Good evening.
I am doing my final project on grapefruit genetic diversity and constructing a phylogenetic tree by comparing two samples of c.maxima, 10 Citrus genus (NCBI results), and outgroups. The outgroup I chose was Zanthoxylum sp or Severinia buxifolia based on the references I had read.
I am doing phylogenetic tree construction using neighborhood joining and maximum likelihood methods with MEGA X. The results shown are different where the outgroup can be seen clearly separated from the ingroup with the Neighborhood joining method. Meanwhile, the out group was included in the in group when using the Maximum Likelihood method. Is this result reasonable? Or should I change the outgroup so that there is a possibility that the results of the two phylogenetic trees are the same?
Please advise.
Thank in advance
Including an outgroup in phylogenetic tree construction is important because it helps to root the tree and determine the direction of evolution. The outgroup is chosen based on its evolutionary distance from the ingroup, meaning it is a taxon that is closely related to the ingroup but not a member of it. The inclusion of the outgroup can affect the placement of the other taxa in the tree, including its position within or outside of the ingroup.
The difference in results between the two methods you used, neighborhood joining and maximum likelihood, could be due to the different algorithms and assumptions used in each method. It is not uncommon for the placement of the outgroup to affect the position of the ingroup in the tree, and the results from each method should be evaluated and compared to each other and to the available literature to determine the most reasonable placement of the taxa.
If you are concerned about the placement of the outgroup and its effect on the results, you could try using a different outgroup that is more distantly related to the ingroup or choose a different method that may be less affected by the outgroup. However, it is important to keep in mind that the choice of outgroup and method should be based on sound evolutionary and statistical principles.
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