10 papers · ranked by Valyu relevance
Fabia U. Battistuzzi, Qiqing Tao, Lance Jones, Koichiro Tamura + 1 more
The RelTime method estimates divergence times when evolutionary rates vary among lineages. It has been shown to perform well in the analysis of empirical and computer simulated datasets. In addition, theoretical analyses show that RelTime relaxes the strict molecular clock throughout a molecular phylogeny. However 11…
Koichiro Tamura, Qiqing Tao, Sudhir Kumar
RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It showed excellent performance in estimating divergence times for both simulated and empirical molecular sequence datasets in which evolutionary rates varied extensively throughout the tree. RelTime is…
Qiqing Tao, Koichiro Tamura, Beatriz Mello, Sudhir Kumar
Confidence intervals (CIs) depict the statistical uncertainty surrounding evolutionary divergence time estimates. They capture variance contributed by the finite number of sequences and sites used in the alignment, deviations of evolutionary rates from a strict molecular clock in a phylogeny, and uncertainty associated…
Beatriz Mello, Qiqing Tao, Sudhir Kumar
Concurrent molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics, and species delimitation studies. Multiple sequence alignments used in these investigations frequently consist of both intra- and inter-species samples (mixed…
Qiqing Tao, Jose Barba-Montoya, Louise A. Huuki, Mary Kathleen Durnan + 1 more
The conventional wisdom in molecular evolution is to apply parameter-rich models of nucleotide and amino acid substitutions for estimating divergence times. However, the actual extent of the difference between time estimates produced by highly complex models compared to those from simple models is yet to be quantified…
Jose Barba-Montoya, Qiqing Tao, Sudhir Kumar
As the number and diversity of species and genes grow in contemporary datasets, two common assumptions made in all molecular dating methods, namely the time-reversibility and stationarity of the substitution process, become untenable. No software tools for molecular dating allow researchers to relax these two…
Sayaka Miura, Koichiro Tamura, Sergei L. Kosakovsky Pond, Louise A. Huuki + 3 more
Pathogen timetrees are phylogenies scaled to time. They reveal the temporal history of a pathogen spread through the populations as captured in the evolutionary history of strains. These timetrees are inferred by using molecular sequences of pathogenic strains sampled at different times. That is, temporally sampled…
Anna B. Neuheimer
For living things, time proceeds relative to body temperature. In this contribution, I describe the biochemical underpinnings of this “biological time” and formalize the Biological Theory of Relativity (BTR). Paralleling Einstein’s Special Theory of Relativity, the BTR describes how time progresses across temporal…
Pavel Sagulenko, Vadim Puller, Richard A. Neher
Mutations that accumulate in the genome of replicating biological organisms can be used to infer their evolutionary history. In case of measurably evolving organisms genomes often reveal their detailed spatio-temporal spread. Such phylodynamic analyses are particularly useful to understand the epidemiology of rapidly…
Zoran Tiganj, Jason A. Cromer, Jefferson E. Roy, Earl K. Miller + 1 more
Cognitive theories suggest that working memory maintains not only the identity of recently-presented stimuli but also a sense of the elapsed time since the stimuli presentation. Previous studies of the neural underpinnings of working memory have focused on sustained firing, which can account for maintenance of the…