Despite the potential model role of the green algal genus Codium for studies of marine speciation and evolution, there have been dif- ficulties with species delimitation and a molecular phylogenetic framework was lacking. In the present study, 74 evolutionarily significant units (ESUs) are delimited using 227 rbcL exon 1 sequences obtained from specimens collected throughout the genus’ range. Several mor- pho-species were shown to be poorly defined, with some clearly in need of lumping and others containing pseudo-cryptic diversity. A phylogenetic hypothesis of 72 Codium ESUs is inferred from rbcL exon 1 and rps3–rpl16 sequence data using a conventional nucleotide substitution model (GTR + C + I), a codon position model and a covariotide (covarion) model, and the fit of a multitude of substitution models and alignment partitioning strategies to the sequence data is reported. Molecular clock tree rooting was carried out because out- group rooting was probably affected by phylogenetic bias. Several aspects of the evolution of morphological features of Codium are dis- cussed and the inferred phylogenetic hypothesis is used as a framework to study the biogeography of the genus, both at a global scale and within the Indian Ocean.
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