Introduction
In eukaryotes, adaptation of populations to novel ecological conditions
often occurs from standing genetic variation (SGV), that is, selectively
relevant variation pre-existing in the ancestor (Orr & Betancourt 2001;
Hermisson & Pennings 2005; Barrett & Schluter 2008; Messer & Petrov
2013; Matuszewski et al. 2015). A puzzle, however, is how SGV is
maintained in the ancestor (Yeaman 2015): if genetic variants are
favored by selection in a novel, derived habitat, should they not be
unfavorable and hence eliminated by purifying selection in the ancestral
habitat? One solution to this paradox is that genetic variants favored
in the derived habitat are maintained as SGV in the ancestor by
continued hybridization (and hence gene flow) between derived and
ancestral populations, thus counteracting the selective removal of these
variants in the latter (Colosimo et al. 2005; Bolnick & Nosil 2007;
Barrett & Schluter 2008; Schluter & Conte 2009; Yeaman & Whitlock
2011; Galloway et al. 2020). An alternative idea is that variants
beneficial within the novel habitat are selectively neutral in the
ancestral population when their frequency is relatively low. While this
must obviously hold for recessive variants (Barrett & Schluter 2008),
quantitative genetic models suggest that when the traits under selection
are highly polygenic (that is, influenced by a great number of loci),
adaptive divergence may generally occur primarily via the establishment
of linkage disequilibrium among alleles and involve only relatively
subtle (or at least incomplete) allele frequency differentiation (Latta
1998; Kremer & Le Corre 2012; Le Corre & Kremer 2012). In this case,
SGV could persist in the ancestor simply because there is no purifying
selection to complete its elimination. The relative importance of these
two not mutually exclusive explanations for the maintenance of SGV, gene
flow-selection balance and selective neutrality, remains unknown and
has, to the best of our knowledge, not been subject to empirical
investigation. An obstacle for doing so is that organismal systems are
required in which adaptive genetic variation can be detected and
quantified in both derived and ancestral populations simultaneously.
We here perform such an investigation in threespine stickleback fish
(Gasterosteus aculeatus ) by focusing on genetic variation
promoting the adaptation of populations to acidic freshwater habitats
after the recent (postglacial) colonization of these habitats by
ancestral marine stickleback. Adaptation to acidic waters likely
involves numerous traits, but particularly obvious elements include the
reduction of external skeletal armor and body size in some acid-adapted
stickleback populations relative to their ancestor (and to standard
freshwater-adapted stickleback) (Figure 1a) (Campbell 1985; Giles 1983,
Bourgeois et al. 1994; Spence et al. 2013; Klepacker et al. 2016;
Magalhaes et al. 2016; Haenel et al. 2019). The function of this
evolution is likely reduced metabolic demands, conferring an advantage
in nutrient-depleted acidic habitats. (Note that for simplicity, we will
use the terms acidic habitats and acidic adaptation throughout this
paper, but we acknowledge that selection may not necessarily be mediated
by pH (alone), but by an associated shortage in dissolved ions).
Although marine threespine stickleback have colonized innumerable
freshwater habitats across the northern hemisphere, morphological
adaptation to acidic habitats is reported from relatively few locations
across the species’ range only (Campbell 1985; Bourgeois et al. 1994;
Klepaker et al. 2013). An exception is North Uist (Outer Hebrides,
Scotland) (Figure 1b), an island on which acidic-adapted stickleback
ecomorphs are common. Due to its particular surface geology (Waterston
et al. 1979), the eastern part of this island harbors numerous acidic
lakes (pH around 5-6) inhabited by archetypal acidic-adapted stickleback
that have likely evolved multiple times independently (Giles 1983;
Spence et al. 2013; Klepacker et al. 2016; Magalhaes et al. 2016; Haenel
et al. 2019). This parallel evolution has occurred though the
deterministic sorting of SGV available in the marine ancestor, because
alleles recruited repeatedly for acidic adaptation are consistently
found in extant marine stickleback breeding in coastal habitats of North
Uist, albeit generally at modest to low frequency (Haenel et al. 2019).
What remains unknown is whether this SGV primarily reflects the
continued flow of acid-favored alleles into marine stickleback by
hybridization, or whether alleles beneficial to acidic adaptation
segregate largely neutrally in marine fish.
To address this question, we here use whole-genome sequence data to
examine SGV in marine stickleback across the Atlantic Ocean. We
hypothesize that if the presence of SGV relevant to acidic adaptation in
marine stickleback around North Uist reflects a balance between gene
flow and purifying selection, the frequency of alleles favored in acidic
habitats should be elevated in marine stickleback breeding around North
Uist compared to marine stickleback sampled from more distant locations.
The reason is that acidic lakes represent an uncommon freshwater habitat
outside North Uist, and the acidic-adapted ecomorphs common on this
island are rare on a worldwide basis. Purifying selection should
therefore vastly outbalance the input of deleterious acidic-favored
alleles by hybridization in marine stickleback far from North Uist.
Alternatively, the frequency of acidic-favored alleles may not be
elevated in marine stickleback breeding around North Uist compared to
marine fish in general, suggesting that purifying selection against
these alleles is weak or absent in marine stickleback at large. As we
show, our data support this latter scenario, thus highlighting selective
neutrality as an underappreciated explanation for the maintenance of
SGV.