Many strains of Metarhizium anisopliae have broad host ranges, but others are specialists and adapted to particular hosts. Patterns of gene duplication, divergence, and deletion in three generalist and three specialist strains were investigated by heterologous hybridization of genomic DNA to genes from the generalist strain Ma2575. As expected, major life processes are highly conserved, presumably due to purifying selection. However, up to 7% of Ma2575 genes were highly divergent or absent in specialist strains. Many of these sequences are conserved in other fungal species, suggesting that there has been rapid evolution and loss in specialist Metarhizium genomes. Some poorly hybridizing genes in specialists were functionally coordinated, indicative of reductive evolution. These included several involved in toxin biosynthesis and sugar metabolism in root exudates, suggesting that specialists are losing genes required to live in alternative hosts or as saprophytes. Several components of mobile genetic elements were also highly divergent or lost in specialists. Exceptionally, the genome of the specialist cricket pathogen Ma443 contained extra insertion elements that might play a role in generating evolutionary novelty. This study throws light on the abundance of orphans in genomes, as 15% of orphan sequences were found to be rapidly evolving in the Ma2575 lineage.It is difficult to trace and reconstruct the evolutionary processes of diversification and radiation of species. In particular, genes that contribute to ecological diversification and the nature of the evolutionary forces acting during this process are poorly understood, partly because genes directly involved in ecological attributes are hard to identify (13). This is not the case with fungi, as they have genes encoding secreted products with specific environmental adaptations, e.g., scavenging nutrients and penetrating host barriers. During its pathogenic life cycle the ubiquitous insect pathogen Metarhizium anisopliae secretes a formidable array of hydrolytic enzymes, antimicrobial compounds, and toxins. These properties, plus its experimental tractability, have made M. anisopliae a common research subject and model system for studying pathogenicity and for developing useful products for medicine, agriculture, and biotechnology (33).The phylogeny of the Metarhizium genus has been well characterized (12). It is a largely clonal organism (4), containing subtypes with wide host ranges (e.g., M. anisopliae var. anisopliae Ma2575) and subtypes that, like M. anisopliae var. acridum Ma324 (used for locust control), show specificity for certain locusts, beetles, crickets, homopterans, etc., and are unable to infect other insects (5). While some specialized lineages, such as M. anisopliae var. acridum, are phylogenetically distant from generalist strains, implying evolutionarily conserved host use patterns, closely related strains can also differ greatly in host range and requirements for germination (16,40,42). Evidence that most specialists arose from generalis...