Herpetological higher taxa nomina 2. Anura Duméril, 1805

Bionomina ◽  
2020 ◽  
Vol 20 (1) ◽  
pp. 1-16
Author(s):  
ALAIN DUBOIS ◽  
THIERRY FRÉTEY
Keyword(s):  
Rank Order ◽  
Phylogenetic Analyses ◽  
Overwhelming Majority ◽  
Higher Taxa

A taxon, traditionally referred to the rank order, encompassing all recent taxa of frogs and their close fossil relatives, is highly supported as holophyletic in all recent phylogenetic analyses of Amphibia. Under the Duplostensional Nomenclatural System, among more than thirty nomina available for this taxon in the literature, two only qualify as sozodiaphonyms: Anura Duméril, 1805 and Salientia Merrem, 1820. The conflict for validity between these two nomina is easily solved by publication dates. The valid nomen for this taxon is therefore Anura Duméril, 1805, which corresponds to the overwhelming majority of uses in the literature, and which should replace all other nomina, authorships and dates sometimes credited to this taxon in publications, catalogues and databases.

Herpetological higher taxa nomina. 7. Lissamphibia Gadow, 1898

Bionomina ◽  
2021 ◽  
Vol 21 (1) ◽  
pp. 73-83
Author(s):  
ALAIN DUBOIS ◽  
THIERRY FRÉTEY
Keyword(s):  
Phylogenetic Relationships ◽  
Rank Order ◽  
Phylogenetic Analyses ◽  
Higher Taxa ◽  
The One

A taxon encompassing all recent taxa of amphibians and their close fossil relatives is highly supported as holophyletic in all recent phylogenetic analyses of amphibians. Under the Duplostensional Nomenclatural System, among twenty nomina available for this taxon, only one, Lissamphibia Gadow, 1898, qualifies as a sozodiaphonym and appears to be the one that should be used for this taxon, traditionally referred to the rank order. However, because of the current uncertainties in the phylogenetic relationships among basal amphibians, the allocation of this nomen to this taxon is still questionable. If it turned out to apply in fact to another, more comprehensive, taxon, its stabilisation under its current acceptation should be realised through an act of archoidy.

Herpetological higher taxa nomina 3. Urodela Duméril, 1805

Bionomina ◽  
2020 ◽  
Vol 20 (1) ◽  
pp. 17-35
Author(s):  
ALAIN DUBOIS ◽  
THIERRY FRÉTEY
Keyword(s):  
Rank Order ◽  
Phylogenetic Analyses ◽  
Higher Taxa

A taxon, traditionally referred to the rank order, encompassing all recent taxa of salamanders and their close fossil relatives, is highly supported as holophyletic in all recent phylogenetic analyses of amphibians. Under the Duplostensional Nomenclatural System, among about thirty nomina available for this taxon in the literature, two only qualify as sozodiaphonyms: Urodela Duméril, 1805 and Caudata Duméril, 1805. The conflict for validity between these two nomina is solved by the Principle of Airesy (first reviser). The valid nomen for this taxon is therefore Urodela Duméril, 1805, which corresponds to the majority of uses in the literature since their creation, and which should replace all other nomina, authorships and dates sometimes credited to this taxon in publications, catalogues and databases.

A combined morphological and molecular phylogeny for sea urchins (Echinoidea: Echinodermata)

1995 ◽  
Vol 347 (1320) ◽  
pp. 213-234 ◽  
Keyword(s):  
Data Base ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Total Evidence ◽  
Morphological Data ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Molecular Sequences ◽  
Higher Taxa ◽  
Stem Group

Phylogenedc reladonships of higher taxa of echinoids have been invesdgated using a 163 character morphological data base and molecular sequences from large and small subunit (LSU and SSU) ribosomal RNA (rRNA) genes. The complete ssu rRNA gene has been sequenced for 21 taxa, with representatives from nine of the 14 extant orders of Echinoidea. Partial LSU sequences, representing the first 400 base pairs (b.p.) from the 5' end were also sequenced for three taxa to complement an existing data base of ten taxa. The two molecular sequences provided a total of 371 variable sites, of which 143 were phylogenetically informative (compared to 145 phylogenetically informative sites from morphological data). Morphological, LSU and SSU data have been analysed separately and together. Morphological and ssu sequence data generate topologies that are not significantly in conflict (under Templeton’s test), but the strong signal pairing arbaciids with clypeasteroids in the LSU derived tree marks the LSU sequence data as anomalous for this taxon. A ‘ total evidence’ approach derived a tree very similar in topology to that derived from morphological data. Rooted on the stem group echinoid Archaeocidaris , our total evidence tree suggested relationships of higher taxa as follows: Gidaroida Phormosomatidae Echinothuriidae Diadematidae Spatangoida Clypeasteroida, Cassiduloida Calycina, Arbacioida Stomopneustidae Glyphocidaridae Temnopleuridae Echinometridae Echinidae, Strongylocentridae. Phylogenetic analyses run both with and without key fossil taxa yielded slightly different topologies. It is important to include fossil taxa in a phylogenetic analysis where there are long stem-group branches or where the crown group is highly derived.

Herpetological higher taxa nomina. 6. Gymnophiona Rafinesque, 1814

Bionomina ◽  
2021 ◽  
Vol 21 (1) ◽  
pp. 39-72
Author(s):  
ALAIN DUBOIS ◽  
THIERRY FRÉTEY
Keyword(s):  
Rank Order ◽  
The Other ◽  
Distinct Class ◽  
Higher Taxa ◽  
Senior Synonym ◽  
Cladistic Analyses ◽  
Made In

A taxon, traditionally referred to the rank order, encompassing all recent taxa of caecilians and their close fossil relatives, is highly supported as holophyletic in all recent cladistic analyses of Amphibia. Under the Duplostensional Nomenclatural System, among 12 nomina available in the literature, only one, Gymnophiona Rafinesque, 1814, qualifies as a sozodiaphonym and should be used for this amphibian taxon. We show here that the authorship of this nomen, as well as of 32 other nomina published in 1814, is ‘Rafinesque’, not ‘Rafinesque-Schmaltz’.            The nomen Apoda Oppel, 1811, that has often been used for this taxon, proves to be a distagmonym and a junior homonym of Apodes Linnaeus, 1758 and five other distagmonyms, and as such it is invalid under DONS.            In total, we identified 34 distinct class-series nomina derived from the stems ἄπους (apous) or Apus in 13 distinct zoological groups, only two of which are valid under DONS Criteria: Apodiformia Wetmore, 1947, for the suborder of Aves currently known as Apodi Wetmore, 1947, and Apodomorpha Sibley, Ahlquist & Monroe, 1988 for the order of Aves currently known as Apodiformes Peters, 1940.                Several other nomenclatural findings were made in the course of this study: [1] in the Teleostei, the nomina "Eupercaria" and "Syngnatharia", like all the other new nomina proposed in the paper by Betancur-R. et al. (2017) are anoplonyms and cannot be used as valid; [2] in the Mammalia, the nomina Cetus and Cetacea should be credited to Brisson (1759); [3] in the Holothuroidea, the nomen Apoda Claus, 1868, currently considered valid under the apograph Apodida, is invalid and should be replaced by the nomen Paractinopoda Ludwig, 1891; [4] in the Isopoda, the subordinal nomen Cymothoida Wägele, 1989 should be replaced by its senior synonym Darwinida Lakshminarayana & Rama Rao, 1977.

scholarly journals Phylogeny and morphologic evolution of the Ordovician Camerata (Class Crinoidea, Phylum Echinodermata)

2017 ◽  
Vol 91 (4) ◽  
pp. 815-828 ◽  
Author(s):  
Selina R. Cole
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Major Group ◽  
Higher Taxa ◽  
Morphologic Evolution ◽  
Phylogenetic Framework ◽  
Selection For

AbstractThe subclass Camerata (Crinoidea, Echinodermata) is a major group of Paleozoic crinoids that represents an early divergence in the evolutionary history and morphologic diversification of class Crinoidea, yet phylogenetic relationships among early camerates remain unresolved. This study conducted a series of quantitative phylogenetic analyses using parsimony methods to infer relationships of all well-preserved Ordovician camerate genera (52 taxa), establish the branching sequence of early camerates, and test the monophyly of traditionally recognized higher taxa, including orders Monobathrida and Diplobathrida. The first phylogenetic analysis identified a suitable outroup for rooting the Ordovician camerate tree and assessed affinities of the atypical dicyclic family Reteocrinidae. The second analysis inferred the phylogeny of all well-preserved Ordovician camerate genera. Inferred phylogenies confirm: (1) the Tremadocian genera Cnemecrinus and Eknomocrinus are sister to the Camerata; (2) as historically defined, orders Monobathrida and Diplobathrida do not represent monophyletic groups; (3) with minimal revision, Monobathrida and Diplobathrida can be re-diagnosed to represent monophyletic clades; (4) family Reteocrinidae is more closely related to camerates than to other crinoid groups currently recognized at the subclass level; and (5) several genera in subclass Camerata represent stem taxa that cannot be classified as either true monobathrids or true diplobathrids. The clade containing Monobathrida and Diplobathrida, as recognized herein, is termed Eucamerata to distinguish its constituent taxa from more basally positioned taxa, termed stem eucamerates. The results of this study provide a phylogenetic framework for revising camerate classification, elucidating patterns of morphologic evolution, and informing outgroup selection for future phylogenetic analyses of post-Ordovician camerates.

Herpetological higher taxa nomina 1. Introduction and methodology

Bionomina ◽  
2020 ◽  
Vol 19 (1) ◽  
pp. 1-56
Author(s):  
ALAIN DUBOIS ◽  
THIERRY FRÉTEY
Keyword(s):  
Rank Order ◽  
Higher Taxa

This work introduces a series of papers devoted to the ascertainment of the valid nomina, under the revised Duplostensional Nomenclatural System (DONS-2), of the highest taxa (from the rank order to the rank class) of recent amphibians and ‘reptiles’. The main general features of the DONS approach to class-series nomenclature (above the rank superfamily) are explained in detail, the DONS-2 procedure for ascertaining the availability, allocation, validity and correctness of class-series nomina is described, and a Glossary of all the technical nomenclatural terms used in this work is provided.

Across the benthic and pelagic realms: a species‐level phylogeny of Benthesicymidae (Crustacea:Decapoda)

2021 ◽  
Vol 35 (7) ◽  
pp. 776
Author(s):  
Alexander L. Vereshchaka ◽  
Dmitry N. Kulagin ◽  
Anastasiia A. Lunina
Keyword(s):  
Phylogenetic Analyses ◽  
Bottom Layer ◽  
Morphological Characters ◽  
Valid Species ◽  
Phylogenetic Study ◽  
Depth Range ◽  
Sea Floor ◽  
Higher Taxa ◽  
Insight Into ◽  
Rare Opportunity

Benthesicymidae is a monophyletic group of Decapoda adapted to a life on the sea-floor, in the near-bottom layer, in the bathy- and in the mesopelagic, within an impressive depth range from a few hundred metres (Gennadas) to several thousand metres (Benthesicymus). Higher taxa are known to conquer all main oceanic biotopes such as the benthic, benthopelagic, and pelagic and a wide depth range but few family-level groups have clades evolved within all these oceanic realms. Therefore, the global fauna of Benthesicymidae provides a rare opportunity for an insight into phylogenetic processes favouring colonisation of all principal oceanic biotopes. The first comprehensive phylogenetic study of Benthesicymidae (all 37 valid species) is based on six molecular markers and 105 morphological characters (including 72 female and male copulatory characters). Analyses resulted in trees with similar topology and the same set of robust clades. Molecular methods based on 167 sequences (84 new) provided better resolution of deeper nodes and generally higher support of the clades, while morphological methods allowed analyses of all valid species of the global fauna. Phylogenetic analyses support the monophyly and robustness of all currently known genera except Gennadas, which was split into Gennadas Bate, 1881, Amalopenaeus Smith, 1882, and Notogennema gen. nov. We also retrieved two major clades for which we erected two new subfamilies: Benthesicyminae subfam. nov. (presumably benthic, genera Altelatipes, Bathicaris, Benthesicymus, and Benthonectes) and Gennadinae subfam. nov. (presumably pelagic, genera Amalopenaeus, Bentheogennema, Benthoecetes, Boreogennema, Gennadas, Maorrancaris, and Notogennema gen. nov.). We revealed two groups of morphological characters, that are interlinked evolutionarily: (1) petasma and thelycum; (2) body, mouthparts, and pereopods. Morphological traits within benthic and pelagic clades are different, a model explaining the differences is proposed. Along with previous studies, our results confirm the idea that the elaboration of the copulatory structures is a key to successful colonisation of the pelagic realm. These results extend our knowledge about evolution in the largest habitual biotope of our planet and phylogenetic processes favouring colonisation of all principal oceanic biotopes.

scholarly journals Specimen-level phylogenetics in paleontology using the Fossilized Birth-Death model with sampled ancestors

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3055 ◽  
Author(s):  
Andrea Cau
Keyword(s):  
Bayesian Methods ◽  
Phylogenetic Analyses ◽  
Phylogenetic Inference ◽  
Parsimony Analysis ◽  
Higher Taxa ◽  
Phylogenetic Methods ◽  
Phylogenetic Framework ◽  
Bayesian Methodologies ◽  
High Diversity ◽  
Birth Death

Bayesian phylogenetic methods integrating simultaneously morphological and stratigraphic information have been applied increasingly among paleontologists. Most of these studies have used Bayesian methods as an alternative to the widely-used parsimony analysis, to infer macroevolutionary patterns and relationships among species-level or higher taxa. Among recently introduced Bayesian methodologies, the Fossilized Birth-Death (FBD) model allows incorporation of hypotheses on ancestor-descendant relationships in phylogenetic analyses including fossil taxa. Here, the FBD model is used to infer the relationships among an ingroup formed exclusively by fossil individuals, i.e., dipnoan tooth plates from four localities in the Ain el Guettar Formation of Tunisia. Previous analyses of this sample compared the results of phylogenetic analysis using parsimony with stratigraphic methods, inferred a high diversity (five or more genera) in the Ain el Guettar Formation, and interpreted it as an artifact inflated by depositional factors. In the analysis performed here, the uncertainty on the chronostratigraphic relationships among the specimens was included among the prior settings. The results of the analysis confirm the referral of most of the specimens to the taxaAsiatoceratodus,Equinoxiodus, LavocatodusandNeoceratodus, but reject those toCeratodusandFerganoceratodus. The resulting phylogeny constrained the evolution of the Tunisian sample exclusively in the Early Cretaceous, contrasting with the previous scenario inferred by the stratigraphically-calibrated topology resulting from parsimony analysis. The phylogenetic framework also suggests that (1) the sampled localities are laterally equivalent, (2) but three localities are restricted to the youngest part of the section; both results are in agreement with previous stratigraphic analyses of these localities. The FBD model of specimen-level units provides a novel tool for phylogenetic inference among fossils but also for independent tests of stratigraphic scenarios.

scholarly journals The flounder organic anion transporter fOat has sequence, function, and substrate specificity similarity to both mammalian Oat1 and Oat3

2006 ◽  
Vol 291 (6) ◽  
pp. R1773-R1780 ◽  
Author(s):  
Amy G. Aslamkhan ◽  
Deborah M. Thompson ◽  
Jennifer L. Perry ◽  
Kelly Bleasby ◽  
Natascha A. Wolff ◽  
...  
Keyword(s):  
Fundulus Heteroclitus ◽  
Xenopus Oocytes ◽  
Rank Order ◽  
Phylogenetic Analyses ◽  
Organic Anion ◽  
Organic Anion Transporter ◽  
Takifugu Rubripes ◽  
Fluorescent Substrate ◽  
Ancestral Gene ◽  
Anion Transporter

The flounder renal organic anion transporter (fOat) has substantial sequence homology to mammalian basolateral organic anion transporter orthologs (OAT1/Oat1 and OAT3/Oat3), suggesting that fOat may have functional properties of both mammalian forms. We therefore compared uptake of various substrates by rat Oat1 and Oat3 and human OAT1 and OAT3 with the fOat clone expressed in Xenopus oocytes. These data confirm that estrone sulfate is an excellent substrate for mammalian OAT3/Oat3 transporters but not for OAT1/Oat1 transporters. In contrast, 2,4-dichlorophenoxyacetic acid and adefovir are better transported by mammalian OAT1/Oat1 than by the OAT3/Oat3 clones. All three substrates were well transported by fOat-expressing Xenopus oocytes. fOat Km values were comparable to those obtained for mammalian OAT/Oat1/3 clones. We also characterized the ability of these substrates to inhibit uptake of the fluorescent substrate fluorescein in intact teleost proximal tubules isolated from the winter flounder ( Pseudopleuronectes americanus) and killifish ( Fundulus heteroclitus). The rank order of the IC50 values for inhibition of cellular fluorescein accumulation was similar to that for the Km values obtained in fOat-expressing oocytes, suggesting that fOat may be the primary teleost renal basolateral Oat. Assessment of the zebrafish ( Danio rerio) genome indicated the presence of a single Oat (zfOat) with similarity to both mammalian OAT1/Oat1 and OAT3/Oat3. The puffer fish ( Takifugu rubripes) also has an Oat (pfOat) similar to mammalian OAT1/Oat1 and OAT3/Oat3 members. Furthermore, phylogenetic analyses argue that the teleost Oat1/3-like genes diverged from a common ancestral gene in advance of the divergence of the mammalian OAT1/Oat1, OAT3/Oat3, and, possibly, Oat6 genes.

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