RAD genotyping reveals fine‐scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus)

Abstract

Deciphering genetic structure and inferring connectivity in marine species have been challenging due to weak genetic differentiation and limited resolution offered by traditional genotypic methods. The main goal of this study was to assess how a population genomics framework could help delineate the genetic structure of the American lobster (Homarus americanus) throughout much of the species' range and increase the assignment success of individuals to their location of origin. We genotyped 10 156 filtered SNPs using RAD sequencing to delineate genetic structure and perform population assignment for 586 American lobsters collected in 17 locations distributed across a large portion of the species' natural distribution range. Our results revealed the existence of a hierarchical genetic structure, first separating lobsters from the northern and southern part of the range (FCT = 0.0011; P-value = 0.0002) and then revealing a total of 11 genetically distinguishable populations (mean FST = 0.00185; CI: 0.0007-0.0021, P-value < 0.0002), providing strong evidence for weak, albeit fine-scale population structuring within each region. A resampling procedure showed that assignment success was highest with a subset of 3000 SNPs having the highest FST . Applying Anderson's (Molecular Ecology Resources, 2010, 10, 701) method to avoid 'high-grading bias', 94.2% and 80.8% of individuals were correctly assigned to their region and location of origin, respectively. Lastly, we showed that assignment success was positively associated with sample size. These results demonstrate that using a large number of SNPs improves fine-scale population structure delineation and population assignment success in a context of weak genetic structure. We discuss the implications of these findings for the conservation and management of highly connected marine species, particularly regarding the geographic scale of demographic independence.

Genetic discontinuity in two high dispersal marine invertebrates in the northwest Atlantic

“…Broader phylogeographic patterns of subdivision between the Gulf of Maine, eastern Nova Scotia, and the GSL are generally consistent with previous studies of intertidal (Dillon and Manzi 1992;Kelly et al 2006;Baker et al 2008) and subtidal species (Kenchington et al 2006;St-Onge et al 2013;Benestan et al 2015). Although the AMOVA results indicated strong regional differentiation for both species, levels of intraspecific genetic variation differed substantially between the species.…”

“…In addition, samples of C. volutator from DGB clustered with samples from the Gulf of Maine (Einfeldt and Addison 2013), but in our collections from DGB, T. obsoleta was genetically identical to the Bay of Fundy, whereas M. petalum was genetically more similar to samples from eastern Nova Scotia. Population genetic studies in other species also show mixed patterns across this transition zone (e.g., Gartner-Kepkay et al 1980;Dillon and Manzi 1992;Addison and Hart 2004;Evans et al 2004;Kelly et al 2006;Kenchington et al 2006;Jennings et al 2009;So et al 2011;Owen and Rawson 2013;St-Onge et al 2013;Benestan et al 2015;Govindarajan et al 2015), but as these studies only sampled one population in or at the mouth of the bay, they provide little resolution to the boundaries of phylogeographic transition. Although many species of marine invertebrates sampled in the Bay of Fundy appear isolated from populations studied elsewhere, incongruence in the location of the break suggests that the physical boundaries to gene flow across the gyre depend on a variety of factors including both dispersal ability and evolutionary history.…”

RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic

“…Interestingly, genomewide divergence was so prominent that background genomic variation (i.e., neutral SNPs) explained an order of magnitude more of the variation between northern and southern groups than observed in native species in the region (e.g., sea scallop, Van Wyngaarden et al., 2017), and locus‐specific F ST values were an order of magnitude larger across the genome than observed in native species [e.g., American lobster, Homarus americanus , Benestan et al. (2015) or sea scallop]. This work builds directly on previous studies describing the spatial variation of these two invasions by providing enhanced genomic and geographic resolution of the differences.…”

Biogeographic, ontogenetic, and environmental variability in larval behaviour of American lobster Homarus americanus

“…More recent ex panded coverage suggests significantly greater genetic structure (Benestan et al 2015) in Atlantic Canada than previously reported. Given the high abundance of lobsters in some environments and large dispersal potential (e.g.…”