Epigenetic modifications are expected to occur at a much faster rate than genetic mutations, potentially causing isolated populations to stochastically drift apart, or if they are subjected to different selective regimes, to directionally diverge. A high level of genome‐wide epigenetic divergence between individuals occupying distinct habitats is therefore predicted. Here, we introduce bisulfite‐converted restriction site associated DNA sequencing (bsRADseq), an approach to quantify the level of DNA methylation differentiation across multiple individuals. This reduced representation method is flexible in the extent of DNA sequence interrogated. We showcase its applicability in three natural systems, each comprising individuals adapted to divergent environments: a diploid plant (Heliosperma, Caryophyllaceae), a tetraploid plant (Dactylorhiza, Orchidaceae) and an animal (Gasterosteusaculeatus, Gasterosteidae). We present a robust bioinformatic pipeline, combining tools for RAD locus assembly, SNP calling, bisulfite‐converted read mapping and DNA methylation calling to analyse bsRADseq data with or without a reference genome. Importantly, our approach accurately distinguishes between SNPs and methylation polymorphism (SMPs). Although DNA methylation frequency between different positions of a genome varies widely, we find a surprisingly high consistency in the methylation profile between individuals thriving in divergent ecological conditions, particularly in Heliosperma. This constitutive stability points to significant molecular or developmental constraints acting on DNA methylation variation. Altogether, by combining the flexibility of RADseq with the accuracy of bisulfite sequencing in quantifying DNA methylation, the bsRADseq methodology and our bioinformatic pipeline open up the opportunity for genome‐wide epigenetic investigations of evolutionary and ecological relevance in non‐model species, independent of their genomic features.
The evolution of threespine sticklebacks in freshwater lakes constitutes a well-studied example of a phenotypic radiation that has produced numerous instances of parallel evolution, but the exact selective agents that drive these changes are not yet fully understood. We present a comparative study across 74 freshwater populations of threespine stickleback in Norway to test whether evolutionary changes in stickleback morphology are consistent with adaptations to physical parameters such as lake depth, lake area, lake perimeter and shoreline complexity, variables thought to reflect different habitats and feeding niches. Only weak indications of adaptation were found. Instead, populations seem to have diversified in phenotypic directions consistent with allometric scaling relationships. This indicates that evolutionary constraints may have played a role in structuring phenotypic variation across freshwater populations of stickleback. We also tested whether the number of lateral plates evolved in response to lake calcium levels, but found no evidence for this hypothesis.
Phenotypic plasticity is a major factor contributing to variation of organisms in nature, yet its evolutionary significance is insufficiently understood. One example system where plasticity might have played an important role in an adaptive radiation is the threespine stickleback (Gasterosteus aculeatus), a fish that has diversified after invading freshwater lakes repeatedly from the marine habitat. The parallel phenotypic changes that occurred in this radiation were extremely rapid. This study evaluates phenotypic plasticity in stickleback body shape in response to salinity in fish stemming from a wild freshwater population. Using a split-clutch design, we detected surprisingly large phenotypically plastic changes in body shape after one generation. Fish raised in salt water developed shallower bodies and longer jaws, and these changes were consistent and parallel across families. Although this work highlights the effect of phenotypic plasticity, we also find indications that constraints may play a role in biasing the direction of possible phenotypic change. The slopes of the allometric relationship of individual linear traits did not change across treatments, indicating that plastic change does not affect the covariation of traits with overall size. We conclude that stickleback have a large capacity for plastic phenotypic change in response to salinity and that plasticity and evolutionary constraints have likely contributed to the phenotypic diversification of these fish.
Phenotypic expression may be and often is influenced by an organism's developmental environment, referred to as phenotypic plasticity. The sperm cells of teleosts have been found to be inactive in the seminal plasma and are activated by osmotic shock for most fish species, through release in either hypertonic (for marine fish) or hypotonic (for freshwater fish) water. If this is the case, the regulatory system of sperm mobility should be reversed in salt- and freshwater fish. We tested this hypothesis by first activating sperm of salt- and freshwater populations of threespine stickleback in salt- and freshwater. The sperm from saltwater stickleback could be activated in either salinity, which matches the freshwater colonization history of the species, whereas the sperm from the freshwater population acted as predicted by the osmotic shock theory and was activated in freshwater only. As the freshwater population used here was calculated to be thousands of years old, we went on to test whether the trait(s) were plastic and sperm from freshwater males still could be activated in saltwater after individuals were exposed to saltwater. After raising freshwater stickleback in saltwater, we found the mature males to have active sperm in both saltwater and freshwater. Further, we also found the sperm of wild-caught freshwater stickleback to be active in saltwater after exposing those mature males to saltwater for only 2 days. This illustrates that the ability for stickleback sperm to be activated in a range of water qualities is an environmentally induced plastic trait.
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