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 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.

scholarly journals Phylogenetic relationships of Malayan gaur with other species of the genus Bos based on cytochrome b gene DNA sequences

2011 ◽  
Vol 10 (1) ◽  
pp. 482-493 ◽  
Author(s):  
M.K.A. Rosli ◽  
S.S. Zakaria ◽  
S.M.F. Syed-Shabthar ◽  
Z.Z. Zainal ◽  
M.N. Shukor ◽  
...  
Keyword(s):  
Cytochrome B ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Cytochrome B Gene

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.

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):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
The Philippines ◽  
I Gene

Reassessment of Phylogenetic Relationships among Pitviper Genera Based on Mitochondrial Cytochrome b Gene Sequences

Copeia ◽  
1997 ◽  
Vol 1997 (2) ◽  
pp. 429 ◽  
Author(s):  
Kenneth W. Cullings ◽  
David J. Morafka ◽  
José Hernandez ◽  
John W. Roberts ◽  
Jose Hernandez
Keyword(s):  
Cytochrome B ◽  
Phylogenetic Relationships ◽  
Cytochrome B Gene ◽  
Mitochondrial Cytochrome ◽  
Gene Sequences ◽  
Mitochondrial Cytochrome B ◽  
Mitochondrial Cytochrome B Gene

A molecular phylogenetic study of Hylopetes (Rodentia: Sciuridae) inferred from mitochondrial cytochrome-b gene

Biologia ◽  
2014 ◽  
Vol 69 (12) ◽  
Author(s):  
Farong Yu ◽  
Xiuzhen Lian ◽  
Zuoping Li ◽  
Mingren Xie
Keyword(s):  
Cytochrome B ◽  
Phylogenetic Relationships ◽  
Cytochrome B Gene ◽  
Phylogenetic Study ◽  
Molecular Phylogenetic Study ◽  
Mitochondrial Cytochrome B ◽  
Distinct Genus ◽  
Molecular Phylogenetic ◽  
Close Genetic Relationship ◽  
Tectonic Movements

AbstractTo elucidate the phylogenetic relationships of Hylopetes, the complete cytochrome-b gene sequences (1,140 bp) were determined from degraded museum specimens for phylogenetic study. The large genetic differences (18.1% to 20.7%) separate Eoglaucomys from Hylopetes as a distinct genus. Phylogenetic relationships reconstructed with maximum parsimony, maximum likelihood, and Bayesian methods show that all Hylopetes were genetically clustered as two major groups, the Indochinese Hylopetes group including H. alboniger and H. phayrei, and the Sundaic group consisting of H. lepidus, H. nigripes, and H. spadiceus. The close genetic relationship and the recent divergence suggest that the Indochinese group rapidly extended to their present distributions with the uplifting of the Himalayas last few million years ago, whereas the oceanic tectonic movements during the Pliocene-Pleistocene resulted in the current geographical distributions of the Sundaic group through alteration of dispersal across the islands of the Sunda Shelf.

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.

Sign in / Sign up

Export Citation Format

Share Document