Bayesian molecular dating: opening up the black box

L Bromham, S Duchêne, X Hua, AM Ritchie… - Biological …, 2018‏ - Wiley Online Library
Molecular dating analyses allow evolutionary timescales to be estimated from genetic data,
offering an unprecedented capacity for investigating the evolutionary past of all species …

[PDF][PDF] Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock

B Mello, CG Schrago - Genome Biology and Evolution, 2024‏ - academic.oup.com
Relaxing the molecular clock using models of how substitution rates change across lineages
has become essential for addressing evolutionary problems. The diversity of rate evolution …

A comprehensive phylogeny and revised taxonomy illuminate the origin and diversification of the global radiation of Papilio (Lepidoptera: Papilionidae)

FL Condamine, R Allio, EL Reboud, JR Dupuis… - Molecular Phylogenetics …, 2023‏ - Elsevier
Abstract The swallowtail genus Papilio (Lepidoptera: Papilionidae) is species rich,
distributed worldwide, and has broad morphological habits and ecological niches. Because …

Whole genome shotgun phylogenomics resolves the pattern and timing of swallowtail butterfly evolution

R Allio, C Scornavacca, B Nabholz… - Systematic …, 2020‏ - academic.oup.com
Evolutionary relationships have remained unresolved in many well-studied groups, even
though advances in next-generation sequencing and analysis, using approaches such as …

Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

TR Simões, MW Caldwell, SE Pierce - BMC biology, 2020‏ - Springer
Background The vast majority of all life that ever existed on earth is now extinct and several
aspects of their evolutionary history can only be assessed by using morphological data from …

Analysis of phylogenomic tree space resolves relationships among marsupial families

DA Duchêne, JG Bragg, S Duchêne… - Systematic …, 2018‏ - academic.oup.com
A fundamental challenge in resolving evolutionary relationships across the tree of life is to
account for heterogeneity in the evolutionary signal across loci. Studies of marsupial …

Combining palaeontological and neontological data shows a delayed diversification burst of carcharhiniform sharks likely mediated by environmental change

B Brée, FL Condamine, G Guinot - Scientific Reports, 2022‏ - nature.com
Estimating deep-time species-level diversification processes remains challenging. Both the
fossil record and molecular phylogenies allow the estimation of speciation and extinction …

Accounting for uncertainty in the evolutionary timescale of green plants through clock-partitioning and fossil calibration strategies

Y Nie, CSP Foster, T Zhu, R Yao, DA Duchêne… - Systematic …, 2020‏ - academic.oup.com
Establishing an accurate evolutionary timescale for green plants (Viridiplantae) is essential
to understanding their interaction and coevolution with the Earth's climate and the many …

Bayesian molecular clock dating using genome-scale datasets

M Dos Reis, Z Yang - Evolutionary genomics: Statistical and …, 2019‏ - Springer
Bayesian methods for molecular clock dating of species divergences have been greatly
developed during the past decade. Advantages of the methods include the use of relaxed …

Linking branch lengths across sets of loci provides the highest statistical support for phylogenetic inference

DA Duchêne, KJ Tong, CSP Foster… - Molecular Biology …, 2020‏ - academic.oup.com
Evolution leaves heterogeneous patterns of nucleotide variation across the genome, with
different loci subject to varying degrees of mutation, selection, and drift. In phylogenetics, the …