DOI: 10.5061/dryad.zs7h44j7h
title: Genetic response to human‐induced habitat changes in the marine environment: A century of evolution of European sprat in Landvikvannet, Norway

description: Habitat changes represent one of the five most pervasive threats to
 biodiversity. However, anthropogenic activities also have the capacity to
 create novel niche spaces to which species respond differently. In 1880,
 one such habitat alterations occurred in Landvikvannet, a freshwater lake
 on the Norwegian coast of Skagerrak, which became brackish after being
 artificially connected to the sea. This lake is now home to the European
 sprat, a pelagic marine fish that managed to develop a self-recruiting
 population in barely few decades. Landvikvannet sprat proved to be
 genetically isolated from the three main populations described for this
 species; i.e. Norwegian fjords, Baltic Sea, and the combination of North
 Sea, Kattegat and Skagerrak. This distinctness was depicted by an accuracy
 self-assignment of 89% and a highly significant FST between the lake sprat
 and each of the remaining samples (average of ≈0.105). The correlation
 between genetic and environmental variation indicated that salinity could
 be an important environmental driver of selection (3.3% of the 91 SNPs
 showed strong associations). Likewise, Isolation by Environment was
 detected for salinity, although not for temperature, in samples not
 adhering to an Isolation by Distance pattern. Neighbour-joining tree
 analysis suggested that the source of the lake sprat is in the Norwegian
 fjords, rather than in the Baltic Sea despite a similar salinity profile.
 Strongly drifted allele frequencies and lower genetic diversity in
 Landvikvannet compared with the Norwegian fjords concur with a founder
 effect potentially associated with local adaptation to low salinity.
 Genetic differentiation (FST) between marine and brackish sprat is larger
 in the comparison Norway- Landvikvannet than in Norway-Baltic, which
 suggests that the observed divergence was achieved in Landvikvannet in
 some 65 generations, i.e., 132 years, rather than gradually over thousands
 of years (the age of the Baltic Sea), thus highlighting the pace at which
 human-driven evolution can happen.
description: Sprat were sampled by commercial fishermen and scientific cruises
 from forty locations in the NE Atlantic. As there is a strong management
 interest in defining stock affiliation of sprat fished in the
 Kattegat–Skagerrak areas, sprat were sampled in these areas both during
 the spring spawning season and outside the spawning season by the pelagic
 fishery. Norwegian fjord samples spanning most of the sprat's
 Norwegian distribution range were also sampled. Sampling was directed
 toward ripe individuals, where possible. However, in some areas, samples
 were mainly taken outside the main spawning season and may thus represent
 both local and migratory individuals of mixed origin.
 DNA was extracted from fin clips stored in ethanol using the
 Qiagen DNeasy 96 Blood & Tissue Kit in 96‐well plates, each of
 which contained two or more negative controls. A
 double‐digest RAD library was constructed from eight sprat genomic DNA
 samples from Hardangerfjorden, comprising a 400–700 base pair region of
 <i>Sbf</i>I‐ and <i>Sph</i>I‐restricted DNA and
 involving individual‐specific inline barcode adapters. The methodology has
 been previously described in detail by Manousaki et al.
 (2015). The library was thereafter sequenced on
 the Illumina MiSeq platform (part of a shared flow cell run, V2 chemistry,
 300 cycle kit, 160 base paired‐end reads). Stacks software v1.47 (Catchen,
 Hohenlohe, Bassham, Amores, & Cresko,
 2013) was used to demultiplex sequence reads and
 identify and score SNPs (de novo assembly; key Stacks parameters m
 (minimum depth of coverage) = 4, <i>M</i> (maximum distance
 allowed between stacks) = 2, <i>n</i> (number of mismatches
 allowed between loci among individuals) = 1). Data were then exported to
 Microsoft Excel for filtering to identify potential SNPs suitable for
 Sequenom‐based multiplex SNP assay. This involved selecting RAD loci
 (trimmed length 135 bases) that contained a single diallelic SNP with at
 least two occurrences of the minor allele among the eight samples and that
 the SNP was positioned between base 41 and base 95, to allow for enough
 flanking sequence for PCR primer design. For the final filtered set, SNP
 locus primer design, amplification, and genotype calling were performed
 using the Sequenom MassARRAY iPLEX Platform, as described by Gabriel,
 Ziaugra, and Tabbaa (2009).
description: Data consists of individual ID, sample and genotypes (SNPs and
 microsatellites, respectively). SNPs have been coded as
 follows: 1(A), 2 (C), 3 (G), 4 (T) and 0 (missing data). Two columns for
 locus. Microsatellites have been coded using the
 fragment size (bp). Two columns per locus.