In simple terms

Genetic diversity: refers to variation in the nucleotides, genes, chromosomes, or whole genomes of organisms within (or among) populations

Genetic structure: Refers to the patterning of the genetic diversity across multiple populations or demes (in a metapopulation).

Formal definitions can be found in classical literature, e.g.:

1- Wright S (1943) Isolation by distance Genetics 28 114-138

2-Wright S (1951) The genetical structure of populations. Annals of Eugenics, 15, 323–354

3-Wright S (1965) The interpretation of population structure by

F-statistics with special regard to systems of mating. Evolution, 19, 395–420

4-Nei (1973) Analysis of Gene Diversity in Subdivided Populations. PNAS, 70, 3321-3323.

See also Jost 2008 GST and its relatives do not measure differentiation. Molecular Ecology. 17, 4015-4026.

thanks, then which estimators are used to describe population genetic diversity and genetic structure, respectively. I was confused.

Both have an array of different metrics most common are:

Genetic diversity: Gene diversity or Heterozygosity (He), Number of alleles per loci, Number of polymorphic loci, allelic richness...

Genetic structure: One will usually use fixation indices (Fst, Gst) to assess genetic differentiation between populations. There are also estimates of genetic distances (e.g. Nei, Cavalli-Sforza and Edwards). Again, see Jost (2008) for alternative view on the use of Fst and Gst. Jost proposes D instead of Gst and derivatives , as a true index of differentiation. Analysis of Molecular Variance (AMOVA; Excoffier 1992) partition the molecular variance (F-statistics) into its components , among groups of populations, among populations within groups and within populations.

thanks a lot, Guillaume de Lafontaine. recently I read some papers on Gst , G'st and Jost'D and Fst, et al., on which estimator they debated could mearsure the genetic differentiation. so which should I use in terms of honeybee population structuring with 10 microsatellite loci .

This is still a much debated question in the literature! The most common metrics is probably still Fst (and derivatives, e.g. W&C theta, etc...). It is implemented in almost any population genetics software.

both parameters Fst and Gst are measured populations genetic diversities rates -between and within. Their are really useful when we study different populations with same genetic and genomic loci

Hi. First, you have to see the distribution of alleles for your STRs. If distribution adjusts better to infinite allele mode (IAM) you should use FST. Instead, If is more like

stepwise mutation model (SMM) you should use RST.

Gst, Fst are parameters we are using for evaluation of populations genetic diversities. Actually -it can be say: population genetic structure or gene pool describes polymorphism of genes or genomic loci -STRs, SNPs, Y-chr & mtDNA haplogroups etc within certain population, as well as Hobs, Hexp. We are checking STRs alleles frequencies for that, as well as biallelic system and haplogroups distribution. But when we want to compare different populations and a diversities between and within them we are using the parameters listed above.

Dear Prof.

Thank you for your information. Could provide me with free program for Genetic structure.

with best regards

khaled

Population genetic structure can be well understood using STRUCTURE software which gives you the possible subgroups based on the genetic data (e.g three subgroups). Then you run analysis of molecular variance (AMOVE) which gives you more information on population genetic diversity through estimating the diversity between individuals within and between the three groups . There is is sowftware called GenLAX which examine if the any of the three groups has specific alleles. 

Population genetic structure is the heterogeneity in allele frequency among the populations caused by limited gene flow. it can be estimated using hierarchial analysis of molecular variance (AMOVA) as implemented in Arlequin version 3.5 (Excoffier et al. 2010).

While genetic diversity is the amount of variation observed between DNA sequences. it can be expressed in the form haplotype and nucleotide diversities using DnaSP software version 4.0 (Rozas et al., 2003), Arlequin version 3.5 (Excoffier et al. 2010).