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

Abstract

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.

Abbreviations

actB :

β-actin

AIC:

Akaike information criterion

BI:

Bayesian inference

BIC:

Bayesian information criterion

cob :

cytochrome b

cox1 :

cytochrome c oxidase subunit 1

DNA:

deoxyribonucleic acid

GTR:

General Time-Reversible

HIV:

human immunodeficiency virus

HKY:

Hasegawa Kishino Yano

hLRT:

hierarchical likelihood ratio tests

JTT:

Jones Taylor Thornton

LBA:

long-branch attraction

LRT:

likelihood ratio test

MCMC:

Markov chain Monte Carlo

ME:

minimum evolution

ML:

maximum likelihood

MP:

maximum parsimony

mtREV:

mitochondrial reversible

NJ:

neighbour-joining

PCR:

polymerase chain reaction

rag1 :

recombination activating gene 1

rRNA:

ribosomal ribonucleic acid

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San Mauro, D., Agorreta, A. Molecular systematics: A synthesis of the common methods and the state of knowledge. Cell Mol Biol Lett 15, 311–341 (2010). https://doi.org/10.2478/s11658-010-0010-8

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Key words

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