12 papers · ranked by Valyu relevance
Jesus Lozano-Fernandez, Mario dos Reis, Philip C.J. Donoghue, Davide Pisani
'Davide Pisani'] Title: Abstract Establishing an accurate timescale for the history of life is crucial to understand evolutionary processes. For this purpose, relaxed molecular clock models implemented in a Bayesian MCMC framework are generally used. However, these methods are time consuming. RelTime, a non-Bayesian…
Sudhir Kumar, Koichiro Tamura
Molecular dating of species divergences has become an important means to add a temporal dimension to the Tree of Life. Increasingly larger datasets encompassing greater taxonomic diversity are becoming available to generate molecular timetrees by using sophisticated methods that model rate variation among lineages.…
Qiqing Tao, Sudip Sharma, Koichiro Tamura, Sudhir Kumar
1.## Introduction The relative rate framework (RRF) is a system of equations that estimate relative rates among lineages exclusively from branch lengths in a phylogeny (Tamura et al. 2018). A lineage emanating from a node consists of the branch connecting to that node (stem) and all the branches in the descendant clade…
Jose Barba-Montoya, Sudip Sharma, Sudhir Kumar
A common practice in molecular systematics is to infer phylogeny and then scale it to time by using a relaxed clock method and calibrations. This sequential analysis practice ignores the effect of phylogenetic uncertainty on divergence time estimates and their confidence/credibility intervals. An alternative is to…
Jose Barba-Montoya, Qiqing Tao, Sudhir Kumar, Barbara Holland
Rapid relaxed-clock dating methods are frequently applied to analyze phylogenomic data sets containing hundreds to thousands of sequences because of their accuracy and computational efficiency. However, the relative performance of different rapid dating methods is yet to be compared on the same data sets, and, thus…
Fernanda P. Costa, Carlos G. Schrago, Beatriz Mello
Advances in genome sequencing techniques produced a significant growth of phylogenomic datasets. This massive amount of data represents a computational challenge for molecular dating with Bayesian approaches. Rapid molecular dating methods have been proposed over the last few decades to overcome these issues. However…
Edward A. Lee, Albert M. K. Cheng
This paper is about better engineering of cyber-physical systems (CPSs) through better models. Deterministic models have historically proven extremely useful and arguably form the kingpin of the industrial revolution and the digital and information technology revolutions. Key deterministic models that have proven…
Alan J S Beavan, Philip C J Donoghue, Mark A Beaumont, Davide Pisani + 1 more
'David T E Bryant'] Title: Abstract Relaxed molecular clock methods allow the use of genomic data to estimate divergence times across the tree of life. This is most commonly achieved in Bayesian analyses where the molecular clock is calibrated a priori through the integration of fossil information. Alternatively…
Jose Barba-Montoya, Jack M Craig, Sudhir Kumar
Reconstructing the global Tree of Life necessitates computational approaches to integrate numerous molecular phylogenies with limited species overlap into a comprehensive supertree. Our survey of published literature shows that individual phylogenies are frequently restricted to specific taxonomic groups due to the…
Qiyu Chen, Chunling Chen, Bo Wang, Zehuan Wang + 3 more
'Yuan Huang' 'Qingwen Sun'] The genus Sabia is a woody climber belonging to the family Sabiaceae, order Proteales. Several species of this genus have been utilized as medicines for treating diseases, such as rheumatic arthritis, traumatism, hepatitis, etc. However, the lack of molecular data has prevented the accurate…
Timm A. Wild, Georg Wilbs, Dina K. N. Dechmann, Jenna E. Kohles + 7 more
'Nils Linek' 'Sierra Mattingly' 'Nina Richter' 'Spyros Sfenthourakis' 'Haris Nicolaou' 'Elena Erotokritou' 'Martin Wikelski'] Time-synchronised data streams from bio-loggers are becoming increasingly important for analysing and interpreting intricate animal behaviour including split-second decision making, group…
Marlyne Meijerink-Bosman, Roger Leenders, Joris Mulder, Lei Shi
The relational event model (REM) facilitates the study of network evolution in relational event history data, i.e., time-ordered sequences of social interactions. In real-life social networks it is likely that network effects, i.e., the parameters that quantify the relative importance of drivers of these social…