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opencc-by-4.0Jan 2021View details →

Dataset for "Phylogenetic structure of European forest vegetation" - Journal of Biogeography (DOI: 10.1111/jbi.14046)

This dataset contains the list of plant occurrences and geographical and environmental attributes of the vegetation-plots analyzed in the paper titled “Phylogenetic structure of European forest vegetation” by Padullés Cubino et al. (2021; Journal of Biogeography; DOI: 10.1111/jbi.14046).  The dataset contains 3 tables: <ol> <li>“Table_taxa.csv”: It includes the list of angiosperm plant taxa in selected vegetation plots.</li> <li>“Table_sites.csv”: It includes data on the environmental variables of plots, their classification into different forest types, their location in 1o × 1o grid cells, and the reference to the original datasets archived in the European Vegetation Archive (EVA; http://euroveg.org/eva-database-participating-databases).</li> <li>“Metadata.csv”: It includes a description of the fields found in the two previous tables.</li> </ol>

→ Fig. 10. FESEM images of the test structure in lagenid foraminifers from Recent, Admiralty Bay, King George Island, West Antarctica (A) and from the Jurassic of Gnaszyn, Poland (B, C). A. Unilocular Procerolagena gracilis Williamson, 1848, MWGUW ZI/67/44/02. B. Unilocular Lagena globosa Montagu, 1803, MWGUW ZI/67/61/09. C. Uniserial Nodosaria pulchra Franke, 1936, MWGUW ZI/67/61/26. Oblique cross-sectional views (A1, A2, A4, B1, B2, C); transverse cross-sectional views, showing single-crystal interlocked bundle structures, inner pores which extend along the entire length of the bundles as well as prominent calcite cleavage (A3, B3). Abbreviations: c, prominent calcite cleavage; ip, inner pore. in Chamber arrangement versus wall structure in the high-rank phylogenetic classification of Foraminifera

→ Fig. 10. FESEM images of the test structure in lagenid foraminifers from Recent, Admiralty Bay, King George Island, West Antarctica (A) and from the Jurassic of Gnaszyn, Poland (B, C). A. Unilocular Procerolagena gracilis Williamson, 1848, MWGUW ZI/67/44/02. B. Unilocular Lagena globosa Montagu, 1803, MWGUW ZI/67/61/09. C. Uniserial Nodosaria pulchra Franke, 1936, MWGUW ZI/67/61/26. Oblique cross-sectional views (A1, A2, A4, B1, B2, C); transverse cross-sectional views, showing single-crystal interlocked bundle structures, inner pores which extend along the entire length of the bundles as well as prominent calcite cleavage (A3, B3). Abbreviations: c, prominent calcite cleavage; ip, inner pore.

Fig. 9 in Chamber arrangement versus wall structure in the high-rank phylogenetic classification of Foraminifera

Fig. 9. FESEM images of "monocrystalline" test structure in Spirillinata → foraminifers from the Jurassic of Gnaszyn, Poland (A) and Recent from Ronsard Bay, Western Australia (B). A. Paalzowella pazdroe Bielecka and Styk, 1969, MWGUW ZI/67/61/27; view of the test cross-section (A1); significantly magnified view of the test cross-section (A2, A4, A5); oblique cross-sectional view of the test showing "monocrystalline" test structure (A3); oblique cross sections of the test showing test composed of a few layers (A6, A7). B. Patellina sp., MWGUW ZI/67/61/22; oblique cross sections of the test showing prominent calcite cleavage (B1, B2).

Fig. 8 in Chamber arrangement versus wall structure in the high-rank phylogenetic classification of Foraminifera

Fig. 8. FESEM images of the test structure in Tubothalamea from the Jurassic of Gnaszyn, Poland. A. Ophthalmidium carinatum Pazdro, 1958, MWGUW → ZI/67/08/5.03; front views of the abraded test surface, showing the extrados and porcelain (A1, A2). B.?Cornuspira radiata (Terquem, 1886), MWGUW ZI/67/55/11; front view of the test surface (B1, B3); oblique view of the test cross section, showing the test as being entirely composed of needle-shaped crystallites (B2, B4). C. Planiinvoluta sp., MWGUW ZI/67/57/13; view of the inner test surface (C1); side view of the test cross section, showing irregular meshwork of needle-shaped crystallites (C2). Abbreviations: e, extrados; p, porcelain.

Fig. 7 in Chamber arrangement versus wall structure in the high-rank phylogenetic classification of Foraminifera

Fig. 7. FESEM images of the test structure in Recent calcareous cemented agglutinated textulariid (Globothalamea; A, B) and miliolid (Tubothalamea; C) → foraminifers from Ronsard Bay, Western Australia. A. Textularia sp., MWGUW ZI/67/55/24, front view of the test, showing agglutinated grains and the calcareous nanogranular matrix (A1); details of test wall (A2, A3). B. Gaudryina sp., MWGUW ZI/67/61/16, front view of the test, showing agglutinated grains and the matrix (B1); details of nanogranular matrix (B2, B3). C. Quinqueloculina arenata Said, 1949, MWGUW ZI/67/57/02, front view of the test (C1); oblique cross-sectional view of test showing foreign particle partially embedded in the irregular meshwork of needle-shaped crystallites (C2). Abbreviations: g, foreign particle; m, calcareous matrix. Arrows indicate pores.

opencc-zeroMay 2022View details →

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The chloroplast genomes of Sanicula (Apiaceae): plastome structure, comparative analyses, and phylogenetic relationships

Sanicula (Apiaceae subfamily Saniculoideae) is a taxonomically difficult genus of medicinal value. Its distribution center is in China, where there are 18 species (11 of which are endemic). To provide plastid genome resources, whole chloroplast genomes of five Sanicula species (S. flavovirens, S. giraldii, S. lamelligera, S. odorata, and S. rubriflora) were sequenced and compared to the previously published S. orthacantha plastome. These genomes exhibit a typical quadripartite structure. All contain 129 different genes, including 84 protein-coding, 37 tRNA, and 8 rRNA genes. Loci rpl2, matK, psbA, and ycf1 are the most variable. Results of maximum likelihood analysis of 90 whole plastome sequences from Apioideae and Saniculoideae and the outgroup Hydrocotyle (Araliaceae) reveal sectional relationships in Sanicula different from the traditional classification system, support the monophyly of Apioideae and its sister group relationship to Saniculoideae, and show concordant topologies to nrDNA ITS and other plastome-based phylogenies. Sanicula orthacantha and S. chinensis form a clade sister group to S. lamelligera and S. odorata, consecutively. These four species comprise a clade sister group to the clade of S. rubriflora and S. flavovirens, with this entire group sister to S. giraldii. The plastid genome resources provided herein will be important for future systematic, evolutionary, phylogenomic, and population-level studies of Sanicula.

opencc-by-4.0Dec 2021View details →

Text-fig. 13. Enamel ultrastructure of I1, Equus hydruntinus (Kabazi 2). a: vertical sections, scale bar = 100 Μm; b: horizontal and vertical arrangement of prisms in the HSB structure, scale bar = 10 Μm; c: unstructured PLEX enamel at the end of the root, scale bar = 100 Μm. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections

Text-fig. 13. Enamel ultrastructure of I1, Equus hydruntinus (Kabazi 2). a: vertical sections, scale bar = 100 Μm; b: horizontal and vertical arrangement of prisms in the HSB structure, scale bar = 10 Μm; c: unstructured PLEX enamel at the end of the root, scale bar = 100 Μm.

opencc-by-4.0Dec 2021View details →

Text-fig. 11. Enamel ultrastructure of first (a) and second (b, c) lower incisors, Equus caballus (konik polski), vertical sections. a: enamel row, scale bar = 100 Μm; b: arranging the prisms in the HSB structure, scale bar = 20 Μm; c: arranging the prisms in PI structure, scale bar = 20 Μm. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections

Text-fig. 11. Enamel ultrastructure of first (a) and second (b, c) lower incisors, Equus caballus (konik polski), vertical sections. a: enamel row, scale bar = 100 Μm; b: arranging the prisms in the HSB structure, scale bar = 20 Μm; c: arranging the prisms in PI structure, scale bar = 20 Μm.

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-4.0Jun 2020View details →

FIGURE 2 in Using community phylogenetics to assess phylogenetic structure in the Fitzcarrald region of Western Amazonia

FIGURE 2 | Ultrametric cladogram of the Fitzcarrald region fish fauna (modified from S2) showing distributions of species in habitats and river basins. Red boxes indicate species presences in: Rivers, Stream, Lakes, Purus, Yuruá, Urubamba and Las Piedras. Note phylogenetic clustering in the Urubamba basin and the stream habitat.

opencc-by-4.0Mar 2015View details →

Fig. 4. Composite phylogenetic hypothesis for 33 in Phylogenetic signal and major ecological shifts in the ecomorphological structure of stream fish in two river basins in Brazil

Fig. 4. Composite phylogenetic hypothesis for 33 stream fish species based on six different studies. Solid circles indicate six taxonomic groups that were significant in the canonical phylogenetic ordination (CPO); they are numerically labeled as follows: 1, Siluriformes/Characiformes; 2, Loricariidae; 3, Farlowella/Rineloricaria; 4, Characidae; 5, Hypostominae; 6, Pimelodella/Rhamdia.