Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families
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 …
for the majority of emerging infections. However, it is unclear whether some virus families …
Mutation and recombination in pathogen evolution: Relevance, methods and controversies
Mutation and recombination drive the evolution of most pathogens by generating the genetic
variants upon which selection operates. Those variants can, for example, confer resistance …
variants upon which selection operates. Those variants can, for example, confer resistance …
Consequences of substitution model selection on protein ancestral sequence reconstruction
The selection of the best-fitting substitution model of molecular evolution is a traditional step
for phylogenetic inferences, including ancestral sequence reconstruction (ASR). However, a …
for phylogenetic inferences, including ancestral sequence reconstruction (ASR). However, a …
Bioinformatics applied to biotechnology: A review towards bioenergy research
The ever-increasing demand for energy, along with worldwide policies aiming sustainability,
resulted in an escalation of research projects focusing on alternative routes for energy …
resulted in an escalation of research projects focusing on alternative routes for energy …
Discovery of novel crustacean and cephalopod flaviviruses: insights into the evolution and circulation of flaviviruses between marine invertebrate and vertebrate hosts
Most described flaviviruses (family Flaviviridae) are disease-causing pathogens of
vertebrates maintained in zoonotic cycles between mosquitoes or ticks and vertebrate hosts …
vertebrates maintained in zoonotic cycles between mosquitoes or ticks and vertebrate hosts …
Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids
The onset of phylogenomics has contributed to the resolution of numerous challenging
evolutionary questions while offering new perspectives regarding biodiversity. However, in …
evolutionary questions while offering new perspectives regarding biodiversity. However, in …
Can sequence phylogenies safely infer the origin of the global virome?
Edward C. Holmes, a, b, c Sebastián Duchêned aMarie Bashir Institute for Infectious
Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia bCharles …
Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia bCharles …
Relative model fit does not predict topological accuracy in single-gene protein phylogenetics
SJ Spielman - Molecular biology and evolution, 2020 - academic.oup.com
It is regarded as best practice in phylogenetic reconstruction to perform relative model
selection to determine an appropriate evolutionary model for the data. This procedure ranks …
selection to determine an appropriate evolutionary model for the data. This procedure ranks …
Impact of the tree prior on estimating clock rates during epidemic outbreaks
Bayesian phylogenetics aims at estimating phylogenetic trees together with evolutionary
and population dynamic parameters based on genetic sequences. It has been noted that the …
and population dynamic parameters based on genetic sequences. It has been noted that the …
New statistical criteria detect phylogenetic bias caused by compositional heterogeneity
In statistical phylogenetic analyses of DNA sequences, models of evolutionary change
commonly assume that base composition is stationary through time and across lineages …
commonly assume that base composition is stationary through time and across lineages …