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C. alta individuals 10 cm in diameter or greater at breast height were sampled from a 9 ha area inside of a large tract of continuous forest. These trees 10 cm in diameter or greater at breast height are the candidate parents. A sample of seeds was also collected from some of these trees. The genotypes of both the trees and the seeds were determined for 10 nuclear microsatellite loci (see Box 2.1 for an introduction to this type of genetic marker). A subset of these data is shown in Table 4.1. The goal of the parentage analysis in this case is to determine the fathers of the seeds given the known mothers in order to estimate the proportion of seeds that resulted from pollen transport within the sampled plot compared with pollen transport from outside the sampled plot.

The first step in a parentage analysis is to examine the genotypes of an individual progeny and its known parent for allelic matches. C. alta seed genotypes are grouped with their known parent in Table 4.2. For example, in Table 4.2 the genotype of seed 1-1 from tree 989 is given in the first row and the genotype of the known maternal parent tree (989) is given in the second row. At each locus, one (or sometimes both) of the alleles found in the known parent genotype is observed in the progeny genotype. For seed 1-1 from tree 989, the known parent contributed the 336 allele at locus A, the 106 allele at locus B, the 165 allele at locus C, the 2 75 allele at locus D, and the

153 allele at locus E. Given those alleles came from the known parent, the true father must have contributed alleles 327, 91, 185, 287, and 153 at loci A through E. This set of single alleles at each diploid locus is called the paternal haplotype. We can now scan the genotypes of the candidate parents to see whether there is any individual with a haplotype that contains all of those alleles (this is normally done with the assistance of a computer program). All candidate parents that have a matching haplotype are possible fathers of seed 1-1 from tree 989. In this case, tree 1946 is the only individual with the required haplotype and so 1946 is possibly the father while all of the other candidate parents are excluded as fathers due to a genetic mismatch at one or more loci in the paternal haplotype. Repeating this process for the next two seeds also excludes all but a single individual as the father.

With the exclusion of all but a single candidate parent, it would seem like certain identification of the true parent has been accomplished. Unfortunately, it is always possible that any non-excluded candidate parent is not the actual parent. There is the possibility, by chance alone, that an individual possesses a genotype with the same haplotype as the true parent. Evaluating the chance that a non-excluded candidate parent (sometimes called an inclusion or an included parent) is not the true parent requires

Table 4.2 Seed progeny genotypes (top row of every three) given with the known maternal parent genotype (middle row of every three) along with the genotype of the most probable paternal parent (bottom row of every three) from the pool of all possible candidate parents. Alleles in the seed progeny that match those in the known maternal parent are underlined. The known maternal parent is also a candidate paternal parent since this species can self-fertilize. Missing data are indicated by zero.

Genotype

Microsatellite locus... A B C D E

989 seed 1-1

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