Duplicated genes and their relevance in the process of speciation

An integral part of evolution, the formation of species, is less well understood than other areas of evolutionary biology. Speciation is a fundamental process that creates the great diversity of species in the world, and a deeper insight into its mechanisms is highly desirable. To achieve this goal, the molecular basis of speciation must be elucidated and characterized in detail. This study uses two approaches to contribute to the understanding of the genetics of speciation: A screen for positively selected, young duplicated genes, and in depth analysis of a proposed "speciation gene", Dnahc8. Young duplicated genes may be positively selected in only one of two diverging populations, and through rapid change create an incompatibility between the two emerging species. To find candidates of this type a microsatellite screen for selective sweeps is conducted, in which microsatellite loci close to the genes in question are typed and assayed for reduced variability. Using a measure developed for this problem, the lnRH statistic, subspecies or populations are compared, and selective sweep loci identified. The screen results in thirteen candidate sweep loci in (sub)species comparisons, and fifteen between populations of the same species. Furthermore, comparisons of lnRH values to synonymous substitution rates (KS) of genes show that the youngest duplicated genes of the set do not seem to be evolving under positive selection. To test whether the duplication time correlates with the divergence time estimated from the synonymous substitutions rate, a subset of duplicate pairs was tested for presence in different mouse species. For most duplicates, KS between copies increases with age, but three pairs have very low KS values that do not correspond to their age. Gene conversion is discussed as a possible explanation for this result. The Dnahc8 gene is already known to cause reproductive isolation between Mus spretus and Mus mus domesticus. It encodes an axonemal dynein protein that is involved in sperm tail formation, and hybrid animals have deformed, immotile sperm. Here, the entire coding sequence of Dnahc8 is determined of six mouse species in addition to the M. m. domesticus sequence already known. In addition, several exons are sequenced in a population sample of M. spretus and the full-length gene sequenced for ten M. m. domesticus. Tests for positive selection based on polymorphism data and codon-based maximum likelihood methods are performed with this data. There is evidence that Dnahc8 may be evolving under relaxed constraint in the lineage of M. m. domesticus. However, no significant evidence for positive selection could be found using any method. In addition to the sequence data, quantitative real time PCR is used to measure the level of expression in eight tissues of seven mouse species. Large differences in expression pattern are identified between M. spretus and M. m. domesticus: Dnahc8 expression is eight fold lower in M. spretus testis compared to M. m. domesticus. Together these results suggest that the nature of the incompatibility caused by Dnahc8 may lie in gene regulation rather than differences in the amino acid sequence.