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FIGURES 10–13 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)

FIGURES 10–13. Male head frontal: (10) L. coomansi SAR09_10_GOM4; (11) L. coomansi holotype; (12) L. sp. cf coomansi SAB12_GOM4; (13) L. pendleburyi SAR13_14_GOM13.

FIGURES 46–51 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)

FIGURES 46–51. Female head frontal detail; h—occipital horn; ot—occipital tube; t—tubercle; th—tubercle horn: (46) L. coomansi SAR11_12_GOM48; (47) L pendleburyi SAR16_GOM8; (48) L. schieli paratype SAR15_GOM6; (49) L. species SAR11_12_GOM33; (50) L. williamsoni SAR13_14_GOM51; (51) L. sp. cf williamsoni SAR11_12_GOM59.

FIGURES 24–27 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)

FIGURES 24–27. Female head dorsal: (24) L pendleburyi SAR16_GOM8; (25) L. schieli paratype SAR15_GOM6; (26) L. williamsoni SAR13_14_GOM51; (27) L. sp. cf williamsoni SAR11_12_GOM59.

FIGURE 3. Phylogenetic reconstruction for 30 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)

FIGURE 3. Phylogenetic reconstruction for 30 specimens of Leptogomphus and three outgroup taxa using the combined COI+ITS dataset. The best Maximum Likelihood tree is shown, with posterior probabilities from the Bayesian Inference analysis also depicted on the branches. Bootstrap values and posterior probabilities are shown if less than 100 or 1.0 respectively. RMNH collection codes are shown for each specimen, as well as the sex of the specimen and an indication of where it was collected.

FIGURE 2. ITS gene tree for 20 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)

FIGURE 2. ITS gene tree for 20 specimens of Leptogomphus and three outgroup taxon. The best Maximum Likelihood tree is shown, with posterior probabilities from the Bayesian Inference analysis also depicted on the branches. Bootstrap values and posterior probabilities are shown if less than 100 or 1.0 respectively. RMNH collection codes are shown for each specimen, as well as the sex of the specimen and an indication of where it was collected.

opennotspecifiedFeb 2019View details →

FIGURE 3 in Molecular phylogenetic analysis of subfamilial placement of Haplotropis Saussure, 1888 (Orthoptera: Pamphagidae) based on mitochondrial and nuclear DNA markers

FIGURE 3. Phylogenetic tree based on the nucleotide sequences of ITS2 region of Pamphagidae. Support values shown as: SH-aLRT support/ ultrafast bootstrap (probability> 80/90 considered significant). The brackets on the right side show subfamily and family clusters.

opennotspecifiedFeb 2019View details →

FIGURE 2 in Molecular phylogenetic analysis of subfamilial placement of Haplotropis Saussure, 1888 (Orthoptera: Pamphagidae) based on mitochondrial and nuclear DNA markers

FIGURE 2. Phylogenetic tree based on the nucleotide sequences of COII mitochondrial gene of Pamphagidae. Support values shown as: SH-aLRT support/ ultrafast bootstrap (probability> 80/90 considered significant). The brackets on the right side show subfamily and family clusters.

opennotspecifiedFeb 2019View details →

FIGURE 1 in Molecular phylogenetic analysis of subfamilial placement of Haplotropis Saussure, 1888 (Orthoptera: Pamphagidae) based on mitochondrial and nuclear DNA markers

FIGURE 1. Phylogenetic tree, based on the nucleotide sequences of COI mitochondrial gene of Pamphagidae. Support values shown as: SH-aLRT support/ultrafast bootstrap (probability> 80/90 considered significant). The brackets on the right side show subfamily and family clusters.

Fig. 3 Chronogram showing the relationships and divergence times for 80 bears, estimated from a concatenated mitochondrial dataset comprising all 13 protein coding and 2 in Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker

Fig. 3 Chronogram showing the relationships and divergence times for 80 bears, estimated from a concatenated mitochondrial dataset comprising all 13 protein coding and 2 ribosomal RNA genes. Groups delimited as species by the GMYC analysis are shown as triangles. The horizontal axis shows the timescale, measured in millions of years.

Fig. 2 Chronogram showing the relationships and divergence times for 357 cetaceans, estimated from a concatenated mitochondrial dataset comprising all 13 protein coding and 2 in Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker

Fig. 2 Chronogram showing the relationships and divergence times for 357 cetaceans, estimated from a concatenated mitochondrial dataset comprising all 13 protein coding and 2 ribosomal RNA genes. Groups delimited as species by the GMYC analysis are shown as triangles. The horizontal axis shows the timescale, measured in millions of years.

Fig. 1 in Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker

Fig. 1 Number of markers analysed in a survey of 109 studies using GMYC published between January 2013 and December 2014. Columns indicate the total number of studies in the sample using the relevant number of markers. The lower dark grey portion of each column refers to the number of studies using only mitochondrial markers, while the upper light grey portion refers to all other studies

Fig. 5 in Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker

Fig. 5 Numbers of species delimited by different mitochondrial genes in GMYC analysis of three datasets: a cetaceans; b bears (Ursidae); and c European whitefish (Coregonus lavaretus) and allies. In each case, the value at which the horizontal axis crosses the vertical axis corresponds to the number of named species (47 cetaceans, 8 bears, 4 whitefish). Columns represent the number of species delimited in the most likely hypotheses identified by GMYC using individual genes, while error bars show the range of species counts found in the 95 % confidence set of species hypotheses generated by GMYC. Genes marked 'NS' did not provide sufficient evidence to reject the one-species null hypothesis (likelihood-ratio test, p> 0.05). Substantial variation is observed between delimitations given by different genes

opencc-zeroDec 2017View details →

dryad32/100

Data from: Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)

Rhododendron arboreum is an ecologically prominent species, which also lends commercial and medicinal benefits in the form of palatable juices and useful herbal drugs. Local abundance and survival of the species under a highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina's platform facilitated the generation of ∼100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out of shorter transcripts predicted 113 167 non-redundant transcripts with an average length of 1164.6 bases. Of these, 71 961 transcripts were categorized based on functional annotations in the Gene Ontology database, whereby 5710 were grouped into 141 pathways and 23 746 encoded for different transcription factors. Transcriptome screening further identified 35 419 microsatellite regions, of which, 43 polymorphic loci were characterized on 30 genotypes. Seven hundred and nineteen transcripts had 811 high-quality single-nucleotide polymorphic variants with a minimum coverage of 10, a total score of 20, and SNP% of 50.

opennotspecifiedFeb 2013View details →

Figure 3 in Localization and transcription patterns of LsVasa, a molecular marker of germ cells in Lepeophtheirus salmonis (Krøyer)

Figure 3. Localization of Lepeophtheirus salmonis Vasa (LsVasa) transcripts. (A) Light microscopy of sexually mature adult female with eggstrings attached. Most of the eggstrings extending from the genital segment have been cropped from the image. The position of various tissues is indicated: ∗ (ovaries), × (oocytes in the genital segment). Subcuticular tissue is found under the cuticula of most of the lice. The area used for in situ hybridization is indicated (+). Scale bar represents 5 mm. (B–F) In situ hybridization using an LsVasa-specific antisense RNA probe showing positive staining as dark colour. Small inserts illustrate corresponding locations in negative controls (using a LsVasa-sense RNA probe). (B) The two ovaries (Ov) of mature adult females. LsVasa transcripts are localized throughout the ovary including both proximal and the more distal zones. Scale bar represents 200 µm. (C) LsVasa is present in immature oocytes in the oviduct (ovd, scale bar 50 µm) as well as in mature oocytes in the unfertilized eggstring (D, scale bar 200 µm). LsVasa is also present in the gonads of earlier developmental stages (E, ovaries of preadult females, scale bar 200 µm) and in adult male testes (F, scale bar 100 µm).

opennotspecifiedFeb 2013View details →

Figure 2 in Localization and transcription patterns of LsVasa, a molecular marker of germ cells in Lepeophtheirus salmonis (Krøyer)

Figure 2. Ontogenic analysis of Lepeophtheirus salmonis Vasa (LsVasa) transcript levels. LsVasa transcripts levels were determined by the use of quantitative reverse transcription-polymerase chain reaction at different developmental stages. Levels were quantified relative to the level found in the nauplius stage. Error bars show 95% confidence intervals calculated from the ΔΔCT values from each dilution.

opennotspecifiedFeb 2013View details →

Figure 1 in Localization and transcription patterns of LsVasa, a molecular marker of germ cells in Lepeophtheirus salmonis (Krøyer)

Figure 1. Domain structure and copy number of Lepeophtheirus salmonis Vasa (LsVasa). (A) LsVasa with position of conserved protein domains. Position of DEAD box helicase core motifs (reviewed by Hilbert et al. 2009) are indicated with Roman numerals: (I) Motif I, (II) Motif Ia, (III) GG doublet, (IV) Motif Ib, (V) Motif II, (VI) Motif III, (VII) Motif IV, (VIII) QxxR, (IX) Motif V and (X) Motif VI. Triangles indicate the position of the three introns. (B) Southern blot using LsVasa as a probe. Genomic DNA was digested with XhoI (lane 1), PstI (lane 2), ClaI (lane 3), KpnI (lane 4), SacI (lane 5) and XbaI (lane 6) and electrophoresed together with a DNA marker (M).

opennotspecifiedDec 2011View details →

FIGURE 1. A in Molecular and morphological diagnostic markers for the Himalayan Ips DeGeer species (Coleoptera: Curculionidae: Scolytinae)

FIGURE 1. A joint phylogenetic tree obtained from the NJ and Bayesian inference for the COI genes of Ips and outgroups. Numbers above the nodes represent bootstrap values and the numbers in parentheses below the nodes indicate Bayesian posterior probabilities.

opennotspecifiedAug 2013View details →

Figure 3 in Phylogeny, phylogeography, and systematics of the American pea crab genus Calyptraeotheres Campos, 1990, inferred from molecular markers

Figure 3. Histogram of Kimura two-parameter genetic distances for (A) the cytochrome oxidase I and (B) the large ribosomal subunit (16S) data sets. Species and number of specimens used for intraspecific and interspecific distance calculations are detailed in Table 1.

opennotspecifiedAug 2013View details →

Figure 4. A in Phylogeny, phylogeography, and systematics of the American pea crab genus Calyptraeotheres Campos, 1990, inferred from molecular markers

Figure 4. A, median-joining haplotype network for cytochrome oxidase I (COI) mtDNA sequences of Calyptraeotheres garthi, including some samples of Calyptraeotheres hernandezi and Calyptraeotheres politus. Area of the circles is proportional to the number of individuals of each haplotype found. White dots represent missing, probably unsampled, haplotypes or extinct lineages. Lines between circles represent additional mutational steps. B, mismatch distributions of C. garthi. Solid lines indicate the observed distribution, and dashed lines indicate the expected distribution. C, Bayesian skyline plot based on COI sequences of C. garthi showing change in population size through time. The y-axis is the product of effective population size (Ne) and generation length (t) on a log scale. The heavy solid line is the median estimated under the assumption of a per site mutation rate of 1.66% million years-1, and the dotted lines indicate 95% highest posterior density regions. Abbreviations: ARI, Arica; CAR, Caraguatatuba; ICU, Isla Cubagua; MDP, Mar del Plata; PMO, Puerto Montt; RIA, Ría de San António; SCL, San Clemente; SOT, El Sótano.