scholarly journals Phylogenetic Analysis of Mitogenomic Data Sets Resolves the Relationship of Seven Macropostrongyloides Species from Australian Macropodid and Vombatid Marsupials

Pathogens ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1042 ◽  
Author(s):  
Tanapan Sukee ◽  
Anson V. Koehler ◽  
Ross Hall ◽  
Ian Beveridge ◽  
Robin B. Gasser ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Mitochondrial Protein ◽  
Parasitic Nematodes ◽  
Data Sets ◽  
Protein Amino Acid ◽  
Protein Coding ◽  
Relationship Of ◽  
The Relationship ◽  
Swamp Wallaby

Nematodes of the genus Macropostrongyloides inhabit the large intestines or stomachs of macropodid (kangaroos and wallabies) and vombatid (wombats) marsupials. This study established the relationships of seven species of Macropostrongyloides using mitochondrial (mt) protein amino acid sequence data sets. Phylogenetic analyses revealed that species of Macropostrongyloides (M. lasiorhini, M. baylisi, M. yamagutii, M. spearei, M. mawsonae and M. woodi) from the large intestines of their hosts formed a monophyletic assemblage with strong nodal support to the exclusion of M. dissimilis from the stomach of the swamp wallaby. Furthermore, the mitochondrial protein-coding genes provided greater insights into the diversity and phylogeny of the genus Macropostrongyloides; such data sets could potentially be used to elucidate the relationships among other parasitic nematodes of Australian marsupials.

Anterastes davrazensis sp. n. (Orthoptera, Tettigoniidae): morphology, song and 16S rDNA phylogeny

Zootaxa ◽  
2012 ◽  
Vol 3401 (1) ◽  
pp. 49 ◽  
Author(s):  
SARP KAYA ◽  
DRAGAN CHOBANOV ◽  
BATTAL ÇIPLAK
Keyword(s):  
New Species ◽  
16S Rdna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
16S Rdna Sequence ◽  
Rdna Sequence Data ◽  
Male Calling ◽  
Relationship Of ◽  
The Relationship

The new species Anterastes davrazensis sp. n. (Orthoptera, Tettigoniidae) is described from south-eastern Turkey. Description, diagnosis and relationships of the new species were studied utilizing morphology, male calling songs and 16S rDNA sequence data from all species in the genus. Morphology and song syllable structure indicate A. davrazensis sp. n. is related to A. uludaghensis. Phylogenetic analyses based on representative haplotypes of 16S rDNA, using Sureyaella bella, Parapholidoptera distincta and Bolua turkiyae as outgroups, also suggested strong support to the relationship of these two species. A. davrazensis sp. n. differs from its closest relative A. uludaghensis by the higher number of stridulatory pegs and the song, consisting of irregular syllable groups.

A novel mitogenomic rearrangement for Odorrana schmackeri (Anura: Ranidae) and phylogeny of Ranidae inferred from thirteen mitochondrial protein-coding genes

2014 ◽  
Vol 35 (3) ◽  
pp. 331-343 ◽  
Author(s):  
Yongmin Li ◽  
Huabin Zhang ◽  
Xiaoyou Wu ◽  
Hui Xue ◽  
Peng Yan ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Mitochondrial Protein ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes

We determined the complete nucleotide sequence of the mitochondrial genome of Odorrana schmackeri (family Ranidae). The O. schmackeri mitogenome (18 302 bp) contained 13 protein-coding genes, 2 rRNA genes, 21 tRNA genes and a single control region (CR). In the new mitogenome, the distinctive feature is the loss of tRNA-His, which could be explained by a hypothesis of gene substitution. The new sequence data was used to assess the phylogenetic relationships among 23 ranid species mostly from China using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic analyses support two families (Ranidae, Dicroglossidae) for Chinese ranids. In Ranidae, we support the genus Amolops should be retained in the subfamily Raninae rather than in a distinct subfamily Amolopinae of its own. Meanwhile, the monophyly of the genus Odorrana was supported. Within Dicroglossidae, four tribes were well supported including Occidozygini, Dicroglossini, Limnonectini and Paini. More mitochondrial genomes and nuclear genes are required to decisively evaluate phylogenetic relationships of ranids.

scholarly journals Mitochondrial Evidence on the Phylogenetic Position of Caecilians (Amphibia: Gymnophiona)

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 765-775
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Tandem Repeats ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Maximum Parsimony Analysis ◽  
Bootstrap Support ◽  
Phylogenetic Position ◽  
Trna Genes ◽  
Data Sets ◽  
Data Set ◽  
Protein Coding

Abstract The complete nucleotide sequence (17,005 bp) of the mitochondrial genome of the caecilian Typhlonectes natans (Gymnophiona, Amphibia) was determined. This molecule is characterized by two distinctive genomic features: there are seven large 109-bp tandem repeats in the control region, and the sequence for the putative origin of replication of the L strand can potentially fold into two alternative secondary structures (one including part of the tRNACys). The new sequence data were used to assess the phylogenetic position of caecilians and to gain insights into the origin of living amphibians (frogs, salamanders, and caecilians). Phylogenetic analyses of two data sets—one combining protein-coding genes and the other combining tRNA genes—strongly supported a caecilian + frog clade and, hence, monophyly of modern amphibians. These two data sets could not further resolve relationships among the coelacanth, lungfishes, and tetrapods, but strongly supported diapsid affinities of turtles. Phylogenetic relationships among a larger set of species of frogs, salamanders, and caecilians were estimated with a mitochondrial rRNA data set. Maximum parsimony analysis of this latter data set also recovered monophyly of living amphibians and favored a frog + salamander (Batrachia) relationship. However, bootstrap support was only moderate at these nodes. This is likely due to an extensive among-site rate heterogeneity in the rRNA data set and the narrow window of time in which the three main groups of living amphibians were originated.

scholarly journals Schroeteria Decaisneana, S. Poeltii, and Ciboria Ploettneriana (Sclerotiniaceae, Helotiales, Ascomycota), Three Parasites on Veronica Seeds: First Report of Teleomorphs in Schroeteria

2021 ◽  
Author(s):  
Hans-Otto Baral ◽  
Peter Rönsch ◽  
Udo Richter ◽  
Alexander Urban ◽  
Julia Kruse ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Similar Species ◽  
Protein Coding ◽  
Ultrastructural Studies ◽  
The Core ◽  
Rdna Sequences ◽  
False Smut ◽  
Relationship Of ◽  
First Time ◽  
The Relationship

Abstract Three little known, morphologically similar species of Sclerotiniaceae which form their apothecia on fallen stromatized Veronica seeds are described and illustrated in detail based on fresh collections or moist chamber cultures of infected seeds: Ciboria ploettneriana, Schroeteria decaisneana, and Schroeteria poeltii. The former two were found on Veronica hederifolia agg. at different sites of temperate central Europe, the latter on V. cymbalaria in a mediterranean region of Spain. The latter two are anamorph-typified and here reported for the first time with their teleomorph.Ciboria ploettneriana was described by Kirschstein as Sclerotiniaploettneriana on seeds of V. hederifolia agg. but is currently treated in Ciboria. Based on the reexamination of four syntype specimens in B it became evident that Kirschstein confused the two species on V. hederifolia. A lectotype is therefore designated for S. ploettneriana.Members of Schroeteria are specific plant parasites infecting fruits of different Veronica spp. Schroeteria has earlier been referred to the Ustilaginales (Basidiomycota) based on its smut-like chlamydospores, but later light-microscopic and ultrastructural studies suggested that it represents a false smut fungus belonging to the Sclerotiniaceae (Helotiales).rDNA sequences were obtained from chlamydospores of Schroeteria bornmuelleri (on V. rubrifolia), S. delastrina (generic type, on Veronica arvensis), S. decaisneana, and S. poeltii, and from apothecia on V. hederifolia agg. and V. cymbalaria seeds. As a result, the anamorph-teleomorph connection could be verified for Schroeteria decaisneana and S. poeltii based on a 100% ITS similarity between both morphs, whereas Ciboria ploettneriana in the here redefined sense could not be connected to an anamorph.Our phylogenetic analyses show that Ciboria ploettneriana belongs in the relationship of Sclerotinia, Stromatinia, and Grovesinia rather than Ciboria, but its placement was not supported. Also Schroeteria poeltii clustered unresolved in this relationship but has a much higher molecular distance to those. The remaining three Schroeteria spp. formed a supported monophyletic group, the Schroeteria core clade, which clustered with medium to low support distantly to a member of the Monilinia alpina group of section Disjunctoriae (M. jezoensis). ITS distances of 5–6.3% were found among members of the Schroeteria core clade, and 13.8–14.7% between the core clade and S. poeltii. The high distance of S. poeltii reflects its deviating chlamydospore morphology.Despite the high heterogeneity in the available ITS and LSU data, Schroeteria is accepted here under inclusion of S. poeltii as a genus distinct from Monilinia, particularly because of its very special anamorphs. A similar heterogeneity in rDNA analyses was observed in Monilinia and other genera of Sclerotiniaceae. Protein-coding genes should be investigated in order to obtain a more natural phylogeny within the Sclerotiniaceae.

Morphological and molecular characterization of Megalobatrachonema hainanensis sp. nov. (Nematoda: Ascaridida), with phylogenetic position of Megalobatrachonema in Cosmocercoidea

2018 ◽  
Vol 94 ◽  
Author(s):  
H.-X. Chen ◽  
L.-P. Zhang ◽  
L. Li
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Hainan Island ◽  
Phylogenetic Position ◽  
Phylogenetic Study ◽  
Its1 Sequence ◽  
Nematode Parasites ◽  
Relationship Of ◽  
The Relationship

Abstract The genus Megalobatrachonema is a rare group of nematode parasites within Ascaridida. The systematic status of Megalobatrachonema in the superfamily Cosmocercoidea (Ascaridida) has long been controversial. The relationship of Megalobatrachonema and Chabaudgolvania remains unsolved. In the present study, a new species of Megalobatrachonema, M. hainanensis sp. nov., was described based on specimens collected in Amolops hainanensis (Boulenger) and Hylarana spinulosa (Smith) (Amphibia: Anura) from Hainan Island, China. The large ribosomal DNA (28S) and internal transcribed spacer (ITS1-5.8S-ITS2) were also sequenced for molecular identification and phylogenetic study. Phylogenetic analyses using maximum likelihood (ML) inference and Bayesian inference (BI) based on 28S and ITS1 sequence data, respectively, supported that Megalobatrachonema is a member of the family Kathlaniidae. In addition, the genetic comparison and phylogenetic results based on ITS1 sequence data also supported that the genus Chabaudgolvania should be considered as a synonym of Megalobatrachonema.

scholarly journals The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1517
Author(s):  
Se-Hwan Cheon ◽  
Min-Ah Woo ◽  
Sangjin Jo ◽  
Young-Kee Kim ◽  
Ki-Joong Kim
Keyword(s):  
Northeast Asia ◽  
Single Copy ◽  
Rrna Genes ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Protein Coding ◽  
Tropical Regions ◽  
Relationship Of ◽  
The Relationship ◽  
Simple Sequence

The genus Zoysia Willd. (Chloridoideae) is widely distributed from the temperate regions of Northeast Asia—including China, Japan, and Korea—to the tropical regions of Southeast Asia. Among these, four species—Zoysia japonica Steud., Zoysia sinica Hance, Zoysia tenuifolia Thiele, and Zoysia macrostachya Franch. & Sav.—are naturally distributed in the Korean Peninsula. In this study, we report the complete plastome sequences of these Korean Zoysia species (NCBI acc. nos. MF953592, MF967579~MF967581). The length of Zoysia plastomes ranges from 135,854 to 135,904 bp, and the plastomes have a typical quadripartite structure, which consists of a pair of inverted repeat regions (20,962~20,966 bp) separated by a large (81,348~81,392 bp) and a small (12,582~12,586 bp) single-copy region. In terms of gene order and structure, Zoysia plastomes are similar to the typical plastomes of Poaceae. The plastomes encode 110 genes, of which 76 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fourteen genes contain single introns and one gene has two introns. Three evolutionary hotspot spacer regions—atpB~rbcL, rps16~rps3, and rpl32~trnL-UAG—were recognized among six analyzed Zoysia species. The high divergences in the atpB~rbcL spacer and rpl16~rpl3 region are primarily due to the differences in base substitutions and indels. In contrast, the high divergence between rpl32~trnL-UAG spacers is due to a small inversion with a pair of 22 bp stem and an 11 bp loop. Simple sequence repeats (SSRs) were identified in 59 different locations in Z. japonica, 63 in Z. sinica, 62 in Z. macrostachya, and 63 in Z. tenuifolia plastomes. Phylogenetic analysis showed that the Zoysia (Zoysiinae) forms a monophyletic group, which is sister to Sporobolus (Sporobolinae), with 100% bootstrap support. Within the Zoysia clade, the relationship of (Z. sinica, Z japonica), (Z. tenuifolia, Z. matrella), (Z. macrostachya, Z. macrantha) was suggested.

scholarly journals Complete Mitogenomic Structure and Phylogenetic Implications of the Genus Ostrinia (Lepidoptera: Crambidae)

Insects ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 232
Author(s):  
Nan Zhou ◽  
Yanling Dong ◽  
Pingping Qiao ◽  
Zhaofu Yang
Keyword(s):  
Control Region ◽  
Ostrinia Nubilalis ◽  
Phylogenetic Analyses ◽  
Structural Elements ◽  
Ostrinia Furnacalis ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Ostrinia Scapulalis ◽  
The Relationship ◽  
Rna Genes

To understand mitogenome characteristics and reveal phylogenetic relationships of the genus Ostrinia, including several notorious pests of great importance for crops, we sequenced the complete mitogenomes of four species: Ostrinia furnacalis (Guenée, 1854), Ostrinia nubilalis (Hübner, 1796), Ostrinia scapulalis (Walker, 1859) and Ostrinia zealis (Guenée, 1854). Results indicate that the four mitogenomes—O. furnacalis, O. nubilalis, O. scapulalis, and O. zealis—are 15,245, 15,248, 15,311, and 15,208 bp in size, respectively. All four mitogenomes are comprised of 37 encoded genes and a control region. All 13 protein-coding genes (PCGs) initiate with ATN and terminate with TAN, with the exception of cox1 that starts with CGA, and cox1, cox2, and nad5 that terminate with an incomplete codon T. All transfer RNA genes (tRNAs) present the typical clover-leaf secondary structure except for the trnS1 (AGN) gene. There are some conserved structural elements in the control region. Our analyses indicate that nad6 and atp6 exhibit higher evolution rates compared to other PCGs. Phylogenetic analyses based on mitogenomes using both maximum likelihood (ML) and Bayesian inference (BI) methods revealed the relationship (O. palustralis + (O. penitalis + (O. zealis + (O. furnacalis + (O. nubilalis + O. scapulalis))))) within Ostrinia.

scholarly journals Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Mammalia ◽  
2019 ◽  
Vol 83 (2) ◽  
pp. 180-189 ◽  
Author(s):  
Adam W. Ferguson ◽  
Houssein R. Roble ◽  
Molly M. McDonough
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Alternative Hypothesis ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Sister Relationship ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Molecular Phylogenetic ◽  
Relationship Of

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

Generic Delimitations and Relationships of the Cape Genera Capnophyllum, Dasispermum, and Sonderina, the North African Genera Krubera and Stoibrax, and a New Monotypic Genus of the Subfamily Apioideae (Apiaceae)

2009 ◽  
Vol 34 (3) ◽  
pp. 580-594 ◽  
Author(s):  
Anthony R. Magee ◽  
Ben-Erik van Wyk ◽  
Patricia M. Tilney ◽  
Stephen R. Downie
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Monotypic Genus ◽  
North African ◽  
African Species ◽  
Dna Sequence Data ◽  
The North ◽  
Relationship Of

Generic circumscriptions and phylogenetic relationships of the Cape genera Capnophyllum, Dasispermum, and Sonderina are explored through parsimony and Bayesian inference analyses of nrDNA ITS and cpDNA rps16 intron sequences, morphology, and combined molecular and morphological data. The relationship of these genera with the North African genera Krubera and Stoibrax is also assessed. Analyses of both molecular data sets place Capnophyllum, Dasispermum, Sonderina, and the only southern African species of Stoibrax (S. capense) within the newly recognized Lefebvrea clade of tribe Tordylieae. Capnophyllum is strongly supported as monophyletic and is distantly related to Krubera. The monotypic genus Dasispermum and Stoibrax capense are embedded within a paraphyletic Sonderina. This complex is distantly related to the North African species of Stoibrax in tribe Apieae, in which the type species, Stoibrax dichotomum, occurs. Consequently, Dasispermum is expanded to include both Sonderina and Stoibrax capense. New combinations are formalized for Dasispermum capense, D. hispidum, D. humile, and D. tenue. An undescribed species from the Tanqua Karoo in South Africa is also closely related to Capnophyllum and the Dasispermum–Sonderina complex. The genus Scaraboides is described herein to accommodate the new species, S. manningii. This monotypic genus shares the dorsally compressed fruit and involute marginal wings with Capnophyllum, but is easily distinguished by its erect branching habit, green leaves, scabrous umbels, and fruit with indistinct median and lateral ribs, additional solitary vittae in each marginal wing, and parallel, closely spaced commissural vittae. Despite the marked fruit similarities with Capnophyllum, analyses of DNA sequence data place Scaraboides closer to the Dasispermum–Sonderina complex, with which it shares the erect habit, green (nonglaucous) leaves, and scabrous umbels.

Mitochondrial DNA dataset suggest that the genus Sphaerirostris Golvan, 1956 is a synonym of the genus Centrorhynchus Lühe, 1911

Parasitology ◽  
2020 ◽  
Vol 147 (10) ◽  
pp. 1149-1157 ◽  
Author(s):  
Nehaz Muhammad ◽  
Suleman ◽  
Munawar Saleem Ahmad ◽  
Liang Li ◽  
Qing Zhao ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Likelihood Methods ◽  
Sister Relationship ◽  
Protein Coding ◽  
Maximum Likelihood Methods ◽  
Relationship Of ◽  
First Time ◽  
Mt Genome ◽  
Rna Genes

AbstractOur present genetic data of Acanthocephala, especially the mitochondrial (mt) genomes, remains very limited. In the present study, the nearly complete mt genome sequences of Sphaerirostris lanceoides (Petrochenko, 1949) was sequenced and determined for the first time based on specimens collected from the Indian pond heron Ardeola grayii (Sykes) (Ciconiiformes: Ardeidae) in Pakistan. The mt genome of S. lanceoides is 13 478 bp in size and contains 36 genes, including 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA genes (rRNAs). Moreover, in order to clarify the phylogenetic relationship of the genera Centrorhynchus and Sphaerirostris, and to test the systematic position of S. lanceoides in the Centrorhynchidae, the phylogenetic analyses were performed using Bayesian inference and maximum likelihood methods, based on concatenated nucleotide sequences of 12 PCGs, rRNAs and tRNAs. The phylogenetic results further confirmed the monophyly of the order Polymorphida and the paraphyly of the order Echinorhynchida in the class Palaeacanthocephala. Our results also challenged the validity of the genus Sphaerirostris (Polymorphida: Centrorhynchidae) and showed a sister relationship between S. lanceoides and S. picae (Rudolphi, 1819).

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