Utilisation and conservation of farm animal genetic resources 55
Chapter 3. What is genetic diversity?
John Woolliams
1,2
and Miguel Toro
3 1
Roslin Institute, Roslin, Midlothian EH25 9PS, United Kingdom
2
Department of Animal and Aquacultural Sciences, Norwegian University of Life Science, Box 1432, Ås, Norway
3
Department of Animal Breeding, National Agriculture and Food Research Institute, Carretera La Coruna km7, 28040 Madrid, Spain
Questions that will be answered in this chapter: What is meant by diversity?
In what ways can diversity be quantiied? To what extent are diferent measures of genetic diversity describing the same
phenomenon? How can we measure change in genetic diversity?
Summary
his chapter surveys the diferent ways in which the diversity we observe within a species can be quantiied. It will consider: 1 how the diversity we observe in the population
of a species can be divided into diferences between breeds, or more generally sub- populations, and diferences within these breeds; 2 how diversity within breeds can
be described by examining the pedigrees of individuals, or examining the sequences of DNA carried by individuals; 3 how a number of diferent approaches have been used
to measure the genetic diversity; and 4 how many of these measures may be related to the concepts of inbreeding.
1. Introduction
Diversity, in its most commonly recognised sense, is the observation of diferent forms and functions between species. However this deinition is too narrow and fails
to recognise that individuals within a species also difer in many characteristics or phenotypes; these phenotypes may be qualitative, such as coat colour or pattern, or
quantitative, such as height and weight. In domestic animals particular phenotypes will have evolved because of their utility to particular human populations. he most
useful concept in quantifying these diferences is the fundamental statistical concept of variance since it can be decomposed into sub components, and in particular, if we
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56 Utilisation and conservation of farm animal genetic resources
John Woolliams and Miguel Toro
have a sum of independent variables each with some variance, then the variance in the sum of the variables is equal to the sum of the variances. his property will be used in
what follows at several points.
We may deine the total diversity in a trait within a species as the variance of the phenotypes. Of course, not all the variance we observe is genetic in origin. For example
whilst we may expect a considerable similarity between identical twins, they will not be totally identical since diferences will arise through the environmental impact of life-
history events from conception onwards. In the study of genetics it is widely assumed as a irst and useful approximation that we can decompose the phenotype into two
independent components one due to genetic efects and one due to environmental efects i.e. P = G + E, where P has total phenotypic variance σ
P 2
, G has total genetic variance σ
G 2
, and E has total environmental variance σ
E 2
. Using the decomposition property of variance for independent efects, described above, we ind σ
P 2
= σ
G 2
+ σ
E 2
, and so the total variance of the phenotypes that is observed can be uniquely decomposed into a
genetic and environmental component. he fraction of the total phenotypic variance that is of genetic origin is called the
broad sense heritability, denoted H
2
. herefore by conducting experiments to estimate H
2
the total genetic variance can be calculated in the population.
However experiments to estimate H
2
are surprisingly diicult since they involve the tracking of individuals with identical genotypes, such as identical twins or clones, and
these can be hard to ind. It is therefore common to focus on a component of the genetic variance, termed the additive genetic variance σ
A 2
. his component has a special utility as it forms that part of the genetic variance that can be used to create changes
in the population mean by selection, and is the variance of the breeding values in the population. he ratio of σ
A 2
with the total phenotypic variance is called the narrow-
sense heritability, denoted h
2
, and unless otherwise stated in the literature, particularly in animal breeding literature, the terms ‘heritability’ and ‘h
2
’ should be interpreted as denoting the narrow-sense heritability as in this book. Falconer and Mackay 1996
give more details on deining breeding values, heritabilities and their derivation. It is relatively easy to obtain information on breeding values from experimental or ield data
and so the genetic variance in the population is oten estimated simply by σ
A 2
. Note that σ
A 2
≤ σ
G 2
and h
2
≤ H
2
. he use of variance to summarise diversity is most obviously applicable in the case of
continuous traits such as height and weight. However it can also be easily applied to qualitative traits where there are two outcomes e.g. say horns or no horns, since the
two classes can be transformed into 0’s and 1’s and variances calculated using these numbers. More diicult are qualitative traits with more than two classes: where these
