Environmental Engineering Reference
In-Depth Information
Box 7.1 Estimating genetic diversity and its use in conservation
and restoration
Measuring genetic diversity. A good quantifi cation of
genetic variation allows assessment of variables that
are important for decision making in conservation
and restoration, including within- and between-
population divergence, local adaptation, inbreeding
and gene fl ow. At the population level, genetic diver-
sity is often measured as (1) P = proportion of loci
that is polymorphic (the fraction of all loci for which
two or more different alleles have been observed),
(2) H = average heterozygosity (the proportion of
loci at which individuals on average are hetero-
zygous, i.e. have two different alleles) and (3)
A = allelic diversity (the average number of alleles
observed per locus). All of these parameters are
generally positively related to fi tness (Reed &
Frankham 2003; Leimu et al . 2006).
Use of near-neutral genetic markers. Different types of
genetic markers can be used as a basis for such
estimates, from DNA or protein to phenotypic vari-
ants. DNA-based markers offer the advantage that
they generally yield a large number of polymorphic
loci. Some of these, like Amplifi ed Fragment Length
Polymorphism (AFLP), are relatively easy to develop,
but lack the ability to discriminate between homozy-
gotes and heterozygotes due to dominant inherit-
ance. Others, like microsatellites (Simple Sequence
Repeats, SSR), do not bear this disadvantage (co-
dominant inheritance) but do take a bit more time to
develop. With the rapidly declining cost of sequenc-
ing, sequence-based markers like Single Nucleotide
Polymorhisms (SNP) are becoming more widely
available, offering opportunities of genotyping vast
numbers of polymorphic loci with co-dominant
inheritance.
Estimating population genetic parameters. From the
distribution of the observed neutral genetic
variation between and within populations and indi-
viduals, a number of basic population genetic
parameters can be assessed. Estimates are based
on deviations of observed heterozygosity from
expected heterozygosity. Any nonrandom mating
amongst individuals included in the sampling results
in a deviation (defi cit) of heterozygotes compared to
those expected in infi nitely large, outbreeding, per-
fectly random mating populations without mutation,
migration or selection (Hardy-Weinberg equilib-
rium). Deviations of subpopulations relative to the
total population (F ST ) indicate population differentia-
tion, while deviations of individuals relative to their
subpopulation (F IS ) indicate inbreeding within popu-
lations. The degree of population differentiation (F ST ,
or G ST , the equivalent for multiple loci) is inversely
related to effective population size N e and the
number of migrants (m) and hence can be used to
infer gene fl ow, while F IS can be used to infer the
degree of inbreeding within populations.
Use of neutral versus quantitative genetic markers.
Genetic diversity based on DNA markers predomi-
nantly assesses neutral molecular variation. Unfor-
tunately, neutral molecular variation generally has
poor predictive power for phenotypic and quan-
titative genetic variation on which natural selec-
tion acts, and that is important in local adaptation
to the environment (Reed & Frankham 2001; McKay
& Latta 2002, and references therein). Therefore,
a combination of studies with neutral and quanti-
tative markers is often advised in conservation
and restoration (Kramer & Havens 2009). Neutral
genetic studies are well suited for assessing gene
fl ow to identify historical and current movement
and mixing of populations, inbreeding and diver-
gence within and between populations. Quantita-
tive genetic trait studies such as common garden,
reciprocal transplant and quantitative trait loci
studies are better suited to estimate fi tness costs
associated with inbreeding, adaptive genetic diver-
sity and adaptive population differentiation. Com-
bining neutral genetic and quantitative genetic
studies are especially useful to dissect adaptive
versus random population genetic divergence. For
instance, the ratio of Q ST to F ST (or G ST ) - where Q ST
is the equivalent of F ST for quantitative trait loci -
has been used to identify traits involved in adaptive
differentiation, that is, traits that show larger popu-
lation divergence (Q ST ) than that observed for
neutral loci (F ST ).
Search WWH ::




Custom Search