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 …
[HTML][HTML] Tightening the requirements for species diagnoses would help integrate DNA-based descriptions in taxonomic practice
FE Rheindt, P Bouchard, RL Pyle… - PLoS …, 2023 - journals.plos.org
Modern advances in DNA sequencing hold the promise of facilitating descriptions of new
organisms at ever finer precision but have come with challenges as the major Codes of …
organisms at ever finer precision but have come with challenges as the major Codes of …
Integrating gene annotation with orthology inference at scale
Annotating coding genes and inferring orthologs are two classical challenges in genomics
and evolutionary biology that have traditionally been approached separately, limiting …
and evolutionary biology that have traditionally been approached separately, limiting …
Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance
Gene tree discordance is expected in phylogenomic trees and biological processes are
often invoked to explain it. However, heterogeneous levels of phylogenetic signal among …
often invoked to explain it. However, heterogeneous levels of phylogenetic signal among …
Redefining possible: combining phylogenomic and supersparse data in frogs
The data available for reconstructing molecular phylogenies have become wildly disparate.
Phylogenomic studies can generate data for thousands of genetic markers for dozens of …
Phylogenomic studies can generate data for thousands of genetic markers for dozens of …
PhyloAcc-GT: A Bayesian method for inferring patterns of substitution rate shifts on targeted lineages accounting for gene tree discordance
An important goal of evolutionary genomics is to identify genomic regions whose substitution
rates differ among lineages. For example, genomic regions experiencing accelerated …
rates differ among lineages. For example, genomic regions experiencing accelerated …
[HTML][HTML] Phylogenetics and the Cenozoic radiation of lampreys
CD Brownstein, TJ Near - Current Biology, 2023 - cell.com
The development of a movable jaw is one of the most important transitions in the
evolutionary history of animals. 1 Jawed vertebrates rapidly diversified after appearing …
evolutionary history of animals. 1 Jawed vertebrates rapidly diversified after appearing …
Fourth report on chicken genes and chromosomes 2022
The chicken continues to hold its position as a leading model organism within many areas of
research, as well as being a major source of protein for human consumption. The First …
research, as well as being a major source of protein for human consumption. The First …
Exon-based phylogenomics and the relationships of African cichlid fishes: tackling the challenges of reconstructing phylogenies with repeated rapid radiations
African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates,
and their propensity for repeated rapid radiation has made them a celebrated model system …
and their propensity for repeated rapid radiation has made them a celebrated model system …
Convergent genomic signatures of local adaptation across a continental-scale environmental gradient
LR Moreira, BT Smith - Science advances, 2023 - science.org
Convergent local adaptation offers a glimpse into the role of constraint and stochasticity in
adaptive evolution, in particular the extent to which similar genetic mechanisms drive …
adaptive evolution, in particular the extent to which similar genetic mechanisms drive …