# Global population genomics redefines domestication and clinical diversity in the Aspergillus flavus–oryzae complex

## TL;DR

This study uses global population genomics to explore the evolutionary history and domestication of Aspergillus flavus and A. oryzae, revealing complex relationships and multiple domestication events.

## Contribution

The paper presents the first global genomic analysis of A. flavus and A. oryzae, uncovering multiple domestication events and challenging current species boundaries.

## Key findings

- A. oryzae likely arose from multiple independent domestication events.
- Clinical A. flavus isolates are found across various clades and mosaic groups.
- The study challenges existing species boundaries and provides insights into evolutionary history and pangenomic architecture.

## Abstract

Aspergillus
flavus is a globally important human pathogen and agricultural contaminant, while its domesticated relative A.
oryzae is widely used in food fermentation and biotechnology. Despite their importance, the evolutionary relationship, population structure and domestication history of these fungi remain unresolved. Here, we present the first global population genomic analysis of 639 A.
flavus and A.
oryzae isolates from clinical, environmental and food-fermentation sources across multiple continents. Our analyses reveal a complex evolutionary landscape comprising well-separated clades interspersed with highly admixed mosaic groups and potential evidence for multiple independent domestication events giving rise to A.
oryzae. Clinical A.
flavus isolates are distributed across several clades and mosaic groups, some overlapping with fermentation strains, highlighting an apparent role of domestication and admixture in shaping pathogen diversity. These results challenge current species boundaries and provide a framework for understanding evolutionary history, taxonomy and pangenomic architecture in these fungi, with broad implications for pathogenicity, food safety, biocontrol and metagenomic surveillance.