As evo devo deals with understanding developmental processes among various living beings on this planet in order to determine ancestral relationship between them.This requires availability of various model systems (better if we have one for each 35 phyla known) so that we can validate all the conserved genes and pathways ,which can be known from the sequence analysis.By checking the expression patterns of evolutionary conserved ones we can reach to the origin of metazoans,because expression is very important in interpreting the function in lower organisms where tools to study loss of function are not well worked out at the moment.

The availability of complete genome sequences allows powerful predictions to be made about the history of life(pointing to the origin of all animals). Imagine that if a gene present in humans or any other chordate, is also found in either an Ecdysozoan(eg:Drosophila) or Lophotrochozoan(eg:Annelids) or Cnidarian animal, then the definite conclusion has to be that this gene was present in Urbilateria(common ancestor to all bilaterians ,which includes ecdysozoans and Lophotrochozoa)as well.Similarly, if a gene is found in both a Ctenophore and a chordate, it must also have been present in Urmetazoa(common ancestor of all animals on this planet).In this way reconstructing the genetic tool kit of the common ancestor of all animals will elucidate the contribution of gene loss and developmental constraints to the evolution of animal body plans.

Some genes like Bmp antagonist Noggin,Wnt inhibitors like Dickkopf are not present not be present in Drosophila and Nematodes genome.But this doesnot mean that these genes were not present in urbilaterian becuase these genes are present in Molluscans (belongs to Lophotrochozoa).So what does this tell us??? This brings a very important aspect of evolution into picture,that of GENE LOS-which constitutes a powerful source for rapid evolutionary changes.Presence of Noggin and Dickkopf in Lophotrochozoans/ chordates but not in Drosophila/nematodes suggests that these proteins were very much part of Urbilaterians but were secondarily lost in C. elegans and Drosophila.It can be assumed the Urbilateria might had all the diverse proteins used in the animal kingdom but some phyla like Drosophila lost some genes during evolution.
We can reconstruct complete Proteins present in Urbilateria or Urmetazoa in silico in order to find out if any of the species available toady retain the whole set.But the chances look very bleak of finding something exactly similar like last common ancestor but finding something close will also be a great achievement.

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