Male-specific Y chromosomes degenerate: they lose most of their protein-coding genes, accumulate repetitive DNA and often acquire a genetically inert heterochromatic structure. In response, X chromosomes often become dosage compensated, again involving epigenetic modifications .
Young sex chromosomes found in many Drosophila species offer a unique opportunity to study the evolution and function of sex chromosomes caught in the act of diverging from autosomes and each other, while acquiring the distinct characteristics seen in older sex chromosomes. Our lab has been pioneering genome-wide comparative and functional analysis of sex chromosomes in Drosophila, including whole-genome sequencing and assembly, transcriptome and chromatin profiling across tissues and development, transgenics, and population genomics, to identify the molecular changes causing sex chromosome differentiation, and the evolutionary forces driving these changes. We have also developed powerful statistical methods for identifying sex-linked genes by sequencing that is applicable to virtually any organism, which has allowed us to study the functional and evolutionary properties of sex chromosomes in several non-model species, including birds, snakes and various insects, in an unprecedented way.