Incongruence in the phylogenomics era

JL Steenwyk, Y Li, X Zhou, XX Shen… - Nature Reviews Genetics, 2023 - nature.com
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 …

Methicillin-resistant Staphylococcus aureus: molecular characterization, evolution, and epidemiology

S Lakhundi, K Zhang - Clinical microbiology reviews, 2018 - journals.asm.org
Staphylococcus aureus, a major human pathogen, has a collection of virulence factors and
the ability to acquire resistance to most antibiotics. This ability is further augmented by …

Independent infections of porcine deltacoronavirus among Haitian children

JA Lednicky, MS Tagliamonte, SK White, MA Elbadry… - Nature, 2021 - nature.com
Coronaviruses have caused three major epidemics since 2003, including the ongoing SARS-
CoV-2 pandemic. In each case, the emergence of coronavirus in our species has been …

Evolution and epidemic spread of SARS-CoV-2 in Brazil

DS Candido, IM Claro, JG De Jesus, WM Souza… - Science, 2020 - science.org
Brazil currently has one of the fastest-growing severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) epidemics in the world. Because of limited available data …

Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil

CM Voloch, R da Silva Francisco Jr… - Journal of …, 2021 - journals.asm.org
Almost simultaneously, several studies reported the emergence of novel severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages characterized by distinct …

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

MF Boni, P Lemey, X Jiang, TTY Lam, BW Perry… - Nature …, 2020 - nature.com
There are outstanding evolutionary questions on the recent emergence of human
coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination …

Virome characterization of game animals in China reveals a spectrum of emerging pathogens

WT He, X Hou, J Zhao, J Sun, H He, W Si, J Wang… - Cell, 2022 - cell.com
Game animals are wildlife species traded and consumed as food and are potential
reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic analysis of …

RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets

DP Martin, A Varsani, P Roumagnac, G Botha… - Virus …, 2021 - academic.oup.com
For the past 20 years, the recombination detection program (RDP) project has focused on
the development of a fast, flexible, and easy to use Windows-based recombination analysis …

The numbers of fungi: is the descriptive curve flattening?

KD Hyde, R Jeewon, YJ Chen, CS Bhunjun… - Fungal Diversity, 2020 - Springer
The recent realistic estimate of fungal numbers which used various algorithms was between
2.2 and 3.8 million. There are nearly 100,000 accepted species of Fungi and fungus-like …

Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies

HB Hassler, B Probert, C Moore, E Lawson… - Microbiome, 2022 - Springer
Abstract Background The 16S rRNA gene is used extensively in bacterial phylogenetics, in
species delineation, and now widely in microbiome studies. However, the gene suffers from …