scholarly journals Sequence changes in six variants of rice tungro bacilliform virus and their phylogenetic relationships

1999 ◽  
Vol 80 (8) ◽  
pp. 2229-2237 ◽  
Author(s):  
Pepito Q. Cabauatan ◽  
Ulrich Melcher ◽  
Koichi Ishikawa ◽  
Toshihiro Omura ◽  
Hiroyuki Hibino ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Open Reading Frames ◽  
Rice Tungro Bacilliform Virus ◽  
Likelihood Methods ◽  
Nucleotide Substitutions ◽  
Rich Region ◽  
Evolutionary Forces ◽  
Maximum Likelihood Methods ◽  
Tree Topologies

The DNA of three biological variants, G1, Ic and G2, which originated from the same greenhouse isolate of rice tungro bacilliform virus (RTBV) at the International Rice Research Institute (IRRI), was cloned and sequenced. Comparison of the sequences revealed small differences in genome sizes. The variants were between 95 and 99% identical at the nucleotide and amino acid levels. Alignment of the three genome sequences with those of three published RTBV sequences (Phi-1, Phi-2 and Phi-3) revealed numerous nucleotide substitutions and some insertions and deletions. The published RTBV sequences originated from the same greenhouse isolate at IRRI 20, 11 and 9 years ago. All open reading frames (ORFs) and known functional domains were conserved across the six variants. The cysteine-rich region of ORF3 showed the greatest variation. When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia (Serdang), similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome. The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony, distance and maximum-likelihood methods. The isolates clustered in three groups: Serdang alone; Ic and G1; and Phi-1, Phi-2, Phi-3 and G2. The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination, as well as substitutions and insertions or deletions, has played a role in the evolution of RTBV variants. The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses.

Phylogenetic relationships among megachiropteran species from the two major islands of the Philippines, deduced from DNA sequences of the cytochrome b gene

2001 ◽  
Vol 79 (9) ◽  
pp. 1671-1677 ◽  
Author(s):  
Severo T Bastian, Jr. ◽  
Kazuaki Tanaka ◽  
Rea Victoria P Anunciado ◽  
Nelson G Natural ◽  
Augusto C Sumalde ◽  
...  
Keyword(s):  
Cytochrome B ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
The Philippines ◽  
Cytochrome B Gene ◽  
Likelihood Methods ◽  
Base Pairs ◽  
Maximum Likelihood Methods ◽  
Pteropus Vampyrus ◽  
Cynopterus Brachyotis

Complete cytochrome b gene sequences (1140 base pairs) in species of Megachiroptera were ascertained in order to deduce their phylogenetic relationships, using samples of Cynopterus brachyotis, Eonycteris spelaea, Ptenochirus jagori, Pteropus vampyrus, and Rousettus amplexicaudatus collected from the islands of Luzon and Mindanao in the Philippines. Genetic divergence between samples of R. amplexicaudatus, E. spelaea, and C. brachyotis was very small. On the other hand, a large genetic distance was detected between species of Megachiroptera. The phylogenetic tree using neighbor-joining, parsimony, and maximum-likelihood methods generated similar topologies, reflecting the evolutionary associations among megachiropteran species. We estimated that Megachiroptera separated from Microchiroptera 50.2 million years ago (MYA), and split further approximately 32.4 MYA, forming three lineages: E. spelaea, R. amplexicaudatus, and P. vampyrus and the P. jagori – C. brachyotis cluster. The third lineage, composed of P. vampyrus and the P. jagori – C. brachyotis cluster, branched out 31.9 MYA. We hypothesize that R. amplexi caudatus diverged from the three members of the subfamily Pteropodinae examined, and its phylogenetic relationship with E. spelaea remains unclear.

scholarly journals Molecular analysis of the hot spot region related to length mutations in wheat chloroplast DNAs. I. Nucleotide divergence of genes and intergenic spacer regions located in the hot spot region.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 873-884 ◽  
Author(s):  
Y Ogihara ◽  
T Terachi ◽  
T Sasakuma
Keyword(s):  
Dna Sequences ◽  
Gene Evolution ◽  
Hot Spot ◽  
Intergenic Spacer ◽  
Open Reading Frames ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Plant Groups ◽  
Nucleotide Divergence ◽  
Chloroplast Dnas

Abstract The nucleotide divergence of chloroplast DNAs around the hot spot region related to length mutation in Triticum (wheat) and Aegilops was analyzed. DNA sequences (ca. 4.5 kbp) of three chloroplast genome types of wheat complex were compared with one another and with the corresponding region of other grasses. The sequences region contained rbcL and psaI, two open reading frames, and a pseudogene, rpl23' (pseudogene for ribosomal protein L23) disrupted by AT-rich intergic spacer regions. The evolution of these genes in the closely related wheat complex is characterized by nonbiased nucleotide substitutions in terms of being synonymous/nonsynonymous, having A-T pressure transitions over transversions, and frequent changes at the third codon position, in contrast with the gene evolution among more distant plant groups where biased nucleotide substitutions have frequently occurred. The sequences of these genes had diverged almost in proportion to taxonomic distance. The sequence of the pseudogene rpl23' changed approximately two times faster than that of the coding region. Sequence comparison between the pseudogene and its protein-coding counterpart revealed different degrees of nucleotide homology in wheat, rice and maize, suggesting that the transposition timing of the pseudogene differed and/or that different rates of gene conversion operated on the pseudogene in the cpDNA of the three plant groups in Gramineae. The intergenic spacer regions diverged approximately ten times faster than the genes. The divergence of wheat from barley, and that from rice are estimated based on the nucleotide similarity to be 1.5, 10 and 40 million years, respectively.

scholarly journals Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae)

2019 ◽  
Vol 69 (1) ◽  
pp. 91-109 ◽  
Author(s):  
Marie K Brandrud ◽  
Juliane Baar ◽  
Maria T Lorenzo ◽  
Alexander Athanasiadis ◽  
Richard M Bateman ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Diploid Species ◽  
Climatic Conditions ◽  
Likelihood Methods ◽  
Allopolyploid Speciation ◽  
Naturally Occurring ◽  
Maximum Likelihood Methods ◽  
History Of ◽  
Challenging Situation ◽  
Age Estimates

Abstract Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here, we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, nonmodel, polyploid plant complexes.

scholarly journals Molecular Phylogeny of the Ant-Decapitating Flies, Genus Apocephalus Coquillett (Diptera: Phoridae)

2018 ◽  
Vol 2 (4) ◽  
Author(s):  
Brian V Brown ◽  
Christine Hayes ◽  
John M Hash ◽  
Paul T Smith
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Likelihood Methods ◽  
Taxonomic Relationships ◽  
Methods Of Analysis ◽  
Maximum Likelihood Methods ◽  
New Synonymy

Abstract The phylogenetic relationships of the large, diverse genus Apocephalus Coquillett are studied using seven loci (16S, COI, NDI, 28S, AK, CAD, and TPI). Both Bayesian and Maximum Likelihood methods were used to analyze the sequences. Pre-existing taxonomic relationships, based on morphology, were largely upheld, with the notable exception of the subgenus Mesophora Borgmeier being placed deep inside the genus. Therefore, Mesophora was synonymized with Apocephalus (new synonymy) and its species referred to as belonging to the Apocephalus wheeleri group. Both methods of analysis recovered similar results, providing what we consider reasonable explanations of the data, based on morphological information.

New contributions towards the understanding of the phylogenetic relationships among economically important fruit flies (Diptera: Tephritidae)

2006 ◽  
Vol 96 (3) ◽  
pp. 279-288 ◽  
Author(s):  
M.D. Segura ◽  
C. Callejas ◽  
M.P. Fernández ◽  
M.D. Ochando
Keyword(s):  
Phylogenetic Relationships ◽  
Fruit Flies ◽  
Bactrocera Cucurbitae ◽  
Likelihood Methods ◽  
Morphological Classification ◽  
Important Group ◽  
Tephritid Species ◽  
The Family ◽  
Maximum Likelihood Methods ◽  
The Many

AbstractFruit flies (Diptera: Tephritidae) are a species-rich and economically important group. The phylogenetic relationships among the many taxa are still to be fully resolved and the monophyly of several groups is still to be confirmed. This paper reports a study of the phylogenetic relationships among 23 economically important tephritid species (representing several major lineages of the family) which examines the sequence of a region of mitochondrial DNA encompassing the cytb, tRNASer and ND1 genes. Substitutions characteristic of particular taxa were found that could help classify members of the family at any developmental stage. The trees obtained by the maximum parsimony, neighbour joining and maximum likelihood methods were generally compatible with present morphological classification patterns. However, the data reveal some characteristics of the phylogenetic relationships of this family that do not agree with present classifications. The results support the probable non-monophyletic nature of the subfamily Trypetinae and suggest that Bactrocera cucurbitae (Coquillet) is more closely related to the genus Dacus than to other species of Bactrocera.

scholarly journals The evolution of the vestibular apparatus in apes and humans

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Alessandro Urciuoli ◽  
Clément Zanolli ◽  
Amélie Beaudet ◽  
Jean Dumoncel ◽  
Frédéric Santos ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
Phylogenetic Reconstruction ◽  
Vestibular Apparatus ◽  
Likelihood Methods ◽  
Geometric Morphometric ◽  
Bony Labyrinth ◽  
Maximum Likelihood Methods ◽  
Geometric Morphometric Analysis ◽  
Fossil Apes

Phylogenetic relationships among extinct hominoids (apes and humans) are controversial due to pervasive homoplasy and the incompleteness of the fossil record. The bony labyrinth might contribute to this debate, as it displays strong phylogenetic signal among other mammals. However, the potential of the vestibular apparatus for phylogenetic reconstruction among fossil apes remains understudied. Here we test and quantify the phylogenetic signal embedded in the vestibular morphology of extant anthropoids (monkeys, apes and humans) and two extinct apes (Oreopithecus and Australopithecus) as captured by a deformation-based 3D geometric morphometric analysis. We also reconstruct the ancestral morphology of various hominoid clades based on phylogenetically-informed maximum likelihood methods. Besides revealing strong phylogenetic signal in the vestibule and enabling the proposal of potential synapomorphies for various hominoid clades, our results confirm the relevance of vestibular morphology for addressing the controversial phylogenetic relationships of fossil apes.

Building and Using Phylogenies

2016 ◽  
Author(s):  
Marc W. Cadotte ◽  
T. Jonathan Davies
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Tree ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Likelihood Methods ◽  
Object Type ◽  
Maximum Likelihood Methods ◽  
R Packages ◽  
Tree Building ◽  
Common Ancestors

This chapter explains how to build a phylogeny for a certain set of species. A phylogenetic tree is a representation of species interrelatedness and conveys information about which taxa share recent common ancestors, which evolutionary groups (clades) species belong to, and the distances (time, genetic, or character differences) separating species. The chapter first considers two R packages called ape and picante for use in analysis of the R phylogenetic object (referred to as a phylo object type), along with a few other packages, before discussing the steps in reconstructing phylogenetic relationships. It also evaluates some tree-building approaches that are easily implemented in R, including distance-based methods and maximum likelihood methods. Finally, it describes ways of finding and adapting available phylogenetic trees, together with tree scaling and rate smoothing.

Discordance between morphological species identification and mtDNA phylogeny in the flesh fly genus Ravinia (Diptera : Sarcophagidae)

2015 ◽  
Vol 29 (1) ◽  
pp. 1 ◽  
Author(s):  
Evan S. Wong ◽  
Gregory A. Dahlem ◽  
Trevor I. Stamper ◽  
Ronald W. DeBry
Keyword(s):  
Cytochrome Oxidase ◽  
Phylogenetic Relationships ◽  
Mitochondrial Gene ◽  
Bootstrap Support ◽  
Likelihood Methods ◽  
Mtdna Phylogeny ◽  
Maximum Likelihood Methods ◽  
Morphological Species ◽  
Cytochrome Oxidase Ii ◽  
Species Definitions

In order to better understand the phylogenetic relationships among species in the genus Ravinia Robineau-Desvoidy, 1863, we analysed data from two mitochondrial gene fragments: cytochrome oxidase I (COI) and cytochrome oxidase II (COII). We used Bayesian inference and maximum likelihood methods to infer phylogenetic relationships. Our results indicate that the genera Ravinia and Chaetoravinia, previously synonymised into the genus Ravinia (sensu lato) are each likely to be monophyletic (posterior probability 1; bootstrap support 85%). We found highly supported paraphyletic relationships among species of Ravinia, with relatively deep splits in the phylogeny. This conflict between the morphological species definitions and the mtDNA phylogeny could be indicative of the presence of cryptic species in Ravinia anxia (Walker, 1849), Ravinia floridensis (Aldrich, 1916), Ravinia lherminieri (Robineau-Desvoidy, 1830), and Ravinia querula (Walker, 1849).

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