 Philosophers have paid particular attention to reticulation in the context of microbial genomics, and for good reason (O’Malley et al. 2010 is a notable special edition dedicated to this topic and is a useful resource). These are often framed as challenges to the phylogenetic approach itself, or, in other cases, how and whether the tools of phylogenetics apply to microbial genomics (Martin 1999; Doolittle 1999). The breadth of HGT in microbial systems has also led to challenges to the more conceptual and metaphysical commitments about species and other phylogenetic units (Franklin 2007).