Individuals are enormously genetically diverse, even when those individuals live close together in the same environments. This high diversity has important implications for sustainable agriculture and for the conservation of biodiversity because genetic diversity allows crops and wild plants and animals to persist in the face of disease and other environmental challenges. Understanding genetic diversity is also important in medicine because individuals have different susceptibility to disease and they can respond differently to the same treatment; this is the foundation of the recent emphasis on "personalized medicine". However, high genetic diversity is surprising because we expect that local populations that share a common gene pool and experience similar environments should be relatively genetically homogenous. This project addresses the debate about why individuals within populations (including humans) are so genetically diverse. Specifically, the research team will test a prominent hypothesis: that high diversity is maintained because rare gene variants confer an advantage to individuals who bear them (i.e., they are favored by natural selection). The project will also identify the genes that are the direct targets of this kind of selection. Because experiments required to answer these questions would be impossible in humans or agricultural species, the project will use a vertebrate animal that has well-known natural history, ecology, and behavior, and for which the genome sequence has recently become available (the Trinidad guppy). These small fish have high genetic diversity for body color, and this research will examine competing ideas about why: (1) fish with rare patterns survive better, or (2) fish with rare patterns reproduce more successfully. This project will also produce educational material and activities for school children. This material will enhance students' understanding of genetics, ecology, and evolutionary biology by using an animal with which many students are already familiar since guppies are popular in home aquariums.
Accounting for the persistence of high genetic diversity in ecologically-important traits is a fundamental problem in population genetics, and one that has fundamental implications for agriculture, medicine, and conservation biology. Debate about what processes maintain variation has led to the development of important population-genetic principles and hypotheses, but the larger question remains unanswered. This project will test the hypothesis that selection that varies in space or time ("balancing selection") maintains genetic diversity in natural populations and will link these selective processes directly to the genetic variants they target. Researchers will combine genomic and ecological approaches in a species exhibiting one of the best-known cases of adaptive polymorphism, the colour patterns in the Trinidadian guppy (Poecilia reticulata). Field and laboratory studies of predator density, reproductive behavior, and color-pattern variation will determine which ecological processes promote genetic variation. Whole-genome sequencing of guppies from 13 natural populations will identify regions of the genome enriched for intermediate-frequency alleles; using data from many populations will allow us to differentiate between loci under balancing selection and those that are polymorphic because of non-selective processes such as random genetic drift and migration. This multipronged approach will enable linking evolutionary processes that maintain variation directly to the genetic variants (polymorphisms) they target.