PT  - JOURNAL ARTICLE
AU  - Miyagi, Miriam
AU  - Morrison, Maike
AU  - Kirkpatrick, Mark
TI  - How many ecological niches are defined by the superabundant marine microbe <em>Prochlorococcus?</em>
AID  - 10.1101/2022.11.29.517206
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.11.29.517206
4099  - http://biorxiv.org/content/early/2022/11/29/2022.11.29.517206.short
4100  - http://biorxiv.org/content/early/2022/11/29/2022.11.29.517206.full
AB  - Determining the identities, frequencies, and memberships of ecotypes in Prochlorococcus and other superabundant microbes (SAMs) is essential to studies of their evolution and ecology. This is challenging, however, because the extremely large population sizes of SAMs likely cause violations of foundational assumptions made by standard methods used in molecular evolution and phylogenetics. Here we present a tree-free likelihood method to identify ecotypes, which we define as populations with genome sequences whose high similarity is maintained by purifying selection. We applied the method to 96 genomes of the superabundant marine cyanobacterium Prochlorococcus and find that this sample is comprised of about 24 ecotypes, substantially more than the five major ecotypes that are generally recognized. The method presented here may prove useful with other superabundant microbes.Competing Interest StatementThe authors have declared no competing interest.