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 …
[HTML][HTML] Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics
In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and
John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the …
John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the …
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 …
A genome-scale phylogeny of the kingdom Fungi
Phylogenomic studies using genome-scale amounts of data have greatly improved
understanding of the tree of life. Despite the diversity, ecological significance, and …
understanding of the tree of life. Despite the diversity, ecological significance, and …
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 …
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
Motivation: The estimation of species phylogenies requires multiple loci, since different loci
can have different trees due to incomplete lineage sorting, modeled by the multi-species …
can have different trees due to incomplete lineage sorting, modeled by the multi-species …
A genomic timescale for placental mammal evolution
The precise pattern and timing of speciation events that gave rise to all living placental
mammals remain controversial. We provide a comprehensive phylogenetic analysis of …
mammals remain controversial. We provide a comprehensive phylogenetic analysis of …
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 …
A species-level phylogeny of extant snakes with description of a new colubrid subfamily and genus
Background With over 3,500 species encompassing a diverse range of morphologies and
ecologies, snakes make up 36% of squamate diversity. Despite several attempts at …
ecologies, snakes make up 36% of squamate diversity. Despite several attempts at …
TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees
Background Sequence data used in reconstructing phylogenetic trees may include various
sources of error. Typically errors are detected at the sequence level, but when missed, the …
sources of error. Typically errors are detected at the sequence level, but when missed, the …