RAD sequencing sheds new light on the genetic structure and local adaptation of European scallops and resolves their demographic histories

Abstract

Recent developments in genomics are advancing our understanding of the processes shaping population structure in wild organisms. In particular, reduced representation sequencing has facilitated the generation of dense genetic marker datasets that provide greater power for resolving population structure, investigating the role of selection and reconstructing demographic histories. We therefore used RAD sequencing to study the great scallop Pecten maximus and its sister species P. jacobeus along a latitudinal cline in Europe. Analysis of 219 samples genotyped at 82,439 single nucleotide polymorphisms clearly resolved an Atlantic and a Norwegian group within P. maximus as well as P. jacobeus , in support of previous studies. Fine-scale structure was also detected, including pronounced differences involving Mulroy Bay in Ireland, where scallops are commercially cultured. Furthermore, we identified a suite of 279 environmentally associated loci that resolved a contrasting phylogenetic pattern to the remaining neutral loci, consistent with ecologically mediated divergence. Finally, demographic inference provided support for the two P. maximus groups having diverged during the last glacial maximum and subsequently expanded, whereas P. jacobeus diverged around 95,000 generations ago and experienced less pronounced expansion. Our results provide an integrative perspective on the factors shaping genome-wide differentiation in a commercially important marine invertebrate.

New insights on the population genetic structure of the great scallop (Pecten maximus) in the English Channel, coupling microsatellite data and demogenetic simulations

“…It appears that even in a species with a high potential for larval dispersal and which displays recent divergence times (i.e. since the last glacial maximum; Vendrami et al, 2019), a weak fine‐scale genetic differentiation between west Start Point and the rest of the English Channel can be identified with refined sampling, as performed in the present study. Given the genetic differentiation observed to the west of Start Point, this area should probably be considered as a distinct management unit in the UK management policy.…”

“…At the European scale, a clear genetic structure was reported between P. maximus samples from northern Norway to Galicia, with the Norwegian populations being differentiated from the other Atlantic populations (Morvezen, Charrier, et al, 2016; Vendrami et al, 2019). At the scale of the British Isles, no significant genetic structure has previously been detected, regardless of the genetic markers employed (i.e.…”

“…allozymes, mitochondrial DNA, microsatellite markers, single‐nucleotide polymorphisms; Beaumont, Morvan, Huelvan, Lucas, & Ansell, 1993; Morvezen, Charrier, et al, 2016; Vendrami et al, 2017; Wilding, Beaumont, & Latchford, 1999), apart from in Mulroy Bay (North of Ireland), suggesting that P. maximus forms a single panmictic population. The genetic differentiation of Mulroy Bay could result from restricted gene flow interactions with other populations combined with the effect of a restocking programme in this area (Vendrami et al, 2019). Yet, at least two genetically differentiated groups of populations in the English Channel have been suggested based on microsatellites (Szostek , 2015): one group including fishing grounds from Falmouth Bay to the Sussex coast, and a second group isolating Cornwall and the Bay of Seine from the rest of the English Channel.…”

Fine-Scale Population Genetic Structure and Parapatric Cryptic Species of Kuruma Shrimp (Marsupenaeus japonicus), Along the Northwestern Pacific Coast of China

“…However, a handful of genetic markers is not appropriate for inferring fine-scale population structure and genetic differentiation, especially in cryptic species (Struck et al, 2018;Pedraza-Marrón et al, 2019). Recent rapid developments in nextgeneration sequencing (NGS) have provided many extraordinary tools with which to study population divergence (Davey et al, 2011;Xu et al, 2016;Clucas et al, 2018;Friedline et al, 2019;Rincon-Sandoval et al, 2019;Vendrami et al, 2019). The genotyping-by-sequencing (GBS) technique can rapidly generate considerable numbers of genome-wide genetic markers, which has revolutionized the field of ecological and evolutionary genomics (Elshire et al, 2012;Andrews et al, 2016;Hume et al, 2018).…”

Demographic inference provides insights into the extirpation and ecological dominance of eusocial snapping shrimps

“…Recent studies have also begun modelling comparative demographic processes across multiple taxa simultaneously (20,(27)(28)(29)(30), including eusocial bees (31) and social spiders (14). These and other studies examine relative patterns of Ne change through time, rather than simply comparing absolute estimates at specific time points (32)(33)(34)(35)(36)(37)(38)(39)(40)(41), an approach that would enable us to test alternative demographic scenarios in eusocial lineages. Moreover, the broad use of coalescent-based methods has shown its robustness as a population genetic tool and can accurately select models and estimate parameters using as few as 3-15 individuals and 10,000 -50,000 single nucleotide polymorphism (SNP) loci (42,43).…”