Alexandra Lesayova writes about the threespine stickleback fish; a promising model organism with respect to gaining a better understanding of the effects of climate change on living organisms, and how understanding the basis of natural selection in response to environmental stresses could be the key to accurate predictions of the effects of climate change.
Climate change is expected to bring environmental shifts so dramatic, that proper genetic adaptation of animals will be required for their survival. Temperature swings and habitat loss have already driven some species to the verge of extinction. On the contrary, there are animals like threespine stickleback fish, which experience large environmental changes seasonally – and adapt accordingly.
Researchers from McGill University in Canada investigated the natural selection among stickleback populations. Specifically, the genomic changes introduced for adaptation to drastic seasonal environmental changes. Not only do these data inform us on historical adaptation to new habitats dating 10 000 years back; they also allow for forecasting how populations might adapt to the future climate change-associated stressors. The latter could help us predict specific survival strategies as well as their potential success.
Threespine stickleback – an ideal model organism
To detect genomic changes introduced in natural selection, we search for parallel evolution, i.e. when very closely related, but independently evolved populations adapt similarly. Many studies on parallel evolution are retrospective: analyses ran when animals were already well-adapted to their current habitat. This way provided some insight into adaptation to freshwater, novel pathogens, or low oxygen environments. It was, however, impossible to unambiguously distinguish the adaptation-associated changes from “noise” – changes introduced by random processes after the studied environmental shift.
Fortunately, the stickleback lifestyle is ideal for monitoring real-time natural selection. Sticklebacks inhabiting estuaries along Californian coasts experience dry summers and rainy winters. During summer, sandbar build-ups isolate estuaries from the ocean. The environmental shift facilitates predator abundance as well as changes habitat structure and water flow. Salinity becomes diversified on the water column, with the top layer formed by freshwater. Stickleback isolation from the ocean thus provides an analogue of the marine-to-freshwater transition – known to have proceeded during post-glacial colonisation 10 000 years ago, when marine populations occupied freshwater. All listed environmental changes are quite drastic, hence fish need to adapt adequately.
Genomic changes linked to environmental adaptation
A research team sampled six estuaries along the California coast at two time points; the sample from the first time point was taken right after winter while the second at the end of summer. With this experimental design, researchers were able to monitor the stickleback’s adaptation to summer conditions. Individuals with genetic changes favouring survival and reproduction survived and provided more offspring, thus the frequency of beneficial genetic changes increased within the populations.
DNA isolated from the pectoral fin was sequenced, to compare the genome between the two time points and map it to the stickleback reference genome. Researchers focused on single nucleotide polymorphisms, i.e. variations at single bases within the individual’s DNA sequence, as they wished to reveal whether or not there are significant changes in allele frequencies within estuaries – and if so, whether the changes were shared among estuaries.
The importance of enhanced ion balance for adaptation
Analyses revealed similar changes in allele frequency across at least three different estuaries. Given the consistency, frequency changes were likely linked to parallel evolution, and identified candidate genes – targets for natural selection. To fully understand evolutionary changes, the team ran gene ontology (GO) analysis. GO informs on functions of specific genes and gene products, essentially revealing molecular functions of the identified candidate genes.
Functional enrichment – overexpression – was, non-surprisingly, found in genes associated with osmoregulation – biological internal control of salt concentrations. Wnk4 and Nalcn encode intracellular salt sensors involved in salinity tolerance. Enhancement was found for the Ccny gene, relevant to salinity adaptation. Natural selection also proceeded on mitogen-activated protein kinase genes, which are genes activated by cell division-inducing substances; particularly those expressed in response to osmotic stress.
To absorb calcium from freshwater, which is hypoosmotic to fish plasma, the enhanced ability for calcium binding and transport is required. Fittingly, gene functions relevant for calcium-sensing, homeostasis, and transport were enriched. Genomic changes for osmoregulation enhancement were indeed consistent with osmotic changes introduced by the marine-to-freshwater transition. Researchers thus likely discovered solutions sticklebacks adopted to survive into the next season.
Current research; providing insight into both the past and future
The consistent genomic changes imply that adaptation can be detected over short timescales – even within a single year where the first few generations already face environmental change, as shown by the isolated estuaries mirroring environmental shifts of post-glacial colonisation. The research team hence gained insight into the genomic changes that likely occurred in the past. Acquiring data over multiple seasonal shifts could confirm the results and provide stronger evidence.
Studying the past might be helpful, as we could predict how populations adapt to stressors brought on by climate change. Having observed the rate at which genetic adaptation can occur is certainly good news, as some species might be well-equipped to overcome the environmental climate challenges to come.
Further investigations of populations in dynamic environments should be carried out with experiments of similar methodologies to the above-mentioned. Doing so would enhance our understanding of the mechanisms behind natural selection and provide useful data which could be used to potentially predict the survival success of other species.
Written by Alexandra Lesayova and edited by Diana Barreiros Jorge