scholarly journals Reassessment of the phylogenetic interrelationships of basal turtles (Testudinata)

2017 ◽  
Author(s):  
Jérémy Anquetin
Keyword(s):  
Phylogenetic Analysis ◽  
Data Matrix ◽  
Late Triassic ◽  
Character State ◽  
Additional Species ◽  
Data Set ◽  
Fossil Species ◽  
Turtle Species ◽  
Phylogenetic Placement ◽  
First Time

Recent discoveries from the Late Triassic and Middle Jurassic have significantly improved the fossil record of early turtles. These new forms offer a unique opportunity to test the interrelationships of basal turtles. Nineteen fossil species are added to the taxon sample of the most comprehensive morphological phylogenetic analysis of the turtle clade. Among these additional species are recently discovered forms (e.g., Odontochelys semitestacea, Eileanchelys waldmani, Condorchelys antiqua), taxa generally omitted from previous analyses (e.g., chengyuchelyids, Sichuanchelys chowi) and species included in a phylogenetic analysis for the first time (Naomichelys speciosa and Siamochelys peninsularis). The coding of several characters is reassessed in light of recent observations, but also in order to reduce unwarranted assumptions on character and character state homologies. Additional characters from previous analyses, as well as five new ones, are also included, resulting in a data matrix of 178 characters scored for 86 turtle species and 7 fossil outgroups.The data set resolves the relationships of most newly included taxa, with the exception of Sichuanchelys chowi and ‘Chengyuchelys’ dashanpuensis. The phylogenetic placement of Heckerochelys romani, Condorchelys antiqua and Eileanchelys waldmani as stem turtles more derived than Kayentachelys aprix but more basal than Meiolania platyceps and Mongolochelys efremovi is corroborated. The relationships of chengyuchelyids remain unclear and more investigation is needed regarding these forms, yet interestingly they are unstable with respect to stem turtles. In contrast to previous analyses, Arundelemys dardeni is placed within pleurosternids. Siamochelys peninsularis falls within xinjiangchelyids. Perhaps the most salient conclusion of the present study is the placement of Naomichelys speciosa as a basal member of a clade uniting meiolaniids, Mongolochelys efremovi and Otwayemys cunicularius. This clade of rather large stem turtles was spread worldwide during the Mesozoic at least and persisted up until the Pleistocene with meiolaniids.

A comparison of methodological approaches to the subfamilial classification of the Naididae (Oligochaeta)

1987 ◽  
Vol 65 (3) ◽  
pp. 691-707 ◽  
Author(s):  
A. F. L. Nemec ◽  
R. O. Brinkhurst
Keyword(s):  
Data Matrix ◽  
Jaccard Coefficient ◽  
Data Set ◽  
Parsimony Method ◽  
Fit Statistics ◽  
Reconstruction Methods ◽  
Linkage Methods ◽  
The Family ◽  
First Time

A data matrix of 23 generic or subgeneric taxa versus 24 characters and a shorter matrix of 15 characters were analyzed by means of ordination, cluster analyses, parsimony, and compatibility methods (the last two of which are phylogenetic tree reconstruction methods) and the results were compared inter alia and with traditional methods. Various measures of fit for evaluating the parsimony methods were employed. There were few compatible characters in the data set, and much homoplasy, but most analyses separated a group based on Stylaria from the rest of the family, which could then be separated into four groups, recognized here for the first time as tribes (Naidini, Derini, Pristinini, and Chaetogastrini). There was less consistency of results within these groups. Modern methods produced results that do not conflict with traditional groupings. The Jaccard coefficient minimizes the significance of symplesiomorphy and complete linkage avoids chaining effects and corresponds to actual similarities, unlike single or average linkage methods, respectively. Ordination complements cluster analysis. The Wagner parsimony method was superior to the less flexible Camin–Sokal approach and produced better measure of fit statistics. All of the aforementioned methods contain areas susceptible to subjective decisions but, nevertheless, they lead to a complete disclosure of both the methods used and the assumptions made, and facilitate objective hypothesis testing rather than the presentation of conflicting phylogenies based on the different, undisclosed premises of manual approaches.

Molecular insights into the phylogenetic placement of the poorly known genus Niceforonia Goin & Cochran, 1963 (Anura: Brachycephaloidea)

Zootaxa ◽  
2018 ◽  
Vol 4514 (4) ◽  
pp. 487
Author(s):  
ANDRÉS R. ACOSTA-GALVIS ◽  
JEFFREY W. STREICHER ◽  
LUIGI MANUELLI ◽  
TRAVIS CUDDY ◽  
RAFAEL O. DE SÁ
Keyword(s):  
Phylogenetic Analysis ◽  
New World ◽  
Taxonomic Revision ◽  
Phylogenetic Inference ◽  
Genetic Distances ◽  
Molecular Phylogenetic Analysis ◽  
Phylogenetic Placement ◽  
Molecular Phylogenetic ◽  
First Time

Among New World direct-developing frogs belonging to the clade Brachycephaloidea (= Terraranae), there are several genera with uncertain phylogenetic placements. One notable example is the genus Niceforonia Goin & Cochran 1963, which includes three species that are endemic to Colombia. Three specimens of the species Niceforonia nana were collected and for the first time the genus is included in a molecular phylogenetic analysis of mitochondrial (mtDNA; 12S and 16S) and nuclear (nucDNA; TYR and RAG1) markers. Molecular phylogenetic inference based on concatenated and separate mtDNA and nucDNA analyses recovered Niceforonia nana nested within Hypodactylus Hedges et al. 2008, rendering the latter genus paraphyletic. Consequently, herein we place the genus Hypodactylus in the synonymy of Niceforonia to resolve the paraphyly and place Niceforonia in the subfamily Hypodactylinae. Based on our revised concept of the genus Niceforonia we conducted preliminary morphological comparisons using specimens and literature descriptions. Finally, Nicefornia nana is quite divergent from other species of Niceforonia (uncorrected genetic distances of ca. 10% 16S and 7% TYR) suggesting that further taxonomic revision may be warranted. 

The enigmatic diapsid Acerosodontosaurus piveteaui (Reptilia: Neodiapsida) from the Upper Permian of Madagascar and the paraphyly of “younginiform” reptiles

2009 ◽  
Vol 46 (9) ◽  
pp. 651-661 ◽  
Author(s):  
Constanze Bickelmann ◽  
Johannes Müller ◽  
Robert R. Reisz
Keyword(s):  
Phylogenetic Analysis ◽  
Data Matrix ◽  
Upper Permian ◽  
Phylogenetic Position ◽  
Ancestral Condition ◽  
Phylogenetic Data ◽  
First Time ◽  
Evolutionary Lineages

A restudy of the Upper Permian diapsid Acerosodontosaurus piveteaui from Madagascar indicates that the bone formerly identified as the quadratojugal is a fragment of a rib. This in turn implies that, in contrast to previous studies, the lower temporal arcade must be considered incomplete and derived relative to the ancestral condition. Since the phylogenetic position of Acerosodontosaurus is poorly understood, the taxon was entered into a modified phylogenetic data matrix of diapsid reptiles, and the purported monophyly of “Younginiformes” was tested for the first time by including all potential members of the clade as separate taxa, as well as other taxa from the same deposits. The results of the phylogenetic analysis do not support the monophyly of “younginiform” reptiles. Instead, most taxa cluster unresolved at the base of Neodiapsida, a finding that has important implications for the understanding of early diapsid evolution because it suggests that early neodiapsids represent several distinct evolutionary lineages. Acerosodontosaurus and Hovasaurus do form a clade, a finding consistent with the stratigraphic age and biogeography of these taxa.

scholarly journals First nearly complete skull of Gallotia auaritae (lower-middle Pleistocene, Squamata, Gallotiinae) and a morphological phylogenetic analysis of the genus Gallotia

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Penélope Cruzado-Caballero ◽  
Carolina Castillo Ruiz ◽  
Arnau Bolet ◽  
Juan Ramón Colmenero ◽  
Julio De la Nuez ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cranial Morphology ◽  
Middle Pleistocene ◽  
Phylogenetic Position ◽  
Fossil Species ◽  
La Palma ◽  
Computed Microtomography ◽  
X Ray Computed ◽  
Cranial Osteology ◽  
First Time

Abstract The Canary Islands are an Atlantic archipelago known for its high number of endemic species. Among the most known endemic vertebrate species are the giant lizards of the genus Gallotia. We describe the cranial osteology of the first almost complete and articulated fossil skull of the taxon Gallotia auaritae, recovered from the lower-middle Pleistocene of the La Palma island. In this work, X-ray computed microtomography images were used to perform an exhaustive phylogenetic analysis where most of the extant and fossil species of the genus Gallotia were included for first time. This analysis recovered a monophyletic Gallotia clade with similar topology to that of molecular analyses. The newly described specimen shares some characters with the group formed by G. bravoana, G. intermedia and G. simonyi, G. auaritae, and its position is compatible with a referral to the latter. Our study adds new important data to the poorly known cranial morphology of G. auaritae, and the phylogenetic analysis reveals an unexpected power of resolution to obtain a morphology-based phylogeny for the genus Gallotia, for inferring the phylogenetic position of extinct species and for helping in the identification of fossil specimens.

Phylogeny of the Mycetophiliformia, with proposal of the subfamilies  Heterotrichinae, Ohakuneinae, and Chiletrichinae for the Rangomaramidae (Diptera, Bibionomorpha)

Zootaxa ◽  
2007 ◽  
Vol 1535 (1) ◽  
pp. 1-92 ◽  
Author(s):  
DALTON DE SOUZA AMORIM ◽  
EIRIK RINDAL
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Sister Group ◽  
Data Matrix ◽  
Southern Brazil ◽  
The Family ◽  
First Time ◽  
A New Species ◽  
Transformation Series

A phylogenetic analysis of the Mycetophiliformia (= Sciaroidea) was performed to determine the relationships among its families and to place the following genera of uncertain position in the system: Heterotricha, Ohakunea, Colonomyia, Freemanomyia, Rhynchoheterotricha, Chiletricha, Afrotricha, Anisotricha, Kenyatricha, Nepaletricha, Sciarosoma, Sciaropota, Insulatricha, Cabamofa, Rogambara, and Starkomyia. Eratomyia n. gen. is described based on a new species from Ecuador. Colonomyia brasiliana sp.n. and Colonomyia freemani sp.n. are described respectively from southern Brazil and Chile. The male of Cabamofa mira Jaschhof is described for the first time. A total of 64 terminal taxa and 137 transformation series (with 202 characters) were included in the data matrix, with a number of new features from thoracic morphology. Willi Hennig’s 1973 system for the higher Bibionomorpha was adopted using the name Mycetophiliformia for the Sciaroidea. The Mycetophiliformia are monophyletic. The family Cecidomyiidae appears as the sister group of the remaining Mycetophiliformia, followed by the Sciaridae. In the preferred topology, the Rangomaramidae appear as the group sister of a clade consisting of (Ditomyiidae + Bolitophilidae + Diadocidiidae + Keroplatidae) and of (Lygistorrhinidae + Mycetophilidae). The topology within the Rangomaramidae is (Chiletrichinae subfam. n. (Heterotrichinae subfam. n. ((Rangomaraminae + Ohakuneinae subfam. n.))). The Chiletrichinae include the genera Kenyatricha, Rhynchoheterotricha, Insulatricha, Chiletricha, and Eratomyia n. gen. Heterotrichinae and Rangomaraminae are monotypic. The subfamily Ohakuneinae includes Ohakunea, Colonomyia, Cabamofa, and Rogambara. The positions of Freemanomyia, Loicia, Taxicnemis, Sciaropota, Starkomyia, Anisotricha, Nepaletricha, and Sciarosoma are considered. Afrotricha might belong to the Sciaridae. The similarities used by many authors to gather the Sciaridae and Mycetophilidae in a clade are shown to be a combination of plesiomorphies and homoplasies.

scholarly journals A New Cynodont from the Late Triassic Los Colorados Formation (Argentina, South America) Reveals a Novel Paleobiogeographic Context for Mammalian Ancestors

2021 ◽  
Author(s):  
L. C. GAETANO ◽  
F. ABDALA ◽  
F. D. SEOANE ◽  
A. TARTAGLIONE ◽  
M. SCHULZ ◽  
...  
Keyword(s):  
Data Matrix ◽  
Late Triassic ◽  
Character State ◽  
New Taxon ◽  
X Rays ◽  
Crown Group ◽  
Unique Character ◽  
New Findings ◽  
Micro Tomography ◽  
Important Center

Abstract Probainognathia is a derived lineage of cynodonts which encompass Mammalia as their crown-group. The profuse record of probainognathians from the Carnian of Argentina contrasts with their Norian representation, with only one named species. Here we describe a new probainognathian, Tessellatia bonapartei gen. et sp. nov., from the Norian Los Colorados Formation of the Ischigualasto-Villa Unión Basin of Argentina. The new taxon, represented by a partial cranium with articulated lower jaws, was analyzed through neutron and X-rays micro-tomography (µCT). The high-resolution neutron µCT data allowed the identification of a unique character state combination, including features inaccessible through traditional techniques. We constructed the largest phylogenetic data-matrix of non-mammalian cynodonts. The new species and its sister-taxon, the Brazilian Therioherpeton, are recovered as probainognathians, closely related to Mammaliamorpha. We conducted the first quantitative paleobiogeographic analysis of non-mammalian cynodonts, focusing in probainognathians. The results indicate that Probainognathia and Mammaliamorpha originated in Brazil, which was an important center of diversification during the Triassic. Finally, China is identified as the ancestral area of Mammaliaformes. These new findings, besides adding to the knowledge of the poorly represented Norian cynodonts from the Los Colorados Formation, are significant to improve our understanding of probainognathian diversity, evolution, and paleobiogeographic history.

scholarly journals Revised phylogenetic analysis of the Aetosauria (Archosauria: Pseudosuchia); assessing the effects of incongruent morphological character sets

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1583 ◽  
Author(s):  
William G. Parker
Keyword(s):  
Phylogenetic Analysis ◽  
Convergent Evolution ◽  
Morphological Character ◽  
Late Triassic ◽  
Parsimony Analysis ◽  
Weak Support ◽  
Selective Pressures ◽  
Body Regions ◽  
High Species Diversity ◽  
First Time

Aetosauria is an early-diverging clade of pseudosuchians (crocodile-line archosaurs) that had a global distribution and high species diversity as a key component of various Late Triassic terrestrial faunas. It is one of only two Late Triassic clades of large herbivorous archosaurs, and thus served a critical ecological role. Nonetheless, aetosaur phylogenetic relationships are still poorly understood, owing to an overreliance on osteoderm characters, which are often poorly constructed and suspected to be highly homoplastic. A new phylogenetic analysis of the Aetosauria, comprising 27 taxa and 83 characters, includes more than 40 new characters that focus on better sampling the cranial and endoskeletal regions, and represents the most comprenhensive phylogeny of the clade to date. Parsimony analysis recovered three most parsimonious trees; the strict consensus of these trees finds an Aetosauria that is divided into two main clades: Desmatosuchia, which includes the Desmatosuchinae and the Stagonolepidinae, and Aetosaurinae, which includes the Typothoracinae. As defined Desmatosuchinae now containsNeoaetosauroides engaeusand several taxa that were previously referred to the genusStagonolepis, and a new clade, Desmatosuchini, is erected for taxa more closely related toDesmatosuchus. Overall support for some clades is still weak, and Partitioned Bremer Support (PBS) is applied for the first time to a strictly morphological dataset demonstrating that this weak support is in part because of conflict in the phylogenetic signals of cranial versus postcranial characters. PBS helps identify homoplasy among characters from various body regions, presumably the result of convergent evolution within discrete anatomical modules. It is likely that at least some of this character conflict results from different body regions evolving at different rates, which may have been under different selective pressures.

Corrigendum to: The phylogenetic placement of Australian Linderniaceae and implications for generic taxonomy

2018 ◽  
Vol 31 (4) ◽  
pp. 373
Author(s):  
Ed Biffin ◽  
W. R. (Bill) Barker ◽  
Bruce Wannan ◽  
Yi-Shuo Liang
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Phylogeny ◽  
Dna Sequences ◽  
Sister Relationship ◽  
Australian Species ◽  
Phylogenetic Placement ◽  
Generic Framework ◽  
Broad Concept ◽  
First Time ◽  
Name Changes

The taxonomy of Linderniaceae has been considered difficult, particularly in the establishment of a stable generic framework. The prevailing approach in Australia and globally has been to adopt a broad concept of Lindernia encompassing several segregates that have at various times been recognised as genera or subgeneric taxa. A recent global conspectus drawing on molecular phylogeny returned Lindernia to a narrower circumscription and also retained several long-recognised and more recently established genera. It included a polyphyletic Vandellia, encompassing many Australian species previously accepted as belonging in Lindernia. Here, we test these generic concepts using the phylogenetic analysis of plastid matK DNA sequences, including representatives of Australian Linderniaceae. We propose a generic taxonomy that resolves existing polyphyly and balances the need for name changes against the information conveyed by generic names. Our concept of Lindernia recognises three monophyletic subgenera. Evidence is insufficient to determine whether Micranthemum should be subsumed in Lindernia or remains a close ally with a sister relationship to it. In light of our findings, we return most of the Australian species to Lindernia; we also establish for the first time: Lindernia subg. Ilysanthes (Raf.) Wannan, W.R.Barker & Y.S.Liang, based on Ilysanthes Raf.; a replacement name Yamazakia W.R.Barker, Y.S.Liang & Wannan for Tittmannia Rchb. nom. rej., with consequential combinations Y. viscosa (Hornem.) W.R.Barker, Y.S.Liang & Wannan, based on Gratiola viscosa Hornem. and Y. pusilla W.R.Barker, Y.S.Liang & Wannan, based on Gratiola pusilla Willd.; and, in expanding Torenia, the combination Tor. anagallis (Burm.f.) Wannan, W.R.Barker & Y.S.Liang, based on Ruellia anagallis Burm.f.

Phylogenetic analysis and taxonomy of the subgenus Gnathopaederus Chapin and related groups of Paederus s.l. (Coleoptera:Staphylinidae:Paederinae)

2009 ◽  
Vol 23 (5) ◽  
pp. 422
Author(s):  
Xiao-Yan Li ◽  
Hong-Zhang Zhou
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Morphological Characters ◽  
Character State ◽  
Robust Solution ◽  
Current Classification ◽  
The Status ◽  
Definition Of ◽  
Taxonomic Studies ◽  
First Time

The paederine genus Paederus s.l. (Coleoptera : Staphylinidae) is a hyperdiverse group of some 500 species worldwide. Although the subtribe Paederina, in which the genus resides, is monophyletic the status of numerous genera and subgenera is questionable and the current classification is likely to be flawed. As part of detailed studies on the paederine fauna of China, we undertook a preliminary morphologically-based phylogenetic analysis to determine the relationships of Paederus (Gnathopaederus) and related subgenera, as a basis for a revision of the subgenus, and as an attempt to provide a better framework for future taxonomic studies on the group as a whole. The analysis was based on 66 adult morphological characters for 30 ingroup taxa, including all six species of P. (Gnathopaederus). The results show that P. (Gnathopaederus) and P. (Paederus), and the genera Megalopaederus, Pachypaederus and Paederidus are monophyletic, and that P. (Eopaederus) and P. (Harpopaederus) are paraphylyetic. However, our analysis did not offer a robust solution to relationships among other clades within Paederus s.l. although it seems clear that Paederus s.l. is not monophyletic with respect to the above genera. The monophyly of P. (Gnathopaederus) is supported by the mandibular basal medial tooth having two cuspids separated dorsoventrally. Based largely on this character state, the definition of the subgenus is refined; six species are recognized, including two new species described from China as follows: P. (G.) daozhenensis, sp. nov. from Guizhou, and P. (G.) jilongensis, sp. nov. from Xizang; three species, P. bursavacua Willers, P. yunnanensis Willers and P. solodovnikovi Willers, are newly assigned to the subgenus according to a revised subgeneric definition. New morphological characters including important secondary sexual characters and sexual dimorphism are described and male genitalia are illustrated for the first time for the type species of the subgenus, P. (G.) szechuanus (Chapin). A key to the six species is presented and the distribution of each species is documented and discussed.

Harnessing the power of phylogenomics to disentangle the directionality and signatures of interkingdom host jumping in the parasitic fungal genus Tolypocladium

Mycologia ◽  
2018 ◽  
Vol 110 (1) ◽  
pp. 104-117 ◽  
Author(s):  
Quandt ◽  
Patterson ◽  
Spatafora
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Gene Clusters ◽  
Host Specialization ◽  
Comparative Genomic ◽  
Character State ◽  
Lineage Sorting ◽  
Additional Species ◽  
Data Set ◽  
Host Jump

Host specialization is common among parasitic fungi; however, there are examples when transitions in host specificity between disparately related hosts have occurred. Here, we examine the interkingdom host jump from insect pathogenicity and mycoparasitism in Tolypocladium. Previous phylogenetic inferences made using only a few genes and with poor support reconstructed an ancestral character state of insect pathogenesis, a transition to mycoparasitism, and reversions to insect pathogenesis. To further explore the directionality and genes underlying the transitions in host, we sequenced two additional species of Tolypocladium (T. capitatum and T. paradoxum) and used phylogenomics to compare two insect pathogens and two mycoparasites. Our whole-genome-scale analysis suggests that the diversification of Tolypocladium species happened relatively quickly and that the truffle parasites form a monophyletic, derived lineage within the genus that is the result of a single ecological transition or host jump from insects to fungi. A significant amount of gene tree/species tree discordance occurs within the data set, and we infer this to be the product of both an historical hybridization event and incomplete lineage sorting that was likely because of the rapid diversification of the clade. Furthermore, comparative genomic analyses revealed a set of genes that are exclusive to the mycoparasitic species. These potentially mycoparasitic gene clusters were characterized by a reduced proportion of secreted proteins when compared with entomopathogen-enriched genes and involved the reshaping of the fungal secretome in the ecological context of mycoparasitism.

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