Evidence for the parallel evolution of head and body shape morphology
across ecomorphs has been shown in previous studies of Arctic charr .
However, even disregarding the notably distinct Dughaill ecomorph pair,
the other three ecomorph pairs show limited evidence of parallelism in
shape morphology despite the parallel evolution of ecomorphs themselves.
Evolutionary divergence and thus phenotypic trajectories are influenced
by the interaction between environmental variation and adaptive genetic
variation. As a result, repeated ecomorph divergences often have very
different phenotypic trajectories for key components of phenotypes, as
seen in three-spine stickleback . Thus, the lack of strict parallelism
seen in our study is likely the result of known differences in the
evolutionary histories of these pairs and differing selective pressures
in their local environments, for example from differences in their
ecosystems or diets . Parallelism can also be generated by other
mechanisms, such as differences in gene expression, post-translational
modifications, and/or alternate splicing . Indeed, differences in
splicing and gene expression patterns showed parallel patterns across
ecomorph pairs in a study on three of the ecomorph pairs we investigated
and provide explanations of alternative adaptive paths.
Of the two traits we tested, head shape had longer phenotypic trajectory
lengths and greater angles, suggesting that the ecomorphs are more
differentiated in head shape from one another and that head shape has
evolved in more distinct directions across lakes. Head shape is well
recognised as an important phenotype for foraging and prey
specialisation, while body shape is important for swimming behaviour and
habitat complexity . The considerable divergence in head shape between
ecomorphs within lakes suggests different prey specialisations
(Garduño-Paz et al. 2012; Hooker et al 2016) while their body shapes and
therefore perhaps swimming behaviours are more subtly different. The
high trajectory angles for head shape suggest notable difference in
foraging across lakes, whether that be due to the lake environments or
the actual species available as prey . For both traits, Loch Tay and
Dughaill showed notably higher trajectory lengths than Awe and na Sealga
and more evolutionary divergence, also seen in the ecomorphs’ genomic
divergence (FST ~1% between ecomorphs
in Awe and na Sealga vs 9% in Dughaill and Tay). This reflects likely
what were previously inferred to be recent sympatric divergences of
ecomorph pairs in Awe and na Sealga while Tay and Dughaill each have
complex histories of divergence and secondary contact between colonising
lineages .
Genomic underpinnings of head and body shape across
lakes:
From our total of 212 SNPs that showed high associations with head
and/or body shape (Figure 2), we found more SNPs associated with body
shape than for head shape. Head shape was controlled by more
large-effect loci relative to body shape and may suggest that head shape
is controlled by fewer genes/pathways. In both cases these will be an
underestimate of actual associations because we have reduced
representation of the genome captured. We found for that for both head
and body shape only a small number of associated SNPs were diverged
between ecomorphs in all four pairs (Figure 3). This is line with what
has been suggested both in other Arctic charr studies and other salmonid
species, in which genetic differentiation between ecomorphs is largely
nonparallel across pairs bar at a few key genes . Further to previous
work, we found that the SNPs shared across pairs were not highly
differentiated between ecomorphs in all pairs suggesting that while
present, they are not critical to underlying the phenotypic differences
in each pair (Figure 4). These results also suggest that the genomic
underpinnings of each phenotype varies across the lakes, likely
contributing to the phenotypic differences we see between pairs. The
polygenic genomic underpinnings of both phenotypes, as indicated by the
numbers of associated SNPs identified, indicate that there are multiple
pathways that can achieve the same phenotypes hence the lack of high
divergence for the same SNPs across all lakes .
Loch Dughaill and in particular Loch Tay often showed notable high
genomic divergence between ecomorphs for many of the associated SNPs for
each trait. Additionally, the associated SNPs for both traits showed
high DXY values compared to the background subsets at
both of these lakes. While increased levels of DXY or
FST compared to genomic background can be indicative of
positive selection , they might also be expected for loci resisting
introgression following secondary contact , as is likely the case in
Loch Tay and Loch Dughaill . The associated SNPs we found are widespread
across the genome (Figure 2) indicating these are not single linked
regions of divergence as found in studies on Atlantic cod and rainbow
trout but instead are diffused and highly polygenic, similar to patterns
for body shape in lake whitefish .
Functional genomic regions for head and body
shape:
Roughly half of the associated SNPs identified for each of head and body
shape were found within or proximal to an annotated gene in the charr
genome. A number of the GO terms that appeared as significantly
overrepresented or enriched in our study have been identified in other
studies investigating adaptive divergences or parallel evolution in
various fish species. Odontogenesis (GO:0042476), sensory perception of
sound (GO:0007605), blood vessel remodelling (GO:0001974), response to
muscle activity (GO:0014850), ventricular trabecula myocardium
morphogenesis (GO:0003222), common-partner SMAD protein phosphorylation
(GO:0007182), cellular response to ethanol (GO:0071361), and
neuromuscular synaptic transmission (GO:0007274) have shown significance
in other Arctic charr studies investigating ecomorph divergence . The GO
terms for associative learning (GO:0008306), regulation of cell shape
(GO:0008360), and UDP-glucuronate biosynthetic process (GO:0006065) also
appear in overrepresented groups in a study on the divergence of a
sympatric lake whitefish species pair (Corgeonus clupeaformis ) in
the USA . Finally, in pupfishes (Cyprinodon. sp. ), the divergent
expression of a number of genes involved in cranial skeletal system
development was seen between different trophic specialists with the GO
term for this process (GO:1904888) significant in our study .
Differences in ossification rate have been related to adaptive
morphological differentiation in other freshwater fish and the over
enrichment or overexpression of genes related to formation of various
bones in our study indicates a similarly important role in adaptive
divergences between ecomorphs of Arctic charr . Indeed, previous work
has noted the importance of differences in bone structure and sizes
between different ecomorphs of Arctic charr .
The QTL database that we have developed allows us to explore whether
rapid replicated diversification of ecomorphs in different salmonid
species is underlined by the use of the same functional regions as has
been previously suggested for salinity tolerance . Our results suggest
that this is true to some extent with QTLs related to body shape in lake
trout and whitefish found in proximity to SNPs that we identified as
being associated with phenotypic differences in Arctic charr ecomorphs.
Whilst we only identified a small number of QTLs located near the
associated SNPs, this is line with other work which suggests that shared
basis for ecomorph divergence across species may be limited . This QTL
marker database will be a valuable resource for future salmonid
research.