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821 results for “Molecular Systematics”
Figure 1 in A global phylogeny of Elysia Risso, 1818 (Gastropoda: Heterobranchia): molecular systematic insights focusing on European taxa and description of a new species
Figure 1. Molecular phylogeny of worldwide Elysia species rooted on genus Bosellia (not shown). Topology is based on Bayesian inference analysis of concatenated dataset (H3 + COI + 16S + 28S). Only one specimen per species is shown according to species delimitation analyses. Bold red species names indicate the species sequenced in this study that are present in European waters. Significant support values are given as ML bootstrap percentages (BS, below branch) and BI posterior probabilities (PP, above branch). Asterisks indicate complete support (PP = 1.0, BS = 100%). Vertical grey bars indicate specimens grouped as species entities by ABGD, GMYC and bPTP methods based on the COI gene. Unfilled vertical bars indicate the specimens grouped as species based on the 16S gene.
Figure 2 in A global phylogeny of Elysia Risso, 1818 (Gastropoda: Heterobranchia): molecular systematic insights focusing on European taxa and description of a new species
Figure 2. Histogram of pairwise genetic COI distances (Kimura parameter) among 638 sequences including all available National Center for Bioinformatics (NCBI) sequences for Elysia, showing barcoding gap; the arrow indicates the threshold that allows to distinguish intraspecific (left) and interspecific (right) distances for the COI region, based on ABGD analyses.
FIGURE 3 in Molecular systematics of the North American chub genus Macrhybopsis (Teleostei: Cyprinidae)
FIGURE 3. Bayesian tree for ND2 in the Platygobio-Macrhybopsis clade and two representatives of the shiner clade (L. umbratilis and H. winchelli). Outgroups excluded. Labels at terminal nodes = haplotype designation; parentheses = locality numbers (Fig. 1). Bold and slightly enlarged locality numbers = M. australis in the Red River clade and M. tetranema in the Northern Plains clade. Asterisks above internal nodes = Bayesian support>0.95; numbers below nodes = maximum parsimony bootstrap support>50%.
FIGURE 2. Bayesian tree for S7 intron 1 in Molecular systematics of the North American chub genus Macrhybopsis (Teleostei: Cyprinidae)
FIGURE 2. Bayesian tree for S7 intron 1 in the Platygobio-Macrhybopsis clade and two representatives of the shiner clade (L. umbratilis and H. winchelli). Outgroups excluded. Labels at terminal nodes = haplotype designation followed by locality numbers in Fig. 1; those beginning with GU or JX are accession numbers for sequences obtained from GenBank. Terminal nodes identified only by river system are Eisenhour's (2004) M. hyostoma. Numbers above internal nodes = Bayesian support ±0.90 (asterisks,>0.95); below nodes = maximum parsimony bootstrap support>50%.
FIGURE 4 in Molecular systematics of the North American chub genus Macrhybopsis (Teleostei: Cyprinidae)
FIGURE 4. Distribution of primary ND2 clades (Fig. 3) in the M. aestivalis complex of species. Clades not designated by genus and species names are from the currently recognized M. hyostoma, except for the Red River clade, which includes both M. australis and M. hyostoma, and the Northern Plains clade, which includes the Arkansas River endemic, M. tetranema with putative M. hyostoma. Question marks signify areas where we failed to collect (Tennessee River) or did not attempt to collect (lower Mississippi River system) specimens although there are historical records of occurrence for representatives (M. cf. hyostoma) of the complex.
FIGURE 1 in Molecular systematics of the North American chub genus Macrhybopsis (Teleostei: Cyprinidae)
FIGURE 1. Sampling localities for Macrhybopsis (see Appendix). Rivers and basins mentioned in the text are as follows: 1 Rio Grande; 2 Pecos; 3 Guadalupe; 4–5 Colorado; 6 Brazos; 7 Angelina; 8 Sabine; 9–16 Red; 17 Pearl; 18 Pascagoula; 19–21 Escambia to Choctawhatchee; 22–23 Mobile Basin below the Fall Line; 24 Tallapoosa; 25–26 Mobile Basin above the fall line; 27 South Canadian; 31 Ninnescah; 27–31 Arkansas; 32 Ouachita; 33 White; 34 Kansas; 35–39 Missouri; 40 Des Moines; 42– 44 Wabash; 45 Licking; 46 South Fork Kentucky; 47 Green.
FIGURE 10. A in Molecular systematics of the heteronemertean genus Dushia (Nemertea Pilidiophora), with descriptions of D. wijnhoffae sp. nov. and D. nigra species complex comb. nov.
FIGURE 10. A Bayesian tree of 42 species of the heteronemertean family Lineidae based on concatenated 16 rRNA, COI, 18S rRNA, 28S rRNA, and histone H3 genes. Support values were generated by a separate partitioned ML bootstrap (BS) analysis with 1000 replicates and posterior probability (PP) of a separate partitioned Bayesian analysis; node support is indicated by BS/PP.
FIGURE 2 in Molecular systematics of the heteronemertean genus Dushia (Nemertea Pilidiophora), with descriptions of D. wijnhoffae sp. nov. and D. nigra species complex comb. nov.
FIGURE 2. Dushia wijnhoffae Schwartz & Norenburg sp. nov. Photomicrographs of transverse sections (A, C–E) (paratype, USNM 1594813), and tangential section (B) (holotype, USNM 1594812). (A) Epidermis and cutis. (B) Dermal muscle components; diagonal muscles are indicated by ">". (C) Section through gonad with dorsoventral muscles and horizontal muscle. (D) Precerebral blood vessels and rhynchodaeum. (E) Cross section through foregut region with prominent longitudinal muscle plate. Scale bars: A, C, D = 100 µm, B = 50 µm, E = 200 µm. Abbreviations: cu, cutis; cv, cephalic vessel; dcm, dermal circular muscle; dlm, dermal longitudinal muscle; dv, dorsoventral muscle fibers; ep, epidermis; fg, foregut; gc, gland cells; go, gonad; hm, horizontal muscle; ilm, body-wall inner longitudinal muscle layer; in, intestinal lumen; lmp, longitudinal muscle plate; lnc, lateral nerve cord; mcm, body-wall middle circular muscle layer; olm, body-wall outer longitudinal muscle layer; rc, rhynchocoel; rd, rhynchodaeum.
FIGURE 9. A in Molecular systematics of the heteronemertean genus Dushia (Nemertea Pilidiophora), with descriptions of D. wijnhoffae sp. nov. and D. nigra species complex comb. nov.
FIGURE 9. A phylogenetic tree of Dushia nigra species complex comb. nov., resulting from the maximum-likelihood analysis ofpartial sequence (513 bp) of the cytochrome c oxidase subunit I gene from 10 specimens collected in Kakeroma, Japan, nine specimens in Okinawa, Japan; and one specimen from Van Phong Bay, Vietnam (Chernyshev 2016; Sundberg et al. 2016); Dushia wijnhoffae sp. nov. is used as an outgroup. Text colors represent body colors of specimens, and numbers near nodes indicate maximum-likelihood bootstrap support value. Vertical bars indicate the results of TCS, ABGD, and PTP analyses.
FIGURE 8 in Molecular systematics of the heteronemertean genus Dushia (Nemertea Pilidiophora), with descriptions of D. wijnhoffae sp. nov. and D. nigra species complex comb. nov.
FIGURE 8. Three haplotype networks (A–C) of Dushia nigra species complex comb. nov., generated by statistical parsimony analysis using partial sequence (513 bp) of the cytochrome c oxidase subunit I gene from 10 specimens collected in Kakeroma, Japan (solid), nine specimens in Okinawa, Japan (oblique stripes); and one specimen from Van Phong Bay, Vietnam (Chernyshev 2016; Sundberg et al. 2016) (vertical stripe). Three kinds of colorations (black, brown, and orange) indicate their body color.
FIGURE 7 in Molecular systematics of the heteronemertean genus Dushia (Nemertea Pilidiophora), with descriptions of D. wijnhoffae sp. nov. and D. nigra species complex comb. nov.
FIGURE 7. Dushia nigra (Stimpson, 1855) species complex comb. nov., transverse section of proboscis (A), showing two, unequal muscle crosses (B, C); post-overlapping parts of muscle crosses are indicated by arrowheads ICHUM 3457. Scale bars: A = 500 µm, B, C = 200 µm. Abbreviations: ge, glandular epithelium; isl, inner strand of proboscis inner longitudinal muscle layer; pd, proboscis diagonal muscle layer; pic, proboscis inner circular muscle layer; pil, proboscis inner longitudinal muscle layer; poc, proboscis outer circular muscle layer; pol, proboscis outer longitudinal muscle layer.
FIGURE 1 in Molecular systematics of the heteronemertean genus Dushia (Nemertea Pilidiophora), with descriptions of D. wijnhoffae sp. nov. and D. nigra species complex comb. nov.
FIGURE 1. Images of Dushia spp., taken in life. (A) Dushia wijnhoffae Schwartz & Norenburg sp. nov. from Puerto Rico. (B–F) Dushia nigra (Stimpson, 1855) species complex comb. nov.: (B) black form, ICHUM 3457, from Onna, Okinawa, Japan; (C) orange form, from Nakijin, Okinawa, caudal cirrus not pictured; (D) brown form, from Kakeroma, Japan; (E, F) black form from Okinawa, showing body fragments regenerating caudal cirrus, 3 days (E) and 10 days (F) after amputation. Scale bars: A–D = 1 cm, E, F = 500 µm. Abbreviations: ao, apical organs; cc, caudal cirrus; cf, horizontal cephalic furrow.
FIGURE 5 in Molecular systematics of the heteronemertean genus Dushia (Nemertea Pilidiophora), with descriptions of D. wijnhoffae sp. nov. and D. nigra species complex comb. nov.
FIGURE 5. Dushia nigra (Stimpson, 1855) species complex comb. nov., transverse sections (A–D, F) (ICHUM 3457), (E) (USNM 1107399). (A) Intestinal region, showing dorsoventral muscles, gonad, and associated horizontal muscles. (B) Rhynchodaeum opening and pre-rhynchostomal blood lacuna. (C) Precerebral region, showing rhynchodeal sphincter (indicated by arrow head). (D) Dorsal cerebral commissure. (E) Pseudocnidae of the proboscis. (F) One of the two muscle crosses between the proboscis circular muscle layer and the endothelium (indicated by two arrow heads). Scale bars: A, B, D = 100 µm, C, E, F = 50 µm. Abbreviations: an, anterior peripheral nerve; cl, cephalic lacuna; cv, cephalic vessel; dg, dorsal ganglion; dv, dorsal ventral muscles of intestinal region; go, gonad; hm, horizontal muscles associated with gonad; ilm, inner longitudinal muscles of body wall; pc, pseudocnidae; pcm, proboscis circular muscle layer; pil, proboscis inner longitudinal muscle layer; pn, proboscis nerve; pnp, proboscis nerve plexus; pol, proboscis outer longitudinal muscle layer; rc, rhynchocoel; rd, rhynchodaeum.
FIGURE 4 in Molecular systematics of the heteronemertean genus Dushia (Nemertea Pilidiophora), with descriptions of D. wijnhoffae sp. nov. and D. nigra species complex comb. nov.
FIGURE 4. Dushia nigra (Stimpson, 1855) species complex comb. nov., transverse sections (A, C–F) (ICHUM 3457), (B) (USNM 1107399). (A) Arrangement of the epidermis and cutis. (B) Oblique section through dermal muscle layers showing dermal gland cells, dermal longitudinal, circular, and associated lattice muscles, and epidermis. (C) Organization of body wall in foregut region, nephridial tubules, and one of the numerous efferent ducts. (D) Precerebral region, showing musculature, rhynchodaeum, and cephalic vessels. (E) Proboscis insertion. (F) Longitudinal muscular plate and nephridial tubules. Scale bars: A, C, F = 50 µm, B, D, E = 100 µm. Abbreviations: cu, cutis; cv, cephalic vessel; dc, dermal gland cells; dcm, dermal circular muscle; ddf, dermal diagonal muscle fibers; dlm, dermal longitudinal muscle; ed, efferent duct; ep, epidermis; ex, excretory collecting tubule; ilm, body-wall inner longitudinal muscle layer; lmp, longitudinal muscle plate; mcm, body-wall middle circular muscle layer; mo, mouth; olm, body-wall outer longitudinal muscle layer; nt, nephridial tubules; pr, proboscis; rd, rhynchodaeum.
FIGURE 3 in Molecular systematics of the heteronemertean genus Dushia (Nemertea Pilidiophora), with descriptions of D. wijnhoffae sp. nov. and D. nigra species complex comb. nov.
FIGURE 3. Dushia wijnhoffae Schwartz & Norenburg sp. nov. (A, B, D) Photomicrographs of transverse sections (paratype, USNM 1594813); (C) photomicrograph of anesthetized animal with cephalic furrows reflected back to expose ciliated glandular ridge; the specimen was destroyed after examination and not extant. (A) Organization of the cerebral ganglia region showing dorsal and ventral ganglia and positions of Bürger type III cells, neurocord cell and neurocord. (B) ×40 magnification of Bürger type III cell and neurocord cell in A. (C) Ciliated and gland cell ridge of cephalic furrow marked by arrow heads. (D) Transverse section through glandular ridge in C, arrow heads mark the cells with elongated cilia, asterisks indicate gland cells. Scale bars: A, B, D = 100 µm, C = 500 µm. Abbreviations: b3, Bürger type III neural cell; cf, cephalic furrow; lnc, lateral nerve cord; nc, neurocord cell; vg, ventral ganglion.
FIGURE 6 in Molecular systematics of the heteronemertean genus Dushia (Nemertea Pilidiophora), with descriptions of D. wijnhoffae sp. nov. and D. nigra species complex comb. nov.
FIGURE 6. Dushia nigra (Stimpson, 1855) species complex comb. nov. Photomicrographs of transverse sections (A–D) (ICHUM 3457) and frontal sections (E, F) (USNM 1107399). (A) Ventral rhynchocoel wall in foregut region. (B) Dorsal ganglion showing Bürger type III neural cells and neurocord cells. (C) Neurocord cells. (D) Transverse section of cephalic furrow posterior to cerebral organ opening showing ciliated cells with elongated cilia (arrow heads) and gland cells (asterisks). (E) Frontal section of intestinal regions showing arrangement of gonads and intestinal diverticula. (F) Spermatozoa. Scale bars: A, B, D, E = 100 µm, C = 50 µm, F = 3 µm. Abbreviations: b3, Bürger type III neural cell; cf, cephalic furrow; cu, cutis; dg, dorsal ganglion; dv, dorsal ventral muscle; fg, foregut lumen; go, gonad; ilm, inner longitudinal muscle; in, lumen of the intestine;; lnc, lateral nerve cord; mcm, middle circular muscle; nc, neurocord cell; olm, outer longitudinal muscle; pr, proboscis; rc, rhynchocoel; rcc, rhynchocoel circular muscle; rcl, rhynchocoel longitudinal muscle, rv, rhynchocoel villus.
Fig. 3 in New insights into the systematics and molecular phylogeny of the Malagasy snake genus Liopholidophis suggest at least one rapid reversal of extreme sexual dimorphism in tail length
Fig. 3 Head drawings of Liopholidophis oligolepis sp. nov. (holotype, ZSM 153/2005) in (a) dorsal and (b) lateral view
Fig. 1 in New insights into the systematics and molecular phylogeny of the Malagasy snake genus Liopholidophis suggest at least one rapid reversal of extreme sexual dimorphism in tail length
Fig. 1 Phylogenetic tree of all Liopholidophis species based on sequences of three mitochondrial and one nuclear gene (16S rRNA, cytb, COI and c-mos). For L. baderi no 16S sequence was available. Bayesian posterior probabilities (10 million generations) are given above branches, parsimony bootstrap values (2,000 replicates) below branches. The relation of tail length/snout-vent length (red: female, blue: male) is given for all species of Liopholidophis, and for Liophidium torquatum, on the right of the species names. Reconstructed values for nodes are given at the branches, as results of parsimony/maximum likelihood (95% confidence interval). The lower figure shows the same tree with sexual dimorphism in relative tail length plotted on taxa (expressed as ratio of relative tail length of males/ females). Ancestral values calculated on ML-reconstructed values for males and females. Symbols show origin (>) and reversal (<) of extreme dimorphism (values 0.43-0.53, i.e. females having relative tail lengths roughly half that of males or lower)
Fig. 4 in Systematics and phylogenetic species delimitation within Polinices s.l. (Caenogastropoda: Naticidae) based on molecular data and shell morphology
Fig. 4 NeighborNet network based on the concatenated data set (COI, 16S, 18S, 28S, H3). Bootstrap values are indicated
Fig. 5 in Molecular and phytochemical systematics of the subtribe Hypochaeridinae (Asteraceae, Cichorieae)
Fig. 5 Overview of the distribution of hypocretenolides within the phylogenetic context of the Hypochaeridinae
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