In many organisms sex is determined by a specific pair of chromosomes (the sex-chromosomes) which differ between males and females. For example, in almost all mammalian species females carry two X chromosomes and males carry one X and one Y. Usually the X chromosome is quite similar to the autosomes; the Y chromosome is the odd one, by having a very low number of genes, and a large amount of teterochromatin and repetitive DNA. Y chromosomes are widespread, and evolved independently in many taxa (Bull 1983). Hence their origin and evolution is a major biological question. Notwithstanding their enormous differences, X and Y are believed to have evolved from an initial state of similarity, more specifically from an ordinary pair of autosomes (Bull 1983). Progressive gene loss from the Y resulted in a mostly degenerated chromosome. Direct evidence for this hypothesis came from the finding that most of the few genes of the Y are shared with the X (e.g., in humans; Skaletsky et al. 2003). Although it is certain that Y chromosomes usually arise from the degeneration of X chromosomes, important questions about their origin and evolution remain unanswered. In our project we will investigate some of these questions (below), using Drosophila ("vinegar flies") and Rhodnius prolixus (a vector of Chaga's Disease) as experimental models. Gene loss and gain are known to play an important role on the evolution of the Y. By studying the gene content of the Y of approximately 300 Drosophila species we will get a clearer picture of these processes. We found that the ancestral Y of Drosophila became part of an autosome in D. pseudoobscura, and was replaced by a new construct of unknown origin. This finding has obvious implications for the origin and evolution of the Y, and raises the question of how frequent this phenomenon is. The study of 300 Drosophila Y will answer this question. A major obstacle to the study of Y chromosomes is their poor assembly in WGS genome projects. We developed most of the available bioinformatics methods to identify the pieces of the Y, but they still produce many false positives. We will improve these methods to allow the study of the Y in a diverse set of organisms that are being sequenced. We will do an in depth study of one of them: We are participating in the genome project of the insect R. prolixus (a vector of Chaga's disease), and it will be carried in a way that is particularly suitable to Identify Y-linked genes. In nature embryos "decide" to develop as males or females by many different forms, but sex- chromosomes are the most popular one. Our own species employ them: males are "XY" and females are "XX". Our project investigates the origin and evolution of the Y chromosomes, using insects. [unreadable] [unreadable] [unreadable]