G. Achaz

How demography shapes linkage disequilibrium with or without recombination

The paper analyzes how demographic factors influence linkage disequilibrium measures under different recombination scenarios and provides recommendations for their use.

Patterns of diversity under loose genetic draft

The paper studies diversity patterns under loose genetic draft using the RIF model, showing that diversity scales as a power law of population size and genealogies converge to Kingman coalescent despite reduced diversity.

Chance favors the prepared genomes: horizontal transfer shapes the emergence of antibiotic resistance mutations in core genes.

This study shows that horizontal gene transfer influences the likelihood of acquiring antibiotic resistance mutations in core genes of E. coli.

Evo-Scope: Fully automated assessment of correlated evolution on phylogenetic trees

Evo-Scope is a fast, automated pipeline to assess correlated evolution on phylogenetic trees, improving previous tools and analyzing antibiotic resistance mutations in Streptococcus pneumoniae.

Interpreting the pervasive observation of U-shaped Site Frequency Spectra

The paper analyzes site frequency spectra across species and finds U-shaped patterns, suggesting that multiple merger coalescent models better fit the data than the standard neutral model.

Simulation of bacterial populations with SLiM

This paper demonstrates how to simulate bacterial populations using SLiM, a forward-in-time simulator, and validates its results against existing tools and theoretical expectations.

A minimal yet flexible likelihood framework to assess correlated evolution

This paper introduces a likelihood framework to assess correlated evolution between two traits on a phylogenetic tree, showing it performs well with datasets of fewer than 100 species.

Testing for population decline using maximal linkage disequilibrium blocks

The paper introduces a population genomics method to detect recent population decline using maximal linkage disequilibrium blocks to assess species conservation status.

The genomic view of diversification

This paper introduces a new framework for modeling gene and species lineage evolution, showing it better explains gene flow-driven incongruences than traditional species tree models.

The rapid divergence of the Antarctic crinoid species Promachocrinus kerguelensis

This study analyzes genetic data from Antarctic crinoids to test the biodiversity pump hypothesis, finding rapid genetic turnover and cryptic speciation within Promachocrinus kerguelensis.

The quiescent X, the replicative Y and the Autosomes

The paper analyzes mutation spectra in human genomes to show that X chromosomes have more indels than autosomes, which are more than Y chromosomes, linking this to quiescent and replicating cell states.

Coalescent Processes With Skewed Offspring Distributions And Non-Equilibrium Demography

This paper develops a coalescent model that jointly estimates reproductive skew and population history, showing that ignoring demography can bias coalescent inferences and demonstrating its application to Japanese sardine data.

Yeast de novo genes preferentially emerge from divergently transcribed, GC-rich intergenic regions

The paper identifies 703 de novo genes in 15 yeast species and finds they preferentially arise from GC-rich intergenic regions near divergent promoters and recombination hotspots.

Accuracy of demographic inferences from Site Frequency Spectrum: The case of the Yoruba population

The paper assesses the accuracy of demographic inferences from the Site Frequency Spectrum (SFS) in the Yoruba population, finding that simple models outperform flexible ones.