Genes on the marsupial Y chromosome

The XX female/XY male sex chromosome system of therian mammals evolved from a homologous pair of autosomes following evolution of a testis-determining factor on the Y chromosome. Over time, male-advantage alleles accumulated around the sex-determining locus leading to suppression of recombination between the X and Y to preserve the male specificity of this region. In the absence of recombination, the Y chromosome serially degraded, resulting in the dimorphic sex chromosomes seen in extant mammals. The highly heterochromatic Y makes traditional "shotgun sequencing" impractical and therefore very few Y chromosomes have been studied in detail. Most knowledge of Y chromosome gene content and structure comes from eutherian mammals. Marsupials occupy a particularly informative phylogenetic position between the bird-mammal divergence and eutherian radiation with the marsupial Y evolving independently from the eutherian Y for 148 million years. In order to understand how the therian Y chromosome has evolved, I focussed on the Y chromosome of an Australian marsupial, the tammar wallaby (Macropus eugenii). The isolation of Y chromosome specific sequences is key to expanding our knowledge of the marsupial Y chromosome. I isolated and characterised clones from a testis cDNA library and two male tammar wallaby BAC libraries using a microdissection derived Y chromosome probe as well as three-dimensional PCR screening. Because the long arm of the tammar wallaby Y chromosome is known to contain heterochromatic sequences shared with the short-arm of the X chromosome, efforts were focussed on the short-arm of the Y to examine the location and arrangement of genes. I identified four novel genes on the tammar wallaby Y, expanding my work to other marsupials to demonstrate that there are at least ten genes which are X/Y shared in three orders of marsupials. This enabled me to develop a model to describe the evolution of the marsupial Y chromosome. The tammar wallaby Y chromosome appears to be an intricate mixture of different repetitive elements; highly iterated elements found throughout the genome, X-Y specific repeats derived from the remnants of a shared NOR and Y-specific repetitive elements. This study catalogued 39 BAC clones mapping to the tammar wallaby Y revealing the structure of the Y to be a convoluted mixture of simple repeats, more complex repetitive elements shared with the X as well as Y-chromosome specific elements, all providing the framework within which the small number of Y genes reside. The gene repertoire of the marsupial Y chromosome implies that multifunctional genes on the proto XY were retained and subsequently specialised on the therian Y, as evidenced by the involvement of human and mouse X-borne homologues (of marsupial Y genes) in brain and testis function. The marsupial Y chromosome has degraded in parallel with the eutherian Y. The common therian ancestor had a Y chromosome with at least twelve X-Y shared genes. Some of these genes evolved male-specific functions and are found today on the Y chromosomes of various marsupial and eutherian mammals. Other genes were gradually pseudogenised and ultimately lost from the Y chromosome in a lineage specific fashion