A Theory-Based Pragmatism for Discovering and Classifying Newly Divergent Species of Bacterial Pathogens

Cohan, Frederick M.; Kopac, Sarah M.

doi:10.1016/b978-0-12-799942-5.00002-0

Cited by 6 publications

(16 citation statements)

References 84 publications

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“…This appears to be happening within agricultural lineages of Rhizobium leguminosarum, where there are five sequence clusters that can each be infected by various symbiosis plasmids that adapt the bacteria to either vetch or clover (133). While these clusters have no known physiological features that would explain their coexistence, they appear to differ in their propensities to be infected by the various symbiosis plasmids (52). Differences in association between plasmid adaptations and bacterial sequence clusters cause the clusters to differ dramatically in the plants they infect.…”

Section: The Genetic Basis Of Early Diversificationmentioning

confidence: 98%

“…When we see a particular microbe taxon, e.g., rabies virus, infecting a huge diversity of bat species, the established taxonomy does not make clear whether we have a generalist virus that can infect dozens of host species or whether there are many specialist viruses that each primarily infect one host lineage. Streicker's work shows the latter, and implores us to fine-tune our systematics to accommodate rapid diversification of pathogens (52).…”

Section: Resource Differences Among Pathogensmentioning

confidence: 99%

“…This is not a bad approximation for animal and plant species, but it is not so useful for bacterial speciology. A recognized bacterial taxon is typically already extremely diverse in physiology, genome content, and ecology, and contains multiple lineages that each hold the species-like properties we have discussed (52)(53)(54)(55)(56).…”

Section: The Focal Species Of Bacterial Speciologymentioning

confidence: 99%

“…The problem is that while the classification scheme of bacterial systematics has focused on finding species that are significantly different from one another in DNA sequence identity, genome content, and physiology (57), the classification is not aimed to ensure that each individual species is homogeneous in any characteristic (52,54,55,58). To pick on a particularly notable example, we would not learn much about speciation by studying the divergence between the closely related Escherichia coli and Escherichia fergusonii species taxa, as lineages within E. coli are already hugely diversified.…”

Section: The Focal Species Of Bacterial Speciologymentioning

confidence: 99%

“…The different styles of dashed lines within ecotype 1 refer to different ephemeral ecotypes; note that only one of these lineages persists to the present. The different weights of solid lines represent different ephemeral ecotypes within ecotype 2 (52). Used with permission from Elsevier.…”

Section: To Identify the Most Newly Divergent Ecotypesmentioning

confidence: 99%

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

Cohan

2017

Microbiol Spectr

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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.

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Section: The Genetic Basis Of Early Diversificationmentioning

confidence: 98%

Section: Resource Differences Among Pathogensmentioning

confidence: 99%

Section: The Focal Species Of Bacterial Speciologymentioning

confidence: 99%

Section: The Focal Species Of Bacterial Speciologymentioning

confidence: 99%

Section: To Identify the Most Newly Divergent Ecotypesmentioning

confidence: 99%

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

Cohan

2017

Microbiol Spectr

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Unlocking the Genomic Taxonomy of the Prochlorococcus Collective

et al. 2020

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Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera: Prochlorococcus, Eurycolium, Prolificoccus, Thaumococcus and Riococcus. The novel genera have distinct genomic and ecological attributes.

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Systematics: The Cohesive Nature of Bacterial Species Taxa

Cohan

2019

Current Biology

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A survey of bacterial genomes suggests that the diversity within recognized species is constrained by a force of cohesion. However, recognized bacterial species do not adhere to another species-like property-that of being the newest lineages that can coexist indefinitely.Are bacterial species real? Species, and indeed taxa at all levels, are real in that they represent clusters of similar organisms that are separated by gaps.That is to say, the gaps between taxa represent intermediate organisms that we can imagine but don't actually exist. This cluster-and-gap pattern emerges inevitably from the genealogical continuity of all organisms, in which some lineages have succeeded to the present whereas others have gone extinct, yielding gaps in

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A Theory-Based Pragmatism for Discovering and Classifying Newly Divergent Species of Bacterial Pathogens

Cited by 6 publications

References 84 publications

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

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

Unlocking the Genomic Taxonomy of the Prochlorococcus Collective

Systematics: The Cohesive Nature of Bacterial Species Taxa

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