Maximum likelihood vs. minimum chi-square-A general comparison with applications to the estimation of recombination fractions in two-point linkage analysis

Abstract

Some relationships between the estimates of recombination fraction in two-point linkage analysis obtained by maximum likelihood, minimum chi-square, and general least squares are derived. These theoretical results are based on an approximation for the multinomial distribution. Applications (theoretical and experimental) with RFLP (restriction fragment length polymorphism) markers for a segregating F2 population are given. The minimum chi-square estimate is slightly larger than the maximum likelihood estimate. For applications, however, both estimates must be considered to be approximately equal. The least squares estimates are slightly different (larger or smaller) from these estimates.Key words: linkage analysis, recombination fraction, maximum likelihood, minimum chi-square, general least squares.