Phylotranscriptomic Insights into the Diversification of EndothermicThunnusTunas

Abstract

Birds, mammals, and certain fishes, including tunas, opahs and lamnid sharks, are endothermic, conserving internally generated, metabolic heat to maintain body or tissue temperatures above that of the environment. Bluefin tunas are commercially important fishes worldwide, and some populations are threatened. They are renowned for their endothermy, maintaining elevated temperatures of the oxidative locomotor muscle, viscera, brain and eyes, and occupying cold, productive high-latitude waters. Less cold-tolerant tunas, such as yellowfin tuna, by contrast, remain in warm-temperate to tropical waters year-round, reproducing more rapidly than most temperate bluefin tuna populations, providing resiliency in the face of large-scale industrial fisheries. Despite the importance of these traits to not only fisheries but also habitat utilization and responses to climate change, little is known of the genetic processes underlying the diversification of tunas. In collecting and analyzing sequence data across 29,556 genes, we found that parallel selection on standing genetic variation is associated with the evolution of endothermy in bluefin tunas. This includes two shared substitutions in genes encoding glycerol-3 phosphate dehydrogenase, an enzyme that contributes to thermogenesis in bumblebees and mammals, as well as four genes involved in the Krebs cycle, oxidative phosphorylation, β-oxidation, and superoxide removal. Using phylogenetic techniques, we further illustrate that the eight Thunnus species are genetically distinct, but found evidence of mitochondrial genome introgression across two species. Phylogeny-based metrics highlight conservation needs for some of these species.

Skeletal muscle and cardiac transcriptomics of a regionally endothermic fish, the Pacific bluefin tuna, Thunnus orientalis

“…Raw reads were published previously in a sister study [56] (BioProject PRJNA495053; Table 1). Between 20 and 27 million paired-end reads were retained after trimming for adapter sequences and low-quality bases for each sample, of which 90.5-98.3% pseudo-aligned to the reference Pacific bluefin tuna transcriptome (Table 1) [56]. This read mapping clustered 48,648 transcripts of the reference transcriptome into 31,610 genes.…”

“…Candidate genes were identified by hypothesised function relating to either to SR or sarcolemmal membrane Ca 2+ cycling or thermogenesis and endothermy, according to previous studies of regionally endothermic fish [56][57][58] or mammals and birds (see Methods). The expression of many of these genes varied by tissue type (Table S1).…”

“…Tissue-specific isoform expression of these genes was also apparent in the muscle samples, with different RYR and SERCA isoforms having higher expression in either the red or white muscle compared to the other (Table S1). None of the candidate genes previously associated with endothermy in tuna [56,57] were differentially expressed in deep red or white muscle compared to superficial red or white muscle, although many isoforms showed tissuespecific expression (Table S1). Myoglobin had higher expression in the red muscle compared to the white muscle, and in the ventricle compared to the atrium, but not in either of the deep versus superficial red or white muscle comparisons.…”

“…All animals were euthanised by pithing, in accordance with protocols from Stanford University. These samples were utilised in a recent phylogenetic study of Thunnus tunas, where RNA extraction and sequencing protocols are outlined [56] (NCBI BioProject 495,053; see Table 1 for BioSample accession numbers of each sample). For two of the individuals (P1 and P2; Table 1), tissue samples were taken from warm, deep red and white muscle at the deepest point the muscle inserts near the centre of the body, superficial red and white muscle were also extracted under the skin near the surface of body.…”

“…Raw reads were pseudo-aligned against a reference Pacific bluefin tuna transcriptome [56] (available from NCBI GenBank BioProject 495,053; GIUO00000000l; version GIUO01000000), using Salmon (v0.8.2) [79] and 200 bootstraps, correcting for sequence-specific bias and GC bias and outputting equivalence class counts. These equivalence class counts were then used to cluster the reference transcriptome into genes, according to shared reads and expression, as well as quantify read counts for each cluster using CORSET (v1.0.7) [80].…”