Phylogenetic analysis is the finding of the genetic relationships among organisms. Phylogeny is the study of an organism’s evolutionary history; it includes time (when), mode (how), and place (where). Systematic is the classification and studying the diversity of organisms based on their phylogenetic relationships. Modern phylogenetics is highly revolutionized by molecular data.
All life on earth shares a common ancestors, Biological evolution is the descent with modifications.
DNA sequence from the common ancestor, two descendent sequences are derived, each of these sequences are started to accumulated the nucleotide substitutions, deletions (mutations) over time. In phylogenetic analysis these mutations are used as molecular markers to reconstruct the evolutionary history of organisms.
When two or more DNA or protein sequences are very similar, these sequences are most likely derived from the common ancestor. Multiple sequences alignment is used to find the similarity between the sequences.
Main assumptions of the phylogenetic Analysis
- Organisms are related by descent from a common ancestor descendant have shared derived characters.
- There are bifurcating patterns for divergence.
- Changes in characteristics are occurred in lineages over time.
Phylogenetic analysis has two major components.
- Phylogenetic inferences (tree building)
- Character and the rate analysis
Phylogenetic/ evolutionary tree is the visual representation of the evolutionary distances between species. There are two types of tree Rooted and unrooted.
- Rooted trees – this tree type shows evolutionary relationships, direction of evolution and the ancestral state
- Unrooted trees – this tree type only shows the Phylogenetic relationships.
In phylogenetic degree of divergence is considered.
The degree of the divergence between two DNA or protein sequences is expressed by as below.
Degree of divergence = n/N
- n – Number of different sites between two sequences (No. of changed characters)
- N – Total number of sites between sequences. (Total number of characters)
E.g – compare the two DNA sequences with 200 base pairs, 10 sites are different, Degree of divergence will be 10/200
True trees Vs Inferred trees
The true tree represents the actual phylogenetic relationships and evolutionary history of the organisms.
Inferred tree is reconstructed by using a specific set of data and the specific methods.
Cladogenesis Vs Anagenesis
- Anagenesis is evolutionary changers occurs along the evolutionary linages
- Cladogenesis is Splitting of an evolutionary lineage into two genetically independent lineages.
- In molecular phylogenetic assume that species are only created by cladogenesis.
Constant Molecular Clock Hypothesis
- For any given macromolecules (a protein or DNA sequence) the evolutionary rate is approximately constant overtime in all evolutionary linages & the rate of substitution of neutral alleles is equal to the mutation rate of neutral alleles
- Mutations are added at a constant rate in related species.
- For distantly related species (Taxa) haven’t constant molecular clock.
- There is no universal molecular clock; because different sites of the molecules, different genes, different regions in genes and different genomes in the same cells.
- Carefully tested and calibrated molecular local clocks are available
- The slope of the graph represents an average rate of change in amino acid sequences.
- This rate is approximately constant
Neutrality of the molecular variants
- This theory describe that many molecular changes (mutations) are not influenced by the natural selection. because advantageous mutations are rare, deleterious mutations are rapidly removed therefore Rate of the substitution of the neural alleles = Rate of the mutation of the neural alleles
- But not all not all molecular changes are neutral.
Gene tree VS Species tree
- Gene tree is the phylogeny of the gene; species tree is the phylogeny of the species
- Gene duplication, paralogy an the lateral gene transfer cause mismatches between gene tree and species tree.
- The branch length of the phylogenetic trees express the amount of evolutionary changes along the branches
Orthologs genes VS Paralogous genes VS Xenologs genes
- Orthologous genes – These genes are connected directly via speciation not duplication. these genes are usually found in species raised from common ancestor.
- Paralogous genes – Duplication of the same gene within a single species (ancestral species). These genes are evolved independently in the species and have different functions.
- Xenologous – horizontal (lateral) gene (matching gene) transfer between organisms.
- Analogous genes – Gene that having similar functions but not arise from the common ancestor mainly due to similar environmental pressure.
In simple terms
- Orthologous genes are found in different species arise from the common ancestor.
- Paralogous genes are duplicate the same gene within the single species (ancestral species).
- Xenologous genes are laterally tranfers between organisms.
| Orthologous genes | Paralogous genes | Xenologs |
| Related via speciation | Related via duplication | Related via transfer between organisms. |
References
- Sequence homology – Wikipedia. (2014, December 8). Sequence Homology – Wikipedia. https://en.wikipedia.org/wiki/Sequence_homology
- M Carr, D. S. (n.d.). Molecular Clock. Molecular Clock. https://www.mun.ca/biology/scarr/Molecular_Clock.html
- sgugenetics / Introduction to Molecular Evolution 2. (n.d.). Sgugenetics / Introduction to Molecular Evolution 2. http://sgugenetics.pbworks.com/w/page/52236355/Introduction%20to%20Molecular%20Evolution%202
- Speciation | bartleby. (n.d.). Speciation | Bartleby. https://www.bartleby.com/subject/science/biology/concepts/speciation
- https://rainbow.ldeo.columbia.edu/courses/v1001/anaclad.html. (n.d.). https://rainbow.ldeo.columbia.edu/courses/v1001/anaclad.html