A. Greenwood

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Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth

by Gennady Boeskorov, Nikolas Nikolaidis, and A. Greenwood

BMC evolutionary biology, Sep 11, 2009

Background Like humans, the living elephants are unusual among mammals in being sparsely covered ... more Background Like humans, the living elephants are unusual among mammals in being sparsely covered with hair. Relative to extant elephants, the extinct woolly mammoth, Mammuthus primigenius, had a dense hair cover and extremely long hair, which likely were adaptations to its subarctic habitat. The fibroblast growth factor 5 (FGF5) gene affects hair length in a diverse set of mammalian species. Mutations in FGF5 lead to recessive long hair phenotypes in mice, dogs, and cats; and the gene has been implicated in hair length ...

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Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology

by Sergios-Orestis Kolokotronis and A. Greenwood

Citation: Scheel DM, Slater GJ, Kolokotronis S-O, Potter CW, Rotstein DS, Tsangaras K, Greenwood ... more

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Negative Purifying Selection Drives Prion and Doppel Protein Evolution

by johan michaux, Serge Morand, Sergios-Orestis Kolokotronis, and A. Greenwood

The prion protein (PrP) when misfolded into the pathogenic conformer PrP Sc is the major causativ... more The prion protein (PrP) when misfolded into the pathogenic conformer PrP Sc is the major causative agent of several lethal transmissible spongiform encephalopathies in mammals. Studies of evolutionary pressure on the corresponding gene using different datasets have yielded conflicting results. In addition, putative PrP or PrP interacting partners with strong similarity to PrP such as the doppel protein have not been examined to determine if the same evolutionary mechanisms apply to prion paralogs or if there are coselected sites that might indicate how and where the proteins interact. We examined several taxonomic groups that contain model organisms of prion diseases focusing on primates, bovids, and an expanded dataset of rodents for selection pressure on the prion gene (PRNP) and doppel gene (PRND) individually and for coevolving sites within. Overall, the results clearly indicate that both proteins are under strong selective constraints with relaxed selection on amino acid residues connecting a-helices 1 and 2.

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Ancient DNA Identification of Early 20th Century Simian T-Cell Leukemia Virus Type 1

by Shannon Hensley, A. Greenwood, and C. Hanni

Molecular Biology and Evolution, 2008

The molecular identification of proviruses from ancient tissues (and particularly from bones) rem... more The molecular identification of proviruses from ancient tissues (and particularly from bones) remains a contentious issue. It can be expected that the copy number of proviruses will be low, which magnifies the risk of contamination with retroviruses from exogenous sources. To assess the feasibility of paleoretrovirological studies, we attempted to identify proviruses from early 20th century bones of museum specimens while following a strict ancient DNA methodology.

format_quoteQuantification revealed older specimens had less nuclear DNA; all samples remained viable for proviral research despite age differences.format_quote

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Assessing the fidelity of ancient DNA sequences amplified from nuclear genes

by Ross Barnett and A. Greenwood

To date, the field of ancient DNA has relied almost exclusively on mitochondrial DNA (mtDNA) sequ... more To date, the field of ancient DNA has relied almost exclusively on mitochondrial DNA (mtDNA) sequences. However, a number of recent studies have reported the successful recovery of ancient nuclear DNA (nuDNA) sequences, thereby allowing the characterization of genetic loci directly involved in phenotypic traits of extinct taxa. It is well documented that postmortem damage in ancient mtDNA can lead to the generation of artifactual sequences. However, as yet no one has thoroughly investigated the damage spectrum in ancient nuDNA. By comparing clone sequences from 23 fossil specimens, recovered from environments ranging from permafrost to desert, we demonstrate the presence of miscoding lesion damage in both the mtDNA and nuDNA, resulting in insertion of erroneous bases during amplification. Interestingly, no significant differences in the frequency of miscoding lesion damage are recorded between mtDNA and nuDNA despite great differences in cellular copy numbers. For both mtDNA and nuDNA, we find significant positive correlations between total sequence heterogeneity and the rates of type 1 transitions (adenine / guanine and thymine / cytosine) and type 2 transitions (cytosine / thymine and guanine / adenine), respectively. Type 2 transitions are by far the most dominant and increase relative to those of type 1 with damage load. The results suggest that the deamination of cytosine (and 5-methyl cytosine) to uracil (and thymine) is the main cause of miscoding lesions in both ancient mtDNA and nuDNA sequences. We argue that the problems presented by postmortem damage, as well as problems with contamination from exogenous sources of conserved nuclear genes, allelic variation, and the reliance on single nucleotide polymorphisms, call for great caution in studies relying on ancient nuDNA sequences.

format_quoteType 1 transitions occur less frequently in nuDNA (15%) than mtDNA (24%); type 2 transitions are more common in nuDNA (78% vs 56%).format_quote

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