scholarly journals Phylogenetic relationships of heteroscleromorph demosponges and the affinity of the genus Myceliospongia (Demospongiae incertae sedis)

2019 ◽  
Author(s):  
Dennis V. Lavrov ◽  
Manuel Maldonado ◽  
Thierry Perez ◽  
Christine Morrow
Keyword(s):  
Molecular Clock ◽  
Phylogenetic Relationships ◽  
Sister Group ◽  
Molecular Data ◽  
Sensu Stricto ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Incertae Sedis ◽  
Middle Paleozoic ◽  
Clade 1

AbstractClass Demospongiae – the largest in the phylum Porifera (Sponges) – encompasses 7,581 accepted species across the three recognized subclasses: Keratosa, Verongimorpha, and Heteroscleromorpha. The latter subclass contains the majority of demosponge species and was previously subdivided into subclasses Heteroscleromorpha sensu stricto and Haploscleromorpha. The current classification of demosponges is the result of nearly three decades of molecular studies that culminated in a formal proposal of a revised taxonomy (Morrow and Cardenas, 2015). However, because most of the molecular work utilized partial sequences of nuclear rRNA genes, this classification scheme needs to be tested by additional molecular markers. Here we used sequences and gene order data from complete or nearly complete mitochondrial genomes of 117 demosponges (including 60 new sequences determined for this study and 6 assembled from public sources) and three additional partial mt-genomes to test the phylogenetic relationships within demosponges in general and Heteroscleromorpha sensu stricto in particular. We also investigated the phylogenetic position of Myceliospongia araneosa – a highly unusual demosponge without spicules and spongin fibers, currently classified as Demospongiae incertae sedis.Our results support the sub-class relationship within demosponges and reveal four main clades in Heteroscleromorpha sensu stricto: Clade 1 composed of Spongillida, Sphaerocladina, and Scopalinida; Clade 2 composed of Axinellida, Biemnida, Bubarida; Clade 3 composed of Tetractinellida and “Rhizomorina” lithistids; and Clade 4 composed of Agelasida, Polymastida, Clionaida, Suberitida, Poecilosclerida, and Tethyida. The four clades appear to be natural lineages that unite previously defined taxonomic orders. Therefore, if those clades are to be systematically interpreted, they will have the rank of superorders (hence S1-S4). We inferred the following relationships among the newly defined clades: (S1(S2(S3+S4))). Analysis of molecular data from Myceliospongia araneosa – first from this species/genus – placed it in S3 as a sister group to Microscleroderma sp. and Leiodermatium sp. (“Rhizomorina”).Molecular clock analysis indicated that the origin of the Heteroscleromorpha sensu stricto as well as the basal split in this group between S1 and the rest of the superorder go back to Cambrian, while the divergences among the three other superorders occurred in Ordovician (with the 95% standard variation from Late Cambrian to Early Silurian). Furthermore most of the proposed orders within Heteroscleromorpha appear to have middle Paleozoic origin, while crown groups within order date mostly to Paleozoic to Mesozoic transition. We propose that these molecular clock estimates can be used to readjust ranks for some of the higher taxa within Heteroscleromorpha.In addition to phylogenetic information, we found several unusual mtgenomic features among the sampled species, broadening our understanding of mitochondrial genome evolution in this group and animals in general. In particular, we found mitochondrial introns within cox2 (first in animals) and rnl (first in sponges).

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.

Dissecting the major African snake radiation: a molecular phylogeny of the Lamprophiidae Fitzinger (Serpentes, Caenophidia)

Zootaxa ◽  
2008 ◽  
Vol 1945 (1) ◽  
pp. 51-66 ◽  
Author(s):  
NICOLAS VIDAL ◽  
WILLIAM R. BRANCH ◽  
OLIVIER S. G. PAUWELS ◽  
S. BLAIR HEDGES ◽  
DONALD G. BROADLEY ◽  
...  
Keyword(s):  
Mitochondrial Protein ◽  
Sister Group ◽  
Molecular Data ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Data Set ◽  
Protein Coding ◽  
Mitochondrial Rrna ◽  
Protein Coding Genes ◽  
History Of

The Elapoidea includes the Elapidae and a large (~60 genera, 280 sp.) and mostly African (including Madagascar) radiation termed Lamprophiidae by Vidal et al. (2007), that includes at least four major groups: the psammophiines, atractaspidines, lamprophiines and pseudoxyrhophiines. In this work, we reviewed the recent taxonomic history of the lamprophiids, and built a data set including two nuclear protein-coding genes (c-mos and RAG2), two mitochondrial rRNA genes (12S and 16S rRNA) and two mitochondrial protein-coding genes (cytochrome b and ND4) for 85 species belonging to 45 genera (thus representing about 75% of the generic diversity and 30% of the specific diversity of the radiation), in order to clarify the phylogenetic relationships of this large and neglected group at the subfamilial and generic levels. To this aim, 480 new sequences were produced. The vast majority of the investigated genera fall into four main monophyletic clusters, that correspond to the four subfamilies mentioned above, although the content of atractaspidines, lamprophiines and pseudoxyrhophiines is revised. We confirm the polyphyly of the genus Stenophis, and the relegation of the genus name Dromophis to the synonymy of the genus name Psammophis. Gonionotophis brussauxi is nested within Mehelya. The genus Lamprophis Fitzinger, 1843 is paraphyletic with respect to Lycodonomorphus Fitzinger, 1843. Lamprophis swazicus is the sister-group to Hormonotus modestus, and may warrant generic recognition. Molecular data do not support the traditional placement of Micrelaps within the Atractaspidinae, but its phylogenetic position, along with that of Oxyrhabdium (previously considered to belong to the Xenodermatidae), requires additional molecular data and they are both treated as Elapoidea incertae sedis. The interrelationships of Psammophiinae, Atractaspidinae, Lamprophiinae, Pseudoxyrhophiinae, Prosymna (13 sp.), Pseudaspis (1 sp.) and Pythonodipsas (1 sp.), Buhoma (2 species), and Psammodynastes (1 sp.) remain unresolved. Finally, the genus Lycognathophis, endemic to the Seychelles, does not belong to the African radiation, but to the Natricidae.

Phylogenetic relationships of the subfamily Pyrgulinae (Gastropoda: Caenogastropoda: Hydrobiidae) with emphasis on the genus Dianella Gude, 1913

Zootaxa ◽  
2005 ◽  
Vol 891 (1) ◽  
pp. 1 ◽  
Author(s):  
Magdalena Szarowska ◽  
Andrzej Falniowski ◽  
FRANK Riedel ◽  
Thomas Wilke
Keyword(s):  
Type Species ◽  
Sister Group ◽  
Molecular Data ◽  
Character Evolution ◽  
Phylogenetic Position ◽  
Sister Group Relationship ◽  
Data Sets ◽  
Sequencing Data ◽  
The Family ◽  
Anatomical Characters

The phylogenetic position of the subfamily Pyrgulinae within the superfamily Rissooidea has been discussed very controversially. Different data sets not only led to different evolutionary scenarios but also to different systematic classifications of the taxon. The present study uses detailed anatomical data for two pyrgulinid taxa, the type species of the subfamily, Pyrgula annulata (Linnaeus, 1767), and the type species of the little known genus Dianella, D. thiesseana (Kobelt, 1878), as well as DNA sequencing data of three gene fragments from representatives of eight rissooidean families to A) infer the phylogenetic position of Pyrgulinae with emphasis on its relationships within the family Hydrobiidae, B) to study the degree of concordance between anatomyand DNAbased phylogenies and C) to trace the evolution of anatomical characters along a multi-gene molecular phylogeny to find the anatomical characters that might be informative for future cladistic analyses. Both anatomical and molecular data sets indicate either a very close or even sister-group relationship of Pyrgulinae and Hydrobiinae. However, there are major conflicts between the two data sets on and above the family level. Notably, Hydrobiidae is not monophyletic in the anatomical analysis. The reconstruction of anatomical character evolution indicates that many of the characters on which the European hydrobioid taxonomy is primarily based upon are problematic. The inability to clearly separate some hydrobiids from other distinct families based on those characters might explain why until only a few years ago, "Hydrobiidae" was a collecting box for numerous rissooidean taxa (mostly species with shells small and lacking any characteristic features). The present study not only stresses the need for comprehensive molecular studies of rissooidean taxa, it also demonstrates that much of the problems surrounding anatomical analyses in rissooidean taxa are due to the lack of comprehensive data for many representatives. In order to aid future comparativeanatomical studies and a better understanding of character evolution in the species-rich family Hydrobiidae, detailed anatomical descriptions for P. annulata and D. thiesseana are provided.Key words: Pyrgulinae, Pyrgula, Dianella, Hydrobiidae, phylogeny, DNA, anatomy, Greece

scholarly journals Cretaceous origin and repeated tertiary diversification of the redefined butterflies

2011 ◽  
Vol 279 (1731) ◽  
pp. 1093-1099 ◽  
Author(s):  
Maria Heikkilä ◽  
Lauri Kaila ◽  
Marko Mutanen ◽  
Carlos Peña ◽  
Niklas Wahlberg
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Bayesian Approaches ◽  
The Family ◽  
Family Level ◽  
Morphological And Molecular Data

Although the taxonomy of the ca 18 000 species of butterflies and skippers is well known, the family-level relationships are still debated. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the superfamilies Papilionoidea, Hesperioidea and Hedyloidea to date based on morphological and molecular data. We reconstructed their phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification along lineages in order to reconstruct their evolutionary history. Our results suggest that the butterflies, as traditionally understood, are paraphyletic, with Papilionidae being the sister-group to Hesperioidea, Hedyloidea and all other butterflies. Hence, the families in the current three superfamilies should be placed in a single superfamily Papilionoidea. In addition, we find that Hedylidae is sister to Hesperiidae, and this novel relationship is supported by two morphological characters. The families diverged in the Early Cretaceous but diversified after the Cretaceous–Palaeogene event. The diversification of butterflies is characterized by a slow speciation rate in the lineage leading to Baronia brevicornis , a period of stasis by the skippers after divergence and a burst of diversification in the lineages leading to Nymphalidae, Riodinidae and Lycaenidae.

Phylogenetic relationships in the lizard genus Diplodactylus Gray and resurrection of Lucasium Wermuth (Gekkota, Diplodactylidae)

2007 ◽  
Vol 55 (3) ◽  
pp. 197 ◽  
Author(s):  
Paul M. Oliver ◽  
Mark N. Hutchinson ◽  
Steven J. B. Cooper
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Arid Zone ◽  
Sister Group ◽  
Molecular Data ◽  
The Other ◽  
Sister Group Relationship ◽  
Considerable Uncertainty ◽  
Biogeographic History ◽  
Species Groups

Diplodactylid geckos offer a model system for investigating the biogeographic history of Australia and adaptive radiations in the arid zone, but there is considerable uncertainty in the systematics of several key genera. We used sequence data from mitochondrial DNA to carry out a comprehensive analysis of phylogenetic relationships of geckos in the genus Diplodactylus. Parsimony and Bayesian analyses were highly concordant and allocated all species to one of two monophyletic clades, one comprising the species placed in the vittatus and conspicillatus species groups, the other comprising species placed in the stenodactylus and steindachneri species groups, plus D. byrnei, formerly in the vittatus group. The distinctness of these two clades is supported by external morphology of the digits, body and limb proportions, and osteology of the bones in the orbital region, and we use these characters to formally define the two clades as genera. We revive and expand the genus Lucasium for D. byrnei, D. steindachneri and the stenodactylus group, with the other species staying in a redefined Diplodactylus. The monotypic Rhynchoedura is distinct from Lucasium, although the Bayesian mtDNA analysis (but not parsimony) gives some support for a sister-group relationship between Lucasium and Rhynchoedura. Molecular data suggest that each of these clades represents a distinct radiation into semiarid and arid terrestrial habitats during the mid-Tertiary, well before the hypothesised Pliocene onset of major aridification.

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.

Molecular phylogeny of Asiatic Short-Tailed Shrews, genus Blarinella Thomas, 1911 (Mammalia: Soricomorpha: Soricidae) and its taxonomic implications

Zootaxa ◽  
2012 ◽  
Vol 3250 (1) ◽  
pp. 43 ◽  
Author(s):  
SHUNDE CHEN ◽  
SHAOYING LIU ◽  
YANG LIU ◽  
KAI HE ◽  
WEICAI CHEN ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Southwest China ◽  
Molecular Data ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Species Status ◽  
Molecular Phylogenetic ◽  
Paraphyletic Group ◽  
Poorly Differentiated ◽  
Taxonomic Implications

The classification and phylogenetic relationships of the genus Blarinella have been traditionally based on morphologicalcharacteristics, and there have been no studies published about the molecular phylogenetic relationships and biogeographyfor this genus. Here, we reconstructed the phylogenetic relationships of the genus Blarinella based on one nuclear (ApoB)and two mitochondrial (cyt-b, 16S rRNA) genes. Our results supported the monophyly of the genus Blarinella and thevalid species status of Blarinella wardi. Nevertheless, two morphologically defined Blarinella species, B. quadraticaudaand B. griselda, were poorly differentiated by molecular data; B. quadraticauda was found embedded within B. griseldamaking the latter a paraphyletic group. These results indicate that B. quadraticauda might be under a budding speciationscenario or is a restricted geographical subspecies of B. griselda. Phylogeographic analyses suggest that diversificationand speciation of Blarinella might have been promoted by vicariance events associated to the complex topography of Southwest China. Further morphological, genetic and ecological studies are necessary to examine these hypotheses.

Early embryology of Vochysiaceae and some insights into its phylogeny and intrafamilial taxonomy

Phytotaxa ◽  
2020 ◽  
Vol 443 (3) ◽  
pp. 211-257
Author(s):  
RENATA CARMO-OLIVEIRA ◽  
LUCIANA NASCIMENTO CUSTÓDIO ◽  
BERTA LANGE DE MORRETES ◽  
PAULO EUGÊNIO OLIVEIRA
Keyword(s):  
Developmental Stages ◽  
Embryo Sac ◽  
Sister Group ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Its Phylogeny ◽  
The Family

Embryological data provides insights into the taxonomy and evolution of angiosperms.  Vochysiaceae is a mostly Neotropical family whose phylogenetic position was greatly influenced by reconstructions based on molecular data, and despite its monosymmetric and oligostemonous flowers, was included as a sister group of polysymmetric and polystemonous Myrtaceae. However, molecular data has yet to resolve the relationships between the genera inside the family. We analysed the early embryology of some species of five out of the six generally accepted Neotropical genera using sequential histological analyses to compare the microsporogenesis and gametogenesis and megasporogenesis and gametogenesis between clades and with the embryology of the well-studied Myrtales. We observed some marked differences in timing and developmental stages, which somewhat corroborate the clades defined from molecular data. Multiple archesporium and embryo sacs, as well as megagametophyte maturation and fertilization long after anthesis, characterized the Qualea-Ruizteranea-Callisthene (QRC) clade, while single embryo sac mature at anthesis characterized the Vochysia-Salvertia (VS) clade. Tri-cellular pollen only occurred in Salvertia convallariodora. Seven of the eight main embryological features supported the Myrtales as present in Vochysiaceae and the remaining one, inner integument with two layers of cells, was observed in some Qualea. Thus, the studied Vochysiaceae embryology conforms very well within the order and only their strongly monosymmetric and oligostemonous flowers are less common among Myrtales.

Relationships and phylogenetic revision of Filistatinella spiders (Araneae : Filistatidae)

2017 ◽  
Vol 31 (6) ◽  
pp. 665 ◽  
Author(s):  
Ivan L. F. Magalhaes ◽  
Martín J. Ramírez
Keyword(s):  
Phylogenetic Relationships ◽  
Sister Group ◽  
Morphological Data ◽  
Incertae Sedis ◽  
The North ◽  
Central Asian ◽  
Phylogenetic Revision ◽  
Fine Morphology ◽  
Arid And Semiarid ◽  
Scanning Electron

Filistatids represent an antique lineage of araneomorph spiders which are most diverse in arid and semiarid regions of the globe. Phylogenetic relationships among its genera are still largely unexplored, and previous studies disagree on the position of the North American Filistatinella Gertsch & Ivie, 1936, which could either be the sister group of all other Prithinae, or deeply nested in the subfamily. We present a new phylogenetic hypothesis based on morphological data, which supports the position of Filistatinella at the base of Prithinae. We also argue that the central Asian Pholcoides Roewer, 1960, hitherto considered incertae sedis in the subfamily, represents the putative sister group of Filistatinella. The latter genus is revised, and we describe its fine morphology in detail using optical and scanning electron microscopy. We redescribe the three previously known species, F. crassipalpis (Gertsch, 1935), F. domestica Desales-Lara, 2012 and F. palaciosi Jiménez & Palacios-Cardiel, 2012. Seven new species are named: F. kahloae, sp. nov. and F. chilindrina, sp. nov. from Mexico; F. pistrix, sp. nov., F. tohono, sp. nov., F. howdyall, sp. nov. and F. hermosa, sp. nov. from south-western USA; and F. spatulata, sp. nov. from the border between the two countries. The phylogenetic relationships among these 10 species are assessed, revealing the monophyly of the genus. http://zoobank.org/urn:lsid:zoobank.org:pub:71820858-545C-43EC-98E1-F9BF490AA3F1

Phylogenetic relationships of Palaeogene ziphodont eusuchians and the status ofPristichampsusGervais, 1853

2012 ◽  
Vol 103 (3-4) ◽  
pp. 521-550 ◽  
Author(s):  
Christopher A. Brochu
Keyword(s):  
Phylogenetic Relationships ◽  
Middle Eocene ◽  
Distinct Species ◽  
Sister Group ◽  
New Combination ◽  
Phylogenetic Position ◽  
Western North America ◽  
Close Relationship ◽  
The Status ◽  
Group A

ABSTRACTEusuchians with deep snouts and labiolingually compressed teeth are known from the Palaeogene of Laurasia. These are usually referred to Pristichampsinae, but the type species,Pristichampsus rollinati, is based on insufficiently diagnostic material and should be treated as a nomen dubium. At least two Lutetian species formerly referred toPristichampsuscan be recognised –Boverisuchus magnifronsin Germany and possibly elsewhere in Europe, andBoverisuchus vorax, new combination, in western North America. Material from the middle Eocene of Italy and Texas may represent distinct species. A phylogenetic analysis confirms their close relationship and also supports a relationship with two Asian forms – early EocenePlanocrania datangensisand PalaeocenePlanocrania hengdongensis. The name Planocraniidae Li 1976 is applied to this group. A distinctive quadrate with a prominent dorsal peak between medial and lateral hemicondyles is known only inBoverisuchus, and although the teeth ofPlanocraniaare flattened, they are not serrated. Planocraniids maintain a phylogenetic position as the sister group to Crocodyloidea+Alligatoroidea, but this part of the tree is unstable and discovery of older, more primitive planocraniids will help resolve conflicts on the phylogenetic relationships of extant crocodylian lineages.

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