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Fig. 8 in Understanding the color variability and resolving taxonomic confusion in the sea cucumber Isostichopus badionotus (Echinodermata, Holothuroidea): a revision of the genus Isostichopus
Fig. 8 (continued on next page). Color patterns and morphological variation of Isostichopus badionotus (Selenka, 1867) (DNA sequences and detailed information of some specimens are indicated in Table 1, see Photo ID column for correspondence). A–U, I'. Specimens with "Chips" color pattern from Bocas del Toro, Panamá (A–I), Neguanje, Colombia (J–L), La Guajira, Colombia (M–Q); juveniles from Neguanje, Colombia (R–U). V–B'. Specimens with "Uniform" pattern from Bocas del Toro (Panama) (V–X), La Guajira, Colombia (Y), Curaçao (Z), Magdalena, Colombia (A'–B'). C'–K'. Specimens with "Reticulated" pattern from Bocas del Toro, Panama (C'–E'), Juvenile from Neguanje, Colombia (F'), Punta Betin, Magdalena, Colombia (G'–I'), La Guajira, Colombia (J'–K'). L'–O'. Specimens with "Black and yellow" pattern from Bocas del Toro, Panamá (L'), Magdalena, Colombia (M'–O'). Photos: A–I, Q, V–X, C'–E', L', O' by G. Borrero; R–U by G. Ospina; J–L by E. Acosta; M–P, Y, J'–K' by E. Ortiz; Z, M' by M. González-Wangüemert; G'–I' by J. Gómez; and A'–B', N' by S. Zea. Scale bars = 10 mm.
Fig. 3D in Understanding the color variability and resolving taxonomic confusion in the sea cucumber Isostichopus badionotus (Echinodermata, Holothuroidea): a revision of the genus Isostichopus
Fig. 3D. Bayesian inference tree of mitochondrial 16S gene fragment. The numbers on the nodes indicate Bayesian posterior probability / Maximum Likelihood (bootstrap %) / Neighbor Joining (bootstrap %). A hyphen (-) indicates that the node was not recovered by a particular method. Specimen ID and color pattern designation as in Fig. 3A. Specimens of I. badionotus (Selenka, 1867) with unknown color pattern are indicated in black color.
Fig. 3C in Understanding the color variability and resolving taxonomic confusion in the sea cucumber Isostichopus badionotus (Echinodermata, Holothuroidea): a revision of the genus Isostichopus
Fig. 3C. Bayesian inference tree of mitochondrial COI-Fr2 gene fragment. The numbers on the nodes indicate Bayesian posterior probability / Maximum Likelihood (bootstrap %) / Neighbor Joining (bootstrap %). A hyphen (-) indicates that the node was not recovered by a particular method. Specimen ID and color pattern designation as in Fig. 3A. Specimens of I. badionotus (Selenka, 1867) from Brazil with unknown color pattern are indicated in black color.
Fig. 3A in Understanding the color variability and resolving taxonomic confusion in the sea cucumber Isostichopus badionotus (Echinodermata, Holothuroidea): a revision of the genus Isostichopus
Fig. 3A. Bayesian inference tree of concatenated sequences of the mitochondrial COI-Fr1 (Barcoding region), COI-Fr2 and 16S gene fragments. The numbers on the nodes indicate Bayesian posterior probability / Maximum Likelihood (bootstrap %) / Neighbor Joining (bootstrap %). A hyphen (-) indicates that a node was absent in the tree estimated by a particular method. Individuals are indicated by the field number, which includes the initial letter of the locality and the color pattern when available (see Table 1, Fig. 1). Text color meaning: green = Isosostichopus maculatus maculatus (Greeff, 1882); blue = I. maculatus phoenius (Clark, 1922); pink = I. badionotus (Selenka, 1867) Chips (CH) pattern; purple = Uniform (U) pattern; red = reticulated (R) pattern; orange = Black and Yellow (BY) pattern. Sequences from GenBank are indicated with their accession number and species ID as included in GenBank (see Table 1). Outgroup species: Apostichopus japonicus (Selenka, 1867) and Stichopus horrens Selenka, 1867.
Fig. 1 in Understanding the color variability and resolving taxonomic confusion in the sea cucumber Isostichopus badionotus (Echinodermata, Holothuroidea): a revision of the genus Isostichopus
Fig. 1 (continued on next page). Color patterns of species and subspecies of Isostichopus Deichmann, 1958. A–J. Isostichopus badionotus (Selenka, 1867). A. Pink background and dark brown spots (Chips pattern – CH) (BT99, Panamá). B. Close-up of A, note large dark brown spots and small dots. C. Light brown background and darker ocellar spots (CH pattern) (INV TEJ1125-Ma10, Colombia). D. Close-up of C, note large ocellar spots and small black dots. E. Uniform black background (Uniform pattern – U) (BT59, Panamá). F. Beige background color with a reticulum of darker brown and yellow papillae (Reticulated pattern – R) (USNM 1659460-BT20, Panamá). G. Close-up of F, reticulated pattern in detail. H. Reticulated pattern with brown papillae (R pattern) (INV TEJ1167-SM4R, Colombia). I. Close-up of H, reticulated pattern in detail. J. Black background and yellow papillae (Black and yellow pattern-BY) (INV TEJ1176-SM13, Colombia). K–Y. Isostichopus maculatus phoenius (Clark, (BI), Maximum Likelihood (ML), and Neighbour-Joining (NJ). BI and ML were performed, using the GTR evolutionary model and NJ using K2P distances. BI was performed with MrBayes ver. 3.2.6 (Ronquist & Huelsenbeck 2003); the data set was run twice, using four Markov chains for ten million generations; trees were sampled every 500th generation, the first 2.5 million generations were discarded, and a 50% majority tree was obtained. ML analysis was performed in MEGA X (Kumar et al. 2018); support was assessed with 1000 bootstrap reiterations.
Fig. 2 in Understanding the color variability and resolving taxonomic confusion in the sea cucumber Isostichopus badionotus (Echinodermata, Holothuroidea): a revision of the genus Isostichopus
Fig. 2 (see previous page). Ossicles of species and subspecies of Isostichopus Deichmann, 1958. A–H. Tables. A. Regular tables present in several parts of the body in the five species (1–2 = lateral view; 3 = top or dorsal view; 4 = ventral view). B. Large, regular tables, only present in I. maculatus maculatus (Greeff, 1882) (lateral view). C. Table with reduced disc, only present in the dorsal body wall of I. macroparentheses (Clark, 1922) adults (lateral view). D. Large tables with disc and spire modified, only present in the top of the dorsal papillae of I. maculatus maculatus – "modified maculatus tables" (lateral view, top view). E. Regular tables present in the ventral body wall and tube feet (top and lateral view). F. Tables with low and incomplete spires, present in the tentacles (top view). G. Tables with circular spire, several pillars, observed in the cloaca of I. fuscus (top and lateral view). H. Large tables with well-developed spires, several pillars forming a very dense and thick crown of spines, present in the mouth membrane and other internal organs (top and lateral view). I–T. Rods. I. Large thin C-shaped rods present in I. macroparentheses. J–K. Thin C, S-shaped rods present in the body wall, papillae and tube feet, and some internal organs. L. Thick C rods and worm-shaped rods present in the dorsal papillae of I. maculatus maculatus and I. maculatus phoenius (Clark, 1922). M. Simple rods present in several internal organs. N. Simple rods present in gonads. O. Simple rods present in the tentacles. P. Cross-shaped rods present in the intestine. Q. Branched rods present in several internal organs. R. Irregular plate-like branched rods present mostly in the anterior cloaca. S. Large, curved rods with quadrangular projections in the middle, present in the papillae. T. Large slightly or strongly curved rods with wide perforated expansions in the middle, present in the tube feet. U–X. Perforated plates. U. Perforated plates from papillae. V. Perforated plate from tube feet. W. End-plate. X. Tridimensional spheres only observed in the respiratory trees of I. macroparentheses. Photos by G. Borrero.
Fig. 3B in Understanding the color variability and resolving taxonomic confusion in the sea cucumber Isostichopus badionotus (Echinodermata, Holothuroidea): a revision of the genus Isostichopus
Fig. 3B. Bayesian inference tree of mitochondrial COI-Fr1 gene fragment. The numbers on the nodes indicate Bayesian posterior probability / Maximum Likelihood (bootstrap %) / Neighbor Joining (bootstrap %). A hyphen (-) indicates that the node was not recovered by a particular method. Specimen ID and color pattern designation as in Fig. 3A. Specimens of I. badionotus (Selenka, 1867) with unknown color pattern are indicated in black color.
Linked collectors and determiners for: Revision of Pazala Moore, 1888: The Graphium (Pazala) alebion and G. (P.) tamerlanus Groups, with Notes on Taxonomic and Distribution Confusions (Lepidoptera: Papilionidae).
Natural history specimen data linked to collectors and determiners held within, "Revision of Pazala Moore, 1888: The Graphium (Pazala) alebion and G. (P.) tamerlanus Groups, with Notes on Taxonomic and Distribution Confusions (Lepidoptera: Papilionidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/5973e41e-4808-4a2f-a220-7afe5c899cff">https://bionomia.net/dataset/5973e41e-4808-4a2f-a220-7afe5c899cff</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/5973e41e-4808-4a2f-a220-7afe5c899cff">https://gbif.org/dataset/5973e41e-4808-4a2f-a220-7afe5c899cff</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: One hundred and sixty years of taxonomic confusion resolved: Belonocnema (Hymenoptera: Cynipidae: Cynipini) gall wasps associated with live oaks in the USA.
Natural history specimen data linked to collectors and determiners held within, "One hundred and sixty years of taxonomic confusion resolved: Belonocnema (Hymenoptera: Cynipidae: Cynipini) gall wasps associated with live oaks in the USA". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/9182a649-923b-4a69-bac0-d41873ded32e">https://bionomia.net/dataset/9182a649-923b-4a69-bac0-d41873ded32e</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/9182a649-923b-4a69-bac0-d41873ded32e">https://gbif.org/dataset/9182a649-923b-4a69-bac0-d41873ded32e</a>. Formatted as a Frictionless Data package.
Supplemental Data for: Lineage diversification and rampant hybridization among subspecies explain taxonomic confusion in the endemic Hawaiian fern Polypodium pellucidum
<p><strong><span>Premise:</span></strong><span> <em>Polypodium pellucidum</em>, a fern endemic to the Hawaiian Islands, encompasses a broad spectrum of morphological and ecological variation, suggesting a complex history involving divergence and hybridization. In contrast to angiosperm systems, spore dispersal in ferns presents a unique opportunity to study how highly dispersible organisms diversify in the dynamic landscape of the archipelago.</span></p> <p><strong><span>Key Results: </span></strong><span>We infer <em>P. pellucidum</em> is monophyletic, dispersing to the Hawaiian archipelago 11.53 to 7.77 Mya, with diversification into extant clades 5.66 to 4.73 Mya. We identify four non-hybrid clades with unique morphologies, ecological niches, and distributions. Additionally, we elucidate several intraspecific hybrid combinations and evidence for undiscovered or extinct 'ghost' lineages contributing to extant hybrids populations. </span></p> <p><strong><span>Conclusions:</span></strong><span> We provide a roadmap for revising the taxonomy of <em>P. pellucidum</em> to account for cryptic lineages and intraspecific hybrids. Geologic succession of the Hawaiian Islands through cycles of volcanism, vegetative succession, and erosion has determined the available habitats and distribution of ecologically specific divergent clades within <em>P. pellucidum, </em>with intraspecific hybrids arising as a result of ecological and or geological transitions, often persisting after the local extinction of their progenitors. This research contributes to our understanding of the evolution of Hawaii's diverse fern flora and allows for better conservation efforts that are often complicated by the presence of cryptic taxa and hybridization.</span></p>
Fig. 8 in Understanding the color variability and resolving taxonomic confusion in the sea cucumber Isostichopus badionotus (Echinodermata, Holothuroidea): a revision of the genus Isostichopus
Fig. 8 (continued).
Supplemental data for: Lineage diversification and rampant hybridization among subspecies explain taxonomic confusion in the endemic Hawaiian fern Polypodium pellucidum
Open the record for dataset details and reuse information.
FIGURES 1–6 in Taxonomic confusion among gall-thrips and host-plants, with three new combinations from the genus Austrothrips (Thysanoptera, Phlaeothripidae)
FIGURES 1–6. Ocnothrips cochinchinensis. (1) head; (2) antenna; (3) pelta and tergites I–II; (4) pronotum; (5) mes and metanotum; (6) type slides.
FIGURE 3. G in Revision of Pazala Moore, 1888: The Graphium (Pazala) alebion and G. (P.) tamerlanus Groups, with Notes on Taxonomic and Distribution Confusions (Lepidoptera: Papilionidae)
FIGURE 3. G. (P.) alebion (Gray, [1853]); upperside above, underside below; scale bar = 10 mm. A–B: ♂, Nanjing, Jiangsu, China; C: ♀, ditto; D: ♀, Jurong, Jiangsu, China; A and C © Jian-Qing Zhu (Shanghai Zoological Park, Shanghai, China).
FIGURE 9. G in Revision of Pazala Moore, 1888: The Graphium (Pazala) alebion and G. (P.) tamerlanus Groups, with Notes on Taxonomic and Distribution Confusions (Lepidoptera: Papilionidae)
FIGURE 9. G. (P.) tamerlanus (Oberthür, 1876); upperside above, underside below; scale bar = 10 mm. A–C: ssp. tamerlanus (Oberthür, 1876), ♂(A–B), Baoxing, Sichuan, China, ♀(C), Pingwu, Sichuan, China, © Peking University; D–F: ssp. kansuensis (O. Bang-Haas, 1933), ♂(D–E), ♀(F), Ningshan, Shaanxi, China.
FIGURE 7 in Revision of Pazala Moore, 1888: The Graphium (Pazala) alebion and G. (P.) tamerlanus Groups, with Notes on Taxonomic and Distribution Confusions (Lepidoptera: Papilionidae)
FIGURE 7. Male genitalia of G. (P.) parus (Nicéville, 1900) from Yulong Xueshan, Lijiang, N.W. Yunnan, China; scale bar = 1.0 mm. All: genitalia as a whole, R.: lateral view of ring, TSU: dorsal view of tegumen, socii and uncus, V.: right valve, Ae.: lateral view of aedeagus, Ju.: ventral view of juxta.
FIGURE 4 in Revision of Pazala Moore, 1888: The Graphium (Pazala) alebion and G. (P.) tamerlanus Groups, with Notes on Taxonomic and Distribution Confusions (Lepidoptera: Papilionidae)
FIGURE 4. Male genitalia of G. (P.) alebion (Gray, [1853]) from Nanjing, Jiangsu, China; scale bar = 1.0 mm. All: genitalia as a whole, R.: lateral view of ring, TSU: dorsal view of tegumen, socii and uncus (lines and arrows indicate the distance measured), V.: right valve, Ae.: lateral view of aedeagus, Ju.: ventral view of juxta.
FIGURE 6. G in Revision of Pazala Moore, 1888: The Graphium (Pazala) alebion and G. (P.) tamerlanus Groups, with Notes on Taxonomic and Distribution Confusions (Lepidoptera: Papilionidae)
FIGURE 6. G. (P.) parus (Nicéville, 1900); upperside above, underside below; scale bar = 10 mm. A: ♂, Weixi, Yunnan, China; B: ♂, Zhongdian, Yunnan, China; C–D: ♂, Yulong Xueshan, Yunnan, China; E: ♀, ditto; ♂, F: Baoxing, Sichuan, China.
FIGURE 10 in Revision of Pazala Moore, 1888: The Graphium (Pazala) alebion and G. (P.) tamerlanus Groups, with Notes on Taxonomic and Distribution Confusions (Lepidoptera: Papilionidae)
FIGURE 10. Male genitalia of G. (P.) tamerlanus tamerlanus (Oberthür, 1876) from Baoxing, Sichuan, China; scale bar = 1.0 mm. All: genitalia as a whole, R.: lateral view of ring, TSU: dorsal view of tegumen, socii and uncus, V.: right valve, Ae.: lateral view of aedeagus, Ju.: ventral view of juxta.
Data from: Barcoding snakeheads (Teleostei, Channidae) revisited: discovering greater species diversity and resolving perpetuated taxonomic confusions
Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group.
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International Brain Laboratory public data
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OpenNeuro
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