Terraces in species tree inference from gene trees. [PDF]
BMC Ecol Evol, 2022 Abstract A terrace in a phylogenetic tree space is a region where all trees contain the same set of subtrees, due to certain patterns of missing data among the taxa sampled, resulting in an identical optimality score for a given data set. This was first investigated in the context of phylogenetic tree estimation from sequence alignments using ...
Habib M +4 more
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Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication. [PDF]
Syst Biol, 2022 Whole-genome duplication (WGD) occurs broadly and repeatedly across the history of eukaryotes and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs.
Xiong H +8 more
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Complexity of the simplest species tree problem. [PDF]
Mol Biol Evol, 2021 The multispecies coalescent model provides a natural framework for species tree estimation accounting for gene-tree conflicts. Although a number of species tree methods under the multispecies coalescent have been suggested and evaluated using simulation,
Zhu T, Yang Z.
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DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition. [PDF]
Syst Biol, 2022 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 including gene duplication and loss, makes the estimation of species trees very ...
Willson J +4 more
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ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy. [PDF]
Mol Biol Evol, 2020 Species tree inference via summary methods that combine gene trees has become an increasingly common analysis in recent phylogenomic studies. This broad adoption has been partly due to the greater availability of genome-wide data and ample recognition ...
Zhang C +3 more
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Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction. [PDF]
Syst Biol, 2021 Ultraconserved genomic elements (UCEs), are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes is agnostic to genetic identity, only selecting loci that are highly conserved, single copy, without ...
Van Dam MH +3 more
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GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene Family Tree Inference under Gene Duplication, Transfer, and Loss. [PDF]
Mol Biol Evol, 2020 Inferring phylogenetic trees for individual homologous gene families is difficult because alignments are often too short, and thus contain insufficient signal, while substitution models inevitably fail to capture the complexity of the evolutionary ...
Morel B +3 more
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Coalescent histories for lodgepole species trees [PDF]
Journal of Computational Biology, 2015 Coalescent histories are combinatorial structures that describe for a given gene tree and species tree the possible lists of branches of the species tree on which the gene tree coalescences take place. Properties of the number of coalescent histories for
Disanto, Filippo, Rosenberg, Noah A.
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Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent. [PDF]
Mol Biol Evol, 2018 The multispecies coalescent provides a natural framework for accommodating ancestral genetic polymorphism and coalescent processes that can cause different genomic regions to have different genealogical histories. The Bayesian program BPP includes a full-
Flouri T, Jiao X, Rannala B, Yang Z.
europepmc +2 more sources
STELAR: a statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency. [PDF]
BMC Genomics, 2020 Species tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, estimating a species tree from a collection of gene trees can be complicated due to the presence of gene tree incongruence
Islam M +4 more
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