Figures & data
Figure 3. (a) Maximum likelihood phylogeny combining concatenated coding sequences from mitochondria and chloroplasts. Ultrafast bootstrapping is shown in the support values, only above 90%. (b) Haplotype network for cox1 from Macrocystis pyrifera. Haplotypes were obtained from Macaya et al. (2010) and Durrant, Barrett, Edgar, Coleman, & Burridge (Citation2015), in which each haplotype represented only one sequence. Mutations are shown as hatch marks in connecting lines. Haplotypes are shaded according to geographic origin. (c) Whole-genome alignment built with MAUVE. Locally Collinear Blocks (LCBs; light red) show high similarities between genomes from southern and northern hemisphere individuals. Below LCB, gene synteny of each genome is shown: ribosomal RNA genes in red, coding genes in white and transfer RNA genes in green. Orange blocks in chloroplast genomes indicate repeat regions.
![Figure 3. (a) Maximum likelihood phylogeny combining concatenated coding sequences from mitochondria and chloroplasts. Ultrafast bootstrapping is shown in the support values, only above 90%. (b) Haplotype network for cox1 from Macrocystis pyrifera. Haplotypes were obtained from Macaya et al. (2010) and Durrant, Barrett, Edgar, Coleman, & Burridge (Citation2015), in which each haplotype represented only one sequence. Mutations are shown as hatch marks in connecting lines. Haplotypes are shaded according to geographic origin. (c) Whole-genome alignment built with MAUVE. Locally Collinear Blocks (LCBs; light red) show high similarities between genomes from southern and northern hemisphere individuals. Below LCB, gene synteny of each genome is shown: ribosomal RNA genes in red, coding genes in white and transfer RNA genes in green. Orange blocks in chloroplast genomes indicate repeat regions.](/cms/asset/ceda20d9-1df8-42a6-ae66-f8c5c5c07663/tapy_a_2193619_f0003_oc.jpg)
Figure 4. Genetic variation distribution of chloroplast and mitochondrial coding proteins. (a) uncorrected pairwise divergence, (b) synonymous substitution rate and (c) nonsynonymous substitution rate.
![Figure 4. Genetic variation distribution of chloroplast and mitochondrial coding proteins. (a) uncorrected pairwise divergence, (b) synonymous substitution rate and (c) nonsynonymous substitution rate.](/cms/asset/2db5147d-5922-4976-8c77-9cf96e7d49df/tapy_a_2193619_f0004_b.gif)
Table 1. The top 10 protein genes with the highest nonsynonymous substitution rates in chloroplast and mitochondrial genomes. dN, nonsynonymous substitution rates; dS, synonymous substitution rates.
Supplemental Material
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Download PDF (276.4 KB)Data availability statement
The data that support the findings of this study are openly available in GenBank (https://www.ncbi.nlm.nih.gov/genbank), accession number ON227496 for mitochondrion and ON227495 for chloroplast.