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Phenotypic differences between closely related taxa or populations can arise through genetic variation or be environmentally induced, in both cases leading to altered transcription of genes during the structural and functional development of the body. Comparative developmental studies of closely related species or variable populations of the same species can help to elucidate the molecular mechanisms related to population divergence and speciation. Studies of Arctic charr (Salvelinus alpinus) and related salmonids have revealed considerable phenotypic variation among populations and in Arctic charr many cases of extensive variation within lakes (resource polymorphism) have been recorded. One example is the four Arctic charr morphs in the ~10.000 year old Lake Thingvallavatn, which differ in numerous morphological and life history traits. We set out to investigate the molecular and developmental roots of this polymorphism by studying gene expression in embryos of three of the morphs reared in a common garden set-up. We performed RNA-sequencing, de-novo transcriptome assembly and compared gene expression among morphs during a timeframe in early development. Expectedly, developmental time was the predominant explanatory variable. As the data were affected by RNA-degradation, an estimate of 3’-bias was the second most common explanatory variable. Morph, both as a independent variable and as interaction with developmental time, affected the expression of numerous transcripts. The majority of transcripts with significant morph effects separated the limnetic and the benthic morphs. However, gene ontology analyses did not reveal clear functional enrichment of transcripts between groups. Verification via qPCR confirmed differential expression of several genes between the morphs, including regulatory genes such as Arid4a and Tsn. The data are consistent with a scenario where genetic divergence has contributed to differential expression of multiple genes and systems during early development of these sympatric Arctic charr morphs.

As biological diversity of the world is increasingly threatened, it is of great importance to map it and study factors that are important for its origin and maintenance. In recent years scientists have increasingly realized that there is a strong relationship between ecological dynamics and micro-evolutionary processes. To increase our understanding on important ecological factors related to the evolution of biological diversity, a comparative approach involving a high number of populations is powerful. Here, I have used this approach in studies on Icelandic Arctic charr ('Salvelinus alpinus') to gain further understanding of the relationship between ecological factors and phenotypic diversity. My results showed that ecological variables were related to phenotypic diversity of fish. For Arctic charr populations in lakes factors like age of bedrock, origin of water and fish community structure were clearly related to morphological diversity. Numerous populations of small benthic charr have evolved in lava springs in Iceland. These charr are morphologically similar, but differ, nevertheless, in important morphological features related to feeding. I found a clear relationship between diversity in morphology and diet and ecological factors among populations. In particular, there were clear differences in morphology and diet between fish coming from habitats where the lava spring flowed on as a stream compared to habitats where the lava spring flowed into a pond. Laboratory rearing experiments showed that phenotypic plasticity is important for morphological diversity. Populations differed in reaction norms for morphology and the level of plasticity was related to current velocity and amount of lava rock in their habitats. This strongly suggests that plastic responses have evolved within populations. Findings of this study strengthen ideas that ecological factors are important for the origin and maintenance of biological diversity. The relationship between phenotype and ecological factors is not only observed when examining large ecological differences but also on a fine scale, when comparing numerous populations that are phenotypically similar. This strongly suggests that for understanding, managing and conserving biological diversity important ecological variables have to be taken into the account.