3.3 The pelagic environment drives species-specific differences in gene expression and reveals signatures of genetic assimilation.
We have shown previously that foraging conditions can have a marked impact on the genotype-phenotype map. Specifically, quantitative trait loci (QTL) for the same trait map to largely distinct regions of the genome when animals are reared under alternate benthic/pelagic foraging conditions (Parson et al., 2016; Zogbaum et al., 2021). We therefore examined expression differences between species within each environment, and documented a marked imbalance in DEGs. Specifically, when only considering animals exposed to pelagic conditions, we found over 3500 DEGs between species, whereas fewer than 1000 DEGs were detected between species when only comparing animals reared under benthic conditions (Table 1, Figure 4A-C). Additionally, when comparing environment-specific DEGs to the total dataset (i.e., combining both environments), we found that over 2500 genes from pelagic animals were represented in the global comparison, whereas only 155 genes from benthic animals overlapped between datasets (Table 1, Figure 4C). These data underscore the importance of environmental context in determining the genetic basis of species-specific bone shapes (Parsons et al 2016; Zogbaum et al, 2021). More specifically, they suggest that the pelagic foraging environment is driving species differences in gene expression within the IOP-RA functional complex.
This trend is drawn out when comparing genes from an additive model (S+E), whereby DEGs were detected at the level of both species and foraging environment (Table S2; Figure 5A). When illustrated in a heatmap, these data support the assertion that species differences in gene expression are driven by the pelagic environment, and reveal patterns consistent with either genetic accommodation or assimilation. Genetic assimilation is a mechanism by which plasticity is lost over evolutionary time as genetic variation that facilitated plasticity in an ancestral population becomes fixed as descendent populations adapt to a specific environment (reviewed by Pigliucci et al., 2006). If we assume that plasticity is ancestral, evidence for genetic assimilation is apparent in several gene clusters (denoted by pink dots, Figure 5A), whereby TRC expression levels are indistinguishable between foraging environments and match those of benthic MZ. Consistent with previous data many of the DEGs identified by this model contribute to cell cycle regulation – e.g., cdc20 , cdca5 , cdca8 ,ccne2 , ccnb1 , ccnb2 , ccnf . A list of all the DEGs in this model can be found in Table S2.
Alternative to genetic assimilation is genetic accommodation, or an increase in genetic plasticity over evolutionary time. We cannot rule out that this is the case, as it is possible that plasticity has been enhanced beyond the ancestral condition in MZ. Regardless, the main conclusion to be drawn from these data is that the evolution of plasticity in this system may be traced to divergent patterns of gene expression associated with cell cycle regulation.
We next performed GO analyses for DEGs between species in each foraging environment. When considering animals reared in the pelagic foraging environment, GO analysis revealed a diversity of biological processes; however, those associated with cell division were among the most enriched in MZ, whereas translation and cell differentiation were among the most enriched processes in TRC (Figure 4D). For animals reared in the benthic environment, comparatively fewer biological processes were enriched in general, consistent with fewer DEGs being identified. Similar to pelagic fishes, this analysis found enrichment of cell cycle genes in MZ, and cell differentiation in TRC (Figure 4E). While a greater number of DEGs, contributing to a larger number of biological processes, underlie species-specific differences in the pelagic environment, there are notable consistencies between environments. Specifically, an increase in cell number seems to be important for skeletal growth in MZ, whereas cell differentiation may shape growth in TRC at the time points when tissues were collected.
Unsurprisingly, enriched GO terms for the additive model are similar to those for MZ in the pelagic environment, and include cell cycle, cell division, and chromosome segregation (Figure 5B). In addition, this analysis found enrichment of cytoskeleton organization, which is critical to many cellular functions relevant to bone formation and plasticity, including mechanotransduction (Gunst & Zhang, 2008), and primary cilia formation (Mirvis et al., 2018), which we and others have found to be necessary for load-induced bone formation (Chen et al., 2016; Moore et al., 2019; Gilbert & Tetrault et al., 2021).