Evolution and Phylogeny of the Diptera: A Molecular Phylogenetic Analysis Using 28S rDNA Sequences

In this study, two new brackish-water species of Macrostomum (M. shenda n. sp. and M. spiriger n. sp.) collected from Shenzhen, China, were described based on morphological, histological, and molecular phylogenetic analyses. Macrostomum shenda n. sp. differs from its congeners in the oblique and non-thickening distal opening of its narrow funnel-shaped stylet. In addition, its sperm have neither bristles nor brush, and are surrounded by an undulating membrane in the mid-body region. In M. spiriger n. sp., the stylet is spirally twisted. Its reproductive apparatus has a seminal bursal pore opening exteriorly. Results of the 18S and 28S rDNA phylogenetic analyses also support the establishments of these two new species. Moreover, the 18S and 28S rDNA sequences of some species within Macrostomum in previous studies have been revised to avoid ambiguity, while Macrostomum dongyuanensis Wang & Sun, 2015 was re-identified as a new record of M. quiritium Kolasa, 1973 from China.

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Two Erysiphe species associated with recent outbreak of soybean powdery mildew: results of molecular phylogenetic analysis based on nuclear rDNA sequences

Mycoscience ◽

10.1007/s102670200049 ◽

2002 ◽

Vol 43 (4) ◽

pp. 333-341 ◽

Cited By ~ 20

Author(s):

Susumu Takamatsu ◽

Yusuke Taguchi ◽

Hyeon-Dong Shin ◽

Urailak Paksiri ◽

Saranya Limkaisang ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Powdery Mildew ◽

Molecular Phylogenetic Analysis ◽

Nuclear Rdna ◽

Rdna Sequences ◽

Recent Outbreak ◽

Molecular Phylogenetic

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A framework for a phylogenetic classification in the genus Cortinarius (Basidiomycota, Agaricales) derived from morphological and molecular data

Canadian Journal of Botany ◽

10.1139/b05-107 ◽

2005 ◽

Vol 83 (11) ◽

pp. 1457-1477 ◽

Cited By ~ 47

Author(s):

Sigisfredo Garnica ◽

Michael Weiß ◽

Bernhard Oertel ◽

Franz Oberwinkler

Keyword(s):

Phylogenetic Analysis ◽

Molecular Data ◽

Internal Transcribed Spacers ◽

Molecular Phylogenetic Analysis ◽

Nuclear Rdna ◽

Ecological Data ◽

Natural Classification ◽

Geographical Patterns ◽

Rdna Sequences ◽

Molecular Phylogenetic

Phylogenetic relationships in the genus Cortinarius with emphasis on European species were studied by integrating a molecular phylogenetic analysis of nuclear rDNA sequences with morphological, chemical, and ecological data. Internal transcribed spacers (ITS1 and ITS2, including 5.8S) and the D1–D2 regions of nuclear rDNA of 262 Cortinarius species including most of the recognised subgenera from Europe, South America, Australia, Tasmania, New Zealand, and Asia were sequenced and analysed by maximum likelihood and neighbour joining. Our morphological and molecular analyses showed considerable disagreement with earlier morphology-based hypotheses concerning the infrageneric delimitations in Cortinarius. We propose a new base for a more natural classification system in Cortinarius involving the taxonomic rearrangement of the species into the following major lineages that we informally designate as “clades” at this time: (1) phlegmacioid species are included in Alluti, Amarescentes, Arguti, Calochroi, Caerulescentes, Percomes, Phlegmacioides, Phlegmacium, Purpurascentes, Scauri, and Vulpini; (2) the Heterocliti clade includes species of the subgenera Leprocybe and Cystogenes ; (3) most of the Myxacium species are included in the Delibuti and Myxacium clades; (4) part of Rozites are included in the Rozites clade; (5) the north-hemispheric species of subgenus Dermocybe are included in the Dermocybe clade and part of the south-hemispheric species in the Splendidi clade; (6) part of Sericeocybe are integrated in the Anomali and Telamonia clades; (7) members of subgenus Cortinarius are assigned to the Cortinarius clade; (8) telamonioid taxa are included in the Obtusi, Renidentes, and Telamonia clades. Several Cortinarius species with peculiar patterns of morphology and basidiome coloration had isolated positions in the sequence analysis, and the evolutionary relationships among the major lineages remained unresolved. Our results suggest the convergent evolution of certain morphological traits across phylogenetically divergent lineages in Cortinarius. However, combinations of features such as pileipellis anatomy, spore shape, veil coloration, basidiome pigments, and stipe shape appear useful to circumscribe clades. Our molecular phylogenetic analysis allows insights in global geographical patterns of species distribution within the major lineages in the genus Cortinarius. The clade structure proposed here could be used as backbone for further more detailed systematic studies.

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Mexicana rubra sp. nov. and Encotyllabe cf. spari Yamaguti, 1934 (Monogenea) of Orthopristis ruber (Cuvier, 1830) from the Brazilian Coast off Rio de Janeiro

Helminthologia ◽

10.1515/helm-2017-0046 ◽

2017 ◽

Vol 54 (4) ◽

pp. 336-347

Author(s):

A. C. A. Camargo ◽

J. L. Luque ◽

C. P. Santos

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Rio De Janeiro ◽

Genetic Data ◽

28S Rdna ◽

Brazilian Coast ◽

Diagnostic Features ◽

Rdna Sequences ◽

28S Rdna Sequences ◽

Partial 18S

Summary Mexicana rubra sp. nov. and Encotyllabe cf. spari are described from the gills of the marine fish Orthopristis ruber (Haemulidae) caught off Rio de Janeiro, Brazil. Morphological, ultrastructural and genetic data are provided. The main diagnostic features of this new species of ectoparasite are a posteriorly bipartite testis, a ventral bar with three deep bowed projections and a dorsal bar with two deep, conspicuous, antero-lateral indentations. Genetic data on Mexicana rubra sp. nov. are based on the ITS1, 5.8S and partial 18S and 28S rDNA. This is the sixth known species of Mexicana Caballero & Bravo-Hollis, 1959, a key to which is also presented. Encotyllabe cf. spari Yamaguti, 1934 is described from the same host, with new ultrastructural data and new partial 18S and 28S rDNA sequences. A phylogenetic analysis based on partial 18S and 28S sequences is undertaken for both species.

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Erratum to “Phylogenetic analysis of the Monocotylidae (Monogenea) inferred from 28S rDNA sequences” [Int. J. Parasitol. 31 (2001) 1253–1263]

International Journal for Parasitology ◽

10.1016/s0020-7519(01)00312-5 ◽

2001 ◽

Vol 31 (13) ◽

pp. 1535

Keyword(s):

Phylogenetic Analysis ◽

28S Rdna ◽

Rdna Sequences ◽

28S Rdna Sequences

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Phylogenetic analysis of the Monocotylidae (Monogenea) inferred from 28S rDNA sequences

International Journal for Parasitology ◽

10.1016/s0020-7519(01)00313-7 ◽

2001 ◽

Vol 31 (13) ◽

pp. 1537-1547 ◽

Cited By ~ 34

Author(s):

Leslie A. Chisholm ◽

Jess A.T. Morgan ◽

Rob D. Adlard ◽

Ian D. Whittington

Keyword(s):

Phylogenetic Analysis ◽

28S Rdna ◽

Rdna Sequences ◽

28S Rdna Sequences

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Phylogenetic relationships of the lower Cyclorrhapha (Diptera: Brachycera) based on 28S rDNA sequences

Insect Systematics & Evolution ◽

10.1163/187631202x00235 ◽

2002 ◽

Vol 33 (4) ◽

pp. 445-456 ◽

Cited By ~ 14

Author(s):

Brian M. Wiegmann ◽

Kenneth P. Collins

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Sister Group ◽

28S Rdna ◽

Morphological Data ◽

Monophyletic Clade ◽

Rdna Sequences ◽

28S Rdna Sequences

AbstractCyclorrhaphan Diptera are an extremely successful clade of ecologically and phylogenenetically important flies. Despite their significance the relationships among lower cyclorrhaphans ('Aschiza') remain controversial in spite of several morphologically based phylogenetic analyses. We sequenced a 2.7-kb fragment of 28S rDNA for taxa representing all lower cyclorrhaphan families (except Ironomyiidae), four schizophoran families, and seven empidoid out-group taxa. Phylogenetic analysis of these data strongly supports a monophyletic Cyclorrhapha (including the enigmatic taxon Opetia nigra) that is divided into two clades - a well-supported Eumuscomorpha (Syrphidae + Pipunculidae + Schizophora), and a weakly-supported Platypezoidea (all non-Eumuscomorpha). Consequently, the former grouping known as Aschiza, which included syrphids and pipunculids, is not a valid monophyletic clade. Within Platypezoidea, most of our analyses place Lonchopteridae as sister group to Opetiidae, and strongly support the monophyly of Sciadoceridae + Phoridae. Among the Eumuscomorpha we do not recover the monophyly of Syrphoidea (Syrphidae + Pipunculidae). Instead, all analyses place Pipunculidae as the sister group to Schizophora. This novel finding has never been proposed based on morphological data and will require more data (both molecular and morphological) and taxa to confirm.

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Systematic revision, cladistics and biogeography of the genus Neogutierrezia Martínez (Coleoptera:Scarabaeidae) and its phylogenetic placement in Rutelinae based on structural alignment of 28S rDNA sequences

Invertebrate Systematics ◽

10.1071/is09035 ◽

2010 ◽

Vol 24 (1) ◽

pp. 81 ◽

Cited By ~ 8

Author(s):

Federico C. Ocampo ◽

Eider Ruiz-Manzanos ◽

Adriana E. Marvaldi

Keyword(s):

Structural Alignment ◽

Phylogenetic Reconstruction ◽

Cladistic Analysis ◽

28S Rdna ◽

Structure Alignment ◽

28S Rrna ◽

Systematic Revision ◽

Rdna Sequences ◽

Molecular Phylogenetic ◽

28S Rdna Sequences

The Argentinean endemic genus Neogutierrezia Martínez, 1953 (Scarabaeidae : Rutelinae) is revised and seven new species are described: N. bicolor Ocampo & Ruiz-Manzanos, sp. nov., N. chelii Ocampo & Ruiz-Manzanos, sp. nov., N. galileoi Ocampo & Ruiz-Manzanos, sp. nov., N. lagosae Ocampo & Ruiz-Manzanos, sp. nov., N. payuniensis Ocampo & Ruiz-Manzanos, sp. nov., N. scutata Ocampo & Ruiz-Manzanos, sp. nov. and N. variabilis Ocampo & Ruiz-Manzanos, sp. nov. Species status is proposed for N. affinis Martínez stat. nov., which was formerly considered as subspecies of N. mirabilis Martínez. The genus Neogutierrezia now includes 10 species distributed in the Monte biogeographic province in Argentina. In order to clarify the systematic placement of the genus Neogutierrezia, a molecular phylogenetic analysis was performed using structurally aligned 28S rDNA sequences (expansion segments D2 and D3) from 23 taxa in Scarabaeoidea, including two representative species of Neogutierrezia. This is the first report of an annotated secondary structure alignment of the D2 and D3 segments of 28S rRNA that spans a wide sample of scarabaeoids, providing a useful homology template for further phylogenetic reconstruction in these and closely related beetles. Results of the molecular parsimony analysis strongly indicate that the genus is closely related to members of the Rutelinae (Scarabaeidae), and thus Neogutierrezia Martínez is transferred from Melolonthinae: Pachydemini to Rutelinae, new placement. A morphological cladistic analysis of the genus was also undertaken, including all the 10 known species in the genus plus two outgroup taxa in Rutelinae, and based on 53 adult characters. The most-parsimonious cladogram provides evidence for the monophyly of the genus, which shows three main clades, distributed in Central Monte and Southern Monte. The adult morphology of the 10 species is described and a key is provided, along with illustrations of the diagnostic characters. The biogeography of species in the genus is discussed.

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Molecular evolutionary relationships of Vietnamese and global pulmonary Paragonimus species in the family paragonimidae and suborder xiphidiata (Platyhelminthes: Trematoda)

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/18/4/15673 ◽

2021 ◽

Vol 18 (4) ◽

pp. 653-662

Author(s):

Nguyen Thi Khue ◽

Pham Thi Khanh Linh ◽

Do Thi Roan ◽

Doan Thi Thanh Huong ◽

Pham Ngoc Doanh ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Analyses ◽

The Philippines ◽

28S Rdna ◽

Evolutionary Relationships ◽

Evolutionary Analysis ◽

North West ◽

Rdna Sequences ◽

The Family ◽

28S Rdna Sequences

Paragonimiasis, caused by Paragonimus species belonging to the family Paragonimidae of the suborder Xiphidiata (Platyhelminthes: Trematoda), often occurs in poor, upland, ethnic minorities, in Vietnam and the world. Asian Paragonimus species are distributed from Japan, South Korea, along with North and Southeast China, North-West and Central Vietnam, the Philippines, Thailand, Bangladesh, India, and Sri Lanka. There are various genetic variants, strains, and genotypes forming different complexes and evolutionary lineages. The 18S, 28S rDNA sequences and the intergenic transcribed spacer regions (ITS-1, ITS-2) of nuclear ribosomal transcription units are commonly used as molecular markers in genetic studies and phylogenetic analyses. We obtained a portion of 28S rDNA (domains D1–D3) of Paragonimus spp. including P. heterotremus (from Vietnam), P. ohirai (Japan), P. iloktsuenensis (Japan), and P. westermani (India and Vietnam) and conducted phylogenetic analysis for molecular evolutionary studies. The results showed that the family Paragonimidae formed the biggest cluster in a phylogenetic tree, which comprises of 46 sequences of 11 species belonging to 11 subgroups, among which the P. westermani complex of strains originating from China, Korea, Japan, India, Philippines, Malaysia, and Vietnam is present. P. westermani complex is arranged in a position of "sister" (sister group) with the subgroup P. siamensis. The P. heterotremus and P. ohirai complexes, and the P. miyazakii, P. harinasutai, P. mexicanus, P. kellicotti, and P. macrorchis complexes are clustered in a common population. P. westermani of Vietnam is in close proximity to the East Asian strains, as of which has been previously reported. P. ohirai and P. iloktsuenensis are considered “sibling” species, sharing the same clade. Phylogenetic analysis using the 28S rDNA sequences directly presented species position and their molecular evolutionary relationships in the families Paragonimidae, Troglotrematidae, Nanophyetidae, and Collyriclidae. Evolutionary analysis has also clarified a number of complex delineation problems and made a clear nomenclature for Paragonimus sp. of Vietnam, in particular, which has scientific grounds merited to recognize as that it is really the P. westermani species.

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Phylogenetic analysis of the superfamily Hemiuroidea (Platyhelminthes, Neodermata:Trematoda) based on partial 28S rDNA sequences

Parasitology ◽

10.1017/s0031182018001841 ◽

2018 ◽

Vol 146 (5) ◽

pp. 596-603 ◽

Cited By ~ 2

Author(s):

Sergey G. Sokolov ◽

Dmitry M. Atopkin ◽

Misako Urabe ◽

Ilya I. Gordeev

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationship ◽

Phylogenetic Relationships ◽

Sister Group ◽

28S Rdna ◽

Monophyletic Group ◽

Rdna Sequences ◽

The Family ◽

Statistical Support ◽

28S Rdna Sequences

AbstractIn the present paper, the phylogenetic relationships between genera, subfamilies and families of the Hemiuroidea are explored. Twelve new sequences of 28 rDNA and data taken from GenBank (NSBI) on 43 species affiliated to 34 genera were included in the analysis. Most of the hemiuroidean trematodes form two highly supported clades (A and B), which are sister groups to each other.Hemipera manterijoined withGonocercaspp. with moderate statistical support. This clade is basal relative to the clades A and B. Сlade A is polytomic and contains representatives of the families Accacoeliidae, Syncoeliidae, Didymozoidae, Hirudinellidae and Sclerodistomidae, and derogenid subfamilies Derogeninae and Halipeginae. At the same time, the Syncoeliidae, Hirudinellidae and Accacoeliidae form a well-supported monophyletic group. The phylogenetic relationship between Derogeninae and Halipeginae is poorly resolved. Сlade B unites the isoparorchiid, bunocotylid, lecithasterid and hemiurid trematodes. Our data re-establishes the family Bunocotylidae, which consists of two subfamilies, Opisthadeninae and Bunocotylinae, and theMachidatrema chilostoma+Hysterolecithoides frontilatusgroup. The Bunocotylidae is the sister group to the Hemiuridae + Lecithasteridae group and the Isoparorchiidae is a basal relative to the representatives of these three hemiuroid families.

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