Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed, and this dating may pose a problem for the widely believed hypothesis that the bipedal creatureAustralopithecus afarensis, which lived some 3.7 million years ago, was ancestral to man and evolved after the human-ape splitting.
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea
A new method for estimating the variance of the difference between log likelihood of different tree topologies is developed by expressing it explicitly in order to evaluate the maximum likelihood branching order among Hominoidea.
Estimating the rate of evolution of the rate of molecular evolution.
A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events…
Performance of a divergence time estimation method under a probabilistic model of rate evolution.
Simulation results demonstrate that the accuracy of divergence time estimation is substantially enhanced when constraints are included and new parameterization more effectively captures the phylogenetic structure of rate evolution on a tree.
Divergence time and evolutionary rate estimation with multilocus data.
Bayesian methods for estimating evolutionary divergence times are extended to multigene data sets, and a technique is described for detecting correlated changes in evolutionary rates among genes.…
An evolutionary model for maximum likelihood alignment of DNA sequences
A parameter-estimation approach which takes into account all possible alignments between two sequences is introduced; the danger of estimating evolutionary parameters from a single alignment is discussed.
A phylogenetic foundation for comparative mammalian genomics.
The largest alignments of amino acid sequence data to date are constructed and a good case is made for the tree shrew as a closer relative of primates than rodents, while also showing a slower rate of evolution in key cell cycle genes.
Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
A maximum likelihood method based on a Markov model that takes into account the unequal transition probabilities among pairs of amino acids and does not assume constancy of rate among different lineages is expected to be powerful in inferring phylogeny among distantly related proteins.
Inching toward reality: An improved likelihood model of sequence evolution
Parameter estimation and alignment procedures that incorporate generalizations to permit approximate treatment of multiple-base insertions and deletions as well as regional heterogeneity of substitution rates are developed.
Time flies, a new molecular time-scale for brachyceran fly evolution without a clock.
Divergence times based on the 28S rDNA and several fossil constraints indicate that the Brachycera originated in the late Triassic or earliest Mesozoic and that all major lower brachyceran fly lineages had near contemporaneous origins in the mid-Jurassic prior to the origin of flowering plants.