I need to differentiate the two species sequences by any DNA quantitative analysis. morphologically those species was identified but genetic variation very is less. what method i should follow?.
Dear Purushothaman Paramasivam,
there are several methods that you can use. If you only have one locus or if you only have loci for mitocondrial segments or for chloroplast segments, I suggest that you use either the GMYC and its variations like the bGMYC (bayesian GMYC) or that you use the PTP method. These two models are similar, but the GMYC requires an ultrametric tree, and PTP don't.
If you have multilocus data, than you can use methods like Brownies, spedeSTEM and BPP.
You can find a Nice review on this link: https://www.researchgate.net/publication/249646273_How_to_fail_at_species_delimitation
Article How to fail at species delimitation
Dear Purushothaman Paramasivam,
there are several methods that you can use. If you only have one locus or if you only have loci for mitocondrial segments or for chloroplast segments, I suggest that you use either the GMYC and its variations like the bGMYC (bayesian GMYC) or that you use the PTP method. These two models are similar, but the GMYC requires an ultrametric tree, and PTP don't.
If you have multilocus data, than you can use methods like Brownies, spedeSTEM and BPP.
You can find a Nice review on this link: https://www.researchgate.net/publication/249646273_How_to_fail_at_species_delimitation
Article How to fail at species delimitation
I adice you to read these papers
- http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0097556
- http://sysbio.oxfordjournals.org/content/63/4/534.short
- http://sysbio.oxfordjournals.org/content/63/2/119.short
Dead Purushothaman Paramasivam,
Following on the answer provided by Manolo Perez, I recommend you to check this publication: http://dx.doi.org/10.1371/journal.pone.0148268
it provides a detailed description on how to use four popular methods for the task in question:
1 - Statistical parsimony analysis
2 - Distance-based clustering
3 - Generalised mixed Yule-coalescent (GMYC) modelling [nicely implemented in the 'split' package of the R environment]
4 - Poisson tree processes (PTP) modelling [nice web-based implementation at http://species.h-its.org/ptp/ ]
As mentioned by Manolo Perez you have to be careful about the type of tree you need as input. There are nice implementations in R to make trees ultrametric.
Best,
Aminael SANCHEZ
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