Abstract
Changes that occur in the genome (or DNA) are pieces of genetic information containing valuable information to reveal the evolutionary history of organisms. As mentioned in the previous chapter, the elucidation of DNA sequences is a major advancement in the field of molecular biology. These advancements allowed sequences to be compared between different organisms, looking at similarities and differences. Through looking at molecular level changes, the reconstruction of phylogenies based on these sequences can be performed. Molecular phylogenies provide insights into the evolutionary relationships among organisms and a closer look at the processes behind species diversity. In addition, molecular phylogenies are also beneficial in the taxonomical classification and identification of organisms. Regarding Chap. 7, we reviewed the principles behind molecular-based techniques like PCR and DNA sequencing, together with examples of each method popular among researchers. In this chapter, we looked at the types of mutations that can occur in the DNA and the terminologies and main concepts of DNA sequence alignment. The principles behind phylogenetic inferences were introduced and the explanation of various models and methods. Finally, guidelines for analysis and practical steps for sequence alignment and the reconstruction of phylogenetic trees were discussed to complete the link between physical specimens, DNA sequences, and phylogenetic trees.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Ajawatanawong, P. (2017). Molecular phylogenetics: Concepts for a newcomer. Advances in Biochemical Engineering/Biotechnology, 160, 185–196. https://doi.org/10.1007/10_2016_49
Arenas, M. (2015). Trends in substitution models of molecular evolution. Frontiers in Genetics, 6, 319–319. https://doi.org/10.3389/fgene.2015.00319
Baldauf, S. L. (2003). Phylogeny for the faint of heart: A tutorial. Trends in Genetics, 19(6), 345–351. https://doi.org/10.1016/s0168-9525(03)00112-4
Baum, D. (2008). Reading a phylogenetic tree: the meaning of monophyletic groups. Nature Education, 1(1), 190.
Carlin, J. (2011). Mutations are the raw materials of evolution. Nature Education Knowledge, 2(1), 10. Retrieved from https://www.nature.com/scitable/knowledge/library/mutations-are-the-raw-materials-of-evolution-17395346/
Chatzou, M., Magis, C., Chang, J. M., Kemena, C., Bussotti, G., Erb, I., & Notredame, C. (2016). Multiple sequence alignment modeling: Methods and applications. Briefings in Bioinformatics, 17(6), 1009–1023. https://doi.org/10.1093/bib/bbv099
De Bruyn, A., Martin, D. P., & Lefeuvre, P. (2014). Phylogenetic reconstruction methods: An overview. Methods in Molecular Biology, 1115, 257–277. https://doi.org/10.1007/978-1-62703-767-9_13
Edgar, R. C. (2004). MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113. https://doi.org/10.1186/1471-2105-5-113
Erickson, K. (2010). The jukes-cantor model of molecular evolution. Primus, 20(5), 438–445. https://doi.org/10.1080/10511970903487705
Felsenstein, J. (1985). Phylogenies and the comparative method. The American Naturalist, 125(1), 1–15.
Garamszegi, L. (2014). Modern phylogenetic comparative methods and their application in evolutionary biology (1st ed.). Springer.
Gibbs, A. J., & McIntyre, G. A. (1970). The diagram, a method for comparing sequences. Its use with amino acid and nucleotide sequences. European Journal of Biochemistry, 16(1), 1–11. https://doi.org/10.1111/j.1432-1033.1970.tb01046.x
Hall, T. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program or windows 95/98/NT. Nucleic Acids Symposium, 41, 95–98.
Hall, B. G. (2005). Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences. Molecular Biology and Evolution, 22(3), 792–802. https://doi.org/10.1093/molbev/msi066
Hogeweg, P., & Hesper, B. (1984). The alignment of sets of sequences and the construction of phyletic trees: An integrated method. Journal of Molecular Evolution, 20(2), 175–186. https://doi.org/10.1007/BF02257378
Holder, M., & Lewis, P. O. (2003). Phylogeny estimation: Traditional and Bayesian approaches. Nature Reviews. Genetics, 4(4), 275–284. https://doi.org/10.1038/nrg1044
Katoh, K. (2021). Multiple sequence alignment. Humana.
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 Research, 30(14), 3059–3066. https://doi.org/10.1093/nar/gkf436
Keith, J. (2017). Bioinformatics (2nd ed.). Humana.
Keller, A., Förster, F., Müller, T., Dandekar, T., Schultz, J., & Wolf, M. (2010). Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. Biology Direct, 5, 4. https://doi.org/10.1186/1745-6150-5-4
Kumar, S., & Filipski, A. (2007). Multiple sequence alignment: In pursuit of homologous DNA positions. Genome Research, 17(2), 127–135. https://doi.org/10.1101/gr.5232407
Kumar, S., & Gadagkar, S. R. (2001). Disparity index: A simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. Genetics, 158(3), 1321–1327. https://doi.org/10.1093/genetics/158.3.1321
Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6), 1547–1549. https://doi.org/10.1093/molbev/msy096
Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., & Higgins, D. G. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23(21), 2947–2948. https://doi.org/10.1093/bioinformatics/btm404
Lemey, P., Salemi, M., & Vandamme, A. (2009). The phylogenetic handbook (2nd ed.). Cambridge University Press.
Li, W. H., & Graur, D. (2000). Fundamentals of molecular evolution. Sinauer Associates.
Li, H., Zhu, D., Zhang, C., Han, H., & Crandall, K. A. (2014). Characteristics and prediction of RNA structure. BioMed Research International, 2014, 690340. https://doi.org/10.1155/2014/690340
Margoliash, E., & Fitch, W. M. (1971). Amino acid sequences and phylogeny. Taxon, 20(1), 51–53. https://doi.org/10.2307/1218533
Nascimento, F. F., Reis, M., & d., & Yang, Z. (2017). A biologist’s guide to Bayesian phylogenetic analysis. Nature Ecology & Evolution, 1(10), 1446–1454. https://doi.org/10.1038/s41559-017-0280-x
Notredame, C., Higgins, D. G., & Heringa, J. (2000). T-coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology, 302(1), 205–217. https://doi.org/10.1006/jmbi.2000.4042
Page, R. D. (1996). TreeView: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences, 12(4), 357–358. https://doi.org/10.1093/bioinformatics/12.4.357
Page, R., & Holmes, E. (1998). Molecular evolution: A phylogenetic approach. Blackwell.
Posada, D. (2009). Bioinformatics for DNA sequence analysis (1st ed.). Humana.
Prasad, P. K., Tandon, V., Biswal, D. K., Goswami, L. M., & Chatterjee, A. (2009). Phylogenetic reconstruction using secondary structures and sequence motifs of ITS2 rDNA of Paragonimus westermani (Kerbert, 1878) Braun, 1899 (Digenea: Paragonimidae) and related species. BMC Genomics, 10(Suppl 3), S25. https://doi.org/10.1186/1471-2164-10-S3-S25
Rambaut, A. (2010). FigTree. Retrieved from http://tree.bio.ed.ac.uk/software/figtree/
Rosenberg, M. S., & Kumar, S. (2003). Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Molecular Biology and Evolution, 20(4), 610–621. https://doi.org/10.1093/molbev/msg067
Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4), 406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Sanderson, M. J., & Shaffer, H. B. (2002). Troubleshooting molecular phylogenetic analyses. Annual Review of Ecology and Systematics, 33(1), 49–72. https://doi.org/10.1146/annurev.ecolsys.33.010802.150509
Selzer, P. M., Marhöfer, R. J., & Koch, O. (2018). Applied bioinformatics—An introduction. Springer.
Shaik, N., Hakeem, K., Banaganapalli, B., & Elango, R. (2019). Essentials of bioinformatics (Vol. 1, 1st ed.). Springer.
Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J. D., & Higgins, D. G. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal omega. Molecular Systems Biology, 7, 539. https://doi.org/10.1038/msb.2011.75
Soltis, P. S., & Soltis, D. E. (2003). Applying the bootstrap in phylogeny reconstruction. Statistical Science, 18(2), 256–267. Retrieved from http://www.jstor.org/stable/3182855
Subbotin, S. A., Sturhan, D., Vovlas, N., Castillo, P., Tambe, J. T., Moens, M., & Baldwin, J. G. (2007). Application of the secondary structure model of rRNA for phylogeny: D2-D3 expansion segments of the LSU gene of plant-parasitic nematodes from the family Hoplolaimidae Filipjev, 1934. Molecular Phylogenetics and Evolution, 43(3), 881–890. https://doi.org/10.1016/j.ympev.2006.09.019
Subbotin, S., Waeyenberge, L., & Moens, M. (2013). Molecular systematics. In R. N. Perry & M. Moens (Eds.), Plant nematology (pp. 40–72). CAB International.
University of California, MoP. (2021). Understanding evolution. Retrieved from http://evolution.berkeley.edu/
Xia, X. (2000). Data analysis in molecular biology and evolution (1st ed.). Springer.
Xia, X. (2017). DAMBE6: New tools for microbial genomics, phylogenetics, and molecular evolution. The Journal of Heredity, 108(4), 431–437. https://doi.org/10.1093/jhered/esx033
Yang, Z., & Rannala, B. (2012). Molecular phylogenetics: Principles and practice. Nature Reviews. Genetics, 13(5), 303–314. https://doi.org/10.1038/nrg3186
Author information
Authors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Thaenkham, U., Chaisiri, K., Hui En Chan, A. (2022). DNA Sequence Alignment and Phylogenetic Inferences: Guidelines for Analysis and the Selection of Appropriate Methods for Molecular Systematics. In: Molecular Systematics of Parasitic Helminths . Springer, Singapore. https://doi.org/10.1007/978-981-19-1786-8_8
Download citation
DOI: https://doi.org/10.1007/978-981-19-1786-8_8
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-19-1785-1
Online ISBN: 978-981-19-1786-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)