No abstract

Prokaryotes demonstrate tremendous variation in gene content, even within individual bacterial clones or lineages. This diversity is made possible by the ability of bacteria to horizontally transfer DNA through a variety of mechanisms, and the extent of such transfer sets them apart from eukaryotes. What has become evident through interrogation of thousands of bacterial genomes is that gene variation is directly related to the ecology of the organism and is driven by continual processes of niche exploration, diversification, and adaptation. Of course, the acquisition of new genes is not necessarily beneficial, resulting in either the removal of that individual through purifying selection or the occurrence of compensatory mutations in the genomic “backbone” (i.e., core genes) that become epistatically linked to the presence accessory genes. There are now numerous examples of relationship between gene variation and niche adaptation. We explore some of those examples here as well as the population genomic footprint left by the dynamics of gene flow, diversification, and adaptation.

Insecticide-resistant Drosophila melanogaster strains represent a resource for the discovery of the underlying molecular mechanisms of cytochrome P450 constitutive over-expression, even if some of these P450s are not directly involved in the resistance phenotype. For example, in select 4,4’-dichlorodiphenyltrichloroethane (DDT) resistant strains the glucocorticoid receptor-like (GR-like) potential transcription factor binding motifs (TFBMs) have previously been shown to be associated with constitutively differentially-expressed cytochrome P450s, Cyp12d1, Cyp6g2 and Cyp9c1. However, insects are not known to have glucocorticoids. The only ortholog to the mammalian glucocorticoid receptor (GR) in D. melanogaster is an estrogen-related receptor (ERR) gene, which has two predicted alternative splice isoforms (ERRa and ERRb). Sequencing of ERRa and ERRb in select DDT susceptible and resistant D. melanogaster strains has revealed a glycine (G) codon insertion which was only observed in the ligand binding domain of ERR from the resistant strains tested (ERR-G). Transgenic flies, expressing the ERRa-G allele, constitutively over-expressed Cyp12d1, Cyp6g2 and Cyp9c1. Only Cyp12d1 and Cyp6g2 were over-expressed in the ERRb-G transgenic flies. Phylogenetic studies show that the G-insertion appeared to be located in a less conserved domain in ERR and this insertion is found in multiple species across the Sophophora subgenera.