The effect of ancient DNA damage on inferences of demographic histories
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The effect of ancient DNA damage on inferences of demographic histories. / Axelsson, Erik; Willerslev, Eske; Gilbert, Marcus Thomas Pius; Nielsen, Rasmus.
In: Molecular Biology and Evolution, Vol. 25, No. 10, 2008, p. 2181-7.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - The effect of ancient DNA damage on inferences of demographic histories
AU - Axelsson, Erik
AU - Willerslev, Eske
AU - Gilbert, Marcus Thomas Pius
AU - Nielsen, Rasmus
N1 - Keywords: Animals; Bayes Theorem; Bison; DNA Damage; Evolution; Evolution, Molecular; Genetic Variation; Genetics, Population; Models, Genetic; Phylogeny; Polymerase Chain Reaction; Population Density; Sequence Analysis, DNA
PY - 2008
Y1 - 2008
N2 - The field of ancient DNA (aDNA) is casting new light on many evolutionary questions. However, problems associated with the postmortem instability of DNA may complicate the interpretation of aDNA data. For example, in population genetic studies, the inclusion of damaged DNA may inflate estimates of diversity. In this paper, we examine the effect of DNA damage on population genetic estimates of ancestral population size. We simulate data using standard coalescent simulations that include postmortem damage and show that estimates of effective population sizes are inflated around, or right after, the sampling time of the ancestral DNA sequences. This bias leads to estimates of increasing, and then decreasing, population sizes, as observed in several recently published studies. We reanalyze a recently published data set of DNA sequences from the Bison (Bison bison/Bison priscus) and show that the signal for a change in effective population size in this data set vanishes once the effects of putative damage are removed. Our results suggest that population genetic analyses of aDNA sequences, which do not accurately account for damage, should be interpreted with great caution.
AB - The field of ancient DNA (aDNA) is casting new light on many evolutionary questions. However, problems associated with the postmortem instability of DNA may complicate the interpretation of aDNA data. For example, in population genetic studies, the inclusion of damaged DNA may inflate estimates of diversity. In this paper, we examine the effect of DNA damage on population genetic estimates of ancestral population size. We simulate data using standard coalescent simulations that include postmortem damage and show that estimates of effective population sizes are inflated around, or right after, the sampling time of the ancestral DNA sequences. This bias leads to estimates of increasing, and then decreasing, population sizes, as observed in several recently published studies. We reanalyze a recently published data set of DNA sequences from the Bison (Bison bison/Bison priscus) and show that the signal for a change in effective population size in this data set vanishes once the effects of putative damage are removed. Our results suggest that population genetic analyses of aDNA sequences, which do not accurately account for damage, should be interpreted with great caution.
U2 - 10.1093/molbev/msn163
DO - 10.1093/molbev/msn163
M3 - Journal article
C2 - 18653730
VL - 25
SP - 2181
EP - 2187
JO - Molecular Biology and Evolution
JF - Molecular Biology and Evolution
SN - 0737-4038
IS - 10
ER -
ID: 9856500