Population Genetics of Sugar Kelp Throughout the Northeastern United States Using Genome-Wide Markers

Abstract

An assessment of genetic diversity of marine populations is critical not only for the understanding and preserving natural biodiversity but also for its commercial potential. As commercial demand rises for marine resources, it is critical to generate baseline information for monitoring wild populations. Furthermore, anthropogenic stressors on the coastal environment, such as warming sea temperatures and overharvesting of wild populations, are leading to the destruction of keystone marine species such as kelps. In this study, we conducted a fine-scale genetic analysis using genome-wide high-density markers on Northwest Atlantic sugar kelp. The population structure for a total of 149 samples from the Gulf of Maine (GOM) and Southern New England (SNE) was investigated using AMOVA, F ST , admixture, and PCoA. Genome-wide association analyses were conducted for six morphological traits, and the extended Lewontin and Krakauer (FLK) test was used to detect selection signatures. Our results indicate that the GOM region is more heterogeneous than SNE. These two regions have large genetic difference (between-location F ST ranged from 0.21 to 0.32) and were separated by Cape Cod, which is known to be the biogeographic barrier for other taxa. We detected one significant SNP (P = 2.03 × 10 −7) associated with stipe length, and 248 SNPs with higher-than-neutral differentiation. The findings of this study provide baseline knowledge on sugar kelp population genetics for future monitoring, managing and potentially restoring wild populations, as well as assisting in selective breeding to improve desirable traits for future commercialization opportunities.

Seascape Genomics of the Sugar Kelp Saccharina latissima along the North Eastern Atlantic Latitudinal Gradient

“…Such overall concordance between SNPs and SSRs, but taking into account the difference in resolutive power between these two types of marker, has been reported in other recent studies of marine and freshwater organisms, including kelp [50], brown trout [74], coral reef-associated fish [75], and pike [73]. The SNP derived H E values that we observed were approximately an order of magnitude lower than those obtained for several western Atlantic S. latissima localities [76]. Whether this difference is due to contrasting demographic histories or different responses of the S. latissima populations on either side of the Atlantic Ocean to environmental change or rather from the different methodologies used to obtain the SNP markers in our study and in [76] is something that should be investigated further.…”

“…The SNP derived H E values that we observed were approximately an order of magnitude lower than those obtained for several western Atlantic S. latissima localities [76]. Whether this difference is due to contrasting demographic histories or different responses of the S. latissima populations on either side of the Atlantic Ocean to environmental change or rather from the different methodologies used to obtain the SNP markers in our study and in [76] is something that should be investigated further.…”

“…The SNP derived H E values that we observed were approximately an order of magnitude lower than those obtained for several western Atlantic S . latissima localities [ 76 ]. Whether this difference is due to contrasting demographic histories or different responses of the S .…”

“…Whether this difference is due to contrasting demographic histories or different responses of the S . latissima populations on either side of the Atlantic Ocean to environmental change or rather from the different methodologies used to obtain the SNP markers in our study and in [ 76 ] is something that should be investigated further.…”

“…Six distinct genetic clusters were delimited, knowledge of which will be helpful for the conservation management of the eastern Atlantic populations of S. latissima as it will allow specific geographic areas containing putatively locally adapted strains to be defined more accurately which is vital for sustainable management of these wild resources for kelp aquaculture. In addition to the recommendation of avoiding the transfer of algae material between disparate genetic clusters and across vast geographic regions because of the potential risks of genetic pollution and/or introduction of foreign pathogens [33,76,112], in the context of spatial and temporal environmental variability, management practices and breeding strategies should also carefully consider the choice of source populations and the selection of varieties suitable for sustainable aquaculture [113]. In this context, the genome-wide outlier scan approach identified several outlier loci that might be involved in differential adaptive responses to the local environmental parameters across our sampling range.…”