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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”.