scholarly journals Less is more stable: arguing for few names in turtle’s taxonomy

2015 ◽  
Author(s):  
Pedro S. R. Romano
Keyword(s):  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Sensu Stricto ◽  
Botanical Nomenclature ◽  
Crown Group ◽  
Diagnostic Characters ◽  
Less Is More ◽  
Phylogenetic Reconstructions ◽  
Stem Species ◽  
Phylogenetic Nomenclature

Background. Beyond the International Codes of Zoological (ICZN) and Botanical Nomenclature and the PhyloCode, there is an alternative taxonomic system for phylogenetic systematics proposed. This phylogenetic nomenclature suggests the elimination of suprageneric names and the use of negative indexes instead of it. This system of nomenclature has a basic principle to identify clades: the presence of nominal heterobathmy, which is analogous to Hennig's "heterobathmy of characters", but applied to taxa names. Here I argue for an extensive use of heterobathmy as basic criteria to determinate “good” nodes to identify higher level taxa names. Methods. I used a previews published dataset (doi:10.5061/dryad.f2h6r) and ran several searches for Most Parsimonious Trees (MPT) using different search algorithms and assumptions in TNT. After that, I compared the results of different searches, mapped the characters transformations, and calculate the Bremer supports. The results were then compared with the current taxonomy proposed for Pelomedusoides, with emphasis on Bothremydidae. Results. The remarkable divergences with the current taxonomy of Bothremydidae are: (1) Kurmademydini and Bothremydini need to be redefined; (2) Cearachelyini and Galianemys lack diagnostic characters and, therefore, are not monophyletic; and (3) Bothremydidae do not possess common diagnostic characters in all MPT, thus, lacks a well supported heterobathmy with its sister-group, Podocnemidinura (=Pan-Podocnemididae). Moreover, the Infrafamily Bothremydodda has Bremer support of 3. However, given that all bothremydids are extinct, it is impossible to define a panstem clade based on a crown group. The result is an unstable nomenclature with more names than necessary. Discussion. The use of heterobathmy is a center point in Hennig's argumentation for phylogenetic reconstruction. Indeed, it implies the zero length collapsing rule applied to cladistic reconstruction (which is the TNT default option). Nonetheless, ambiguous characters or several equal MPT can imply on phylogenetic reconstructions that lack a consistent heterobathmy (i.e.: a common diagnostic character in the ancestor eidophoront of a given node in all MPT; as is the case of Bothremydidae). A possible solution is to use the suffix “formes” to designate extinct lineages with stem-species when some nodes are not well supported in a given phylogeny. In the example presented here, it would consist on naming ICZN’s Bothremydodda as “Bothremydidae” (sensu stricto) and ICZN’s Bothremydidae (sensu lato, i.e.: including stem-Bothremydidae) as “Bothremydidiformes” and avoid naming each node of the consensus tree unless it has high Bremer support. By taking into account this delimitation criterion, we can propose a more stable and clean taxonomy.

scholarly journals Less is more stable: arguing for few names in turtle’s taxonomy

2015 ◽  
Author(s):  
Pedro S. R. Romano
Keyword(s):  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Sensu Stricto ◽  
Botanical Nomenclature ◽  
Crown Group ◽  
Diagnostic Characters ◽  
Less Is More ◽  
Phylogenetic Reconstructions ◽  
Stem Species ◽  
Phylogenetic Nomenclature

Background. Beyond the International Codes of Zoological (ICZN) and Botanical Nomenclature and the PhyloCode, there is an alternative taxonomic system for phylogenetic systematics proposed. This phylogenetic nomenclature suggests the elimination of suprageneric names and the use of negative indexes instead of it. This system of nomenclature has a basic principle to identify clades: the presence of nominal heterobathmy, which is analogous to Hennig's "heterobathmy of characters", but applied to taxa names. Here I argue for an extensive use of heterobathmy as basic criteria to determinate “good” nodes to identify higher level taxa names. Methods. I used a previews published dataset (doi:10.5061/dryad.f2h6r) and ran several searches for Most Parsimonious Trees (MPT) using different search algorithms and assumptions in TNT. After that, I compared the results of different searches, mapped the characters transformations, and calculate the Bremer supports. The results were then compared with the current taxonomy proposed for Pelomedusoides, with emphasis on Bothremydidae. Results. The remarkable divergences with the current taxonomy of Bothremydidae are: (1) Kurmademydini and Bothremydini need to be redefined; (2) Cearachelyini and Galianemys lack diagnostic characters and, therefore, are not monophyletic; and (3) Bothremydidae do not possess common diagnostic characters in all MPT, thus, lacks a well supported heterobathmy with its sister-group, Podocnemidinura (=Pan-Podocnemididae). Moreover, the Infrafamily Bothremydodda has Bremer support of 3. However, given that all bothremydids are extinct, it is impossible to define a panstem clade based on a crown group. The result is an unstable nomenclature with more names than necessary. Discussion. The use of heterobathmy is a center point in Hennig's argumentation for phylogenetic reconstruction. Indeed, it implies the zero length collapsing rule applied to cladistic reconstruction (which is the TNT default option). Nonetheless, ambiguous characters or several equal MPT can imply on phylogenetic reconstructions that lack a consistent heterobathmy (i.e.: a common diagnostic character in the ancestor eidophoront of a given node in all MPT; as is the case of Bothremydidae). A possible solution is to use the suffix “formes” to designate extinct lineages with stem-species when some nodes are not well supported in a given phylogeny. In the example presented here, it would consist on naming ICZN’s Bothremydodda as “Bothremydidae” (sensu stricto) and ICZN’s Bothremydidae (sensu lato, i.e.: including stem-Bothremydidae) as “Bothremydidiformes” and avoid naming each node of the consensus tree unless it has high Bremer support. By taking into account this delimitation criterion, we can propose a more stable and clean taxonomy.

scholarly journals Morphological and molecular differences between the Amphiamerican populations of Antillesoma (Sipuncula: Antillesomatidae), with the description of a new species

2019 ◽  
Vol 67 (S5) ◽  
pp. S101-S109
Author(s):  
Itzahí Silva-Morales ◽  
Mónica J. López-Aquino ◽  
Valentina Islas-Villanueva ◽  
Fernando Ruiz-Escobar ◽  
J. Rolando Bastida-Zavala
Keyword(s):  
Marine Invertebrates ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Molecular Data ◽  
Sensu Stricto ◽  
Genetic Distances ◽  
Likelihood Method ◽  
Tropical Eastern Pacific ◽  
Mexican Pacific ◽  
The Caribbean

Introduction: The sipunculans are a group of marine invertebrates that have been little studied in the tropical eastern Pacific (TEP). Antillesoma antillarum is a species belonging to the monospecific family Antillesomatidae, considered widely distributed in tropical and subtropical localities across the globe. Objective: The main objective of this work was to examine the morphological and molecular differences between specimens from both coasts of tropical America to clarify the taxonomy of this species. Methods: We examined the morphology with material from the Mexican Caribbean and southern Mexican Pacific. To perform molecular analyses, two sequences of the COI molecular marker were obtained from specimens collected in Panteón Beach, Oaxaca, southern Mexican Pacific, and compared with four sequences identified as A. antillarum in GenBank, all of them from different localities. A phylogenetic reconstruction was performed with the maximum likelihood method and genetic distances were calculated with the Kimura 2P model and compared to reference values. Results: The phylogenetic analysis revealed three different lineages of Antillesoma that are well supported by bootstrap values: Antillesoma antillarum sensu stricto from the Caribbean Sea and Florida; a sister group to the one represented by our samples from the Mexican Pacific; and a third group from Thailand. Conclusion: Based on morphological traits and molecular data, Antillesoma mexicanum sp. nov. is described from the Mexican Pacific, differing from A. antillarum in the trunk papillae, color patterns and, additionally, the specimens from the Caribbean attain significantly bigger trunk sizes than the ones Pacific.

scholarly journals The phylogeny and taxonomic status of the Chlorocystini (sensu stricto) (Homoptera, Tibicinidae)

1995 ◽  
Vol 65 (4) ◽  
pp. 201-231 ◽  
Author(s):  
A.J. de Boer
Keyword(s):  
Computer Program ◽  
Computer Analysis ◽  
Phylogenetic Reconstruction ◽  
Taxonomic Status ◽  
Sister Group ◽  
Sensu Stricto ◽  
Complete Data ◽  
Data Matrix ◽  
A Posteriori

The “Baeturia and related genera complex”, as defined earlier (De Boer, 1990) by shared aedeagal characters, is identified as the tribe Chlorocystini (sensu stricto). The Prasiini (sensu stricto) are identified as the sister group of the Chlorocystini (sensu stricto), while the genus Muda is recognized as the nearest outgroup. The phylogeny and biogeography of the sister group and outgroup is briefly discussed. Baeturia kuroiwae Matsumura is transferred to the genus Muda. A phylogenetic reconstruction of all 147 species of the Chlorocystini (sensu stricto) is presented, based on 154 characters and 409 character states. The computer program PAUP 3.1.1 (Swofford, 1993) was used for analysing the data; the genera Prasia and Muda were used as outgroups in this analysis. The results obtained from the computer analysis were slightly modified a posteriori, favouring some presumably phylogenetically important characters over strongly fluctuating ones. These final modifications were carried out with the aid of the computer program MacClade 3.0 (Maddison & Maddison, 1992). A complete data matrix and a list of characters and character states are given in an appendix; for descriptions and illustrations of these characters one is referred to previous publications.

A new species of Contomastix (Squamata, Teiidae) supported by total evidence, with remarks on diagnostic characters defining the genus

2019 ◽  
pp. 23-36
Author(s):  
Mario. R. Cabrera
Keyword(s):  
New Species ◽  
Geographic Distribution ◽  
Phylogenetic Reconstruction ◽  
Total Evidence ◽  
Molecular Evidence ◽  
Proximal Margin ◽  
Diagnostic Characters ◽  
Morphological Differences ◽  
A New Species ◽  
Molecular Characters

Formerly Cnemidophorus was thought to be the most speciose genus of Teiidae. This genus comprised four morphological groups that were later defined as four different genera, Ameivula, Aurivela, Cnemidophorus and Contomastix. The last appears as paraphyletic in a recent phylogenetic reconstruction based on morphology, but monophyletic in a reconstruction using molecular characters. Six species are allocated to Contomastix. One of them, C. lacertoides, having an extensive and disjunct geographic distribution in Argentina, Uruguay and Brazil. Preliminary analyses revealed morphological differences among its populations, suggesting that it is actually a complex of species. Here, we describe a new species corresponding to the Argentinian populations hitherto regarded as C. lacertoides, by integrating morphological and molecular evidence. Furthermore, we demonstrate that the presence of notched proximal margin of the tongue is a character that defines the genus Contomastix.

Review of Eohiodon (Teleostei: Osteoglossomorpha) from western North America, with a phylogenetic reassessment of Hiodontidae

1997 ◽  
Vol 71 (6) ◽  
pp. 1109-1124 ◽  
Author(s):  
Li Guo-Qing ◽  
Mark V. H. Wilson ◽  
Lance Grande
Keyword(s):  
North America ◽  
Sister Group ◽  
Sensu Stricto ◽  
Valid Species ◽  
Western North America ◽  
Extant Species ◽  
The Family ◽  
Fossil Records ◽  
Fossil Genus ◽  
Freshwater Teleosts

Review of recently collected material of Eohiodon from North America suggests that there are two valid species, E. rosei (Hussakof) and E. woodroffi Wilson. Eohiodon falcatus Grande is identical to E. woodruffi in known skeletal features and nearly all meristic features and is treated as a junior synonym of the latter. The fossil genus Eohiodon Cavender differs from Hiodon Lesueur, which is known from both fossil and extant species, in numerous meristic and osteological features. The caudal skeleton in Eohiodon is nearly identical to that in Hiodon.The traditionally accepted Notopteroidei, containing Lycopteridae, Hiodontidae, and Notopteridae, is a polypheletic group. The Asian fossil family Lycopteridae is not more closely related to Hiodontidae than it is to other taxa in the Osteoglossomorpha, but is sister to all other Osteoglossomorpha. The Hiodontiformes sensu stricto, including only the family Hiodontidae, is the sister-group of the Osteoglossiformes. This family is not more closely related to notopterids than to other taxa in Osteoglossiformes. The Notopteridae are most closely related to the Mormyroidea; together they and the fossil family Ostariostomidae constitute the sister-group of the Osteoglossoidei.Fossil records of Hiodontiformes sensu stricto and Notopteroidei indicate a widespread pre-Neogene biogeographic range of these freshwater teleosts, suggesting that extinction must have been involved in the Cenozoic evolution of these two osteoglossomorph sublineages.

Rediagnosis of the squat lobster genus Gastroptychus Caullery, 1896, with a new genus Sternostylus and a new family Sternostylidae (Crustacea: Decapoda: Anomura: Chirostyloidea)

Zootaxa ◽  
2018 ◽  
Vol 4524 (1) ◽  
pp. 77 ◽  
Author(s):  
KEIJI BABA ◽  
SHANE T. AHYONG ◽  
KAREEN E. SCHNABEL
Keyword(s):  
Type Species ◽  
Anterior Margin ◽  
New Genus ◽  
Sister Group ◽  
Sensu Stricto ◽  
The Other ◽  
Squat Lobster ◽  
Terminal Spine ◽  
New Family ◽  
Left And Right

The chirostyloidean squat lobster genus Gastroptychus Caullery, 1896 is revised and is split into two genera: Gastroptychus sensu stricto (type species, Ptychogaster spinifer A. Milne-Edwards, 1880) and Sternostylus new genus (type species, Ptychogaster formosus Filhol, 1884). Gastroptychus sensu stricto, is restricted to nine species with a sternal plastron, at sternite 3, abruptly demarcated from the preceding sternites (excavated sternum) by a distinct step forming a well-defined transverse or concave anterior margin at the articulation with maxillipeds 3, the maxillipeds 3 widely separated, with the distal parts accommodated in the excavated sternum between the left and right maxillipeds 3 when folded, and the P2–4 dactyli with the terminal spine demarcated by a suture. Sternostylus new genus, represented by 12 species, has the sternite 3 anteriorly bluntly produced medially and steeply sloping anterodorsally to the anterior sternite, with a pair of spines directly behind the anterior margin, the left and right maxillipeds 3 adjacent, and the P2–4 dactyli ending in an indistinctly demarcated corneous spine. The above-mentioned characters of Gastroptychus are consistent with Chirostylidae sensu stricto. Published molecular phylogenies indicate, however, that Sternostylus is the sister group to all the other Chirostylidae, and is designated the type genus of a new family, Sternostylidae. 

scholarly journals The genome of the blind soil-dwelling and ancestrally wingless dipluran Campodea augens, a key reference hexapod for studying the emergence of insect innovations

2019 ◽  
Author(s):  
Mosè Manni ◽  
Felipe A. Simao ◽  
Hugh M. Robertson ◽  
Marco A. Gabaglio ◽  
Robert M. Waterhouse ◽  
...  
Keyword(s):  
Draft Genome ◽  
Gene Families ◽  
Sister Group ◽  
Sensu Stricto ◽  
Comparative Genomic ◽  
Gene Repertoire ◽  
Animal Group ◽  
Origin And Evolution ◽  
Genomic Analyses ◽  
Metabolism Gene

AbstractThe dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gbp draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion which might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behaviour, and duplicated apoptotic genes might underlie its high regenerative potential.The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.

First plesiosaur remains from the lower Cretaceous of the Neuquén Basin, Argentina

2003 ◽  
Vol 77 (4) ◽  
pp. 784-789 ◽  
Author(s):  
Dario G. Lazo ◽  
Marcela Cichowolski
Keyword(s):  
Lower Cretaceous ◽  
Sister Group ◽  
Monophyletic Group ◽  
Phylogenetic Position ◽  
Crown Group ◽  
Marine Reptiles ◽  
Stem Group ◽  
Neuquen Basin ◽  
Neuquén Basin

Plesiosaurs constitute a monophyletic group whose stratigraphical range is uppermost Triassic to uppermost Cretaceous (Brown, 1981). They were large predatory marine reptiles, highly adapted for submarine locomotion, with powerful paddle-like limbs and heavily reinforced limb girdles (Saint-Seine, 1955; Romer, 1966; Carroll, 1988; Benton, 1990). The Plesiosauria clade belongs to the Sauropterygia, which has recently been hypothesized as the sister-group of the Ichthyosauria. Together with that clade they form the Euryapsida (Caldwell, 1997). The Sauropterygia can be subdivided into relatively plesiomorphic stem-group taxa from the Triassic (Placodonts, Nothosauroids, and Pistosauroids), and the obligatorily marine crown-group Plesiosauria (Rieppel, 1999). Plesiosaurs are traditionally divided into two superfamilies: Plesiosauroidea, with usually small heads and long necks; and Pliosauroidea, with larger heads and shorter necks (Welles, 1943; Persson, 1963; Brown, 1981). Plesiosauroidea contains three families: Plesiosauridae, Cryptoclididae, and Elasmosauridae (Brown, 1981; Brown and Cruickshank, 1994). The validity of the Polycotylidae Cope, 1869, has long been questioned and its phylogenetic position among Plesiosauria debated, as many consider it to be related to the Pliosauridae or to be a sister-group of the Elasmosauridae (Sato and Storrs, 2000; O'Keefe, 2001).

The description of a cryptic species related to the pan-Amazonian frog Allobates femoralis (Boulenger 1883) (Anura: Aromobatidae)

Zootaxa ◽  
2010 ◽  
Vol 2406 (1) ◽  
pp. 1 ◽  
Author(s):  
PEDRO IVO SIMÕES ◽  
ALBERTINA P. LIMA ◽  
IZENI PIRES FARIAS
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Sister Group ◽  
Sensu Stricto ◽  
Left Bank ◽  
Genetic Introgression ◽  
Nucleotide Substitutions ◽  
Advertisement Calls ◽  
Allobates Femoralis

We describe a new species of litter frog from western Brazilian Amazon previously referred to as Allobates femoralis (Boulenger 1883). The new species is allopatric to A. femoralis and its known occurrence is restricted to terra-firme forests on the left bank of the upper Madeira River and southeastern State of Acre. This species is distinguished from A. femoralis and from other species in the A. femoralis group by presenting two-note advertisement calls and conspicuous reddish-orange color on ventral surfaces of hind limbs and posterior abdomen. Phylogenetic analyses based on a fragment of the 16S rRNA mitochondrial gene suggest the new species is the sister group to a clade referred to as A. femoralis occurring in southern State of Acre, from which it is distinguished by six unambiguous nucleotide substitutions, in addition to exclusive advertisement calls and color patterns. The new species is more distantly related to A. femoralis sensu stricto occurring near the A. femoralis type locality in the Peruvian Amazon. Summarizing evidence from molecular phylogenetic analysis, genetic distances and available data on advertisement calls, we identify one possible case of genetic introgression between lineages in this group and highlight the potential for the description of more species within the A. femoralis complex.

scholarly journals Phylogenetic relationships among extinct and extant turtles: the position of Pleurodira and the effects of the fossils on rooting crown-group turtles

2010 ◽  
Vol 79 (3) ◽  
pp. 93-106 ◽  
Author(s):  
Juliana Sterli
Keyword(s):  
Phylogenetic Relationships ◽  
Sister Group ◽  
Molecular Data ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Separate Analysis ◽  
Crown Group ◽  
Rapid Radiation ◽  
Present Contribution ◽  
Origin And Evolution

The origin and evolution of the crown-group of turtles (Cryptodira + Pleurodira) is one of the most interesting topics in turtle evolution, second perhaps only to the phylogenetic position of turtles among amniotes. The present contribution focuses on the former problem, exploring the phylogenetic relationships of extant and extinct turtles based on the most comprehensive phylogenetic dataset of morphological and molecular data analyzed to date. Parsimony analyses were conducted for different partitions of data (molecular and morphological) and for the combined dataset. In the present analysis, separate analyses of the molecular data always retrieve Pleurodira allied to Trionychia. Separate analysis of the morphological dataset, by contrast, depicts a more traditional arrangement of taxa, with Pleurodira as the sister group of Cryptodira, being Chelonioidea the most basal cryptodiran clade. The simultaneous analysis of all available data retrieves all major extant clades as monophyletic, except for Cryptodira given that Pleurodira is retrieved as the sister group of Trionychia. The paraphyly of Cryptodira is an unorthodox result, and is mainly caused by the combination of two factors. First, the molecular signal allies Pleurodira and Trionychia. Second, the morphological data with extinct taxa locates the position of the root of crown-group Testudines in the branch leading to Chelonioidea. This study highlights major but poorly explored topics of turtle evolution: the alternate position of Pleurodira and the root of crown turtles. The diversification of crown turtles is characterized by the presence of long external branches and short internal branches (with low support for the internal nodes separating the major clades of crown turtles), suggesting a rapid radiation of this clade. This rapid radiation is also supported by the fossil record, because soon after the appearance of the oldest crown-group turtles (Middle-Late Jurassic of Asia) the number and diversity of turtles increases remarkably. This evolutionary scenario of a rapid diversification of modern turtles into the major modern lineages is likely the reason for the difficulty in determining the interrelationships and the position of the root of crown-group turtles.

Sign in / Sign up

Export Citation Format

Share Document