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Extracting DNA from museum bird eggs, and whole genome amplification of archive DNA
We present a comprehensive protocol for extracting DNA from egg membranes and other internal debris recovered from the interior of blown museum bird eggs. A variety of commercially available DNA extraction methods were found to be applicable. DNA sequencing of polymerase chain reaction (PCR) products for a 176-bp fragment of mitochondrial DNA was successful for most egg samples (> 78%) even though the amount of DNA extracted (mean = 14.71 ± 4.55 ng/µL) was significantly less than that obtained for bird skin samples (mean = 67.88 ± 4.77 ng/µL). For PCR and sequencing of snipe (Gallinago) DNA, we provide eight new primers for the ‘DNA barcode’ region of COI mtDNA. In various combinations, the primers target a range of PCR products sized from 72 bp to the full ‘barcode’ of 751 bp. Not all possible combinations were tested with archive snipe DNA, but we found a significantly better success rate of PCR amplification for a shorter 176-bp target compared with a larger 288-bp fragment (67% vs. 39%). Finally, we explored the feasibility of whole genome amplification (WGA) for extending the use of archive DNA in PCR and sequencing applications. Of two WGA approaches, a PCR-based method was found to be able to amplify whole genomic DNA from archive skins and eggs from museum bird collections. After WGA, significantly more archive egg samples produced visible PCR products on agarose (56.9% before WGA vs. 79.0% after WGA). However, overall sequencing success did not improve significantly (78.8% compared with 83.0%).
History
Journal
Molecular ecology resourcesVolume
8Issue
3Pagination
551 - 560Publisher
WileyLocation
London, EnglandPublisher DOI
ISSN
1755-098XeISSN
1755-0998Language
engPublication classification
C1.1 Refereed article in a scholarly journalCopyright notice
2008, WileyUsage metrics
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Categories
Keywords
COI mtDNADNA barcodingDNA extractionGallinagomuseum collectionsWGAScience & TechnologyLife Sciences & BiomedicineBiochemistry & Molecular BiologyEcologyEvolutionary BiologyEnvironmental Sciences & EcologyMULTIPLE DISPLACEMENT AMPLIFICATIONGENETIC-VARIATIONPOPULATIONBOTTLENECKIDENTIFICATIONCONSEQUENCESCOLLECTIONSPATTERNSSAMPLESEXTINCT