The posterior and the prior in Bayesian phylogenetics

ME Alfaro, MT Holder - Annu. Rev. Ecol. Evol. Syst., 2006 - annualreviews.org
Bayesian analysis has enjoyed explosive growth in phylogenetics over the past five years.
Accompanying this popularity has been increased focus on the meaning of the posterior …

RASP 4: ancestral state reconstruction tool for multiple genes and characters

Y Yu, C Blair, X He - Molecular biology and evolution, 2020 - academic.oup.com
With the continual progress of sequencing techniques, genome-scale data are increasingly
used in phylogenetic studies. With more data from throughout the genome, the relationship …

Recovering speciation and extinction dynamics based on phylogenies

T Stadler - Journal of evolutionary biology, 2013 - academic.oup.com
Phylogenetic trees of only extant species contain information about the underlying
speciation and extinction pattern. In this review, I provide an overview over the different …

Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees

MR Smith - Bioinformatics, 2020 - academic.oup.com
Abstract Motivation The Robinson–Foulds (RF) metric is widely used by biologists, linguists
and chemists to quantify similarity between pairs of phylogenetic trees. The measure tallies …

Horizontal gene transfer among genomes: the complexity hypothesis

R Jain, MC Rivera, JA Lake - Proceedings of the National …, 1999 - National Acad Sciences
Increasingly, studies of genes and genomes are indicating that considerable horizontal
transfer has occurred between prokaryotes. Extensive horizontal transfer has occurred for …

Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

JL Geoghegan, S Duchêne, EC Holmes - PLoS pathogens, 2017 - journals.plos.org
The cross-species transmission of viruses from one host species to another is responsible
for the majority of emerging infections. However, it is unclear whether some virus families …

Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous

A Ghezelayagh, RC Harrington, ED Burress… - Nature Ecology & …, 2022 - nature.com
Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and account for
more than a quarter of all living vertebrate species. Previous time-calibrated phylogenies …

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

K Nyakatura, ORP Bininda-Emonds - BMC biology, 2012 - Springer
Background Although it has proven to be an important foundation for investigations of
carnivoran ecology, biology and evolution, the complete species-level supertree for …

[图书][B] Mathematical classification and clustering

B Mirkin - 2013 - books.google.com
I am very happy to have this opportunity to present the work of Boris Mirkin, a distinguished
Russian scholar in the areas of data analysis and decision making methodologies. The …

Missing data, incomplete taxa, and phylogenetic accuracy

JJ Wiens - Systematic biology, 2003 - academic.oup.com
The problem of missing data is often considered to be the most important obstacle in
reconstructing the phylogeny of fossil taxa and in combining data from diverse characters …