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Catalán, Ana (2014): Local adaptation of gene regulation in natural populations of Drosophila melanogaster. Dissertation, LMU München: Faculty of Biology



The central goal of this dissertation is to understand the genetic and functional aspects of how populations adapt to new or changing environments. Genetic variation within a population, either at protein coding genes or at regulatory elements, provides the substrate upon which natural selection can act to drive adaptation. There is considerable evidence that changes in gene expression account for a large proportion of morphological, physiological and behavioral variation between and within species that can contribute to adaptation and speciation. Due to the major role that gene expression changes can have in shaping phenotypes, the first three chapters of this dissertation deal with the study of how changes in gene expression can facilitate adaptation. I use Drosophila melanogaster from ancestral and derived regions of the species' range as a model system for studying local adaptation. In chapter 1, I perform high-throughput RNA-sequencing (RNA-seq) of brain tissue of flies from an ancestral (Zimbabwe) and a derived (the Netherlands) population. The whole brain transcriptome was assayed for differences in gene expression between African and European flies in order to understand how differences in brain expression may lead to local adaptation. I found over 300 candidate genes that differed significantly in expression between the populations, including a cluster of genes on chromosome arm 3R that showed reduced expression in Europe and genetic evidence for positive selection. Other candidate genes involved in stress response, olfaction and detoxification were also identified. Additionally, I compared brain gene expression between males and females and found an enrichment of sex-biased genes on the X chromosome. Chapter 2 presents a detailed study of one of the candidate genes identified in chapter 1. The metallothionein gene, MtnA, shows over four-fold higher expression in the brain of European flies than of African flies. I found a derived deletion in the 3’ untranslated region (UTR) of MtnA that segregates at high frequency within the Dutch population, but is absent from the Zimbabwean population. The presence of the deletion was perfectly associated with the observed variation in MtnA expression. When additional populations of D. melanogaster were screened for the presence of the deletion, I found that it showed a clinal distribution that was significantly correlated with latitude and temperature. Furthermore, using population genetic data and a selective sweep analysis I show that the MtnA locus is evolving under positive selection. In Chapter 3 I report a population genetic analysis of the enhancer region of CG9505, a gene that shows significantly higher expression in European than in African populations of D. melanogaster. A previous study found that there was very low nucleotide polymorphism in the enhancer region of CG9509 in flies from the Netherlands, a pattern that is consistent with a selective sweep. I analyzed an additional set of five populations from Zambia, Egypt, Malaysia, France and Germany in order to gain a better understanding of how selection has affected the evolution of this enhancer. I found that there is a depletion of nucleotide diversity in all of the non-sub-Saharan populations (Egypt, Malaysia, France and Germany), which share a common high-frequency derived haplotype. Population genetic analyses suggest that a selective sweep took place in the enhancer region of CG9509 just after D. melanogaster migrated out of sub-Saharan Africa. Finally, in chapter 4 I performed in situ hybridizations to examine the expression of tissue-specific reporter genes in the D. melanogaster testis. In the male germline of D. melanogaster, reporter genes that reside on the X chromosome show a reduction in expression relative to those located on the autosomes. This phenomenon was demonstrated by randomly inserting reporter gene constructs on the X chromosome and the autosomes. By doing in situ hybridizations on testis of flies having reporter gene insertions on the X chromosome and autosomes, I could show that the expression difference mainly occurs in meiotic and post-meiotic cells. For most constructs, expression was very low or absent in the testis apex, which is enriched with pre-meiotic cells. These results suggest that the suppression of X-linked gene expression in the Drosophila male germline occurs through a different mechanism than the MSCI (meiotic sex chromosome inactivation) known to occur in mammals.