Cryptic species of Didymobothrium rudolphii (Cestoda: Spathebothriidea) from the sand sole, Solea lascaris, off the Portuguese coast, with an analysis of their molecules, morphology, ultrastructure and phylogeny

SUMMARYDidymobothrium rudolphii (Cestoda: Spathebothriidea) was collected seasonally from the sand sole, Solea lascaris, off the northern, central and southern areas of the Portuguese coast. Morphological and molecular analyses were conducted in order to examine the possible existence of cryptic species and to facilitate the circumscription of their morphological boundaries. Data were compared between D. rudolphii specimens from each of the 3 geographical areas and 4 seasons, and principal components analysis of 18 morphological characters was used to detect differences. Two distinct genotypes were present with sequence divergences of 1·9% and 2·1% in the large subunit (lsrDNA) and second internal transcribed spacer (ITS-2) of ribosomal DNA (rDNA), respectively. The less common ‘central’ genotype was present only off the central area from summer to winter, whereas the ‘common’ genotype was present throughout the year off the northern and southern areas, but only during spring in the central area. No sequence variation was found within each genotype. The presence of 2 distinct genetic entities was supported by morphological analyses, which showed the ‘central’ genotype specimens to be more slender and elongate, although morphometric ranges overlapped considerably for most characters. Molecular phylogenetic analysis of 4 of the 5 known genera of the Spathebothriidea showed Spathebothrium to be the earliest branching lineage and the 2 genotypes of Didymobothrium formed a sister group to Cyathocephalus. The concordance of genetic differences with variation in host diet according to season and locality could account for sympatric speciation occurring in the central region of the Portuguese coast.

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Phylogenetic reassignment of basal cyclostome braconid parasitoid wasps (Hymenoptera) with description of a new, enigmatic Afrotropical tribe with a highly anomalous 28S D2 secondary structure

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlaa037 ◽

2020 ◽

Vol 190 (3) ◽

pp. 1002-1019 ◽

Cited By ~ 1

Author(s):

Donald L J Quicke ◽

Sergey A Belokobylskij ◽

Yves Braet ◽

Cornelis van Achterberg ◽

Paul D N Hebert ◽

...

Keyword(s):

Sequence Data ◽

Elongation Factor ◽

Sequence Divergence ◽

Sister Group ◽

Morphological Characters ◽

Dna Sequence Data ◽

Elongation Factor 1 Alpha ◽

Molecular Phylogenetic ◽

Molecular Dataset ◽

First Time

Abstract A new tribe of braconid wasps provisionally included in the Rhyssalinae, Laibaleini trib. nov., type genus Laibalea gen. nov. (type species Laibalea enigmatica sp. nov.), from Kenya and the Central African Republic, is described. A molecular dataset, with emphasis on basally derived taxa based on four gene fragments (28S D2–D3 expansion region, COI barcode, elongation factor 1-alpha and 16S ribosomal DNA), was analysed both alone and in combination with a morphological dataset. Molecular phylogenetic placement of the new species into an existing subfamily is complicated by the extreme sequence divergence of the three sequences obtained for Laibalea. In both the combined sequence analysis and the combined DNA plus morphological tree, Laibalea is recovered as a sister group to the Rhyssalinae plus all non-cyclostome lineage braconids excluding Mesostoinae, Maxfischeriinae and Aphidiinae. A consensus of morphological characters and molecular analyses suggests inclusion of Laibalea either in the otherwise principally Holarctic subfamily Rhyssalinae or perhap more basally, in the principally Gondwanan Mesostoinae s.l., although we cannot exclude the possibility that it might represent a separate basal lineage. We place Laibalea in its own tribe, provisionally included in Rhyssalinae. The DNA sequence data are presented for several genera for the first time. Avga, the type genus of Avgini, is shown not to belong to Mesostoinae s.l. or Hormiinae, but its exact relationships remain uncertain. The generic compositions of Rhyssalinae and Mesostoinae s.l. are revised. Anachyra, Apoavga, Neptihormius, Neoavga and Opiopterus are shown to belong to Mesostoinae s.s. A key to the tribes of Rhyssalinae is provided.

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Amanita glarea, a new species in section Vaginatae from Pakistan

Phytotaxa ◽

10.11646/phytotaxa.306.2.3 ◽

2017 ◽

Vol 306 (2) ◽

pp. 135 ◽

Cited By ~ 1

Author(s):

SANA JABEEN ◽

MUNAZZA KIRAN ◽

SADIQ ULLAH ◽

ANDREW W. WILSON ◽

GREGORY M. MUELLER ◽

...

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Internal Transcribed Spacer ◽

Large Subunit ◽

Morphological Characters ◽

Nucleotide Sequences ◽

Phylogenetic Data ◽

Molecular Phylogenetic ◽

A New Species ◽

Molecular Phylogenetic Data

A new species, Amanita glarea, is described and illustrated from Pakistan. Molecular phylogenetic data derived from internal transcribed spacer (ITS) and nuclear ribosomal large subunit (LSU) regions along with morphological characters make it distinct from other currently known Amanita species. Amanita glarea is characterized by a grayish brown, slightly umbonate, pileus having universal veil remnants and striate margins, a long ringless stipe with a saccate volva bearing yellowish brown patches on the verrucose surface, inamyloid globose to subglobose basidiospores, and a filamentous pileipellis with some inflated round to elongated cells. Phylogenetic analysis of nuclear ribosomal ITS and LSU nucleotide sequences resolve A. glarea with other taxa in Amanita section Vaginatae.

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Molecular phylogeny of Acrobeloides and Cephalobus (Nematoda: Cephalobidae) reveals paraphyletic taxa and recurrent evolution of simple labial morphology

Nematology ◽

10.1163/156854106779799178 ◽

2006 ◽

Vol 8 (6) ◽

pp. 819-836 ◽

Cited By ~ 16

Author(s):

Steven Nadler ◽

Ashleigh Smythe

Keyword(s):

Molecular Phylogeny ◽

Large Subunit ◽

Taxonomic Revision ◽

Morphological Characters ◽

Lateral Field ◽

The Core ◽

Morphological Taxonomy ◽

Dominant Feature ◽

The Family ◽

Molecular Phylogenetic

AbstractMembers of the family Cephalobidae (Nematoda) are among the most common and morphologically striking soil nematodes. Many members of Cephalobidae have extensive lip elaborations called probolae, but two taxonomically problematic genera, Acrobeloides and Cephalobus, have simple, low probolae. We sequenced a portion of the nuclear large subunit ribosomal DNA for 33 cultures of Acrobeloides and Cephalobus. A phylogenetic analysis of these data, plus sequences representing other members of Cephalobina, revealed a core clade of 22 closely related taxa, but did not represent Acrobeloides and Cephalobus as monophyletic. The dominant feature used in morphological taxonomy of Cephalobidae, the lip region, was homoplastic according to the molecular phylogenetic hypothesis. Contrary to previous suggestions, taxa with simple probolae have arisen multiple times from taxa with complex probolae. Cultures were also examined for mode of reproduction (presumed parthenogenetic vs sexual) and three morphological characters commonly used in generic diagnoses: the shape of the corpus in profile; the number of lateral incisures; and the terminal extent of the lateral field. Most cultures, including all 22 members of the core clade, lacked males and were presumed to be parthenogenetic, but several independent origins of sexually reproducing taxa were found. Of the morphological characters, only the corpus shape was consistent with the molecular phylogeny, however, the utility of this character is also questioned. Many genera with complex probolae were also paraphyletic, including Nothacrobeles, Zeldia and Cervidellus, indicating the need for more comprehensive phylogenies and a broad taxonomic revision of the family.

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Description of Ruehmaphelenchus fujiensis n. sp. (Tylenchomorpha: Aphelenchoididae) isolated from dead wood of Quercus crispula from Yamanashi, Japan

Nematology ◽

10.1163/15685411-bja10072 ◽

2021 ◽

pp. 1-18

Author(s):

Natsumi Kanzaki

Keyword(s):

New Species ◽

Cryptic Species ◽

Botrytis Cinerea ◽

Ribosomal Rna ◽

Dead Wood ◽

Large Subunit ◽

Small Subunit ◽

Quercus Crispula ◽

Female Tail ◽

Molecular Phylogenetic

Summary Three undescribed Ruehmaphelenchus species were isolated from dead wood of Quercus crispula collected in three different localities in Japan. One of these three species was successfully cultured using Botrytis cinerea as its food fungus and is described and figured as R. fujiensis n. sp. The new species is characterised by the following features: male tail, conical with or without a projection; female tail, conical with variously shaped terminal mucron or projection; and male spicule possessing a relatively long and triangular condylus. The new species is close to, or almost a cryptic species of R. digitulus, i.e., the typological characters and morphometric values of these two species are mostly overlapping. In a molecular phylogenetic relationship inferred from near-full-length small subunit (18S) and D2-D3 expansion segments of the large subunit (28S) of ribosomal RNA, the new species is close to R. asiaticus, R. digitulus, R. formosanus, and Ruehmaphelenchus sp. NKZ202; however, it was clearly separated from these species.

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Molecular phylogenetic analysis reveals two new species of Discosia from Italy

Phytotaxa ◽

10.11646/phytotaxa.203.1.3 ◽

2015 ◽

Vol 203 (1) ◽

pp. 37 ◽

Cited By ~ 1

Author(s):

Wenjing Li ◽

Jian-kui Liu ◽

D. Jayarama Bhat ◽

Erio Camporesi ◽

Dong-QING DAI ◽

...

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Internal Transcribed Spacer ◽

Large Subunit ◽

Morphological Characters ◽

Fruiting Bodies ◽

Forensic Dna ◽

Two New Species ◽

Molecular Phylogenetic ◽

Large Subunit Rdna

Two fresh collections of Discosia were made from dead leaves of Fagus sylvatica in Italy. As these collections could not be cultured, the fruiting bodies were directly used for sequencing using a Forensic DNA Extraction Kit. Based on analyses of the concatenated internal transcribed spacer regions of the nrDNA operon (ITS) and large subunit rDNA (LSU) gene sequences, as well as morphological characters, the fresh collections are introduced as two new species, namely D. italica and D. fagi. Phylogenetically, these two species are distinct from all other Discosia species. Morphologically, D. italica is somewhat similar with D. fagi, but can be distinguished using dimension of conidiomata and conidiogenous cells. Descriptions and illustrations of the new taxa are provided herein.

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Description of Bursaphelenchus kiyoharai n. sp. (Tylenchina: Aphelenchoididae) with remarks on the taxonomic framework of the Parasitaphelenchinae Rühm, 1956 and Aphelenchoidinae Fuchs, 1937

Nematology ◽

10.1163/138855410x552652 ◽

2011 ◽

Vol 13 (7) ◽

pp. 787-804 ◽

Cited By ~ 24

Author(s):

Natsumi Kanzaki ◽

Noritoshi Maehara ◽

Takuya Aikawa ◽

Hayato Masuya ◽

Robin M. Giblin-Davis

Keyword(s):

New Species ◽

Large Subunit ◽

Morphological Characters ◽

Small Subunit ◽

Mountain Range ◽

Biodiversity Survey ◽

Phylogenetic Status ◽

Molecular Phylogenetic ◽

Taxonomic Framework ◽

Definition Of

Abstract A Bursaphelenchus species was isolated from an ambrosia beetle, Xyleborus seriatus, during a biodiversity survey of entomophilic nematodes in a conserved forest in the Shirakami mountain range, Aomori, Japan. The nematode has several interesting morphological characters that do not fit the morphological definition of Bursaphelenchus, e.g., males have a tail spike instead of a bursal flap and lack the P1 ventral single papilla, and females have a very long and tapering tail (filiform). The molecular phylogenetic status of the new species inferred by the near-full-length small subunit (SSU: 18S) and the D2/D3 expansion segments of the large subunit (LSU: 28S) suggests, however, that the nematode is included in the B. fungivorus group, and is most closely related to B. thailandae and B. willibaldi. Despite these unique morphological characters, its spicule morphology, which is almost identical to that of B. gonzalezi, B. thailandae and B. willibaldi, and vulval structure, i.e., lacking a vulval flap, are in accordance with the molecular phylogenetic status of the nematode. The new species, which shows evidence of secondary loss of the bursal flap and P1 papilla, is described herein as B. kiyoharai n. sp. The typological descriptions of the genus and Parasitaphelenchinae were reconsidered and the taxonomic framework of the Aphelenchoidinae and Parasitaphelenchinae revised. Bursaphelenchus asiaticus n. comb. is proposed for Ruehmaphelenchus asiaticus.

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A multi-gene phylogeny of Chlorophyllum (Agaricaceae, Basidiomycota): new species, new combination and infrageneric classification

MycoKeys ◽

10.3897/mycokeys.32.23831 ◽

2018 ◽

Vol 32 ◽

pp. 65-90 ◽

Cited By ~ 9

Author(s):

Zai-Wei Ge ◽

Adriaana Jacobs ◽

Else C. Vellinga ◽

Phongeun Sysouphanthong ◽

Retha van der Walt ◽

...

Keyword(s):

New Species ◽

Rna Polymerase Ii ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Elongation Factor ◽

Morphological Characters ◽

Nuclear Ribosomal Dna ◽

New Combination ◽

Infrageneric Classification ◽

Molecular Phylogenetic

Taxonomic and phylogenetic studies of Chlorophyllum were carried out on the basis of morphological differences and molecular phylogenetic analyses. Based on the phylogeny inferred from the internal transcribed spacer (ITS), the partial large subunit nuclear ribosomal DNA (nrLSU), the second largest subunit of RNA polymerase II (rpb2) and translation elongation factor 1-α (tef1) sequences, six well-supported clades and 17 phylogenetic species are recognised. Within this phylogenetic framework and considering the diagnostic morphological characters, two new species, C.africanum and C.palaeotropicum, are described. In addition, a new infrageneric classification of Chlorophyllum is proposed, in which the genus is divided into six sections. One new combination is also made. This study provides a robust basis for a more detailed investigation of diversity and biogeography of Chlorophyllum.

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A molecular phylogenetic approach to Longidoridae (Nematoda: Dorylaimida)

Nematology ◽

10.1163/1568541054192108 ◽

2005 ◽

Vol 7 (1) ◽

pp. 111-124 ◽

Cited By ~ 69

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.

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A molecular phylogenetic analysis of Diuris (Orchidaceae) based on AFLP and ITS reveals three major clades and a basal species

Australian Systematic Botany ◽

10.1071/sb08029 ◽

2009 ◽

Vol 22 (1) ◽

pp. 1 ◽

Cited By ~ 3

Author(s):

James O. Indsto ◽

Peter H. Weston ◽

Mark A. Clements

Keyword(s):

Phylogenetic Analyses ◽

Sister Group ◽

Morphological Characters ◽

Molecular Data ◽

Total Evidence ◽

Bootstrap Support ◽

Its2 Region ◽

Molecular Phylogenetic ◽

Strong Bootstrap Support ◽

Evidence Analysis

Diuris is a terrestrial orchid genus of at least 61 and possibly more than 100 species, restricted to Australia except for one species endemic in Timor. Distinctive species groups have respective eastern and western centres of distribution. Although species affinities have been vaguely understood for many years, no formal infrageneric treatment has been undertaken as Diuris possesses few reliable morphological characters for a classification system. We have undertaken cladistic parsimony and Bayesian phylogenetic analyses of Diuris by using the ITS1–5.8S–ITS2 region of nuclear rDNA and morphological characters, with a subset of samples also studied by amplified fragment length polymorphism (AFLP) as an independent test of phylogenetic relationships. Four major clades with strong bootstrap support were resolved and are named here according to a recently published classification; D. sulphurea forms a lineage (subg. Paradiuris) of its own that is well supported as the sister to the rest of Diuris. Two other major eastern clades contained species related to D. maculata (subg. Xanthodiuris) and D. punctata (subg. Diuris), respectively. Although these latter two subgenera are genetically well resolved, there is minimal genetic variation at species level, consistent with recent, rapid speciation. A fourth clade (subg. Hesperodiuris) has a centre of distribution in Western Australia, and has more genetic and morphological variation than the eastern subgenera. Total evidence analysis provides support for the western clade being sister group to the two eastern subgenera Diuris and Xanthodiuris; however, this relationship was not resolved by molecular data. Hybridisation is known to be common among species within subgenera Diuris and Xanthodiuris. Instances of incongruence between different datasets were found suggestive of hybridisation events between species of different sections of Diuris.

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A phylogenetic analysis of filarial nematodes: comparison with the phylogeny of Wolbachia endosymbionts

Parasitology ◽

10.1017/s0031182000007149 ◽

2001 ◽

Vol 122 (1) ◽

pp. 93-103 ◽

Cited By ~ 240

Author(s):

M. CASIRAGHI ◽

T.J.C. ANDERSON ◽

C. BANDI ◽

C. BAZZOCCHI ◽

C. GENCHI

Keyword(s):

Sister Group ◽

Morphological Characters ◽

Coi Gene ◽

Phylogenetic Study ◽

Sister Group Relationship ◽

Rrna Gene ◽

Data Sets ◽

Gene Sequences ◽

Filarial Nematodes ◽

Molecular Phylogenetic

Infection with the endosymbiotic bacteria Wolbachia is widespread in filarial nematodes. Previous studies have suggested concordance between the phylogeny of Wolbachia with that of their nematode hosts. However, there is only one published molecular phylogenetic study of filarial species, based on the 5S rRNA gene spacer. The phylogeny proposed by this study is partially incongruent with previous classifications of filarial nematodes, based on morphological characters. Furthermore, both traditional classifications and molecular phylogenies are, in part, inconsistent with the phylogeny of Wolbachia. Here we report mitochondrial cytochrome oxidase I (COI) gene sequences for 11 species of filaria and for another spirurid nematode which was included as an outgroup. In addition, 16S rRNA, wsp and ftsZ gene sequences were generated for the Wolbachia of several filarial species, in order to complete the available data sets and further resolve the phylogeny of Wolbachia in nematodes. We used these data to evaluate whether nematode and Wolbachia phylogenies are concordant. Some of the possible phylogenetic reconstructions based on COI gene were congruent with the phylogeny of Wolbachia and supported the grouping of the rodent filaria Litomosoides sigmodontis with the lymphatic filariae (i.e. Brugia spp. and Wuchereria spp.) and the sister group relationship of Dirofilaria spp. and Onchocerca spp. However, the placement of the Wolbachia-free filaria Acanthocheilonema viteae is ambiguous and dependent on the phylogenetic methods used.

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