Dear all I'm very grateful for the suggestions received. Here are the replies: Request: Hi all, I'm trying to use the approach suggested in SPAGeDi 1.2 (O. Hardy and X. Vekemans 2007) to test for the existence of a significant phylogeographic signal, using mtDNA sequence data. However there is an issue that is not entirely clear to me: in cases when a Nst > Gst > 0 but the slope of pairwise Nst vs geographic distance is not significant, what could be plausible explanations? Can anyone give me any suggestions about this issue or can suggest some paper, book, that could be of help if further questions or doubts storm me? many thanks Marco Carriso ----- Answers: Dear Marco, there are two different issues in the problem you are describing. One is whether there is some phylogenetic signal in your mtDNA data on top of the differences in haplotype frequencies among populations (the Nst versus Gst comparison), and the other whether the genetic differentiation that you observe has a spatial component (does or not fit an isolation by distance pattern). When you are applying the test implemented in Spagedi that gives Nst>Gst, you are implicitly assuming an Island model of migration, with GST measuring average genetic differentiation among populations due to differences in haplotype frequencies, and Nst measuring average genetic differentiation taking into account differences in haplotype frequencies plus phylogenetic differences among haplotypes. Your observation that Nst>Gst suggests that the set of distinct haplotypes that are co-occuring whithin populations are on average more similar to each other than random sets of haplotypes at the total species level. Another way to put it, is to say that genetic drift along cannot explain the data and thus the mutational process is participating to genetic differentiation among populations. When you are computing the slope of the regression of pairwise Nst vs geographic distance, you are implicitly assuming an Isolation by distance model (i.e. restricted dispersal), and if the slope is ot significantly different than zero this means that this model should be rejected. Hence in your case there is no clear spatial component in genetic differentiation. It may be that the slope for Gst is significant but not the one on Nst. This could happen simply because of the larger variance of the estimates of pairwise Nst as compared to pairwise Gst. best regards, Xavier Vekemans -- Xavier VEKEMANS Laboratoire de Genetique et Evolution des Populations Vegetales GEPV - UMR CNRS 8016 Batiment SN2 Universite des Sciences et Technologies de Lille - Lille 1 59655 Villeneuve d'Ascq Cedex FRANCE Tel: +33 3 2043 6753 - Fax: +33 3 2043 6979 http://www.univ-lille1.fr/gepv=0A=C2=A0=0A=C2=A0=0A=C2 Hi Marco, you might obtain such pattern if you have a complex history of colonisation by long term differentiated gene pools (Nst>Gst) that spread over large and/or disjunct areas because you could have comparable proportions of pairs of populations belonging to distinct gene pools at short distance and at large distance. For an example, have a look at http://www.pierroton.inra.fr/genetics/ComEvol/Atelier-Phylogeo/OHardy_phylogeography.pdfp.6. Best, Olivier Olivier Hardy Chercheur qualifié FNRS Service Eco-Ethologie Evolutive - CP 160/12 Université Libre de Bruxelles 50 Av. F. Roosevelt 1050 Bruxelles Belgique Tel: +32 (0)2 650 6585 Fax: +32 (0)2 650 2445 email: ohardy@ulb.ac.be marcocarriso@yahoo.it