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nearly complete genomic haplotype, each expressed in a different random genetic background. A hemiclone is equivalent to the offspring that would be produced by randomly picking a group of eggs from the base population and then fertilizing each egg with a cloned copy of the same sperm.

STAGE 3: MEASURING GENETIC VARIATION

To measure genetic variation for an arbitrary trait in the base population, multiple genomic haplotypes are independently sampled, cytogenetically cloned, and used to construct clonal amplification lines (Fig. 3.3). Next, hemiclones are constructed independently two or more times from each clonal amplification line, and the phenotypic value of each individual in each hemiclone is measured. Finally, random-effects analysis of variance is used to partition phenotypic variation among and between hemiclones to estimate additive genetic variance among hemiclones (Chippindale et al., 2001). Individuals within a hemiclone share half of their genetic variation in common, so that two times the additive genetic variation among hemiclones divided by the total phenotypic variation approximates the heritability of the trait in the base population.

The additive genetic variation among hemiclones contains no nonadditive dominance variation, nor epistatic variation between alleles that reside in the genomic haplotype of a hemiclone and those in its genetic background. It does, however, potentially contain nonadditive epistatic variation between nonallelic genes that reside in the same genomic haplotype. Epistasis can occur between nonallelic genes that reside in genomic haplotypes inherited from (i) the father, (ii) the mother, or (iii) a mixture of these two. Only epistasis between genes that both reside in the paternal haplotype are included in the measure of additive genetic variation among hemiclones (a quarter of the four possible pair-wise types). The inclusion of some epistatic variation in the estimate of additive genetic variation is not unique to hemiclonal analysis. In fact, because of the lack of recombination in male Drosophila, it is a confound that is shared in common with most forms of quantitative genetic analysis with Drosophila. For example, a paternal half-sib design to estimate additive genetic variance includes epistatic variance among alleles that reside on the same chromosome because lack of recombination in male Drosophila keeps these alleles together during meiosis. Similarly, the well-known North Carolina II breeding design (Comstock and Robinson, 1952) also confounds additive and epistatic variation, when applied to D. melanogaster, because the protocol uses balancer chromosomes that cause whole chromosomes to segregate like single giant supergenes (e.g., see Hughes, 1997).

In effect the hemiclonal analysis technique of estimating additive ge-



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