This function estimates Fst between population pairs based on Weir and Cockerham's theta (Weir & Cockerham 1984) adapted for pairwise comparison from a GENEPOP data object (Rousset 2008). Missing genotype values in the GENEPOP file ("0000" or "000000") are simply ignored.

1 | ```
thetaWC.pair(popdata)
``` |

`popdata` |
Population data object created by read.genepop function from a GENEPOP file. |

Weir and Cockerham (1984) derived an unbiased estimator of a coancestry coefficient (theta) based on a random effect model. It expresses the extent of genetic heterogeneity within the population. The second stage common approach is to investigate the detailed pattern of the population structure, based on a measure of genetic difference between pairs of subpopulations (demes). We call this by pairwise Fst. This function follows the formula of Weir and Cockerham's theta with the sample size *r* = 2. Given the pair, our finite sample correction multiplies *a* of Weir & Cockerham's theta by (*r* - 1) / *r* (equation 2 in p.1359 of Weir & Cockerham 1984).

Matrix of estimated pairwise Fst by theta with finite sample correction.

Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada

Rousset F (2008) Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. *Mol. Ecol. Resources*, 8, 103-106.

Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. *Evolution*, 38, 1358-1370.

`read.genepop`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
# Example of GENEPOP file
data(data.JSM)
cat(data.JSM$MS.genepop, file="JSM_MS_genepop.txt", sep="\n")
cat(data.JSM$popname, file="JSM_popname.txt", sep=" ")
# Data load
# Prepare your GENEPOP file and population name file in the working directory
# (Here, these files were provided as "JSM_MS_genepop.txt" and "JSM_popname.txt".)
popdata <- read.genepop(genepop="JSM_MS_genepop.txt", popname="JSM_popname.txt")
# theta estimation
result.theta.pair <- thetaWC.pair(popdata)
write.csv(result.theta.pair, "result_thetaWCpair.csv", na="")
print(as.dist(result.theta.pair))
``` |

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