Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla

Abstract

Any two lineages, no matter how distant they are now, began their divergence as one population splitting into two lineages that could coexist indefinitely. The rate of origin of higher-level taxa is therefore the product of the rate of speciation times the probability that two new species coexist long enough to reach a particular level of divergence. Here I have explored these two parameters of disparification in bacteria. Owing to low recombination rates, sexual isolation is not a necessary milestone of bacterial speciation. Rather, irreversible and indefinite divergence begins with ecological diversification, that is, transmission of a bacterial lineage to a new ecological niche, possibly to a new microhabitat but at least to new resources. Several algorithms use sequence data from a taxon of focus to identify phylogenetic groups likely to bear the dynamic properties of species. Identifying these newly divergent lineages allows us to characterize the genetic bases of speciation, as well as the ecological dimensions upon which new species diverge. Speciation appears to be least frequent when a given lineage has few new resources it can adopt, as exemplified by photoautotrophs, C1 heterotrophs, and obligately intracellular pathogens; speciation is likely most rapid for generalist heterotrophs. The genetic basis of ecological divergence may determine whether ecological divergence is irreversible and whether lineages will diverge indefinitely into the future. Long-term coexistence is most likely when newly divergent lineages utilize at least some resources not shared with the other and when the resources themselves will coexist into the remote future.

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

“…Some species show multiple peaks of divergence for high values of d , consistent with the presence of subspecies [36], ecotypes [53, 54], or other strong forms of population structure. These coarse groupings have been observed previously and are not our primary focus here.…”

Potential Enterotoxicity of Phylogenetically Diverse Bacillus cereus Sensu Lato Soil Isolates from Different Geographical Locations

“…An extensive study on the dynamics of bacterial speciation showed that among individual bacterial species, so-called ecotypes comprising ecologically distinct bacterial populations can occur [35]. In B. cereus s.l., seven thermal ecotypes adapted to different thermal niches were proposed [36], which correlate well with ribosomal protein profiles [37] and the group's phylogeny [22].…”

Subtle biogeochemical regimes in the Indian Ocean revealed by spatial and diel frequency of Prochlorococcus haplotypes

“…Perhaps the best example of a highly diverse and widely distributed microbe is Prochlorococcus , a global marine cyanobacterium with phylogenetic clades that are known to partition the ocean based on light, temperature, and iron, often referred to as “ecotypes” (Moore et al ; Bouman et al ; Johnson et al ; Rusch et al ). The term ecotype is traditionally defined as ecologically and phylogenetically distinct bacterial populations that can coexist indefinitely (Cohan ). Prochlorococcus ecotypes include the low light clades (eLL), the high‐light, low‐temperature clade (eHL‐I); the high‐light, high‐temperature clade (eHL‐II); and, most recently, two high‐light but low‐iron clades (eHL‐III, eHL‐IV) (Johnson et al ; Rusch et al ).…”