Microorganisms from the bacterial and archaeal domains of the tree of life comprise the greatest breadth of biodiversity on earth. Yet the essential evolutionary process of speciation (through which biodiversity is generated) is poorly understood in microbes. At issue is the fundamental question of whether gene flow among individuals of clonally reproducing microorganisms is rapid enough to provide coherence within – and prevent speciation between – coexisting lineages.
Researchers used complete sequencing of microbial genomes to observe speciation in action. They looked at Archaea called Sulfolobus islandicus gathered from a geothermal hot spring from the Mutnovsky Volcano in Kamchatka, Russia, whose physical isolation allows us to pinpoint evolutionary processes to one location. Contrary to the theoretical predictions for microbes, they were able to provide evidence that two novel lineages are in the process of becoming ecologically distinct and evolutionarily independent despite the fact that they recombine. The divergence is not happening uniformly across the genome because certain genomic regions are more prone to become differentiated between species than others. This genomic view of the process of speciation occurring within a single natural microbial population contributes to our understanding of the generation of biodiversity in Archaea and furthers our understanding of speciation across the tree of life.
Patterns of Gene Flow Define Species of Thermophilic Archaea. (2012) PLoS Biol 10(2): e1001265. doi:10.1371/journal.pbio.1001265
Despite a growing appreciation of their vast diversity in nature, mechanisms of speciation are poorly understood in Bacteria and Archaea. Here we use high-throughput genome sequencing to identify ongoing speciation in the thermoacidophilic Archaeon Sulfolobus islandicus. Patterns of homologous gene flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia, demonstrate higher levels of gene flow within than between two persistent, coexisting groups, demonstrating that these microorganisms fit the biological species concept. Furthermore, rates of gene flow between two species are decreasing over time in a manner consistent with incipient speciation. Unlike other microorganisms investigated, we do not observe a relationship between genetic divergence and frequency of recombination along a chromosome, or other physical mechanisms that would reduce gene flow between lineages. Each species has its own genetic island encoding unique physiological functions and a unique growth phenotype that may be indicative of ecological specialization. Genetic differentiation between these coexisting groups occurs in large genomic ”continents,” indicating the topology of genomic divergence during speciation is not uniform and is not associated with a single locus under strong diversifying selection. These data support a model where species do not require physical barriers to gene flow but are maintained by ecological differentiation.