Extended Data Fig. 5: Maximum likelihood phylogenies of cockle mtDNA and CedBTN genomes.
From: Somatic evolution of marine transmissible leukemias in the common cockle, Cerastoderma edule
a, Maximum likelihood cockle mtDNA phylogeny. Midpoint-rooted tree of deconvoluted mtDNA haplotypes, including sample codes for normal (‘N0’) and tumor samples (‘T’; colored by mtDNA lineage). The nine identified mtDNA lineages are labeled. Bootstrap support values (n = 1000 replicates) are shown for all nodes. b, Maximum likelihood CedBTN nuclear phylogeny from genotyped SNVs. Phylogenetic tree inferred from a subset of 833,007 BTN-specific SNVs, including 30,000 randomly selected SNVs from each of the ancestral variant sets (‘A0’, ‘A1’, ‘A2’) and all the non-ancestral (postdivergence) SNVs in each nuclear lineage, which were genotyped across 61 tumor samples. Tips are colored according to mtDNA lineage (where information is available); sample labels are colored according to nuclear CedBTN lineage. Bootstrap support values (n = 1000 replicates) are shown for all nodes. Samples subjected to whole-genome amplification (WGA) are indicated by asterisks. Sample EICE18_910H is a case of co-infection by cells from mtDNA lineages BTN1-HT4 and BTN2-HT2 (Fig. 2e,f).
