I am working on DNA barcoding of two closely related plant species. I have used 5 marker regions for my analysis. How to calculate theta, theta prime, coalescent depth and minimum interspecific distance? How to discriminate between two closely related species by Inter and intra-specific genetic distance?
How to calculate barcode gap and how this gap is determining the species discrimination?
Barcode gap: http://wwwabi.snv.jussieu.fr/public/abgd/. The basic idea is that, when looking at the distribution pairwise genetic distances, we can define "clusters" (=species?) as groups of individuals which have lower distances than to individuals in other clusters. The linked program is very easy to use and does this automatically.
Theta: A decent estimate of population mutation rate can be derived by calculating the maximum intraspecific distance (see above and below)
Minimum/maximum inter/ intra- specific distance: Just get a distance matrix get the values needed from it (e.g. maximum intraspecific distance for species A is the largest distance calculated from pairwise comparisons of conspecifics for species A). I think the linked program ABGD (above) will give you a distance matrix
Tree height, coalescence rate, etc: https://github.com/joaks1/pyule Use this nice and easy command-line program.
Thank you very much Sir for your valuable guidance. Sir, I have aligned fasta file and MEGA pairwise distance files which I have uploaded and ran the analysis in ABGD but I am not able to interpret the results. Sir, which partition should I take?
Sir, if you kindly help me in this regard, I will be highly grateful to you.
Dear Biswajit,
ABGD shows a series of results. First a bar-chart of genetic distance distribution (JC or K2P accvording to your selection) a cumulative curve of the same and also a reconstructed tree with the suggested groups. Someting like this.
In the three you can see the groups reconstructed.
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