For example in the figures I have attached you will notice that CAB 1583 in Example 1 clusters with Candida diddensiae, however in Example 2 this is not the case. I am sure the one tree I have created and the methodology behind it is incorrect though but I am looking for some experienced input. I have created two different phylogenetic trees using MEGA X software and I would like to know why in each case I get a different result in terms of where the strain I have collected groups in each tree. So if we can justify that using public data from GenBank in a large dataset in my family. Also it is not possible to extract DNA and sequence 3,60,000 angiosperms while proposing new system of classification, so I think that in every system of classification there might be some errors and speculations. But in my family there are more than 40+ members, so their internal variation might not be justified in that sense, in the tree. 5/10 specimens in consideration when they built new tree. The key vital point is that, in the classification they used small set of data, like they took, as for e.g. Like did they follow the classification or not, if not where are the dissimilarities, are there any morphological variations that can be related with that variation, if yes, then considering morphology it can be proposed to transfer the position of an existing clade.all these things. So I wanted to validate the use of matK gene/other genes, if it can justify the systemic position of the members of my working family. So in that sense it is not possible to test different genes (rbcL, matK.etc) at the same time, also intergenic spacers (ITS, rpoC1, trnH-psbA etc).
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