Molecular phylogeny of earthworms (Annelida:Crassiclitellata) based on 28S, 18S and 16S gene sequences

2012 ◽  
Vol 26 (2) ◽  
pp. 213 ◽  
Author(s):  
Samuel W. James ◽  
Seana K. Davidson
Keyword(s):  
Molecular Phylogeny ◽  
Morphological Character ◽  
Strong Support ◽  
Molecular Data ◽  
Character Evolution ◽  
Taxon Sampling ◽  
Gene Sequences ◽  
Bayesian Analyses ◽  
16S Gene

Relationships among, and content of, earthworm families have been controversial and unstable. Here we analyse molecular data from 14 Crassiclitellata families represented by 54 genera, the non-crassiclitellate ‘earthworms’ of the Moniligastridae, plus several clitellate outgroups. Complete 28S and 18S gene sequences and a fragment of the 16S gene analysed separately or in concatenated Bayesian analyses indicate that most previously proposed suprafamilial taxa within the Crassiclitellata are para- or polyphyletic. There is strong support for the Metagynophora, which consists of the Crassiclitellata and Moniligastridae. The most basal within-Clitellata branch leads to the small families Komarekionidae, Sparganophilidae, Kynotidae, and Biwadrilidae, found in widely separated areas. A clade composed of Lumbricidae, Ailoscolecidae, Hormogastridae, Criodrilidae and Lutodrilidae appears near the base of the tree, but Criodrilidae and Biwadrilidae are not closely related because the former is sister to the Hormogastridae + Lumbricidae clade. The Glossoscolecidae is here separated into two families, the Glossoscolecidae s.s. and the Pontoscolecidae (fam. nov.). The Megascolecidae is monophyletic within a clade including all acanthodrilid earthworms. There is strong support for the Benhamiinae (Acanthodrilidae s.l.) as sister to Acanthodrilidae + Megascolecidae, but taxon sampling within other acanthodrilid groups was not sufficient to reach further conclusions. The resulting trees support revised interpretations of morphological character evolution.’

Molecular phylogeny of the spoonbills (Aves: Threskiornithidae) based on mitochondrial DNA

Zootaxa ◽  
2010 ◽  
Vol 2603 (1) ◽  
pp. 53 ◽  
Author(s):  
R. TERRY CHESSER ◽  
CAROL K. L. YEUNG ◽  
CHENG-TE YAO ◽  
XIU-HUA TIAN ◽  
SHOU-HSIEN LI
Keyword(s):  
Mitochondrial Dna ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Sister Group ◽  
Molecular Data ◽  
Mitochondrial Genes ◽  
Bayesian Analyses ◽  
Limited Sampling

Spoonbills (genus Platalea) are a small group of wading birds, generally considered to constitute the subfamily Plataleinae (Aves: Threskiornithidae). We reconstructed phylogenetic relationships among the six species of spoonbills using variation in sequences of the mitochondrial genes ND2 and cytochrome b (total 1796 bp). Topologies of phylogenetic trees reconstructed using maximum likelihood, maximum parsimony, and Bayesian analyses were virtually identical and supported monophyly of the spoonbills. Most relationships within Platalea received strong support: P. minor and P. regia were closely related sister species, P. leucorodia was sister to the minor-regia clade, and P. alba was sister to the minor-regia-leucorodia clade. Relationships of P. flavipes and P. ajaja were less well resolved: these species either formed a clade that was sister to the four-species clade, or were successive sisters to this clade. This phylogeny is consistent with ideas of relatedness derived from spoonbill morphology. Our limited sampling of the Threskiornithinae (ibises), the putative sister group to the spoonbills, indicated that this group is paraphyletic, in agreement with previous molecular data; this suggests that separation of the Threskiornithidae into subfamilies Plataleinae and Threskiornithinae may not be warranted.

scholarly journals Muellerella, a lichenicolous fungal genus recovered as polyphyletic within Chaetothyriomycetidae (Eurotiomycetes, Ascomycota)

2019 ◽  
Vol 64 (2) ◽  
pp. 367-381
Author(s):  
Lucia Muggia ◽  
Sergio Pérez-Ortega ◽  
Damien Ertz
Keyword(s):  
Environmental Samples ◽  
Strong Support ◽  
Morphological Diversity ◽  
Molecular Data ◽  
Taxon Sampling ◽  
Phylogenetic Placement ◽  
Monophyletic Lineage ◽  
Black Fungi ◽  
Culture Dependent ◽  
Multilocus Phylogeny

AbstractMolecular data and culture-dependent methods have helped to uncover the phylogenetic relationships of numerous species of lichenicolous fungi, a specialized group of taxa that inhabit lichens and have developed diverse degrees of specificity and parasitic behaviors. The majority of lichenicolous fungal taxa are known in either their anamorphic or teleomorphic states, although their anamorph-teleomorph relationships have been resolved in only a few cases. The pycnidium-forming Lichenodiplis lecanorae and the perithecioid taxa Muellerella atricola and M. lichenicola were recently recovered as monophyletic in Chaetothyriales (Eurotiomycetes). Both genera are lichenicolous on multiple lichen hosts, upon which they show a subtle morphological diversity reflected in the description of 14 species in Muellerella (of which 12 are lichenicolous) and 12 in Lichenodiplis. Here we focus on the teleomorphic genus Muellerella and investigate its monophyly by expanding the taxon sampling to other species occurring on diverse lichen hosts. We generated molecular data for two nuclear and one mitochondrial loci (28S, 18S and 16S) from environmental samples. The present multilocus phylogeny confirms the monophyletic lineage of the teleomorphic M. atricola and M. lichenicola with their L. lecanorae-like anamorphs, but places the rest of the Muellerella species studied in two different monophyletic lineages with strong support. The first, Muellerella spp. 1, is nested within some new lineages of black fungi isolated from different epilithic lichen thalli, while the second, Muellerella spp. 2, is closely related to the Verrucariales. Based on these results, we reappraise the phylogenetic placement of Muellerella and suggest its polyphyly within Chaetothyriomycetidae.

A molecular phylogeny of the Grunts (Perciformes: Haemulidae) inferred using mitochondrial and nuclear genes

Zootaxa ◽  
2011 ◽  
Vol 2966 (1) ◽  
pp. 37 ◽  
Author(s):  
MILLICENT D. SANCIANGCO ◽  
LUIZ A. ROCHA ◽  
KENT E. CARPENTER
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Strong Support ◽  
Morphological Characters ◽  
Cyt B ◽  
Bayesian Analyses ◽  
Mitochondrial Coi ◽  
Outgroup Species ◽  
Molecular Studies ◽  
Upper Jaw

We infer a phylogeny of haemulid genera using mitochondrial COI and Cyt b genes and nuclear RAG1, SH3PX3, and Plagl2 genes from 56 haemulid species representing 18 genera of the expanded haemulids (including the former inermiids) and ten outgroup species. Results from maximum parsimony, maximum likelihood, and Bayesian analyses show strong support for a monophyletic Haemulidae with the inclusion of Emmelichthyops atlanticus. The former inermiids did not form a clade indicating that the highly protrusible upper jaw specialization to planktivory evolved more than once within Haemulidae. The subfamilies Haemulinae and Plectorhinchinae, currently diagnosed by eight morphological characters, most notably the number of chin pores and the origin of the retractor dorsalis, are also recovered from these analyses with the Haemulinae sister to the Plectorhinchinae. Plectorhinchus is monophyletic only with the inclusion of Diagramma. Within the Haemulinae, Pomadasys and Conodon are polyphyletic. In addition, Anisotremus is monophyletic only with the inclusion of Genyatremus and Conodon nobilis, and Haemulon is monophyletic only with the inclusion of Xenistius. These results suggest that further morphological and molecular studies are needed to revise the limits of several haemulid genera.

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.

Molecular phylogeny of the mud lobsters and mud shrimps (Crustacea : Decapoda : Thalassinidea) using nuclear 18S rDNA and mitochondrial 16S rDNA

2002 ◽  
Vol 16 (6) ◽  
pp. 839 ◽  
Author(s):  
C. C. Tudge ◽  
C. W. Cunningham
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
16S Rdna ◽  
18S Rdna ◽  
Strong Support ◽  
Ribosomal Genes ◽  
Bayesian Analyses ◽  
The Family ◽  
Mitochondrial 16S Rdna

Partial sequences of the 18S nuclear and 16S mitochondrial ribosomal genes were obtained for 14�species of thalassinidean shrimp (families Callianassidae, Laomediidae, Strahlaxiidae, Thalassinidae and Upogebiidae) and a further six species in related decapod infraorders (families Aeglidae, Astacidae, Lithodidae, Palinuridae, Raninidae and Scyllaridae). Maximum-likelihood and Bayesian analyses show equivocal support for the monophyly of the Thalassinidea, but show strong support for division of the infraorder into two major clades. This dichotomy separates representatives in the Upogebiidae, Laomediidae and Thalassinidae from those in the Strahlaxiidae and Callianassidae. The Laomediidae is shown to be paraphyletic, with the thalassinid species, Thalassina squamifera, being placed on a branch between Axianassa and a clade comprising Jaxea and Laomedia, the three current laomediid genera. For a monophyletic Laomediidae, the family Axianassidae should be resurrected for the genus Axianassa.

Molecular phylogeny of the Brazilian endemic genus Orthophytum (Bromelioideae, Bromeliaceae) and its implications on morphological character evolution

2014 ◽  
Vol 77 ◽  
pp. 54-64 ◽  
Author(s):  
Rafael B. Louzada ◽  
Katharina Schulte ◽  
Maria das Graças L. Wanderley ◽  
Daniele Silvestro ◽  
Georg Zizka ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Morphological Character ◽  
Character Evolution ◽  
Endemic Genus

scholarly journals Phylogenetic Analyses of Molecular Data and Reconstruction of Morphological Character Evolution in Asian Impatiens section Semeiocardium (Balsaminaceae)

2016 ◽  
Vol 40 (4) ◽  
pp. 1063-1074 ◽  
Author(s):  
Saroj Ruchisansakun ◽  
Timotheüs van der Niet ◽  
Steven B. Janssens ◽  
Pramote Triboun ◽  
Jiranan Techaprasan ◽  
...  
Keyword(s):  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Character Evolution

scholarly journals Improvements in the fossil record may largely resolve the conflict between morphological and molecular estimates of mammal phylogeny

2018 ◽  
Author(s):  
Robin M. D. Beck ◽  
Charles Baillie
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Fossil Record ◽  
Morphological Character ◽  
Molecular Data ◽  
Morphological Data ◽  
Ancestral State ◽  
Case Scenario ◽  
State Reconstruction ◽  
Consensus View

AbstractMorphological phylogenies of mammals continue to show major conflicts with the robust molecular consensus view of their relationships. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships, particularly for fossil taxa for which, in most cases, molecular data is unlikely to ever become available. We tested this under a hypothetical “best case scenario” by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive molecular phylogeny of mammals, and then seeing what effect inclusion of these predicted ancestors had on unconstrained analyses of morphological data. We found that this resulted in topologies that are highly congruent with the molecular consensus, even when simulating the effect of incomplete fossilisation. Most strikingly, several analyses recovered monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record may be sufficient to largely reconcile morphological and molecular phylogenies of mammals, even with current morphological character sets.

Alternaria caricicola, a new species of Alternaria in the section Nimbya from Iran

Phytotaxa ◽  
2019 ◽  
Vol 405 (2) ◽  
pp. 65
Author(s):  
ABDOLLAH AHMADPOUR
Keyword(s):  
New Species ◽  
Molecular Phylogeny ◽  
Morphological Character ◽  
Morphological Characters ◽  
Undescribed Species ◽  
Gene Sequences ◽  
Narrow Channels ◽  
Gapdh Gene ◽  
Plant Families ◽  
A New Species

Alternaria section Nimbya, currently contains six species which are pathogens of members of the Juncaceae and Cyperaceae plant families. The prominent morphological character in the members of this section is internal compartmentation of conidia into conspicuous angular lumina interconnected by narrow channels through the transverse distosepta and fewer transverse eusepta. In the study on fungi from culm lesions of Carex sp. (Cyperaceae) from West Azarbaijan province, Iran, four isolates with typical characteristics of Alternaria were isolated and studied taxonomically. Based on combination of morphological characters and molecular phylogeny based on ITS–rDNA and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene sequences, the isolates represent a new undescribed species of Alternaria in the section Nimbya, which is described here as Alternaria caricicola sp. nov. The new species is characterized by straight to slightly curved obclavate conidia with 6–14 transverse distosepta, 1–4 darkened eusepta, and an unbranched, tapering apical beak. A detailed description and illustrations are provided and compared with similar taxa in the section Nimbya.

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