I'm currently doing some work with molecular identification of flies using the COI region for my masters. All the flies came from the same location. These particular three flies were identified as Peckia (sarcodexia) lambens after Genbank search. Following alignment and tree building using reference sequences obtained from Genbank, two of the three flies showed 100 percent identity with each other (where as they showed slightly lower with the third fly). On the tree, they clustered more closely together on a sub branch on their own, whereas the third fly clustered with a reference sequence. I'm not really sure how to explain this. Any ideas?
Any population comprises individuals that are more or less related to each other. Think of how your identical twin sisters would cluster together with you on a branch outside of them because they have identical genotypes and your is slightly different because you came equipped with a unique genotype.
so the tree you have is completely compatible with simple genetic variation in a population of a species. What is your reference sequence? Same species? Same population? How many total sequences do you have?
hmm that makes sense Thank you! I thought perhaps it’s something like an identical twin situation but wondered if I was being too simplistic. my reference sequences were from a different population (drawn from Genbank) my flies are from one area in Jamaica the ref sequences from USA and Columbia. I was trying to identify these flies based on their sequence i was unable to identify them to species using morphological means. Interestingly the third fly clustered closer with Columbia sequence than the other two flies from Jamaica.
these flies were part of a bigger tree that featured 10 of my own sequences representing 5 species along with about 22 reference sequences.
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