26.5: Possible Theoretical and Practical Issues with Discussed Approach

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A special point must be made about distances. Since distances are typically calculated between aligned gene sequences, most current tree reconstruction methods rely on heavily conserved genes, as non-conserved genes would not give information on species without those genes. This causes the ignoring of otherwise useful data. Therefore, there are some algorithms that try to take into account less conserved genes in reconstructing trees but these algorithms tend to take a long time due to the NP-Hard nature of reconstructing trees.

Additionally, aligned sequences are still not explicit in regards to the events that created them. That is, combinations of speciation, duplication, loss, and horizontal gene transfer (hgt) events are easy to mix up because only current DNA sequences are available. (see [11] for a commentary on such theoretical issues) A duplication followed by a loss would be very hard to detect. Additionally, a duplication followed by a speciation could look like an HGT event. Even the probabilities of events happening is still contested, especially horizontal gene transfer events.

Another issue is that often multiple marker sequences are concatenated and the concatenated sequence is used to calculate distance and create trees. However, this approach assumes that all the concatenated genes had the same history and there is debate over if this is a valid approach given that events such as hgt and duplications as described above could have occurred differently for different genes. [8] is an article showing how different phylogenetic relationships were found depending on if the tree was created using multiple genes concatenated together or if it was created using each of the individual genes. Conversely, additional [4] claims that while hgt is prevalent, orthologs used for phylogenetic reconstruction are consistent with a single tree of life. These two issues indicate that there is clearly debate in the field on a non arbitrary way to define species and to infer phylogenetic relationships to recreate the tree of life.