Cladistic Analysis of Restriction Endonuclease Cleavage Maps Within a Maximum-Likelihood Framework

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Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades

<p>Abstract</p> <p>Background</p> <p>Rodentia is the most diverse order of placental mammals, with extant rodent species representing about half of all placental diversity. In spite of many morphological and molecular studies, the family-level relationships among rodents and the location of the rodent root are still debated. Although various datasets have already been analyzed to solve rodent phylogeny at the family level, these are difficult to combine because they involve different taxa and genes.</p> <p>Results</p> <p>We present here the largest protein-coding dataset used to study rodent relationships. It comprises six nuclear genes, 41 rodent species, and eight outgroups. Our phylogenetic reconstructions strongly support the division of Rodentia into three clades: (1) a "squirrel-related clade", (2) a "mouse-related clade", and (3) Ctenohystrica. Almost all evolutionary relationships within these clades are also highly supported. The primary remaining uncertainty is the position of the root. The application of various models and techniques aimed to remove non-phylogenetic signal was unable to solve the basal rodent trifurcation.</p> <p>Conclusion</p> <p>Sequencing and analyzing a large sequence dataset enabled us to resolve most of the evolutionary relationships among Rodentia. Our findings suggest that the uncertainty regarding the position of the rodent root reflects the rapid rodent radiation that occurred in the Paleocene rather than the presence of conflicting phylogenetic and non-phylogenetic signals in the dataset.</p

RESEARCH ARTICLE Mutations to Less-Preferred Synonymous Codons in a Highly Expressed Gene of Escherichia coli: Fitness and Epistatic Interactions

Codon-tRNA coevolution to maximize protein production has been, until recently, the domi-nant hypothesis to explain codon-usage bias in highly expressed bacterial genes. Two pre-dictions of this hypothesis are 1) selection is weak; and 2) similar silent replacements at different codons should have similar fitness consequence. We used an allele-replacement strategy to change five specific 3rd-codon-position (silent) sites in the highly expressed Escherichia coli ribosomal protein gene rplQ from the wild type to a less-preferred alterna-tive. We introduced the five mutations within a 10-codon region. Four of the silent sites were chosen to test the second prediction, with a CTG to CTA mutation being introduced at two closely linked leucine codons and an AAA to AAGmutation being introduced at two closely linked lysine codons. We also introduced a fifth silent mutation, a GTG to GTA mutation at a valine codon in the same genic region. We measured the fitness effect of the individual mutations by competing each single-mutant strain against the parental wild-type strain, using a disrupted form of the araA gene as a selectively neutral phenotypic marker to distin-guish between strains in direct competition experiments. Three of the silent mutations had a fitness effect of |s |&gt; 0.02, which is contradictory to the prediction that selection will be weak. The two leucine mutations had significantly different fitness effects, as did the two lysine mutations, contradictory to the prediction that similar mutations at different codons should have similar fitness effects. We also constructed a strain carrying all five silent mutations in combination. Its fitness effect was greater than that predicted from the individual fitness val-ues, suggesting that negative synergistic epistasis acts on the combination allele

Total effective doublings (± 1 s.d.), relative fitness values (± 1 s.d.) and selection coefficients for the mutant genotypes constructed in this study, based on competition experiments between the Ara^-, <i>rplQ</i> substrains and the wild-type <i>E</i>. <i>coli</i> K-12 substrain MG1655.

<p>Total effective doublings (± 1 s.d.), relative fitness values (± 1 s.d.) and selection coefficients for the mutant genotypes constructed in this study, based on competition experiments between the Ara^-, <i>rplQ</i> substrains and the wild-type <i>E</i>. <i>coli</i> K-12 substrain MG1655.</p

Mutations to Less-Preferred Synonymous Codons in a Highly Expressed Gene of <i>Escherichia coli</i>: Fitness and Epistatic Interactions

<div><p>Codon-tRNA coevolution to maximize protein production has been, until recently, the dominant hypothesis to explain codon-usage bias in highly expressed bacterial genes. Two predictions of this hypothesis are 1) selection is weak; and 2) similar silent replacements at different codons should have similar fitness consequence. We used an allele-replacement strategy to change five specific 3rd-codon-position (silent) sites in the highly expressed <i>Escherichia coli</i> ribosomal protein gene <i>rplQ</i> from the wild type to a less-preferred alternative. We introduced the five mutations within a 10-codon region. Four of the silent sites were chosen to test the second prediction, with a CTG to CTA mutation being introduced at two closely linked leucine codons and an AAA to AAG mutation being introduced at two closely linked lysine codons. We also introduced a fifth silent mutation, a GTG to GTA mutation at a valine codon in the same genic region. We measured the fitness effect of the individual mutations by competing each single-mutant strain against the parental wild-type strain, using a disrupted form of the <i>araA</i> gene as a selectively neutral phenotypic marker to distinguish between strains in direct competition experiments. Three of the silent mutations had a fitness effect of |s| > 0.02, which is contradictory to the prediction that selection will be weak. The two leucine mutations had significantly different fitness effects, as did the two lysine mutations, contradictory to the prediction that similar mutations at different codons should have similar fitness effects. We also constructed a strain carrying all five silent mutations in combination. Its fitness effect was greater than that predicted from the individual fitness values, suggesting that negative synergistic epistasis acts on the combination allele.</p></div

Change in folding energy (ΔΔG) of the <i>rplQ</i> mRNA for the five single-mutant strains generated in this study.

<p>Change in folding energy (ΔΔG) of the <i>rplQ</i> mRNA for the five single-mutant strains generated in this study.</p

Silent mutations generated for this study.

<p>The five mutations introduced into the wild-type <i>rplQ</i> gene <i>en bloc</i> to create the <i>rplQ</i>m5 allele and singly to create the <i>rplQ</i>mL44, <i>rplQ</i>mL38, <i>rplQ</i>mK40, <i>rplQ</i>m42, and <i>rplQ</i>mV47 alleles are indicated. The region shown is the segment that is excised by digestion of <i>rplQ</i> with <i>Bcg</i> I. Codons in which the silent mutations were placed are shaded. Positions in the <i>E</i>. <i>coli</i> MG1655 genomic sequence (Genbank accession U00096) are shown for each mutant nucleotide.</p

Predicted and observed fitness of the quintuple-mutant allele.

<p>Error bars indicated ± two standard deviation units (for the predicted fitness) or the 95% confidence interval (for the observed fitnesses). The predicted fitness for the quintuple-mutant strain was calculated after assigning a fitness of 1.0 to the two single-mutant strains with observed fitness > 1.0, but with the observed among-replicate variance for all five single-mutant alleles being used to calculate the standard deviation of the predicted fitness.</p

Fitness of mutant strains as determined from competition experiments against wild-type <i>E</i>. <i>coli</i> K-12 MG1655.

<p>Error bars denote one standard deviation for each experiment.</p