[PDF][PDF] The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis

RAD Castro, S Borrell, S Gagneux - FEMS microbiology reviews, 2021 - academic.oup.com
Tuberculosis (TB) has been responsible for the greatest number of human deaths due to an
infectious disease in general, and due to antimicrobial resistance (AMR) in particular. The …

Sweepstakes reproductive success via pervasive and recurrent selective sweeps

E Árnason, J Koskela, K Halldórsdóttir, B Eldon - Elife, 2023 - elifesciences.org
Highly fecund natural populations characterized by high early mortality abound, yet our
knowledge about their recruitment dynamics is somewhat rudimentary. This knowledge gap …

How does evolution work in superabundant microbes?

DA Filatov, M Kirkpatrick - Trends in Microbiology, 2024 - cell.com
Marine phytoplankton play crucial roles in the Earth's ecological, chemical, and geological
processes. They are responsible for about half of global primary production and drive the …

Interpreting the pervasive observation of U-shaped Site Frequency Spectra

F Freund, E Kerdoncuff, S Matuszewski… - PLoS …, 2023 - journals.plos.org
The standard neutral model of molecular evolution has traditionally been used as the null
model for population genomics. We gathered a collection of 45 genome-wide site frequency …

Simultaneous inference of past demography and selection from the ancestral recombination graph under the beta coalescent

K Korfmann, TPP Sellinger, F Freund… - Peer Community …, 2024 - peercommunityjournal.org
The reproductive mechanism of a species is a key driver of genome evolution. The standard
Wright-Fisher model for the reproduction of individuals in a population assumes that each …

Inference of coalescence times and variant ages using convolutional neural networks

J Nait Saada, Z Tsangalidou, M Stricker… - Molecular Biology …, 2023 - academic.oup.com
Accurate inference of the time to the most recent common ancestor (TMRCA) between pairs
of individuals and of the age of genomic variants is key in several population genetic …

Genealogical structure changes as range expansions transition from pushed to pulled

G Birzu, O Hallatschek… - Proceedings of the …, 2021 - National Acad Sciences
Range expansions accelerate evolution through multiple mechanisms, including gene
surfing and genetic drift. The inference and control of these evolutionary processes …

Population Genomic Evidence for a Repeated Introduction and Rapid Expansion of the Fungal Maize Pathogen Setosphaeria turcica in Europe

M Vidal-Villarejo, F Freund, H Hanekamp… - Genome Biology and …, 2023 - academic.oup.com
Modern agricultural practices, climate change, and globalization foster the rapid spread of
plant pathogens, such as the maize fungal pathogen Setosphaeria turcica, which causes …

Determinants of rapid adaptation in species with large variance in offspring production

K Korfmann, M Temple‐Boyer, T Sellinger… - Molecular …, 2024 - Wiley Online Library
The speed of population adaptation to changing biotic and abiotic environments is
determined by the interaction between genetic drift, positive selection and linkage effects …

How do monomorphic bacteria evolve? The Mycobacterium tuberculosis complex and the awkward population genetics of extreme clonality

C Stritt, S Gagneux - Peer Community Journal, 2023 - peercommunityjournal.org
Exchange of genetic material through sexual reproduction or horizontal gene transfer is
ubiquitous in nature. Among the few outliers that rarely recombine and mainly evolve by de …