[图书][B] Phylogeny: discrete and random processes in evolution
M Steel - 2016 - SIAM
The idea that all life on earth traces back to a common origin dates back at least to Charles
Darwin's Origin of Species. Ever since, biologists have tried to piece together parts of this …
Darwin's Origin of Species. Ever since, biologists have tried to piece together parts of this …
An evolutionary epigenetic clock in plants
Molecular clocks are the basis for dating the divergence between lineages over
macroevolutionary timescales (~ 105 to 108 years). However, classical DNA-based clocks …
macroevolutionary timescales (~ 105 to 108 years). However, classical DNA-based clocks …
Assessing parameter identifiability in phylogenetic models using data cloning
The success of model-based methods in phylogenetics has motivated much research aimed
at generating new, biologically informative models. This new computer-intensive approach …
at generating new, biologically informative models. This new computer-intensive approach …
Identifiability of two-tree mixtures for group-based models
Phylogenetic data arising on two possibly different tree topologies might be mixed through
several biological mechanisms, including incomplete lineage sorting or horizontal gene …
several biological mechanisms, including incomplete lineage sorting or horizontal gene …
Identifiability of large phylogenetic mixture models
JA Rhodes, S Sullivant - Bulletin of mathematical biology, 2012 - Springer
Phylogenetic mixture models are statistical models of character evolution allowing for
heterogeneity. Each of the classes in some unknown partition of the characters may evolve …
heterogeneity. Each of the classes in some unknown partition of the characters may evolve …
The potential role of androgenesis in cytoplasmic–nuclear phylogenetic discordance
In many organisms, gene trees based on nuclear markers and those based on cytoplasmic
markers (chloroplasts or mitochondria) sometimes indicate quite different relationships …
markers (chloroplasts or mitochondria) sometimes indicate quite different relationships …
Complex models of sequence evolution require accurate estimators as exemplified with the invariable site plus gamma model
The invariable site plus model (I is widely used to model rate heterogeneity among
alignment sites in maximum likelihood and Bayesian phylogenetic analyses. The proof that …
alignment sites in maximum likelihood and Bayesian phylogenetic analyses. The proof that …
[HTML][HTML] Consistency and identifiability of the polymorphism-aware phylogenetic models
Polymorphism-aware phylogenetic models (PoMo) constitute an alternative approach for
species tree estimation from genome-wide data. PoMo builds on the standard substitution …
species tree estimation from genome-wide data. PoMo builds on the standard substitution …
Can we avoid “SIN” in the house of “no common mechanism”?
M Steel - Systematic biology, 2011 - academic.oup.com
In “no common mechanism”(NCM) models of character evolution, each character can evolve
on a phylogenetic tree under a partially or totally separate process (eg, with its own branch …
on a phylogenetic tree under a partially or totally separate process (eg, with its own branch …
Parameter identifiability for a profile mixture model of protein evolution
A profile mixture (PM) model is a model of protein evolution, describing sequence data in
which sites are assumed to follow many related substitution processes on a single …
which sites are assumed to follow many related substitution processes on a single …