Dear professors
Respectfully, i know that sequences can help us to reveal the most common ancestor in phylogenetic studies. However, in genetic diversity studies using IRAP, SSR, markers etc, i want to know if it is possible to estimate Tmarca? If the answer is yes, How? which software can help us?
I will appreciate if anyone can help me.
Regards
Dear Atena,
in order to reconstruct the past (evolutionary history) you will need a model that tells you how your marker of choice changed over time - providing a direct link with time or, e.g., with number of generations.
With DNA sequence data we can apply such kind of models and can further use either mutational/substitional rates to get the parameter "time" into any type of calculations and/or simulations.
However, this is not possible (or biased by many flaws) with marker sets such as AFLPs (0/1 matrix), or SSRs. Of course, there are models when using microsats etc., but with increasing (phylo)genetic distance the models will not work at all.
If you have divergence time estimate from given phylogenetic trees then there are methods to use AFLPs in a coalescent framework - but this is highly critisized.
Just a few thoughts ... and not comprehensive, of course,
Marcus
Dear Markus Koch,
So many thanks for the recommendation.
As I understood, I can not estimate Tmarca using 0 & 1 data (absence and presence of bands, respectively) assessed by genetic diversity markers (e.g., SSR, IRAP, etc).
Atena Eslami Some early publications (before wide-range DNA sequence analysis) consider presence of a common ancestor for genotypes within the same species based on 0/1 data, but there is no validation of such conclusions.
Stich B, Melchinger AE, Frisch M, Maurer HP, Heckenberger M, Reif JC. Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theoretical and Applied Genetics. 2005 Aug 1;111(4):723-30.
Russell JR, Fuller JD, Macaulay M, Hatz BG, Jahoor A, Powell W, Waugh R. Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theoretical and Applied genetics. 1997 Sep 1;95(4):714-22.
Hi Alex Ignatov,
So many thanks for the answer. I have the same idea. Only sequences with the correct models can estimate the Tmarca, but would you please send the references of these articles for me? I am really curious to find out how they did this.
Dear @Atena Eslami
Quite a while ago I did my PhD on evolutionary taxonomy of a family of fish (Platycephalidae) using allozyme markers. I tested various methods of coding these markers and found that a binary coding system proved to be the best. Details can be found in:
Phylogeny of Australian species of flatheads (Teleostei, Platycephalidae) as determined by allozyme electrophoresis
CP Keenan - Journal of Fish Biology, 1991, Vol39: 237-249
I hope this helps.
Cheers, Clive Keenan
Hi @Clive Keenan
So many thanks for the answer.
I can not found the link. Would you please write it again?
Regards
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