@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.}
}
@article {138,
	title = {Prospects of barcoding the Italian wild dendroflora: oaks reveal severe limitations to tracking species identity},
	journal = {Molecular Ecology ResourcesMolecular Ecology Resources},
	volume = {11},
	number = {1},
	year = {2011},
	pages = {72-83},
	publisher = {Blackwell Publishing Ltd},
	abstract = {DNA barcoding may be particularly important in influencing ecology, economic issues, and the fundamental crisis facing biodiversity as a standardized, species-level identification tool for taxonomy assessment. Trees play important roles in the conservation of many land ecosystems, the wood trade, and the definition of biogeographical processes; nevertheless, peculiar biological, evolutionary and taxonomical features will probably constitute an intriguing challenge to barcoders. We examined whether four marker regions (trnh-psba, rbcL, rpoc1, matK) proposed by the Consortium for the Barcode of Life (CBOL) matched species taxonomy in a preliminary tree biodiversity survey of Italian forested land. Our objective was to provide a test of future in situ applications of DNA barcodes by evaluating the efficacy of species discrimination under the criteria of uniformity of methods and natural co-occurrence of the species in the main forest ecosystems. Fifty-two species were included in a floristic study. We obtained 73\% total discrimination success, with trnH-psbA as the best performing marker and oaks as the least responsive plants to the markers used. A further taxon-based study of Quercus (thirty specimens, 12 species) revealed that this genus is refractory to barcoding (0\% discrimination success), a probable consequence of low variation rate at the plastid genome level, hybridization, and the incidence of biogeography. We conclude that some species-rich tree genera in small geographical regions may prove exceptionally difficult to barcode. Until more efficient markers are developed, we recommend that improved and diversified sampling (multiple locations of sympatric and co-occurring congenerics) be embraced as a timely and important goal for the precise assessment of haplotype specificity to facilitate the productive application of barcoding in practice.},
	keywords = {DNA barcoding, forest trees, Italy, Quercus, regional sampling},
	isbn = {1755-0998},
	author = {Piredda, Roberta and Simeone, Marco C. and Attimonelli, Marcella and Bellarosa, Rosanna and Schirone, Bartolomeo}
}
