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 …
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
Background Evolutionary histories can be discordant across the genome, and such
discordances need to be considered in reconstructing the species phylogeny. ASTRAL is …
discordances need to be considered in reconstructing the species phylogeny. ASTRAL is …
Integrative approaches for species delimitation in Ascomycota
Biodiversity loss from disturbances caused by human activities means that species are
disappearing at an ever increasing rate. The high number of species that have yet to be …
disappearing at an ever increasing rate. The high number of species that have yet to be …
Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits
INTRODUCTION The ruminants are one of the most successful mammalian lineages,
exhibiting extensive morphological and ecological diversity and containing several key …
exhibiting extensive morphological and ecological diversity and containing several key …
Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow
The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent
vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 …
vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 …
Contentious relationships in phylogenomic studies can be driven by a handful of genes
Phylogenomic studies have resolved countless branches of the tree of life, but remain
strongly contradictory on certain, contentious relationships. Here, we use a maximum …
strongly contradictory on certain, contentious relationships. Here, we use a maximum …
StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates
HA Ogilvie, RR Bouckaert… - Molecular biology and …, 2017 - academic.oup.com
Fully Bayesian multispecies coalescent (MSC) methods like* BEAST estimate species trees
from multiple sequence alignments. Today thousands of genes can be sequenced for a …
from multiple sequence alignments. Today thousands of genes can be sequenced for a …
Six reference-quality genomes reveal evolution of bat adaptations
Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity
and unique immunity. High-quality genomes are crucial for understanding the molecular …
and unique immunity. High-quality genomes are crucial for understanding the molecular …
Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology
One of the lasting controversies in phylogenetic inference is the degree to which specific
evolutionary models should influence the choice of methods. Model‐based approaches to …
evolutionary models should influence the choice of methods. Model‐based approaches to …