- Phylogenetic trees are constructed by choosing an optimal tree, which is itself based on some model of evolutionary change. This approach is known as cladistics approach. Now, if there is any dispute regarding the parent model, then the entire phylogenetic tree would go wrong.
- Every organism’s genome organization is different. A more complex organism will have totally different phylogenetic tree in comparison to a less complex organism. Genome organization, of various organisms in the present scenario is changing generation after generation; so, it is becoming more and more difficult to interpret the exact phylogenetic tree.
- In reproductive cycle, genome is passed from parents to offspring. This type of gene transfer is known as vertical gene transfer. And phylogenetic trees are constructed on the basis of these vertical gene transfers. But actually evolutionary mechanisms are effected by horizontal gene transfers also, which are nowhere considered in construction of phylogenetic trees.
- Each organism contains the DNA inherited from its parents. A single nucleotide change in DNA results in change in the daughter genome. Thus, it is assumed that the tree derived from any one gene would look like tree from any other gene.
- Above all, tree construction method and quality of data affect the reliability of phylogenetic tree.
- Lastly, phylogenetic tree building utilizes lot of computational time. This increases tediousness and cost of the task.
