Molecular‐clock methods for estimating evolutionary rates and timescales

SYW Ho, S Duchêne - Molecular ecology, 2014 - Wiley Online Library
The molecular clock presents a means of estimating evolutionary rates and timescales using
genetic data. These estimates can lead to important insights into evolutionary processes and …

Bayesian molecular clock dating of species divergences in the genomics era

M Dos Reis, PCJ Donoghue, Z Yang - Nature Reviews Genetics, 2016 - nature.com
Five decades have passed since the proposal of the molecular clock hypothesis, which
states that the rate of evolution at the molecular level is constant through time and among …

RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language

S Höhna, MJ Landis, TA Heath, B Boussau… - Systematic …, 2016 - academic.oup.com
Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite
of models. Consequently, users of these software packages are simultaneously forced to …

A general species delimitation method with applications to phylogenetic placements

J Zhang, P Kapli, P Pavlidis, A Stamatakis - Bioinformatics, 2013 - academic.oup.com
Motivation: Sequence-based methods to delimit species are central to DNA taxonomy,
microbial community surveys and DNA metabarcoding studies. Current approaches either …

The fossilized birth–death process for coherent calibration of divergence-time estimates

TA Heath, JP Huelsenbeck… - Proceedings of the …, 2014 - National Acad Sciences
Time-calibrated species phylogenies are critical for addressing a wide range of questions in
evolutionary biology, such as those that elucidate historical biogeography or uncover …

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 …

Bayesian total-evidence dating reveals the recent crown radiation of penguins

A Gavryushkina, TA Heath, DT Ksepka… - Systematic …, 2017 - academic.oup.com
The total-evidence approach to divergence time dating uses molecular and morphological
data from extant and fossil species to infer phylogenetic relationships, species divergence …

An unbiased molecular approach using 3′-UTRs resolves the avian family-level tree of life

H Kuhl, C Frankl-Vilches, A Bakker… - Molecular Biology …, 2021 - academic.oup.com
Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of
birds are still resolved controversially in different analyses or are considered unresolvable …

[图书][B] Molecular evolution: a statistical approach

Z Yang - 2014 - books.google.com
Studies of evolution at the molecular level have experienced phenomenal growth in the last
few decades, due to rapid accumulation of genetic sequence data, improved computer …

Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case

MD Reis, GF Gunnell, J Barba-Montoya… - Systematic …, 2018 - academic.oup.com
Primates have long been a test case for the development of phylogenetic methods for
divergence time estimation. Despite a large number of studies, however, the timing of …