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Jon Mallatt - One of the best experts on this subject based on the ideXlab platform.
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Ribosomal RNA genes and deuterostome phylogeny revisited: more cyclostomes, elasmobranchs, reptiles, and a brittle star.
Molecular Phylogenetics and Evolution, 2007Co-Authors: Jon Mallatt, Christopher J. WinchellAbstract:This is an expanded study of the relationships among the deuterostome animals based on combined, nearly complete 28S and 18S rRNA genes (>3925 nt.). It adds sequences from 20 more taxa to the approximately 45 sequences used in past studies. Seven of the new taxa were sequenced here (brittle star Ophiomyxa, lizard Anolis, turtle Chrysemys, sixgill shark Hexanchus, electric ray Narcine, Southern Hemisphere lamprey Geotria, and Atlantic hagfish Myxine for 28S), and the other 13 were from GenBank and the literature (from a chicken, dog, rat, human, three lungfishes, and several ray-finned fishes, or Actinopterygii). As before, our alignments were based on secondary structure but did not account for base pairing in the stems of rRNA. The new findings, derived from likelihood-based tree-reconstruction methods and by testing hypotheses with parametric bootstrapping, include: (1) brittle star joins with sea star in the echinoderm clade, Asterozoa; (2) with two hagfishes and two lampreys now available, the cyclostome (jawless) fishes remain monophyletic; (3) Hexanchiform sharks are monophyletic, as Hexanchus groups with the frilled shark, Chlamydoselachus; (4) turtle is the sister taxon of all other amniotes; (5) bird is closer to the lizard than to the mammals; (6) the bichir Polypterus is in a monophyletic Actinopterygii; (7) Zebrafish Danio is the sister taxon of the other two teleosts we examined (trout and perch); (8) the South American and African lungfishes group together to the exclusion of the Australian lungfish. Other findings either upheld those of the previous rRNA-based studies (e.g., echinoderms and hemichordates group as Ambulacraria; orbitostylic sharks; batoids are not derived from any living lineage of sharks) or were obvious (monophyly of mammals, gnathostomes, vertebrates, echinoderms, etc.). Despite all these findings, the rRNA data still fail to resolve the relations among the major groups of deuterostomes (tunicates, Ambulacraria, cephalochordates and vertebrates) and of gnathostomes (chondrichthyans, lungfishes, coelacanth, actinopterygians, amphibians, and amniotes), partly because tunicates and lungfishes are rogue taxa that disrupt the tree. Nonetheless, parametric bootstrapping showed our RNA-gene data are only consistent with these dominant hypotheses: (1) deuterostomes consist of Ambulacraria plus Chordata, with Chordata consisting of tunicates and 'vertebrates plus cephalochordates'; and (2) lungfishes are the closest living relatives of tetrapods.
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Phylogeny of elasmobranchs based on LSU and SSU ribosomal RNA genes.
Molecular phylogenetics and evolution, 2004Co-Authors: Christopher J. Winchell, Andrew P. Martin, Jon MallattAbstract:The dominant view of the phylogeny of living elasmobranchs, based on morphological characters, is that batoids (skates and rays) are derived sharks, joined with saw sharks, and angel sharks in the clade Hypnosqualea [S. Shirai, Squalean Phylogeny: A New Framework of 'Squaloid' Sharks and Related Taxa, Hokkaido University Press, Sapporo, 1992]. By contrast, a recent molecular-phylogenetic study based on mitochondrial genes for 12S and 16S rRNA and tRNA valine [C.J. Douady et al., Mol. Phylogenet. Evol., 26 (2003) 215-221] supported the older view that batoids and sharks are separate lineages. Here, we tested these two different views using combined, nuclear large-subunit and small-subunit rRNA gene sequences ( approximately 5.3kb) from 22 elasmobranchs, two chimeras, and two bony fishes. We used maximum likelihood, maximum parsimony, minimum evolution, and Bayesian inference for tree reconstruction, and found the large-subunit rRNA gene to contain far more signal than the small-subunit gene for resolving this mostly Mesozoic radiation. Our findings matched those of in separating batoids from sharks and in statistically rejecting Hypnosqualea. The angel shark (Squatina) was the sister group to squaliforms (dogfish sharks), and our findings are consistent with the idea that "orbitostylic" sharks form a monophyletic group (squaliforms+the hexanchiform Chlamydoselachus+Squatina+Pristiophorus). In the galeomorph sharks, however, lamniforms grouped with orectolobiforms, opposing the widely accepted 'lamniform+carcharhiniform' grouping. A tree based on the mitochondrial gene for cytochrome b also supported a separation of sharks and batoids, in contrast to Hypnosqualea. Among elasmobranchs, variation in the evolutionary rates of the nuclear rRNA genes was higher than that of cytochrome b genes, mainly due to the relatively rapid evolution of rRNA in some carcharhiniforms. In conclusion, several different molecular studies now refute the Hypnosqualea hypothesis of elasmobranch interrelationships.
Christopher J. Winchell - One of the best experts on this subject based on the ideXlab platform.
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Ribosomal RNA genes and deuterostome phylogeny revisited: more cyclostomes, elasmobranchs, reptiles, and a brittle star.
Molecular Phylogenetics and Evolution, 2007Co-Authors: Jon Mallatt, Christopher J. WinchellAbstract:This is an expanded study of the relationships among the deuterostome animals based on combined, nearly complete 28S and 18S rRNA genes (>3925 nt.). It adds sequences from 20 more taxa to the approximately 45 sequences used in past studies. Seven of the new taxa were sequenced here (brittle star Ophiomyxa, lizard Anolis, turtle Chrysemys, sixgill shark Hexanchus, electric ray Narcine, Southern Hemisphere lamprey Geotria, and Atlantic hagfish Myxine for 28S), and the other 13 were from GenBank and the literature (from a chicken, dog, rat, human, three lungfishes, and several ray-finned fishes, or Actinopterygii). As before, our alignments were based on secondary structure but did not account for base pairing in the stems of rRNA. The new findings, derived from likelihood-based tree-reconstruction methods and by testing hypotheses with parametric bootstrapping, include: (1) brittle star joins with sea star in the echinoderm clade, Asterozoa; (2) with two hagfishes and two lampreys now available, the cyclostome (jawless) fishes remain monophyletic; (3) Hexanchiform sharks are monophyletic, as Hexanchus groups with the frilled shark, Chlamydoselachus; (4) turtle is the sister taxon of all other amniotes; (5) bird is closer to the lizard than to the mammals; (6) the bichir Polypterus is in a monophyletic Actinopterygii; (7) Zebrafish Danio is the sister taxon of the other two teleosts we examined (trout and perch); (8) the South American and African lungfishes group together to the exclusion of the Australian lungfish. Other findings either upheld those of the previous rRNA-based studies (e.g., echinoderms and hemichordates group as Ambulacraria; orbitostylic sharks; batoids are not derived from any living lineage of sharks) or were obvious (monophyly of mammals, gnathostomes, vertebrates, echinoderms, etc.). Despite all these findings, the rRNA data still fail to resolve the relations among the major groups of deuterostomes (tunicates, Ambulacraria, cephalochordates and vertebrates) and of gnathostomes (chondrichthyans, lungfishes, coelacanth, actinopterygians, amphibians, and amniotes), partly because tunicates and lungfishes are rogue taxa that disrupt the tree. Nonetheless, parametric bootstrapping showed our RNA-gene data are only consistent with these dominant hypotheses: (1) deuterostomes consist of Ambulacraria plus Chordata, with Chordata consisting of tunicates and 'vertebrates plus cephalochordates'; and (2) lungfishes are the closest living relatives of tetrapods.
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Phylogeny of elasmobranchs based on LSU and SSU ribosomal RNA genes.
Molecular phylogenetics and evolution, 2004Co-Authors: Christopher J. Winchell, Andrew P. Martin, Jon MallattAbstract:The dominant view of the phylogeny of living elasmobranchs, based on morphological characters, is that batoids (skates and rays) are derived sharks, joined with saw sharks, and angel sharks in the clade Hypnosqualea [S. Shirai, Squalean Phylogeny: A New Framework of 'Squaloid' Sharks and Related Taxa, Hokkaido University Press, Sapporo, 1992]. By contrast, a recent molecular-phylogenetic study based on mitochondrial genes for 12S and 16S rRNA and tRNA valine [C.J. Douady et al., Mol. Phylogenet. Evol., 26 (2003) 215-221] supported the older view that batoids and sharks are separate lineages. Here, we tested these two different views using combined, nuclear large-subunit and small-subunit rRNA gene sequences ( approximately 5.3kb) from 22 elasmobranchs, two chimeras, and two bony fishes. We used maximum likelihood, maximum parsimony, minimum evolution, and Bayesian inference for tree reconstruction, and found the large-subunit rRNA gene to contain far more signal than the small-subunit gene for resolving this mostly Mesozoic radiation. Our findings matched those of in separating batoids from sharks and in statistically rejecting Hypnosqualea. The angel shark (Squatina) was the sister group to squaliforms (dogfish sharks), and our findings are consistent with the idea that "orbitostylic" sharks form a monophyletic group (squaliforms+the hexanchiform Chlamydoselachus+Squatina+Pristiophorus). In the galeomorph sharks, however, lamniforms grouped with orectolobiforms, opposing the widely accepted 'lamniform+carcharhiniform' grouping. A tree based on the mitochondrial gene for cytochrome b also supported a separation of sharks and batoids, in contrast to Hypnosqualea. Among elasmobranchs, variation in the evolutionary rates of the nuclear rRNA genes was higher than that of cytochrome b genes, mainly due to the relatively rapid evolution of rRNA in some carcharhiniforms. In conclusion, several different molecular studies now refute the Hypnosqualea hypothesis of elasmobranch interrelationships.
Jennifer A. Lane - One of the best experts on this subject based on the ideXlab platform.
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Morphology of the braincase in the Cretaceous hybodont shark Tribodus limae (Chondrichthyes: Elasmobranchii), based on CT scanning. American Museum Novitates
2016Co-Authors: Jennifer A. LaneAbstract:The braincase of the Lower Cretaceous hybodont shark Tribodus limae is examined using high-resolution CT scanning, and its internal and external morphology is described based on three-dimensional digital reconstructions. This study represents the first in-depth examination of a hybodont braincase using CT scanning and digital imaging technology. The braincase of an additional Lower Cretaceous hybodont, Egertonodus basanus, is also digitally reconstructed and compared to Tribodus. A reconstruction of cranial nerves and blood vessels in Tribodus is presented on the basis of preserved foramina. The braincase of Tribodus shares many features with those of Egertonodus and neoselachians, providing further support for the sister-group relationship between hybodonts and extant elasmobranchs. CT scans confirm that in both Tribodus and Egertonodus the glossopharyngeal and vagus canals converge and exit from a common foramen (also found in Chlamydoselachus). In both of the hybodonts examined, the trochlear nerve exits the braincase anterior to the optic nerve, a possible hybodont synapomorphy. Separate foramina for the two rami of the octaval nerve are present in both Tribodus and Egertonodus, and may represent an additional hybodont synapomorphy. Also, both taxa have three separate foramina for th
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Morphology of the Braincase in the Cretaceous Hybodont Shark Tribodus limae (Chondrichthyes: Elasmobranchii), Based on CT Scanning
American Museum Novitates, 2010Co-Authors: Jennifer A. LaneAbstract:Abstract The braincase of the Lower Cretaceous hybodont shark Tribodus limae is examined using high-resolution CT scanning, and its internal and external morphology is described based on three-dimensional digital reconstructions. This study represents the first in-depth examination of a hybodont braincase using CT scanning and digital imaging technology. The braincase of an additional Lower Cretaceous hybodont, Egertonodus basanus, is also digitally reconstructed and compared to Tribodus. A reconstruction of cranial nerves and blood vessels in Tribodus is presented on the basis of preserved foramina. The braincase of Tribodus shares many features with those of Egertonodus and neoselachians, providing further support for the sister-group relationship between hybodonts and extant elasmobranchs. CT scans confirm that in both Tribodus and Egertonodus the glossopharyngeal and vagus canals converge and exit from a common foramen (also found in Chlamydoselachus). In both of the hybodonts examined, the trochlear ...
Toshihiko Toida - One of the best experts on this subject based on the ideXlab platform.
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RESEARCH ARTICLE Composition of Glycosaminoglycans in Elasmobranchs including Several Deep-Sea Sharks: Identification of Chondroitin/ Dermatan Sulfate from the Dried Fins of
2016Co-Authors: Isurus Oxyrinchus, Prionace Glauca, Kyohei Higashi, Yoshiki Takeuchi, Ann Mukuno, Hideyuki Tomitori, Masaki Miya, Robert J. Linhardt, Toshihiko ToidaAbstract:Shark fin, used as a food, is a rich source of glycosaminoglyans (GAGs), acidic polysaccha-rides having important biological activities, suggesting their nutraceutical and pharmaceuti-cal application. A comprehensive survey of GAGs derived from the fin was performed on 11 elasmobranchs, including several deep sea sharks. Chondroitin sulfate (CS) and hyaluronic acid (HA) were found in Isurus oxyrinchus, Prionace glauca, Scyliorhinus torazame, Deania calcea, Chlamydoselachus anguineus,Mitsukurina owatoni,Mustelus griseus and Dasyatis akajei, respectively. CS was only found from Chimaera phantasma, Dalatias licha, and Odontaspis ferox, respectively. Characteristic disaccharide units of most of the CS were comprised of C- and D-type units. Interestingly, substantial amount of CS/dermatan sulfate (DS) was found in the dried fin (without skin and cartilage) of Isurus oxyrinchus and Prionace glauca. 1H-NMR analysis showed that the composition of glucuronic acid (GlcA) and iduro-nic acid (IdoA) in shark CS/DS was 41.2 % and 58.8 % (Isurus oxyrinchus), 36.1 % and 63.9 % (Prionace glauca), respectively. Furthermore, a substantial proportion of this CS/DS consisted of E-, B- and D-type units. Shark CS/DS stimulated neurite outgrowth of hippo
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Composition of Glycosaminoglycans in Elasmobranchs including Several Deep-Sea Sharks: Identification of Chondroitin/Dermatan Sulfate from the Dried Fins of Isurus oxyrinchus and Prionace glauca
PloS one, 2015Co-Authors: Kyohei Higashi, Yoshiki Takeuchi, Ann Mukuno, Hideyuki Tomitori, Masaki Miya, Robert J. Linhardt, Toshihiko ToidaAbstract:Shark fin, used as a food, is a rich source of glycosaminoglyans (GAGs), acidic polysaccharides having important biological activities, suggesting their nutraceutical and pharmaceutical application. A comprehensive survey of GAGs derived from the fin was performed on 11 elasmobranchs, including several deep sea sharks. Chondroitin sulfate (CS) and hyaluronic acid (HA) were found in Isurus oxyrinchus, Prionace glauca, Scyliorhinus torazame, Deania calcea, Chlamydoselachus anguineus, Mitsukurina owatoni, Mustelus griseus and Dasyatis akajei, respectively. CS was only found from Chimaera phantasma, Dalatias licha, and Odontaspis ferox, respectively. Characteristic disaccharide units of most of the CS were comprised of C- and D-type units. Interestingly, substantial amount of CS/dermatan sulfate (DS) was found in the dried fin (without skin and cartilage) of Isurus oxyrinchus and Prionace glauca. 1H-NMR analysis showed that the composition of glucuronic acid (GlcA) and iduronic acid (IdoA) in shark CS/DS was 41.2% and 58.8% (Isurus oxyrinchus), 36.1% and 63.9% (Prionace glauca), respectively. Furthermore, a substantial proportion of this CS/DS consisted of E-, B- and D-type units. Shark CS/DS stimulated neurite outgrowth of hippocampal neurons at a similar level as DS derived from invertebrate species. Midkine and pleiotrophin interact strongly with CS/DS from Isurus oxyrinchus and Prionace glauca, affording Kd values of 1.07 nM, 6.25 nM and 1.70 nM, 1.88 nM, respectively. These results strongly suggest that the IdoA-rich domain of CS/DS is required for neurite outgrowth activity. A detailed examination of oligosaccharide residues, produced by chondroitinase ACII digestion, suggested that the IdoA and B-type units as well as A- and C-type units were found in clusters in shark CS/DS. In addition, it was discovered that the contents of B-type units in these IdoA-rich domain increased in a length dependent manner, while C- and D-type units were located particularly in the immediate vicinity of the IdoA-rich domain.
Norton Hiller - One of the best experts on this subject based on the ideXlab platform.
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AN EARLY CENOZOIC NEOSELACHIAN SHARK FAUNA FROM THE SOUTHWEST PACIFIC
Palaeontology, 2008Co-Authors: Al A. Mannering, Norton HillerAbstract:Abstract: An early Cenozoic shark fauna, comprising at least 16 taxa, is described from Paleocene sedimentary rocks on the South Island of New Zealand. Although representing a remote Southern Hemisphere location, the fauna includes forms closely comparable to contemporary species from the Northern Hemisphere, in addition to the new species Chlamydoselachus keyesi and Centroselachus goordi. Comparison with closely related extant species suggests the fauna may be interpreted as a deep water one, typical of the outer continental shelf and upper slope. However, after palaeogeography, sedimentology and mineralogy of the enclosing rock, and the nature of similar faunas from elsewhere are taken into consideration, the fauna is interpreted to have occupied a mid-shelf environment.