1. How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher-Wright mutation-selection framework.

    Biology Letters 11(4):20141031 (2015) PMID 25854546 PMCID PMC4424610

    First principles of population genetics are used to obtain formulae relating the non-synonymous to synonymous substitution rate ratio to the selection coefficients acting at codon sites in protein-coding genes. Two theoretical cases are discussed and two examples from real data (a chloroplast ge...
  2. Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci.

    Systematic Biology 64(2):267 (2015) PMID 25503979 PMCID PMC4380039

    Genetic sequence data provide information about the distances between species or branch lengths in a phylogeny, but not about the absolute divergence times or the evolutionary rates directly. Bayesian methods for dating species divergences estimate times and rates by assigning priors on them. In...
  3. Characterization of the Uncertainty of Divergence Time Estimation under Relaxed Molecular Clock Models Using Multiple Loci.

    Systematic Biology 64(2):267 (2015) PMID 25503979

    Genetic sequence data provide information about the distances between species or branch lengths in a phylogeny, but not about the absolute divergence times or the evolutionary rates directly. Bayesian methods for dating species divergences estimate times and rates by assigning priors on them. In...
  4. A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome.

    Methods in Molecular Biology 1201:65 (2015) PMID 25388108

    The ratio of non-synonymous to synonymous substitutions (dN/dS) is a useful measure of the strength and mode of natural selection acting on protein-coding genes. It is widely used to study patterns of selection on protein genes on a genomic scale-from the small genomes of viruses, bacteria, and ...
  5. A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome.

    Methods in Molecular Biology 1201:65 (2015) PMID 25388108

    The ratio of non-synonymous to synonymous substitutions (dN/dS) is a useful measure of the strength and mode of natural selection acting on protein-coding genes. It is widely used to study patterns of selection on protein genes on a genomic scale-from the small genomes of viruses, bacteria, and ...
  6. A Beginners Guide to Estimating the Non-synonymous to Synonymous Rate Ratio of all Protein-Coding Genes in a Genome.

    Methods in Molecular Biology 1201:65 (2015) PMID 25388108

    The ratio of non-synonymous to synonymous substitutions (dN/dS) is a useful measure of the strength and mode of natural selection acting on protein-coding genes. It is widely used to study patterns of selection on protein genes on a genomic scale-from the small genomes of viruses, bacteria, and ...
  7. The impact of the rate prior on Bayesian estimation of divergence times with multiple Loci.

    Systematic Biology 63(4):555 (2014) PMID 24658316 PMCID PMC4055871

    Bayesian methods provide a powerful way to estimate species divergence times by combining information from molecular sequences with information from the fossil record. With the explosive increase of genomic data, divergence time estimation increasingly uses data of multiple loci (genes or site p...
  8. Bayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons.

    Molecular Biology and Evolution 31(7):1902 (2014) PMID 24748652 PMCID PMC4069626

    The nonsynonymous/synonymous rate ratio (ω = d(N)/d(S)) is an important measure of the mode and strength of natural selection acting on nonsynonymous mutations in protein-coding genes. The simplest such analysis is the estimation of the d(N)/d(S) ratio using two sequences. Both heuristic countin...
  9. The impact of the rate prior on Bayesian estimation of divergence times with multiple Loci.

    Systematic Biology 63(4):555 (2014) PMID 24658316 PMCID PMC4055871

    Bayesian methods provide a powerful way to estimate species divergence times by combining information from molecular sequences with information from the fossil record. With the explosive increase of genomic data, divergence time estimation increasingly uses data of multiple loci (genes or site p...
  10. Bayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons.

    Molecular Biology and Evolution 31(7):1902 (2014) PMID 24748652 PMCID PMC4069626

    The nonsynonymous/synonymous rate ratio (ω = d(N)/d(S)) is an important measure of the mode and strength of natural selection acting on nonsynonymous mutations in protein-coding genes. The simplest such analysis is the estimation of the d(N)/d(S) ratio using two sequences. Both heuristic countin...
  11. Bayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons.

    Molecular Biology and Evolution 31(7):1902 (2014) PMID 24748652 PMCID PMC4069626

    The nonsynonymous/synonymous rate ratio (ω = d(N)/d(S)) is an important measure of the mode and strength of natural selection acting on nonsynonymous mutations in protein-coding genes. The simplest such analysis is the estimation of the d(N)/d(S) ratio using two sequences. Both heuristic countin...
  12. A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.

    Genetics 197(1):257 (2014) PMID 24532780 PMCID PMC4012484

    We develop a maximum penalized-likelihood (MPL) method to estimate the fitnesses of amino acids and the distribution of selection coefficients (S = 2Ns) in protein-coding genes from phylogenetic data. This improves on a previous maximum-likelihood method. Various penalty functions are used to pe...
  13. A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.

    Genetics 197(1):257 (2014) PMID 24532780 PMCID PMC4012484

    We develop a maximum penalized-likelihood (MPL) method to estimate the fitnesses of amino acids and the distribution of selection coefficients (S = 2Ns) in protein-coding genes from phylogenetic data. This improves on a previous maximum-likelihood method. Various penalty functions are used to pe...
  14. A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.

    Genetics 197(1):257 (2014) PMID 24532780 PMCID PMC4012484

    We develop a maximum penalized-likelihood (MPL) method to estimate the fitnesses of amino acids and the distribution of selection coefficients (S = 2Ns) in protein-coding genes from phylogenetic data. This improves on a previous maximum-likelihood method. Various penalty functions are used to pe...
  15. Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates.

    Genome Biology and Evolution 6(1):213 (2014) PMID 24398377 PMCID PMC3914689

    Vomeronasal receptor genes have frequently been invoked as integral to the establishment and maintenance of species boundaries among mammals due to the elaborate one-to-one correspondence between semiochemical signals and neuronal sensory inputs. Here, we report the most extensive sample of vome...
  16. Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates.

    Genome Biology and Evolution 6(1):213 (2014) PMID 24398377 PMCID PMC3914689

    Vomeronasal receptor genes have frequently been invoked as integral to the establishment and maintenance of species boundaries among mammals due to the elaborate one-to-one correspondence between semiochemical signals and neuronal sensory inputs. Here, we report the most extensive sample of vome...
  17. Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals.

    Biology Letters 10(1):20131003 (2014) PMID 24429684 PMCID PMC3917342

    O'Leary et al. (O'Leary et al. 2013 Science 339, 662-667. (doi:10.1126/science.1229237)) performed a fossil-only dating analysis of mammals, concluding that the ancestor of placentals post-dated the Cretaceous-Palaeogene boundary, contradicting previous palaeontological and molecular studies tha...
  18. Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals.

    Biology Letters 10(1):20131003 (2014) PMID 24429684 PMCID PMC3917342

    O'Leary et al. (O'Leary et al. 2013 Science 339, 662-667. (doi:10.1126/science.1229237)) performed a fossil-only dating analysis of mammals, concluding that the ancestor of placentals post-dated the Cretaceous-Palaeogene boundary, contradicting previous palaeontological and molecular studies tha...
  19. Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons?

    Genetics 195(1):195 (2013) PMID 23792953 PMCID PMC3761301

    Several studies have reported a negative correlation between estimates of the nonsynonymous to synonymous rate ratio (ω = dN/dS) and the sequence distance d in pairwise comparisons of the same gene from different species. That is, more divergent sequences produce smaller estimates of ω. Explanat...
  20. Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons?

    Genetics 195(1):195 (2013) PMID 23792953 PMCID PMC3761301

    Several studies have reported a negative correlation between estimates of the nonsynonymous to synonymous rate ratio (ω = dN/dS) and the sequence distance d in pairwise comparisons of the same gene from different species. That is, more divergent sequences produce smaller estimates of ω. Explanat...