New approaches for inferring phylogenies in the presence of paralogs
The availability of whole genome sequences was expected to supply essentially unlimited
data for phylogenetics. However, strict reliance on single-copy genes for this purpose has …
data for phylogenetics. However, strict reliance on single-copy genes for this purpose has …
Identifying and addressing methodological incongruence in phylogenomics: A review
JF Fleming, A Valero‐Gracia… - Evolutionary …, 2023 - Wiley Online Library
The availability of phylogenetic data has greatly expanded in recent years. As a result, a
new era in phylogenetic analysis is dawning—one in which the methods we use to analyse …
new era in phylogenetic analysis is dawning—one in which the methods we use to analyse …
Weighting by gene tree uncertainty improves accuracy of quartet-based species trees
Phylogenomic analyses routinely estimate species trees using methods that account for
gene tree discordance. However, the most scalable species tree inference methods, which …
gene tree discordance. However, the most scalable species tree inference methods, which …
Concordance and discordance in the phylogenomics of the wrasses and parrotfishes (Teleostei: Labridae)
Phylogenomic analysis of large genome-wide sequence data sets can resolve phylogenetic
tree topologies for large species groups, help test the accuracy of and improve resolution for …
tree topologies for large species groups, help test the accuracy of and improve resolution for …
Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci
The atypoid mygalomorphs include spiders from three described families that build a diverse
array of entrance web constructs, including funnel-and-sheet webs, purse webs, trapdoors …
array of entrance web constructs, including funnel-and-sheet webs, purse webs, trapdoors …
Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance
Gene tree discordance is expected in phylogenomic trees and biological processes are
often invoked to explain it. However, heterogeneous levels of phylogenetic signal among …
often invoked to explain it. However, heterogeneous levels of phylogenetic signal among …
The multispecies coalescent model outperforms concatenation across diverse phylogenomic data sets
A statistical framework of model comparison and model validation is essential to resolving
the debates over concatenation and coalescent models in phylogenomic data analysis. A …
the debates over concatenation and coalescent models in phylogenomic data analysis. A …
To what extent current limits of phylogenomics can be overcome?
Current phylogenomic methods are still a long way from implementing a realistic genome
evolution model. An ideal approach would require a general joint analysis of genomic …
evolution model. An ideal approach would require a general joint analysis of genomic …
Dissecting incongruence between concatenation-and quartet-based approaches in phylogenomic data
Topological conflict or incongruence is widespread in phylogenomic data. Concatenation-
and coalescent-based approaches often result in incongruent topologies, but the causes of …
and coalescent-based approaches often result in incongruent topologies, but the causes of …
Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study on Pseudapis Bees
Summarizing individual gene trees to species phylogenies using two-step coalescent
methods is now a standard strategy in the field of phylogenomics. However, practical …
methods is now a standard strategy in the field of phylogenomics. However, practical …