Determination of the adequate number of individuals and AFLP markers to use when studying genetic differentiation among intraspecific populations.
Medina, Raul*,1, Barbosa, Pedro1, Christman, Mary2, 1 Department of Entomology, College Park, Maryland, USA2 Department of Animal and Avian Sciences, College Park, Maryland, USA
ABSTRACT- Since their development, AFLP have been widely used in biology. Particularly, in organisms where little or nothing is known about their genome. Genotypic differentiation among cultivars, strains and populations of several species have been explored using this technique. Cluster analysis methods using AFLP have been applied to visualize these differences and to test all sort of systematics, evolutionary biology and population ecology hypotheses. However, this research is potentially flawed because there is no way of knowing whether the number of individuals and markers used to generate similarity matrices, and associated cluster analyses, are sufficient to validly represent the genome of field populations of a species. Indeed, there are no agreed upon criteria for determining the appropriate number of individuals and markers for such representations. We present a method for determining the number of individuals to collect and the number of markers to consider when representing genetic profiles of populations. The proposed method uses bootstrap analysis to construct curves representing the standard error of the Jaccard index (SESim curves) at different number of individuals by number of marker combinations. The point at which a SESim curve reach a value smaller than 0.045 indicates the minimum number of individuals by markers to use for the cluster analysis. This method is used in our study investigating genotypic differentiation of the parasitoid Aleiodes nolophanae Ashmead (Hymenoptera: Braconidae) ovipositing on Plathypena scabra F. (Lepidoptera Noctuidae) on two different crops (alfalfa and soybean). We have found no genotypic differentiation among parasitoids ovipositing green cloverworm larvae on different host plant species and weak genotypic differentiation among parasitoids from different collection sites. AFLP data from the processionary moth, Thaumatopea pityocampa Denis and Schiffermüller (Lepidoptera: Thaumetopoeidae), in which strong genotypic differentiation have been found among different sites, is used to validate the proposed method. We found that as predicted, the more differentiated T. pytiocampa populations required lower number of markers to describe genetic differentiation among collection sites.
Key words: aflp, sample size, genetic differentiation, braconidae
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