Population Genetics
| Population genetics is the study of the distributions and changes of allele frequencies in a population, as it is subject to four main processes: mutation, selection, genetic drift and genetic recombination. Studies in population genetics are often useful in classifying individuals into populations. Standard approach is to sample DNA from members of a potential source population, and using these samples to estimate allele frequency in each population. The likelihood that a genotype originated from the population is computed using the estimated allele frequency. Individuals of unknown origin can be assigned to populations according to these likelihoods. |  |
Preliminary analysis
GeneMapper pre-processing
Microsatellite markers, also known as short tandem repeats (STRs),
are polymorphic DNA loci consisting of a repeated nucleotide
sequence. The number of repeat units varies in a population, thereby creating
multiple alleles for a microsatellite locus.
In a typical microsatellite analysis, microsatellite loci are amplified by PCR using fluorescently labeled forward and unlabeled reverse primers. The PCR amplicons are separated by size using
electrophoresis; then the dye labeled products are identified by
fluorescence detection. You can then use the GeneMapper Software
to size and genotype the alleles.
Downstream analysis softwares
Running structure
The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.
Running Arlequin
Arlequin: An Integrated Software for Population Genetics Data Analysis. The goal of Arlequin is to provide the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples.
Running GenAlEx
GenAlEx offers a wide range of population genetic analysis options for the full spectrum of genetic markers within the Microsoft Excel environment on both PC and Macintosh computers.
PowerMarker
PowerMarker delivers a data-driven, integrated analysis environment (IAE) for genetic data. The IAE integrates data management, analysis and visualization in a user-friendly graphical user interface.
Convert utility tool
CONVERT is a user-friendly, 32-bit Windows program that facilitates ready transfer of co-dominant, diploid genotypic data amongst commonly used population genetic software packages.