Fig. 3: Phylosymbiosis-like pattern and nucleotide diversity overlap of holobiont members between individuals of C. concentrica.

Illumina metagenomes of microbial cell fractions of individuals CC1-CC4 are used for analysis. a The analysis for phylosymbiosis-like patterns between sponge host genetics and community composition of the sponge host viromes (HiC-linked), the cellular microbiomes, and the viromes of cellular microbial symbionts (HiC-linked). The maximum likelihood tree of the sponge host is inferred from the consensus sequences of sponge ribosomal protein S6e in sponge individuals. The tree scale is shown. The tree is rooted to CC4 as its sequence shows the largest deviation from the others. Branch support value is based on 1000 iterations of ultrafast bootstrapping in IQ-TREE. The community compositions are clustered based on Bray-Curtis dissimilarity using the average method. The information on virus-host links is based on the results of Fig. 2. RF, Robinson-Foulds test (one-sided test). b The analysis for phylosymbiosis-like patterns between the popANI relationships of bacterial symbionts and the community compositions of their viromes. The virome compositions are clustered based on Bray-Curtis dissimilarity using the average method. RF, Robinson-Foulds test (one-sided test). c and d popANIs (c) and SGCs (d) of the sponge host viromes, cellular microbial symbionts, and their viromes between sponge individuals in comparison with the phylogenetic distance of the sponge host. For boxplots, data points of independent samples and the sample sizes are shown. The center lines represent median values. Box limits represent upper and lower quartiles. Whiskers represent 1.5 × interquartile range. Outliers are detected based on chi-squared scores using the R package outliers and are shown as dark red points. e and f Consensus trees of sample clusters based on popANIs (e) and SGCs (f) of cellular microbial symbionts (n = 33). Source data are provided as a Source Data file.