@article {154,
	title = {Outlier loci highlight the direction of introgression in oaks},
	journal = {Molecular EcologyMolecular Ecology},
	volume = {22},
	number = {2},
	year = {2013},
	pages = {450-462},
	abstract = {Loci considered to be under selection are generally avoided in attempts to infer past demographic processes as they do not fit neutral model assumptions. However, opportunities to better reconstruct some aspects of past demography might thus be missed. Here we examined genetic differentiation between two sympatric European oak species with contrasting ecological dynamics (Quercus robur and Quercus petraea) with both outlier (i.e. loci possibly affected by divergent selection between species or by hitchhiking effects with genomic regions under selection) and nonoutlier loci. We sampled 855 individuals in six mixed forests in France and genotyped them with a set of 262 SNPs enriched with markers showing high interspecific differentiation, resulting in accurate species delimitation. We identified between 13 and 74 interspecific outlier loci, depending on the coalescent simulation models and parameters used. Greater genetic diversity was predicted in Q.~petraea (a late-successional species) than in Q.~robur (an early successional species) as introgression should theoretically occur predominantly from the resident species to the invading species. Remarkably, this prediction was verified with outlier loci but not with nonoutlier loci. We suggest that the lower effective interspecific gene flow at loci showing high interspecific divergence has better preserved the signal of past asymmetric introgression towards Q.~petraea caused by the species{\textquoteright} contrasting dynamics. Using markers under selection to reconstruct past demographic processes could therefore have broader potential than generally recognized.},
	keywords = {asymmetric introgression, divergent selection, gene flow barriers, genetic assignment, outlier loci, Quercus petraea, Quercus robur, single nucleotide polymorphism},
	isbn = {1365-294X},
	author = {Guichoux, E. and Garnier-G{\'E}R{\'E}, P. and Lagache, L. and Lang, T. and Boury, C. and Petit, R. J.}
}
@article {136,
	title = {Two highly validated multiplexes (12-plex and 8-plex) for species delimitation and parentage analysis in oaks (<i>Quercus </i>spp.)},
	journal = {Molecular Ecology ResourcesMolecular Ecology Resources},
	volume = {11},
	number = {3},
	year = {2011},
	pages = {578-585},
	publisher = {Blackwell Publishing Ltd},
	abstract = {Abstract Multiplex PCR is a fast and cost-effective technique allowing increased genotyping throughput of microsatellites. We developed two multiplexes for Quercus petraea and Q.~robur, a 12-plex of EST-SSRs (eSSRs) and an 8-plex of genomic SSRs (gSSRs). We studied the origin of allele calling errors at the human reader and software levels. We showed that the robustness of allele identification can be improved by binning on raw peak sizes prior to genetic data analysis. We checked through simulation the power of these markers for species delimitation and hybrid detection. The resolution achieved with all 20 markers was greatly improved compared to that of previous studies based on a subset of the markers. Preliminary PCR tests suggest that these multiplexes might be useful to study other oak species as well. The strategy used for multiplex microsatellite development (from PCR conditions to the definition of allele calling rules) should be broadly applicable.},
	keywords = {manual binning, microsatellites, molecular identification, Quercus spp.},
	isbn = {1755-0998},
	author = {Guichoux, E. and Lagache, L. and Wagner, S. and Leger, P. and Petit, R. J.}
}
