Extended Data Fig. 1: The maximum-likelihood phylogenomic tree of 523 high-light (HL) adapted Prochlorococcus genomes (26 isolates’ genomes and 497 high-quality SAGs from HLII, HLI, HLIII/IV), constructed with IQ-TREE based on concatenated single-copy orthologous genes at the amino acid level and rooted with low-light (LL) adapted clade I (LLI) genomes.
From: Prochlorococcus have low global mutation rate and small effective population size
To help show the fine phylogenetic structure within the HLII clade, all distant relatives (LLI, HLIII/IV, HLI and HLVI) were pruned. Solid circles at the nodes indicate the frequency of the group defined by that node greater than 90 out of the 100 bootstrapped replicates. The phylogeny is visualized and annotated with iTOL. From the outer to inner rings: (1) denotes the 15 HLII isolates used in Bobay and Ochman (2018) for defining the species ‘Prochlorococcus marinus’ by ConSpeciFix. (2) denotes the 93 genomes (13 isolates and 80 high quality SAGs) used for Ne estimation by Kashtan et al (2014), among which 80 HLII SAGs were classified into seven backbone subpopulations and are marked with corresponding color strips; (3)-(6) represents the season, water depth, longitude and latitude of the samples they collected, respectively; (7) shows the identity of the SAGs or isolates. Colored stars at the tips of the phylogeny differentiate the strains of distinct sources (that is, ocean, cruise, and station). Strains without the above information are not marked at the tips. The strain P. marinus AS9601 subjected to unbiased global mutation rate determination is highlighted in deep blue. Cells with the genome id highlighted with blue, pink, green, and orange compose the population MC0, MC1, MC4, and MC16, respectively, delineated by PopCOGenT. Other populations delineated by PopCOGenT were highlighted with light yellow, with each consisting of at least three non-redundant genomes (Supplementary Table 3). (8) illustrates the progressive extensions of the four main populations (MC0, MC1, MC4, and MC16) defined by PopCOGenT, with arrows marking the most recent common ancestor of each extension. The purpose of this analysis is to estimate the impact of population delineation on Ne estimates. Both πS and Ne were estimated for the extended groups (left bottom). The ConSpeciFix grouped all 418 HLII members (23 isolates and 395 high-quality SAGs) into one species except 11 strains (marked with purple triangles), which ConSpeciFix inappropriately reported as distantly related relatives to the defined species.
