The phylogenomic species concept
Classifying microbes has always been difficult because they are constantly evolving and changing, but nevertheless they have an accepted place on the tree of life. Although modern molecular techniques are of great help to microbial taxonomists, 16S rRNA gene sequencing has limitations when it comes to differentiating between species of bacteria. In this article in Microbiology Today (pdf) Jim Staley proposes an alternative approach – the phylogenomic species concept:
Speciation is the process whereby organisms evolve to form new strains and species. Like speciation in plants and animals, bacterial speciation is driven by ecological and geographical factors. For example, consider the bacteria that have evolved to become pathogens of specific plant and animal species. These pathogenic bacterial species are illustrative products of ecological speciation. Geographic separation in which divergence to form new species is caused by mutation, selection and genetic drift, is common in animals and plants. Evidence for the effect of geographic factors on bacterial speciation has been more difficult to establish. Recently, however, Rachel Whitaker and colleagues showed that Sulfolobus islandicus, a thermoacidophilic archaeon isolated from globally separated hot springs, forms different clades depending on the their location. Strains isolated from hot springs in Iceland differ from those from Yellowstone and Lassen National Parks of North America, and these groups differ from strains isolated from Kamchatka, Russia. This finding indicates that geography also plays a role in bacterial speciation and quite probably a major one, although more research is needed to better understand the importance and commonality of it among bacteria and archaea…
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Tags: Bacteria, Biology, Microbiology, Science
I tend to favor the Ecotype Species Concept. The problem with Genotypic Clusters is that species are thought of as more than just clusters of closely related, similar organisms. Species must retain Fundamental Dynamic Properties: 1. Different species exploit different ecological niches 2. Genetic divergence within species is constrained by forces of cohesion and 3. Different species have different evolutionary fates. So how do bacteria maintain forces of cohesion? Bacteria are part of an extremely large, asexual population where genetic exchange and drift doesn’t constrain diversity significantly. The Ecotype Species Concept is based upon the concept of Periodic Selection:
An adaptive mutation sets into motion a round of natural selection that purges the population of nearly all its diversity at all loci. The adaptive mutant and all its clonal descendants eventually replace the other cells of the population by outcompeting them. Thus, diversity is accumulated for a period of time and then brought to zero after a period of selection.
An Ecotype is defined a set of strains using the same ecological niche, such that an adaptive mutant from within the ecotype outcompetes, to extinction, all other strains of the same ecotype, but can’t drive to extinction strains from other ecotypes.
But, then there is the issue of Permanent Divergence:
If periodic selection continues a new mutant can never escape the diversity purging effects of the selection process.
An adaptive mutant MUST acquire a new locus that allows it to take advantage of a new resource; this allows the new mutant and its clonal descendants to form a separate ecotype
Periodic selection imposes a cap on the phenotypic and sequence divergence within a bacterial ecotype.
As indicated by the PSC, Genotypic clusters correspond to ecotypes: Each ecotype, Ancestral and Mutant, appears as a monophyletic group and as a distinct cluster. Molecular variations are patterned along ecological gradients. In summation, speciation in bacteria only requires ecological divergence and is limited by the rate of mutation.
The major problem then is defining ecological niches and then identifying the adaptive mutants at the genome level. Up to this point I would concede that the PSC and Ecotype Species Concept are fundamentally the same. The largest difference between the two, and the biggest drawback to the PSC is that is relies heavily on the use of MLSA. MLSA only looks at a very small subset of genes and in most instances would miss adaptive mutants. The Ecotype Species Concept is just that . . .a concept. Currently, I don’t believe scientists have the right tools to define Ecotypes. Once we begin to better define ecological niches we may know where to look and what to look at.