Measwring and Testing Genetic Differentiation With Ordered Versus Unordered Alleles

Abstract

Estimates and variances of diversity and differentiation measures in subdivided populations are proposed that can be applied to haplotypes (ordered alleles such as DNA sequences, which may contain a record of their own histories). Hence, two measures of differentiation can be compared for a single data set: one (GST) that makes use only of the allelic frequencies and the other (NST) for which similarities between the haplotypes are taken into account in addition. Tests are proposed to compare NST and GST with zero and with each other. The difference between NST and GST can be caused by several factors, including sampling artefacts, unequal effect of mutation rates and phylogeographic structure. The method presented is applied to a published data set where a nuclear DNA sequence had been determined from individuals of a grasshopper distributed in 24 regions of Europe. Additional insights into the genetic subdivision of these populations are obtained by progressively combining related haplotypes and reanalyzing the data each time.

Flightlessness in insects enhances diversification and determines assemblage structure across whole communities

“…A similar pattern, albeit less pronounced, was also found for G ST (unweighted genetic distance among haplotypes). This difference between N ST and G ST is consistent with Pons & Petit [33], who point out that N ST will be more informative than G ST , as haplotype variation is more efficiently used when ordered alleles are considered, leading to a more powerful test for genetic structure. Significant differences in N ST between royalsocietypublishing.org/journal/rspb Proc.…”

“…Two measures of population genetic differentiation were estimated to quantify phylogeographic structure within LMDHs: G ST which considers only allelic frequencies, and N ST which takes into account genetic distances between alleles, thus incorporating a phylogenetic weight in the measure [33]. LMDHs sampled from a minimum of two populations and comprising more than three overall individuals were selected to estimate G ST and N ST : (i) within each island, considering sampling sites as populations, (ii) among islands, where islands are considered as a single site, and (iii) pairwise among islands, using Spagedi 1.4b [34] with 10 000 permutations and K2P distances.…”

Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence of Chamaesium (Apiaceae)

“…Haplotype diversity ( H d ) ( Nei and Tajima, 1981 ) and nucleotide diversity (π) ( Nei and Li, 1979 ) for each population were calculated using DNAsp v5.1 ( Librado and Rozas, 2009 ) to verify the degrees and patterns of diversity. PERMUT ( Pons and Petit, 1996 ) was used to access the total diversity ( H T ), within-population diversity ( H S ) and population differentiation indices ( G ST and N ST ) ( Grivet and Petit, 2002 ). We also used a U-statistic to test the phylogeographic structure by comparing G ST and N ST , which can indicate the presence of phylogeographic structure.…”

The DNA history of a lonely oak: Quercus humboldtii phylogeography in the Colombian Andes

“…For the purpose of describing the genetic variation within populations, haplotype richness, rarefied haplotype richness, genetic diversity with unordered alleles (h sensu Pons & Petit, 1996), and nonstandardized genetic diversity with ordered alleles (v sensu Pons & Petit, 1996) were calculated for the 22 sampling locations (226 individuals) using cpSSR loci and the programs SPAGeDi 1.1 (Hardy & Vekemans, 2002) and Arlequin 3.5.2.2 (Excoffier & Lischer, 2010).…”