scholarly journals Phylogenetic Relationships within the Nematode Subfamily Phascolostrongylinae (Nematoda: Strongyloidea) from Australian Macropodid and Vombatid Marsupials

2020 ◽  
Vol 9 (1) ◽  
pp. 9
Author(s):  
Tanapan Sukee ◽  
Ian Beveridge ◽  
Ahmad Jawad Sabir ◽  
Abdul Jabbar
Keyword(s):  
Large Intestine ◽  
Phylogenetic Relationships ◽  
Strong Support ◽  
Taxonomic Revision ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Unexpected Finding ◽  
Generic Level ◽  
Grey Kangaroo ◽  
Generic Composition

The strongyloid nematode subfamily Phascolostrongylinae comprises parasites of the large intestine and stomach of Australian macropods and wombats. In this study, we tested the phylogenetic relationships among the genera of the Phascolostrongylinae using the first and second internal transcribed spacers of the nuclear ribosomal DNA. Monophyly was encountered in the tribe Phascolostrongylinea comprising two genera, Phascolostrongylus and Oesophagostomoides, found exclusively in the large intestine of wombats. The tribe Hypodontinea, represented by the genera Hypodontus and Macropicola from the ileum and large intestine of macropods, was also found to be monophyletic. The tribe Macropostrongyloidinea, comprising the genera Macropostrongyloides and Paramacropostrongylus, was paraphyletic with the species occurring in the stomach grouping separately from those found in the large intestines of their hosts. However, Macropostrongyloidesdissimilis from the stomach of the swamp wallaby and Paramacropostrongylus toraliformis from the large intestine of the eastern grey kangaroo were distinct from their respective congeners. This study provided strong support for the generic composition of the tribe Phascolostrongylinea. The unexpected finding of M. dissimilis and P. toraliformis being distantly related to their respective congeners suggests a requirement for future taxonomic revision that may warrant separation of these species at the generic level.

scholarly journals Phylogenetic Relationships within the Nematode Subfamily Phascolostrongylinae (Nematoda: Strongyloidea) from Australian Macropodid and Vombatid Marsupials

2020 ◽  
Author(s):  
Tanapan Sukee ◽  
Ian Beveridge ◽  
Ahmad Jawad Sabir ◽  
Abdul Jabbar
Keyword(s):  
Large Intestine ◽  
Phylogenetic Relationships ◽  
Strong Support ◽  
Taxonomic Revision ◽  
Unexpected Finding ◽  
Generic Level ◽  
Grey Kangaroo ◽  
Generic Composition ◽  
Second Internal Transcribed Spacer ◽  
Strongyloid Nematode

Abstract Background: The strongyloid nematode subfamily Phascolostrongylinae are parasites of the large intestine and stomach of Australian macropods (Macropodidae) and wombats (Vombatidae). Based on morphological classifications, the Phascolostrongylinae is comprised of seven genera belonging to three tribes (Phascolostrongylinea, Macropostrongyloidinea, and Hypodontinea). The phylogenetic relationships among the genera of the Phascolostrongylinae were tested using the first and second internal transcribed spacer (ITS+) sequences of the ribosomal DNA. Results: Monophyly was encountered in the tribe Phascolostrongylinea comprising two genera, Phascolostrongylus and Oesophagostomoides, found exclusively in the large intestine of wombats. The tribe Hypodontinea, represented by the genera Hypodontus and Macropicola from the ileum and large intestine of macropods was also found to be monophyletic, but with low support. The tribe Macropostrongyloidinea comprising the genera Macropostrongyloides and Paramacropostrongylus was paraphyletic with the species occurring in the stomach grouping separately to those found in the large intestines of their hosts. Finally, Macropostrongyloides dissimilis from the stomach of the swamp wallaby and Paramacropostrongylus toraliformis from the large intestine of the eastern grey kangaroo were distinct from their respective congeners. Conclusion: The current study provided strong support for the generic composition of the tribe Phascolostrongylinea and low support for the tribe Hypodontinea. However, the relationships within the tribe Macropostrongyloidinea are more complex and its monophyly was not supported by the current ITS+ dataset. The unexpected finding of M. dissimilis and P. toraliformis being distantly related to their respective congeners suggests a requirement for future taxonomic revision which may warrant separation of these species at the generic level.

Phylogenetic relationships based on nuclear and plastid DNA sequences reveal recent diversification and discordant patterns of morphological evolution of the Chilean genera of Gilliesieae (Amaryllidaceae: Allioideae)

2020 ◽  
Vol 194 (1) ◽  
pp. 84-99
Author(s):  
Inelia Escobar ◽  
Eduardo Ruiz-Ponce ◽  
Paula J Rudall ◽  
Michael F Fay ◽  
Oscar Toro-Núñez ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Incomplete Lineage Sorting ◽  
Morphological Evolution ◽  
Strong Support ◽  
Plastid Dna ◽  
Lineage Sorting ◽  
Generic Level ◽  
Molecular Analyses ◽  
Floral Diversity

Abstract Gilliesieae are a South American tribe of Amaryllidaceae characterized by high floral diversity. Given different taxonomic interpretations and proposals for generic and specific relationships, a representative phylogenetic analysis is required to clarify the systematics of this group. The present study provides a framework for understanding phylogenetic relationships and contributing to the development of an appropriate taxonomic treatment of Gilliesieae. Molecular analyses, based on nuclear (ITS) and plastid DNA sequences (trnL-F and rbcL), resolve with strong support the monophyly of the tribe and the differentiation of two major clades. Clade I comprises the genera Gilliesia, Gethyum and Solaria and Clade II includes Miersia and Speea. These well-supported clades are mostly congruent with vegetative and karyotype characters rather than, e.g., floral symmetry. At the generic level, all molecular analyses reveal the paraphyly of Gilliesia and Miersia. Gethyum was found to be paraphyletic, resulting in the confirmation of Ancrumia as a distinct genus. Several instances of incongruent phylogenetic signals were found among data sets. The calibrated tree suggests a recent diversification of the tribe (Pliocene–Pleistocene), a contemporary process of speciation in which instances of hybridization and incomplete lineage sorting could explain patterns of paraphyly and incongruence of floral morphology.

scholarly journals Phylogenetic relationships of the nematode subfamily Phascolostrongylinae from macropodid and vombatid marsupials inferred using mitochondrial protein sequence data

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Tanapan Sukee ◽  
Ian Beveridge ◽  
Anson V. Koehler ◽  
Ross Hall ◽  
Robin B. Gasser ◽  
...  
Keyword(s):  
Amino Acid ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Mitochondrial Protein ◽  
Amino Acid Sequences ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
Data Sets ◽  
Sister Relationship

Abstract Background The subfamily Phascolostrongylinae (Superfamily Strongyloidea) comprises nematodes that are parasitic in the gastrointestinal tracts of macropodid (Family Macropodidae) and vombatid (Family Vombatidae) marsupials. Currently, nine genera and 20 species have been attributed to the subfamily Phascolostrongylinae. Previous studies using sequence data sets for the internal transcribed spacers (ITS) of nuclear ribosomal DNA showed conflicting topologies between the Phascolostrongylinae and related subfamilies. Therefore, the aim of this study was to validate the phylogenetic relationships within the Phascolostrongylinae and its relationship with the families Chabertiidae and Strongylidae using mitochondrial amino acid sequences. Methods The sequences of all 12 mitochondrial protein-coding genes were obtained by next-generation sequencing of individual adult nematodes (n = 8) representing members of the Phascolostrongylinae. These sequences were conceptually translated and the phylogenetic relationships within the Phascolostrongylinae and its relationship with the families Chabertiidae and Strongylidae were inferred from aligned, concatenated amino acid sequence data sets. Results Within the Phascolostrongylinae, the wombat-specific genera grouped separately from the genera occurring in macropods. Two of the phascolostrongyline tribes were monophyletic, including Phascolostrongylinea and Hypodontinea, whereas the tribe Macropostrongyloidinea was paraphyletic. The tribe Phascolostrongylinea occurring in wombats was closely related to Oesophagostomum spp., also from the family Chabertiidae, which formed a sister relationship with the Phascolostrongylinae. Conclusion The current phylogenetic relationship within the subfamily Phascolostrongylinae supports findings from a previous study based on ITS sequence data. This study contributes also to the understanding of the phylogenetic position of the subfamily Phascolostrongylinae within the Chabertiidae. Future studies investigating the relationships between the Phascolostrongylinae and Cloacininae from macropodid marsupials may advance our knowledge of the phylogeny of strongyloid nematodes in marsupials. Graphical Abstract

Revisiting phylogenetic relationships in Phoradendreae (Viscaceae): utility of the trnL-F region of chloroplast DNA and presence of a homoplasious inversion in the intergenic spacer

Botany ◽  
2017 ◽  
Vol 95 (3) ◽  
pp. 247-258 ◽  
Author(s):  
Vanessa E.T.M. Ashworth
Keyword(s):  
Chloroplast Dna ◽  
Phylogenetic Relationships ◽  
Nucleotide Substitution ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Nuclear Ribosomal Dna ◽  
Morphological Data ◽  
Maximum Parsimony Analysis ◽  
Tropical Species ◽  
F Region

The utility of the trnL-F region of the chloroplast DNA for inferring relationships in 26 taxa in the mistletoe tribe Phoradendreae (Viscaceae) was compared with that of sequences from three regions of the nuclear ribosomal DNA (nrDNA). Chloroplast- and nuclear-inferred phylogenies generally were congruent based on maximum parsimony analysis of nucleotide substitution data. Results suggested that the intron and intergenic spacer of the chloroplast partition were not sufficiently variable to resolve phylogenetic relationships among either close relatives or more distantly related species. The distribution of insertions and deletions generally supported the phylogeny inferred from nucleotide substitution data. However, presence or absence of a 59-nucleotide inversion in the trnL-F intergenic spacer of eight Phoradendron species showed no agreement with the topology inferred from molecular and morphological data. Combined analyses of the nuclear partitions and the chloroplast region (with the homoplasious inversion inserted in reverse orientation) provided strong support for P. californicum as sister to a clade uniting North American species and not as sister to a clade comprising more tropical species. Consistent with results from previous studies using nrDNA, a lineage in the Phoradendron leucarpum complex (comprising subsp. leucarpum and macrophyllum) was strongly supported, but subspecies tomentosum was not confidently placed.

Phylogenetic relationships of three tribes of cloacinine nematodes (Strongylida: Chabertiidae) from macropodid marsupials

2018 ◽  
Vol 93 (04) ◽  
pp. 486-493 ◽  
Author(s):  
N.B. Chilton ◽  
F. Huby-Chilton ◽  
A. Koehler ◽  
R.B. Gasser ◽  
I. Beveridge
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Host Genus ◽  
Single Host

AbstractThe phylogenetic relationships of 42 species of cloacinine nematodes belonging to three tribes (Coronostrongylinea, Macropostrongylinea and Zoniolaiminea) were examined based on sequence data of the first and second internal transcribed spacers (ITS-1 and ITS-2) of the nuclear ribosomal DNA. All nematodes examined are parasites of Australian macropodid marsupials. None of the three nematode tribes was monophyletic. Paraphyly was also encountered in three genera: Papillostrongylus, Monilonema and Wallabinema. Species within the genus Thallostonema were limited to a single host genus (i.e. Thylogale), whereas species within the five principal genera (Coronostrongylus, Macropostrongylus, Popovastrongylus, Wallabinema and Zoniolaimus) were found to occur in multiple host genera. Potential modes of evolution among these nematodes are discussed.

Phylogenetic relationships in Dermocybe and related Cortinarius taxa based on nuclear ribosomal DNA internal transcribed spacers

1997 ◽  
Vol 75 (4) ◽  
pp. 519-532 ◽  
Author(s):  
Y. J. Liu ◽  
S. O. Rogers ◽  
Y. J. Liu ◽  
J. F. Ammirati
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Herbarium Specimens ◽  
Data Reorganization ◽  
Taxonomic Groups

The genus Cortinarius Fr. (Cortinariaceae, Agaricales) is divided into four or more subgenera. Dermocybe (Fr.) Sacc. has been recognized as either a subgenus of Cortinarius or a separate genus, distinguished in part by the presence of various anthraquinonic pigments. Nucleotide sequences of ribosomal DNA 5.8S and internal transcribed spacers were used to investigate the phylogenetic relationships among species of Dermocybe and selected taxa from subgenera of Cortinarius. Sequence data from 47 herbarium specimens representing 31 taxa (28 species plus 3 varieties) of Dermocybe and Cortinarius were analyzed using parsimony, maximum likelihood, and neighbor joining. In general, molecular data support the morphological groupings of the taxa, although they more closely correspond to biochemical (anthraquinone and other) analyses. Phylogenetic trees showed that, while the sections Dermocybe and Malicoriae are monophyletic, and the concolorous or almost concolorous red species (section Sanguineae, such as D. sanguinea and relatives) together formed a coherent clade, the subgenus Dermocybe sensu lato itself is polyphyletic. Cortinarius californicus clusters with taxa in Cortinarius, subgenus Telamonia, section Armillati. Dermocybe olivaceopicta is more closely related to other subgenera of Cortinarius than to Dermocybe. Within the genus Cortinarius, certain of the subgenera may actually represent coherent genera. Of the subgenera examined, Telamonia, Phlegmacium, and possibly Sericeocybe appear to represent well defined taxonomic groupings. However, current assignments of taxa within Leprocybe and Myxacium were inconsistent with the molecular data. Reorganization of some taxa and taxonomic groups is suggested. Key words: Dermocybe, Cortinarius, molecular phylogeny, rDNA, ITS1, ITS2.

Eight new species of Siphoderina Manter, 1934 (Digenea, Cryptogonimidae) infecting Lutjanidae and Haemulidae (Perciformes) off Australia

2008 ◽  
Vol 53 (4) ◽  
Author(s):  
Terrence Miller ◽  
Thomas Cribb
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Large Subunit ◽  
Strong Support ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Evolutionary Divergence ◽  
New Combinations ◽  
Closely Related Species ◽  
History Of

AbstractWe report nine species, eight of which are new, of cryptogonimids belonging to Siphoderina Manter, 1934 from the intestine and pyloric caeca of five species of Lutjanidae (Lutjanus adetii, L. argentimaculatus, L. carponotatus, L. fulviflamma and L. russelli) and one species of Haemulidae (Plectorhinchus gibbosus) recovered from Heron and Lizard Islands off the Great Barrier Reef, Moreton Bay and Ningaloo Reef in Western Australia. We also report the metacercariae of two species from an atherinid fish, Atherinomorus capricornensis, from near Heron Island. Morphological analysis of the species reported here was augmented by DNA sequence analyses utilizing data from the internal transcribed spacers (ITS) 1 and 2, large subunit (LSU) and 5.8S nuclear ribosomal DNA to explore the integrity of the species and their biogeographic distributions. The analysis found strong support for the integrity of Siphoderina and found that it is the sister-taxon to Beluesca Miller et Cribb, 2007. Sequencing included multiple replicates and no intraspecific variation was observed between any of the taxa over the rDNA regions examined. Sequence data from the ITS and LSU regions were analysed with that of species of Beluesca, Caulanus Miller et Cribb, 2007, Chelediadema Miller et Cribb, 2007, Latuterus Miller et Cribb, 2007, Neometadena Hafeezullah et Siddiqi, 1970 and Retrovarium Miller et Cribb, 2007 which all also infect lutjanids or haemulids. Some closely related species of Siphoderina infect only distantly related fishes among the haemulids and lutjanids whereas others form clusters in association with clusters of closely related lutjanids. This pattern suggests a history of some co-evolutionary divergence together with significant host switching. Pseudallacanthochasmus Velasquez, 1961 is considered a synonym of Siphoderina and the new combinations S. grandispinus (Velasquez, 1961) n. comb. and S. magnivesiculum (Gaevskaya et Aljoshkina, 1985) n. comb. are proposed. As a result of the new species described here and these new combinations, Siphoderina now contains 43 species, making it by far the largest genus of the Cryptogonimidae.

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