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Figs 30–35 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)

Figs 30–35. Variation of the male palps, left palps, prolateral views. 30–33. Loxosceles tolantongo sp. nov. 30–32. Tourist Center Grutas de Tolantongo, Municipality of Cardonal, Hidalgo (type locality). 33. 500 m west of the entrance No. 5 to the Tourist Center Grutas de Tolantongo, Municipality of Cardonal, Hidalgo. 34–35. Loxosceles jaca Gertsch & Ennik, 1983. 2.5 km north of Jacala de Ledezma, Municipality of Jacala de Ledezma, Hidalgo. Scale bars = 0.5 mm.

Fig. 56 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)

Fig. 56. Maximum likelihood tree inferred from the concatenated matrix (CO1 + ITS2) of species of Loxosceles Heineken & Lowe, 1832 from Mexico. Colors of branches and bars indicate different species. Numbers above bars represent the delimitation methods: 1 = morphology (M); 2 = neighbor joining (NJ); 3 = ABGD with initial partitions (IP); 4–5 = ABGD with recursive partitions (RP); 6 = GMYC yule analysis; 7 = GMYC coalescent analysis; 8 bPTP with ML; 9 = bPTP with IB. Numbers below bars represent species recovered for each delimitation method. Red numbers correspond to Bayesian posterior probabilities, black numbers are bootstrap support values from the ML analysis.

Figs 20–25 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)

Figs 20–25. Loxosceles tolantongo sp. nov., ♂ holotype (CNAN-T01317). 20–22. Left palp, prolateral, dorsal and retrolateral views, respectively. 23–25. Detail of the bulb and embolus, retrolateral, dorsal and apical views, respectively. Scale bars: 20–22 = 0.5 mm; 23–25 = 0.2 mm.

Fig. 54 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)

Fig. 54. Maximum likelihood tree inferred from CO1 gene of species of Loxosceles Heineken & Lowe, 1832 from Mexico. Colors of branches and bars indicate different species. Numbers above bars represent the delimitation methods: 1 = morphology (M); 2 = neighbor joining (NJ); 3 = ABGD with initial partitions (IP); 4–6 = ABGD with recursive partitions (RP); 7 = GMYC yule analysis; 8 = GMYC coalescent analysis; 9 = bPTP with ML; 10 = bPTP with IB. Numbers below bars represent species recovered for each delimitation method. Red numbers on branches correspond to Bayesian posterior probabilities, black numbers are bootstrap support values from the ML analysis.

opencc-by-4.0Oct 2022View details →

Fig. 6. ITS2 in A huge undescribed diversity of the subgenus Hystricochaetonotus (Gastrotricha, Chaetonotidae, Chaetonotus) in Central Europe

Fig. 6. ITS2 of the subgenus Hystricochaetonotus Schwank, 1990. A. Putative consensus secondary structure. The central loop radiates four unequally long helices. The first two helices are highly conserved, while the two following helices are much less conserved. For localization of helix 10, which is made by the interaction of 3'-end of 5.8S and 5'-end of 28S, see Fig. 7. B. Two different views on the tertiary structure, showing that helices II and IV run in parallel. C. Structure logos of helices I‒IV. The height of a base is proportional to its frequency in the multiple sequence alignment.

opencc-by-4.0Jun 2024View details →

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

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).

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-4.0Feb 2014View details →

Fig. 3. Maximum likelihood tree constructed from 38 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and relatives using a in Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences

Fig. 3. Maximum likelihood tree constructed from 38 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and relatives using a transition/transversion rate ratio of 1.6. Branch lengths are proportional to the number of expected nucleotide substitutions per site.

opencc-by-4.0Jun 2019View details →

Nematode ITS2 Database

Nematode ITS2 database These are the sequence and taxonomy files for the Nematode ITS2 database.  This database was created with <a href="https://github.com/ucvm/markerDB">markerDB</a>. Please see that repository for full details on the file formats.  The main database consists of the "seqs_nr.fasta" and the associated "taxonomy_nr.txt".  These contain the non-redundant ITS2 sequences. The database is available in some other common formats used for assigning taxonomy and are listed below<code>.</code> <ul> <li>dada2: dada2’s <code>assignTaxonomy</code> function</li> <li>rdp: to train a custom RDP database with the <code>rRDP</code> Bioconductor package (this is pretty much the same as <code>assignTaxonomy</code>)</li> <li>mothur: a fasta file and paired mothur taxonomy file. Works with the <a href="https://www.nemabiome.ca/">Nemabiome</a> pipeline. An alignment is also written out that should work with mothur, but can also be used for other pipelines as needed.</li> <li>idtaxa: a fasta file and taxonomy file for <a href="https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0521-5">IDTAXA</a>.</li> </ul>

opencc-by-4.0Dec 2019View details →

Fig. 5. Parsimony splits network constructed from a per and ITS2 concatenated sequence data set. Heterozygous specimens are indicated with A and B in Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism

Fig. 5. Parsimony splits network constructed from a per and ITS2 concatenated sequence data set. Heterozygous specimens are indicated with A and B. 'bufonivora_EUROPE_A' represents a consistent haplotype present in all 12 samples from Europe (Table 1), of which just two were heterozygous ('bufonivora_frog' and 'bufonivora_NLWi'). 'bufonivora_CAN' and 'elongata_CAN' are represented by two samples each, none of which were heterozygous. Scale bar represents expected changes per site.

opencc-by-4.0Dec 2021View details →

Fig. 4. Maximum likelihood tree generated using ITS1-5.8S-ITS2 in Morphological and molecular description of Pallisentis roparensis n. sp. (Acanthocephala: Quadrigyridae) infecting the freshwater cat fish Wallago attu from Ropar Wetland, Punjab, India

Fig. 4. Maximum likelihood tree generated using ITS1-5.8S-ITS2 gene sequence of Pallisentis roparensis and the sequences of related taxa downloaded from GenBank. Numbers near internal nodes show ML bootstrap clade frequencies.

opencc-by-4.0Aug 2024View details →

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