Dear All,
I really wanted to know the concept of molecuar clock in phylogenetics, and can it be determined via any software, if yes what are the prerequisites???
Dear Sonal,
As per the concept of molecular clock, i am quoting some lines from "Essential Bioinformatics" by Xiong, hope it will give you the basic understanding. The lines goes as follows:
"To define the direction of an evolution path, a tree must be rooted. In a
rooted tree, all the sequences under study have a common ancestor or root node from
which a unique evolutionary path leads to all other nodes. Obviously, a rooted tree is
more informative than an unrooted one. To convert an unrooted tree to a rooted tree,
one needs to first determine where the root is.
Strictly speaking, the root of the tree is not known; the common ancestor is already
extinct. In practice, however, it is often desirable to define the root of a tree. There are
two ways to define the root of a tree. One is to use an outgroup, which is a sequence
that is homologous to the sequences under consideration, but separated from those
sequences at an early evolutionary time. Outgroups are generally determined from
independent sources of information. For example, a bird sequence can be used as a
root for the phylogenetic analysis of mammals based on multiple lines of evidence
that indicate that birds branched off prior to all mammalian taxa in the ingroup.
Outgroups are required to be distinct from the ingroup sequences, but not too distant
from the ingroup. Using too divergent sequences as an outgroup can lead to errors in
tree construction. In the absence of a good outgroup, a tree can be rooted using the
midpoint rooting approach, in which the midpoint of the two most divergent groups
judged by overall branch lengths is assigned as the root. This type of rooting assumes
that divergence from root to tips for both branches is equal and follows the “molecular
clock” hypothesis.
Molecular clock is an assumption by which molecular sequences evolve at constant
rates so that the amount of accumulated mutations is proportional to evolutionary
time. Based on this hypothesis, branch lengths on a tree can be used to estimate
divergence time. This assumption of uniformity of evolutionary rates, however, rarely
holds true in reality."
To estimate the molecular clock tests you can use the below mentioned software
HYPHY (Reference: S.L. Kosakovsky et al.(2005) Bioinformatics 21:676-679).
Best wishes,
Amit
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