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The Fusarium oxysporum species complex ( FOSC) causes disease in plants and animals, but is also widely dispersed in natural ecosystems without evidence of disease. The present study screened a population representing natural ecosystems across the Australian continent for the putative effector genes pisatin demethylase 1 ( PDA1), pectate lyase ( pelD), secreted gene expression ( SGE1) and secreted in xylem ( SIX). The genes pelD and SGE1 were prevalent in the natural isolates, PDA1 was present at an intermediate level, whereas SIX genes were detected at low levels. Phylogenies of these putative effector genes were compared to the EF-1α species phylogeny to determine the likely modes of gene transmission: vertical gene transfer ( VGT) and horizontal gene transfer ( HGT). There was evidence of both modes of gene transmission within the F. oxysporum isolates. PDA1, pelD and SGE1 were likely to be only vertically inherited, whereas the SIX genes had evidence for both VGT and HGT. The phylogenetic relationships of SIX genes in isolates from natural ecosystems and formae speciales from agro-ecosystems were also established. These findings have important implications for the evolution of effectors in the FOSC. [ABSTRACT FROM AUTHOR]