[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 …
Major revisions in pancrustacean phylogeny and evidence of sensitivity to taxon sampling
The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group
of animals on earth, containing over 80% of animal species and half of animal biomass. It …
of animals on earth, containing over 80% of animal species and half of animal biomass. It …
StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates
HA Ogilvie, RR Bouckaert… - Molecular biology and …, 2017 - academic.oup.com
Fully Bayesian multispecies coalescent (MSC) methods like* BEAST estimate species trees
from multiple sequence alignments. Today thousands of genes can be sequenced for a …
from multiple sequence alignments. Today thousands of genes can be sequenced for a …
Misconceptions on missing data in RAD-seq phylogenetics with a deep-scale example from flowering plants
DAR Eaton, EL Spriggs, B Park… - Systematic …, 2017 - academic.oup.com
Restriction-site associated DNA (RAD) sequencing and related methods rely on the
conservation of enzyme recognition sites to isolate homologous DNA fragments for …
conservation of enzyme recognition sites to isolate homologous DNA fragments for …
To include or not to include: the impact of gene filtering on species tree estimation methods
With the increasing availability of whole genome data, many species trees are being
constructed from hundreds to thousands of loci. Although concatenation analysis using …
constructed from hundreds to thousands of loci. Although concatenation analysis using …
Defining coalescent genes: theory meets practice in organelle phylogenomics
JJ Doyle - Systematic biology, 2022 - academic.oup.com
The species tree paradigm that dominates current molecular systematic practice infers
species trees from collections of sequences under assumptions of the multispecies …
species trees from collections of sequences under assumptions of the multispecies …
StarBeast3: adaptive parallelized Bayesian inference under the multispecies coalescent
As genomic sequence data become increasingly available, inferring the phylogeny of the
species as that of concatenated genomic data can be enticing. However, this approach …
species as that of concatenated genomic data can be enticing. However, this approach …
The perfect storm: gene tree estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant ancient angiosperm clade, Malpighiales
The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life.
The development of the multispecies coalescent model and improved gene tree estimation …
The development of the multispecies coalescent model and improved gene tree estimation …
Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data
Genomic data have had a profound impact on nearly every biological discipline. In
systematics and phylogenetics, the thousands of loci that are now being sequenced can be …
systematics and phylogenetics, the thousands of loci that are now being sequenced can be …
Analysis of a rapid evolutionary radiation using ultraconserved elements: evidence for a bias in some multispecies coalescent methods
Rapid evolutionary radiations are expected to require large amounts of sequence data to
resolve. To resolve these types of relationships many systematists believe that it will be …
resolve. To resolve these types of relationships many systematists believe that it will be …