Skip to main content
SpringerLink
Log in
Book cover

Ancient DNA pp 93–105Cite as

Whole-Genome Capture of Ancient DNA Using Homemade Baits

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1963))

Abstract

For many archaeological and paleontological samples, the relative content of endogenous compared to contaminant DNA is low. In such cases, enriching sequencing libraries for endogenous DNA, prior to sequencing can make the final research project more cost-effective. Here, we present an in-solution enrichment protocol based on homemade baits that can be applied to recover complete nuclear genomes from ancient remains. The approach is based on the preparation of DNA baits by biotinylated adapter ligation. The procedure has been developed for use with human remains but can be adapted to other species or target regions by choosing the appropriate template DNA from which to build the capture baits. By using homemade rather than commercially acquired baits, this protocol may offer increased flexibility and cost efficiency.

This is a preview of subscription content, log in via an institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   119.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD   159.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Dabney J, Meyer M, Pääbo S (2013) Ancient DNA Damage. Cold Spring Harb Perspect Biol 5:a012567. https://doi.org/10.1101/cshperspect.a012567

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Gamba C, Hanghøj K, Gaunitz C, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Bradley DG, Orlando L (2016) Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing. Mol Ecol Resour 16:459–469. https://doi.org/10.1111/1755-0998.12470

    Article  CAS  PubMed  Google Scholar 

  3. Gansauge M-T, Meyer M (2013) Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat Protoc 8:737–748. https://doi.org/10.1038/nprot.2013.038

    Article  CAS  PubMed  Google Scholar 

  4. Fortes GG, Paijmans JLA (2015) Analysis of whole mitogenomes from ancient samples. arXiv:150305074 [q-bio]

    Google Scholar 

  5. Gamba C, Jones ER, Teasdale MD, McLaughlin RL, Gonzalez-Fortes G, Mattiangeli V, Domboróczki L, Kővári I, Pap I, Anders A, Whittle A, Dani J, Raczky P, Higham TFG, Hofreiter M, Bradley DG, Pinhasi R (2014) Genome flux and stasis in a five millennium transect of European prehistory. Nat Commun 5:5257. https://doi.org/10.1038/ncomms6257

    Article  CAS  PubMed  Google Scholar 

  6. Pinhasi R, Fernandes D, Sirak K, Novak M, Connell S, Alpaslan-Roodenberg S, Gerritsen F, Moiseyev V, Gromov A, Raczky P, Anders A, Pietrusewsky M, Rollefson G, Jovanovic M, Trinhhoang H, Bar-Oz G, Oxenham M, Matsumura H, Hofreiter M (2015) Optimal ancient DNA yields from the inner ear part of the human petrous bone. PLoS One 10:e0129102. https://doi.org/10.1371/journal.pone.0129102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Alberti F, Gonzalez J, Paijmans JLA, Basler N, Preick M, Henneberger K, Trinks A, Rabeder G, Conard NJ, Münzel SC, Joger U, Fritsch G, Hildebrandt T, Hofreiter M, Barlow A (2018) Optimized DNA sampling of ancient bones using Computed Tomography scans. Mol Ecol Resour. https://doi.org/10.1111/1755-0998.12911

  8. Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, Berger B, Economou C, Bollongino R, Fu Q, Bos KI, Nordenfelt S, Li H, de Filippo C, Prüfer K, Sawyer S, Posth C, Haak W, Hallgren F, Fornander E, Rohland N, Delsate D, Francken M, Guinet J-M, Wahl J, Ayodo G, Babiker HA, Bailliet G, Balanovska E, Balanovsky O, Barrantes R, Bedoya G, Ben-Ami H, Bene J, Berrada F, Bravi CM, Brisighelli F, Busby GBJ, Cali F, Churnosov M, Cole DEC, Corach D, Damba L, van Driem G, Dryomov S, Dugoujon J-M, Fedorova SA, Gallego Romero I, Gubina M, Hammer M, Henn BM, Hervig T, Hodoglugil U, Jha AR, Karachanak-Yankova S, Khusainova R, Khusnutdinova E, Kittles R, Kivisild T, Klitz W, Kučinskas V, Kushniarevich A, Laredj L, Litvinov S, Loukidis T, Mahley RW, Melegh B, Metspalu E, Molina J, Mountain J, Näkkäläjärvi K, Nesheva D, Nyambo T, Osipova L, Parik J, Platonov F, Posukh O, Romano V, Rothhammer F, Rudan I, Ruizbakiev R, Sahakyan H, Sajantila A, Salas A, Starikovskaya EB, Tarekegn A, Toncheva D, Turdikulova S, Uktveryte I, Utevska O, Vasquez R, Villena M, Voevoda M, Winkler CA, Yepiskoposyan L, Zalloua P, Zemunik T, Cooper A, Capelli C, Thomas MG, Ruiz-Linares A, Tishkoff SA, Singh L, Thangaraj K, Villems R, Comas D, Sukernik R, Metspalu M, Meyer M, Eichler EE, Burger J, Slatkin M, Pääbo S, Kelso J, Reich D, Krause J (2014) Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513:409–413. https://doi.org/10.1038/nature13673

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Jones ER, Gonzalez-Fortes G, Connell S, Siska V, Eriksson A, Martiniano R, McLaughlin RL, Llorente MG, Cassidy LM, Gamba C, Meshveliani T, Bar-Yosef O, Müller W, Belfer-Cohen A, Matskevich Z, Jakeli N, Higham TFG, Currat M, Lordkipanidze D, Hofreiter M, Manica A, Pinhasi R, Bradley DG (2015) Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nat Commun 6:8912. https://doi.org/10.1038/ncomms9912

    Article  CAS  PubMed  Google Scholar 

  10. Jones ER, Zarina G, Moiseyev V, Lightfoot E, Nigst PR, Manica A, Pinhasi R, Bradley DG (2017) The Neolithic transition in the Baltic was not driven by admixture with early European farmers. Curr Biol 27:576–582. https://doi.org/10.1016/j.cub.2016.12.060

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. González-Fortes G, Jones ER, Lightfoot E, Bonsall C, Lazar C, Grandal-d’Anglade A, Garralda MD, Drak L, Siska V, Simalcsik A, Boroneanţ A, Romaní JRV, Rodríguez MV, Arias P, Pinhasi R, Manica A, Hofreiter M (2017) Paleogenomic evidence for multi-generational mixing between Neolithic farmers and Mesolithic hunter-gatherers in the lower Danube basin. Curr Biol 27:1801–1810.e10. https://doi.org/10.1016/j.cub.2017.05.023

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Cassidy LM, Martiniano R, Murphy EM, Teasdale MD, Mallory J, Hartwell B, Bradley DG (2016) Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome. Proc Natl Acad Sci 113:368–373. https://doi.org/10.1073/pnas.1518445113

    Article  CAS  PubMed  Google Scholar 

  13. Paijmans JLA, Barnett R, Gilbert MTP, Zepeda-Mendoza ML, Reumer JWF, de VJ, Zazula G, Nagel D, Baryshnikov GF, Leonard JA, Rohland N, Westbury MV, Barlow A, Hofreiter M (2017) Evolutionary history of Saber-toothed cats based on ancient mitogenomics. Curr Biol 27:3330–3336.e5. https://doi.org/10.1016/j.cub.2017.09.033

    Article  CAS  PubMed  Google Scholar 

  14. Fortes GG, Grandal-d’Anglade A, Kolbe B, Fernandes D, Meleg IN, García-Vázquez A, Pinto-Llona AC, Constantin S, de Torres TJ, Ortiz JE, Frischauf C, Rabeder G, Hofreiter M, Barlow A (2016) Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears. Mol Ecol 25:4907–4918. https://doi.org/10.1111/mec.13800

    Article  CAS  PubMed  Google Scholar 

  15. Posth C, Renaud G, Mittnik A, Drucker DG, Rougier H, Cupillard C, Valentin F, Thevenet C, Furtwängler A, Wißing C, Francken M, Malina M, Bolus M, Lari M, Gigli E, Capecchi G, Crevecoeur I, Beauval C, Flas D, Germonpré M, van der Plicht J, Cottiaux R, Gély B, Ronchitelli A, Wehrberger K, Grigorescu D, Svoboda J, Semal P, Caramelli D, Bocherens H, Harvati K, Conard NJ, Haak W, Powell A, Krause J (2016) Pleistocene mitochondrial genomes suggest a single major dispersal of non-Africans and a Late Glacial population turnover in Europe. Curr Biol 26:827–833. https://doi.org/10.1016/j.cub.2016.01.037

    Article  CAS  PubMed  Google Scholar 

  16. Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PLF, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Albert FW, de la Rasilla M, Fortea J, Rosas A, Lachmann M, Hannon GJ, Pääbo S (2010) Targeted Investigation of the Neandertal genome by array-based sequence capture. Science 328:723–725. https://doi.org/10.1126/science.1188046

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Castellano S, Parra G, Sanchez-Quinto FA, Racimo F, Kuhlwilm M, Kircher M, Sawyer S, Fu Q, Heinze A, Nickel B, Dabney J, Siebauer M, White L, Burbano HA, Renaud G, Stenzel U, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajkovi D, Kucaneljko GI, Shunkov MV, Derevianko AP, Viola B, Meyer M, Kelso J, Andres AM, Paabo S (2014) Patterns of coding variation in the complete exomes of three Neandertals. Proc Natl Acad Sci 111:6666–6671. https://doi.org/10.1073/pnas.1405138111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Haak W, Lazaridis I, Patterson N, Rohland N, Mallick S, Llamas B, Brandt G, Nordenfelt S, Harney E, Stewardson K, Fu Q, Mittnik A, Bánffy E, Economou C, Francken M, Friederich S, Pena RG, Hallgren F, Khartanovich V, Khokhlov A, Kunst M, Kuznetsov P, Meller H, Mochalov O, Moiseyev V, Nicklisch N, Pichler SL, Risch R, Rojo Guerra MA, Roth C, Szécsényi-Nagy A, Wahl J, Meyer M, Krause J, Brown D, Anthony D, Cooper A, Alt KW, Reich D (2015) Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522:207–211. https://doi.org/10.1038/nature14317

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Fu Q, Meyer M, Gao X, Stenzel U, Burbano HA, Kelso J, Paabo S (2013) DNA analysis of an early modern human from Tianyuan Cave, China. Proc Natl Acad Sci 110:2223–2227. https://doi.org/10.1073/pnas.1221359110

    Article  PubMed  PubMed Central  Google Scholar 

  20. King TE, Fortes GG, Balaresque P, Thomas MG, Balding D, Delser PM, Neumann R, Parson W, Knapp M, Walsh S, Tonasso L, Holt J, Kayser M, Appleby J, Forster P, Ekserdjian D, Hofreiter M, Schürer K (2014) Identification of the remains of King Richard III. Nat Commun 5:5631. https://doi.org/10.1038/ncomms6631

    Article  CAS  PubMed  Google Scholar 

  21. Mathieson I, Lazaridis I, Rohland N, Mallick S, Patterson N, Roodenberg SA, Harney E, Stewardson K, Fernandes D, Novak M, Sirak K, Gamba C, Jones ER, Llamas B, Dryomov S, Pickrell J, Arsuaga JL, de Castro JMB, Carbonell E, Gerritsen F, Khokhlov A, Kuznetsov P, Lozano M, Meller H, Mochalov O, Moiseyev V, Guerra MAR, Roodenberg J, Vergès JM, Krause J, Cooper A, Alt KW, Brown D, Anthony D, Lalueza-Fox C, Haak W, Pinhasi R, Reich D (2015) Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528:499–503. https://doi.org/10.1038/nature16152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Lazaridis I, Nadel D, Rollefson G, Merrett DC, Rohland N, Mallick S, Fernandes D, Novak M, Gamarra B, Sirak K, Connell S, Stewardson K, Harney E, Fu Q, Gonzalez-Fortes G, Jones ER, Roodenberg SA, Lengyel G, Bocquentin F, Gasparian B, Monge JM, Gregg M, Eshed V, Mizrahi A-S, Meiklejohn C, Gerritsen F, Bejenaru L, Blüher M, Campbell A, Cavalleri G, Comas D, Froguel P, Gilbert E, Kerr SM, Kovacs P, Krause J, McGettigan D, Merrigan M, Merriwether DA, O’Reilly S, Richards MB, Semino O, Shamoon-Pour M, Stefanescu G, Stumvoll M, Tönjes A, Torroni A, Wilson JF, Yengo L, Hovhannisyan NA, Patterson N, Pinhasi R, Reich D (2016) Genomic insights into the origin of farming in the ancient Near East. Nature 536:419–424. https://doi.org/10.1038/nature19310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Carpenter ML, Buenrostro JD, Valdiosera C, Schroeder H, Allentoft ME, Sikora M, Rasmussen M, Gravel S, Guillén S, Nekhrizov G, Leshtakov K, Dimitrova D, Theodossiev N, Pettener D, Luiselli D, Sandoval K, Moreno-Estrada A, Li Y, Wang J, Gilbert MTP, Willerslev E, Greenleaf WJ, Bustamante CD (2013) Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am J Hum Genet 93:852–864. https://doi.org/10.1016/j.ajhg.2013.10.002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Schroeder H, Ávila-Arcos MC, Malaspinas A-S, Poznik GD, Sandoval-Velasco M, Carpenter ML, Moreno-Mayar JV, Sikora M, Johnson PLF, Allentoft ME, Samaniego JA, Haviser JB, Dee MW, Stafford TW, Salas A, Orlando L, Willerslev E, Bustamante CD, Gilbert MTP (2015) Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean. Proc Natl Acad Sci 112:3669–3673. https://doi.org/10.1073/pnas.1421784112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Olalde I, Schroeder H, Sandoval-Velasco M, Vinner L, Lobón I, Ramirez O, Civit S, García Borja P, Salazar-García DC, Talamo S, María Fullola J, Xavier Oms F, Pedro M, Martínez P, Sanz M, Daura J, Zilhão J, Marquès-Bonet T, Gilbert MTP, Lalueza-Fox C (2015) A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK cultures. Mol Biol Evol 32:3132–3142. https://doi.org/10.1093/molbev/msv181

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Maricic T, Whitten M, Pääbo S (2010) Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS One 5:e14004. https://doi.org/10.1371/journal.pone.0014004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Horn S (2012) Target enrichment via DNA hybridization capture. In: Hofreiter M, Shapiro B (eds) Ancient DNA, 1st edn. Humana Press, Totowa, NJ, pp 177–188

    Chapter  Google Scholar 

  28. Hodges E, Rooks M, Xuan Z, Bhattacharjee A, Benjamin Gordon D, Brizuela L, Richard McCombie W, Hannon GJ (2009) Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat Protocols 4:960–974. https://doi.org/10.1038/nprot.2009.68

    Article  CAS  PubMed  Google Scholar 

  29. Meyer M, Kircher M (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc 2010:pdb.prot5448. https://doi.org/10.1101/pdb.prot5448

    Article  PubMed  Google Scholar 

  30. Paijmans JLA, Baleka S, Henneberger K, Taron UH, Trinks A, Westbury MV, Barlow A (2017) Sequencing single-stranded libraries on the Illumina NextSeq 500 platform. arXiv:171111004 [q-bio]

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy

    Gloria González Fortes

  2. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Johanna L. A. Paijmans

Authors
  1. Gloria González Fortes
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Johanna L. A. Paijmans
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA

    Beth Shapiro

  2. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Axel Barlow

  3. Tromsø University Museum, UiT—The Arctic University of Norway, Tromsø, Norway

    Peter D. Heintzman

  4. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Michael Hofreiter

  5. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Johanna L. A. Paijmans

  6. Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil

    André E. R. Soares

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

González Fortes, G., Paijmans, J.L.A. (2019). Whole-Genome Capture of Ancient DNA Using Homemade Baits. In: Shapiro, B., Barlow, A., Heintzman, P., Hofreiter, M., Paijmans, J., Soares, A. (eds) Ancient DNA. Methods in Molecular Biology, vol 1963. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9176-1_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-9176-1_11

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9175-4

  • Online ISBN: 978-1-4939-9176-1

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation