Molecular phylogeny of the Annelida

2000 ◽  
Vol 78 (11) ◽  
pp. 1873-1884 ◽  
Author(s):  
Damhnait McHugh
Keyword(s):  
Molecular Analysis ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Nuclear Gene ◽  
Sister Group ◽  
The Body ◽  
Sister Group Relationship ◽  
Molecular Evidence ◽  
Gene Sequences ◽  
Sister Relationship

Traditionally, the Annelida has been classified as a group comprising the Polychaeta and the Clitellata. Recent phylogenetic analyses have led to profound changes in the view that the Annelida, as traditionally formulated, is a natural, monophyletic group. Both molecular and morphological analyses support placement of the Siboglinidae (formerly the Pogonophora) as a derived group within the Annelida; there is also evidence, based on molecular analysis of the nuclear gene elongation factor-1α, that the unsegmented echiurids are derived annelids. While monophyly of the Clitellata is well-supported by both molecular and morphological analyses, there is no molecular evidence to support monophyly of the polychaete annelids; the Clitellata fall within a paraphyletic polychaete grade. Relationships among groups of polychaete annelids have not yet been resolved by molecular analysis. Within the Clitellata, paraphyly of the Oligochaeta was indicated in a phylogenetic analysis of cytochrome c oxidase I, which supported a sister relationship between the leeches, including an acanthobdellid and a branchiobdellid, and two of the four oligochaetes in the analysis. There is some evidence from analysis of 18S rRNA sequences for a sister-group relationship between the clitellates and the taxon Aeolosoma. There is no agreement regarding the body form of the basal annelid, and while molecular analyses provide strong support for the Eutrochozoa, the identity of sister-group to the Annelida among the Eutrochozoa remains enigmatic. It is recommended that future investigations include additional conserved gene sequences and expanded taxon sampling. It is likely that the most productive approach to resolving annelid phylogeny, and thus increasing our understanding of annelid evolution, will come from combined analyses of several gene sequences.

A Phylogenetic Analysis and Taxonomic Revision of Bartonia (Gentianaceae: Gentianeae), Based on Molecular and Morphological Evidence

2009 ◽  
Vol 34 (1) ◽  
pp. 162-172 ◽  
Author(s):  
Katherine G. Mathews ◽  
Niall Dunne ◽  
Emily York ◽  
Lena Struwe
Keyword(s):  
Phylogenetic Analyses ◽  
Strong Support ◽  
Taxonomic Revision ◽  
Sister Group ◽  
Species Boundaries ◽  
Morphological Evidence ◽  
Phylogenetic Study ◽  
Sister Group Relationship ◽  
Internal Transcribed Spacer Region ◽  
Test Species

A phylogenetic study and taxonomic revision of the four currently accepted species of Bartonia (Gentianaceae, subtribe Swertiinae) were conducted in order to test species boundaries and interspecific relationships. Species boundaries were examined based on measurements of key quantitative and qualitative morphological characters as given in the original descriptions. Phylogenetic analyses were performed using molecular data from the nuclear internal transcribed spacer region and chloroplast DNA (trnL intron through the trnL-F spacer), separately and combined using parsimony and Bayesian methodologies, incorporating outgroups from subtribes Swertiinae and Gentianinae. The morphological study revealed that characters of one species, B. texana, represent a subset of the morphological variation found within B. paniculata, but that B. paniculata, B. verna, and B. virginica could all be separated from one another. The molecular phylogenetic analyses all found B. texana to nest in a clade with the two recognized subspecies of B. paniculata (subsp. paniculata and subsp. iodandra), making the latter paraphyletic. Bartonia texana is here reduced to subspecific rank, as Bartonia paniculata subsp. texana. Also, the phylogenetic analyses showed strong support for a sister group relationship between B. verna and B. virginica, as opposed to between B. paniculata and B. virginica as has been previously suggested.

Phylogenetic relationships in Hypomyces and allied genera, with emphasis on species growing on wood-decaying homobasidiomycetes

2000 ◽  
Vol 77 (12) ◽  
pp. 1756-1768 ◽  
Author(s):  
Kadri Põldmaa ◽  
Ellen Larsson ◽  
Urmas Kõljalg
Keyword(s):  
Maximum Likelihood ◽  
Sexual Reproduction ◽  
Phylogenetic Relationships ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Sister Group ◽  
28S Rdna ◽  
The Other ◽  
Molecular Evidence

To infer phylogenetic relationships among species of Hypomyces (Fr.) Tul and allied genera, partial sequences of the 28S rDNA were obtained for 21 strains representing 19 species. On the basis of these data and 38 sequences obtained from GenBank, phylogenetic analyses were performed using the programs PAUP and Pee-Wee. Hypomyces appears to be paraphyletic, with species having wet-conidial phialidic anamorphs more closely related to other genera. Hypomyces chrysostomus Berk & Broome is a sister group to the clade that includes species of Aphysiostroma Barrasa et al., Arachnocrea Moravec, and Hypocrea Fr. Based on morphological and molecular evidence, a new genus, Sporophagomyces, is described for Hypomyces chrysostomus and two allied species. Hypomyces broomeanus Tul. forms one clade with species of Sphaerostilbella Sacc. and is transferred to this genus. The recognition of Arachnocrea is justified. The integration of Cladobotryum Nees species that are not known to undergo sexual reproduction with Hypomyces species that possess Cladobotryum anamorphs receives strong support, but the whole complex of these species appears to be paraphyletic. However, constraint trees, which require monophyly of all these ana- and pleo-morphic species, do not appear significantly less likely than the other trees obtained under maximum likelihood or parsimony criteria. For the remaining species of Hypomyces, four distinct lineages are distinguished.

A molecular phylogenetic approach to Longidoridae (Nematoda: Dorylaimida)

Nematology ◽  
2005 ◽  
Vol 7 (1) ◽  
pp. 111-124 ◽  
Author(s):  
Yu He ◽  
Sergei A. Subbotin ◽  
Tatiana V. Rubtsova ◽  
Franco Lamberti ◽  
Derek J.F. Brown ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Strong Support ◽  
Nuclear Gene ◽  
Sister Group ◽  
Bayesian Posterior Probability ◽  
Molecular Phylogenetic ◽  
Secondary Structure Models ◽  
Outgroup Taxon ◽  
Lsu Rrna

Abstract The Longidoridae are a group of ectoparasitic nematodes including two subfamilies and six genera with hundreds of species. Sequences of the D2 and D3 expansion region of the large subunit (LSU) rRNA nuclear gene were amplified and used to reconstruct the phylogeny of longidorids. Phylogenetic analyses with maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) were performed with one outgroup taxon and 62 longidorid sequences. Confidence of inferred clades was assessed by non-parametric bootstrapping for MP and Bayesian posterior probability for ML. All analyses placed Paralongidorus species as an inner group within the otherwise monophyletic genus Longidorus. The genus Xiphinema, except for X. americanum-group species, was placed as the sister group of Longidorus with strong support from the ML and BI analyses. The X. americanum-group was strongly supported as an exclusive clade to other genus Xiphinema species. The position of the Xiphidorus clade was not well resolved and the phylogenetic analyses did not support it as a sister group to Longidorus as previously inferred from morphology. Secondary structure models were constructed for the D2/D3 region of LSU rRNA for all studied species. It was found that sequence-based and structural morphometric rRNA phylogenies were incongruent.

Phylogeny of the semiaquatic bugs (Hemiptera-Heteroptera, Gerromorpha)

2008 ◽  
Vol 39 (4) ◽  
pp. 431-460 ◽  
Author(s):  
Jakob Damgaard
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Sister Group ◽  
Morphological Characters ◽  
Mitochondrial Genes ◽  
Simultaneous Analysis ◽  
Sister Group Relationship ◽  
Individual Character ◽  
Aquatic Bugs

AbstractThe phylogeny of semi-aquatic bugs (Hemiptera-Heteroptera: Gerromorpha) was tested in parsimony analyses of 64 morphological characters and approximately 2.5 kb of DNA sequence data from the mitochondrial genes encoding COI+II and 16SrRNA and the nuclear gene encoding 28SrRNA. The taxon sample included representatives of all families and most subfamilies of Gerromorpha and a selection of outgroup taxa representing the two basal infraorders of Heteroptera, Enicocephalomorpha and Dipsocoromorpha, and two families of Nepomorpha. A simultaneous analysis (SA) of all data, and with gaps scored as fifth state characters, gave a single most parsimonious tree with all families resolved as monophyletic, except the Veliidae, where Microveliinae + Haloveliinae, Veliinae, Rhagoveliinae, Perittopinae, and Ocelloveliinae were resolved as successive sister groups to the Gerridae, thus confirming earlier statements about paraphyly of this family. The Gerridae + Veliidae clade was strongly supported, but otherwise only the Gerridae + Veliidae less Ocelloveliinae and the Gerridae itself had support. These three clades could all be diagnosed on apomorphic morphological characters, although no characters diagnosing the Gerridae were without convergences or present in all included taxa. While the Ocelloveliinae, Veliinae and Haloveliinae could not be diagnosed on convincing apomorphies, the Microveliinae + Haloveliinae, and their sister group relationship with the Gerridae, could be diagnosed on rather strong morphological synapomorphies, suggesting that Gerridae could be expanded to include these two veliid subfamilies, while Ocelloveliinae, and perhaps the remaining veliid subfamilies, could be elevated to new families. In Gerridae, the Ptilomerinae + Halobatinae was sister group to all other subfamilies, while the Rhagadotarsinae + Trepobatinae was sister group to a clade comprising the Gerrinae, Eotrechinae, Cylindrostethinae and Charmatometrinae. Most relationships in this clade were poorly supported and diagnosed, and Cylindrostethinae was surprisingly found to be paraphyletic. The sister group to the Gerridae + Veliidae clade was a strongly supported clade comprising the Paraphrynoveliidae and Macroveliidae, and this, and the lack of convincing synapomorphies for Paraphrynoveliidae, suggest that these two small families could be synonymized. For the basal relationships of Gerromorpha, the Mesoveliidae was strongly supported sister group to all other families, while the Hebridae, Hermatobatidae and Hydrometridae formed a poorly supported and poorly diagnosed sister group to the Gerridae + Veliidae + Paraphrynoveliidae + Macroveliidae clade. The unexpected sister group relationship between Hermatobatidae and Hydrometridae was moderately supported, and could be diagnosed on two synapomorphies, thus giving a new hypothesis about the relationships of these very divergent families. Phylogenetic analyses of individual character partitions gave less resolved and less supported relationships, and the mitochondrial genes COI+II and 16SrRNA contributed negative hidden partitioned Bremer support (HPBS) to the simultaneous analysis tree, probably due to homoplasy caused by saturation effects.

A description of the second species of the genus Bleptus Eaton, 1885 (Ephemeroptera: Heptageniidae) from Japan, and phylogenetic relationships of two Bleptus mayflies inferred from mitochondrial and nuclear gene sequences

Zootaxa ◽  
2021 ◽  
Vol 4974 (2) ◽  
pp. 333-360
Author(s):  
KOJI TOJO ◽  
KEN MIYAIRI ◽  
YUTO KATO ◽  
AYANA SAKANO ◽  
TOMOYA SUZUKI
Keyword(s):  
Phylogenetic Analyses ◽  
Ribosomal Subunit ◽  
Nuclear Gene ◽  
Taxonomic Status ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gene Sequences ◽  
Molecular Phylogenetic ◽  
Black Band ◽  
Relationship Of

A new mayfly species, Bleptus michinokuensis sp. nov. (Ephemeroptera: Heptageniidae) is described on the basis of specimens of male and female adults and mature nymphs collected at a seepage zone of a small freshwater branch of the ‘Tachiya-zawa-gawa’ River located amongst the northern foothills of Mt. Gassan (Shonai-machi Town, Yamagata Prefecture, Japan). This new Bleptus species is characterized by its clear fore and hind wings. That is, they neither exhibit the distinct black band on the fore wings, nor the characteristic darkened margins along the edges of both the fore and hind wings. Rather it has a blackish colored terminal half of its fore legs (i.e., tibial, tarsal and pretarsal segments). These features differ clearly when comparing them to the other known species, Bleptus fasciatus Eaton. The information and data describing the habitat and distribution range of this new species are also noted. We also examined and discussed the genetic relationship of two Bleptus mayflies to settle the taxonomic status, inferred from the partially sequenced cytochrome c oxidase subunit I (COI) and large mitochondrial ribosomal subunit (16S rRNA) genes, and also the nuclear internal transcribed spacer 2 (ITS2) gene sequences. Consequently, phenetic and molecular phylogenetic analyses agreed well in terms of clustering. 

scholarly journals On a remarkable new species of <i>Tharsis</i>, a Late Jurassic teleostean fish from southern Germany: its morphology and phylogenetic relationships

Fossil Record ◽  
2019 ◽  
Vol 22 (1) ◽  
pp. 1-23 ◽  
Author(s):  
Gloria Arratia ◽  
Hans-Peter Schultze ◽  
Helmut Tischlinger
Keyword(s):  
New Species ◽  
Late Jurassic ◽  
Strong Support ◽  
Sister Group ◽  
Common Species ◽  
Upper Jurassic ◽  
Morphological Characters ◽  
Morphological Description ◽  
Sister Group Relationship ◽  
Southern Germany

Abstract. A complete morphological description, as preservation permits, is provided for a new Late Jurassic fish species (Tharsis elleri) together with a revision and comparison of some morphological features of Tharsis dubius, one of the most common species from the Solnhofen limestone, southern Germany. An emended diagnosis of the genus Tharsis – now including two species – is presented. The new species is characterized by a combination of morphological characters, such as the presence of a complete sclerotic ring formed by two bones placed anterior and posterior to the eye, a moderately short lower jaw with quadrate-mandibular articulation below the anterior half of the orbit, caudal vertebrae with neural and haemal arches fused to their respective vertebral centrum, and parapophyses fused to their respective centrum. A phylogenetic analysis based on 198 characters and 43 taxa is performed. Following the phylogenetic hypothesis, the sister-group relationship Ascalaboidae plus more advanced teleosts stands above the node of Leptolepis coryphaenoides. Both nodes have strong support among teleosts. The results confirm the inclusion of Ascalabos, Ebertichthys and Tharsis as members of this extinct family. Tharsis elleri n. sp. (LSID urn:lsid:zoobank.org:act:6434E6F5-2DDD-48CF-A2B1-827495FE46E6, date: 13 December 2018) is so far restricted to one Upper Jurassic German locality – Wegscheid Quarry near Schernfeld, Eichstätt – whereas Tharsis dubius is known not only from Wegscheid Quarry, but also from different localities in the Upper Jurassic of Bavaria, Germany, and Cerin in France.

scholarly journals Placozoa and Cnidaria are sister taxa

2017 ◽  
Author(s):  
Christopher E. Laumer ◽  
Harald Gruber-Vodicka ◽  
Michael G. Hadfield ◽  
Vicki B. Pearse ◽  
Ana Riesgo ◽  
...  
Keyword(s):  
Strong Support ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Large Dataset ◽  
Animal Evolution ◽  
Phylogenetic Placement ◽  
The Matrix ◽  
Show Evidence ◽  
Animal Phylogeny ◽  
Reduced Forms

AbstractThe phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for Cnidaria and Bilateria (=Planulozoa), also seen in most published work to date, depending on the orthologues selected to construct the matrix. We demonstrate that a majority of genes show evidence of compositional heterogeneity, and that the support for Planulozoa can be assigned to this source of systematic error. In interpreting this placozoan-cnidarian clade, we caution against a peremptory reading of placozoans as secondarily reduced forms of little relevance to broader discussions of early animal evolution.

scholarly journals Discovery of a new family of amphibians from northeast India with ancient links to Africa

2012 ◽  
Vol 279 (1737) ◽  
pp. 2396-2401 ◽  
Author(s):  
Rachunliu G. Kamei ◽  
Diego San Mauro ◽  
David J. Gower ◽  
Ines Van Bocxlaer ◽  
Emma Sherratt ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Northeast India ◽  
Sister Group Relationship ◽  
New Family ◽  
Ancient Lineage ◽  
Molecular Phylogenetic ◽  
Threatened Habitats

The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group relationship with the exclusively African family Herpelidae. Relaxed molecular clock analyses indicate that these lineages diverged in the Early Cretaceous, about 140 Ma. The discovery adds a major branch to the amphibian tree of life and sheds light on both the evolution and biogeography of caecilians and the biotic history of northeast India—an area generally interpreted as a gateway between biodiversity hotspots rather than a distinct biogeographic unit with its own ancient endemics. Because of its distinctive morphology, inferred age and phylogenetic relationships, we recognize the newly discovered caecilian radiation as a new family of modern amphibians.

scholarly journals Molecular evidence and marine snake origins

2005 ◽  
Vol 1 (2) ◽  
pp. 227-230 ◽  
Author(s):  
Michael S.Y Lee
Keyword(s):  
Molecular Phylogeny ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Morphological Data ◽  
Molecular Evidence ◽  
Gene Sequences ◽  
Molecular Analyses ◽  
Marine Origin ◽  
Molecular Tree

A molecular phylogeny was used to refute the marine scenario for snake origins. Nuclear gene sequences suggested that snakes are not closely related to living varanid lizards, thus also apparently contradicting proposed relationships between snakes and marine mosasaurs (usually considered to be varanoids). However, mosasaurs share derived similarities with both snakes and living varanids. A reanalysis of the morphological data suggests that, if the relationships between living taxa are constrained to the proposed molecular tree, with fossil forms allowed to insert in their optimal positions within this framework, mosasaurs cluster with snakes rather than with varanids. Combined morphological and molecular analyses also still unite marine lizards with snakes. Thus, the molecular data do not refute the phylogenetic evidence for a marine origin of snakes.

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