1. Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar's forests past.

    PNAS 113(29):8049 (2016) PMID 27432945 PMCID PMC4961119

    Phylogeographic analysis can be described as the study of the geological and climatological processes that have produced contemporary geographic distributions of populations and species. Here, we attempt to understand how the dynamic process of landscape change on Madagascar has shaped the distr...
  2. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference.

    Genome Biology and Evolution 8(2):330 (2016) PMID 26733575 PMCID PMC4779606

    Placental mammals comprise three principal clades: Afrotheria (e.g., elephants and tenrecs), Xenarthra (e.g., armadillos and sloths), and Boreoeutheria (all other placental mammals), the relationships among which are the subject of controversy and a touchstone for debate on the limits of phyloge...
  3. Bayesian molecular clock dating of species divergences in the genomics era.

    Nature Reviews: Genetics 17(2):71 (2016) PMID 26688196

    Five decades have passed since the proposal of the molecular clock hypothesis, which states that the rate of evolution at the molecular level is constant through time and among species. This hypothesis has become a powerful tool in evolutionary biology, making it possible to use molecular sequen...
  4. Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales.

    Current Biology 25(22):2939 (2015) PMID 26603774 PMCID PMC4651906

    The timing of divergences among metazoan lineages is integral to understanding the processes of animal evolution, placing the biological events of species divergences into the correct geological timeframe. Recent fossil discoveries and molecular clock dating studies have suggested a divergence o...
  5. Dating Tips for Divergence-Time Estimation.

    Trends in Genetics 31(11):637 (2015) PMID 26439502

    The molecular clock is the only viable means of establishing an accurate timescale for Life on Earth, but it remains reliant on a capricious fossil record for calibration. 'Tip-dating' promises a conceptual advance, integrating fossil species among their living relatives using molecular/morpholo...
  6. Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales

    Current Biology (2015)

    The timing of divergences among metazoan lineages is integral to understanding the processes of animal evolution, placing the biological events of species divergences into the correct geological time frame. Recent fossil discoveries and molecular clock dating studies have suggested a d...
  7. 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...
  8. 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...
  9. 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 ...
  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. 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...
  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. 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...
  14. 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...
  15. 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...
  16. Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny.

    Proceedings of the Royal Society B: Biological ... 279(1742):3491 (2012) PMID 22628470 PMCID PMC3396900

    The fossil record suggests a rapid radiation of placental mammals following the Cretaceous-Paleogene (K-Pg) mass extinction 65 million years ago (Ma); nevertheless, molecular time estimates, while highly variable, are generally much older. Early molecular studies suffer from inadequate dating me...
  17. Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models.

    Genetics 190(3):1101 (2012) PMID 22209901 PMCID PMC3296245

    Estimation of the distribution of selection coefficients of mutations is a long-standing issue in molecular evolution. In addition to population-based methods, the distribution can be estimated from DNA sequence data by phylogenetic-based models. Previous models have generally found unimodal dis...
  18. An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations.

    Molecular Ecology 20(17):3653 (2011) PMID 21806691

    In barley, the eukaryotic translation initiation factor 4E (eIF4E) gene situated on chromosome 3H is recognized as an important source of resistance to the bymoviruses Barley yellow mosaic virus and Barley mild mosaic virus. In modern barley cultivars, two recessive eIF4E alleles, rym4 and rym5,...
  19. Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times.

    Molecular Biology and Evolution 28(7):2161 (2011) PMID 21310946

    The molecular clock provides a powerful way to estimate species divergence times. If information on some species divergence times is available from the fossil or geological record, it can be used to calibrate a phylogeny and estimate divergence times for all nodes in the tree. The Bayesian metho...
  20. Charting the host adaptation of influenza viruses.

    Molecular Biology and Evolution 28(6):1755 (2011) PMID 21109586 PMCID PMC3098510

    Four influenza pandemics have struck the human population during the last 100 years causing substantial morbidity and mortality. The pandemics were caused by the introduction of a new virus into the human population from an avian or swine host or through the mixing of virus segments from an anim...