Gradual speciation: Further entangling the tree of life

Abstract

The Tree of Life is a useful framework for providing evolutionary context to the distribution of genotypes and phenotypes among extant lineages. Organisms are placed into hierarchical groups defined by vertical inheritance, thereby allowing one to trace the origin of evolutionary novelty. The utility of the Tree of Life in understanding bacterial evolution has been criticized because pervasive lateral gene transfer confounds interpretation of current gene repertoires; organismal relationships inferred from constituent genes are muddled by the presence of numerous genes with disparate evolutionary histories. Here, I discuss gradual speciation as another stumbling block to the construction of a bacterial Tree of Life. Recombination events between bacterial strains affect only small regions of the chromosome; therefore, different chromosomal regions in sibling species have experienced their last recombination event at different times. Genetic isolation is established in a stepwise fashion over the course of tens of millions of years. During this extended time frame, descendent taxa may be the process of genetic isolation from each other before their parent population has finished the process of gaining genetic isolation from other lineages. As a result, the relationships among sibling species are necessarily ambiguous. This phylogenetic reticulation does not reflect lack of data, or the impact of transfer among extant lineages; rather, it bespeaks the fundamental lack of strict, hierarchical relationships among evolving taxa. As a result, interpretation of character states must balance parsimony with intrinsic phylogenetic ambiguity.