Genome-wide markers reveal geographical isolation by distance and barriers as well as local heterogeneity in the genetic structure of a seagrass

Gene flow is a crucial concept in the delineation of conservation units for natural populations of a species. Seagrasses are marine species targeted for conservation because their abundance has declined worldwide during the last century. However, we cannot determine how to delineate conservation units with inadequate knowledge of the genetic structure of seagrasses. This study explored the genetic structure of Zostera marina L. (eelgrass) populations in three semi-enclosed areas using single nucleotide polymorphisms within abundant, genome-wide loci. Genome-wide markers revealed that the genetic structure was isolated by geographical distance and barriers through a narrow strait in an area with linear dimensions less than 200 km. The genetic distance created by the barrier was 6.7 times the genetic distance due to 100 km of geographic distance. The markers revealed the intra-site variability in genetic structure and the heterogeneity among sites on scales less than ~10 km that had not been recognized previously. Our results imply that the use of genomic tools will focus seagrass conservation efforts more locally than before and that assessing relative genetic differences can make delineating conservation units a reality. Identifying the evolutionary and quantitative meaning of genetic differences will be a next challenge for delineating seagrass conservation units.