A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level

Abstract

Microsatellites are powerful molecular markers, used commonly to estimate intraspecific genetic distances. With the exception of band sharing similarity index, available distance measures were developed specifically for diploid organisms and are unsuited for comparisons of polyploids. Here, we present a simple method for calculation of microsatellite genotype distances, which takes into account mutation processes and permits comparison of individuals with different ploidy levels. This method should provide a valuable tool for intraspecific analyses of polyploid organisms, which are widespread among plants and some animal taxa. An illustration is given using data from the planarian flatworm Schmidtea polychroa (Platyhelminthes).

Microsatellite marker isolation and cultured strain identification in Carassius auratus gibelio

“…In this case, one allele was recognized to be duplicated in one of the two bands (Ohara et al 1999). Pairwise distances between multilocus genotypes were calculated using the method first described by Bruvo et al (2004). The obtained distance matrices then served to construct the neighbor-joining tree with MEGA software version 3.1 (http://www.megasoftware.net/mega.html).…”

Poppr: an R package for genetic analysis of populations with clonal or partially clonal reproduction

“…Typical analyses in poppr start with summary statistics for diversity, rarefaction, evenness, MLG counts, and calculation of distance measures such as Bruvo's distance, providing a suitable stepwise mutation model appropriate for microsatellite markers [25]. Poppr will define MLGs in your data set, show where they cross populations, and can produce graphs and tables of MLGs by population that can be used for further analysis with the R package vegan [24].…”

“…Poppr complements and builds on previously existing R packages including adegenet and vegan [22][23][24] while implementing tools novel to R significantly facilitating data import, population genetic analyses, and graphing of clonal or partially clonal populations. These tools include among others: analysis across hierarchies of populations, subsetting of populations, clone-censoring, Bruvo's genetic distance [25], the index of association and related statistics [17,18], and bootstrap support for trees based on Bruvo's distance. By providing a centralized suite of tools appropriate for many data types, this package represents a novel and useful resource specifically tailored for analysis of clonal populations.…”

Best Practices for Population Genetic Analyses

“…Distances for sequence data are easily calculated using one of the nucleotide substitution models present in the dist.dna() function in the ape R package (Paradis et al 2004), but are only applicable to haplotype data. For simple sequence repeats (SSR) data, if one can assume that the alleles mutate in a stepwise fashion, Bruvo's distance, as implemented in poppr, polysat, and Genodive is appropriate for all ploidy levels (Bruvo et al 2004;Clark and Jasieniuk 2011;Kamvar et al 2014;Meirmans and Van Tienderen 2004). Calculating genetic distance for polyploid data are challenging because of ambiguity of heterozygous genotypes (e.g., a tetraploid heterozygote with alleles A and T could be ATTT, AATT, or AAAT).…”

“…Calculating genetic distance for polyploid data are challenging because of ambiguity of heterozygous genotypes (e.g., a tetraploid heterozygote with alleles A and T could be ATTT, AATT, or AAAT). Bruvo et al (2004) addressed this with three models that account for allelic ambiguity, all of which are implemented in both polysat and poppr. For polyploid SSR data that doesn't follow a stepwise mutation model one can use the methods implemented in the meandist.matrix2() function in polysat or turn Bruvo's distance into the simple mismatch distance by multiplying all fragment lengths by 1,000 as demonstrated in Metzger et al (2015).…”