Genetic structure of Metarhizium species in western USA: Finite populations composed of divergent clonal lineages with limited evidence for recent recombination

Abstract

Globally distributed, soil associated Metarhizium species used in insect biological control are evidently facultatively sexual and obligately outcrossing, yet sexual morphs have not been observed for most species and corroboration that they recombine in nature remains limited. Community-wide genetic diversity of Metarhizium species among 480 soil isolates from 14 states of western USA was investigated to assess the contributions of clonality and recombination in determining each species’ population structure. Seven species, varying greater than 100-fold in relative abundance, were identified by phylogenetic analysis of 5′ EF1-α (5TEF), including M. robertsii (n = 372), M. guizhouense (n = 37), M. brunneum (n = 37), M. lepidiotae (n = 14), M. pemphigi (n = 11), M. anisopliae (n = 7) and M. pingshaense (n = 2). Analyses of composite multilocus genotypes integrating 5TEF sequences, multilocus microsatellites and mating type idiomorphs conducted on a subset of 239 isolates revealed that all species populations display pronounced clonal structure. Following clone-correction procedures to remove redundant clonal genotypes and collapse clonal lineages, each species’ population sample was determined to be composed of a dozen or fewer genetically unique individuals. Thus, the Metarhizium community inhabiting western USA is conservatively estimated to comprise as few as 34 distinct genetic individuals, with a single, geographically ubiquitous clonal lineage of M. robertsii constituting 45% of total isolates. M. robertsii was the only population determined to be in linkage equilibrium. However, the high proportion of private alleles differentiating most M. robertsii clonal lineages argues against contemporary panmixia, thus the recombination signal detected may be historical. Nevertheless, within M. robertsii, M. brunneum and M. guizhouense there are closely related genotypes of opposite mating type, which suggests that if recombination is contemporary, it likely occurs between closely related individuals. The restricted number of genetic individuals observed throughout western North American Metarhizium species may signify that these represent peripheral populations descended from limited numbers of founders among which there has been little recombination relative to the extent of clone expansion and within-clone genetic divergence.