It is common knowledge that internal nodes are ancestral and external nodes are of recent origin in a haplotype network. But most of the median joining haplotype networks published in articles are found to be unrooted. In such cases, how can we infer the internal most frequent haplotypes as ancestral ones?. A similar issue happened in my analysis too.
When I performed dating of those haplotypes and constructed a phylogenetic tree, the internal node which was considered to be ancestral in haplotype network found much recently diverged than the external ones.
May I know your opinions..............
The center of the star-like and the most frequent haplotype will always be seen as the ancestral haplotype. But I think it would be better to confirm it by the outgroup.
About the dating problem, it is weird. May I asked how you perform the dating?
Hi Rahul,
Median-Joining Networks and Reduced Median Networks (unrooted phylogenetic network, is a kind of kind of splits graph), are two methods popular in population genetics, especially used as haplotype networks.
Haplotype networks are usually drawn unrooted, where the root location is often unknown. However, sometimes a root is provided, and the splits graph is interpreted as a directed network, like starting with an unrooted phylogenetic tree and adding a root (via an outgroup), so the rooted tree can be interpreted as a genealogical history. From an unrooted to a rooted tree, each branch acquires a direction and the internal nodes become hypothetical ancestors.
This is problematic as each edge acquires an unambiguous direction, as for a tree, but not every internal node can necessarily be interpreted as a hypothetical ancestor.
To avoid misinterpretation (bad usage) you have to recognize that a rooted splits graph does not explicitly represent a phylogeny, because reticulations in the graph represent uncertainty not genealogy.
Please read this article:
Computer programs for population genetics data analysis: a survival guide. Excoffier, Laurent, and Gerald Heckel. Nature Reviews Genetics 7.10 (2006): 745-758 (a good review).
and also these books :
ReCombinatorics: The Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks by Dan Gusfield
Phylogenetic Networks: Concepts, Algorithms and Applications by Daniel H. Huson,Regula Rupp,Celine Scornavacca
Hope this could help you.
I really thank Mr. Cherifi for spending his valuable time to clarify my doubt clearly. I will describe ancestral relationship only with the Phylogenetic tree because it is more authentic.
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