Outlier SNPs enable food traceability of the southern rock lobster, Jasus edwardsii

Abstract

Recent advances in next generation sequencing have enhanced the resolution of population genetic studies of non-model organisms through increased marker generation and sample throughput. Using double digest restriction siteassociated DNA sequencing (ddRADseq), we investigated the population structure of the commercially important southern rock lobster, Jasus edwardsii, in Australia and New Zealand with the aim of identifying a panel of SNP markers that could be used to trace country of origin. Four ddRADseq libraries comprising a total of 91 individuals were sequenced on the Illumina MiSeq platform and demultiplexed reads were used to create a reference catalog of loci. Individual reads were then mapped to the reference catalog and variant calling was performed. We have characterized two single nucleotide polymorphism (SNP) panels comprised in total of 656 SNPs. The first panel contained 535 neutral SNPs, and the second, 121 outlier SNPs that were characteristic of being putatively under selection. Both neutral and outlier SNP panels showed significant differentiation between the two countries, with the outlier loci demonstrating much larger FST values (FST outlier SNP panel = 0.134, P < 0.0001; FST neutral SNP panel = 0.022, P < 0.0001). Assignment tests performed with the outlier SNP panel allocated 100% of the individuals to country of origin, demonstrating the usefulness of these markers for food traceability of J. edwardsii.

Outlier SNPs detect weak regional structure against a background of genetic homogeneity in the Eastern Rock Lobster, Sagmariasus verreauxi

“…Early population genetic studies, limited to a small number of neutrally evolving genetic markers, often lacked statistical power to detect population divergence (Ouborg et al 1999; Allendorf 2017) characteristic of many marine species (Allendorf et al 2010); reinforcing the assumption of high connectivity between populations in the marine environment. However, with the advent of powerful genomic techniques, large panels of Single Nucleotide Polymorphisms (SNPs) have increased genetic resolution, enabling studies to detect weak, but significant population differentiation within marine species (Benestan et al 2015;Araneda et al 2016;Villacorta-Rath et al 2016).…”

“…The higher genetic divergence detected in these loci is potentially caused by environmental selection, however it should be noted that outlier loci may also be detected due to Type I error or demographic processes, such as range-expansions and pre-or post-zygotic isolation (Bierne et al 2011). Nevertheless, outlier loci are often more powerful than neutral SNPs in delineating genetic structure and reliably assigning individuals to sampling regions in species exhibiting genetic structure (Freamo et al 2011;Milano et al 2014;Araneda et al 2016;Villacorta-Rath et al 2016). Furthermore, if outlier SNPs can be linked to biological function, they may provide useful insight into the ecological drivers of adaptation within their environment.…”

“…Separate management strategies exist for both countries based on the results of an early genetic assessment, which used six mitochondrial regions, indicating separate genetic populations in NSW and NZ (Brasher et al 1992). While S. verreauxi are yet to be assessed with high resolution genetic markers, SNPs recently confirmed a trans-Tasman genetic break in the co-distributed, closely related, commercially important Southern Rock Lobster, Jasus edwardsii (Villacorta-Rath et al 2016). Oceanographic models indicate that trans-Tasman gene flow for both species of lobster is possible due to their long PLDs (Chiswell et al 2003); microsatellite studies have indicated that for J. edwardsii, trans-Tasman gene flow occurs at levels low enough to maintain genetic structure (Thomas and Bell 2013).…”

Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)

“…In this study we used existing ddRADseq sequence databases of two closely related marine lobster species, Jasus edwardsii 15 (N = 42) and Sagmariasus verreauxi (N = 55), to design probes for target enrichment re-sequencing. We then evaluated the efficiency and reproducibility of the target enrichment approach, and determined the practical utility of this method for population genomic studies within all marine spiny lobster species of the genus Jasus in modern (N = 40) and museum collection (N = 39) specimens.…”

SNP discovery in European lobster (Homarus gammarus) using RAD sequencing

“…These advances have also led to the development of small panels of informative SNPs (e.g. Nielsen et al 2012;Villacorta-Rath et al 2016) that are likely to be useful for assessments of genetic structure, population assignment and connectivity. In this study, we used restriction-site associated DNA (RAD) sequencing to isolate and characterise 96 novel SNP markers in H. gammarus.…”