Introduction
Understanding how eco-evolutionary processes and environmental factors
drive population differentiation and adaptation remain key challenges in
evolutionary biology. Besides informing about the origin and dynamics of
biodiversity, knowledge about drivers can promote successful management
and protection of populations and species. For differentiation to occur
populations must be at least partially reproductively separated. That
geographically isolated (allopatric) populations experience such
reproductive separation is self-evident. However, reproductive isolation
may also arise through other mechanisms that restrict gene flow. For
example, the Isolation By Distance model
(IBD; Wright, 1943) proposes that there
is a negative association between geographic distance and gene flow,
which should translate into clinal population structures with higher
degrees of differentiation on longer distances. Apart from geographical
dispersal boundaries, ecological factors can influence the degree of
gene flow (Rundle & Nosil, 2005).
Differences in ecology and environmental preferences (e.g.different ecotypes) can instigate population differentiation via
Isolation By Environment (IBE; Sexton,
Hangartner, & Hoffmann, 2014; Wang &
Bradburd, 2014). There is also potential for population genetic
structure to evolve as a result of Isolation By Time (IBT), whereby
reproductive separation occurs between groups of individuals due to
differences in reproductive timing (Hendry
& Day, 2005).
Differences in ecology and/or environmental preferences are generally
accompanied by divergent selection. The evolution of different local
adaptations can cause a feed-back loop that reinforces the reproductive
separation and speeds up the differentiation process
(a case of IBE often referred to as
Isolation by Adaptation (IBA); Nosil, Egan, & Funk, 2008). The
reinforcing effect is likely of particular importance when such
divergent selection acts upon traits directly connected to reproductive
isolation and reproductive success, e.g. habitat preferences
(Hendry, Nosil, & Rieseberg, 2007),
spawning segregation (Nosil, 2012), or
early life history traits (Momigliano et
al., 2017), and it might ultimately lead to ‘ecological speciation’
(Schluter & Rambaut, 1996).
Northern temperate freshwater fish species present good opportunities to
study differentiation and eco-evolutionary dynamics
(Hume, Recknagel, Bean, Adams, & Mable,
2018). It was not until after the retreat of the glaciers (15,000 –
10,000 years ago) that many areas were colonized via range expansions
(Petit et al., 2003;
Rowe, Heske, Brown, & Paige, 2004). The
geographical isolation in glacial refugia, in combination with the
subsequent range expansions, means that there has been opportunities for
founder events, bottlenecks, divergent selection, and adaptions to local
conditions to influence genetic structure and diversity, and the
different contemporary ecotypes that can be observed today have likely
evolved during this time. In aquatic systems, gene flow is generally
expected to be high due to the lack of apparent dispersal boundaries
(Gagnaire et al., 2015;
Puebla, Bermingham, & McMillan, 2012).
Despite this, genetic structuring has been reported within open and
connected waterbodies (Bergek & Björklund,
2007; Momigliano et al., 2017;
Nordahl et al., 2019;
Rosenbaum et al., 2009;
Willing et al., 2010; ), even on small
spatial scales, which is likely due to ecological and environmental
heterogeneity imposing limits to gene flow. One example of such a system
is the Baltic Sea, one of the largest brackish-water ecosystems in the
world, that exhibits steep environmental north-south gradients in
salinity and temperature (Bendtsen,
Söderkvist, Dahl, Hansen, & Reker, 2007). This makes the Baltic Sea an
excellent system for studies of differentiation and local adaptation
(e.g. in Guo, DeFaveri, Sotelo, Nair, &
Merilä, 2015; Guo, Li, & Merilä, 2016).
One of the most common, coastal, predatory fish species in the Baltic
Sea is pike (Esox lucius ). Pike plays an important role in many
aquatic ecosystems by regulating abundances of species in lower trophic
levels (Donadi et al., 2017). It is an
economically important species for both recreational and commercial
fishing (Lehtonen, Leskinen, Selen, &
Reinikainen, 2009; Pierce, Tomcko, &
Schupp, 1995), and an established model species in studies of ecology
and evolution (Forsman et al., 2015). It
is originally a freshwater species, but it has managed to colonise
brackish waters with salinities up to approximately 15 ppt (Craig 2008).
This range expansion has been accompanied by the evolution of three
different ecotypes that differ with regard to migratory behaviour. The
original ecotype (freshwater) spend the entire life in freshwater,
whilst the other ecotypes (anadromous and resident) spend either part
of, or their entire life, in saline (brackish) waters. The two latter
ecotypes co-exist in the coastal waters of the Baltic Sea during most of
the year (Westin & Limburg, 2002), and
separate only for a short period during spawning when the anadromous
individuals migrate to freshwater localities whilst the resident ecotype
stays in the brackish coastal waters
(Engstedt, Stenroth, Larsson, Ljunggren,
& Elfman, 2010; Larsson et al., 2015;
Muller, 1986). An important feature of
pike in the Baltic Sea, which affects the population structure of the
species (Nordahl et al., 2019), is their
homing behaviour (Engstedt, Engkvist, &
Larsson, 2014; Larsson et al., 2015;
Tibblin, Forsman, Borger, & Larsson,
2016), i.e. the adults return to their natal spawning ground for
reproduction (Engstedt et al., 2014;
Engstedt et al., 2010;
Jacobsen et al., 2017;
Muller, 1986).
While a previous study of pike in the Baltic Sea has indicated genetic
differentiation between the resident and anadromous ecotypes
(Nordahl et al., 2019), studies of the
genetic structuring within the ecotypes show conflicting results. Some
studies suggest weak structuring (Laikre
et al., 2005; Wennerström, Olsson,
Ryman, & Laikre, 2016), whilst others report fine-scaled genetic
structuring among anadromous populations, and point to a role of
isolation by distance (Möller, Winkler,
Richter, & Bastrop, 2020; Nordahl et
al., 2019; Sunde, Yildirim, Tibblin, &
Forsman, 2020a). There is also evidence to suggest that environmental
differences among spawning locations have resulted in adaptive
phenotypic differentiation in various traits, including salinity
tolerance (Sunde, Tamario, Tibblin,
Larsson, & Forsman, 2018), temperature tolerance
(Sunde, Larsson, & Forsman, 2019),
vertebral number (Tibblin, Berggren,
Nordahl, Larsson, & Forsman, 2016), body size and growth rate
(Tibblin et al., 2015), early life
history traits, and reproductive investment
(Berggren, Nordahl, Tibblin, Larsson, &
Forsman, 2016). Pike in the Baltic Sea therefore offers possibilities
to study differentiation at different levels (between allopatric and
sympatric populations, and within and among ecotypes), to evaluate the
contributions to genetic structure of different types of reproductive
isolation (such as IBD, IBE, IBA, and IBT), and to investigate the
potential genetic underpinnings of local adaptations.
Increased knowledge into these issues is also important for management.
Declines in pike populations in the Baltic Sea have been observed during
the last decades (Lehtonen et al., 2009;
Ljunggren et al., 2010;
Nilsson, Flink, & Tibblin, 2019;
Olsson, 2019), and extensive management
actions, such as restoration of spawning habitats and fisheries
regualtions, have been implemeted to counteract this negative trend
(Larsson et al., 2015;
Nilsson et al., 2019). Despite this,
abundances remain low, and there is a need to increase the understanding
to aid successful management. Previous population assignments have
mainly been based on studies utilizing neutral microsatellite markers
(Bekkevold, Jacobsen, Hemmer‐Hansen, Berg,
& Skov, 2015; Eschbach et al., 2019;
Möller et al., 2020;
Nordahl et al., 2019;
Wennerström et al., 2016; but see Sunde
et al., 2020b). Informed decisions regarding management and
conservation efforts require knowledge about how the combination of
stochastic and deterministic processes shape genetic structure and
diversity. This in turn requires that population genetic studies use
molecular markers that capture variation also in coding regions
(Sunde et al., 2020a). To investigate
genetic structure and decipher the roles of different ecological and
evolutionary processes for differentiation and adaptation in pike, we
therefore performed a population genetic study utilizing Restriction
Site Associated DNA sequencing (RADseq). For this we used 11 populations
spanning 8.7 degrees in latitude, from Denmark (Askeby) in the south to
Umeå in northern Sweden (Figure 1, Table 1 ), that experience
different environmental conditions (e.g. ice cover, light,
salinity, temperature, prey species, competition, and predation). The
populations represented all three ecotypes (freshwater, anadromous and
resident) and, to our knowledge, this is the first population genetic
study of pike that includes populations of all three ecotypes.
The RADseq method yields thousands of Single Nucleotide Polymorphisms
(SNPs) residing in both coding (functional) and non-coding (mainly
selectively neutral) genomic regions
(Andrews, Good, Miller, Luikart, &
Hohenlohe, 2016). Thus, comparisons of genetic structure and diversity
obtained using separate analyses of neutral and functional SNPs, can
inform about the roles of both stochastic and deterministic processes
(Andrews et al., 2016;
de Villemereuil & Gaggiotti, 2015; ). In
the present study, we therefore investigated genetic structure using
both neutral and adaptive SNP datasets. In addition, we performed
outlier analyses to identify loci putatively under selection and to
pinpoint environmental factors contributing to evolutionary divergence
among ecotypes and populations.