Abstract
Species distribution describes the spatial arrangement and spread of individuals within a species across its geographic range. Multiple factors, such as disturbance, dispersal distance and ability, population dynamics, and human-made barriers can all affect species distributions. Freshwater ecosystems are among the most threatened habitats on Earth. Human activity, such as the building of dams, can greatly impact not only the environmental conditions of freshwater ecosystems, but also the connectivity between rivers, lakes, and the coast. Altered connectivity between populations, especially in the case of diadromous fishes, can interrupt natural migrations, dispersal distances and population connectivity. Some diadromous species undergo landlocking, where populations become restricted to freshwater, losing their marine phase. Landlocking can result in behavioural, morphological, and genetic changes in populations as they adapt to new environmental conditions.
Landlocked fish populations provide an opportunity to unravel adaptive responses to extreme environmental change. The overarching aim of this thesis is therefore to examine the genetic responses of three diadromous fish species that have undergone landlocking in New Zealand. This involved quantifying the genetic isolation of populations with distance, geographic location, and environment, and examining differential gene expression between diadromous and landlocked populations.
Genotyping by Sequencing (GBS) was used to obtain single nucleotide polymorphism data for populations of kōaro (Galaxias brevipinnis) across diadromous, landlocked, and offshore island populations in New Zealand. Population structuring and differences in genetic diversity were observed between and among diadromous and landlocked populations, illustrating the critical role of landlocking and isolation, but also the effect of spatially-explicit selection pressures that likely play a key role in populations’ evolutionary histories.
RNA sequencing was then used to explore the differential gene expression responses within landlocked populations compared to diadromous populations in two species: the common bully (Gobiomorphus cotidianus) and the common smelt (Retropinna retropinna). In both cases RNA-Seq data provided the first assembled and annotated transcriptomes for these species. The comparisons illustrated differences between treatments, sexes, and life histories under freshwater and salinity treatments. Gene ontogeny suggested that some of the differences in expression were in responses to divergent viral and pathogen communities. In Retropinna retropinna populations, differential gene expression was notably observed between mainland populations and insular (Chatham Island) populations.
It was noticed that landlocking and isolation from the sea didn’t result in a decrease of within-population genetic diversity, but instead local selection pressures likely play a key role on species evolutionary histories. However, the exposure to salinity treatments resulted in differential regulation of genes in common bully and common smelt. Additionally, it was revealed that landlocked fish might be influenced more by selective pressures alongside the shift in salinity, such as locality-specific water temperature to the loss of migratory behaviours.