Mutation and recombination in pathogen evolution: Relevance, methods and controversies

Miguel Arenas, Natalia M. Araujo, Catarina Branco, Nadine Castelhano, Eduardo Castro-Nallar, Marcos Pérez-Losada

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)


Mutation and recombination drive the evolution of most pathogens by generating the genetic variants upon which selection operates. Those variants can, for example, confer resistance to host immune systems and drug therapies or lead to epidemic outbreaks. Given their importance, diverse evolutionary studies have investigated the abundance and consequences of mutation and recombination in pathogen populations. However, some controversies persist regarding the contribution of each evolutionary force to the development of particular phenotypic observations (e.g., drug resistance). In this study, we revise the importance of mutation and recombination in the evolution of pathogens at both intra-host and inter-host levels. We also describe state-of-the-art analytical methodologies to detect and quantify these two evolutionary forces, including biases that are often ignored in evolutionary studies. Finally, we present some of our former studies involving pathogenic taxa where mutation and recombination played crucial roles in the recovery of pathogenic fitness, the generation of interspecific genetic diversity, or the design of centralized vaccines. This review also illustrates several common controversies and pitfalls in the analysis and in the evaluation and interpretation of mutation and recombination outcomes.

Original languageEnglish
Pages (from-to)295-306
Number of pages12
JournalInfection, Genetics and Evolution
Publication statusPublished - Sep 2018


  • Evolutionary analysis
  • HBV evolution
  • HIV-1 evolution
  • Mutation
  • Pathogen evolution
  • Recombination

ASJC Scopus subject areas

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Microbiology (medical)
  • Infectious Diseases


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