The genomic basis of adaptive differentiation between closely related morphs of Arctic charr

Abstract

Exploring the genetic basis of ecological diversification is crucial to understand how diversity is generated and maintained. The overall aim of this thesis is to disentangle the genetic basis behind the ecological differentiation of the Arctic charr in lake Thingvallavatn (Iceland), where this species has diverged genetically and phenotypically into four morphs along the benthic-limnetic ecological axis. Here I focused on studying the genetic underpinnings behind the phenotypic traits involved in this well-characterised case of ecological differentiation: (1) the morphology associated with benthic and limnetic ecologies and (2) the discrete size differentiation. To tackle this, a variety of methodological approaches was used: 1) geometric morphometrics to characterise morphological differentiation across morphs, 2) QTL mapping to map those traits onto the genome, and 3) population genomic approaches to look at the genetic underpinnings behind discrete body size differentiation across morphs. For the geometric morphometrics and the QTL mapping parts of the study, laboratory reared families from the lake were established and for the population genomics part fish were collected from the lake. Throughout this thesis I provide evidence for a genetic basis behind body size and shape in the Thingvallavatn system. QTL mapping revealed that the relative size of the head, maxilla shape and peduncle depth were attributed to single QTL with moderate to high effects, likely complemented with other QTL of small effects. Additionally, genome scans unveiled highly differentiated genomic regions shared between the small and large morph pairs, including a region containing the glypican-6 gene, which is highly conserved in vertebrate evolution, playing a role in cell proliferation and growth. This work significantly contributes to our understanding of ecological diversification and opens avenues for further research in salmonid and other freshwater systems.