Deep Evolutionary Analysis
Evolutionary analysis for deep, ancient relationships
It is often quite challenging to work out evolutionary relationships far in the past, between bacteria, archaea, and eukaryotes.
There are layers of similarity you can expect to find:
Sequence similarity: if similar sequences are found in a blast protein search, they are probably orthologous (barring amino acid content problems)
Protein family similarity: the sequences may not be found by straight-forward blast, but there may be conserved residues, characteristic of a protein family. Such patterns are usually found with psi-blast, or in databases like pfam and interpro.
Protein fold/superfamily: Even psi-blast or pfam do not recognise enough conserved residues to detect the similarity, although the sequences do ultimately have a common ancestor. They will share the same protein fold (SCOP database for example, or interpro). In this case, careful work is needed: is the fold a common one that evolved multiple times? Are the proteins with the same ultimate fold actually paralogues that have been recruited in parallel for the same function in DNA replication?
Different fold family: if the proteins that carry out the same function do not share the same fold, they probably evolved independently and were recruited for DNA replication separately.
There's some argument in the literature about the ancient relationships among bacteria, archaea, and eukaryotes, although it is mostly believed bacteria diverged from the common ancestor of archaea and eukaryotes, which diverged later. The time frame is also not clear in the literature. It is also possible, and believed particularly possible early in the history of life on earth, that genes were transferred between different species (Lateral or Horizontal Gene Transfer).
Additional Websites
--ThomasHuber 13:34, 24 April 2007 (EST)
