RelTime relaxes the strict molecular clock throughout the phylogeny

FU Battistuzzi, Q Tao, L Jones… - Genome Biology and …, 2018 - academic.oup.com
The RelTime method estimates divergence times when evolutionary rates vary among
lineages. Theoretical analyses show that RelTime relaxes the strict molecular clock …

Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model

J Douglas, R Zhang, R Bouckaert - PLoS computational biology, 2021 - journals.plos.org
Relaxed clock models enable estimation of molecular substitution rates across lineages and
are widely used in phylogenetics for dating evolutionary divergence times. Under the …

Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times

M Reis, Z Yang - Molecular biology and evolution, 2011 - academic.oup.com
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 …

Dating the molecular clock in fungi–how close are we?

ML Berbee, JW Taylor - Fungal Biology Reviews, 2010 - Elsevier
Integration of fungal evolution with the dates of plate tectonic movements, paleoecology, and
the evolution of plants and animals requires a molecular clock. Imperfect though they may …

An evaluation of different partitioning strategies for Bayesian estimation of species divergence times

K Angelis, S Álvarez-Carretero, M Dos Reis… - Systematic …, 2018 - academic.oup.com
The explosive growth of molecular sequence data has made it possible to estimate species
divergence times under relaxed-clock models using genome-scale data sets with many …

Calibrating the Tree of Life: fossils, molecules and evolutionary timescales

F Forest - Annals of Botany, 2009 - academic.oup.com
Background Molecular dating has gained ever-increasing interest since the molecular clock
hypothesis was proposed in the 1960s. Molecular dating provides detailed temporal …

Phylogenies of extant species are consistent with an infinite array of diversification histories

S Louca, MW Pennell - BioRxiv, 2019 - biorxiv.org
Time-calibrated molecular phylogenies of extant species (“extant timetrees”) are widely used
for estimating the dynamics of speciation and extinction rates and reconstructing …

Notes on the birth–death prior with fossil calibrations for Bayesian estimation of species divergence times

M Dos Reis - … Transactions of the Royal Society B …, 2016 - royalsocietypublishing.org
Constructing a multi-dimensional prior on the times of divergence (the node ages) of species
in a phylogeny is not a trivial task, in particular, if the prior density is the result of combining …

[HTML][HTML] Using the fossil record to evaluate timetree timescales

CR Marshall - Frontiers in Genetics, 2019 - frontiersin.org
The fossil and geologic records provide the primary data used to established absolute
timescales for timetrees. For the paleontological evaluation of proposed timetree timescales …

Teasing apart molecular-versus fossil-based error estimates when dating phylogenetic trees: a case study in the birch family (Betulaceae)

F Forest, V Savolainen, MW Chase, R Lupia… - Systematic …, 2005 - ingentaconnect.com
Fossils are widely used as calibration points in molecular-based dating studies, but their
placement on a phylogenetic tree of extant species is always highly problematic. We explore …