Discussion
Knowledge of evolutionary and demographic processes is crucial for our
understanding of how native species will respond to biological invasion
and the mechanisms that facilitate or inhibit their co-existence with
invasive species. We investigated the interaction between adaptation and
demography to gain insight into the persistence of a native gastropod
(Amnicola limosus ) following approximately 12 years of exposure
to an invasive predator, the round goby, in the Upper St. Lawrence
River. Our genomic results indicate that A. limosus has locally
adapted to the invasion in the span of \(\leq\)12 generations. We also
find evidence for adaptation to differences in water calcium over the
longer geological history of the ecosystem. Despite evidence of local
adaptation in invaded populations, they are experiencing demographic
decline, whereas refuge populations show relative stability. While these
results could imply that the low-calcium refuge populations have the
potential to provide migrants and generate demographic and genetic
rescue of invaded populations, this hypothesis was not supported. We
detected restricted gene flow and strong population structure between
the physiological refuge and invaded populations. Moreover, we found
evidence that individuals in uninvaded refuges appear to be maladapted
for life history traits, showing low fitness overall. Therefore, despite
the current persistence of native A. limosus gastropods in the
Upper St. Lawrence River system following the invasion by round gobies,
this native gastropod could become vulnerable due to reductions in
effective population sizes and limited potential for genetic rescue of
impacted populations by the populations in physiological refugia.
Genomic signatures of local adaptation to round goby
invasion and low water calcium.
Our genomic data (population structure, Fig. 5 and environmental
association analyses, Fig. 2) provide general evidence for local
adaptation to the two distinct environment types in A. limosus ,
i.e., low calcium/goby absent and high calcium/goby present. The
exceptions were for two populations (RAF-LCGP and PDC-HCGA) that
experienced inverse conditions for selection than the other sampled
populations, both clustering with the invaded populations. For RAF-LCGP,
the results support strong selection from goby predation even under
lower calcium conditions, which are less optimal environmental
conditions for round goby feeding and performance (Iacarella &
Ricciardi, 2015). For PDC-HCGA, the results suggest strong migration
from adjacent invaded sites, which was confirmed by our demographic
analyses (see below). PDC-HCGA itself remained uninvaded despite higher
water calcium concentrations, likely because the site was located within
a wetland, which provides less optimal conditions for round-goby
establishment due to the substrate properties (Astorg et al., 2021).
Our EA analyses with Baypass and poolFreqDiff potentially allowed us to
disentangle the signals of the two putative selective pressures (i.e.,
the effect of selection from goby predation at invaded sites and low
calcium levels at uninvaded sites), even though invasion status and
calcium concentration were strongly correlated. We found SNPs uniquely
associated with invasion status and calcium concentration, which can be
interpreted as signatures of local adaptation to predation by the round
goby fish, and to the more limiting calcium concentrations at uninvaded
sites. However, a more comprehensive understanding of the relative roles
of these distinct selection mechanisms on genomic variation will require
functional validation and ideally a different sampling design that
includes additional sites with less correlation between these two
environmental factors. Due to the unavailability of an annotated
reference genome for A. limosus or a closely related species, we
were unable to investigate putative physiological functions of the SNPs
showing significant differentiation between environment types.
Adaptation to calcium likely involves different functions from
adaptation to predation. Differences in calcium concentrations between
the water masses from the two rivers are related to the geological
characteristics of the river watersheds and therefore represent
environmental differences over the long evolutionary history of this
species in the St. Lawrence River. On the other hand, predation from the
invasive round goby on mollusks is a recent and novel stressor in the
St. Lawrence River. Putative physiological functions that would be worth
investigating in future studies include transmembrane calcium transport
and biomineralization pathways that might be involved in adaptation to
low calcium concentration (Clark et al., 2020), as well as shell
development regulatory genes that could play a role in the evolution of
smaller-sized shells at maturity, which has been observed in populations
subject to goby predation (Kipp et al., 2012; Johnson et al., 2019).
(Mal)adaptive responses to round goby invasion and water
calcium levels
Our results from the reciprocal transplant experiment give insight into
potential adaptive and maladaptive responses in life history traits
between SL (HCGP) and OR (LCGA) populations to divergent calcium
concentrations and round goby predation regimes (Fig. 3). Indeed, we
found important differences in life-history traits (fecundity and
survival as fitness components) between the populations from the two
habitat types. Both fecundity and survival were higher in the HCGP
populations than in the uninvaded LCGA populations, regardless of water
treatment. The potential for local adaptation to the calcium gradient is
suggested by a slight home advantage in fecundity for populations from
both habitats in their origin water versus transplant water (water
treatment LCGA vs HCGP), although the interaction between origin and
treatment water was not significant. While our laboratory reciprocal
transplant experiment could indicate that A. limosus responded to
round goby invasion through shifts in life-history traits, populations
from the uninvaded habitats are also possibly maladapted, as shown by
low fitness across treatment water and goby cue treatments. This
suggests the LCGA populations might be generally maladapted (Brady et
al., 2019), which could occur through a trade-off of adaptation to low
calcium water, as intracellular transport of calcium is energetically
costly (Clark et al., 2020). In addition, individuals from the Ottawa
River might allocate more resources toward calcium transport and be less
able to invest in life-history traits such as reproduction.
Survival rates between populations varied widely, especially for the
HCGP populations. This could reflect potential local (mal)adaptation to
other biotic or abiotic parameters that we did not consider in the
present study (e.g., temperature, substrate, nutrient availability, and
food quality). As it was conducted within a single generation, we
acknowledge that our reciprocal transplant experiment did not allow us
to differentiate plastic vs genetic vs maternal effects on the measured
traits. However, our genomic results support the idea that the
life-history differences observed between the two population types could
be at least partially explained by adaptive genetic differences between
the environments.
Demographic and genetic effects of the invasion.
Given prior findings showing a decline in gastropod population abundance
following invasion by round gobies, we hypothesized that invaded
populations might suffer from population bottlenecks and reduced genetic
diversity. However, we did not find a negative effect of the invasion on
genetic diversity (Fig. 4), with high levels of nucleotide diversity
found in all populations. The nucleotide diversity reported here is
relatively high compared to other species observed across phyla (Leffler
et al., 2012), although lower than what has been observed in other
gastropod species (Redak et al., 2021; Oswald et al., 2022). The
slightly negative Tajima’s D found in all populations indicates that
there was an excess of rare alleles compared to the neutral model, which
could reflect a recent population expansion or positive selection.
However, our demographic analysis revealed the occurrence of genetic
bottlenecks or reductions in Ne in invaded populations,
and even in one refuge population (Table 1, Table S2). This reduction in
Ne was only followed by recovery in one of the cases,
hinting at a possible case of genetic rescue (i.e., due to an increase
in genetic diversity), although the results must be interpreted with
caution as there was considerable uncertainty around the parameter
estimates. The source of migrants that could potentially be generating a
rescue is also presently unknown and is unlikely to be due to the
migration from the low-calcium physiological refugia populations as the
gene flow in this direction was non-significant. Further validation of
the potential for genetic rescue would require obtaining census data and
collecting new genomic samples targeted at identifying the potential
source populations and quantifying the level of hybridization in
recipient-invaded populations (Fitzpatrick et al., 2020).
Surprisingly, the effective population size reductions did not trigger
major declines in genetic diversity levels (Fig. 4). This could be due
to low but significant gene flow (0.1 < 4Nem
< 11; Hämälä et al., 2018) within habitats, as suggested by
the gene flow estimates detected between PDC-HCGA and GOY-HCGP
populations and the lower FST within clusters (Table S2,
Fig. 5). Similar rates as observed here have been shown to be sufficient
to maintain genetic diversity despite low effective population size
(Gompert et al., 2021). Invaded populations thus do not appear to be
currently in need of genetic rescue from refuge populations to recover
genetic diversity, or perhaps genetic rescue has already occurred or is
ongoing and is the reason for the high genetic diversity observed at
invaded sites.
Interaction between local adaptation and demographic/genetic
rescue
A core goal of this study was to determine if local adaptation could
interact with demographic and genetic rescue. We found relatively low or
non-significant levels of gene flow between the populations from the two
habitat types (from LCGA refugia to HCGP populations and inversely), but
high gene flow within habitat types (Table S2).
Pairwise-FST values were within the range of what has
been observed in other egg-laying marine gastropod species . Thus, our
analyses of gene flow indicate that refuge populations in low calcium
habitats do not provide migrants to invaded populations, and this is
further supported by the significant pattern of isolation by environment
(Wang & Bradburd, 2014). This pattern could be generated by selection
against migrants (Nosil et al., 2008; Orsini et al., 2013; Tigano &
Friesen, 2016) related to calcium limitation and round goby predation.
Individuals from the LCGA populations had lower fitness overall compared
to HCGP populations and thus might have low reproductive output and
survival in invaded habitats. Given that goby predation has been shown
to cause selection for smaller shell sizes at maturity (Kipp et al.,
2012), LCGA individuals might be also more vulnerable to predation than
HCGP individuals if they are more conspicuous due to larger shell sizes.
Similarly, hybrids might be selected against if intermediate phenotypes
have lower fitness in their local environment (Thompson et al., 2022).
In addition, because individuals from uninvaded populations have lower
reproductive output and survival, they provide a more limited
demographic subsidy to invaded populations. This will depend on the
magnitude of the relative fitness difference between source and
recipient populations (i.e., how detrimental migrant alleles will be in
the recipient populations; Bolnick & Nosil, 2007). The recent
adaptation to goby predation could have thus reinforced the existing
effect of isolation by environment from the adaptation to low calcium,
thereby limiting the potential of low calcium physiological refugia to
provide migrants necessary for both the demographic and genetic rescue
of invaded populations.
In contrast to the low gene flow found between LCGA and HCGP
populations, gene flow was relatively high between the wetland refuge
PDC-HCGA and the invaded population GOY-HCGP, although it did not result
in Ne recovery from the bottleneck in the latter (Table
S2). Wetland habitats provide refuge from goby predation by reducing
their abundance at a local scale and are known to enhance fish and
macroinvertebrate diversity (Astorg et al., 2021; Morissette et al.,
2023). Their role as a refuge has also been previously recognized in
other invaded systems (Reid et al., 2013). Given the prevalence of
wetlands in the Upper St. Laurence River (Morissette et al., 2023),
wetland refugia with high calcium concentration thus have the potential
to provide migrants to invaded sites, particularly due to the lower
adaptive divergence between these populations. This suggests that
migration of individuals from larger wetland refuge populations might be
providing not only a demographic subsidy (demographic rescue; Hufbauer
et al., 2015) but could also be replenishing the genetic diversity if
indeed it was lost due to population declines in invaded populations
(genetic rescue; Whiteley et al., 2015). The role of wetlands as a
refuge and their potential implication in the demographic and genetic
rescue of invaded gastropod populations therefore warrants further
investigation.
Based on our demographic modeling and population structure results
(Table S2, Fig. 5), populations from high calcium habitats are more
likely to be exchanging migrants, which appears to be sufficient for
preserving genetic diversity. However, this beneficial effect of gene
flow might have limitations as shown by the absence of effective
population size recovery in two out of three populations for which we
detected a bottleneck (Table 1). This is particularly important because
strong selection such as that detected in the invaded populations can
also lead to reduced population sizes and drift, with negative effects
on population fitness (Falk et al., 2012). The net outcome of this
conflict between adaptation to the invasive predator and low calcium
concentrations, and genetic rescue, will thus depend on the severity of
population decline in recipient populations (Hufbauer et al., 2015), the
extent of adaptive differentiation between populations in each habitat
type, and the rate of immigration from high calcium wetland populations.
Potential limitations of genetic rescue during population
management.
This study documents the impact of an aquatic invasive predator on
evolutionary and demographic processes in a native prey species.
Evaluating the potential evolutionary impacts of invasive species on
native species is important because they can lead to surprising,
unforeseen negative effects, such as the disruption of existing local
adaptation . Although genetic rescue has been proposed as a valuable
tool for the conservation of small, isolated populations (Whiteley et
al., 2015; Ralls et al., 2018), it has also been recognized that genetic
rescue carries the risk of outbreeding depression if there is an
adaptive genetic divergence between source and recipient populations
(Frankham et al., 2011). The present study highlights a case from
natural, unmanaged populations where the potential for genetic rescue
from physiological refugia is potentially limited by adaptive
divergence, and only appears to be possible in the presence of migration
from refuge populations of similar habitat types. This implies that the
presence of physiological refugia will not necessarily translate into
the demographic or genetic rescue of imperiled populations if strong
genetic differentiation exists between refuge and recipient populations,
for example stemming from isolation by environment. It thus reiterates
the importance of considering the local (mal) adaptation of donor and
recipient populations during managed introductions that aim to produce
genetic rescue (Hoffmann et al., 2021).