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FIGURE 2. Majority rule consensus Bayesian tree created from the remaining 7500 in Preliminary use of DNA sequences for Dohrniphora (Diptera: Phoridae) phylogeny and taxonomy
FIGURE 2. Majority rule consensus Bayesian tree created from the remaining 7500 trees after burn-in. Branch support values are posterior probabilities.
FIGURE 1 in Preliminary use of DNA sequences for Dohrniphora (Diptera: Phoridae) phylogeny and taxonomy
FIGURE 1. Strict consensus tree of four equally parsimonious trees derived from ND1, COI, CAD, and 16S gene regions (2815 bp). Tree length = 3238 steps. CI = 0.48. RI = 0.43. Branch support values are bootstrap (%)/ Bremer support indicies.
Data underlying RSOS-210474: Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for Lantern Shark taxonomy (Chondrichthyes: Etmopteridae)
<p>After initial detection of target archival DNA of a 116 year old syntype specimen of the Smooth Lanternshark, <i>Etmopterus pusillus</i> in a single stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4,599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has a 12 times coverage and a length of 16,741 basepairs. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple <i>E. pusillus</i> samples from various distant localities as well as sequences from a morphological similar species, the Shortfin Smooth Lantern Shark <i>Etmopterus joungi</i>. Results confirm the almost global distribution of <i>E. pusillus</i> and suggest <i>E. joungi </i>to be a junior synonym of <i>E. pusillus</i>. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet-collection type specimen for taxonomy.</p>
Figure 6 in Species boundaries in Philaethria butterflies: an integrative taxonomic analysis based on genitalia ultrastructure, wing geometric morphometrics, DNA sequences, and amplified fragment length polymorphisms
Figure 6. Evolutionary relationships of Philaethria based on DNA sequences from specimens of Philaethria wernickei (southern population; Atlantic Rain Forest) and individuals previously described as Philaethria pygmalion (northern population; Amazon Forest), depicted by the green shading (grey in print version). Philaethria diatonica and Philaethria dido were used to root the tree. Purple (grey) circles represent individuals from the Atlantic Rain Forest and black triangles indicate samples from the Amazon Basin. A, consensus Bayesian tree based on mitochondrial (cytochrome oxidase subunit I, Co-I) and nuclear [triose-phosphate isomerase (Tpi), wingless (Wg), and tyrosine hydroxylase (TH)] DNA sequences. Posterior probabilities are shown above branches. Bootstrap node support based on maximum likelihood analysis is indicated below branches. Asterisks indicate node support lower than 70%. B, Median-joining network based on mtDNA and nuclear loci sequence data describing the relationship between haplotypes (purple indicates southern population, and black, northern population). Nucleotide substitutions are shown on the branches as small transverse bars. Circle size is proportional to haplotype frequency.
Figure 2 in Species boundaries in Philaethria butterflies: an integrative taxonomic analysis based on genitalia ultrastructure, wing geometric morphometrics, DNA sequences, and amplified fragment length polymorphisms
Figure 2. Location of linear measurements (A) and schematic representation (B, C) of Philaethria wings showing veins and landmarks adopted in this study. A, hind wing dorsal and ventral (detail) views, showing measured vectors. B, fore wing. C, hind wing. See Appendix S2 for details on morphological definitions of landmarks.
Figure 4 in Species boundaries in Philaethria butterflies: an integrative taxonomic analysis based on genitalia ultrastructure, wing geometric morphometrics, DNA sequences, and amplified fragment length polymorphisms
Figure 4. Linear variation in hind wing size and medial postdiscal bands for Philaethria wernickei and Philaethria pygmalion (left column), and in relation to latitude when samples from the two species are combined (right column). A, D, hind wing length. B, E, hind wing length/postdiscal band ratio (AB/DE). C, F, inner and medial postdiscal band ratio (EF/DF). See Fig. 2A for details on wing position of corresponding measurements. Numbers above boxes indicate the number of specimens measured in each class.
Figure 1 in Species boundaries in Philaethria butterflies: an integrative taxonomic analysis based on genitalia ultrastructure, wing geometric morphometrics, DNA sequences, and amplified fragment length polymorphisms
Figure 1. Geographical distributions of Philaethria wernickei and Philaethria pygmalion, and corresponding variation in male genitalia ultrastructure and ventral hind wing colour. A, shaded areas show distribution ranges proposed by Constantino & Salazar (2010) for P. wernickei (green) and P. pygmalion (red); green circles and red triangles represent collection localities of the material analysed in this study. B, variation in valva's cucullus, external view. C, variation in the colour pattern of hind wing surface, ventral view.
Figure 3 in Species boundaries in Philaethria butterflies: an integrative taxonomic analysis based on genitalia ultrastructure, wing geometric morphometrics, DNA sequences, and amplified fragment length polymorphisms
Figure 3. Male genitalia of Philaethria wernickei and Philaethria pygmalion. A, P. wernickei, lateral view. B, P. pygmalion, lateral view. C, schematic representation of generalized genitalia for both, in lateral view. D, F, H, J, scanning electron micrographs of P. wernickei; E, G, I, K, scanning electron micrographs of P. pygmalion. D, E, ampulla external view. F, G, ampulla internal view. H, I, ampulla ornamentation in detail. J, K, fultura inferior distal end. Scale bars = 150, 30, and 100 μm, for D–G, H–I, and J–K, respectively.
Figure 8 in Species boundaries in Philaethria butterflies: an integrative taxonomic analysis based on genitalia ultrastructure, wing geometric morphometrics, DNA sequences, and amplified fragment length polymorphisms
Figure 8. STRUCTURE-based clustering of Philaethria wernickei individuals from low (0–10°S) to high (20–25°S) latitudes (north and south populations, respectively) based on amplified fragment length polymorphism loci. Each individual is represented by a vertical line divided into segments of different colour that represent genetic clusters (K) from 1–4.
Figure 7 in Species boundaries in Philaethria butterflies: an integrative taxonomic analysis based on genitalia ultrastructure, wing geometric morphometrics, DNA sequences, and amplified fragment length polymorphisms
Figure 7. Multilocus consensus Bayesian tree based on cytochrome oxidase subunit I (Co-I), triose-phosphate isomerase (Tpi), wingless (Wg), and tyrosine hydroxylase (TH) sequences from specimens of Philaethria wernickei (Atlantic Rain Forest, purple circles) and individuals previously described as Philaethria pygmalion (Amazon Forest, black triangles) depicted by the green shading (grey in print version). Philaethria pygmalion and Philaethria dido were used to root the tree. Posterior probabilities are shown above branches and bootstrap node support based on maximum likelihood analysis is indicated below branches. Asterisks indicate node support lower than 70%.
FIGURE 2 in Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus
FIGURE 2. Scatter plot for the number of transitions (s) and transversions (v) versus TN distance of ITS1 and ITS2 in pairwise comparisons between spider mites.
FIGURE 1 in Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus
FIGURE 1. Scatter plot for the number of transitions (s) and transversions (v) versus TN distance of COI gene in pairwise comparisons between spider mites, (a) all codon positions; (b) third codon position.
FIGURE 5 in Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus
FIGURE 5. ML tree based on ITS2 sequences. Sequence data for the ITS2 was aligned from a total of 23 individuals from nine species. Demodex folliculorum and D. canis (GenBank nos. AM904564 and GU299785, respectively) were selected as the outgroups of ITS2 tree. Numbers on the branches indicate the percentage bootstrap values (>50) based on NJ bootstrapping with ML settings (1,000 replicates).
FIGURE 3 in Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial DNA and nuclear gene sequences
FIGURE 3. Phylogeography of Gongylomorphus skinks in Mauritius based on 1102bp of combined mtDNA sequence data. Lower-case letters refer to collection localities in Fig. 1 and Table 1. Haplotype networks are drawn with the areas of circles proportional to number of individuals observed; dots represent unobserved haplotypes, and lines between them each represent a single nucleotide substitution. Filled circles represent samples collected from extant populations, and open circles samples from extinct ones.
FIGURE 2 in Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial DNA and nuclear gene sequences
FIGURE 2. Bayesian maximum likelihood tree for extinct and extant Gongylomorphus skinks and a range of outgroup taxa, based on 1473 bp of combined mitochondrial (12S rRNA, cytochrome b) and nuclear (c-mos) DNA sequence. Numbers adjacent to nodes indicate: Bayesian posterior probability/MP bootstrap support values for analyses conducted using all samples (top line, if present), and only a subset of samples with full-length sequence for all three genes (bottom or only line). Letters a-s indicate the sampling locality in Mauritius for each specimen (Fig. 1, Table 1). Letters in bold are specimens which were sequenced for all three genes. Letters suffixed by an * are specimens that represent extinct populations.
FIGURE 1 in Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial DNA and nuclear gene sequences
FIGURE 1. (A) Map of the west Indian Ocean showing the location of the Mascarene islands. (B) Mauritius showing collection localities for Gongylomorphus bojerii skinks used in the present study. (C) Mauritius showing collection localities for Gongylomorphus 'orange-tail' and G. fontenayi skinks used in the present study. * indicates extinct populations.
Figure 6 in DNA sequencing reveals unexpected Recent diversity and an ancient dichotomy in the American marsupial genus Marmosops (Didelphidae: Thylamyini)
Figure 6. Lateral view of posterior braincase of Marmosops (Sciophanes) pinheiroi (A, AMNH 267345) and Marmosops (Marmosops) noctivagus (B, MUSM 13288) illustrating diagnostic subgeneric morphologies of the squamosal (green) and petrosal (yellow). Abbreviations: als, alisphenoid; exo, exoccipital; lspc, lateral surface of pars canalicularis (of petrosal); par, parietal; pet, petrosal; sps, sulcus for the prootic sinus (of petrosal); sq, squamosal; srza, squamosal root of zygomatic arch; ssf, subsquamosal foramen.
Figure 5 in DNA sequencing reveals unexpected Recent diversity and an ancient dichotomy in the American marsupial genus Marmosops (Didelphidae: Thylamyini)
Figure 5. Phylogeny of Marmosops obtained by Bayesian analysis of a concatenated-gene [cytochrome b + breast cancer activating 1 (CYTB + BRCA1)] data set. Terminals are putative species recovered by general mixed Yule coalescent model analyses of CYTB plus Marmosops juninensis (uniquely represented by a BRCA1 sequence). Filled semicircles at internal nodes indicate high support (posterior probability ≥ 0.95, bootstrap ≥ 75%). Abbreviations: BI, Bayesian inference; ML, maximum likelihood.
Figure 3 in DNA sequencing reveals unexpected Recent diversity and an ancient dichotomy in the American marsupial genus Marmosops (Didelphidae: Thylamyini)
Figure 3. Collection localities for sequenced specimens of Atlantic Forest species included in subgenus II of Marmosops. Progressively darker shading indicates the following elevations: pale grey ≥ 500 m, medium grey ≥ 1000 m, and dark grey ≥ 2000 m.
Figure 2 in DNA sequencing reveals unexpected Recent diversity and an ancient dichotomy in the American marsupial genus Marmosops (Didelphidae: Thylamyini)
Figure 2. Collection localities for sequenced specimens of subgenus I of Marmosops. Progressively darker shading indicates the following elevations: pale grey ≥ 500 m, medium grey ≥ 1000 m, dark grey ≥ 2000 m, and darkest grey ≥ 3000 m.
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