Thank you to all who responded to my question posted last week, original question and responses below. Cheers, Rhiannon I am a PhD student working on an annual plant which is highly inbreeding and seeds are dispersed either passively or by ants. I would like to perform some fine-scale spatial genetic structure (SGS) analyses on mapped samples collected at very close distances to each other, using microsatellites, to infer 'neighbourhood size', the scale of gene flow by rare pollination events and seed dispersal, and to see if habitat changes correlate with genetic differentiation. Could anyone recommend any software programs for such SGS analyses that do not require the species/populations to be in Hardy-Weinberg equilibrium? *** Dear Crichton, I suggest to use Spagedi 1.3. (http://ebe.ulb.ac.be/ebe/Software.html). This is very good program and, actualy all using this program. Regarding the Hardy-Weiwberg equilibrium, I suggest to use the Loissele et al. (1995) method. This method not assume HW equilibrium. Best regards, Alexandre *** Dear Rhiannon, software for analysis of spatial genetic structure by essence do not assume that the genotype frequencies correspond to Hardy-Weinberg expectations, as spatial genetic structure is a deviation from random mating, a major hypothesis of H-W model. If your markers are co-dominant, then you can use any software for SGS analysis, including Spagedi by my colleague Olivier Hardy and myself (see Vekemans & Hardy 2004 Molecular Ecology 13:921- for practical considerations on SGS analyses and a review of the empirical literature considering among others the effect of mating system on patterns of SGS; and Hardy & Vekemans 2002 Mol. Ecol. Notes 2:618- for a description of the software, available at http://ebe.ulb.ac.be/ebe/Software.html), but there are many others. best regards, Xavier Vekemans *** Hi, Depending on how many plants & markers, and particularly what proportion of the (local) population you are surveying in each generation, you could presumably take a pedigree-based approach (and infer the relationships between all the sampled plants)? For example, Masterbayes: http://wildevolution.biology.ed.ac.uk/jhadfield/software.html http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2006.03050.x/abstract http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2010.03438.x/pdf http://cran.r-project.org/web/packages/MasterBayes/vignettes/Tutorial.pdf I imagine this might work if you are looking at (e.g.) all candidate parents in an area plus several seeds from each mother in that area. Regards! Darren *** I'd suggest spatial autocorrelation. It can be done on the Genalax package and has been used on lots of botanical species. It's particularly appropriate where you have individuals (rather than populations) spread across an area and want to make inferences about connectivity. I've attached a paper I've used it on (although it's not a perfect example of it's use by any means. However, it should give you the references you need to investigate further! Cheers, Andrew (Paper: Griffiths et al, Evolutionary Applications, 2009) *** Hi, my software SPAGeDi should be fine for this (http://ebe.ulb.ac.be/ebe/Software.html). Best, Olivier -- Rhiannon Crichton