We study the evolution of genes and gene expression using the fruit fly Drosophila melanogaster as a model system. Current projects focus on variation in gene expression between populations and sexes, as well as the population genetic and functional analysis of gene regulatory elements.
Photo: Amanda Glaser-Schmitt.
In general, we are interested in understanding the molecular basis of adaptation. We study the evolution of genes and gene expression using the fruit fly Drosophila melanogaster as a model system. Our research can be divided into three major areas:
Differences in gene expression are thought to underlie many of the phenotypic differences between species and populations. Transcriptomic technologies, such as high-throughput RNA sequencing (RNA-seq), have made it possible to identify the genes that differ in expression between species or vary in expression among individuals of the same species. Such studies have revealed that there is considerable expression divergence between closely related species, as well as abundant expression variation within species. Furthermore, there are extensive differences in gene expression between males and females of the same species. A current challenge in evolutionary genetics is to identify the specific genetic changes responsible for differences in gene expression and to determine how these changes impact an organism's fitness.
We are studying gene expression variation within and between populations of the fruit fly Drosophila melanogaster, a species that has its origin in sub-Saharan Africa and only relatively recently has become a successful colonizer of other word-wide habitats. In order to better understand the role of gene regulatory changes in adaptation, we conduct both genome-wide and candidate-gene studies using flies from ancestral and derived populations. The long-term goal is to identify specific genetic polymorphisms that underlie gene expression divergence and to determine the population genetic mechanisms that are responsible for maintaining them in natural populations. A further goal is to determine the effect that variation in gene expression has on an organismal phenotype that may be subject to natural selection.
It is well established that new protein-coding genes can emerge from existing genes via duplication or by the fission/fusion of coding sequences. More recently, an alternative mechanism has gained increasing attention, namely de novo gene emergence. De novo genes originate from non-coding DNA by acquiring a novel open reading frame (ORF) and the ability to be transcribed and translated. We study the earliest stages of de novo gene formation by identifying newly-evolved, expressed open reading frames (neORFs) in the genomes of several Drosophila species, including multiple inbred lines of each species. These data allow us to determine the evolutionary and population dynamics of de novo genes and characterize the features that allow them to spread throughout a population or species.
Photo: John Parsch
Similar to humans, Drosophila have chromosomal sex determination, with females having two X chromosomes and males having one X and one Y chromosome. The male-specific Y chromosome is highly degenerated and contains very few genes. The X chromosome, in contrast, contains many genes (about 17% of the genes in the Drosophila genome) that are expressed in both sexes. The difference in copy number between males and females makes the X chromosome subject to unique evolutionary forces and gene regulatory mechanisms. For example, in male somatic cells, the expression of genes on the X chromosome is increased in order to compensate for it being present in only one copy. This process is known as dosage compensation. In the male germline, dosage compensation does not occur and expression of the X chromosome is suppressed through a mechanism similar to the meiotic sex chromosome inactivation (MSCI) known in mammals.
We are studying the suppression of X-linked gene expression in the male germline to better understand this form of sex-, chromosome-, and tissue-specific regulation. For example, we are working to identify and characterize mutant strains that are defective in male germline X suppression in order to elucidate the genes and molecular mechanisms responsible for this unique type of regulation and how they influence genome evolution.
Professor
Evolutionary and Functional Genomics
Glaser-Schmitt A, Lemoine M, Kaltenpoth M, Parsch J. (2024) Pervasive tissue-, genetic background-, and allele-specific gene expression effects in Drosophila melanogaster. PLoS Genet. 20:e1011257.
Glaser-Schmitt A, Ramnarine TJS, Parsch J. (2023) Rapid evolutionary change, constraints and the maintenance of polymorphism in natural populations of Drosophila melanogaster. Mol Ecol. 17024.
Grandchamp A, Kühl L, Lebherz M, Brüggemann K, Parsch J, Bornberg-Bauer E. (2023) Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster. Genome Res. 33, 872-890.
Belyi A, Argyridou E, Parsch J (2020) The influence of chromosomal environment on X-linked gene expression in Drosophila melanogaster. Genome Biology and Evolution. 12:2391-2402.
