Do polymorphic loci require large sample sizes to estimate genetic
distances?

S T Kalinowski1

1Department of Ecology, Montana State University, Bozeman, MT 59717, USA

Correspondence to: ST Kalinowski, Department of Ecology, Montana State
University, Bozeman, MT 59717, USA. E-mail: skalinowski{at}montana.edu

Abstract

The coefficient of variation of estimates of three genetic distances
(standard genetic distance of Nei, chord distance, FST) was examined with
computer simulation to determine if large samples (per population) are
necessary to precisely estimate genetic distances at loci with high levels
of polymorphism. These simulations showed that loci with high mutation rates
produce estimates of genetic distance with lower coefficients of variation
than loci with lower mutation rates - without requiring larger sample sizes
from each population. In addition, the rate at which increasing sample sizes
decreases the coefficient of variation of estimates of genetic distances was
shown to be approximately determined by the value of FST between the
populations being sampled. When FST was greater than 0.05, sampling fewer
than 20 individuals (per population) should be sufficient. When FST was less
than 0.01, sampling 100 individuals (per population) or more will be useful.

Heredity (2005) 94, 33-36. doi:10.1038/sj.hdy.6800548
Published online 25 August 2004

Keywords

genetic distance; estimation; sampling; study design; mutation rate

Introduction

Evolutionary and conservation geneticists frequently rely on neutral
molecular data to describe population structure. In the past 30 years, a
parade of molecular markers have been used, from blood proteins to
microsatellites. This progression has been motivated, at least in part, by a
search for loci with more variation. Loci with many alleles, such as
microsatellite loci, have unprecedented ability to detect and describe
genetic differences between populations (eg Hedrick, 1999; Kalinowski,
2002a).

However, loci with scores of alleles have forced population geneticists to
re-evaluate how genotypic data are analyzed and interpreted. The most
fundamental result of this re-evaluation has been increased awareness that
statistically significant genetic differences are not always biologically or
evolutionarily significant (eg Waples, 1998; Hedrick, 1999). One question
that has received little attention in the literature is how high levels of
polymorphism affect study design. This may be because most geneticists using
highly polymorphic microsatellite loci have already concluded that large
sample are needed to estimate genetic distances at loci with many alleles.
All the literature that I am aware of supports this belief. For example, Nei
(1978) analyzed the sampling variances of his genetic distances, and
concluded that 'more individuals should be examined when heterozygosity is
high than when it is low.' Baverstock and Moritz (1996) concluded that 'it
is clear that large sample sizes are needed' to describe population
structure at hypervariable loci. Most recently, Ruzzante (1998) used
computer simulations to show that polymorphic loci have high sampling
variances when sample size is small. Each of these authors, however,
examined the relationship between samples sizes and sampling variance.

This focus on sampling variance has been misleading for two reasons. First,
genetic distances are derived measures of genetic differentiation. They do
not necessarily have high sampling variances when estimates of allele
frequencies are imprecise. For example, high mutation rates usually decrease
the sampling variance of FST. Second, sampling variances are not always an
appropriate measure of precision to compare study design strategies.
Consider the standard genetic distance, DS, between two populations that
have been isolated for t generations. The sampling variance of DS will be
higher at loci with high mutation rates than at loci with low mutation
rates. However, the parametric genetic distance will also be higher

 Full Text at Nature Heredity
http://www.nature.com/cgi-taf/DynaPage.taf?file=/hdy/journal/v94/n1/full/6800548a.html

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