Molecular and morphometric characterisation of Xiphinema globosum Sturhan, 1978 (Nematoda: Longidoridae) from Spain

Nematology ◽  
2011 ◽  
Vol 13 (1) ◽  
pp. 17-28 ◽  
Author(s):  
Blanca Landa ◽  
Carolina Cantalapiedra-Navarrete ◽  
Juan Palomares-Rius ◽  
Pablo Castillo ◽  
Carlos Gutiérrez-Gutiérrez
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Matrix Representation ◽  
Natural Environments ◽  
28S Rrna ◽  
Parsimony Method ◽  
Rdna Genes ◽  
Supertree Method ◽  
The Matrix ◽  
Relationship Of

AbstractDuring a recent nematode survey in natural environments of the Los Alcornocales Regional Park narrow valleys, viz., the renowned 'canutos' excavated in the mountains that maintain a humid microclimate, in southern Spain, an amphimictic population of Xiphinema globosum was identified. Morphological and morphometric studies on this population fit the original and previous descriptions and represent the first report from Spain and southern Europe. Molecular characterisation of X. globosum from Spain using D2-D3 expansion regions of 28S rRNA, 18S rRNA and ITS1-rRNA is provided and maximum likelihood and Bayesian inference analysis were used to reconstruct phylogenetic relationships within X. globosum and other Xiphinema species. A supertree solution of the different phylogenetic trees obtained in this study and in other published studies using rDNA genes are presented using the matrix representation parsimony method (MRP) and the most similar supertree method (MSSA). The results revealed a closer phylogenetic relationship of X. globosum with X. diversicaudatum, X. bakeri and with some sequences of unidentified Xiphinema spp. deposited in GenBank.

Molecular characterisation and phylogenetic relationships of sedentary nematodes of the genus Meloinema Choi & Geraert, 1974 (Nematoda: Tylenchida)

Nematology ◽  
2020 ◽  
pp. 1-9
Author(s):  
Sergei A. Subbotin ◽  
Donggeun Kim
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
Sister Relationship ◽  
The Family ◽  
18S Rrna Genes ◽  
Relationship Of

Summary Molecular characterisation of two species of Meloinema: M. chitwoodi from Oregon, USA, and M. odesanens from South Korea, is given based on the partial 18S rRNA, the D2-D3 of 28S rRNA, ITS rRNA, and COI gene sequences. In the phylogenetic trees, Meloinema clustered with Meloidogyne, in a basal position and more closely with Meloidogyne indica and M. nataliei. The Shimodaira-Hasegawa (SH) maximum likelihood testing of an alternative topology with two gene fragments (D2-D3 of 28S rRNA and 18S rRNA genes) did not reject a sister relationship of Meloidogyne and Meloinema. Molecular results confirmed the view of Siddiqi (2000) that Meloidogyne and Meloinema evolved from a Pratylenchidae-type ancestor. The clade Meloinema + Meloidogyne + Nacobbus was rejected by the SH test of the D2-D3 of 28S rRNA gene sequence dataset. The molecular results suggested that the genus Nacobbus should be placed not in the Meloidogynidae, but in a separate subfamily, the Nacobbinae, under the family Pratylenchidae.

scholarly journals Polynomial Supertree Methods Revisited

2011 ◽  
Vol 2011 ◽  
pp. 1-21 ◽  
Author(s):  
Malte Brinkmeyer ◽  
Thasso Griebel ◽  
Sebastian Böcker
Keyword(s):  
Simulation Study ◽  
Phylogenetic Trees ◽  
Optimization Problem ◽  
Matrix Representation ◽  
Distance Matrix ◽  
Extensive Simulation ◽  
Supertree Method ◽  
Pros And Cons ◽  
To Come ◽  
Supertree Methods

Supertree methods allow to reconstruct large phylogenetic trees by combining smaller trees with overlapping leaf sets into one, more comprehensive supertree. The most commonly used supertree method, matrix representation with parsimony (MRP), produces accurate supertrees but is rather slow due to the underlying hard optimization problem. In this paper, we present an extensive simulation study comparing the performance of MRP and the polynomial supertree methods MinCut Supertree, Modified MinCut Supertree, Build-with-distances, PhySIC, PhySIC_IST, and super distance matrix. We consider both quality and resolution of the reconstructed supertrees. Our findings illustrate the tradeoff between accuracy and running time in supertree construction, as well as the pros and cons of voting- and veto-based supertree approaches. Based on our results, we make some general suggestions for supertree methods yet to come.

scholarly journals Molecular and morphological characterisation of Sphaeronema alni Turkina & Chizhov, 1986 (Nematoda: Sphaeronematidae) from Spain compared with a topotype population from Russia

Nematology ◽  
2010 ◽  
Vol 12 (4) ◽  
pp. 649-659 ◽  
Author(s):  
Juan Palomares-Rius ◽  
Nicola Vovlas ◽  
Sergei A. Subbotin ◽  
Alberto Troccoli ◽  
Carolina Cantalapiedra-Navarrete ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Castanea Sativa ◽  
Rrna Gene ◽  
28S Rrna ◽  
Rflp Profile ◽  
Basal Clade ◽  
Pcr Rflp ◽  
First Time ◽  
Partial 18S

Abstract The occurrence of a male-less population of Sphaeronema alni parasitising chestnut (Castanea sativa) roots and inducing a stelar syncytium is reported for the first time in Pola de Somiedo (Oviedo province), Spain. Morphometric and molecular characters of the Spanish population matched those of a topotype population from Russia. SEM observations showed swollen females having the first lip annulus wider than the second and appearing as a cap-like, circumoral elevation. The second-stage juveniles, having a single band in the lateral fields, were characterised by a non-annulated dome-shaped lip region derived from the fusion of the oral disc with all the lip sectors and lip annuli, and showing slit-like amphidial apertures and an oval prestoma. The sequences of the D2-D3 expansion segments of 28S rRNA, partial 18S rRNA and ITS rRNA gene for the Spanish and topotype populations of S. alni were congruent and matched those deposited in GenBank for another population from Germany, thereby confirming their conspecificity. A PCR-RFLP profile of D2-D3 of 28S rRNA for identification of this species was also provided. The phylogenetic relationships between S. alni populations and representatives of the suborder Criconematina, as inferred from analysis of partial 18S rRNA and D2-D3 of 28S gene sequences obtained in this and previous studies, indicated that S. alni formed a basal clade on the majority consensus Bayesian phylogenetic trees, standing together with Meloidoderita sp. or alone. These findings provide additional evidence of the need to clarify the position of Sphaeronema within Criconematina and its relationships with representatives of Tylenchulinae.

Systematic status of the caridean families Gnathophyllidae Dana and Hymenoceridae Ortmann (Crustacea : Decapoda): a preliminary examination based on nuclear rDNA sequences

2007 ◽  
Vol 21 (6) ◽  
pp. 613 ◽  
Author(s):  
M. Mitsuhashi ◽  
Y. W. Sin ◽  
H. C. Lei ◽  
T.-Y. Chan ◽  
K. H. Chu
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Rrna Genes ◽  
28S Rrna ◽  
Nuclear Rdna ◽  
Rdna Sequences ◽  
Preliminary Examination ◽  
The Family ◽  
Close Relationship ◽  
Paraphyletic Assemblage

The systematic positions of the caridean families Gnathophyllidae and Hymenoceridae are inferred based on analyses of nuclear 18S rRNA and 28S rRNA genes. The phylogenetic trees based on 18S rRNA and 28S rRNA from selected species of one genus of the family Gnathophyllidae, two genera of the family Hymenoceridae, one genus of the family Anchistioididae, eight genera of the subfamily Pontoniinae and five genera of the subfamily Palaemoninae show a close relationship between Hymenoceridae, Gnathophyllidae and Pontoniinae, with the last group constituting a paraphyletic assemblage. This result concurs with the morphology of maxilla in the first zoea, but not the shape of the third maxilliped in adults, based on which Gnathophyllidae and Hymenoceridae are treated as families. Molecular analysis supports the similarities in larval morphology between Hymenoceridae, Gnathophyllidae and Pontoniinae and therefore draws into question the familial status of the former two groups.

Phylogeny of hymenolepidids (Cestoda: Cyclophyllidea) from mammals: sequences of 18S rRNA and COI genes confirm major clades revealed by the 28S rRNA analyses

2021 ◽  
Vol 95 ◽  
Author(s):  
B. Neov ◽  
G.P. Vasileva ◽  
G. Radoslavov ◽  
P. Hristov ◽  
D.T.J. Littlewood ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
18S Rrna ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Rrna Genes ◽  
Host Switching ◽  
28S Rrna ◽  
Mitochondrial Cytochrome ◽  
Rapid Radiation ◽  
18S Rrna Genes

Abstract The aim of the study is to test a hypothesis for the phylogenetic relationships among mammalian hymenolepidid tapeworms, based on partial (D1–D3) nuclear 28S ribosomal RNA (rRNA) genes, by estimating new molecular phylogenies for the group based on partial mitochondrial cytochrome c oxidase I (COI) and nuclear 18S rRNA genes, as well as a combined analysis using all three genes. New sequences of COI and 18S rRNA genes were obtained for Coronacanthus integrus, C. magnihamatus, C. omissus, C. vassilevi, Ditestolepis diaphana, Lineolepis scutigera, Spasskylepis ovaluteri, Staphylocystis tiara, S. furcata, S. uncinata, Vaucherilepis trichophorus and Neoskrjabinolepis sp. The phylogenetic analyses confirmed the major clades identified by Haukisalmi et al. (Zoologica Scripta 39: 631–641, 2010): Ditestolepis clade, Hymenolepis clade, Rodentolepis clade and Arostrilepis clade. While the Ditestolepis clade is associated with soricids, the structure of the other three clades suggests multiple evolutionary events of host switching between shrews and rodents. Two of the present analyses (18S rRNA and COI genes) show that the basal relationships of the four mammalian clades are branching at the same polytomy with several hymenolepidids from birds (both terrestrial and aquatic). This may indicate a rapid radiation of the group, with multiple events of colonizations of mammalian hosts by avian parasites.

Whale falls, multiple colonisations of the deep, and the phylogeny of Hesionidae (Annelida)

2015 ◽  
Vol 29 (2) ◽  
pp. 105 ◽  
Author(s):  
Mindi Summers ◽  
Fredrik Pleijel ◽  
Greg W. Rouse
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
16S Rrna ◽  
Deep Sea ◽  
Phylogenetic Relationships ◽  
18S Rrna ◽  
Shallow Waters ◽  
28S Rrna ◽  
Mitochondrial Cytochrome ◽  
New Members

Phylogenetic relationships within Hesionidae Grube, 1850 are assessed via maximum parsimony and maximum likelihood analyses of mitochondrial (cytochrome c oxidase subunit I and 16S rRNA) and nuclear (18S rRNA, and 28S rRNA) data. The analyses are based on 42 hesionid species; six of these being new species that are described here. The new species, all from deep (>200 m depth) benthic environments (including whale falls) in the eastern Pacific, are Gyptis shannonae, sp. nov., Neogyptis julii, sp. nov., Sirsoe sirikos, sp. nov., Vrijenhoekia ketea, sp. nov., Vrijenhoekia falenothiras, sp. nov., and Vrijenhoekia ahabi, sp. nov. The molecular divergence among the new members of Vrijenhoekia is pronounced enough to consider them cryptic species, even though we cannot distinguish among them morphologically. Our results also showed that the subfamily Hesioninae Grube, 1850, as traditionally delineated, was paraphyletic. We thus restrict Hesioninae to include only Hesionini Grube, 1850 and refer the remaining members to Psamathinae Pleijel, 1998. The present study increases the number of hesionid species associated with whale falls from one to six and markedly increases the number of described deep-sea hesionid taxa. There appear to have been multiple colonisations of the deep sea from shallow waters by hesionids, though further sampling is warranted.

Three new small nucleolar RNAs that are psoralen cross-linked in vivo to unique regions of pre-rRNA

1993 ◽  
Vol 13 (7) ◽  
pp. 4382-4390
Author(s):  
O J Rimoldi ◽  
B Raghu ◽  
M K Nag ◽  
G L Eliceiri
Keyword(s):  
Small Rnas ◽  
18S Rrna ◽  
Rnase H ◽  
Antisense Oligodeoxynucleotide ◽  
28S Rrna ◽  
Small Nucleolar Rnas ◽  
Rrna Sequence ◽  
Nucleolar Rna ◽  
Nucleolar Rnas

We have recently described three novel human small nucleolar RNA species with unique nucleotide sequences, which were named E1, E2, and E3. The present article describes specific psoralen photocross-linking in whole HeLa cells of E1, E2, and E3 RNAs to nucleolar pre-rRNA. These small RNAs were cross-linked to different sections of pre-rRNA. E1 RNA was cross-linked to two segments of nucleolar pre-rRNA; one was within residues 697 to 1163 of the 5' external transcribed spacer, and the other one was between nucleotides 664 and 1021 of the 18S rRNA sequence. E2 RNA was cross-linked to a region within residues 3282 to 3667 of the 28S rRNA sequence. E3 RNA was cross-linked to a sequence between positions 1021 and 1639 of the 18S rRNA sequence. Primer extension analysis located psoralen adducts in E1, E2, and E3 RNAs that were enriched in high-molecular-weight fractions of nucleolar RNA. Some of these psoralen adducts might be cross-links of E1, E2, and E3 RNAs to large nucleolar RNA. Antisense oligodeoxynucleotide-targeted RNase H digestion of nucleolar extracts revealed accessible segments in these three small RNAs. The accessible regions were within nucleotide positions 106 to 130 of E1 RNA, positions 24 to 48 and 42 to 66 of E2 RNA, and positions 7 to 16 and about 116 to 122 of E3 RNA. Some of the molecules of these small nucleolar RNAs sedimented as if associated with larger structures when both nondenatured RNA and a nucleolar extract were analyzed.

MRHS solver based on linear algebra and exhaustive search

2018 ◽  
Vol 12 (3) ◽  
pp. 143-157 ◽  
Author(s):  
Håvard Raddum ◽  
Pavol Zajac
Keyword(s):  
Linear Algebra ◽  
Matrix Representation ◽  
Equation System ◽  
Exhaustive Search ◽  
Binary Matrix ◽  
Algebraic Attacks ◽  
The Matrix ◽  
Speed Up ◽  
Symmetric Key

Abstract We show how to build a binary matrix from the MRHS representation of a symmetric-key cipher. The matrix contains the cipher represented as an equation system and can be used to assess a cipher’s resistance against algebraic attacks. We give an algorithm for solving the system and compute its complexity. The complexity is normally close to exhaustive search on the variables representing the user-selected key. Finally, we show that for some variants of LowMC, the joined MRHS matrix representation can be used to speed up regular encryption in addition to exhaustive key search.

Sign in / Sign up

Export Citation Format

Share Document