Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset

KP Hendriks, C Kiefer, IA Al-Shehbaz, CD Bailey… - Current biology, 2023 - cell.com
The mustard family (Brassicaceae) is a scientifically and economically important family,
containing the model plant Arabidopsis thaliana and numerous crop species that feed …

Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria

D Megrian, N Taib, AL Jaffe, JF Banfield… - Nature Microbiology, 2022 - nature.com
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 …

Diversity and compositional changes in the gut microbiota of wild and captive vertebrates: a meta-analysis

A Alberdi, G Martin Bideguren, O Aizpurua - Scientific Reports, 2021 - nature.com
The gut microbiota is recognised as an essential asset for the normal functioning of animal
biology. When wild animals are moved into captivity, the modified environmental pressures …

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution

TL Kaufmann, M Petkovic, TBK Watkins, EC Colliver… - Genome biology, 2022 - Springer
Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome
doubling (WGD) play key roles in cancer evolution and provide information for the complex …

Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis

O Xie, JM Morris, AJ Hayes, RJ Towers… - Nature …, 2024 - nature.com
Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of human
infection with invasive disease incidence and clinical manifestations comparable to the …

Erosion of heterogeneous rock drives diversification of Appalachian fishes

MF Stokes, D Kim, SF Gallen, E Benavides, BP Keck… - Science, 2023 - science.org
The high levels of biodiversity supported by mountains suggest a possible link between
geologic processes and biological evolution. Freshwater biodiversity is high not only in …

Phosphonate production by marine microbes: exploring new sources and potential function

M Acker, SL Hogle, PM Berube… - Proceedings of the …, 2022 - National Acad Sciences
Phosphonates are organophosphorus metabolites with a characteristic CP bond. They are
ubiquitous in the marine environment, their degradation broadly supports ecosystem …

Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy

Y Bussi, R Kapon, Z Reich - PloS one, 2021 - journals.plos.org
Information theoretic approaches are ubiquitous and effective in a wide variety of
bioinformatics applications. In comparative genomics, alignment-free methods, based on …

Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance

BT Smith, J Merwin, KL Provost, G Thom… - Systematic …, 2023 - academic.oup.com
Gene tree discordance is expected in phylogenomic trees and biological processes are
often invoked to explain it. However, heterogeneous levels of phylogenetic signal among …

Handling logical character dependency in phylogenetic inference: extensive performance testing of assumptions and solutions using simulated and empirical data

TR Simões, OV Vernygora, BAS de Medeiros… - Systematic …, 2023 - academic.oup.com
Logical character dependency is a major conceptual and methodological problem in
phylogenetic inference of morphological data sets, as it violates the assumption of character …