Loci important to acidic adaptation and their allele frequencies
across Atlantic stickleback
Our analysis of genetic structure revealed striking genome-wide evidence
of selection, including between acidic and basic ecomorphs. To
investigate how polymorphisms important to acidic adaptation are
maintained as SGV in marine stickleback, we searched for loci
consistently involved in acidic adaptation based on the genome-wide
comparison of acidic versus basic poolSeq data (Figure 2;
differentiation profiles across all chromosomes are presented in Figure
S2). This identified 50 independent adaptive SNPs nearly fixed for
alternative alleles between the two freshwater
ecomorphs (AFD 0.851
- 0.960; genome-wide median differentiation was 0.145) (Figure 3a; all
adaptive SNPs are characterized in Table S3, and associated genes listed
in .Table S4). These adaptive SNPs recovered many of the genome regions
identified as important to acidic-basic differentiation in Haenel et al.
(2019), based on partly independent specimen panels and a different
analytical approach. Specifically, 15 of the 19 regions of highest
acidic-basic differentiation inferred in Haenel et al. 2019 (i.e., the
regions containing the ‘top core SNPs’ in that study) also exhibited a
marker qualifying as adaptive SNP in the present investigation (Figure
3a, Figure S3). However, given the much higher (whole-genome) marker
resolution, the present study also identified numerous novel regions
(Figure 3a, Figure S2). Haplotype networks derived from genotypes phased
across 5 kb around three exemplary adaptive SNPs indicated that these
markers generally represent longer DNA tracts differentiated between the
ecomorphs (Figure 3b). Across these exemplary regions, acidic
stickleback populations generally shared closely related haplotypes
distinct from the haplotypes prevailing in marine (and basic) fish,
although sometimes acidic individuals exhibited marine haplotypes
(chromosome IX and XI) and vice versa (chromosome XI).
At the adaptive SNPs, marine stickleback generally exhibited lower
frequencies for the alleles characteristic of acidic fish (acidic
alleles; median frequency across all SNP by marine sample combinations:
0.30) than for the alleles typical of the basic populations (median
frequency 0.70) (Figure 4a; Table. S3).
Also, the acidic
alleles occurred at a
lower overall frequency at the adaptive SNPs than at the baseline SNPs
not under consistent acidic-basic divergence (median frequency across
all baseline SNP by marine sample combinations: 0.46). These findings
are in line with observations in Haenel et al. (2019) and indicate that
alleles presumably important for the adaptation to ecologically highly
derived acidic habitats tend to be unfavorable in ancestral marine
stickleback when occurring at high frequency. Interestingly, however, we
found no indication that the frequency of the acidic allele at the
adaptive SNPs was elevated in marine samples collected around North Uist
compared to samples from more distant locations (Figure 4a;
compatibility intervals for the median frequency of the acidic alleles
for all samples are presented in Figure S4); the frequency of these
alleles was highly stable across all our marine samples. This key
finding was reproduced when considering exclusively the subset of
adaptive SNPs at which the acidic allele proved the minor allele withinall marine samples (n = 21; indicated in Table S3) (Figure 4b,
Figure S4; median frequency across all SNP by marine sample
combinations: 0.10); that is, the subset of markers at which purifying
selection in marine stickleback appears particularly plausible because
acidic adaptation involves a particularly strong shift away from the
ancestral allele frequency.
The finding of similar frequencies of alleles important to adaptation to
acidic waters across Atlantic marine stickleback challenges perpetual
antagonism between gene flow and purifying selection (Schluter & Conte
2009; Bassham et al. 2018; Galloway et al. 2020) as a sufficient
explanation for the maintenance of adaptive SGV in the ocean. Instead,
we propose that acidic alleles can persist neutrally in marine
populations when occurring at moderate to low frequencies. Purifying
selection certainly plays a role, but primarily by impeding these
alleles from rising to high frequency in marine stickleback. Note that
the average frequency of the acidic alleles in the ocean was still
around 0.3 (Figure 4a, Figure S4); at many adaptive loci, a substantial
proportion of marine stickleback are thus expected to be homozygous for
the acidic allele, so that purifying selection should still be effective
even when these alleles were recessive. We therefore argue that the
reason for the persistence of acidic alleles in marine populations is
not their recessivity, but their selective neutrality when relatively
uncommon. This interpretation supports quantitative genetic models under
which polygenic adaptation can be achieved by moderate allele frequency
shifts (Latta 1998; Kremer & Le Corre 2012; Le Corre & Kremer 2012).
An important caveat to consider is that although acidic habitats and the
associated stickleback ecomorphs (Figure 1a) are exceptionally common on
North Uist and rare elsewhere (Campbell 1985; Bourgeois et al. 1994;
Klepaker et al. 2013), the potential of marine populations to hybridize
with acidic-adapted freshwater stickleback was not explicitly
manipulated or controlled among our Atlantic marine samples. Is it
plausible that gene flow from acidic-adapted to marine stickleback is
more widespread than we assume, sufficiently so to raise acidic alleles
to substantial frequencies in marine stickleback all across the Atlantic
despite purifying selection? In our view, the marine samples from the
North Sea (DE, NL) refute this concern: western mainland Europe is
densely populated and its Ichthyofauna is well investigated, but acidic
stickleback ecomorphs have to our knowledge not been reported. Gene flow
of acidic alleles into marine fish thus appears highly unlikely across
this region, and yet the frequencies of acidic alleles are not reduced
in these specific marine samples (Figure 4, Figure S4), consistent with
the selective neutrality of these alleles when occurring at the
frequencies observed in marine fish. Similar reasoning applies to marine
stickleback around Iceland, because highly acidic freshwater habitats
seem to be absent in Iceland (Magalhaes et al. 2021).