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Fig. 9 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule

Fig. 9. Evolutionary hypothesis of interrelationships among the four free-living litostomatean lineages studied. This scenario was suggested on the basis of morphology and the consensus secondary structure of the ITS2 molecules. CK – circumoral kinety, DB – dorsal brush, OB – oral bulge, OO – oral bulge opening, P – proboscis, PE – perioral kinety, PR – preoral kineties, SK – somatic kineties.

Fig. 5 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule

Fig. 5. Quartet likelihood-mapping showing distribution of phylogenetic signal in the 18S-A and the CON-1 alignment for three possible relationships among the four main free-living litostomatean lineages studied. The corners of the triangles show the percentage of fully resolved trees, i.e., phylogenetically informative signal. The rectangular areas show the percentage of trees that are in conflict. The central triangle shows the percentage of unresolved star-like trees, i.e., phylogenetically uninformative signal. Coding of free-living litostomatean lineages: H – Haptorida, P – Pleurostomatida, R – Rhynchostomatia, S – Spathidiida.

Fig. 4 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule

Fig. 4. Super-network of 66 free-living litostomatean taxa constructed from 80 randomly selected post-burn-in trees from the Bayesian inference of the 18S-A–D, ITSR-C and ITSR-D as well as the CON-1 and CON-2 alignments. The super-network was constructed in the program SplitsTree, using the Z-closure option, tree size weighted mean, ten runs, and the refined heuristic technique. For details on taxa and characteristics of the alignments analyzed, see Supplementary Table S1 and S2.

Fig. 3 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule

Fig. 3. Phylogeny based on the 18S rRNA gene and the ITS1-5.8S-ITS2 region of 56 free-living litostomatean taxa (alignment CON-1). Posterior probabilities for the Bayesian inference and bootstrap values for maximum likelihood were mapped onto the 50% majority rule ML tree. Dashes indicate posterior probabilities below 0.50 and ML bootstrap values below 50%. The scale bar indicates five substitutions per ten nucleotide positions. For details on taxa, evolutionary model used, and characteristics of the CON-1 alignment, see Supplementary Table S1 and S2.

Fig. 1 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule

Fig. 1. Phylogeny based on the 18S rRNA gene of 64 free-living litostomatean taxa (alignment 18S-A). Posterior probabilities for Bayesian inference and bootstrap values for maximum likelihood were mapped onto the 50% majority rule Bayesian consensus tree. Dashes indicate ML bootstrap values below 50%. Sequences in bold were obtained during this study. The scale bar indicates two substitutions per one hundred nucleotide positions. For details on taxa, evolutionary model used, and characteristics of the 18S-A alignment, see Supplementary Table S1 and S2.

Fig. 8 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule

Fig. 8. Structure logo of ITS2 helices II and III in various higher litostomatean taxa. The height of a base is proportional to its frequency in multiple sequence alignments.

Fig. 2 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule

Fig. 2. Phylogeny based on the ITS1-5.8S-ITS2 region of 60 free-living litostomatean taxa (alignment ITSR-A). Posterior probabilities for Bayesian inference and bootstrap values for maximum likelihood were mapped onto the best ML tree. Dashes indicate posterior probabilities below 0.50 and ML bootstrap values below 50%. Sequences in bold were obtained during this study. The scale bar indicates nine substitutions per one hundred nucleotide positions. For details on taxa, evolutionary model used, and characteristics of the ITSR-A alignment, see Supplementary Table S1 and S2.

Fig. 7 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule

Fig. 7. Consensus secondary structure of ITS2 helices II and III in various higher litostomatean taxa.

opencc-by-4.0Aug 2015View details →

Figure 2. PAM250 matrix for the encoded sequence-Secondary Structure Prediction of Protein using Resilient Back Propagation Learning Algorithm

The PAM matrix (Dayhoff et al., 1978) describes the probability that original amino acid will be replaced by another amino acid over a defined evolutionary interval. The unit of evolutionary divergence is defined as the interval in which 1% of the amino acids have been changed between two sequences. The work uses PAM250, which assumes the occurrence of 250- point mutations per 100 amino acids. So, for the given the protein sequence GIVEQCCASVCSLYQLENYCN, A will be replaced by 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -7 -5 -1 as shown in Figure 2.

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Improving phonetic alignment by handling secondary sequence structures

Supplementary material accompanying the paper "Improving phonetic alignment by handling secondary sequence structures". The data consists of 5 files: <ul> <li>gold_standard.psa : the gold standard used in the analysis in PSA format</li> <li> sca-secondary.psa : the output of the algorithm with the secondary extension</li> <li>sca-traditional.psa : the output of the traditional algorithm</li> <li>sca-secondary-diff.psa : the differences of the secondary extension compared to the GS</li> <li>sca-traditional-diff.psa : the differences of the traditional algorithm compared to the GS</li> </ul> For a description of the file-format used in this dataset, please refer to the LingPy tutorial under http://lingpy.org.

opengpl-2.0Jun 2012View details →

dryad32/100

Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure

Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD-seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans-Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three data sets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD-seq based approaches for the resolution of complex spatial patterns, resolves a region of trans-Atlantic secondary contact in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression.

opencc-zeroDec 2014View details →

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FIGURE. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)

FIGURE. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined.

opennotspecifiedNov 2021View details →

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Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure

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publicSep 2015View details →

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Data from: Secondary structure models of 18S and 28S rRNAs of the true bugs based on complete rDNA sequences of Eurydema maracandica Oshanin, 1871 (Heteroptera: Pentatomidae)

The sequences of 18S and 28S rDNAs have been used as molecular markers to resolve phylogenetic relationships of Heteroptera for two decades. The complete sequences of 18S rDNAs have been used in many studies, while in most studies only partial sequences of 28S rDNAs have been used due to technical difficulties of amplifying the complete lengths. In this study, we amplified the complete 18S and 28S rDNA sequences of Eurydema maracandica Oshanin, 1871, and reconstructed the secondary structure models of the corresponding rRNAs. In addition, and more importantly, all of the length variable regions of 18S rRNA were compared among 37 families of Heteroptera based on 140 sequences, and the D3 region of 28S rRNA was compared among 51 families based on 84 sequences. It was found that 8 length variable regions could potentially serve as molecular synapomorphies for some monophyletic groups. Therefore discoveries of more molecular synapomorphies for specific clades can be anticipated from amplification of complete 18S and 28S rDNAs of more representatives of Heteroptera.

opencc-zeroDec 2012View details →

Fig. 6 in Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule

Fig. 6. Consensus secondary structure of the ITS2 molecule of free-living litostomateans. The ITS2 molecule shows an internal loop, radiating two helices. There is an A-G bulge in the stem of helix III.

Figure 3 from: Xie Q, Yu S, Wang Y, Rédei D, Bu W (2013) Secondary structure models of 18S and 28S rRNAs of the true bugs based on complete rDNA sequences of Eurydema maracandica Oshanin, 1871 (Heteroptera, Pentatomidae). ZooKeys 319: 363-377. https://doi.org/10.3897/zookeys.319.4178

Figure 3 - The 3'-half part of secondary structure model of 28S rRNA of Eurydema maracandica. The numbers D8 to D11 represent four LVRs.

Figure 4 from: Xie Q, Yu S, Wang Y, Rédei D, Bu W (2013) Secondary structure models of 18S and 28S rRNAs of the true bugs based on complete rDNA sequences of Eurydema maracandica Oshanin, 1871 (Heteroptera, Pentatomidae). ZooKeys 319: 363-377. https://doi.org/10.3897/zookeys.319.4178

Figure 4 - Secondary structure models of LVR W of Naboidea and Cimicoidea. These sequences are from 15 genera, 19 species of Naboidea and Cimicoidea. The species names and GenBank Accession numbers are as follow: Nabidae (a) Nabis ferus EF487300 (b) Nabis flavomarginatus GQ258424 (c) Himacerus apterus GQ258425; Lyctocoridae (d) Lyctocoris beneficus EF487298; Anthocoridae (e) Anthocoris sp. AY252319 (f) Anthocoris confusus EF487297 (g) Anthocoris montanus EF487307 (h) Tetraphleps aterrimus EF487295 (i) Amphiareus obscuriceps EF487301 (j) Orius agilis EF487296 (k) Physopleurella armata EF487308 (l) Montandoniola moraguesi EF487310 (m) Xylocoris cerealis GQ258395 (n) Bilia sp. GQ258406 (o) Buchananiella crassicornis GQ258407 (p) Lasiochilus japonicus GQ258410 (q) Lasiochilus luceonotatus GQ258411; Cimicidae (r) Cimex lectularius GQ258396; Curaliidae (s) Curalium cronini EU683128.

Figure 1 from: Xie Q, Yu S, Wang Y, Rédei D, Bu W (2013) Secondary structure models of 18S and 28S rRNAs of the true bugs based on complete rDNA sequences of Eurydema maracandica Oshanin, 1871 (Heteroptera, Pentatomidae). ZooKeys 319: 363-377. https://doi.org/10.3897/zookeys.319.4178

Figure 1 - Secondary structure model of 18S rRNA of Eurydema maracandica. The bases marked in black represent length-conservative regions, and the bases labeled as capital letters B to W in red represent 13 LVRs. CP and NC represent monophyletic groups Cimicomorpha+Pentatomomorpha and Naboidea+Cimicoidea, respectively. Base pairing is indicated as follows: standard canonical pairs by lines (G–C, A–U), wobble G:U pairs by dots (G·U), A:G or A:C pairs by open circles (A○G, A○C), and other non-canonical pairs by filled circles (e.g., A●A).

Figure 2 from: Xie Q, Yu S, Wang Y, Rédei D, Bu W (2013) Secondary structure models of 18S and 28S rRNAs of the true bugs based on complete rDNA sequences of Eurydema maracandica Oshanin, 1871 (Heteroptera, Pentatomidae). ZooKeys 319: 363-377. https://doi.org/10.3897/zookeys.319.4178

Figure 2 - The 5'-half part of secondary structure model of 28S rRNA of Eurydema maracandica. The numbers D2 to D7 represent six LVRs. PM, GO and AL represent monophyletic groups Paraphrynoveliidae+Macroveliidae, Gelastocoridae+Ochteridae and Acanthosomatidae+Lestoniidae, respectively.