plant surface microbiology.pdf

7 Statistical analysis
28 Analysis of Microbial Population Genetics 561
Introduction
The studies of microbial population genetics with molecular methods are
often characterised by an extremely high number of samples and by a high
number of molecular markers. As a consequence, an immediate interpretation
of the results can be difficult unless powerful statistical techniques are
used in order to describe the structure of the populations and to highlight the
contributions of its components (Mengoni and Bazzicalupo 2002).
Methods and Procedure
Statistical treatment of data in microbial population genetics include at least
four different levels of analysis:
1. Quantification of the genetic diversity within the population
2. Measurement of genetic distances between strains
3. Analysis of the genetic structure
4. Analysis of the genetic relationships among populations.
Several methods can be used to address each of these points. Here, a brief
summary of the principal parameters and software used is provided.
The molecular data obtained from RAPD,AFLP, and ITS-RFLP analyses are
usually bands in a gel or peaks in a chromatogram. These data are transformed
into a matrix of state binary vectors (molecular haplotype) for each
individual isolate using a compiler such as Microsoft Excel or similar. Bands
and peaks of equal sizes are interpreted as identical and intensity is not considered
as a difference. The molecular haplotype of each isolate is expressed
as a vector of zeroes (for the absence of the band) or ones (for its presence),
assuming that bands represent independent loci.
1. The quantification of genetic diversity within the population can be done
using several parameters. The most commonly used are the gene diversity,
the average gene diversity over loci and the mean number of pairwise differences
between haplotypes.
The gene diversity is equivalent to the expected heterozygosity for diploid
data. It is defined as the probability that two randomly chosen molecular
haplotypes are different in the sample.
The average gene diversity over loci is defined as the probability that two
individuals are different for a randomly chosen locus. These two parameters
vary from 0 (all isolates identical) to 1 (maximum diversity).
The mean number of pair-wise differences simply calculates the mean
number of differences between all pairs of molecular haplotypes in the
population. The computation of these three parameters is performed with
Arlequin software (Schneider et al. 1997).
2. For the measurement of the genetic distances between strains, several
methods can be applied. The basic principle is the ratio of bands shared by