Genetic analyses from ancient DNA

Authors: S. Päabo, H. Poinar, D. Serre, V. Jaenicke-Despres, J. Hebler, N. Rohland, M. Kuch, J. Krause, L. Vigilant, and M. Hofreiter
Journal: Annu. Rev. Genet. 2004. 38:645–79

About 20 years ago, DNA sequences were separately described from the quagga (a type of zebra) and an ancient Egyptian individual. What made these DNA sequences exceptional was that they were derived from 140- and 2400-year-old specimens. However, ancient DNA research, defined broadly as the retrieval of DNA sequences from museum specimens, archaeological finds, fossil remains, and other unusual sources of DNA, only really became feasible with the advent of techniques for the enzymatic amplification of specific DNA sequences. Today, reports of analyses of specimens hundreds, thousands, and even millions of years old are almost commonplace. But can all these results be believed? In this paper,we critically assess the state of ancient DNA research. In particular, we discuss the precautions and criteria necessary to ascertain to the greatest extent possible that results represent authentic ancient DNA sequences. We also highlight some significant results and areas of promising future research.

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Single nucleotide polymorphism (SNP) discovery in mammals: a targeted-gene approach

Authors: N. Aitken, S. Smith, C. Schwarz, P.A. Morin
Journal: Mol Ecol. – 13(6):1423-3 (June 2004)

Single nucleotide polymorphisms (SNPs) have rarely been exploited in nonhuman and nonmodel organism genetic studies. This is due partly to difficulties in finding SNPs in species where little DNA sequence data exist, as well as to a lack of robust and inexpensive genotyping methods. We have explored one SNP discovery method for molecular ecology, evolution, and conservation studies to evaluate the method and its limitations for population genetics in mammals. We made use of ‘CATS’ (or ‘EPIC’) primers to screen for novel SNPs in mammals. Most of these primer sets were designed from primates and/or rodents, for amplifying intron regions from conserved genes. We have screened 202 loci in 16 representatives of the major mammalian clades. Polymerase chain reaction (PCR) success correlated with phylogenetic distance from the human and mouse sequences used to design most primers; for example, specific PCR products from primates and the mouse amplified the most consistently and the marsupial and armadillo amplifications were least successful. Approximately 24% (opossum) to 65% (chimpanzee) of primers produced usable PCR product(s) in the mammals tested. Products produced generally high but variable levels of readable sequence and similarity to the expected genes. In a preliminary screen of chimpanzee DNA, 12 SNPs were identified from six (of 11) sequenced regions, yielding a SNP on average every 400 base pairs (bp). Given the progress in genome sequencing, and the large numbers of CATS-like primers published to date, this approach may yield sufficient SNPs per species for population and conservation genetic studies in nonmodel mammals and other organisms.

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Characterization of 15 single nucleotide polymorphism markers for chimpanzees (Pan troglodytes)

Authors: S. Smith , N. Aitken , C. Schwarz , P.A. Morin
Journal: Mol Ecol Notes – 4, 348-51 (2004)

We report the characterization of 15 new single nucleotide polymorphism markers for a threatened species, the chimpanzee (Pan troglodytes), developed using a targeted gene approach. These markers are derived from the Y chromosome and autosomal regions of the genome and show frequency differences between chimpanzee subspecies from central and western Africa. These single nucleotide polymorphism markers are the first to be designed for the genotyping of wild chimpanzee populations and will provide a useful addition to the genetic tools employed for the conservation management of this threatened species.

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Isolation of nucleic acids and cultures from fossil ice and permafrost

Authors: E. Willerslev, A.J. Hansen and H.N. Poinar
Journal: TRENDS in Ecology and Evolution – Vol.19 – No.3 (March 2004)

Owing to their constant low temperatures, glacial ice and permafrost might contain the oldest nucleic acids and microbial cells on Earth, which could prove key to reconstructing past ecosystems and for the planning of missions to other planets. However, recent claims concerning viable cells and microbial nucleic acids obtained from ice- and permafrost cores from hundreds of thousands to millions of years old are not properly authenticated and the findings could be the result of contamination. Here, we discuss the processes that restrict the long-term survival of DNA and/or RNA molecules in ice and permafrost, and highlight sources of contamination that could result in false claims. Additionally, we present a set of precautions, controls and criteria to help ensure that future cultures and sequences are authentic.

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Molecular evidence of tuberculosis induced hypertophic osteopathy in a 16th-century Iroquoian dog

Authors: R.R. Bathurst and J.L. Barta
Journal: Journal of Archaeological Science – 31:917-925 (2004)

A fully articulated dog skeleton excavated from a 16th-century Neutral Iroquoian site in Ontario, Canada displays a distinctive osteological condition known as hypertrophic osteopathy (HPO). Ancient DNA (aDNA) analysis of the dog has isolated Mycobacterium tuberculosis complex DNA, linking the secondary condition of HPO to tuberculosis (TB) and representing the oldest known case of TB yet to be discovered in the domestic dog. We emphasize that dogs should be considered as potential reservoirs of TB into the Americas.

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