Genomic DNA variation confirmed Seriola lalandi comprises three different populations in the Pacific, but with recent divergence

H K A Premachandra,Wayne O’Connor,Celine H Frère,Ido Bar,Nguyen Hong Nguyen,Wayne Knibb,Stewart Fielder,Adam Miller,Yutaka Takeuchi,Fabiola Lafarga-De La Cruz

doi:10.1038/s41598-017-07419-x

Abstract

Captive breeding programs and aquaculture production have commenced worldwide for the globally distributed yellowtail kingfish (Seriola lalandi), and captive bred fingerlings are being shipped from the Southern Hemisphere to be farmed in the Northern Hemisphere. It was recently proposed that Pacific S. lalandi comprise at least three distinct species that diverged more than 2 million years ago. Here, we tested the hypothesis of different “species” in the Pacific using novel genomic data (namely single nucleotide polymorphisms and diversity array technology markers), as well as mtDNA and DNA microsatellite variation. These new data support the hypothesis of population subdivision between the Northeast Pacific, Northwest Pacific and South Pacific, and genetic divergence indicates restriction to the gene flow between hemispheres. However, our estimates of maximum mtDNA and nuclear DNA divergences of 2.43% and 0.67%, respectively, were within the ranges more commonly observed for populations within species than species within genera. Accordingly our data support the more traditional view that S. lalandi in the Pacific comprises three distinct populations rather than the subdivisions into several species.

Highlights

Commercial aquaculture of yellowtail kingfish (Seriola lalandi Valenciennes, 1833, Carangidae) has recently commenced around the world
Analysis of the mitochondrial DNA (mtDNA) cytochrome oxidase subunit I (COI) fragments sequenced in this study identified 15 haplotypes containing a total of 28 polymorphic sites (GenBank accession numbers: MF167270 – MF167284; Table 1)
One haplotypes were shared between South Pacific locations (Chile, New South Wales: NSW and South Australia: SA); two haplotypes were shared between USA and Mexico (Fig. 1)

Summary

Introduction

Commercial aquaculture of yellowtail kingfish (Seriola lalandi Valenciennes, 1833, Carangidae) has recently commenced around the world. The use of DNA microsatellite data has been challenged for genetic analyses on the grounds of its extremely high mutation rate, size homoplasy, irregularities in mutation process and degradation over time[28, 29]; it is questionable how well evolutionary rates for DNA microsatellite sequences reflect those across the whole genome[30] Likewise, it is of concern how well just a few nuclear genes reflect whole genome evolution and divergence due to the possibility of locus specific anomalous evolutionary rates[31, 32]. It is of concern how well just a few nuclear genes reflect whole genome evolution and divergence due to the possibility of locus specific anomalous evolutionary rates[31, 32] To address these concerns arising from the use of traditional markers to resolve phylogenetics, we carried out partial genome sequencing of S. lalandi from different Pacific regions to reassess the genetic structure of Pacific S. lalandi populations. This allowed comparison of diversity estimates obtained by traditional methods (mtDNA sequences and DNA microsatellite alleles from new data of this report and previously published mtDNA data) with new estimates, provided for the first time, from partial genomic sequencing

Methods

Results

Conclusion