A practical guide to design and assess a phylogenomic study
J Lozano-Fernandez - Genome Biology and Evolution, 2022 - academic.oup.com
Over the last decade, molecular systematics has undergone a change of paradigm as high-
throughput sequencing now makes it possible to reconstruct evolutionary relationships …
throughput sequencing now makes it possible to reconstruct evolutionary relationships …
Estimating phylogenetic trees from genome‐scale data
The heterogeneity of signals in the genomes of diverse organisms poses challenges for
traditional phylogenetic analysis. Phylogenetic methods known as “species tree” methods …
traditional phylogenetic analysis. Phylogenetic methods known as “species tree” methods …
Evolutionary history of Coleoptera revealed by extensive sampling of genes and species
Beetles (Coleoptera) are the most diverse and species-rich group of insects, and a robust,
time-calibrated phylogeny is fundamental to understanding macroevolutionary processes …
time-calibrated phylogeny is fundamental to understanding macroevolutionary processes …
To include or not to include: the impact of gene filtering on species tree estimation methods
With the increasing availability of whole genome data, many species trees are being
constructed from hundreds to thousands of loci. Although concatenation analysis using …
constructed from hundreds to thousands of loci. Although concatenation analysis using …
Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life
Much progress has been achieved in disentangling evolutionary relationships among
species in the tree of life, but some taxonomic groups remain difficult to resolve despite …
species in the tree of life, but some taxonomic groups remain difficult to resolve despite …
Phylogenomic subsampling and the search for phylogenetically reliable loci
N Mongiardino Koch - Molecular biology and evolution, 2021 - academic.oup.com
Phylogenomic subsampling is a procedure by which small sets of loci are selected from
large genome-scale data sets and used for phylogenetic inference. This step is often …
large genome-scale data sets and used for phylogenetic inference. This step is often …
Avoiding missing data biases in phylogenomic inference: an empirical study in the landfowl (Aves: Galliformes)
Production of massive DNA sequence data sets is transforming phylogenetic inference, but
best practices for analyzing such data sets are not well established. One uncertainty is …
best practices for analyzing such data sets are not well established. One uncertainty is …
Phylogenomic interrogation of Arachnida reveals systemic conflicts in phylogenetic signal
PP Sharma, ST Kaluziak… - Molecular biology …, 2014 - academic.oup.com
Chelicerata represents one of the oldest groups of arthropods, with a fossil record extending
to the Cambrian, and is sister group to the remaining extant arthropods, the mandibulates …
to the Cambrian, and is sister group to the remaining extant arthropods, the mandibulates …
Analysis of a rapid evolutionary radiation using ultraconserved elements: evidence for a bias in some multispecies coalescent methods
Rapid evolutionary radiations are expected to require large amounts of sequence data to
resolve. To resolve these types of relationships many systematists believe that it will be …
resolve. To resolve these types of relationships many systematists believe that it will be …
Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes
Phylogenomic studies using genome-wide datasets are quickly becoming the state of the art
for systematics and comparative studies, but in many cases, they result in strongly supported …
for systematics and comparative studies, but in many cases, they result in strongly supported …