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Article
Open AccessWhole genome phylogeny of Gallus: introgression and data-type effects
Previous phylogenetic studies that include the four recognized species of Gallus have resulted in a number of distinct topologies, with little agreement. Several factors could lead to the failure to converge on a...
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Article
Tempo and timing of ecological trait divergence in bird speciation
Organismal traits may evolve either gradually or in rapid pulses, but the relative importance of these modes in the generation of species differences is unclear. Additionally, while pulsed evolution is frequen...
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Article
Open AccessErratum to: The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms
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Article
Open AccessThe relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms
Although homologous recombination affects the efficacy of selection in populations, the pattern of recombination rate evolution and its effects on genome evolution across plants are largely unknown. Recombinat...
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Chapter and Conference Paper
Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic re...
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Article
Open AccessData access for the 1,000 Plants (1KP) project
The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridi...
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Article
Scombroid Fishes Provide Novel Insights into the Trait/Rate Associations of Molecular Evolution
The study of which life history traits primarily affect molecular evolutionary rates is often confounded by the covariance of these traits. Scombroid fishes (billfishes, tunas, barracudas, and their relatives)...
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Article
Open AccessFrom algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous...
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Article
Open AccessA scalable method for identifying frequent subtrees in sets of large phylogenetic trees
We consider the problem of finding the maximum frequent agreement subtrees (MFASTs) in a collection of phylogenetic trees. Existing methods for this problem often do not scale beyond datasets with around 100 t...
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Article
Open AccessEfficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence
Gene tree - species tree reconciliation problems infer the patterns and processes of gene evolution within a species tree. Gene tree parsimony approaches seek the evolutionary scenario that implies the fewest ...
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Article
Open AccessConsensus properties for the deep coalescence problem and their application for scalable tree search
To infer a species phylogeny from unlinked genes, phylogenetic inference methods must confront the biological processes that create incongruence between gene trees and the species phylogeny. Intra-specific gen...
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Chapter and Conference Paper
GTP Supertrees from Unrooted Gene Trees: Linear Time Algorithms for NNI Based Local Searches
Gene tree parsimony (GTP) problems infer species supertrees from a collection of rooted gene trees that are confounded by evolutionary events like gene duplication, gene duplication and loss, and deep coalesce...
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Chapter
Variation in Rates of Molecular Evolution in Plants and Implications for Estimating Divergence Times
For nearly as long as molecular sequence data have been available for plants, they have been used to construct phylogenetic hypotheses and date the origin and diversification of clades (e.g., Boulter et al. 19...
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Chapter
Identifying the Phylogenetic Context of Whole-Genome Duplications in Plants
Although evolutionary biologists have long recognized the transformative evolutionary potential of whole-genome duplications (WGDs) in plants, identifying the precise phylogenetic location of WGDs presents man...
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Chapter and Conference Paper
Algorithms for Knowledge-Enhanced Supertrees
Supertree algorithms combine smaller phylogenetic trees into a single, comprehensive phylogeny, or supertree. Most supertree problems are NP-hard, and often heuristics identify supertrees with anomalous or unw...
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Chapter and Conference Paper
Fast Local Search for Unrooted Robinson-Foulds Supertrees
A Robinson-Foulds (RF) supertree for a collection of input trees is a comprehensive species phylogeny that is at minimum total RF distance to the input trees. Thus, an RF supertree is consistent with the maxim...
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Chapter and Conference Paper
The Deep Coalescence Consensus Tree Problem is Pareto on Clusters
Phylogenetic methods must account for the biological processes that create incongruence between gene trees and the species phylogeny. Deep coalescence, or incomplete lineage sorting creates discord among gene ...
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Chapter and Conference Paper
Algorithms for Rapid Error Correction for the Gene Duplication Problem
Gene tree - species tree reconciliation problems infer the patterns and processes of gene evolution within the context of an organismal phylogeny. In one example, the gene duplication problem seeks the evoluti...
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Article
Open AccessRobinson-Foulds Supertrees
Supertree methods synthesize collections of small phylogenetic trees with incomplete taxon overlap into comprehensive trees, or supertrees, that include all taxa found in the input trees. Supertree methods bas...
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Article
Open AccessEfficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models
Genomic data provide a wealth of new information for phylogenetic analysis. Yet making use of this data requires phylogenetic methods that can efficiently analyze extremely large data sets and account for proc...
