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Publications

Members of the McMaster Ancient DNA Centre are active in different research projects.

Comparison of methods in the recovery of nucleic acids from archival formalin-fixed paraffin-embedded autopsy tissues

Here we report a systematic comparison of formalin-fixed paraffin-embedded tissue kits for RNA and DNA extraction. Overall, TrimGen's WaxFree and phenol-chloroform methods recovered the largest DNA yields, while Ambion's RecoverAll kit recovered the largest quantity of amplifiable RNA.

Jan 15, 2010

A quantitative approach to detect and overcome PCR inhibition in ancient DNA extracts

PCR inhibition remains a consistent problem for PCR amplification, particular in situations when the target DNA is in low-abundance or heavily degraded. Here we report an analysis on the identification of PCR inhibition and some recommendations to circumvent/alleviate inhibition in degraded samples.

Sep 11, 2009

Time-Dependency of Molecular Rates in Ancient DNA Datasets, a Sampling Artifact?

Here we examine how a variety of factors (including calibration methods, sequence length, etc) affect divergence estimates in BEAST.

Jul 01, 2009

Agouti sequence polymorphism in coyotes and specific sequence differences from wolves and dogs

Here we report an examination of the alleles found in Canadian wild canids (wolves and coyotes) for the Agouti locus. Our analysis revealed that the Agouti locus did not vary in wild canids from domesticated dogs, although differences were observed in the surrounding regions.

Jul 13, 2007

Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA

We report the sequencing of a remarkably well-preserved Siberian woolly mammoth. Using a metagenomics approach we sequenced about 28 million reads of which 45.4% were identified as mammoth. The high percentage of endogenous DNA should enable the completion of its full genome.

Jan 20, 2006

Tarsus determination in Drosophila melanogaster

Here we report our work looking into tarsus determination in Drosophila as it relates to ANTP cell autonomous or noncell autonomous determination.

Aug 21, 2005

Osteocalcin protein sequences of Neanderthals and modern primates

Here we report the oldest fossil primate protein sequences from two approximately 75 thousand year old Neanderthals, as well as modern sequences from chimpanzee, gorilla, and orangutan. These sequences of bone osteocalcin lack hydroxylation of Proline-9 in Pan, Pongo, and Homo may reflect response to a selective pressure related to a decline in vitamin C in the diet during omnivorous dietary adaptation.

Mar 22, 2005

Long-Term Survival of Ancient DNA in Egypt: Response to Zink and Nerlich (2003)

A response to the arguments about the survival of ancient DNA in Egypt and the likelihood of retrial of ancient DNA from Egyptian remains.

Jan 01, 2005

Genetic analyses from ancient DNA

A critical assessment of the state of ancient DNA research and a review of some significant contributions and promising future research areas.

Jul 30, 2004