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Table 1 Selected examples of applications of molecular evolution and selection studies

From: Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry

Application type Description Citation Computational approach
Control of HIV infection Protein function study of HIV restriction properties in TRIM5α [40] Codon model tests for selection
Model species selection for pharmaceutical discovery Assessment of pharmacological target homology [42] Phylogenetic analyses of gene families
HIV vaccine development Assessment of phylogenetic diversity in viral proteins and antibodies; identification of conserved epitopes [50,53] Phylogenetic analyses and codon model tests for selection
Flu epidemics prediction; vaccine strain selection Modeling of antigenic dynamics of flu over time [54] Phylogenetic diffusion model of antigenic evolution
Prediction of HIV progression Monitoring the synonymous substitution rates in viral protein samples from HIV-positive patients over time [67] “Relaxed-clock” modeling of codon evolution
Evaluating epidemics dynamics and the effect of public health interventions Estimating the rates of transmission, recovery, sampling, and the effective reproductive number [81-83] Birth-death phylogenetic models
Flu epidemics prediction; vaccine strain selection Modeling adaptive epitope changes and deleterious mutations outside the epitopes in flu from one year to the next [93] Molecular evolution modeling over viral genealogies
Crop resistance Identifying the resistant variants of the Pi-ta gene in rice that is used to control rice blast disease [96] Analyses of genetic diversity and evolution
Mapping disease associations; complex disease biology; development personalized medicine Genome studies identifying sites of genomic diversification, associations with diseases, estimating fitness of mutations [73,74] Evolutionary analyses of genomic constraints, genome-wide association studies
*Disease biology; identification of vaccine targets Population genomics of the sexually transmitted bacteria Chlamydia trachomatis [97] Genome-wide evolutionary analyses of conservation by codon models and population genetics approaches
*Disease biology Adaptation in the cavity causing bacteria Streptococcus mutans [98] Genome-wide evolutionary analyses of conservation and demography
*Conservation and biodiversity; climate change Evaluating hybridization of blue whale subspecies in southern hemisphere [99] Population genetics analyses
*Impact of climate change Evaluating the interplay between global climate change, genetic diversity and species interactions and community structure [100] Evaluation of intraspecific genetic diversity by population genetics approaches
  1. *Highlighted in the 2013 editorial “Highlights in applied evolutionary biology” in the peer-reviewed journal “Evolutionary Applications”.