@article {149,
	title = {Mitochondrial barcodes are diagnostic of shared refugia but not species in hybridizing oak gallwasps},
	journal = {Molecular EcologyMolecular Ecology},
	year = {2012},
	pages = {no-no},
	publisher = {Blackwell Publishing Ltd},
	abstract = {Mitochondrial DNA barcodes provide a simple taxonomic tool for systematic and ecological research, with particular benefit for poorly studied or species-rich taxa. Barcoding assumes genetic diversity follows species boundaries; however, many processes disrupt species-level monophyly of barcodes leading to incorrect classifications. Spatial population structure, particularly when shared across closely related and potentially hybridizing taxa, can invalidate barcoding approaches yet few data exist to examine its impacts. We test how shared population structure across hybridizing species impacts upon mitochondrial barcodes by sequencing the cytochrome b gene for 518 individuals of four well-delimited Western Palaearctic gallwasp species within the Andricus quercuscalicis species group. Mitochondrial barcodes clustered individuals into mixed-species clades corresponding to refugia, with no difference in within- and between-species divergence. Four nuclear genes were also sequenced from 4 to 11 individuals per refugial population of each species. Multi-locus analyses of these data supported established species, with no support for the refugial clustering across species seen in mitochondrial barcodes. This pattern is consistent with mitochondrial introgression among populations of species sharing the same glacial refugium, such that mitochondrial barcodes identify a shared history of population structure rather than species. Many taxa show phylogeographic structure across glacial refugia, suggesting that mitochondrial barcoding may fail when applied to other sets of co-distributed, closely related species. Robust barcoding approaches must sample extensively across population structure to disentangle spatial from species-level variation. Methods incorporating multiple unlinked loci are also essential to accommodate coalescent variation among genes and provide power to resolve recently diverged species.},
	keywords = {DNA barcoding, introgression, multi-locus, spatial population structure},
	isbn = {1365-294X},
	author = {Nicholls, James A. and Challis, Richard J. and Mutun, Serap and Stone, Graham N.}
}
@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}
}
