相关论文: Bayesian phylogenetic estimation of fossil ages

We apply a self-consistent and robust Bayesian statistical approach to determining the ages, distances, and ZAMS masses of 28 field DA white dwarfs with ages of approximately 4 to 8 Gyrs. Our technique requires only quality optical and…

Estimation of molecular evolutionary divergence times requires models of rate change. These vary with regard to the assumption of what quantity is penalized. The possibilities considered are the rate of evolution, the log of the rate of…

Age-disaggregated health data is crucial for effective public health planning and monitoring. Monitoring under-five mortality, for example, requires highly detailed age data since the distribution of potential causes of death varies…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this…

The Bayesian method is noted to produce spuriously high posterior probabilities for phylogenetic trees in analysis of large datasets, but the precise reasons for this over-confidence are unknown. In general, the performance of Bayesian…

Background: Continuous traits evolution of a group of taxa that are correlated through a phylogenetic tree is commonly modelled using parametric stochastic differential equations to represent deterministic change of trait through time,…

As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…

Background. Conventional phylogenetic clustering approaches rely on arbitrary cutpoints applied a posteriori to phylogenetic estimates. Although in practice, Bayesian and bootstrap-based clustering tend to lead to similar estimates, they…

The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…

Bayesian inference is a popular and widely-used approach to infer phylogenies (evolutionary trees). However, despite decades of widespread application, it remains difficult to judge how well a given Bayesian Markov chain Monte Carlo (MCMC)…

Phylogenetic comparative methods correct for shared evolutionary history among a set of non-independent organisms by modeling sample traits as arising from a diffusion process along on the branches of a possibly unknown history. To…

Divergence time estimation is crucial to provide temporal signals for dating biologically important events, from species divergence to viral transmissions in space and time. With the advent of high-throughput sequencing, recent Bayesian…

Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…

Updated evolutionary and pulsational model predictions are combined in order to interpret the properties of Galactic Classical Cepheids in the Gaia Data Release 2. In particular, the location of the instability strip boundaries and the…

We present an update of our on-going effort to improve the precision of white dwarf cosmochronology via careful analyses of white dwarf photometry in open clusters. To improve the precision of white dwarf and main sequence age analysis, we…

There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…

Motivation: The construction of statistics for summarizing posterior samples returned by a Bayesian phylogenetic study has so far been hindered by the poor geometric insights available into the space of phylogenetic trees, and ad hoc…

Genetic sequence data of pathogens are increasingly used to investigate transmission dynamics in both endemic diseases and disease outbreaks; such research can aid in development of appropriate interventions and in design of studies to…

Rate variation among the sites of a molecular sequence is commonly found in applications of phylogenetic inference. Several approaches exist to account for this feature but they do not usually enable the investigator to pinpoint the sites…