analysis in MrBayes.
FIGURE 2. The tree represents a 50 in A molecular phylogeny of the Grunts (Perciformes: Haemulidae) inferred using mitochondrial and nuclear genes
FIGURE 2. The tree represents a 50% majority rule consensus of the Bayesian topology (numbers represent the posterior probability of the clades), with bootstrap values from MP and ML mapped onto the topology. MP, ML, and Bayesian analyses produced similar topologies (MP: TL = 12,869, consistency index CI = 0.2372, retention index RI = 0.4450; ML: Ln Likelihood = -54309.4503) with differences mostly on nodes with low bootstrap support. The numbers on branches are MP and ML bootstrap values and posterior probabilities from Bayesian analysis, respectively. Asterisks indicate a bootstrap value of 100% for MP and ML and 1.0 for Bayesian analysis. Nodes with less than 50% bootstrap value are marked with an X if the clade had less than 50% support in any of the MP, ML, or Bayesian analyses.
FIGURE 3 in Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial DNA and nuclear gene sequences
FIGURE 3. Phylogeography of Gongylomorphus skinks in Mauritius based on 1102bp of combined mtDNA sequence data. Lower-case letters refer to collection localities in Fig. 1 and Table 1. Haplotype networks are drawn with the areas of circles proportional to number of individuals observed; dots represent unobserved haplotypes, and lines between them each represent a single nucleotide substitution. Filled circles represent samples collected from extant populations, and open circles samples from extinct ones.
FIGURE 2 in Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial DNA and nuclear gene sequences
FIGURE 2. Bayesian maximum likelihood tree for extinct and extant Gongylomorphus skinks and a range of outgroup taxa, based on 1473 bp of combined mitochondrial (12S rRNA, cytochrome b) and nuclear (c-mos) DNA sequence. Numbers adjacent to nodes indicate: Bayesian posterior probability/MP bootstrap support values for analyses conducted using all samples (top line, if present), and only a subset of samples with full-length sequence for all three genes (bottom or only line). Letters a-s indicate the sampling locality in Mauritius for each specimen (Fig. 1, Table 1). Letters in bold are specimens which were sequenced for all three genes. Letters suffixed by an * are specimens that represent extinct populations.
FIGURE 1 in Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial DNA and nuclear gene sequences
FIGURE 1. (A) Map of the west Indian Ocean showing the location of the Mascarene islands. (B) Mauritius showing collection localities for Gongylomorphus bojerii skinks used in the present study. (C) Mauritius showing collection localities for Gongylomorphus 'orange-tail' and G. fontenayi skinks used in the present study. * indicates extinct populations.
FIGURE 6 in Taxonomic status of Velinoides Matsumura (Hemiptera: Reduviidae: Harpactorinae) inferred from mitochondrial and nuclear genes
FIGURE 6. Maximum parsimony phylogenies from the analysis based on cyt b sequences. Above the nodes are MP bootstrap values (>50%), ML bootstrap values (>50%), and ME bootstrap values (>50%), from left to right, respectively. Below the nodes are decay indices. The asterisks indicate bootstrap values smaller than 50%.
FIGURE 9 in Taxonomic status of Velinoides Matsumura (Hemiptera: Reduviidae: Harpactorinae) inferred from mitochondrial and nuclear genes
FIGURE 9. Maximum parsimony phylogenies from the analysis based on the combined data (COI, 16S rRNA and 28S rRNA gene sequences). Above the nodes are MP bootstrap values (>50%), ML bootstrap values (>50%), and ME bootstrap values (>50%), from left to right, respectively. Below the nodes are decay indices. The asterisks indicate bootstrap values smaller than 50%.
FIGURES 1–5. Relationship between K2P in Taxonomic status of Velinoides Matsumura (Hemiptera: Reduviidae: Harpactorinae) inferred from mitochondrial and nuclear genes
FIGURES 1–5. Relationship between K2P+Γ distances and uncorrected pairwise sequence distances for each gene partition. 1. Scatter plot graphic for third positions of COI; 2. COI; 3. cyt b; 4. 16S rRNA; 5. 28S rRNA.
FIGURE 8 in Taxonomic status of Velinoides Matsumura (Hemiptera: Reduviidae: Harpactorinae) inferred from mitochondrial and nuclear genes
FIGURE 8. Maximum likelihood phylogram based on combined data (16S rRNA and 28S rRNA gene sequences). The topology was reconstructed under the TVM + I + G model of nucleotide substitution, -log likelihood = 2660.77. Above the nodes are bootstrap support values derived from MP, ML and ME analysis, from left to right, respectively. Below the nodes are decay indices. The asterisks indicate bootstrap values smaller than 50%. All unambiguous morphological characters used in this study are mapped on this topology and are indicated on the right.
FIGURE 10 in Taxonomic status of Velinoides Matsumura (Hemiptera: Reduviidae: Harpactorinae) inferred from mitochondrial and nuclear genes
FIGURE 10. Maximum parsimony phylogram based on combined cyt b, COI, 16S rRNA and 28S rRNA gene sequences (length = 1398, CI = 0.631, and RI = 0.443). Above the nodes are bootstrap support values derived from MP, ML and ME analysis, from left to right, respectively. Below the nodes are decay indices. The asterisks indicate bootstrap values smaller than 50%. All unambiguous morphological characters used in this study are mapped on this topology and are indicated on the right.
FIGURE 7 in Taxonomic status of Velinoides Matsumura (Hemiptera: Reduviidae: Harpactorinae) inferred from mitochondrial and nuclear genes
FIGURE 7. Phylogenetic tree of Coranus Curtis based on COI gene (K2P model) using distance method (minimum evolution). Bootstrap values (1000 replications) are shown above nodes.
Figure 3 in An underground burst of diversity - a new look at the phylogeny and taxonomy of the genus Talpa Linnaeus, 1758 (Mammalia: Talpidae) as revealed by nuclear and mitochondrial genes
Figure 3. The Bayesian phylogeny of the genus Talpa as inferred from the complete cytb gene sequence. The designations are as in Figure 3. The outgroup (representatives of the genera Euroscaptor, Mogera, Parascaptor, Scaptochirus and tribes Desmanini, Scalopini and Condylurini) is not shown.
Figure 4 in An underground burst of diversity - a new look at the phylogeny and taxonomy of the genus Talpa Linnaeus, 1758 (Mammalia: Talpidae) as revealed by nuclear and mitochondrial genes
Figure 4. Species tree of Talpa produced by the *BEAST algorithm using the Bayesian multispecies coalescent approach. Values above the branches correspond to Bayesian posterior probabilities.
Figure 2 in An underground burst of diversity - a new look at the phylogeny and taxonomy of the genus Talpa Linnaeus, 1758 (Mammalia: Talpidae) as revealed by nuclear and mitochondrial genes
Figure 2. The Bayesian phylogeny of the genus Talpa as inferred from a concatenated alignment of four nuclear genes. Values above the branches correspond to Bayesian posterior probabilities (BPP) in MrBayes and bootstrap support (1000 pseudoreplicates) in ML and MP analyses, correspondingly. Representatives of the genera Euroscaptor, Mogera, Parascaptor, Scaptochirus and tribes Desmanini, Scalopini and Condylurini are used as outgroups.
Figure 1 in An underground burst of diversity - a new look at the phylogeny and taxonomy of the genus Talpa Linnaeus, 1758 (Mammalia: Talpidae) as revealed by nuclear and mitochondrial genes
Figure 1. Map of sampling localities for specimens of the genus Talpa used in this study. Localities 1–37 are listed in Table 1 (original material), localities 38–57 correspond to the sequences retrieved from GenBank and are listed in Supporting Information 1.
Figure 5 in An underground burst of diversity - a new look at the phylogeny and taxonomy of the genus Talpa Linnaeus, 1758 (Mammalia: Talpidae) as revealed by nuclear and mitochondrial genes
Figure 5. Timescale of major divergence events among Talpa based on nuclear concatenation (BEAST). The divergence times correspond to the mean posterior estimate of their age in Myr. The grey bars represent the 95% HPD interval. Numbers above the branches correspond to posterior probabilities for each node.
Figure 5 in The tail tells the tale: taxonomy and biogeography of some Atlantic Chelidonura (Gastropoda: Cephalaspidea: Aglajidae) inferred from nuclear and mitochondrial gene data
Figure 5. Mating sequence of two individuals of Chelidonura berolina belonging to two different colour forms. Single digit numbers indicate the sequence of events. Multiple digit numbers indicated the time at which the photographs were taken.
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