Phylogenetic tree construction step by step

Construction of Phylogenetic tree

1. Phylogenetic Tree Construction By, Anushka Singh Samruddhi Gosavi Shami Gurav Tejas Somwanshi Submitted To : Dr. Nandini Kotharkar

2. Introduction to Phylogenetic Tree Construction Phylogenetic trees are used to represent the evolutionary relationships between organisms. Phylogenetic trees, also known as the "Tree of Life," are like intricate family trees depicting the evolutionary relationships between organisms. These branching diagrams visualize how different species arose from a common ancestor through countless generations. Constructing these trees is no small feat, and it involves a meticulous four-step process:

3. Gather Evidence: Identify  homologous sequences  (DNA/protein) from different organisms. These sequences act as clues to evolutionary relationships. Sequence Alignment: Use bioinformatics tools to  align  the sequences side-by-side. This highlights similarities and differences between sequences. Choose Tree Inference Method: Distance-based:  Calculate evolutionary distances between sequences based on mutations. Character-based:  Analyze changes in individual characters (nucleotides/amino acids) across lineages. Visualize the Tree: Use software to generate a  phylogenetic tree  with branches and nodes. This tree depicts the evolutionary relationships between the organisms. FOUR STEPS ARE:

4. The Evolution of Taxonomy Taxonomy, the science of categorizing and classifying organisms, has evolved significantly over time. It has been shaped by pivotal moments and the contributions of great minds, each building upon the work of their predecessors. Let's explore the major milestones in the evolution of taxonomy from the pre- Darwinian era to modern computational methods.

5. Types of Phylogenetic Trees 1 3 2 Cladograms Chronograms indicate the timing of evolutionary events and can be used to estimate divergence times. Chronograms Phylograms Cladograms depict evolutionary relationships based on shared characteristics among species. Phylograms show the amount of evolutionary change that has taken place in a particular lineage

6. Methods for Phylogenetic Tree Construction 1 Distance-Based Methods Construct trees based on the amount of genetic divergence between species. 2 Maximum Parsimony Minimizing the total number of evolutionary changes to build a tree. 3 Maximum Likelihood Finding the tree that maximizes the probability of the observed data. 4 Bayesian Inference Uses probability to estimate the likelihood of trees given the data.

7. Softwares

8. Softwares

9. Softwares PAUP (Phylogenetic Analysis Using Parsimony): Offers flexibility for advanced users but may have a less user-friendly interface compared to newer options

10. Softwares PHYML (Phylogenetic Maximum Likelihood): Researchers working with large datasets and seeking a balance between speed, accuracy, and user-friendliness .

11. Softwares Phylip (Phylogeny Inference Package) : Maximum parsimony method, distance matrix and likelihood methods A powerful tool for experienced researchers in the field of phylogenetics..

12. Applications of Phylogenetic Tree: E nriches our understanding of how genes, genomes, species evolve. Classification Answering biological questions Forensics Identifying pathogens Phylogenetics now informs the Linnaean classification of new species.

13. Applications of Phylogenetic Tree: E nriches our understanding of how genes, genomes, species evolve. Classification Answering biological questions Forensics Identifying pathogens Phylogenetics can help to inform conservation policy when conservation biologists have to make tough decisions about which species they try to prevent from becoming extinct

14. Applications of Phylogenetic Tree: E nriches our understanding of how genes, genomes, species evolve. Classification Answering biological questions Forensics Identifying pathogens Phylogenetics is used to assess DNA evidence presented in court cases to inform situations

15. Applications of Phylogenetic Tree: E nriches our understanding of how genes, genomes, species evolve. Classification Answering biological questions Forensics Identifying pathogens Used to learn more about a new pathogen outbreak

16. Applications of Phylogenetic Tree: E nriches our understanding of how genes, genomes, species evolve. Potential applications of phylogenetics: Classification Answering biological questions Forensics Identifying pathogens

17. Challenges Throughout

18. Challenges Throughout

19. Challenges Throughout

20. Challenges Throughout

21. Challenges Throughout

22. Challenges Throughout