Assessing the fidelity of ancient DNA sequences amplified from nuclear genes

Jonas Binladen; Carsten Henrik Wiuf; M. Thomas P. Gilbert; Michael Bunce; Ross Barnett; Greger Larson; Alex D. Greenwood; James Haile; Simon Y. W. Ho; Anders J. Hansen; Eske Willerslev

doi:10.1534/genetics.105.049718

Assessing the fidelity of ancient DNA sequences amplified from nuclear genes

Jonas Binladen, Carsten Henrik Wiuf, M. Thomas P. Gilbert, Michael Bunce, Ross Barnett, Greger Larson, Alex D. Greenwood, James Haile, Simon Y. W. Ho, Anders J. Hansen, Eske Willerslev

86 Citations (Scopus)

Abstract

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.
Udgivelsesdato: 2006 Feb

Original language	English
Journal	Genetics
Volume	172
Issue number	2
Pages (from-to)	733-41
ISSN	0016-6731
DOIs	https://doi.org/10.1534/genetics.105.049718
Publication status	Published - 2006

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10.1534/genetics.105.049718

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@article{c4e442109d0e11debc73000ea68e967b,

title = "Assessing the fidelity of ancient DNA sequences amplified from nuclear genes",

abstract = "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. Udgivelsesdato: 2006 Feb",

author = "Jonas Binladen and Wiuf, {Carsten Henrik} and Gilbert, {M. Thomas P.} and Michael Bunce and Ross Barnett and Greger Larson and Greenwood, {Alex D.} and James Haile and Ho, {Simon Y. W.} and Hansen, {Anders J.} and Eske Willerslev",

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year = "2006",

doi = "10.1534/genetics.105.049718",

language = "English",

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pages = "733--41",

journal = "Genetics",

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TY - JOUR

T1 - Assessing the fidelity of ancient DNA sequences amplified from nuclear genes

AU - Binladen, Jonas

AU - Wiuf, Carsten Henrik

AU - Gilbert, M. Thomas P.

AU - Bunce, Michael

AU - Barnett, Ross

AU - Larson, Greger

AU - Greenwood, Alex D.

AU - Haile, James

AU - Ho, Simon Y. W.

AU - Hansen, Anders J.

AU - Willerslev, Eske

N1 - 024ER Times Cited:22 Cited References Count:49

PY - 2006

Y1 - 2006

N2 - 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. Udgivelsesdato: 2006 Feb

AB - 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. Udgivelsesdato: 2006 Feb

U2 - 10.1534/genetics.105.049718

DO - 10.1534/genetics.105.049718

M3 - Journal article

C2 - 16299392

SN - 0016-6731

VL - 172

SP - 733

EP - 741

JO - Genetics

JF - Genetics

IS - 2

ER -