Animal DNA in PCR reagents plagues ancient DNA research

Leonard, Jennifer A.; Shanks, Orin C.; Hofreiter, Michael; Kreuz, Eva; Hodges, Larry; Ream, Walt; Wayne, Robert K.; Fleischer, Robert C.

doi:10.1016/j.jas.2006.10.023

Cited by 148 publications

(125 citation statements)

References 39 publications

(32 reference statements)

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“…However, it is also important to note that standard European/Indian subcontinental/Chinese haplotypes such as 8 would result if either the specimens or laboratory procedures were contaminated with any amount of modern chicken DNA. The contamination of laboratory consumables is a well known problem when working with ancient samples of domestic species (20), which tend to be widespread but not genetically diverse.…”

Section: Phylogenetic Position Of Archaeological Pacific and Pre-columentioning

confidence: 99%

Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA

Gongora

Rawlence

Mobegi

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

100

145

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European chickens were introduced into the American continents by the Spanish after their arrival in the 15th century. However, there is ongoing debate as to the presence of pre-Columbian chickens among Amerindians in South America, particularly in relation to Chilean breeds such as the Araucana and Passion Fowl. To understand the origin of these populations, we have generated partial mitochondrial DNA control region sequences from 41 native Chilean specimens and compared them with a previously generated database of Ϸ1,000 domestic chicken sequences from across the world as well as published Chilean and Polynesian ancient DNA sequences. The modern Chilean sequences cluster closely with haplotypes predominantly distributed among European, Indian subcontinental, and Southeast Asian chickens, consistent with a European genetic origin. A published, apparently pre-Columbian, Chilean specimen and six pre-European Polynesian specimens also cluster with the same European/Indian subcontinental/Southeast Asian sequences, providing no support for a Polynesian introduction of chickens to South America. In contrast, sequences from two archaeological sites on Easter Island group with an uncommon haplogroup from Indonesia, Japan, and China and may represent a genetic signature of an early Polynesian dispersal. Modeling of the potential marine carbon contribution to the Chilean archaeological specimen casts further doubt on claims for pre-Columbian chickens, and definitive proof will require further analyses of ancient DNA sequences and radiocarbon and stable isotope data from archaeological excavations within both Chile and Polynesia.Araucana chicken ͉ Gallus gallus ͉ pre-Columbian chicken ͉ control region

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Section: Phylogenetic Position Of Archaeological Pacific and Pre-columentioning

confidence: 99%

Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA

Gongora

Rawlence

Mobegi

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

100

145

View full text Add to dashboard Cite

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“…Importantly, we obtained PCR products of the expected length from six of the 39 modern control samples using the same primers and amplification conditions as were applied to the ancient samples; the remaining control samples produced no PCR products of the expected length. In-depth FLX sequencing of the products generated a total of 32,874 sequence reads, all of which derive from common laboratory contaminants-cow, pig, or mouse (30) or, in one case, bacterial DNA-and not from megafauna taxa such as mammoth or horse. Amplification of low-level laboratory contaminants is expected when no other target DNA is present (31).…”

Section: Resultsmentioning

confidence: 99%

Ancient DNA reveals late survival of mammoth and horse in interior Alaska

Haile

Froese

MacPhee

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

244

181

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Causes of late Quaternary extinctions of large mammals (''megafauna'') continue to be debated, especially for continental losses, because spatial and temporal patterns of extinction are poorly known. Accurate latest appearance dates (LADs) for such taxa are critical for interpreting the process of extinction. The extinction of woolly mammoth and horse in northwestern North America is currently placed at 15,000 -13,000 calendar years before present (yr BP), based on LADs from dating surveys of macrofossils (bones and teeth). Advantages of using macrofossils to estimate when a species became extinct are offset, however, by the improbability of finding and dating the remains of the last-surviving members of populations that were restricted in numbers or confined to refugia. Here we report an alternative approach to detect 'ghost ranges' of dwindling populations, based on recovery of ancient DNA from perennially frozen and securely dated sediments (sedaDNA). In such contexts, sedaDNA can reveal the molecular presence of species that appear absent in the macrofossil record. We show that woolly mammoth and horse persisted in interior Alaska until at least 10,500 yr BP, several thousands of years later than indicated from macrofossil surveys. These results contradict claims that Holocene survival of mammoths in Beringia was restricted to ecologically isolated high-latitude islands. More importantly, our finding that mammoth and horse overlapped with humans for several millennia in the region where people initially entered the Americas challenges theories that megafaunal extinction occurred within centuries of human arrival or were due to an extraterrestrial impact in the late Pleistocene.extinction ͉ permafrost ͉ megafauna ͉ Beringia

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“…Historic squirrel specimens were amplified using 52 different primer sets, some of which were mammal ''universal'' (n = 23), and some of which were designed for these squirrels, and will be referred to here as ''specific'' primer sets (n = 29). When possible, the universal primers were designed to exclude human and cow, two ubiquitous contaminants in commercial reagents (Leonard et al 2007 City, CA, USA), 2.5 mM MgCl 2 , 0.8 mM dNTPs (0.2 mM each), 1 lM of each primer, 1.25 U AmpliTaq Gold DNA polymerase (Applied Biosystems) and between 10 and 50 ng of DNA. The PCR program started with an initial denaturation step of 95°C for 10 min followed by 36 cycles of 95°C for 30 s, annealing of 50-60°C for 30 s and extension of 72°C for 45 s; with a final extension of 72°C for 10 min.…”

Section: Introductionmentioning

confidence: 99%

Nuclear copies of mitochondrial genes: another problem for ancient DNA

et al. 2010

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The application of ancient DNA techniques is subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characterization of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplification of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occurred. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were utilized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another complication for ancient DNA studies, but it also suggests that more extensive inclusion of nuclear markers in ancient DNA studies should be feasible.R.-J. den Tex · J. A. Leonard (&)

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Animal DNA in PCR reagents plagues ancient DNA research

Cited by 148 publications

References 39 publications

Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA

Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA

Ancient DNA reveals late survival of mammoth and horse in interior Alaska

Nuclear copies of mitochondrial genes: another problem for ancient DNA

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