Genomic signatures of environmental selection despite near‐panmixia in summer flounder

Abstract

Rapid environmental change is altering the selective pressures experienced by marine species. While adaptation to local environmental conditions depends on a balance between dispersal and natural selection across the seascape, the spatial scale of adaptation and the relative importance of mechanisms maintaining adaptation in the ocean are not well understood. Here, using population assignment tests, Approximate Bayesian Computation (ABC), and genome scans with double‐digest restriction‐site associated DNA sequencing data, we evaluated population structure and locus–environment associations in a commercially important species, summer flounder (Paralichthys dentatus), along the U.S. east coast. Based on 1,137 single nucleotide polymorphisms across 232 individuals spanning nearly 1,900 km, we found no indication of population structure across Cape Hatteras, North Carolina (FST = 0.0014) or of isolation by distance along the coast using individual relatedness. ABC estimated the probability of dispersal across the biogeographic break at Cape Hatteras to be high (95% credible interval: 7%–50% migration). However, we found 15 loci whose allele frequencies were associated with at least one of four environmental variables. Of those, 11 were correlated with bottom temperature. For summer flounder, our results suggest continued fisheries management as a single population and identify likely response mechanisms to climate change. Broadly speaking, our findings suggest that spatial balancing selection can manifest in adaptive divergence on regional scales in marine fish despite high dispersal, and that these conditions likely result in the widespread distribution of adaptive alleles and a high potential for future genetic adaptation in response to changing environmental conditions. In the context of a rapidly changing world, a landscape genomics perspective offers a useful approach for understanding the causes and consequences of genetic differentiation.

Genotyping‐by‐sequencing illuminates high levels of divergence among sympatric forms of coregonines in the Laurentian Great Lakes

“…Despite these advancements, delineating discrete conservation units can still be problematic. For example, taxonomic uncertainty can lead to confusion regarding species boundaries (Bickford et al, 2007;Hey, Waples, Arnold, Butlin, & Harrison, 2003), and observed phenotypic, spatial, temporal, or behavioral differences can be opposed by apparent genetic panmixia (Als et al, 2011;Hoey & Pinsky, 2018;Palm, Dannewitz, Prestegaard, & Wickström, 2009). Perhaps no other group embodies the challenges of defining conservation units better than the coregonines.…”

Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America

“…SNPs produced from high-throughput sequencing have led to the identification of previously undetected population structure in a number of marine and terrestrial species K E Y W O R D S connectivity, genotype-by-sequencing, management recommendations, Olympia oyster, outlier loci, population genomics (Everett et al, 2016;Reitzel, Herrera, Layden, Martindale, & Shank, 2013;Van Wyngaarden et al, 2016). Compared to the Atlantic coast of North America (Hoey & Pinsky, 2018), studies utilizing genomewide SNPs for marine taxa from the Pacific coast are far fewer in number and have been limited to regional spatial scales (De Wit & Palumbi, 2013;Drinan et al, 2018;Gleason & Burton, 2016;Larson et al, 2014;Martinez, Buonaccorsi, Hyde, & Aguilar, 2017) or in the number of sampling sites (Pespeni, Oliver, Manier, & Palumbi, 2010;Tepolt & Palumbi, 2015). This study is the first of my knowledge to utilize thousands of SNPs to extensively survey the rangewide population structure of a marine species along this coast.…”

High-frequency temperature variability mirrors fixed differences in thermal limits of the massive coralPorites lobata(Dana, 1846)

“…Dempster, 1955;Kawecki and Ebert, 2004;Levene, 1953;Ravigné et al, 2004;Scheiner, 1993). Local adaptation is expected to evolve in populations with limited connectivity, but if environmentally driven selection is strong enough, adaptive differentiation can still accumulate despite ongoing gene flow (Feder et al, 2012;Hoey and Pinsky, 2018). In the marine environment, reproduction via broadcast spawning and gamete mixing at the sea surface favor the dispersal potential (i.e.…”