File:Fmicb-03-00213-a006 (14237654457).jpg

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Source: Front. Microbiol., 19 June 2012 | doi:10.3389/fmicb.2012.00213 Diversity and distribution of marine Synechococcus: multiple gene phylogenies for consensus classification and development of qPCR assays for sensitive measurement of clades in the ocean Nathan A. Ahlgren and Gabrielle Rocap

Figure A6. Phylogenetic tree based on concatenation of four loci: the 16S rDNA gene, the ITS, ntcA, and rpoC1. Tree construction, bootstrap analysis, and taxa and clade labels as the same as described in Figure A1 except that bootstrap values at the nodes were obtained using three methods: (neighbor joining, HKY + i + g model, 100 replicates/neighbor joining, Jukes–Cantor model, 1000 replicates/maximum likelihood, GTRGAMMA model, 1000 replicates). Phylogeny based on 1,129 core genes from strains with sequenced genomes support the division of strains subcluster 5.1 into two groups 5.1A (blue bar) and 5.1B (solid red bar) (Dufresne et al., 2008). The four loci concatenated phylogeny in Figure A6 also supports the grouping of 5.1A strains, including clade XV. Strains in clades VII, CRD1, and XVI cluster with other 5.1B strains in clades V and VI with high bootstrap support, however it is unclear if these additional new strains without sequenced genomes form a single monophyletic cluster with all 5.1B strains (dashed red line).
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Author Phylogeny Figures

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