Cellular & Molecular Biology Letters

, Volume 15, Issue 2, pp 311–341 | Cite as

Molecular systematics: A synthesis of the common methods and the state of knowledge

  • Diego San MauroEmail author
  • Ainhoa Agorreta


The comparative and evolutionary analysis of molecular data has allowed researchers to tackle biological questions that have long remained unresolved. The evolution of DNA and amino acid sequences can now be modeled accurately enough that the information conveyed can be used to reconstruct the past. The methods to infer phylogeny (the pattern of historical relationships among lineages of organisms and/or sequences) range from the simplest, based on parsimony, to more sophisticated and highly parametric ones based on likelihood and Bayesian approaches. In general, molecular systematics provides a powerful statistical framework for hypothesis testing and the estimation of evolutionary processes, including the estimation of divergence times among taxa. The field of molecular systematics has experienced a revolution in recent years, and, although there are still methodological problems and pitfalls, it has become an essential tool for the study of evolutionary patterns and processes at different levels of biological organization. This review aims to present a brief synthesis of the approaches and methodologies that are most widely used in the field of molecular systematics today, as well as indications of future trends and state-of-the-art approaches.

Key words

Molecular systematics Phylogenetic inference Molecular evolution Phylogeny Evolutionary analysis Evolutionary hypothesis Divergence time 

Abbreviations used




Akaike information criterion


Bayesian inference


Bayesian information criterion


cytochrome b


cytochrome c oxidase subunit 1


deoxyribonucleic acid


General Time-Reversible


human immunodeficiency virus


Hasegawa Kishino Yano


hierarchical likelihood ratio tests


Jones Taylor Thornton


long-branch attraction


likelihood ratio test


Markov chain Monte Carlo


minimum evolution


maximum likelihood


maximum parsimony


mitochondrial reversible




polymerase chain reaction


recombination activating gene 1


ribosomal ribonucleic acid


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Copyright information

© © Versita Warsaw and Springer-Verlag Wien 2010

Authors and Affiliations

  1. 1.Department of ZoologyThe Natural History MuseumLondonUK
  2. 2.Department of Zoology and EcologyUniversity of NavarraPamplonaSpain

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