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RAD genotyping reveals fine‐scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the A merican lobster ( H omarus americanus )
Author(s) -
Benestan Laura,
Gosselin Thierry,
Perrier Charles,
SainteMarie Bernard,
Rochette Rémy,
Bernatchez Louis
Publication year - 2015
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/mec.13245
Subject(s) - biology , homarus , population , genetic structure , population genetics , range (aeronautics) , genotyping , evolutionary biology , effective population size , ecology , genetics , genotype , genetic variation , crustacean , gene , demography , materials science , sociology , composite material
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 ( H omarus americanus ) throughout much of the species’ range and increase the assignment success of individuals to their location of origin. We genotyped 10 156 filtered SNP s 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 ( F CT = 0.0011; P ‐value = 0.0002) and then revealing a total of 11 genetically distinguishable populations (mean F ST = 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 SNP s having the highest F ST . 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 SNP s 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.