Rapid Diversification of Marine Picophytoplankton with Dissimilar Light-Harvesting Structures Inferred from Sequences of Prochlorococcus and Synechococcus (Cyanobacteria) Ena Urbach, 1 David J. Scanlan, 2 Daniel L. Distel, 3 John B. Waterbury, 3 Sallie W. Chisholm 1 1 Ralph M. Parsons Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA 2 Department of Biological Sciences, University of Warwick, Gibbet Hill Rd. Coventry CV4 7AL, United Kingdom 3 Woods Hole Oceanographic Institution, Woods Hole MA 02543, USA Received: 18 January 1997 / Accepted: 18 May 1997 Abstract. Cultured isolates of the unicellular plank- tonic cyanobacteria Prochlorococcus and marine Syn- echococcus belong to a single marine picophytoplankton clade. Within this clade, two deeply branching lineages of Prochlorococcus, two lineages of marine A Synecho- coccus and one lineage of marine B Synechococcus ex- hibit closely spaced divergence points with low bootstrap support. This pattern is consistent with a near- simultaneous diversification of marine lineages with di- vinyl chlorophyll b and phycobilisomes as photosyn- thetic antennae. Inferences from 16S ribosomal RNA sequences including data for 18 marine picophytoplank- ton clade members were congruent with results of psbB and petB and D sequence analyses focusing on five strains of Prochlorococcus and one strain of marine A Synechococcus. Third codon position and intergenic re- gion nucleotide frequencies vary widely among members of the marine picophytoplankton group, suggesting that substitution biases differ among the lineages. Nonethe- less, standard phylogenetic methods and newer algo- rithms insensitive to such biases did not recover different branching patterns within the group, and failed to cluster Prochlorococcus with chloroplasts or other chlorophyll b-containing prokaryotes. Prochlorococcus isolated from surface waters of stratified, oligotrophic ocean provinces predominate in a lineage exhibiting low G + C nucleotide frequencies at highly variable positions. Key words: Prochlorococcus — Synechococcus — Cyanobacteria — Picophytoplankton — Photosynthetic picoplankton — Prochlorophyte — Molecular evolution — Gene clusters Introduction Prochlorococcus and Synechococcus, the dominant pi- cophytoplankton in the world’s open oceans, are unicel- lular cyanobacteria with different photosynthetic pig- ments (Li and Wood 1988; Olson et al. 1990; Campbell et al. 1994). Prochlorococcus uniquely possesses divinyl chlorophylls a and b (8-vinyl chlorophylls a and b, chl a 2 and chl b 2 ), and lacks phycobilisomes observable by transmission electron microscopy (Chisholm et al. 1988, 1992). The Prochlorococcus chlorophyll a/b-binding an- tenna protein is similar to CP43', a Chl a-binding protein induced by iron stress in other cyanobacteria (LaRoche et al. 1996). Synechococcus contains monovinyl chloro- phyll a (chl a 1 ), similar to plastids and most cyanobac- teria, and light harvesting phycobilisomes with numerous polypeptide subunits and covalently bound bilin chromo- phores. Synechococcus phycobilisomes are homologous to structures in rhodophyte plastids, cyanelles, and most cyanobacteria (Bryant 1991). * Present Address: (E.U.), Department of Microbiology, Nash Hall, Oregon State University, Corvallis, OR 97331, USA; (D.L.D.), Bio- chemistry, Microbiology, and Molecular Biology Department, 5735 Hitchner Hall, University of Maine, Orono, ME 04469, USA Correspondence to: E. Urbach J Mol Evol (1998) 46:188–201 © Springer-Verlag New York Inc. 1998