A survey of genome wide sequence differences and comprehensive phenotypic differences of many isolates of Saccharomyces cerevisiae and S. paradoxus revealed an apparent paradox of low phenotypic diversity in S. paradoxus while having great genotypic diversity while the opposite is seen in S. cerevisiae. This paradox may be resolved by the understanding of adaptation of populations to their environments where complex traits are composed of linked antagonistic QTLs which can be broken up to reveal phenotypic diversity due to genetic interactions arising from outbreeding. An initial testable model will be described that may account for various observations.