Concordance between phylogenomics and growth in describing cryptic speciation of little tunny (Euthynnus alletteratus, Scombridae)

Abstract The little tunny ( Euthynnus alletteratus, Scombridae) have great economic importance with a large volume of catches. Recently, both the south-eastern and northern stocks were found to be at high and moderate risk of overfishing, respectively. Here we investigated the stock structure of E. alletteratus and the phylogenetic relationships through a combination of genetic, genomic and growth analysis. Genetic data consisted of mtDNA CR sequences that defined 263 haplotypes amongst 633 individuals from nine locations. The genomic data consisted of 37,888 SNPs obtained by sequencing 89 individuals. Growth data was derived from characterizing a total of 466 dorsal fin spines from 207 individuals from Northeast Atlantic and 259 individuals from Tropical Southeast Atlantic. A pronounced genetic discontinuity was detected by genetic (mtDNA CR) and genomic markers (SNPs) concordant with different growth patterns for the northern and tropical individuals. Thus, genetic and biological data support the hypothesis of cryptic speciation of Euthynnus within the Atlantic Ocean, consisting of a Northern subtropical-temperate species and a Tropical species. Further, population differentiation was detected within the two species, with both species containing at least three subpopulations, and revealing a more complex population structure than envisioned before.