Genomic landscape of the global oak phylogeny
The tree of life is highly reticulate, with the history of population divergence emerging from
populations of gene phylogenies that reflect histories of introgression, lineage sorting and …
populations of gene phylogenies that reflect histories of introgression, lineage sorting and …
Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees
MR Smith - Bioinformatics, 2020 - academic.oup.com
Abstract Motivation The Robinson–Foulds (RF) metric is widely used by biologists, linguists
and chemists to quantify similarity between pairs of phylogenetic trees. The measure tallies …
and chemists to quantify similarity between pairs of phylogenetic trees. The measure tallies …
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria
The division and cell wall (dcw) gene cluster in Bacteria comprises 17 genes encoding key
steps in peptidoglycan synthesis and cytokinesis. To understand the origin and evolution of …
steps in peptidoglycan synthesis and cytokinesis. To understand the origin and evolution of …
Fossils improve phylogenetic analyses of morphological characters
N Mongiardino Koch… - Proceedings of the …, 2021 - royalsocietypublishing.org
Fossils provide our only direct window into evolutionary events in the distant past.
Incorporating them into phylogenetic hypotheses of living clades can help time-calibrate …
Incorporating them into phylogenetic hypotheses of living clades can help time-calibrate …
Tackling rapid radiations with targeted sequencing
In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have
persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large …
persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large …
Integrating full and partial genome sequences to decipher the global spread of canine rabies virus
Despite the rapid growth in viral genome sequencing, statistical methods face challenges in
handling historical viral endemic diseases with large amounts of underutilized partial …
handling historical viral endemic diseases with large amounts of underutilized partial …
Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets
MR Smith - Biology letters, 2019 - royalsocietypublishing.org
Phylogenetic analysis aims to establish the true relationships between taxa. Different
analytical methods, however, can reach different conclusions. In order to establish which …
analytical methods, however, can reach different conclusions. In order to establish which …
A new classification of Carex (Cyperaceae) subgenera supported by a HybSeq backbone phylogenetic tree
T Villaverde, P Jimenez-Mejias… - Botanical Journal of …, 2020 - academic.oup.com
The field of systematics is experiencing a new molecular revolution driven by the increased
availability of high-throughput sequencing technologies. As these techniques become more …
availability of high-throughput sequencing technologies. As these techniques become more …
Robust analysis of phylogenetic tree space
MR Smith - Systematic Biology, 2022 - academic.oup.com
Phylogenetic analyses often produce large numbers of trees. Mapping trees' distribution in
“tree space” can illuminate the behavior and performance of search strategies, reveal …
“tree space” can illuminate the behavior and performance of search strategies, reveal …
Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study on Pseudapis Bees
Summarizing individual gene trees to species phylogenies using two-step coalescent
methods is now a standard strategy in the field of phylogenomics. However, practical …
methods is now a standard strategy in the field of phylogenomics. However, practical …