Molecular Systematics, Taxonomy and Distribution of the Pyrrhura Picta–Leucotis Complex

Introduction: The relationships within the Pyrrhura species complex are partly unresolved. In this study, a comprehensive phylogenetic analysis of the Pyrrhura picta-leucotis complex was carried out, covering all species except P. subandina. Material and Methods: We made a morphological analysis of 745 preserved specimens of all the taxa in different museums. Nucleotide sequences of the mitochondrial cytochrome gene were generated and used to reconstruct a molecular phylogeny of Pyrrhura. Results and Discussion: Our results show that the complex is divided into 6 main groups comprising 15 species. P. dilutissima, regarded up to now as a subspecies of P. peruviana, acquires species status and three new subspecies are described. We also provide evidence that P. roseifrons is a paraphyletic group, indicating the existence of probably 3 lineages of which 2 deserve species status.

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Population structure of the Monocelis lineata (Proseriata, Monocelididae) species complex assessed by phylogenetic analysis of the mitochondrial Cytochrome c Oxidase subunit I (COI) gene

Genetics and Molecular Biology ◽

10.1590/s1415-47572009005000076 ◽

2009 ◽

Vol 32 (4) ◽

pp. 864-867 ◽

Cited By ~ 20

Author(s):

Daria Sanna ◽

Tiziana Lai ◽

Paolo Francalacci ◽

Marco Curini-Galletti ◽

Marco Casu

Keyword(s):

Phylogenetic Analysis ◽

Population Structure ◽

Cytochrome C ◽

Cytochrome C Oxidase ◽

Species Complex ◽

Coi Gene ◽

Mitochondrial Cytochrome ◽

Oxidase Subunit ◽

Mitochondrial Cytochrome C

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Molecular Phylogeny of Jacanas and its Implications for Morphologic and Biogeographic Evolution

The Auk ◽

10.1093/auk/117.1.22 ◽

2000 ◽

Vol 117 (1) ◽

pp. 22-32 ◽

Cited By ~ 1

Author(s):

Linda A. Whittingham ◽

Frederick H. Sheldon ◽

Stephen T. Emlen

Keyword(s):

Phylogenetic Analysis ◽

Maximum Likelihood ◽

Molecular Phylogeny ◽

Cytochrome B ◽

New World ◽

Mitochondrial Cytochrome ◽

Biogeographic Pattern ◽

Mitochondrial Cytochrome B

Abstract We compared sequences of mitochondrial cytochrome-b and ND5 genes in a phylogenetic analysis of seven species of jacanas, representing all six genera and including the Greater Painted-snipe (Rostratula benghalensis) as an outgroup. When analyzed separately by parsimony and maximum-likelihood bootstrapping, the two genes produced consistent trees, although the ND5 tree was better resolved than the cytochrome-b tree. When combined, the data from the two genes produced a fully resolved tree that was identical to the ND5 tree. This tree had the following form: ((((Irediparra, Microparra), Metopidius), Actophilornis), ((Jacana jacana, J. spinosa), Hydrophasianus)), Rostratula. The phylogeny consists of two major clades that were known to traditional and phylogenetic taxonomists. It also contains sister taxa that are geographically disjunct: the New World Jacana and Asian Hydrophasianus, and the African Microparra and Australian Irediparra. We postulate that this biogeographic pattern results from the extinction of intervening African and Asian taxa, respectively.

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Phylogenetic Analysis of Northern Hair Seals Based on Nucleotide Sequences of the Mitochondrial Cytochrome b Gene

Journal of Mammalogy ◽

10.2307/1382609 ◽

1995 ◽

Vol 76 (4) ◽

pp. 1178-1185 ◽

Cited By ~ 13

Author(s):

S. Mouchaty ◽

J. A. Cook ◽

G. F. Shields

Keyword(s):

Phylogenetic Analysis ◽

Cytochrome B ◽

Nucleotide Sequences ◽

Cytochrome B Gene ◽

Mitochondrial Cytochrome ◽

Mitochondrial Cytochrome B ◽

Mitochondrial Cytochrome B Gene

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Phylogenetic analysis of the mitochondrial cytochrome oxidase subunit I gene of five species of the Culicoides imicola species complex

Medical and Veterinary Entomology ◽

10.1046/j.1365-2915.2002.00356.x ◽

2002 ◽

Vol 16 (2) ◽

pp. 139-146 ◽

Cited By ~ 43

Author(s):

Y.-M. Linton ◽

A. J. Mordue luntz ◽

R. H. Cruickshank ◽

R. Meiswinkel ◽

P. S. Mellor ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Cytochrome Oxidase ◽

Species Complex ◽

Mitochondrial Cytochrome ◽

Cytochrome Oxidase Subunit ◽

Cytochrome Oxidase Subunit I ◽

Mitochondrial Cytochrome Oxidase Subunit ◽

Culicoides Imicola ◽

Mitochondrial Cytochrome Oxidase ◽

I Gene

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Re-Evaluation of the Podosphaera tridactyla Species Complex in Australia

Journal of Fungi ◽

10.3390/jof7030171 ◽

2021 ◽

Vol 7 (3) ◽

pp. 171

Author(s):

Reannon L. Smith ◽

Tom W. May ◽

Jatinder Kaur ◽

Tim I. Sawbridge ◽

Ross C. Mann ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Powdery Mildew ◽

Species Complex ◽

Taxonomic Revision ◽

Stone Fruit ◽

Prunus Species ◽

Wide Range ◽

Unidentified Species ◽

The Rose ◽

Generation Sequencing

The Podosphaera tridactyla species complex is highly variable morphologically and causes powdery mildew on a wide range of Prunus species, including stone fruit. A taxonomic revision of the Po. tridactyla species complex in 2020 identified 12 species, seven of which were newly characterised. In order to clarify which species of this complex are present in Australia, next generation sequencing was used to isolate the fungal ITS+28S and host matK chloroplast gene regions from 56 powdery mildew specimens of stone fruit and ornamental Prunus species accessioned as Po. tridactyla or Oidium sp. in Australian reference collections. The specimens were collected in Australia, Switzerland, Italy and Korea and were collected from 1953 to 2018. Host species were confirmed using matK phylogenetic analysis, which identified that four had been misidentified as Prunus but were actually Malusprunifolia. Podosphaera species were identified using ITS+28S phylogenetic analysis, recognising three Podosphaera species on stone fruit and related ornamental Prunus hosts in Australia. These were Po.pannosa, the rose powdery mildew, and two species in the Po. tridactyla species complex: Po. ampla, which was the predominant species, and a previously unidentified species from peach, which we describe here as Po. cunningtonii.

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Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽

10.3390/pathogens10010041 ◽

2021 ◽

Vol 10 (1) ◽

pp. 41

Author(s):

Marcos Godoy ◽

Daniel A. Medina ◽

Rudy Suarez ◽

Sandro Valenzuela ◽

Jaime Romero ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Genetic Variation ◽

Sequence Analysis ◽

Molecular Phylogeny ◽

Phylogenetic Trees ◽

Genomic Segment ◽

Double Stranded Rna ◽

The Family ◽

Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

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Molecular record for the first authentication of Isaria cicadae from Vietnam

Open Life Sciences ◽

10.1515/biol-2021-0074 ◽

2021 ◽

Vol 16 (1) ◽

pp. 711-718

Author(s):

Thuan Duc Lao ◽

Hanh Van Trinh ◽

Loi Vuong ◽

Luyen Tien Vu ◽

Thuy Ai Huyen Le ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Genomic Dna ◽

Morphological Analysis ◽

Phylogenetic Analyses ◽

Neighbor Joining ◽

Pcr Assay ◽

Parsimony Method ◽

Maximum Parsimony Method ◽

Cordyceps Cicadae ◽

High Bootstrap

Abstract The entomopathogenic fungus T011, parasitizing on nymph of Cicada, collected in the coffee garden in Dak Lak Province, Vietnam, was preliminarily morphologically identified as Isaria cicadae, belonged to order Hypocreales and family Clavicipitaceae. To ensure the authenticity of T011, phylogenetic analysis of the concatenated set of multiple genes including ITS, nrLSU, nrSSU, Rpb1, and Tef1 was applied to support the identification. Genomic DNA was isolated from dried sample T011. The PCR assay sequencing was applied to amplify ITS, nrLSU, nrSSU, Rpb1, and Tef1 gene. For phylogenetic analysis, the concatenated data of both target gens were constructed with MEGAX with a 1,000 replicate bootstrap based on the neighbor-joining, maximum likelihood, maximum parsimony method. As the result, the concatenated data containing 62 sequences belonged to order Hypocreales, families Clavicipitaceae, and 2 outgroup sequences belonged to order Hypocreales, genus Verticillium. The phylogenetic analysis results indicated that T011 was accepted at subclade Cordyceps and significantly formed the monophyletic group with referent Cordyceps cicadae (Telemorph of Isaria cicadae) with high bootstrap value. The phylogenetically analyzed result was strongly supported by our morphological analysis described as the Isaria cicadae. In summary, phylogenetic analyses based on the concatenated dataset were successfully applied to strengthen the identification of T011 as Isaria cicadae.

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