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. 2010 Mar 5;15(2):311–341. doi: 10.2478/s11658-010-0010-8

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

Diego San Mauro 1,✉, Ainhoa Agorreta 1,2
PMCID: PMC6275913  PMID: 20213503

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.

Key words: Molecular systematics, Phylogenetic inference, Molecular evolution, Phylogeny, Evolutionary analysis, Evolutionary hypothesis, Divergence time

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Abbreviations used

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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