Incongruence in the phylogenomics era

JL Steenwyk, Y Li, X Zhou, XX Shen… - Nature Reviews Genetics, 2023 - nature.com
Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …

Formation of the Isthmus of Panama

A O'Dea, HA Lessios, AG Coates, RI Eytan… - Science …, 2016 - science.org
The formation of the Isthmus of Panama stands as one of the greatest natural events of the
Cenozoic, driving profound biotic transformations on land and in the oceans. Some recent …

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

R Bouckaert, TG Vaughan… - PLoS computational …, 2019 - journals.plos.org
Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent
years with major new advances in nearly all aspects of the joint modelling of evolutionary …

MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space

F Ronquist, M Teslenko, P Van Der Mark… - Systematic …, 2012 - academic.oup.com
Since its introduction in 2001, MrBayes has grown in popularity as a software package for
Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With …

BEAST 2: a software platform for Bayesian evolutionary analysis

R Bouckaert, J Heled, D Kühnert… - PLoS computational …, 2014 - journals.plos.org
We present a new open source, extensible and flexible software platform for Bayesian
evolutionary analysis called BEAST 2. This software platform is a re-design of the popular …

Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)

A Rambaut, TT Lam, L Max Carvalho… - Virus …, 2016 - academic.oup.com
Gene sequences sampled at different points in time can be used to infer molecular
phylogenies on a natural timescale of months or years, provided that the sequences in …

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

RO Prum, JS Berv, A Dornburg, DJ Field, JP Townsend… - Nature, 2015 - nature.com
Although reconstruction of the phylogeny of living birds has progressed tremendously in the
last decade, the evolutionary history of Neoaves—a clade that encompasses nearly all living …

Real-time, portable genome sequencing for Ebola surveillance

J Quick, NJ Loman, S Duraffour, JT Simpson, E Severi… - Nature, 2016 - nature.com
The Ebola virus disease epidemic in West Africa is the largest on record, responsible for
over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is …

Whole-genome analyses resolve early branches in the tree of life of modern birds

ED Jarvis, S Mirarab, AJ Aberer, B Li, P Houde, C Li… - Science, 2014 - science.org
To better determine the history of modern birds, we performed a genome-scale phylogenetic
analysis of 48 species representing all orders of Neoaves using phylogenomic methods …

Evolutionary history, potential intermediate animal host, and cross‐species analyses of SARS‐CoV‐2

X Li, J Zai, Q Zhao, Q Nie, Y Li, BT Foley… - Journal of medical …, 2020 - Wiley Online Library
To investigate the evolutionary history of the recent outbreak of severe acute respiratory
syndrome coronavirus 2 (SARS‐CoV‐2) in China, a total of 70 genomes of virus strains from …