Visualization of Distinct DNA Regions of the Modern Human Relatively to a Neanderthal Genome

  • Diogo PratasEmail author
  • Morteza Hosseini
  • Raquel M. Silva
  • Armando J. Pinho
  • Paulo J. S. G. Ferreira
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10255)


Species-specific DNA regions are segments that are unique or share high dissimilarity relatively to close species. Their discovery is important, because they allow the localization of evolutionary traits that are often related to novel functionalities and, sometimes, diseases.

We have detected distinct DNA regions specific in the modern human, when compared to a Neanderthal high-quality genome sequence obtained from a bone of a Siberian woman. The bone is around 50,000 years old and the DNA raw data totalizes more than 418 GB. Since the data size required for localizing efficiently such events is very high, it is not practical to store the model on a table or hash table. Thus, we propose a probabilistic method to map and visualize those regions. The time complexity of the method is linear. The computational tool is available at

The results, computed in approximately two days using a single CPU core, show several regions with documented neanderthal absent regions, namely genes associated with the brain (neurotransmiters and synapses), hearing, blood, fertility and the immune system. However, it also shows several undocumented regions, that may express new functions linked with the evolution of the modern human.


DNA patterns Bloom filters Ancient DNA Paleogenomics 



We thank Martin Kircher, for very helpful comments and explanations, and Cláudio Teixeira, for computational infrastructures. This work was funded by FEDER (Programa Operacional Factores de Competitividade - COMPETE) and by National Funds through the FCT - Foundation for Science and Technology, in the context of the projects UID/CEC/00127/2013, UID/BIM/04501/2013, PTCD/EEI-SII/6608/2014 and the grant SFRH/BPD/111148/2015 to RMS.


  1. 1.
    Pratas, D., Silva, R.M., Pinho, A.J., Ferreira, P.J.S.G: Detection and visualisation of regions of human DNA not present in other primates. In: Proceedings of the 21st RecPad 2015, Faro, Portugal, October 2015Google Scholar
  2. 2.
    Rahman, M.S., Alatabbi, A., Athar, T., Crochemore, M., et al.: Absent words and the (dis)similarity analysis of DNA sequences: an experimental study. BMC Res. Notes 9(1), 186 (2016)CrossRefGoogle Scholar
  3. 3.
    Krings, M., Stone, A., Schmitz, R.W., Krainitzki, H., et al.: Neandertal DNA sequences and the origin of modern humans. Cell 90(1), 19–30 (1997)CrossRefGoogle Scholar
  4. 4.
    Green, R.E., Krause, J., Ptak, S.E., Briggs, A.W., et al.: Analysis of one million base pairs of Neanderthal DNA. Nature 444(7117), 330–336 (2006)CrossRefGoogle Scholar
  5. 5.
    Noonan, J.P., Coop, G., Kudaravalli, S., Smith, D., et al.: Sequencing and analysis of Neanderthal genomic DNA. Science 314(5802), 1113–1118 (2006)CrossRefGoogle Scholar
  6. 6.
    Green, R.E., Malaspinas, A.S., Krause, J., Briggs, A.W., et al.: A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134(3), 416–426 (2008)CrossRefGoogle Scholar
  7. 7.
    Green, R.E., Krause, J., Briggs, A.W., Maricic, T., et al.: A draft sequence of the Neandertal genome. Science 328(5979), 710–722 (2010)CrossRefGoogle Scholar
  8. 8.
    Reich, D., Green, R.E., Kircher, M., Krause, J., et al.: Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468(7327), 1053–1060 (2010)CrossRefGoogle Scholar
  9. 9.
    Prüfer, K., Racimo, F., Patterson, N., Jay, F., et al.: The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505(7481), 43–49 (2014)CrossRefGoogle Scholar
  10. 10.
    Fu, Q., Hajdinjak, M., Moldovan, O.T., Constantin, S., et al.: An early modern human from Romania with a recent Neanderthal ancestor. Nature 524(7564), 216–219 (2015)CrossRefGoogle Scholar
  11. 11.
    Skoglund, P., Northoff, B.H., Shunkov, M.V., Derevianko, A.P., et al.: Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. PNAS 111(6), 2229–2234 (2014)CrossRefGoogle Scholar
  12. 12.
    Hofreiter, M., Jaenicke, V., Serre, D., von Haeseler, A., et al.: DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucl. Acids Res. 29(23), 4793–4799 (2001)CrossRefGoogle Scholar
  13. 13.
    Briggs, A.W., Stenzel, U., Johnson, P.L., Green, R.E., et al.: Patterns of damage in genomic DNA sequences from a Neandertal. PNAS 104(37), 14616–14621 (2007)CrossRefGoogle Scholar
  14. 14.
    Silva, R.M., Pratas, D., Castro, L., Pinho, A.J., Ferreira, P.J.S.G.: Three minimal sequences found in Ebola virus genomes and absent from human DNA. Bioinformatics 31(15), 2421–2425 (2015)CrossRefGoogle Scholar
  15. 15.
    Bloom, B.H.: Space/time trade-offs in hash coding with allowable errors. Commun. ACM 13(7), 422–426 (1970)CrossRefzbMATHGoogle Scholar
  16. 16.
    Lin, Y.L., Pavlidis, P., Karakoc, E., Ajay, J., Gokcumen, O.: The evolution and functional impact of human deletion variants shared with archaic hominin genomes. Mol. Biol. Evol. (2015).
  17. 17.
    Qu, R., Sang, Q., Xu, Y., Feng, R., et al.: Identification of a novel homozygous mutation in MYO3A in a chinese family with DFNB30 non-syndromic hearing impairment. Int. J. Pediatr. Otorhinolaryngol. 84, 43–47 (2016)CrossRefGoogle Scholar
  18. 18.
    Silva, I.M., Rosenfeld, J., Antoniuk, S.A., Raskin, S., Sotomaior, V.S.: A 1.5 Mb terminal deletion of 12p associated with autism spectrum disorder. Gene 542(1), 83–86 (2014)CrossRefGoogle Scholar
  19. 19.
    Baker, K., Gordon, S.L., Grozeva, D., van Kogelenberg, M., et al.: Identification of a human synaptotagmin-1 mutation that perturbs synaptic vesicle cycling. J. Clin. Invest. 125(4), 1670 (2015)Google Scholar
  20. 20.
    Meyer, M., Kircher, M., Gansauge, M.T., Li, H., et al.: A high-coverage genome sequence from an archaic Denisovan individual. Science 338(6104), 222–226 (2012)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Diogo Pratas
    • 1
    Email author
  • Morteza Hosseini
    • 1
  • Raquel M. Silva
    • 1
  • Armando J. Pinho
    • 1
  • Paulo J. S. G. Ferreira
    • 1
  1. 1.IEETA/DETI/iBiMEDUniversity of AveiroAveiroPortugal

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