I have a total of 74 CO1 sequences, all with 576 bp representing 4 different Isopod species. They are so similar that when looking at the alignment, one would think they are the same species. I have made a haplotype network in PopART using TCS analysis which gave 23 haplotypes. It has become apparent that many haplotypes are represented by more than 1 species. What are the possible explanations for this? Can two (or more) species share an identical sequence of this lenght? Is there a software i can use to se which sequence belong to which haplotype and how would i use such a software? Any other analysis i should consider?
Thank you!
Have you considered performing a genetic structure analysis (with STRUCTURE: https://web.stanford.edu/group/pritchardlab/structure.html or ADMIXTURE: http://dalexander.github.io/admixture/index.html?)
Both tools (and others, based on the same principle) may help you clarify the number of genetic clusters/groups and each sequence's membership.
In PopART you can also output a list of identical sequences, if this is what you wanted to know.
I think i found a solution. I uploaded a fasta file to DNAsp, saved the data as a haplotype file which contained the haplotypes and sequences belonging to each of them. I then restructured my nexus file to match the data from the haplotype file. This gave me a network displaying haplotypes at the nodes. A traits block with species illustrated how many of each species are present at each node. Any thoughts on this approach? Thank you so much for your answers!
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