Evaluating summary methods for multilocus species tree estimation in the presence of incomplete lineage sorting
Species tree estimation is complicated by processes, such as gene duplication and loss and
incomplete lineage sorting (ILS), that cause discordance between gene trees and the …
incomplete lineage sorting (ILS), that cause discordance between gene trees and the …
On the robustness to gene tree estimation error (or lack thereof) of coalescent-based species tree methods
The estimation of species trees using multiple loci has become increasingly common.
Because different loci can have different phylogenetic histories (reflected in different gene …
Because different loci can have different phylogenetic histories (reflected in different gene …
The performance of coalescent-based species tree estimation methods under models of missing data
Background Estimation of species trees from multiple genes is complicated by processes
such as incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer …
such as incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer …
Challenges in species tree estimation under the multispecies coalescent model
B Xu, Z Yang - Genetics, 2016 - academic.oup.com
The multispecies coalescent (MSC) model has emerged as a powerful framework for
inferring species phylogenies while accounting for ancestral polymorphism and gene tree …
inferring species phylogenies while accounting for ancestral polymorphism and gene tree …
Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased
The development and application of coalescent methods are undergoing rapid changes.
One little explored area that bears on the application of gene-tree-based coalescent …
One little explored area that bears on the application of gene-tree-based coalescent …
A comparative study of SVDquartets and other coalescent-based species tree estimation methods
Background Species tree estimation is challenging in the presence of incomplete lineage
sorting (ILS), which can make gene trees different from the species tree. Because ILS is …
sorting (ILS), which can make gene trees different from the species tree. Because ILS is …
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 …
Species tree inference methods intended to deal with incomplete lineage sorting are robust to the presence of paralogs
Many recent phylogenetic methods have focused on accurately inferring species trees when
there is gene tree discordance due to incomplete lineage sorting (ILS). For almost all of …
there is gene tree discordance due to incomplete lineage sorting (ILS). For almost all of …
Estimating phylogenetic trees from genome‐scale data
The heterogeneity of signals in the genomes of diverse organisms poses challenges for
traditional phylogenetic analysis. Phylogenetic methods known as “species tree” methods …
traditional phylogenetic analysis. Phylogenetic methods known as “species tree” methods …
DISCO: species tree inference using multicopy gene family tree decomposition
Species tree inference from gene family trees is a significant problem in computational
biology. However, gene tree heterogeneity, which can be caused by several factors …
biology. However, gene tree heterogeneity, which can be caused by several factors …