PAML: a program package for phylogenetic analysis by maximum likelihood

Yang, Ziheng

doi:10.1093/bioinformatics/13.5.555

Cited by 4,328 publications

(4,689 citation statements)

References 7 publications

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“…The F84 + G model was applied independently to each of the within-gene partitions such as codon positions for vWF and cytb or stems and loops for 12S. Model parameters were estimated with the use of baseml software (PAML version 3.14; Yang, 1997). Branch lengths and their covariance matrices were calculated with estbranche-dna program (Multidistribute package; Thorne and Kishino, 2002).…”

Section: Molecular Clocks and Divergence Timementioning

confidence: 99%

Molecular phylogeny of the Cricetinae subfamily based on the mitochondrial cytochrome b and 12S rRNA genes and the nuclear vWF gene

Neumann

Michaux

Lebedev

et al. 2006

Molecular Phylogenetics and Evolution

100

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Despite some popularity of hamsters as pets and laboratory animals there is no reliable phylogeny of the subfamily Cricetinae available so far. Contradicting views exist not only about the actual number of species but also concerning the validity of several genera. We used partial DNA sequences of two mitochondrial (cytochrome b, 12S rRNA) and one partial nuclear gene (von Willebrand Factor exon 28) to provide a first gene tree of the Cricetinae based on 15 taxa comprising six genera. According to our data, Palaearctic hamsters fall into three distinct phylogenetic groups: Phodopus, Mesocricetus, and Cricetus-related species which evolved during the late Miocene about 7-12 MY ago. Surprisingly, the genus Phodopus, which was previously thought to have appeared during the Pleistocene, forms the oldest clade. The largest number of extant hamster genera is found in a group of Cricetus-related hamsters. The genus Cricetulus itself proved to be not truly monophyletic with Cricetulus migratorius appearing more closely related to Tscherskia, Cricetus, and Allocricetulus. We propose to place the species within a new monotypic genus. Molecular clock calculations are not always in line with the dating of fossil records. DNA based divergence time estimates as well as taxonomic relationships demand a reevaluation of morphological characters previously used to identify fossils and extant hamsters.

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Section: Molecular Clocks and Divergence Timementioning

confidence: 99%

Molecular phylogeny of the Cricetinae subfamily based on the mitochondrial cytochrome b and 12S rRNA genes and the nuclear vWF gene

Neumann

Michaux

Lebedev

et al. 2006

Molecular Phylogenetics and Evolution

100

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“…The same sequence alignments used in phylogenetic analyses were analyzed using branch models constrained by the a priori gene phylogeny allowing for (model R1) a single x ratio among branches and clades as well as nested models allowing two (model R2), three (model R3), or four (model R4) xÕs for different clades in the gene phylogeny. All models were implemented using PAML, version 3.14 (Yang 1997). Likelihood ratio test (LRT) statistics were calculated as twice the difference between log-likelihoods for more complex versus a nested less complex model, and compared with a chi-squared distribution with degrees of freedom equal to the difference in the number of parameters between models (Goldman and Yang 1994).…”

Section: Codon Substitution Modelsmentioning

confidence: 99%

“…A likelihood test comparing Model A with Model A null constitutes test 2 of Zhang et al (2005). Sites and branch-sites models were implemented using PAML, version 3.14 (Yang 1997). Because of multiple local optima in likelihood searches, sites and branch-sites models were run a minimum of three times using different initial xÕs.…”

Section: Codon Substitution Modelsmentioning

confidence: 99%

“…For our analyses we treated the putative DNA binding domain as distinct from the N-terminus region of FLO. Based on ML estimates for 11 rate categories (10 constrained between 0 and 1, and 1 allowing x > 1) from sites model M8, posterior probabilities for each site (codon) were estimated using the empirical Bayes approach of Nielsen and Yang (1998), implemented in PAML version 3.14 (Yang 1997). Estimated xÕs are calculated as the average over site classes weighted by the posterior probability that the codon belongs to that site class.…”

Section: Codon Substitution Modelsmentioning

confidence: 99%

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Relaxed Selection Among Duplicate Floral Regulatory Genes in Lamiales

2006

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Abstract. Polyploidization is a prevalent mode of genome diversification within plants. Most gene duplicates arising from polyploidization (paralogs) are typically lost, although a subset may be maintained under selection due to dosage, partitioning of gene function, or acquisition of novel functions. Because they experience selection in the presence of other duplicate loci across the genome, interactions among genes may also play a significant role in the maintenance of paralogs resulting from polyploidization. Previously, we identified duplicates of the genes LFY/FLO and AP3/DEF that directly interact in a floral regulatory pathway and are thought to be the result of ancient polyploidization in the Lamiales (> 50 mya). Although duplicates of MADS box genes including AP3/DEF are common throughout the angiosperm lineage, LFY/FLO duplicates in Lamiales are the first reported outside of tetraploid taxa. In order to explore hypotheses for the joint preservation of these interacting floral regulatory genes including novel LFY/FLO paralogs, here we clone FLO and DEF duplicates from additional Lamiales taxa and apply codon substitution models to test how selection acts on both genes following duplication. We find acceleration in the ratio of nonsynonymous-to-synonymous nucleotide substitutions for one (FLO) or both (DEF) paralogs that appears to be due to relaxed purifying selection as opposed to positive selection and shows a different pattern among functional domains of these genes. Several mechanisms are discussed that might be responsible for preservation of co-orthologs of FLO and DEF in Lamiales, including interactions among the genes of this regulatory pathway.

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“…Li's method (Li, 1993), using the diverge function from the GCG 10.2 package, Ina's method 1 (Ina, 1995, implementation downloaded from ftp://nig.ac.jp), and a maximumlikelihood method (Goldman and Yang, 1994;Yang and Nielsen, 2000) as implemented in the PAML package (Yang, 1997).…”

Section: Substitution Rate Estimationmentioning

confidence: 99%

Gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria

Schaber

Rispe²,

Wernegreen

et al. 2005

Gene

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Most endosymbiotic bacteria have extremely reduced genomes, accelerated evolutionary rates, and strong AT base compositional bias thought to reflect reduced efficacy of selection and increased mutational pressure. Here, we present a comparative study of evolutionary forces shaping five fully sequenced bacterial endosymbionts of insects. The results of this study were three-fold: (i) Stronger conservation of high expression genes at not just nonsynonymous, but also synonymous, sites. (ii) Variation in amino acid usage strongly correlates with GC content and expression level of genes. This pattern is largely explained by greater conservation of high expression genes, leading to their higher GC content. However, we also found indication of selection favoring GC-rich amino acids that contrasts with former studies. (iii) Although the specific nutritional requirements of the insect host are known to affect gene content of endosymbionts, we found no detectable influence on substitution rates, amino acid usage, or codon usage of bacterial genes involved in host nutrition. D

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PAML: a program package for phylogenetic analysis by maximum likelihood

Cited by 4,328 publications

References 7 publications

Molecular phylogeny of the Cricetinae subfamily based on the mitochondrial cytochrome b and 12S rRNA genes and the nuclear vWF gene

Molecular phylogeny of the Cricetinae subfamily based on the mitochondrial cytochrome b and 12S rRNA genes and the nuclear vWF gene

Relaxed Selection Among Duplicate Floral Regulatory Genes in Lamiales

Gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria

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