scholarly journals Mitochondrial DNA Phylogeny of Babblers (Timaliidae)

The Auk ◽  
2003 ◽  
Vol 120 (1) ◽  
pp. 35-54
Author(s):  
Alice Cibois
Keyword(s):  
Mitochondrial Dna ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Molecular Data ◽  
Mitochondrial Genes ◽  
Dna Phylogeny ◽  
Traditional Classification ◽  
Phylogenetic Hypotheses

Abstract The systematics of the babblers (Timaliidae) and related members of the Old World insectivorous passerines have been particularly difficult. To clarify our understanding of this group, phylogenetic relationships were constructed using sequences of three mitochondrial genes (cytochrome b, rRNA 12S and 16S). The results indicated that several species traditionally placed among babblers, the shrike babblers (Pteruthius) and the Gray-chested Thrush Babbler (Kakamega poliothorax), are not related to the Timaliidae, but belong to other passerine groups. Furthermore, the phylogenetic hypotheses inferred from molecular data suggest that the babblers assemblage includes two other oscine taxa traditionally considered to be distantly related, Sylvia (Sylviidae) and Zosterops (Zosteropidae). The polyphyly of several babbler genera is discussed, with particular attention to the laughingthrushes (genera Garrulax and Babax) for which the phylogeny is compared to previous hypotheses of relationships. Results from different tests under the maximum-parsimony and maximum-likelihood criteria indicate the rejection of the hypothesis of monophyly for the laughingthrushes group. Thus, the molecular phylogeny challenges the traditional classification of the Timaliidae.

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 Molecular phylogeny of the Taeniapterini (Diptera: Micropezidae) using nuclear and mitochondrial DNA, with a reclassification of the genus Taeniaptera Macquart

2015 ◽  
Vol 46 (5) ◽  
pp. 411-430 ◽  
Author(s):  
Morgan D. Jackson ◽  
Stephen A. Marshall ◽  
Jeffrey H. Skevington
Keyword(s):  
Mitochondrial Dna ◽  
Bayesian Inference ◽  
Molecular Phylogeny ◽  
Maximum Parsimony ◽  
New World ◽  
Molecular Data ◽  
Species Group ◽  
Mitochondrial Genes ◽  
Paraphyletic Group ◽  
Total Dna

DNA molecular data are used to generate a phylogeny for the micropezid subfamily Taeniapterinae. Thirty-two taeniapterine species were sampled, including 10 of the 20 New World genera recognized by Steyskal, as well as one genus formerly treated as a synonym of Poecilotylus Hennig (Hemichaeta Steyskal). Five species from the Micropezinae were included as outgroups. A total DNA dataset of 4705 bp, including mitochondrial genes (12S and cytochrome c oxidase I (COI)) and nuclear coding genes (wingless and CAD), was analysed using maximum parsimony and Bayesian inference. The genus Taeniaptera Macquart was found to be non-monophyletic with respect to the remainder of the Taeniapterini analysed here. Taeniaptera is restricted to the Taeniaptera trivittata Macquart species group, Mitromyia Cresson is resurrected to contain the Taeniaptera grata (Wulp) species group, and Paragrallomyia Hendel is resurrected to contain most species previously considered Taeniaptera. Poecilotylus is recognized as a paraphyletic group awaiting further research.

Molecular phylogeny of the butterfly tribe Baorini Doherty, 1886 (Hesperiidae, Hesperiinae) in China

Zootaxa ◽  
2019 ◽  
Vol 4565 (1) ◽  
pp. 108 ◽  
Author(s):  
WEIBIN JIANG ◽  
HAIYAN HE ◽  
YUANYUAN LI ◽  
YING WANG ◽  
CHEN GE ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Species Diversity ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Mitochondrial Genes ◽  
Nuclear Genes ◽  
Large Group ◽  
The Status

The butterfly tribe Baorini Doherty, 1886 is a large group of skippers. In this study, a total of 8 genera and 41 species of putative members of this tribe, which represent most of the generic diversity and nearly all the species diversity of the group in China, were sequenced for two mitochondrial genes and three nuclear genes (2084 bp). Phylogenetic relationships and subdivision of this tribe were investigated and the status of the genera are discussed. Partitioned maximum likelihood analyses were performed based on the combined dataset. Our results suggest that the data are split into two well-supported clades in the phylogeny tree. This analysis also represents the most complete phylogenetic analysis of the tribe Baorini in China to date, and includes several genera and species that have been previously excluded from published phylogenies of this group. 

scholarly journals Debating phylogenetic relationships of the scleractinian Psammocora: molecular and morphological evidences

2007 ◽  
Vol 76 (1) ◽  
pp. 35-54 ◽  
Author(s):  
Francesca Benzoni ◽  
Fabrizio Stefani ◽  
Jaroslaw Stolarski ◽  
Michel Pichon ◽  
Guillaume Mitta ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Molecular Data ◽  
Genetic Distances ◽  
The Other ◽  
Congeneric Species ◽  
Genetic Affinity ◽  
Phylogenetic Structure ◽  
Skeletal Structures ◽  
The Family

The phylogenetic relationships of the scleractinian genus Psammocora with the other genera traditionally included in the family Siderastreidae and some Fungiidae are assessed based on combined skeletal and molecular data. P. explanulata differs from the other examined congeneric species (P. contigua, P. digitata, P. nierstraszi , P. profundacella, P. superficialis, and P. stellata) in possessing interstomatous septa between adult corallites, costae, and in having continuous buttress-like structures joining septal faces (i.e., fulturae) which typically occur in fungiids. These characters are shared with Coscinaraea wellsi but not with the remainder of the examined siderastreids (the congeneric C. columna, and Anomastraea irregularis, Horastrea indica, Pseudosiderastrea tayamai, Siderastrea savignyana) whose septa are interconnected by typical synapticulae. Most of the examined species form septa with distinct transverse groups of centers of calcification, a biomineralization pattern typical of the Robusta clade. The observations on skeletal structures corroborate the results of the ITS2 and 5.8S molecular phylogeny. C. wellsi and P. explanulata are phylogenetically very close to each other and show closer genetic affinity with the examined Fungiidae (Halomitra pileus, Herpolitha limax, Fungia paumotensis, and Podabacia crustacea) than with the other species in the genera Psammocora and Coscinaraea, or with any other siderastreid. Our results show that neither Psammocora nor Coscinaraea are monophyletic genera. The high genetic distances between the species of Siderastreidae, especially between Pseudosiderastrea tayamai and Siderastrea savignyana on one side and the other genera on the other, suggest a deep divergence in the phylogenetic structure of the family.

Molecular phylogeny of the weevil genus Kyklioacalles Stüben, with descriptions of a new subgenus Glaberacalles and two new species (Curculionidae: Cryptorhynchinae)

Zootaxa ◽  
2010 ◽  
Vol 2662 (1) ◽  
pp. 28 ◽  
Author(s):  
PETER E. STÜBEN ◽  
JONAS J. ASTRIN
Keyword(s):  
New Species ◽  
Molecular Phylogeny ◽  
Bayesian Analysis ◽  
Morphological Differentiation ◽  
Molecular Data ◽  
Mitochondrial Genes ◽  
Morphological Evidence ◽  
New Subgenus ◽  
Western Palearctic ◽  
Two New Species

A molecular phylogeny of the western Palearctic weevil genus Kyklioacalles Stüben, 1999 is presented, combining two mitochondrial genes (CO1 and 16S) in a Bayesian analysis. Based on molecular data, the validity of the subspecies Kyklioacalles punctaticollis punctaticollis (Lucas, 1849) and Kyklioacalles punctaticollis meteoricus (Meyer, 1909) is discussed and the morphological differentiation of the endophalli and known distributions of both subspecies are verified. Glaberacalles subg. n. (formerly Kyklioacalles punctaticollis-group) and two new species are described, Kyklioacalles atlasicus sp.n. from Morocco and Kyklioacalles plantapilosus sp.n. from Spain. Kyklioacalles berberi (Stüben, 2005), comb. n. and Kyklioacalles olcesei (Tournier, 1873) comb. n. are transferred from Acalles Schoenherr. The molecular results further advocate a transfer of Onyxacalles pyrenaeus (Boheman, 1844) to Kyklioacalles; however this is not supported by morphological evidence. Kyklioacalles almadensis Stüben, 2004 syn. n. (Spain) is synonymized with Kyklioacalles bupleuri Stüben, 2004 (Tunisia). A catalogue of all 40 (sub-)species of Kyklioacalles is given and a key of the species of the subgenus Glaberacalles is presented.

Morphological phylogeny and review of the generic classification of Colletinae (Hymenoptera: Colletidae)

2020 ◽  
Author(s):  
Rafael R Ferrari ◽  
Laurence Packer
Keyword(s):  
Functional Traits ◽  
Strong Support ◽  
Molecular Data ◽  
The Other ◽  
Molecular Phylogenies ◽  
Phylogenetic Hypotheses

Abstract The bee subfamily Colletinae includes 542 species, the vast majority of which (518 spp.) belong to Colletes. The generic placement of the remaining 24 species has been controversial, resulting in several classifications being proposed. Despite several recently published molecular phylogenies of Colletinae, it remains unknown (1) what morphological synapomorphies support the recognized genera, (2) in which direction some relevant functional traits (e.g. basitibial plate) have evolved and (3) whether morphology supports the available molecular data. Herein, we provide a morphological phylogeny of Colletinae, which was constructed through parsimony analyses of 186 characters. In total, 50 ingroup species were included representing all major lineages of Colletes (29 spp.), plus all but three of the non-Colletes species of Colletinae (21 spp.). Trees were estimated through equal weights and extended implied weighting. Both provide strong support for the monophyly of Colletinae and indicate that the subfamily is defined by four unique synapomorphies. Our results also confirm recent phylogenetic hypotheses showing that Colletinae can be subdivided into two major clades: one comprising the reciprocally monophyletic Mourecotelles and Xanthocotelles; the other includes Colletes plus Hemicotelles, which are also reciprocally monophyletic. We also provide a fully illustrated key to facilitate generic identification of the Colletinae.

The phylogenetic relationships of Paramesotriton (Caudata: Salamandridae) based on partial mitochondrial DNA gene sequences

Zootaxa ◽  
2012 ◽  
Vol 3150 (1) ◽  
pp. 59
Author(s):  
XIAOMING GU ◽  
HUI WANG ◽  
RONGRONG CHEN ◽  
YINGZHOU TIAN ◽  
SONG LI
Keyword(s):  
Mitochondrial Dna ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
16S Rdna ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Mitochondrial Gene ◽  
Sister Group ◽  
Species Group ◽  
Close Phylogenetic Relationship

We examined phylogenetic relationships among newst of the genus Paramesotriton using partial mitochondrial gene se-quences, including the ND2-tRNATyr region (1415 bp) and the 12S rDNA-tRNAVal -16S rDNA region (1774 bp), from 42individuals of 10 recognized Paramesotriton species and outgroups by Bayesian inference (BI), Maximum likelihood(ML) and Maximum Parsimony (MP) methods. We found that, (1) Laotriton laoensis is the sister group of Paramesotri-ton, (2) the genus Paramesotriton is monophyletic, composed of either the P. caudopunctatus species group and the P.chinensis species group, or the subgenera Allomesotriton and Paramesotriton (3) P. longliensis and P. zhijinensis shouldbe placed in the P. caudopunctatus species group or subgenus Allomesotriton; (4) P. fuzhongensis is not a junior synonym of P. chinensis, and there is a close phylogenetic relationship between P. fuzhongensis and P. guangxiensis.

Phylogenetic relationships and classification of the Malagasy pseudoxyrhophiine snake genera Geodipsas and Compsophis based on morphological and molecular data

Zootaxa ◽  
2007 ◽  
Vol 1517 (1) ◽  
pp. 53-62 ◽  
Author(s):  
FRANK GLAW ◽  
ZOLTÁN T. NAGY ◽  
MIGUEL VENCES
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Close Relationships ◽  
Original Description ◽  
Molecular Data ◽  
Morphological Data ◽  
Molecular Phylogenetic ◽  
Species Groups ◽  
Morphological And Molecular Data

Based on a specimen found at Montagne d'Ambre in northern Madagascar morphologically agreeing with Compsophis albiventris Mocquard, 1894, we report on the rediscovery of this enigmatic snake genus and species and its molecular phylogenetic relationships. Compsophis albiventris, considered to be the only representative of its genus and unreported since its original description, bears strong morphological similarities to species of Geodipsas Boulenger, 1896. A molecular phylogeny based on DNA sequences of three mitochondrial and nuclear genes (complete cytochrome b, fragments of 16S rRNA and c-mos) in Compsophis albiventris and three Geodipsas species corroborated close relationships between C. albiventris and Geodipsas boulengeri, and showed that the genera Compsophis and Geodipsas together form a monophyletic unit. Despite the general similarities, morphological data and chromatic features support the existence of two species groups, corresponding to Compsophis and Geodipsas. We consequently consider Geodipsas as a subgenus of Compsophis and transfer all species currently in Geodipsas into the genus Compsophis.

scholarly journals Molecular Phylogeny of the Ant-Decapitating Flies, Genus Apocephalus Coquillett (Diptera: Phoridae)

2018 ◽  
Vol 2 (4) ◽  
Author(s):  
Brian V Brown ◽  
Christine Hayes ◽  
John M Hash ◽  
Paul T Smith
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Likelihood Methods ◽  
Taxonomic Relationships ◽  
Methods Of Analysis ◽  
Maximum Likelihood Methods ◽  
New Synonymy

Abstract The phylogenetic relationships of the large, diverse genus Apocephalus Coquillett are studied using seven loci (16S, COI, NDI, 28S, AK, CAD, and TPI). Both Bayesian and Maximum Likelihood methods were used to analyze the sequences. Pre-existing taxonomic relationships, based on morphology, were largely upheld, with the notable exception of the subgenus Mesophora Borgmeier being placed deep inside the genus. Therefore, Mesophora was synonymized with Apocephalus (new synonymy) and its species referred to as belonging to the Apocephalus wheeleri group. Both methods of analysis recovered similar results, providing what we consider reasonable explanations of the data, based on morphological information.

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