Skip to main content
SpringerLink
Log in

Molecular Phylogenetics: Concepts for a Newcomer

  • Chapter
  • First Online:
Network Biology

Part of the book series: Advances in Biochemical Engineering/Biotechnology ((ABE,volume 160))

Abstract

Molecular phylogenetics is the study of evolutionary relationships among organisms using molecular sequence data. The aim of this review is to introduce the important terminology and general concepts of tree reconstruction to biologists who lack a strong background in the field of molecular evolution. Some modern phylogenetic programs are easy to use because of their user-friendly interfaces, but understanding the phylogenetic algorithms and substitution models, which are based on advanced statistics, is still important for the analysis and interpretation without a guide. Briefly, there are five general steps in carrying out a phylogenetic analysis: (1) sequence data preparation, (2) sequence alignment, (3) choosing a phylogenetic reconstruction method, (4) identification of the best tree, and (5) evaluating the tree. Concepts in this review enable biologists to grasp the basic ideas behind phylogenetic analysis and also help provide a sound basis for discussions with expert phylogeneticists.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 229.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 299.99
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

Institutional subscriptions

References

  1. Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133–141

    Article  CAS  Google Scholar 

  2. Senés-Guerrero C, Schüßler A (2016) A conserved arbuscular mycorrhizal fungal core-species community colonizes potato roots in the Andes. Fungal Divers 77:317–333

    Article  Google Scholar 

  3. Baele G, Suchard MA, Rambaut A, Lemey P (2016) Emerging concepts of data integration in pathogen phylodynamics. Syst Biol. p ii: syw054

    Google Scholar 

  4. Bentley SD, Parkhill J (2015) Genomic perspectives on the evolution and spread of bacterial pathogens. Proc Biol Sci 282:20150488

    Article  Google Scholar 

  5. Kenah E, Britton T, Halloran ME, Longini IM Jr (2016) Molecular infectious disease epidemiology: survival analysis and algorithms linking phylogenies to transmission trees. PLoS Comput Biol 12, e1004869

    Article  Google Scholar 

  6. Chang AB, Lin R, Keith Studley W, Tran CV, Saier MH Jr (2004) Phylogeny as a guide to structure and function of membrane transport proteins. Mol Membr Biol 21:171–181

    Article  CAS  Google Scholar 

  7. Carrillo-Araujo M, Taş N, Alcántara-Hernández RJ, Gaona O, Schondube JE, Medellín RA, Jansson JK, Falcón LI (2015) Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies. Front Microbiol 6:447

    Article  Google Scholar 

  8. Martiny JBH, Jones SE, Lennon JT, Martiny AC (2015) Microbiomes in light of traits: a phylogenetic perspective. Science 350:aac9323

    Google Scholar 

  9. Matsen FA (2015) Phylogenetics and the human microbiome. Syst Biol 64:e26–e41

    Article  Google Scholar 

  10. Lumbsch HT, Leavitt SD (2011) Goodbye morphology? A paradigm shift in the delimitation of species in lichenized fungi. Fungal Divers 50:59–72

    Article  Google Scholar 

  11. Hillis DM (1987) Molecular versus morphological approaches to systematics. Ann Rev Ecol Syst 18:23–42

    Article  Google Scholar 

  12. Case RJ, Boucher Y, Dahllöf I, Holmström C, Doolittle WF, Kjelleberg S (2007) Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 73:278–288

    Article  CAS  Google Scholar 

  13. Ettoumi B, Guesmi A, Brusetti L, Borin S, Najjari A, Boudabous A, Cherif A (2013) Microdiversity of deep-sea Bacillales isolated from Tyrrhenian sea sediments as revealed by ARISA, 16S rRNA gene sequencing and BOX-PCR fingerprinting. Microbes Environ 28:361–369

    Article  Google Scholar 

  14. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    Article  CAS  Google Scholar 

  15. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, Whitman WB, Euzéby J, Amann R, Rosselló-Móra R (2014) Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 12:635–645

    Article  CAS  Google Scholar 

  16. Nadler SA (1995) Advantages and disadvantages of molecular phylogenetics: a case study of ascaridoid nematodes. J Nematol 27:423–432

    CAS  Google Scholar 

  17. Poretsky R, Rodriguez-R LM, Luo C, Tsementzi D, Konstantinidis KT (2014) Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. PLoS One 9, e93827

    Article  Google Scholar 

  18. Zhang N, Zeng L, Shan H, Ma H (2012) Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms. New Phytol 195:923–937

    Article  CAS  Google Scholar 

  19. Patwardhan A, Ray S, Roy A (2014) Molecular markers in phylogenetic studies—a review. J Phylogenetics Evol Biol 2:2

    Google Scholar 

  20. Rokas A, Holland PWH (2000) Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 15:454–459

    Article  CAS  Google Scholar 

  21. Ajawatanawong P, Baldauf SL (2013) Evolution of protein indels in plants, animals and fungi. BMC Evol Biol 13:140

    Google Scholar 

  22. Baldauf SL, Palmer JD (1993) Animals and fungi are each other’s closest relatives: congruent evidence from multiple proteins. Proc Natl Acad Sci U S A 90:11558–11562

    Article  CAS  Google Scholar 

  23. Chernikova D, Motamedi S, Csürös M, Koonin EV, Rogozin IB (2011) A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes. Biol Direct 6:26

    Article  CAS  Google Scholar 

  24. Janečka JE, Miller W, Pringle TH, Wiens F, Zitzmann A, Helgen KM, Springer MS, Murphy WJ (2007) Molecular and genomic data identify the closest living relative of primates. Science 318:792–794

    Article  Google Scholar 

  25. Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113

    Article  Google Scholar 

  26. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  CAS  Google Scholar 

  27. Katoh K, Standley DM (2013) MAFFT Multiple Sequence Alignment Software Version 7: improvements in performance and usability. Mol Biol Evol 30:772–780

    Article  CAS  Google Scholar 

  28. Katoh K, Standley DM (2016) A simple method to control over-alignment in the MAFFT multiple sequence alignment program. Bioinformatics 32:1933–1942

    Article  CAS  Google Scholar 

  29. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539

    Article  Google Scholar 

  30. Ajawatanawong P, Atkinson GC, Watson-Haigh NS, Mackenzie B, Baldauf SL (2012) SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments. Nucleic Acids Res 40:W340–W347

    Article  CAS  Google Scholar 

  31. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552

    Article  CAS  Google Scholar 

  32. Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56:564–577

    Article  CAS  Google Scholar 

  33. Jukes TH, Cantor CR (1969) In: Munro HN (ed) Mammalian protein metabolism. Academic, New York, pp 121–123

    Google Scholar 

  34. Kimura MA (1980) Simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  Google Scholar 

  35. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  Google Scholar 

  36. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160–174

    Article  CAS  Google Scholar 

  37. 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 10:512–526

    CAS  Google Scholar 

  38. Liò P, Goldman N (1998) Models of molecular evolution and phylogeny. Genome Res 8:1233–1244

    Article  Google Scholar 

  39. Sullivan J, Joyce P (2005) Model selection in phylogenetics. Annu Rev Ecol Evol Syst 36:445–466

    Article  Google Scholar 

  40. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818

    Article  CAS  Google Scholar 

  41. Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25:1253–1256

    Article  CAS  Google Scholar 

  42. Dayhoff MO, Schwartz R, Orcutt BC (1978) A model of evolutionary change in proteins. In: Atlas of protein sequence and structure, vol 5, supplement 3rd edn. Nat Biomed Res Found. pp 345–358

    Google Scholar 

  43. Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 89:10915–10919

    Article  CAS  Google Scholar 

  44. Stewart CB (1993) The powers and pitfalls of parsimony. Nature 361:603–607

    Article  CAS  Google Scholar 

  45. Rannala B, Yang Z (1996) Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J Mol Evol 43:304–311

    Article  CAS  Google Scholar 

  46. Alfaro ME, Holder MT (2006) The posterior and the prior in Bayesian phylogenetics. Annu Rev Ecol Evol Syst 37:19–42

    Article  Google Scholar 

  47. Holder M, Lewis PO (2003) Phylogeny estimation: traditional and Bayesian approaches. Nat Rev Genet 4:275–284

    Article  CAS  Google Scholar 

  48. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310–2314

    Article  CAS  Google Scholar 

  49. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 7:754–755

    Article  Google Scholar 

  50. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542

    Article  Google Scholar 

  51. Lartillot N, Lepage T, Blanquart S (2009) PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Phylogenetics 25:2286–2288

    CAS  Google Scholar 

  52. Lartillot N, Philippe H (2004) A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 21:1095–1109

    Article  CAS  Google Scholar 

  53. Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969–1973

    Article  CAS  Google Scholar 

  54. Baldauf SL (2003) Phylogeny for the faint of heart: a tutorial. Trends Genet 19:345–351

    Article  CAS  Google Scholar 

Download references

Acknowledgement

I thank Prof. Prasit Palittapongarnpim and Dr. Nancy Irwins for comments on this review. This work was funded by Mahidol University.

Author information

Authors and Affiliations

  1. Department of Microbiology, Faculty of Science, Mahidol University, 272 Rama VI, Rachathewi, Bangkok, 10400, Thailand

    Pravech Ajawatanawong

Authors
  1. Pravech Ajawatanawong
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Pravech Ajawatanawong .

Editor information

Editors and Affiliations

  1. Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Science, Little Rock, Arkansas, USA

    Intawat Nookaew

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing AG

About this chapter

Cite this chapter

Ajawatanawong, P. (2016). Molecular Phylogenetics: Concepts for a Newcomer. In: Nookaew, I. (eds) Network Biology. Advances in Biochemical Engineering/Biotechnology, vol 160. Springer, Cham. https://doi.org/10.1007/10_2016_49

Download citation

Publish with us

Policies and ethics

Search

Navigation