Skip to main content
SpringerLink
Log in

A Beginner’s Guide to Phylogenetics

Microbial Ecology volume 66, pages 1–4 (2013)Cite this article

Abstract

Metagenomics and the development of high throughput next generation sequencing capabilities have forced significant development in the field of phylogenetics: the study of the evolutionary relatedness of the planet’s inhabitants. Herein, I review the major tree-building strategies, challenges and opportunities which exist in this rapidly expanding field of evolutionary biology.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2

References

  1. Sleator RD (2011) Phylogenetics. Arch Microbiol 193:235–239. doi:10.1007/s00203-011-0677-x

    Article  PubMed  CAS  Google Scholar 

  2. Knapp S (2009) On the origin of species by means of natural selection. Nature 460:577–577

    Google Scholar 

  3. Sleator RD (2010) An overview of the processes shaping protein evolution. Sci Prog 93:1–6

    Article  PubMed  Google Scholar 

  4. Lopez P, Bapteste E (2009) Molecular phylogeny: reconstructing the forest. C R Biol 332:171–182

    Article  PubMed  CAS  Google Scholar 

  5. Loman NJ, Constantinidou C, Chan JZM, Halachev M, Sergeant M, Penn CW, Robinson ER, Pallen MJ (2012) High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 10:599–606. doi:10.1038/Nrmicro2850

    Article  PubMed  CAS  Google Scholar 

  6. Rotilio D, Della Corte A, D’Imperio M, Coletta W, Marcone S, Silvestri C, Giordano L, Di Michele M, Donati MB (2012) Proteomics: bases for protein complexity understanding. Thromb Res 129:257–262. doi:10.1016/j.thromres.2011.12.035

    Article  PubMed  CAS  Google Scholar 

  7. Sleator RD (2012) Proteins: form and function. Bioeng Bugs 3(2):80–85. doi:10.4161/bbug.18303

    Google Scholar 

  8. Sleator RD, Shortall C, Hill C (2008) Metagenomics. Lett Appl Microbiol 47:361–366. doi:10.1111/j.1472-765X.2008.02444.x

  9. Naidoo N, Pawitan Y, Soong R, Cooper DN, Ku CS (2011) Human genetics and genomics a decade after the release of the draft sequence of the human genome. Hum Genomics 5:577–622

    Article  PubMed  CAS  Google Scholar 

  10. Culligan EP, Sleator RD, Marchesi JR, Hill C (2012) Functional metagenomics reveals novel salt tolerance loci from the human gut microbiome. ISME J 6:1916–1925. doi:10.1038/ismej.2012.38

    Article  PubMed  CAS  Google Scholar 

  11. Feeney A, Sleator RD (2012) The human gut microbiome: the ghost in the machine. Future Microbiol 7:1235–1237. doi:10.2217/fmb.12.105

    Article  PubMed  CAS  Google Scholar 

  12. Manning T, Sleator RD, Walsh P (2013) Naturally selecting solutions: the use of genetic algorithms in bioinformatics. Bioengineered 4(5). doi:10.4161/bioe.23041

  13. Forterre P, Gadelle D (2009) Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms. Nucl Acids Res 37:679–692. doi:10.1093/nar/gkp032

    Article  PubMed  CAS  Google Scholar 

  14. Yang Z, Rannala B (2012) Molecular phylogenetics: principles and practice. Nat Rev Genet 13:303–314. doi:10.1038/nrg3186

    Article  PubMed  CAS  Google Scholar 

  15. Kumar S, Filipski AJ, Battistuzzi FU, Kosakovsky Pond SL, Tamura K (2012) Statistics and truth in phylogenomics. Mol Biol Evol 29:457–472. doi:10.1093/molbev/msr202

    Article  PubMed  CAS  Google Scholar 

  16. Dagan T (2011) Phylogenomic networks. Trends Microbiol 19:483–491. doi:10.1016/j.tim.2011.07.001

    Article  PubMed  CAS  Google Scholar 

  17. Lespinats S, Grando D, Marechal E, Hakimi MA, Tenaillon O, Bastien O (2011) How Fitch-Margoliash algorithm can benefit from multi dimensional scaling. Evol Bioinform 7:61–85. doi:10.4137/Ebo.S7048

    Google Scholar 

  18. Takahashi K, Nei M (2000) Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 17:1251–1258

    Article  PubMed  CAS  Google Scholar 

  19. Soltis DE, Soltis PS (2003) The role of phylogenetics in comparative genetics. Plant Physiol 132:1790–1800

    Article  PubMed  CAS  Google Scholar 

  20. Li SY, Pearl DK, Doss H (2000) Phylogenetic tree construction using Markov chain Monte Carlo. J Am Stat Assoc 95:493–508. doi:10.2307/2669394

    Article  Google Scholar 

  21. Larget B, Simon DL (1999) Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol Biol Evol 16:750–759

    Article  CAS  Google Scholar 

  22. Wrobel B (2008) Statistical measures of uncertainty for branches in phylogenetic trees inferred from molecular sequences by using model-based methods. J Appl Genet 49:49–67

    Article  PubMed  Google Scholar 

  23. Hernandez Fernandez M, Vrba ES (2005) A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants. Biol Rev Camb Philos Soc 80:269–302

    Article  PubMed  Google Scholar 

  24. Brocchieri L (2001) Phylogenetic inferences from molecular sequences: review and critique. Theor Popul Biol 59:27–40. doi:10.1006/tpbi.2000.1485

    Article  PubMed  CAS  Google Scholar 

  25. Lawrence JG (2002) Gene transfer in bacteria: speciation without species? Theor Popul Biol 61:449–460

    Article  PubMed  Google Scholar 

  26. Puigbo P, Wolf Y, Koonin E (2009) Search for a ‘Tree of Life’ in the thicket of the phylogenetic forest. J Biol 8:59

    Article  PubMed  Google Scholar 

  27. Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6:361–375

    Article  PubMed  CAS  Google Scholar 

  28. Karlin S (1998) Global dinucleotide signatures and analysis of genomic heterogeneity. Curr Opin Microbiol 1:598–610

    Article  PubMed  CAS  Google Scholar 

  29. Pallen MJ, Wren BW (2007) Bacterial pathogenomics. Nature 449:835–842. doi:10.1038/Nature06248

    Article  PubMed  CAS  Google Scholar 

  30. Bullman S, Lucey B, Sleator RD (2012) Molecular diagnostics: the changing culture of medical microbiology. Bioeng Bugs 3:1–7. doi:10.4161/bbug.3.1.19011

    Article  PubMed  Google Scholar 

  31. Dorrell N, Hinchliffe SJ, Wren BW (2005) Comparative phylogenomics of pathogenic bacteria by microarray analysis. Curr Opin Microbiol 8:620–626

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

RDS is coordinator of the FP7-PEOPLE-2012-IAPP grant ClouDx-i.

Author information

Authors and Affiliations

  1. Department of Biological Sciences, Cork Institute of Technology, Rossa Avenue, Bishopstown, Cork, Ireland

    Roy D. Sleator

Authors
  1. Roy D. Sleator
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Roy D. Sleator.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Sleator, R.D. A Beginner’s Guide to Phylogenetics. Microb Ecol 66, 1–4 (2013). https://doi.org/10.1007/s00248-013-0236-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-013-0236-x

Keywords

search

Navigation