Basics of constructing Phylogenetic tree.ppt
- 2. What Is Phylogentic tree? It is defined as a diagrammatic representation of evolutionary relationships among living organisms. This diagrammatic representation represents how different species evolved from a series of common ancestors. The phylogenetic tree can also be defined as the two-dimensional graph representing the evolutionary relationship between an organism from various other organisms.
- 3. 3 Phylogenetics is the science of the pattern of evolution Evolutionary biology versus phylogenetics - Evolutionary biology is the study of the processes that generate diversity - Phylogenetics is the study of the pattern of diversity produced by those processes
- 4. Phylogentic tree Node: a branchpoint in a tree (a presumed ancestral OTU) Branch: defines the relationship between the taxa in terms of descent and ancestry Topology: the branching patterns of the tree Branch length (scaled trees only): represents the number of changes that have occurred in the branch Root: the common ancestor of all taxa Clade: a group of two or more taxa or DNA sequences that includes both their common ancestor and all their descendents Operational Taxonomic Unit (OTU): taxonomic level of sampling selected by the user to be used in a study, such as individuals, populations, species, genera, or bacterial strains
- 5. True Clade 5 • A true clade is a monophyletic group that contains a common ancestor and all of its descendants. • A paraphyletic group is one that has a common ancestor but does not contain all of the descendants. • A polyphyletic group does not have a unique common ancestor for all the descendants.
- 6. 6 The central problem of phylogenetics: 1. How do we determine the relationships between species? 2. Use evidence from shared characteristics, not differences 3. Use homologies, not analogies 4. Use derived condition, not ancestral a. synapomorphy - shared derived characteristic b. plesiomorphy - ancestral characteristic Cladistics is phylogenetics based on synapomorphies. 1. Cladistic classification creates and names taxa based only on synapomorphies. 2. This is the principle of monophyly 3. monophyletic, paraphyletic, polyphyletic 4. Cladistics is now the preferred approach to phylogeny
- 7. Phylogenetic trees There are many ways of drawing a tree A E D C B = A E D C B E D C B A = E C D B A A E D C B A E D C B = = A E D C B no meaning
- 8. A E D C B A E D C B Bifurcation Trifurcation = / Bifurcation versus Multifurcation (e.g. Trifurcation) Multifurcation (also called polytomy): a node in a tree that connects more than three branches. A multifurcation may represent a lack of resolution because of too few data available for inferring the phylogeny (in which case it is said to be a soft multifurcation) or it may represent the hypothesized simultaneous splitting of several lineages (in which case it is said to be a hard multifurcation). Phylogenetic trees
- 9. Trees can be scaled or unscaled (with or without branch lengths) A E D C B A E D C B A E D C B A E D C B u n i t u n i t Phylogenetic trees Phylogram is a type of phylogenetic tree that represents the evolutionary relationships among organisms by showing both the branching pattern and the amount of evolutionary divergence. Phylograms are scaled, which means that the branch lengths are proportional to the amount of evolutionary divergence. Cladogram is a type of phylogenetic tree that displays only the branching pattern of evolutionary relationships among organisms. Cladograms are unscaled, which means that the branch lengths do not reflect the amount of evolutionary divergence between taxa or operational taxonomic units (OTUs).
- 10. Trees can be unrooted or rooted D A C B Unrooted tree A C B D Root Rooted tree D A C B Root A C B D Root Root Phylogenetic trees Unrooted trees do not have a specified root node and show only the branching pattern of the evolutionary relationships among taxa or OTUs, without any information about their common ancestor. Rooted trees are trees that have a specified root node, which represents the common ancestor of all the organisms in the tree.
- 11. Trees can be unrooted or rooted Unrooted tree A C B D 4 3 5 2 1 These trees show five different evolutionary relationships among the taxa! Rooted tree 1 B A C D Rooted tree 2 A B C D Rooted tree 3 A B C D Rooted tree 4 C D A B Rooted tree 5 D C A B Phylogenetic trees
- 12. How to root? Use information from ancestors A C B D 4 3 5 2 1 Use statistical tools will root trees automatically (e.g. mid-point rooting) A B C D 10 2 3 5 2 d ( A , D ) = 1 0 + 3 + 5 = 1 8 M i d p o i n t= 1 8 /2 = 9 Phylogenetic trees
- 13. Using “outgroups” A C B D 4 3 5 2 1 outgroup How to root? Phylogenetic trees - the outgroup should be a taxon known to be less closely related to the rest of the taxa (ingroups) - it should ideally be as closely related as possible to the rest of the taxa while still satisfying the above condition
- 14. Exercise: rooted/unrooted; scaled/unscaled A E D C B A E D C B A E D C B A E D C B A E D C B A E D C B A E D C B F Phylogenetic trees
- 15. What are useful characters? Use homologies, not analogies! - Homology: common ancestry of two or more character states - Analogy: similarity of character states not due to shared ancestry - Homoplasy: a collection of phenomena that leads to similarities in character states for reasons other than inheritance from a common ancestor (e.g. convergence, parallelism, reversal) Homoplasy is huge problem in morphology data sets! Cactaceae (cactus spines are modified leaves) Euphorbiaceae (euphorb spines are modified shoots) Phylogenetic trees
- 16. 1. Using Homologous Features 16 • Once a group splits into two distinct groups they evolve independently of one another. However, they retain many of the features of their common ancestor. • Any feature shared by two or more species and inherited from a common ancestor are said to be homologous. • Homologous features can be heritable traits, such as anatomical structures, DNA sequences, or similar proteins. Phylogenetic trees
- 17. Ancestral vs. Derived Traits • During the course of evolution, traits change. The original shared trait is termed the ancestral trait and the trait found in the newly evolved organism being examined is termed the derived trait. • Any feature shared by two or more species that is inherited from a common ancestor is said to be homologous. The limbs above are homologous structures, having similar bones. Phylogenetic trees
- 18. Analogous Structures • Analogous structures are those that are similar in structure but are not inherited from a common ancestor. • While the bones found in the wings of birds and bats are homologous, the wing itself is analogous. The wing structure did not evolve from the same ancestor. The physics necessary for flight is the selection pressure responsible for the similar shape of the wings. Examine airplane wings! Analogous structures should NOT be used in establishing phylogenies . Phylogenetic trees
- 19. 19
- 20. 2. Using Molecular Clocks The molecular clock hypothesis argues that DNA and protein sequences mutate at a constant rate over time among different organisms and that the number of genetic differences between organisms can give us an estimation of when they last shared a common ancestor. Genomic sequencing, computer software and systematics are able to identify these molecular homologies. The more closely related two organisms are, the more their DNA sequences will be alike. The colored boxes represent DNA homologies. Phylogenetic trees
- 21. The molecular clock is a method used to estimate the amount of time needed for a certain amount of evolutionary change. This is done by analyzing biomolecular data, such as the number of changes or substitutions in nucleotide sequences of DNA and RNA, or the amino acid sequence of proteins. Substitution is a type of mutation where one nucleotide is replaced by another. Asuming that the nucleotide or amino acid sequences mutate at a constant rate, the number of substitutions over time is equivalent to the evolutionary rate. For this reason, the molecular clock is also known as the gene clock or the evolutionary clock. 2. Using Molecular Clocks Phylogenetic trees
- 22. 22 Answer: https://www.thetech.org/ask-a- geneticist/articles/2019/ho w-build-phylogenetic-tree/ How do scientists construct phylogenetic trees and know the degree of relatedness between living organisms by DNA? Do they just look for similarities between the whole genomes? Or just specific genes? Or RNA? Or what exactly?” Phylogenetic trees
- 24. 24 The methods to construct phylogenetic trees can be classified into two major types: 1. Distance-based methods Distance-based tree construction methods involve calculating evolutionary distances between sequences by using substitution models, which are then used to construct a distance matrix. Using the distance matrix, a phylogenetic tree is constructed. The two popular distance-based methods are UPGMA and NJ. Phylogenetic trees Methods to construct phylogenetic trees
- 25. 25 2. Character-Based Methods Character-based methods involve analyzing sequence data by directly examining the sequence characters, rather than relying on pairwise distance comparisons. These methods evaluate all sequences at once by analyzing one character or site at a time. Character-based methods are generally considered more accurate than distance- based methods. However, character-based methods are more computationally intensive and require more sophisticated statistical models. The maximum parsimony (MP) and maximum likelihood (ML) methods are the two most commonly used character-based tree construction methods. Phylogenetic trees Methods to construct phylogenetic trees