Incongruence in the phylogenomics era
Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …
Toward a fully resolved fungal tree of life
In this review, we discuss the current status and future challenges for fully elucidating the
fungal tree of life. In the last 15 years, advances in genomic technologies have …
fungal tree of life. In the last 15 years, advances in genomic technologies have …
Plastid phylogenomic insights into relationships of all flowering plant families
Background Flowering plants (angiosperms) are dominant components of global terrestrial
ecosystems, but phylogenetic relationships at the familial level and above remain only …
ecosystems, but phylogenetic relationships at the familial level and above remain only …
New methods to calculate concordance factors for phylogenomic datasets
We implement two measures for quantifying genealogical concordance in phylogenomic
data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF) …
data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF) …
Fast coalescent-based computation of local branch support from quartet frequencies
Species tree reconstruction is complicated by effects of incomplete lineage sorting,
commonly modeled by the multi-species coalescent model (MSC). While there has been …
commonly modeled by the multi-species coalescent model (MSC). While there has been …
A genomic perspective on hybridization and speciation
BA Payseur, LH Rieseberg - Molecular ecology, 2016 - Wiley Online Library
Hybridization among diverging lineages is common in nature. Genomic data provide a
special opportunity to characterize the history of hybridization and the genetic basis of …
special opportunity to characterize the history of hybridization and the genetic basis of …
PhyloNetworks: a package for phylogenetic networks
PhyloNetworks is a Julia package for the inference, manipulation, visualization, and use of
phylogenetic networks in an interactive environment. Inference of phylogenetic networks is …
phylogenetic networks in an interactive environment. Inference of phylogenetic networks is …
Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting
C Solís-Lemus, C Ané - PLoS genetics, 2016 - journals.plos.org
Phylogenetic networks are necessary to represent the tree of life expanded by edges to
represent events such as horizontal gene transfers, hybridizations or gene flow. Not all …
represent events such as horizontal gene transfers, hybridizations or gene flow. Not all …
Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
Background The use of transcriptomic and genomic datasets for phylogenetic reconstruction
has become increasingly common as researchers attempt to resolve recalcitrant nodes with …
has become increasingly common as researchers attempt to resolve recalcitrant nodes with …
Mouse genomic variation and its effect on phenotypes and gene regulation
We report genome sequences of 17 inbred strains of laboratory mice and identify almost ten
times more variants than previously known. We use these genomes to explore the …
times more variants than previously known. We use these genomes to explore the …