Origins and evolution of extreme life span in Pacific Ocean rockfishes

Abstract

Pacific Ocean rockfishes (genus Sebastes) exhibit extreme variation in life span, with some species being among the most long-lived extant vertebrates. We de novo assembled the genomes of 88 rockfish species and from these identified repeated signatures of positive selection in DNA repair pathways in long-lived taxa and 137 longevity-associated genes with direct effects on life span through insulin signaling and with pleiotropic effects through size and environmental adaptations. A genome-wide screen of structural variation reveals copy number expansions in the immune modulatory butyrophilin gene family in long-lived species. The evolution of different rockfish life histories is coupled to genetic diversity and reshapes the mutational spectrum driving segregating CpG→TpG variants in long-lived species. These analyses highlight the genetic innovations that underlie life history trait adaptations and, in turn, how they shape genomic diversity.

Figure 1 -. Genome assemblies and relationships among rockfish species:

A) Ultrametric tree of the rockfish species sequenced in this study and their associated maximum lifespans along with representative images (node timing confidence intervals in light blue) created using IQ-tree, ASTRAL and BPPR. Asterisks indicate individuals for which long-read sequencing-based genomes were assembled. B) The density of rockfish species (heatmap colors) throughout the Pacific Ocean. C) Genome assembly statistics for 81 species, blue and pink represent N(x)-contig lengths while orange indicate N(x) scaffold lengths.

Figure 2 –. Genetic underpinnings of lifespan adaptations:

A) Distribution of pathway enrichment P-values for genes under positive selection in short- and long-lived species. B) Schematics of the 16 DNA replication/repair/maintenance genes exhibiting positive selection in long-lived rockfish. Domain structure (bottom), grey lines indicate putative functional consequence of rockfish amino acid compared to human (PROVEAN score). Red and green bars indicate mutations distinct from all non-long-lived taxa colored by SIFT score - Tolerated (green) / Damaging (red). C) Schematic representation of relative evolutionary rate test and D) P-value distribution of genes from relative evolutionary rate test (RERconverge) of correlation between evolutionary rate and individual traits. Lifespan and the individual components of a predictive linear model of lifespan (E) are used as traits. Gene names are highlighted for the top 12 genes associated with the linear model residual as a trait in addition to four other significant gene candidates previously associated with aging (full gene list in Table S14). E) Linear regression model between maximum lifespan and predicted lifespan based on body size and depth for different species. F) Proportion of variation in lifespan explained by size, depth, and the residual from the linear model. G) Relative evolutionary rates of six genes involved in glucose, insulin, and nutrient signaling four of which have been associated with aging in other taxa (Table S14). H) Ternary plot of 91 lifespan associated genes plotted as a function of the relative importance along linear model axes with dotted line at 50% (inset with gene labels) and heatmaps of pathway enrichment along axes (I).

Figure 3 –. Lifespan associated butyrophilin gene duplications:

A) Miami plot of proportion of 100bp regions with significant phylogenetic least squares linear model (PGLS) correlations between read-depth inferred copy number and lifespan (10kb windows) across the S. aleutianus reference genome. B) Manhattan plot of ~250kb chromosome 1 butyrophilin locus and copy number association in C. Butyrophilin genes shown in orange. D) Protein structural organization of BTN and BTNL gene family members. E) Genome structure of the butyrophilin locus in the S. aleutianus genome assembly. Segmental duplications are highlighted above a self-alignment of the locus to show the underlying duplication architecture with genes below. F) Karyotypes of chromosomes 1 and 22 in S. aleutianus (color indicates gene-density) highlighting the two butyrophilin gene family clusters in Sebastes species.

Figure 4 -. Life history transitions are associated with patterns of diversity:

A) Nucleotide diversity across 88 different species. B) MSMC based estimates of effective population sizes grouped by lifespan quartile over the last ~10⁶ generations and averaged N_e grouped by lifespan quartile in C or grouped by size quartile in D. Box and whisker plots indicate the median and interquartile range (IQR) with tails at the min and maximum values within 1.5*IQR. P-values from PGLS linear model.

Figure 5 –. Shifts in life history traits reshape the mutational spectrum of segregating genetic variation:

A) Survival curves for 34 rockfish species. Humans, shown for comparison, exhibit similar maximum lifespans to many rockfish species but different survival curves (Type I versus Type III survival). B) Rockfish fecundity (births per season) plotted as a function of age. C) Reproductive value plotted as a function of age. D) Generation times estimated from survival and fecundity plotted as a function of lifespan. E) Association of segregating single nucleotide variant mutation types with lifespan across all trinucleotide contexts. Asterisks indicate age-associated mutational profiles significant after multiple testing correction (q<0.05). F) The proportion of segregating CpG->TpG mutations as a function of maximum lifespan.