Variation in reproductive compatibility between sexual partners, from both the same and different populations, plays a pivotal role in the evolution of reproductive traits, sociality, reproductive isolation, speciation, and ultimately levels of biological diversity. However, the genetic mechanisms causing variation in reproductive compatibility between sexual partners are currently unclear, which compromises our ability to predict: (1) the evolutionary trajectory of sexually selected traits, (2) when social versus pair breeding systems will evolve, (3) the occurrence and rate of population divergence, and (4) the biological underpinnings of variation in offspring growth and survival resulting from both within and between population matings. To date it has been difficult to address these issues because it requires identifying the molecular basis of variation in reproductive compatibility within and between populations that have diverged over different periods of time. Here we aim to resolve these issues by: 1. Identifying genes that explain variation in reproductive success caused by reproductive compatibility between sexual partners. 2. Identifying differentiated regions across the genome between populations that have diverged across a gradient of evolutionary time. 3. Testing if the processes causing reproductive isolation originated within ancestral populations by examining if the genes influencing hybridisation success also determine reproductive compatibility within populations. 4. Examining the biological function of genes present in the genomic regions that explain variation in reproductive compatibility both within and between populations. This research will be conducted on three different populations (S. camelus australis, S. camelus massaicus, S. camelus domesticus) of ostriches that represent a gradient of genetic divergence (estimated range from 0.1 to 1 mya)10 kept at the Western Cape experimental research station. These populations constitute an ideal system to evaluate the genetics of reproductive incompatibility for the following reasons: (i) since 1992, ~250 randomly chosen pairs have been closely monitored each year. Many individuals have remained in the breeding population for several years and some of these have been switched between sexual partners each year whereas others have remained with the same partner. This allows gene-interactions between sexual partners to be examined whilst controlling for the effects of mate choice and yearly variation. (ii) During each breeding season detailed data on the number of eggs laid, egg mass, embryo development (fertility), hatching success, offspring growth, disease outbreaks and offspring survival have been recorded for each of the three populations and their hybrids. This has generated a dataset totalling 4024 breeding attempts involving 1421 individuals resulting in over 90000 offspring; (iii) for each of the three populations there are pedigrees available ranging from 3 to 8 generations and quantitative genetic analyses on pure populations suggest levels of heritability in reproductive and offspring traits are up to ~45%; (iv) individuals from all three populations produce fertile offspring when paired together, although evidence suggests there is reduced fitness of hybrid and individuals discriminate against sexual partners from different populations; and (v) the ostrich genome has just been sequenced, assembled and made publicly available.