Applying the Biological Species Concept to Bacteria

Introgression is not limited to Eukaryotes.

Over the years, I have written several blog posts about species concepts (see for example here and here). I argued that most biologists currently follow the General Lineage Concept or the Evolutionary Species Concept, which both regard species as independently evolving lineages. Laypeople are probably most familiar with the Biological Species Concept (or BSC), defining species as “a group of organisms that can successfully interbreed and produce fertile offspring.” However, this concept can be difficult to apply in certain situations, such when populations are geographically isolated and will never meet. Another common criticism is that the BSC cannot be applied to Bacteria because they do not reproduce sexually. You can imagine my surprise when I came across a recent paper in the journal Genome Biology where researchers applied the BSC to Bacteria:

Some bacteria can engage in gene flow via homologous recombination and this observation has led a growing number of researchers to suggest that bacterial species and speciation might be best defined using the same evolutionary theory developed for sexual organisms; the biological species concept (BSC).

Introgression and Recombination

Awa Diop and her colleagues studied more than 30,000 bacterial genomes. First, they classified these genomes into species by using a cut-off value of 94% genetic similarity in a set of core genes. This arbitrary threshold is commonly applied to delineate bacterial “species”. In this study, however, it mainly allowed the researchers to create a set of “species” for further analyses. To determine whether there has been introgression between these different bacterial “species”, the researchers calculated the ratio between homoplasmic (h) and non-homoplasic (m) alleles. A homoplasmic allele is a genetic variant that is not the result of inheritance from parent to offspring (i.e. vertical inheritance). Instead, such an allele can be the outcome of introgression between bacterial species (i.e. horizontal transfer) or convergent evolution (i.e. bacteria that independently acquire the same mutation). Clonal species – that reproduce asexually – are expected to have few homoplasmic alleles and thus a low h/m ratio. Introgression will result in an increased h/m ratio due to the accumulation of homoplasmic alleles.

In addition, introgression will be accompanied by recombination, the exchange of homologous sections of chromosomes. This process leads to the breakdown of linkage between certain alleles – also known as linkage disequilibrium (LD) – across chromosomes. Clonal species don’t engage in recombination and will thus show no reduction in linkage disequilibrium.

The researchers simulated bacterial genomes without gene flow and compared these patterns – in terms of h/m ratio and LD – with the actual data. These analyses revealed that most bacterial “species” showed signs of introgression and only 2.6% were truly clonal. Some kind of sexual reproduction among Bacteria seems to be more common than we expected.

Genomic analyses pointed to high levels of gene flow (or introgression) between bacterial species. From: Diop et al. (2022).

MEPS

Although the level of introgression among bacterial “species” varied extensively (see figure above), it correlated nicely with sequence similarity. The more similar two species are on a genetic level, the higher the level of introgression uncovered in this study. This pattern can be explained by the observation that homologous recombination requires nearly identical stretches of DNA (also known as MEPS, Minimal Efficient Processing Segments). As genomes diverge, the density of these MEPS decreases and recombination becomes less likely. The relationship reported in this study shows a rapid reduction in introgression between 2% and 10% of sequence divergence. This result explains why an arbitrary threshold to define species of about 95% has been so useful in the past. However, introgression occurred between species that were 90% to 98% divergent. The exact threshold for bacterial species boundaries will thus depend on the study system. There is no silver bullet.

The relationship between sequence identify and level of introgression shows a sharp turn at ca. 90% sequence divergence. From: Diop et al. (2022).

From Bacteria to Birds

You might be wondering why I am covering a paper about bacterial species on a blog dedicated to birds. There are two main reasons: (1) I have a broad interest and don’t want to limit myself to literature on avian hybridization, and (2) you can learn a lot from other study systems. In this case, I noticed an interesting parallel between the arbitrary species threshold in birds (ca. 2% divergence in mitochondrial genes) and in Bacteria (ca. 95% divergence in core genes). These thresholds can be useful as a starting point, but are not always reliable (see for example this blog post). Moreover, this study confirmed a growing consensus among biologists studying speciation: introgression is more common than we previously thought. It doesn’t matter whether we are talking about Bacteria or birds.

References

Diop, A., Torrance, E. L., Stott, C. M., & Bobay, L. M. (2022). Gene flow and introgression are pervasive forces shaping the evolution of bacterial species. Genome Biology23(1), 1-19.

Featured image: Neisseria gonorrhoeae © Dr. Norman Jacobs | Wikimedia Commons

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