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Predicting evolution from the shape of genealogical trees

Richard A Neher, Colin A Russell, Boris I Shraiman

eLife · 2014 · CC BY

doi:10.7554/elife.03568 (opens in a new tab)

Abstract

Given a sample of genome sequences from an asexual population, can one predict its evolutionary future? Here we demonstrate that the branching patterns of reconstructed genealogical trees contains information about the relative fitness of the sampled sequences and that this information can be used to predict successful strains. Our approach is based on the assumption that evolution proceeds by accumulation of small effect mutations, does not require species specific input and can be applied to any asexual population under persistent selection pressure. We demonstrate its performance using historical data on seasonal influenza A/H3N2 virus. We predict the progenitor lineage of the upcoming influenza season with near optimal performance in 30% of cases and make informative predictions in 16 out of 19 years. Beyond providing a tool for prediction, our ability to make informative predictions implies persistent fitness variation among circulating influenza A/H3N2 viruses.

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References 37

  1. 1.
    Integrating influenza antigenic dynamics with molecular evolution · 2014
    No notice
  2. 2.

    Bhatt S Holmes EC Pybus OG 2011 The genomic rate of molecular adaptation of the human influenza A virus. Molecular Biology and Evolution28:2443–2451. doi:.

    Not in our library10.1093/molbev/msr044 (opens in a new tab)

  3. 3.

    Brunet E Derrida B Mueller AH Munier S 2007 Effect of selection on ancestry: an exactly soluble case and its phenomenological generalization. Physical review E Statistical, nonlinear and soft matter physics76:041104. doi:.

    Not in our library10.1103/physreve.76.041104 (opens in a new tab)

  4. 4.

    Bush RM Bender CA Subbarao K Cox NJ Fitch WM 1999 Predicting the evolution of human influenza A. Science286:1921–1925. doi:.

    Not in our library10.1126/science.286.5446.1921 (opens in a new tab)

  5. 5.

    Cohen E Kessler DA Levine H 2005 Front propagation up a reaction rate gradient. Physical review. E, Statistical, nonlinear, and soft matter physics72:066126. doi:.

    Not in our library10.1103/physreve.72.066126 (opens in a new tab)

  6. 6.

    Dayarian A Shraiman BI 2014 How to Infer Relative Fitness from a Sample of Genomic Sequences. Genetics113:160986. doi:.

    Not in our library10.1534/genetics.113.160986 (opens in a new tab)

  7. 7.

    Desai MM Fisher DS 2007 Beneficial mutation selection balance and the effect of linkage on positive selection. Genetics176:1759–1798. doi:.

    Not in our library10.1534/genetics.106.067678 (opens in a new tab)

  8. 8.

    Desai MM Walczak AM Fisher DS 2013 Genetic diversity and the structure of genealogies in rapidly adapting populations. Genetics193:565–585. doi:.

    Not in our library10.1534/genetics.112.147157 (opens in a new tab)

  9. 9.

    Falconer DS Mackay TFC 1996 Introduction to quantitative genetics. Pearson.

    Not in our library

  10. 10.

    Felsenstein J 2003 Inferring Phylogenies. Sinauer associates ISBN 0878931775.

    Not in our library

  11. 11.
    Stability-mediated epistasis constrains the evolution of an influenza protein · 2013
    No notice
  12. 12.

    Goyal S Balick DJ Jerison ER Neher RA Shraiman BI Desai MM 2012 Dynamic mutation-selection balance as an evolutionary attractor. Genetics191:1309–1319. doi:.

    Not in our library10.1534/genetics.112.141291 (opens in a new tab)

  13. 13.

    Hallatschek O 2011 The noisy edge of traveling waves. Proceedings of the National Academy of Sciences of USA108:1783–1787. doi:.

    Not in our library10.1073/pnas.1013529108 (opens in a new tab)

  14. 14.

    Hampson AW 2002 Influenza. In: Potter CW, editor. London: Elsevier p. 49–85.

    Not in our library

  15. 15.

    Koel BF Burke DF Bestebroer TM van der Vliet S Zondag GC Vervaet G Skepner E Lewis NS Spronken MI Russell CA Eropkin MY Hurt AC Barr IG de Jong JC Rimmelzwaan GF Osterhaus AD Fouchier RA Smith DJ 2013 Substitutions near the receptor binding site determine major antigenic change during influenza virus evolution. Science342:976–979. doi:.

    Not in our library10.1126/science.1244730 (opens in a new tab)

  16. 16.

    Koelle K Cobey S Grenfell B Pascual M 2006 Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science314:1898–1903. doi:.

    Not in our library10.1126/science.1132745 (opens in a new tab)

  17. 17.
    Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2 · 2014
    No notice
  18. 18.

    Łuksza M Lässig M 2014 A predictive fitness model for influenza. Nature507:57–61. doi:.

    Not in our library10.1038/nature13087 (opens in a new tab)

  19. 19.

    Mézard M Montanari A 2009 Information, Physics, and Computation. Oxford University Press.

    Not in our library

  20. 20.

    Neher RA 2013 Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation. Annual review of Ecology, evolution, and Systematics44:195–215. doi:.

    Not in our library10.1146/annurev-ecolsys-110512-135920 (opens in a new tab)

  21. 21.

    Neher RA Hallatschek O 2013 Genealogies of rapidly adapting populations. Proceedings of the National Academy of Sciences of USA110:437–442. doi:.

    Not in our library10.1073/pnas.1213113110 (opens in a new tab)

  22. 22.

    Neher RA Shraiman BI 2011 Genetic draft and quasi-neutrality in large facultatively sexual populations. Genetics188:975–996. doi:.

    Not in our library10.1534/genetics.111.128876 (opens in a new tab)

  23. 23.

    Nelson MI Holmes EC 2007 The evolution of epidemic influenza. Nature Reviews Genetics8:196–205. doi:.

    Not in our library10.1038/nrg2053 (opens in a new tab)

  24. 24.

    Nimwegen EV Crutchfield JP Huynen M 1999 Neutral evolution of mutational robustness. Proceedings of the National Academy of Sciences96:9716–9720. doi:.

    Not in our library10.1073/pnas.96.17.9716 (opens in a new tab)

  25. 25.

    Oliphant T 2007 Python for Scientific Computing. Computing in Science & Engineering9:10–20. doi:.

    Not in our library10.1109/mcse.2007.58 (opens in a new tab)

  26. 26.

    Plotkin JB Dushoff J Levin SA 2002 Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus. Proceedings of the National Academy of Sciences of USA99:6263–6268. doi:.

    Not in our library10.1073/pnas.082110799 (opens in a new tab)

  27. 27.

    Price MN Dehal PS Arkin AP 2009 FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Molecular Biology and Evolution26:1641–1650. doi:.

    Not in our library10.1093/molbev/msp077 (opens in a new tab)

  28. 28.

    Rouzine IM Coffin JM 2007 Highly fit ancestors of a partly sexual haploid population. Theoretical population biology71:239–250. doi:.

    Not in our library10.1016/j.tpb.2006.09.002 (opens in a new tab)

  29. 29.

    Rouzine IM Wakeley J Coffin JM 2003 The solitary wave of asexual evolution. Proceedings of the National Academy of Sciences of USA100:587–592. doi:.

    Not in our library10.1073/pnas.242719299 (opens in a new tab)

  30. 30.

    Russell CA Jones TC Barr IG Cox NJ Garten RJ Gregory V Gust ID Hampson AW Hay AJ Hurt AC de Jong JC Kelso A Klimov AI Kageyama T Komadina N Lapedes AS Lin YP Mosterin A Obuchi M Odagiri T Osterhaus AD Rimmelzwaan GF Shaw MW Skepner E Stohr K Tashiro M Fouchier RA Smith DJ 2008 The global circulation of seasonal influenza A (H3N2) viruses. Science320:340. doi:.

    Not in our library10.1126/science.1154137 (opens in a new tab)

  31. 31.

    Shih AC Hsiao TC Ho MS Li WH 2007 Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution. Proceedings of the National Academy of Sciences of USA104:6283–6288. doi:.

    Not in our library10.1073/pnas.0701396104 (opens in a new tab)

  32. 32.

    Smith DJ Lapedes AS de Jong JC Bestebroer TM Rimmelzwaan GF Osterhaus AD Fouchier RA 2004 Mapping the antigenic and genetic evolution of influenza virus. Science305:371–376. doi:.

    Not in our library10.1126/science.1097211 (opens in a new tab)

  33. 33.

    Squires RB Noronha J Hunt V Garca-Sastre A Macken C Baumgarth N Suarez D Pickett BE Zhang Y Larsen CN Ramsey A Zhou L Zaremba S Kumar S Deitrich J Klem E Scheuermann RH 2012 Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza and Other Respiratory Viruses6:404. doi:.

    Not in our library10.1111/j.1750-2659.2011.00331.x (opens in a new tab)

  34. 34.

    Strelkowa N Lässig M 2012 Clonal interference in the evolution of influenza. Genetics192:671–682. doi:.

    Not in our library10.1534/genetics.112.143396 (opens in a new tab)

  35. 35.

    Tsimring L Levine H Kessler D 1996 RNA virus evolution via a fitness-space model. Physical Review Letters76:4440–4443. doi:.

    Not in our library10.1103/physrevlett.76.4440 (opens in a new tab)

  36. 36.

    Wiley DC Wilson IA Skehel JJ 1981 Structural identification of the antibody-binding sites of Hong Kong influenza haemagglutinin and their involvement in antigenic variation. Nature289:373–378. doi:.

    Not in our library10.1038/289373a0 (opens in a new tab)

  37. 37.

    Zanini F Neher RA 2012 FFPopSim: an efficient forward simulation package for the evolution of large populations. Bioinformatics28:3332–3333. doi:.

    Not in our library10.1093/bioinformatics/bts633 (opens in a new tab)

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