[HTML][HTML] Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics
In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and
John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the …
John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the …
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 …
groups, Laurasiatheria (eg dogs, bats, whales), Euarchontoglires (eg humans, rodents …
Bayesian inference of species trees from multilocus data
J Heled, AJ Drummond - Molecular biology and evolution, 2009 - academic.oup.com
Until recently, it has been common practice for a phylogenetic analysis to use a single gene
sequence from a single individual organism as a proxy for an entire species. With …
sequence from a single individual organism as a proxy for an entire species. With …
Is a new and general theory of molecular systematics emerging?
SV Edwards - Evolution, 2009 - academic.oup.com
The advent and maturation of algorithms for estimating species trees—phylogenetic trees
that allow gene tree heterogeneity and whose tips represent lineages, populations and …
that allow gene tree heterogeneity and whose tips represent lineages, populations and …
The gene tree delusion
MS Springer, J Gatesy - Molecular phylogenetics and evolution, 2016 - Elsevier
Higher-level relationships among placental mammals are mostly resolved, but several
polytomies remain contentious. Song et al.(2012) claimed to have resolved three of these …
polytomies remain contentious. Song et al.(2012) claimed to have resolved three of these …
Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
J Gatesy, MS Springer - Molecular phylogenetics and evolution, 2014 - Elsevier
Large datasets are required to solve difficult phylogenetic problems that are deep in the Tree
of Life. Currently, two divergent systematic methods are commonly applied to such datasets …
of Life. Currently, two divergent systematic methods are commonly applied to such datasets …
Avoiding missing data biases in phylogenomic inference: an empirical study in the landfowl (Aves: Galliformes)
Production of massive DNA sequence data sets is transforming phylogenetic inference, but
best practices for analyzing such data sets are not well established. One uncertainty is …
best practices for analyzing such data sets are not well established. One uncertainty is …
Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable …
The inference of the evolutionary history of a collection of organisms is a problem of
fundamental importance in evolutionary biology. The abundance of DNA sequence data …
fundamental importance in evolutionary biology. The abundance of DNA sequence data …
Estimating species phylogenies using coalescence times among sequences
The estimation of species trees (phylogenies) is one of the most important problems in
evolutionary biology, and recently, there has been greater appreciation of the need to …
evolutionary biology, and recently, there has been greater appreciation of the need to …
[HTML][HTML] Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes
The current classification of angiosperms is based primarily on concatenated plastid
markers and maximum likelihood (ML) inference. This approach has been justified by the …
markers and maximum likelihood (ML) inference. This approach has been justified by the …