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Figure 4 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES

Figure 4. Time-calibrated Bayesian inference tree generated using concatenated internal and external transcribed spacer data. The values at the nodes indicate mean divergence dates, and the horizontal bars indicate 95% highest posterior density ranges for the age at each node. The green bar indicates the consensus age of the closure of the Panama Isthmus (age based on Leigh et al., 2013; O'Dea et al., 2016). BOL, Bolivia; BRA, Brazil; CAR, Caribbean; COL, Colombia; CRC, Costa Rica; ECU, Ecuador; MEX, Mexico; NIC, Nicaragua; PER, Peru; USA, United States of America; VEN, Venezuela.

Figure 3 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES

Figure 3. Bayesian inference tree of combined internal and external transcribed spacer data. Posterior probabilities> 0.9 are given above the branches. The red text indicates South American species. Leaf figures indicate opposite and alternate phyllotaxy. Chromosome numbers are based on Moreira & Cavalcanti (2020) and Panero & Strother (2021). BOL, Bolivia; BRA, Brazil; CAR, Caribbean; COL, Colombia; CRC, Costa Rica; ECU, Ecuador; MEX, Mexico; NA, North America; NIC, Nicaragua; PER, Peru; SA, South America; VEN, Venezuela.

Figure 2 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES

Figure 2. Total distribution of Verbesina in North America, Central America, the Caribbean, and South America. (Data accessed from GBIF, https://www.gbif.org/).

Figure 1 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES

Figure 1. Morphological characters in Verbesina. A, Tree of Verbesina floribunda Gardner; B, subshrubby habit of V. bipinnatifida Baker; C, capitulum of V. luetzelburgii Mattf.; D, capitulum of V. bipinnatifida; E, cypsela of V. bipinnatifida; F, cypsela of V. floribunda; G, scanning electron micrograph (SEM) of the verrucous cypsela surface of V. macrophylla (Cass.) S.F.Blake; H, inflorescence of V. macrophylla; I, pinnatipartite leaf of V. macrophylla; J, SEM of the scalariform cypsela surface of V. glabrata Hook. & Arn.; K, inflorescence of V. glabrata; L, entire leaf of V. glabrata. Vouchers: C, G.L. Moreira et al. 118 (CEN); D–E, G.L. Moreira et al. 116 (CEN); F, G.L. Moreira et al. 101 (CEN). Scale bars: C, 8 mm; D, 4 mm; E, 2 mm; F, 4 mm; G and J, 200 μm. Photographs: G. L. Moreira.

Figure 5 in Genetic difference between two Schistosoma japonicum isolates with contrasting cercarial shedding patterns revealed by whole genome sequencing

Figure 5. Gene ontology enrichment analysis of genes from genome regions with strong selective signals.

Figure 2 in Genetic difference between two Schistosoma japonicum isolates with contrasting cercarial shedding patterns revealed by whole genome sequencing

Figure 2. Box plots of diversity, Tajima's D of S. japonicum and their FST. (A) Nucleotide diversity estimated in 100-kb windows sliding in 10-kb steps throughout the genome. (B) Tajima's D estimated within a nonoverlapping 100-kb window throughout the genome. (C) pairwise FST computed in 100-kb windows sliding in 10-kb steps throughout the genome.

Figure 4 in Genetic difference between two Schistosoma japonicum isolates with contrasting cercarial shedding patterns revealed by whole genome sequencing

Figure 4. Distribution of p ratios (pST/pHX) and FST values calculated in 100-kb windows sliding in 10-kb steps throughout the genome. Data points colored red and blue were identified as selected regions in ST (red dots) and in HX (blue dots), respectively. These points correspond to the 5% left and right tails of the empirical p ratio distribution, where the p ratios are 0.092 and 1.643, respectively (vertical dashed lines), and the 5% right tail of the empirical FST distribution, where FST is 0.965 (horizontal dashed line).

Figure 3 in Genetic difference between two Schistosoma japonicum isolates with contrasting cercarial shedding patterns revealed by whole genome sequencing

Figure 3. Box plots of diversity and relationship of two sample groups. (A) Nucleotide diversity estimated in 100-kb windows sliding in 10-kb steps throughout the genome. (B) Tajima's D estimated within a nonoverlapping 100-kb window throughout the genome. (C) FST between computed in 100-kb windows sliding in 10-kb steps throughout the genome.

opencc-by-4.0Jun 2024View details →

UNITE+INSD 2024 Fungal ITS, ITS1, and ITS2 Reference Sequences

<p>These datasets were created from the 2024 release (Abarenkov et al. 2024) of the UNITE+INSD database as reference sequences for and by dnabarcoder (Vu et al. 2022). The ITS1 and ITS2 sequences were extracted using ITSx (Bengtsson-Palme et al. 2013).</p>

opencc-by-4.0Aug 2011View details →

Fig. 4 in MITOCHONDRIAL 16S AND 12S rRNA SEQUENCE ANALYSIS IN FOUR SALMONID SPECIES FROM ROMANIA

Fig. 4. Majority with bootstrap support consensus trees for combined data (16S rRNA and 12S rRNA). (a) Combined data Neighbor Joining tree, distance model Kimura 2 Parameters, transition/transversion ratio 2.3; (b) combined data Maximum Parsimony tree; (c) combined data Maxi-

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Fig. 3. Majority with bootstrap support consensus trees for 12S in MITOCHONDRIAL 16S AND 12S rRNA SEQUENCE ANALYSIS IN FOUR SALMONID SPECIES FROM ROMANIA

Fig. 3. Majority with bootstrap support consensus trees for 12S rRNA. (a) 12S rRNA Maximum Parsimony tree; (b) 12S rRNA Neighbor Joining tree, distance model Kimura 2 Parameters, transi-

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Fig. 2. Majority with bootstrap support consensus trees for 16S in MITOCHONDRIAL 16S AND 12S rRNA SEQUENCE ANALYSIS IN FOUR SALMONID SPECIES FROM ROMANIA

Fig. 2. Majority with bootstrap support consensus trees for 16S rRNA. (a) 16S rRNA Neighbor Joining tree, distance model Kimura 2 Parameters, transition/transversion ratio 2.3; (b) 16S rRNA Maximum Parsimony tree; (c) 16S rRNA Maximum Likelihood tree

opencc-by-nc-nd-4.0Jul 2024View details →

Comic strips sequences to develop narratives in the Storytelling in Sequence Task (STST)

<p>                                                  <strong>       Comic strips sequences to develop narratives in theStorytelling in Sequence Task (STST)</strong></p> <p>  </p> <p>The stimuli presented in the 9 following pages were developed by Sophie Courchesne and Sonia Routhier, under the supervision of Marion Fossard, as part of a master’s essay in speech and language pathology at Laval University, Quebec City, Canada.</p> <p>The Storytelling in Sequence Task (STST) was then introduced in a paper of Fossard, Achim, et al., published in 2018 in the journal Frontiers in Psychology.</p> <p><strong>To cite this material :</strong></p> <p>Courchesne, S., & Routhier, S. (2009). Tâche de narration d’histoires en séquence et son analyse référentielle (Essai de maîtrise, Université Laval). Université Laval, Québec, Canada.</p> <p>Fossard M, Achim AM (co-first authors), Roussier-Vercruyssen L, Gonzales S, Bureau A, Champagne-Lavau M. (2018). Referential choices in a collaborative storytelling task: Discourse stages and referential complexity matter. Frontiers in Psychology: Language Sciences, vol. 9, article 176. doi: 10.3389/fpsyg.2018.00176</p> <p><em>TERMES OF USE :</em> This material belongs to Marion Fossard and her research team. Its use is allowed in research or in clinical settings if the following conditions are met:</p> <div>·All commercial use is prohibited;</div> <div>·The source must be cited in all publications involving the use of this material;</div> <div>·No Modifications must can made without the consent of Marion Fossard (<u><a href="mailto:marion.fossard@unine.ch">marion.fossard@unine.ch</a></u>);</div> <div>·All clinical use is done while recognizing the limitations of the test.</div>

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.