Evolutionary medicine
- Using positive selection to identify the pathogenic mechanisms of HIV in human.
- Using the evolutionary analyzes to identify new disease out breaks.
- Learn about the origin of the diseases.
- Identify the diseases resistance mechanisms in other hosts to identify the better treatments.
Population studies – population structure and the subdivisions.
Studying mating systems
Breeding studies
Character evolution
Some other indirect applications
- Ecological problems
- Conservational biology
- Life history
- Forensic issues
- Pathology related issues
Phylogenetic analysis approach is rapidly increased due to
- Development of the explicit and objective methods for phylogenetic history.
- New data are formed in molecular biology.
- Statistical approaches to evaluate and incorporate phylogenetic information.
- Gene trees allow new views of old problems.
Controversies in phylogenetic Analysis
- Types of characters and different methods of the analysis. – Different types of data (distance and the discrete data) required different models of data analysis.
- Homology and similarity in molecular systematics. – Molecular homology can be divided into orthologous (same gene in different species) and paralogous (same gene in the same species), Positional homology of the DNA bands needs to be considered.
- Gene tree and the species trees.
- Reliability of evolutionary rates – correlation between estimates of sequence divergence and the divergence time is depends on the assumptions and data that used.
- Neutrality of the molecular variants – most of the molecular variants are not influenced by the natural selection.
- Data quality and the presentations – Accuracy of primary data, verification of the genetic basis, hybridization, repeatability of DNA fragment data, technical quality of data, sequence alignments…,is considered for reliable analysis.
Things that needs to be considered when selecting the phylogenetic analysis method
- Efficiency : refers to speed of the analysis method
- Data requirements : how much data is needed to generate a reasonable output.
- Consistency : method will meets on the correct answer for given enough data
- Robustness : methods can handle minor violations of its assumptions and it still produce accurate estimation of the phylogeny.