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Codon Positions (codon + position)
Kinds of Codon Positions Selected AbstractsEFFECT OF TAXON SAMPLING, CHARACTER WEIGHTING, AND COMBINED DATA ON THE INTERPRETATION OF RELATIONSHIPS AMONG THE HETEROKONT ALGAE,JOURNAL OF PHYCOLOGY, Issue 2 2003Leslie R. Goertzen Nuclear ribosomal small subunit and chloroplast rbcL sequence data for heterokont algae and potential outgroup taxa were analyzed separately and together using maximum parsimony. A series of taxon sampling and character weighting experiments was performed. Traditional classes (e.g. diatoms, Phaeophyceae, etc.) were monophyletic in most analyses of either data set and in analyses of combined data. Relationships among classes and of heterokont algae to outgroup taxa were sensitive to taxon sampling. Bootstrap (BS) values were not always predictive of stability of nodes in taxon sampling experiments or between analyses of different data sets. Reweighting sites by the rescaled consistency index artificially inflates BS values in the analysis of rbcL data. Inclusion of the third codon position from rbcL enhanced signal despite the superficial appearance of mutational saturation. Incongruence between data sets was largely due to placement of a few problematic taxa, and so data were combined. BS values for the combined analysis were much higher than for analyses of each data set alone, although combining data did not improve support for heterokont monophyly. [source] Population genetic studies of Alouatta belzebul from the Amazonian and Atlantic ForestsAMERICAN JOURNAL OF PRIMATOLOGY, Issue 5 2008F.F. Nascimento Abstract Cytochrome b DNA sequence data (ca. 1,140,bp) of 66 Alouatta belzebul from the Amazonian and the Atlantic Forests of Brazil were used for phylogenetic reconstructions and population studies. Our sample consisted of 60 specimens from the Amazonian Forest (captured in 1984 and 1998 in Pará-PA state) and six specimens from the Atlantic Forest (Paraíba-PB state). We found 32 haplotypes, 23 in PA-1984 (with 12 present in more than one individual), 11 in PA-1998 (with two present in more than one individual), and a single haplotype in the PB sample. Animals from PA-1984 and PA-1998 shared three haplotypes while animals from Pará and Paraíba did not share any haplotype. We found 57 variable sites, consisting of 53 transitions and four transversions, with most replacements occurring at third codon position (77.19%) and less frequently at first and second positions (10.53 and 12.28%, respectively). Genetic distance between all haplotypes varied between 0 and 1.2%. Nucleotide diversity estimates between PA-1984 haplotypes and PA-1998 haplotypes were the same (,=0.01), and haplotype diversity estimates were very similar (h=0.96 and 0.93 for PA-1984 and PA-1998, respectively). Maximum parsimony, median-joining, split decomposition, and TCS showed that PA and PB haplotypes had not drastically diverged and that subsequent radiation within these regions was not apparent. No temporal structure was found between PA-1984 and PA-1998. The sum of square deviation estimate for PA-1984 equaled 0.01 (P=0.23), in agreement with a hypothetical model of sudden expansion contrary to PA-1998 whose sum of square deviation estimate (0.40; P=0.04) was not compatible with this model, although the small sample size of PA-1998 as well as the smaller area of capture could have also accounted for this result. Fu's Fs and R2 statistical neutrality tests corroborated these propositions. Lack of drastic differentiation was attributable to the once existing connection between the Atlantic and the Amazonian forests at a non-distant past. Am. J. Primatol. 70:423,431, 2008. © 2007 Wiley-Liss, Inc. [source] Population genetic studies of Alouatta caraya (Alouattinae, Primates): inferences on geographic distribution and ecologyAMERICAN JOURNAL OF PRIMATOLOGY, Issue 10 2007Fabrícia F. Do Nascimento Abstract Cytochrome b DNA sequence data (ca. 1,140,bp) of 44 Alouatta caraya, including 42 specimens from three localities of Brazil and two from Bolivia, were used for phylogenetic reconstructions and population studies. Seventeen haplotypes were identified, eight of which were present in more than one individual. Seven of these eight haplotypes were shared by individuals from a same locality and one by individuals from two localities. We found 26 variable sites along the entire gene, consisting of 18 transitions and eight transversions; most replacements occurring at the third codon position (65.39%) in contrast to first and second positions (26.92 and 7.69%, respectively). In the sample collected at Chapada dos Guimarães (Brazil), nucleotide and haplotype diversity estimates were ,=0.002325 and h=0.8772, respectively. Maximum parsimony analysis grouped all haplotypes in two clades, separating Bolivian haplotypes from Brazilian haplotypes, the grouping of which did not show a straightforward correspondence with geographic distribution. Median-joining and TCS network pointed to haplotypes 11 or 12 as the most likely ancestral ones. Mismatch distribution and the goodness-of-fit test (SSD estimate=0.0027; P=0.6999) indicated that the population from Chapada dos Guimarães experienced a demographic expansion, in agreement with the median-joining star-like pattern, although this finding could not be confirmed by Fu's Fs test. Am. J. Primatol. 69:1093,1104, 2007. © 2007 Wiley-Liss, Inc. [source] Mitochondrial genome data alone are not enough to unambiguously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Arthropoda)CLADISTICS, Issue 6 2004Stephen L. Cameron An analysis of the relationships of the major arthropod groups was undertaken using mitochondrial genome data to examine the hypotheses that Hexapoda is polyphyletic and that Collembola is more closely related to branchiopod crustaceans than insects. We sought to examine the sensitivity of this relationship to outgroup choice, data treatment, gene choice and optimality criteria used in the phylogenetic analysis of mitochondrial genome data. Additionally we sequenced the mitochondrial genome of an archaeognathan, Nesomachilis australica, to improve taxon selection in the apterygote insects, a group poorly represented in previous mitochondrial phylogenies. The sister group of the Collembola was rarely resolved in our analyses with a significant level of support. The use of different outgroups (myriapods, nematodes, or annelids + mollusks) resulted in many different placements of Collembola. The way in which the dataset was coded for analysis (DNA, DNA with the exclusion of third codon position and as amino acids) also had marked affects on tree topology. We found that nodal support was spread evenly throughout the 13 mitochondrial genes and the exclusion of genes resulted in significantly less resolution in the inferred trees. Optimality criteria had a much lesser effect on topology than the preceding factors; parsimony and Bayesian trees for a given data set and treatment were quite similar. We therefore conclude that the relationships of the extant arthropod groups as inferred by mitochondrial genomes are highly vulnerable to outgroup choice, data treatment and gene choice, and no consistent alternative hypothesis of Collembola's relationships is supported. Pending the resolution of these identified problems with the application of mitogenomic data to basal arthropod relationships, it is difficult to justify the rejection of hexapod monophyly, which is well supported on morphological grounds. © The Willi Hennig Society 2004. [source] Studies on codon usage in Thermoplasma acidophilum and its possible implications on the occurrences of lateral gene transferJOURNAL OF BASIC MICROBIOLOGY, Issue 5 2005S. K. Gupta Codon usage studies have been carried out on the coding sequences of Thermoplasma acidophilum, which is an archaeon and grows at very low pH and high temperature. Overall codon usage data analysis indicates that all the four bases are almost equifrequent at the third position of codons, which is expected (since genomic GC % of this genome is about 46%). However, multivariate statistical analysis indicates that there are two major trends in the codon usage variation among the genes in this organism. In the first major trend it is observed that genes having G and C ending codons are clustered at one end while, A and T ending ones are clustered at the other end. We have also found a significant positive correlation between the expressivities of genes and GC contents at the synonymous third codon positions. In the second major trend, it is seen that the genes are clustered into three distinct parts. A comparative analyses of codon usage data of T. acidophilum and Sulfolobus solfataricus reveals that one of the three clusters of genes of T. acidophilum is very similar to a considerable number of S. solfataricus genes, suggesting possible occurrences of lateral gene transfer between these two microorganisms as reported by earlier workers. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] PHYLOGENY OF THE DASYCLADALES (CHLOROPHYTA, ULVOPHYCEAE) BASED ON ANALYSES OF RUBISCO LARGE SUBUNIT (rbcL) GENE SEQUENCES,JOURNAL OF PHYCOLOGY, Issue 4 2003Frederick W. Zechman The phylogeny of the green algal Order Dasycladales was inferred by maximum parsimony and Bayesian analyses of chloroplast-encoded rbcL sequence data. Bayesian analysis suggested that the tribe Acetabularieae is monophyletic but that some genera within the tribe, such as Acetabularia Lamouroux and Polyphysa Lamouroux, are not. Bayesian analysis placed Halicoryne Harvey as the sister group of the Acetabularieae, a result consistent with limited fossil evidence and monophyly of the family Acetabulariaceae but was not supported by significant posterior probability. Bayesian analysis further suggested that the family Dasycladaceae is a paraphyletic assemblage at the base of the Dasycladales radiation, casting doubt on the current family-level classification. The genus Cymopolia Lamouroux was inferred to be the basal-most dasycladalean genus, which is also consistent with limited fossil evidence. Unweighted parsimony analyses provided similar results but primarily differed by the sister relationship between Halicoryne Lamouroux and Bornetella Munier-Chalmas, thus supporting the monophyly of neither the families Acetabulariaceae nor Dasycladaceae. This result, however, was supported by low bootstrap values. Low transition-to-transversion ratios, potential loss of phylogenetic signal in third codon positions, and the 550 million year old Dasycladalean lineage suggest that dasyclad rbcL sequences may be saturated due to deep time divergences. Such factors may have contributed to inaccurate reconstruction of phylogeny, particularly with respect to potential inconsistency of parsimony analyses. Regardless, strongly negative g1 values were obtained in analyses including all codon positions, indicating the presence of considerable phylogenetic signal in dasyclad rbcL sequence data. Morphological features relevant to the separation of taxa within the Dasycladales and the possible effects of extinction on phylogeny reconstruction are discussed relative to the inferred phylogenies. [source] Introduction of a Nuclear Marker for Phylogenetic Analysis of NepenthaceaePLANT BIOLOGY, Issue 6 2006H. Meimberg Abstract: Nepenthaceae, the pitcher plants of the Old World tropics show a remarkable diversity in SE Asia, especially on the islands of Borneo and Sumatra. This region is considered as a secondary center of diversity. Sequence analysis of the cpDNA trnK intron supports this hypothesis showing the species of the Malay Archipelago as neighbour group to the isolated species from Sri Lanka, the Seychelles, and Madagascar. Based on phylogenetic reconstructions an origin of recent Nepenthaceae in the Indian subcontinent is assumed. A recent investigation focused on a non-plastid, translocated copy of the trnK intron has revealed an incongruence to tree topology based on the cpDNA trnK intron. Although the translocated copy emerged as insufficient for phylogenetic reconstruction of Nepenthaceae some taxa showed, contrary to the cpDNA dataset, relatively high distances to the rest of the taxa. These results indicated that the phylogeny of the trnK intron could not reflect true phylogenetic relationships. We investigated the peptide transferase 1 (PTR1), to develop a phylogenetic marker that is based on a nuclear low copy gene in Nepenthes. All sequences obtained were probably functional, indicated by the ratio of point mutations of the single codon positions in exon and intron regions. Comparative analysis showed that this locus is of similar variability as the cpDNA trnK intron and, contrary to the translocated copy of trnK, potential useful for phylogenetic reconstruction. While in parts congruent to the plastid trnK intron phylogeny, a higher divergence of some sequences in PRT1 and in the previously reported, non cpDNA dataset indicates that remnants of an older species stock persisted east of Wallace's line and on the Sunda Shelf. This suggests that plastid haplotypes existing today in the main distribution center of the Nepenthaceae could be descendants of more recently dispersed lineages that had been transmitted to an old species stock. [source] Molecular phylogeny and evolution of the Asian lineage of vole genus Microtus (Rodentia: Arvicolinae) inferred from mitochondrial cytochrome b sequenceBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2010ANNA A. BANNIKOVA To examine phylogenetic relationships within the Asian lineage of voles (Microtus) belonging to subgenus Alexandromys, the mitochondrial cytochrome b gene (cytb) was sequenced for its representatives, and the results were compared with the cytogenetic, morphological, and paleontological data. In all the trees inferred from maximum likelihood, parsimony, and Bayesian phylogenetic analyses, the Asian clade is subdivided into highly supported Alexandromys s.s. and moderately supported Pallasiinus lineages. Four subclades are recovered within Alexandromys: (1) Microtus maximowiczii and Microtus sachalinensis; (2) Microtus miiddendorffii s.l., Microtus mongolicus and Microtus gromovi; (3) Microtus fortis; and (4) Microtus limnophilus. Thus, M. limnophilus demonstrates clear affinities to Alexandromys s.s. but not to Microtus oeconomus (subgenus Pallasiinus), which was always regarded as its sibling species. The results obtained indicate M. mongolicus as a member of Alexandromys but not of the Microtus arvalis group, thus being concordant with the cytogenetic data. The mitochondrial data support the species status of M. gromovi; moreover, its placement as a part of a trichotomy with M. miiddendorffii s.l. and M. mongolicus contradicts the traditional affiliation of M. gromovi with M. maximowiczii. The divergence rate of cytb third position transversions in Microtus is estimated at approximately 8% per Myr, which corresponds to approximately 30% per Myr for all substitution types at all codon positions. The maximum likelihood distance based on complete sequence showed a tendency for a progressive underestimation of divergence and time for older splits. According to our molecular clock analysis employing nonlinear estimation methods, the split between Alexandromys and Pallasiinus and basal radiation within Alexandromys date back to approximately 1.2 Mya and 800 Kya, respectively. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 595,613. [source] The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequencesBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2005MASAKI MIYA In a previous study based on 100 whole mitochondrial genome (mitogenome) sequences, we sought to provide a new perspective on the ordinal relationships of higher ray-finned fish (Actinopterygii). The study left unexplored the phylogenetic ,position, of, toadfishes, (order, Batrachoidiformes),, as, data, were, unavailable, owing, to, technical, difficulties. In the present study, we successfully determined mitogenomic sequences for two toadfish species (Batrachomoeus trispinosus and Porichthys myriaster) and found that the difficulties resulted from unusual gene arrangements and associated repetitive non-coding sequences. Unambiguously aligned, concatenated mitogenomic sequences (13 461 bp) from 102 higher actinopterygians (excluding the ND6 gene and control region) were divided into five partitions (1st, 2nd and 3rd codon positions of the protein-coding genes, tRNA genes and rRNA genes) and partitioned Bayesian analyses were conducted. The resultant phylogenies strongly suggest that the toadfishes are not members of relatively primitive higher actinopterygians (Paracanthopterygii), but belong to a crown group of actinopterygians (Percomorpha), as was demonstrated for ophidiiform eels (Ophidiiformes) and anglerfishes (Lophiiformes) in the previous study. We propose revised limits of major unranked categories for higher actinopterygians and a new name (Berycomorpha) for a clade comprising two reciprocally paraphyletic orders (Beryciformes and Stephanoberyciformes) based on the present mitogenomic phylogenies. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 85, 289,306. [source] | ||||||||||