Asymmetric oceanographic processes mediate connectivity and population genetic structure, as revealed by RADseq, in a highly dispersive marine invertebrate (Parastichopus californicus)

Abstract

Marine populations are typically characterized by weak genetic differentiation due to the potential for long-distance dispersal favouring high levels of gene flow. However, strong directional advection of water masses or retentive hydrodynamic forces can influence the degree of genetic exchange among marine populations. To determine the oceanographic drivers of genetic structure in a highly dispersive marine invertebrate, the giant California sea cucumber (Parastichopus californicus), we first tested for the presence of genetic discontinuities along the coast of North America in the northeastern Pacific Ocean. Then, we tested two hypotheses regarding spatial processes influencing population structure: (i) isolation by distance (IBD: genetic structure is explained by geographic distance) and (ii) isolation by resistance (IBR: genetic structure is driven by ocean circulation). Using RADseq, we genotyped 717 individuals from 24 sampling locations across 2,719 neutral SNPs to assess the degree of population differentiation and integrated estimates of genetic variation with inferred connectivity probabilities from a biophysical model of larval dispersal mediated by ocean currents. We identified two clusters separating north and south regions, as well as significant, albeit weak, substructure within regions (F = 0.002, p = .001). After modelling the asymmetric nature of ocean currents, we demonstrated that local oceanography (IBR) was a better predictor of genetic variation (R = .49) than geographic distance (IBD) (R = .18), and directional processes played an important role in shaping fine-scale structure. Our study contributes to the growing body of literature identifying significant population structure in marine systems and has important implications for the spatial management of P. californicus and other exploited marine species.

Detection of environmental and morphological adaptation despite high landscape genetic connectivity in a pest grasshopper (Phaulacridium vittatum)

“…Analyses to detect selection were conducted on the full SNP data set, which included all SNPs per RAD tag but excluded tightly linked loci identified using plink version 1.9 (Purcell et al, ; with one marker from each pair excluded with R 2 > 0.8; following Xuereb, Benestan, et al, ). We used two F ST outlier detection methods to assess congruence across approaches: (a) outflank (Whitlock & Lotterhos, ) and (b) bayescan 2.1 (Foll & Gaggiotti, ).…”

Comparing Pool‐seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster (Homarus americanus) as a case study

“…Uncovering population genomic structure of species characterized by large effective population size and/or high migration rate may be challenging since this often translates into a lack or very weak genetic differentiation and spatial genomic structure (Gagnaire et al, 2015;Holliday et al, 2017;Neale & Kremer, 2011;Waples, 1998). Recent studies suggested that increasing the number of samples and markers genotyped can improve the detection of subtle genetic structure in nonmodel species such as the polar bear (Viengkone et al, 2016), the candlefish (Candy et al, 2015), the American lobster (Benestan et al, 2015), the silvery lightfish (Rodriguez-Ezpeleta, Álvarez, & Irigoien, 2017), the Tasmanian devil (Hendricks et al, 2017), or the sea cucumber (Xuereb et al, 2018).…”

East is East and West is West: Population genomics and hierarchical analyses reveal genetic structure and adaptation footprints in the keystone species Paracentrotus lividus (Echinoidea)

“…Furthermore, the analysis of outlier loci has revealed additional levels of structuring in many cases (Milano et al, ; Vandamme et al, ) showing trade‐offs between selection and dispersal (Carreras et al, ). This additional improvement of population genomics, when compared to conventional population genetics, is especially relevant in marine organisms, as they include widely dispersing species and feature large population sizes rendering genetic differentiation across populations difficult to detect (Lamichhaney et al, ; Xuereb et al, ). For this reason, the inclusion of adaptive genetic variation is necessary to identify population structuring mediated by local adaptation to environmental conditions (Sandoval‐Castillo, Robinson, Hart, Strain, & Beheregaray, ).…”