Genomic Mapping of Speciation-Related Traits in Hybridizing Sculpins (Cottus)

European freshwater sculpins, Cottus rhenanus and Cottus perifretum, have formed hybrid lineages (invasive Cottus) in the Lower River Rhine. The hybrid Cottus particularly resembles one of its ancestral species, C. perifretum, in phenotypic features. This contrasts with the fact that the invasive genome is thoroughly admixed. It is hence of interest to investigate the genetic basis of phenotypic traits that represent differentiation among Cottus species, and then to learn about the evolution of these traits in the hybrid lineage. This dissertation combined genetic mapping and quantitative trait loci (QTL) mapping methods with next generation sequencing and candidate gene analysis to explore the genomic basis of Cottus hybrid traits that are observed in nature. Two independent groups of interspecific F2 crosses were generated between C. perifretum and C. rhenanus. EST libraries representing the parental species and invasive Cottus were sequenced using the Roche 454 GS-FLX platform. These reads were assembled into contigs that were mapped against 5 teleost model fish genomes and protein databases. 252 diagnostic SNPs were developed and typed for all F2 crosses using Illumina GoldenGate genotyping Assay. A consensus map was constructed that contains 24 linkage groups (LG) with a total length of 1575.4 cM which is in agreement with available karyotype information for Cottus. The highest conserved synteny of the Cottus map was found with the stickleback genome in which 97.3% of the homologous markers agree among linkage groups. This underlines that the stickleback genome provides an excellent reference to explore the Cottus genome. We have employed genetic and QTL mapping to detect transmission distortion regions as signs for hybrid genetic incompatibilities in the parental species as well as sex determination (SD) regions. This allows the exploration of correlations between SD and genetic incompatibilities to test whether effects related to Haldane’s rule contribute to the observed differentiation in natural hybridizing Cottus. A male heterogametic (XY) SD region was found in different LGs in the two parental species of invasive Cottus. Conserved synteny with sequenced fish genomes reveals that SD in Cottus is not based on the same genomic regions found in model organisms. Signs for genetic incompatibilities were not restricted to males, not linked to SD regions and mostly specific to single mapping families. This indicates a fast evolutionary turnover of SD in Cottus, and does not provide evidence for fitness effects related to Haldane’s rule. As a whole, the incompatibility factors and SD loci identified here are not likely to cause intrinsic selection that could affect the gene pool of natural hybrids in a simple and predictable way. Two morphological traits, scale-like prickling and body shape, vary among Cottus species and are extreme in the hybrid lineage. The Ectodysplasin (EDA) signaling pathway provides promising candidates to investigate the genetic basis of prickling because it is well known to affect the development of scales in fishes. To test whether the EDA signaling pathway also controls natural variation of Cottus, we identified and mapped Cottus EDA signaling pathway components and performed QTL mapping analysis for prickling and body shape. A highly significant QTL that affects prickling in all F2 crosses was detected in an interval that contains the EDA receptor (Edar) gene in Cottus LG 3 but none of the other EDA pathway genes. The same QTL region also has a strong effect on body shape. An investigation of gene structures suggests that the genomic architecture of the Edar gene makes it a more suitable target for evolutionary changes than other components in this pathway. Ancestral allele frequencies within EDA pathway gene regions in the invasive gene pool show that Edar has the genomic ancestry preference for C. perifretum (85%-96%). This correlates with the phenotypic similarity of invasive Cottus with that parental species. The Edar carrying QTL is currently the best candidate that strongly determines the visible phenotypic variation of hybrid Cottus in the River Rhine system. EDA signaling constitutes a key adaptive trait in sticklebacks and our results suggest that the same pathway may also cause conspicuous variation of prickling in Cottus.