Mammal madness: is the mammal tree of life not yet resolved?

NM Foley, MS Springer… - … Transactions of the …, 2016 - royalsocietypublishing.org
Most molecular phylogenetic studies place all placental mammals into four superordinal
groups, Laurasiatheria (eg dogs, bats, whales), Euarchontoglires (eg humans, rodents …

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 …

TreeTime: Maximum-likelihood phylodynamic analysis

P Sagulenko, V Puller, RA Neher - Virus evolution, 2018 - academic.oup.com
Mutations that accumulate in the genome of cells or viruses can be used to infer their
evolutionary history. In the case of rapidly evolving organisms, genomes can reveal their …

[HTML][HTML] So many genes, so little time: a practical approach to divergence-time estimation in the genomic era

SA Smith, JW Brown, JF Walker - PloS one, 2018 - journals.plos.org
Phylogenomic datasets have been successfully used to address questions involving
evolutionary relationships, patterns of genome structure, signatures of selection, and gene …

Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates

K Tamura, Q Tao, S Kumar - Molecular biology and evolution, 2018 - academic.oup.com
RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in
a phylogeny. It shows excellent performance in estimating divergence times for both …

An evolutionary epigenetic clock in plants

N Yao, Z Zhang, L Yu, R Hazarika, C Yu, H Jang… - Science, 2023 - science.org
Molecular clocks are the basis for dating the divergence between lineages over
macroevolutionary timescales (~ 105 to 108 years). However, classical DNA-based clocks …

Scalable relaxed clock phylogenetic dating

EM Volz, SDW Frost - Virus evolution, 2017 - academic.oup.com
Molecular clock models relate observed genetic diversity to calendar time, enabling
estimation of times of common ancestry. Many large datasets of fast-evolving viruses are not …

Symbiosis in eukaryotic evolution

P López-García, L Eme, D Moreira - Journal of theoretical biology, 2017 - Elsevier
Abstract Fifty years ago, Lynn Margulis, inspiring in early twentieth-century ideas that put
forward a symbiotic origin for some eukaryotic organelles, proposed a unified theory for the …

Estimating timetrees with MEGA and the TimeTree resource

B Mello - Molecular biology and evolution, 2018 - academic.oup.com
The main outcome of molecular dating, the timetree, provides crucial information for
understanding the evolutionary history of lineages and is a requirement of several …

Divergence-time estimates for hominins provide insight into encephalization and body mass trends in human evolution

HP Püschel, OC Bertrand, JE O'reilly, R Bobe… - Nature ecology & …, 2021 - nature.com
Quantifying speciation times during human evolution is fundamental as it provides a
timescale to test for the correlation between key evolutionary transitions and extrinsic factors …