Encyclopedia of Metagenomics

2015 Edition
| Editors: Karen E. Nelson

Phylogenetics, Overview

Phylogenetics: A Root and Branch Analysis of the Tree of Life
  • Roy Sleator
Reference work entry
DOI: https://doi.org/10.1007/978-1-4899-7478-5_708


Evolutionary relatedness


Phylogenetics, derived from the Greek terms phylon (meaning “tribe”) and genetikos (meaning “genitive” or origin), is the study of the evolutionary history of species, organisms, genes, or proteins through the construction and analysis of mathematical entities known as trees or phylogenies.


Darwin’s The Origin of Species marked the birth of phylogeny, a discipline whose primary aims are to classify all living organisms, grouping all extant descendants of a given ancestor within specific groups or clades; to provide insights into the shared properties of members within each clade; and to allow retro direction, i.e., the ability to infer ancestral properties based on observable characteristics of extant organisms.

A significant limitation of traditional morphology-based phylogeny approaches is the fact that reconstructing ancient evolutionary events requires a vast sum of character changes. Furthermore, many of these morphological...

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  1. Andersson JO, Sjogren AM, Horner DS, Murphy CA, Dyal PL, Svard SG, Logsdon JR JM, Ragan MA, Hirt RP, Roger AJ. A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. BMC Genomics. 2007;8:51.PubMedCentralPubMedGoogle Scholar
  2. Archibald JM, Rogers MB, Toop M, Ishida K, Keeling PJ. Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans. Proc Natl Acad Sci U S A. 2003;100:7678–83.PubMedCentralPubMedGoogle Scholar
  3. Brocchieri L. Phylogenetic inferences from molecular sequences: review and critique. Theor Popul Biol. 2001;59:27–40.PubMedGoogle Scholar
  4. Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 2005;6:361–75.PubMedGoogle Scholar
  5. Forterre P, Gadelle D. Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms. Nucl Acids Res. 2009;37:679–92.PubMedCentralPubMedGoogle Scholar
  6. Hernandez Fernandez M, Vrba ES. A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants. Biol Rev Camb Philos Soc. 2005;80:269–302.PubMedGoogle Scholar
  7. Karlin S, Bucher P, Brendel V, Altschul SF. Statistical methods and insights for protein and DNA sequences. Annu Rev Biophys Biophys Chem. 1991;20:175–203.PubMedGoogle Scholar
  8. Karlin S, Zuker M, Brocchieri L. Measuring residue associations in protein structures. Possible implications for protein folding. J Mol Biol. 1994;239:227–48.PubMedGoogle Scholar
  9. Lawrence JG. Gene transfer in bacteria: speciation without species? Theor Popul Biol. 2002;61:449–60.PubMedGoogle Scholar
  10. Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science. 1993;262:208–14.PubMedGoogle Scholar
  11. Lopez P, Bapteste E. Molecular phylogeny: reconstructing the forest. C R Biol. 2009;332:171–82.PubMedGoogle Scholar
  12. Puigbo P, Wolf Y, Koonin E. Search for a ‘Tree of Life’ in the thicket of the phylogenetic forest. J Biol. 2009;8:59.PubMedCentralPubMedGoogle Scholar
  13. Sapp J. The structure of microbial evolutionary theory. Stud Hist Philos Biol Biomed Sci. 2007;38:780–795.Google Scholar
  14. Sleator RD. An overview of the processes shaping protein evolution. Sci Prog. 2010;93:1–6.PubMedGoogle Scholar
  15. Sleator RD. Phylogenetics. Arch Microbiol. 2011;193:235–9.PubMedGoogle Scholar
  16. Sleator RD, Shortall C, Hill C. Metagenomics. Lett Appl Microbiol. 2008;47:361–6.PubMedGoogle Scholar
  17. Soltis DE, Soltis PS. The role of phylogenetics in comparative genetics. Plant Physiol. 2003a;132:1790–800.PubMedCentralPubMedGoogle Scholar
  18. Soltis PS, Soltis DE. Applying the bootstrap in phylogeny reconstruction. Stat Sci. 2003b;18:256–67.Google Scholar
  19. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28:2731–9.PubMedCentralPubMedGoogle Scholar
  20. Wrobel B. Statistical measures of uncertainty for branches in phylogenetic trees inferred from molecular sequences by using model-based methods. J Appl Genet. 2008;49:49–67.PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of Biological SciencesCork Institute of TechnologyCorkIreland