Single base errors in PCR products from avian museum specimens and their effect on estimates of historical genetic diversity
- 244 Downloads
Conservation genetic studies often employ DNA extracts from museum specimens for comparisons with extant populations to monitor temporal changes in genetic diversity. Here, we report on artifact base changes in mitochondrial DNA sequences amplified from relatively recent (≤ 35 years) museum specimens of indigobirds (Vidua spp.). Single base errors were confirmed by replicate sequencing and included both double peaks and artifact substitutions at rates of ∼3 × 10−4 and ∼1 × 10−4 per base-pair, respectively, resulting in one or more errors or ambiguities in an 1100 base pair sequence in 21% of 219 samples. Most errors involved C→T changes on the L-strand, presumably due to deamination of cytosine in the template. The error rates encountered here bias comparisons of haplotype number between historical and extant populations, such that the ‘loss’ of artifact haplotypes present in a historical sample could be incorrectly attributed to a population decline or bottleneck. Sequencing errors due to miscoding lesions in template DNA have so far been reported only from ancient and formalin-fixed tissue, but they may also affect relatively recent museum samples, as shown here, and perhaps also non-invasive samples that typically yield low-quality DNA.
KeywordsPCR artifact Sequence error Museum samples Indigobirds Population decline
Field work from 1966 to the present has been supported and facilitated by numerous agencies and individuals. Jeff Tetrault assisted with the replicate sequencing. The work was supported by the Austrian Science Fund (P17380-B06; J-2044), the National Science Foundation (IOB 9412399; DEB 0089757), and the Dr. Heinrich-Jörg-Stiftung (Karl-Franzens-Universität Graz, Austria).
- Cooper A (1994) DNA from museum specimens. In: Herrmann B, Herrmann S (eds) Ancient DNA: recovery and analysis of genetic material from paleontological, archeological, museum, medical and forensic specimens. Springer, New YorkGoogle Scholar
- MacHugh DE, Troy CS, McCormick F, Olsaker I, Eythórsdóttir E, Bradley DG (1999) Early medieval cattle remains from a Scandinavian settlement in Dublin: genetic analysis and comparison with extant breeds. Proc R Soc Lond B 354:99–109Google Scholar
- Payne RB, Sorenson MD (2002). Museum collections as sources of genetic data. In: R. van den Elzen (ed) Bird Collections in Europe: promotion of science in ornithology. Alexander Koenig Research Institute and Museum of Zoology Proceedings, Vol. 2, Bonn, GermanyGoogle Scholar
- Swofford DL (2002) PAUP* 4.0b10: Phylogenetic analysis using parsimony. Sinauer, Sunderland MassachusettsGoogle Scholar