Impacts of taxon-sampling schemes on Bayesian tip dating under the fossilized birth-death process

A Luo, C Zhang, QS Zhou, SYW Ho… - Systematic Biology, 2023 - academic.oup.com
Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and
fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful …

A simulation-based evaluation of tip-dating under the fossilized birth–death process

A Luo, DA Duchêne, C Zhang, CD Zhu… - Systematic …, 2020 - academic.oup.com
Bayesian molecular dating is widely used to study evolutionary timescales. This procedure
usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based …

Bayesian tip-dated phylogenetics in paleontology: topological effects and stratigraphic fit

B King - Systematic Biology, 2021 - academic.oup.com
The incorporation of stratigraphic data into phylogenetic analysis has a long history of
debate but is not currently standard practice for paleontologists. Bayesian tip-dated (or …

Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies

Q Tao, J Barba-Montoya, S Kumar - Bioinformatics, 2021 - academic.oup.com
Motivation Precise time calibrations needed to estimate ages of species divergence are not
always available due to fossil records' incompleteness. Consequently, clock calibrations …

Accounting for calibration uncertainty: Bayesian molecular dating as a “doubly intractable” problem

S Guindon - Systematic Biology, 2018 - academic.oup.com
This study introduces a new Bayesian technique for molecular dating that explicitly
accommodates for uncertainty in the phylogenetic position of calibrated nodes derived from …

Total-evidence dating under the fossilized birth–death process

C Zhang, T Stadler, S Klopfstein, TA Heath… - Systematic …, 2016 - academic.oup.com
Bayesian total-evidence dating involves the simultaneous analysis of morphological data
from the fossil record and morphological and sequence data from recent organisms, and it …

[HTML][HTML] Ignoring fossil age uncertainty leads to inaccurate topology and divergence time estimates in time calibrated tree inference

J Barido-Sottani, NMA Van Tiel, MJ Hopkins… - Frontiers in Ecology …, 2020 - frontiersin.org
Time calibrated trees are challenging to estimate for many extinct groups of species due to
the incompleteness of the rock and fossil records. Additionally, the precise age of a sample …

Bayesian dating of shallow phylogenies with a relaxed clock

RP Brown, Z Yang - Systematic biology, 2010 - academic.oup.com
Bayesian methods are increasingly being used to estimate divergence times without the
restrictive assumption of a global clock. Little is known about their reliability for shallow …

tipdatingbeast: an r package to assist the implementation of phylogenetic tip‐dating tests using beast

A Rieux, CE Khatchikian - Molecular Ecology Resources, 2017 - Wiley Online Library
Molecular tip dating of phylogenetic trees is a growing discipline that uses DNA sequences
sampled at different points in time to coestimate the timing of evolutionary events with rates …

Integrating fossil observations into phylogenetics using the fossilized birth–death model

AM Wright, DW Bapst, J Barido-Sottani… - Annual Review of …, 2022 - annualreviews.org
Over the past decade, a new set of methods for estimating dated trees has emerged.
Originally referred to as the fossilized birth–death (FBD) process, this single model has …