Abstract
Evolution is the dynamic process where a species or population undergo change in heritable characteristics. The study of evolution is called evolutionary biology. The role of computational tools and algorithms has become important for the study of evolutionary process. The key molecular aspect of evolution is sequence variation which is detected by comparing DNA or protein sequences. Different computational tools have been developed to align the obtained sequences and identification of sequence variation. Phylogenetics is a representation of similarity or dissimilarity among the species or genes or proteins. The variation of DNA sequence occurs by substitution of the bases and thereby it affects amino acid sequence. Evolutionary dating has become a crucial tool for estimation of species divergence. The application of evolutionary genomics is spanning from studying human evolution to the evolution of varieties of viruses. Many viruses pose serious threats to human health. Thus, studying viral evolution has become extremely important from biomedical aspect.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Benvenuto D, Giovanetti M, Salemi M, Prosperi M, De Flora C, Junior Alcantara LC, Ciccozzi M (2020) The global spread of 2019-nCoV: a molecular evolutionary analysis. Pathog Glob Health 114(2):64–67. https://doi.org/10.1080/20477724.2020.1725339
Bouckaert R, Vaughan TG, Barido-Sottani J, Duchene S, Fourment M, Gavryushkina A, Drummond AJ (2019) BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol 15(4):e1006650. https://doi.org/10.1371/journal.pcbi.1006650
Bromham L, Duchene S, Hua X, Ritchie AM, Duchene DA, Ho SYW (2018) Bayesian molecular dating: opening up the black box. Biol Rev Camb Philos Soc 93(2):1165–1191. https://doi.org/10.1111/brv.12390
Brudno M, Poliakov A, Minovitsky S, Ratnere I, Dubchak I (2007) Multiple whole genome alignments and novel biomedical applications at the VISTA portal. Nucleic Acids Res 35:W669–W674. https://doi.org/10.1093/nar/gkm279
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Hayashizaki Y (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38(6):626–635. https://doi.org/10.1038/ng1789
Choi KR, Jang WD, Yang D, Cho JS, Park D, Lee SY (2019) Systems metabolic engineering strategies: integrating systems and synthetic biology with metabolic engineering. Trends Biotechnol 37(8):817–837. https://doi.org/10.1016/j.tibtech.2019.01.003
Corel E, Pathmanathan JS, Watson AK, Karkar S, Lopez P, Bapteste E (2018) MultiTwin: a software suite to analyze evolution at multiple levels of organization using multipartite graphs. Genome Biol Evol 10(10):2777–2784. https://doi.org/10.1093/gbe/evy209
Dehghan S, Seto J, Liu EB, Ismail AM, Madupu R, Heim A, Seto D (2019) A zoonotic adenoviral human pathogen emerged through genomic recombination among human and nonhuman simian hosts. J Virol 93:18. https://doi.org/10.1128/JVI.00564-19
Dellicour S, Baele G, Dudas G, Faria NR, Pybus OG, Suchard MA, Lemey P (2018) Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak. Nat Commun 9(1):2222. https://doi.org/10.1038/s41467-018-03763-2
Duchemin W, Anselmetti Y, Patterson M, Ponty Y, Berard S, Chauve C, Tannier E (2017) DeCoSTAR: reconstructing the ancestral organization of genes or genomes using reconciled phylogenies. Genome Biol Evol 9(5):1312–1319. https://doi.org/10.1093/gbe/evx069
Dumas L, Kim YH, Karimpour-Fard A, Cox M, Hopkins J, Pollack JR, Sikela JM (2007) Gene copy number variation spanning 60 million years of human and primate evolution. Genome Res 17(9):1266–1277. https://doi.org/10.1101/gr.6557307
Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinf 5:113. https://doi.org/10.1186/1471-2105-5-113
Futuyma DJ, Kirkpatrick M (2017) Evolution, 4th edn. Sinauer Associates, Inc., Sunderland
Garrigan D (2013) POPBAM: tools for evolutionary analysis of short read sequence alignments. Evol Bioinformatics Online 9:343–353. https://doi.org/10.4137/EBO.S12751
Goerner-Potvin P, Bourque G (2018) Computational tools to unmask transposable elements. Nat Rev Genet 19(11):688–704. https://doi.org/10.1038/s41576-018-0050-x
Green RE, Krause J, Ptak SE, Briggs AW, Ronan MT, Simons JF, Paabo S (2006) Analysis of one million base pairs of Neanderthal DNA. Nature 444(7117):330–336. https://doi.org/10.1038/nature05336
Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52(5):696–704. https://doi.org/10.1080/10635150390235520
Guindon S, Lethiec F, Duroux P, Gascuel O (2005) PHYML online--a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33:W557–W559. https://doi.org/10.1093/nar/gki352
Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22(2):160–174. https://doi.org/10.1007/BF02101694
Hastings WK (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97
Haubold B, Weihei T (2006) Phylogeny introduction to evolutionary biology: an evolutionary approach. Berhauser Verlag, Basel, pp 143–168
Ho SY, Duchene S (2014) Molecular-clock methods for estimating evolutionary rates and timescales. Mol Ecol 23(24):5947–5965. https://doi.org/10.1111/mec.12953
Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17(8):754–755. https://doi.org/10.1093/bioinformatics/17.8.754
Ismail AM, Cui T, Dommaraju K, Singh G, Dehghan S, Seto J, Seto D (2018) Genomic analysis of a large set of currently-and historically-important human adenovirus pathogens. Emerg Microbes Infect 7(1):10. https://doi.org/10.1038/s41426-017-0004-y
Jariani A, Warth C, Deforche K, Libin P, Drummond AJ, Rambaut A, Theys K (2019) SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination. Virus Evol 5(1):vez003. https://doi.org/10.1093/ve/vez003
Jobin M, Schurz H, Henn BM (2018) IMPUTOR: phylogenetically aware software for imputation of errors in next-generation sequencing. Genome Biol Evol 10(5):1248–1254. https://doi.org/10.1093/gbe/evy088
Karim S, NourEldin HF, Abusamra H, Salem N, Alhathli E, Dudley J, Kumar S (2016) e-GRASP: an integrated evolutionary and GRASP resource for exploring disease associations. BMC Genomics 17(Suppl 9):770. https://doi.org/10.1186/s12864-016-3088-1
Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30(14):3059–3066. https://doi.org/10.1093/nar/gkf436
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120. https://doi.org/10.1007/BF01731581
Krause J, Lalueza-Fox C, Orlando L, Enard W, Green RE, Burbano HA, Paabo S (2007) The derived FOXP2 variant of modern humans was shared with Neandertals. Curr Biol 17(21):1908–1912. https://doi.org/10.1016/j.cub.2007.10.008
Kumar S, Nei M, Dudley J, Tamura K (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9(4):299–306. https://doi.org/10.1093/bib/bbn017
Lai A, Bergna A, Acciarri C, Galli M, Zehender G (2020) Early phylogenetic estimate of the effective reproduction number of SARS-CoV-2. J Med Virol 92(6):675–679. https://doi.org/10.1002/jmv.25723
Li K, Yan S, Wang N, He W, Guan H, He C, Su S (2020a) Emergence and adaptive evolution of Nipah virus. Transbound Emerg Dis 67(1):121–132. https://doi.org/10.1111/tbed.13330
Li J, Zhang S, Li B, Hu Y, Kang XP, Wu XY, Jiang T (2020b) Machine learning methods for predicting human-adaptive influenza A viruses based on viral nucleotide compositions. Mol Biol Evol 37(4):1224–1236. https://doi.org/10.1093/molbev/msz276
Liu SQ, Deng CL, Yuan ZM, Rayner S, Zhang B (2015) Identifying the pattern of molecular evolution for Zaire ebolavirus in the 2014 outbreak in West Africa. Infect Genet Evol 32:51–59. https://doi.org/10.1016/j.meegid.2015.02.024
Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21(6):1087–1092
Nater A, Burri R, Kawakami T, Smeds L, Ellegren H (2015) Resolving evolutionary relationships in closely related species with whole-genome sequencing data. Syst Biol 64(6):1000–1017. https://doi.org/10.1093/sysbio/syv045
Nei M, Kumar S (2000) Molecular evoution and phylogenetics. Oxford University Press, Oxford
Noonan JP (2010) Neanderthal genomics and the evolution of modern humans. Genome Res 20(5):547–553. https://doi.org/10.1101/gr.076000.108
Nuin P A, Wang Z, Tillier ER (2006) The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics 7:471. https://doi.org/10.1186/1471-2105-7-471
Park Y, Casey D, Joshi I, Zhu J, Cheng F (2020) Emergence of new disease: how can artificial intelligence help? Trends Mol Med 26(7):627–629. https://doi.org/10.1016/j.molmed.2020.04.007
Remita MA, Halioui A, Malick Diouara AA, Daigle B, Kiani G, Diallo AB (2017) A machine learning approach for viral genome classification. BMC Bioinf 18(1):208. https://doi.org/10.1186/s12859-017-1602-3
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61(3):539–542. https://doi.org/10.1093/sysbio/sys029
Sankararaman S, Mallick S, Dannemann M, Prufer K, Kelso J, Paabo S, Reich D (2014) The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507(7492):354–357. https://doi.org/10.1038/nature12961
Sauquet H (2013) A practical guide to molecular dating. Comptes Rendus Palevol 12(6):355–367
Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Miller W (2000) PipMaker--a web server for aligning two genomic DNA sequences. Genome Res 10(4):577–586. https://doi.org/10.1101/gr.10.4.577
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312–1313. https://doi.org/10.1093/bioinformatics/btu033
Sumner JG, Jarvis PD, Fernandez-Sanchez J, Kaine BT, Woodhams MD, Holland BR (2012) Is the general time-reversible model bad for molecular phylogenetics? Syst Biol 61(6):1069–1074. https://doi.org/10.1093/sysbio/sys042
Tajima F, Nei M (1984) Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol 1(3):269–285. https://doi.org/10.1093/oxfordjournals.molbev.a040317
Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10(3):512–526. https://doi.org/10.1093/oxfordjournals.molbev.a040023
Wang Y, Waters J, Leung ML, Unruh A, Roh W, Shi X, Navin NE (2014) Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 512(7513):155–160. https://doi.org/10.1038/nature13600
Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24(8):1586–1591. https://doi.org/10.1093/molbev/msm088
Yao H, Chen M, Tang Z (2019) Analysis of synonymous codon usage bias in flaviviridae virus. Biomed Res Int 2019:5857285. https://doi.org/10.1155/2019/5857285
Zehender G, Lai A, Bergna A, Meroni L, Riva A, Balotta C, Galli M (2020) Genomic characterization and phylogenetic analysis of SARS-COV-2 in Italy. J Med Virol. https://doi.org/10.1002/jmv.25794
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Banerjee, S. (2021). Computational Evolutionary Biology. In: Singh, V., Kumar, A. (eds) Advances in Bioinformatics. Springer, Singapore. https://doi.org/10.1007/978-981-33-6191-1_5
Download citation
DOI: https://doi.org/10.1007/978-981-33-6191-1_5
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-33-6190-4
Online ISBN: 978-981-33-6191-1
eBook Packages: Computer ScienceComputer Science (R0)