Fossil avian eggshell preserves ancient DNA

Charlotte L Oskam; James Seymour Haile; Emma McLay; Paul Rigby; Morten Erik Allentoft; Maia E. Olsen; Camilla Bengtsson; Gifford H. Miller; Jean-Luc Schwenninger; Christopher Jacomb; Richard Walter; Alexander Baynes; Joe Dortch; Michael Parker-Pearson; Tom Gilbert; Richard N. Holdaway; Eske Willerslev; Michael Bunce

doi:10.1098/rspb.2009.2019

Fossil avian eggshell preserves ancient DNA

Charlotte L Oskam, James Seymour Haile, Emma McLay, Paul Rigby, Morten Erik Allentoft, Maia E. Olsen, Camilla Bengtsson, Gifford H. Miller, Jean-Luc Schwenninger, Christopher Jacomb, Richard Walter, Alexander Baynes, Joe Dortch, Michael Parker-Pearson, Tom Gilbert, Richard N. Holdaway, Eske Willerslev, Michael Bunce

88 Citations (Scopus)

Abstract

Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has approximately 125 times lower bacterial load than bone, making it a highly suitable substrate for high-throughput sequencing approaches. Importantly, the preservation of DNA in Pleistocene eggshell from Australia and Holocene deposits from Madagascar indicates that eggshell is an excellent substrate for the long-term preservation of DNA in warmer climates. The successful recovery of DNA from this substrate has implications in a number of scientific disciplines; most notably archaeology and palaeontology, where genotypes and/or DNA-based species identifications can add significantly to our understanding of diets, environments, past biodiversity and evolutionary processes.

Original language	English
Journal	Royal Society of London. Proceedings B. Biological Sciences
Volume	277
Issue number	1690
Pages (from-to)	1991-2000
Number of pages	10
ISSN	0962-8452
DOIs	https://doi.org/10.1098/rspb.2009.2019
Publication status	Published - 7 Jul 2010

Keywords

Animals
Australia
Birds
DNA
DNA, Mitochondrial
Dromaiidae
Ducks
Egg Shell
Extinction, Biological
Fossils
Madagascar
Microscopy, Confocal
Molecular Sequence Data
New Zealand
Paleontology
Polymerase Chain Reaction
Sequence Analysis, DNA
Strigiformes

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Oskam, C. L., Haile, J. S., McLay, E., Rigby, P., Allentoft, M. E., Olsen, M. E., Bengtsson, C., Miller, G. H., Schwenninger, J-L., Jacomb, C., Walter, R., Baynes, A., Dortch, J., Parker-Pearson, M., Gilbert, T., Holdaway, R. N., Willerslev, E., & Bunce, M. (2010). Fossil avian eggshell preserves ancient DNA. Royal Society of London. Proceedings B. Biological Sciences, 277(1690), 1991-2000. https://doi.org/10.1098/rspb.2009.2019

Oskam, CL, Haile, JS, McLay, E, Rigby, P, Allentoft, ME, Olsen, ME, Bengtsson, C, Miller, GH, Schwenninger, J-L, Jacomb, C, Walter, R, Baynes, A, Dortch, J, Parker-Pearson, M, Gilbert, T, Holdaway, RN, Willerslev, E & Bunce, M 2010, 'Fossil avian eggshell preserves ancient DNA', Royal Society of London. Proceedings B. Biological Sciences, vol. 277, no. 1690, pp. 1991-2000. https://doi.org/10.1098/rspb.2009.2019

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title = "Fossil avian eggshell preserves ancient DNA",

abstract = "Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has approximately 125 times lower bacterial load than bone, making it a highly suitable substrate for high-throughput sequencing approaches. Importantly, the preservation of DNA in Pleistocene eggshell from Australia and Holocene deposits from Madagascar indicates that eggshell is an excellent substrate for the long-term preservation of DNA in warmer climates. The successful recovery of DNA from this substrate has implications in a number of scientific disciplines; most notably archaeology and palaeontology, where genotypes and/or DNA-based species identifications can add significantly to our understanding of diets, environments, past biodiversity and evolutionary processes.",

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author = "Oskam, {Charlotte L} and Haile, {James Seymour} and Emma McLay and Paul Rigby and Allentoft, {Morten Erik} and Olsen, {Maia E.} and Camilla Bengtsson and Miller, {Gifford H.} and Jean-Luc Schwenninger and Christopher Jacomb and Richard Walter and Alexander Baynes and Joe Dortch and Michael Parker-Pearson and Tom Gilbert and Holdaway, {Richard N.} and Eske Willerslev and Michael Bunce",

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doi = "10.1098/rspb.2009.2019",

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T1 - Fossil avian eggshell preserves ancient DNA

AU - Oskam, Charlotte L

AU - Haile, James Seymour

AU - McLay, Emma

AU - Rigby, Paul

AU - Allentoft, Morten Erik

AU - Olsen, Maia E.

AU - Bengtsson, Camilla

AU - Miller, Gifford H.

AU - Schwenninger, Jean-Luc

AU - Jacomb, Christopher

AU - Walter, Richard

AU - Baynes, Alexander

AU - Dortch, Joe

AU - Parker-Pearson, Michael

AU - Gilbert, Tom

AU - Holdaway, Richard N.

AU - Willerslev, Eske

AU - Bunce, Michael

PY - 2010/7/7

Y1 - 2010/7/7

N2 - Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has approximately 125 times lower bacterial load than bone, making it a highly suitable substrate for high-throughput sequencing approaches. Importantly, the preservation of DNA in Pleistocene eggshell from Australia and Holocene deposits from Madagascar indicates that eggshell is an excellent substrate for the long-term preservation of DNA in warmer climates. The successful recovery of DNA from this substrate has implications in a number of scientific disciplines; most notably archaeology and palaeontology, where genotypes and/or DNA-based species identifications can add significantly to our understanding of diets, environments, past biodiversity and evolutionary processes.

AB - Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has approximately 125 times lower bacterial load than bone, making it a highly suitable substrate for high-throughput sequencing approaches. Importantly, the preservation of DNA in Pleistocene eggshell from Australia and Holocene deposits from Madagascar indicates that eggshell is an excellent substrate for the long-term preservation of DNA in warmer climates. The successful recovery of DNA from this substrate has implications in a number of scientific disciplines; most notably archaeology and palaeontology, where genotypes and/or DNA-based species identifications can add significantly to our understanding of diets, environments, past biodiversity and evolutionary processes.

KW - Animals

KW - Australia

KW - Birds

KW - DNA

KW - DNA, Mitochondrial

KW - Dromaiidae

KW - Ducks

KW - Egg Shell

KW - Extinction, Biological

KW - Fossils

KW - Madagascar

KW - Microscopy, Confocal

KW - Molecular Sequence Data

KW - New Zealand

KW - Paleontology

KW - Polymerase Chain Reaction

KW - Sequence Analysis, DNA

KW - Strigiformes

U2 - 10.1098/rspb.2009.2019

DO - 10.1098/rspb.2009.2019

M3 - Journal article

C2 - 20219731

SN - 0962-8452

VL - 277

SP - 1991

EP - 2000

JO - Proceedings of the Royal Society B: Biological Sciences

JF - Proceedings of the Royal Society B: Biological Sciences

IS - 1690

ER -

Fossil avian eggshell preserves ancient DNA

Abstract

Keywords

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