Biology Reference
In-Depth Information
pathogens and cyanobacteria. Doolittle and Bapteste (2007) questioned the fundamental belief
over the existence of a universal TOL and proposed an alternative path for tree-building known
as “pattern pluralism”. This theory recognizes the existence of different evolutionary models for
different taxa or at different levels or for different purposes. According to them, it provides a good
alternative instead of searching for an impractical universal TOL. But Koonin (2009) is of the view
that the evolutionary tree introduced by Darwin need not be abandoned altogether because (i) it
is possible to construct phylogenetic trees representing accurately the evolution in individual gene
families, and (ii) congruent trees can be obtained for large sets of orthologous genes. There are two
alternatives. One is to represent a highly consensus tree of highly conserved genes showing the LGT
events. The second is to present a complex network with cross-connections representing the phases
of LGT that cannot be represented as a tree. Eisen (1998) and Eisen and Fraser (2003) emphasized
the need to combine the studies on whole genome sequences (genomics) and the evolutionary
studies (phylogeny) together into a new composite area known as 'phylogenomics'. According to
them, LGT being a rare event has not distorted the structure of the tree. The diversity of prokaryotic
genomes seems to be very enormous as revealed by the presence of good number of new genes in
every sequenced genome (Tettelin
et al
., 2005). The total number of genes present in a given species
is termed as 'pangenome'.
The root of the TOL:
The classifi cation proposed by Woese
et al
. (1990) envisages that the rooting
of the TOL is between the eubacteria and archaebacteria and that the eukaryotes were identifi ed
as specifi c relatives of archaebacteria. It means the archaebacteria constitute a more recent group
than that of eubacteria. Then which are the ancestors of eubacteria and archaebacteria that might
have constituted the root from which evolution had taken place? The eubacterial group consists of
gram-positive, gram-negative bacteria and cyanobacteria. So it means the prokaryotes consist of
two-distinct and non-overlapping (i.e. monophyletic) groups that are not specifi cally related to each
other than either was to the eukaryotes. Based on the presence of specifi c sequences of amino acids in
proteins, known as 'signature sequences' (also termed as 'indels'), Gupta (1998) emphasized that: (a)
Archaebacteria are monophyletic and are distinct from other prokaryotes. This conclusion is further
supported by phylogenies based on gene sequences of 16s rRNA, DNA replication, transcription,
translation, t-RNA splicing, histones and theTcp-1 chaperonins. (b) Based on the signature sequences
present in proteins such as HSP70, glutamine synthetase 1 (GSI) and glutamate-1-semialdehyde 2,1-
aminomutase the archaebacteria are closely related to gram-positive bacteria. (c) Signature sequences
also indicate that
Deinococcus
and
Thermus
group of bacteria are intermediates in the transition from
gram-positive to gram-negative bacteria. (d) Among the gram-negative bacteria, cyanobacteria
constitute one of the deepest branching divisions specifi cally related to
Deinococcus
-
Thermus
group.
This close relationship between these two groups is also revealed by the signature sequences unique
to proteins such as DnaJ-Hsp40 and elongation factor TE-Ts sequences. These results are suggestive
of a common ancestor for these two groups of prokaryotes. However, due to the existence of common
signature sequences in other proteins such as Hsp60, acetolactate synthase and asparginyl-tRNA
synthetase cyanobacteria are shown to be closer to gram-negative bacteria as well. So exclusive of
Deinococcus
-
Thermus
group, cyanobacteria might have had a common ancestor with gram-negative
bacteria. These evidences further point out to the suggestion that: (i)
Deinococcus
-
Thermus
group of
bacteria are more ancestral than cyanobacteria; (ii)
Deinococcus-Thermus
group and cyanobacteria are
not the ancestors of other gram-negative bacteria but branched off from the early ancestors. It is also
probable that extensive LGT events might have taken place in between
Deinococcus
-
Thermus
group
and cyanobacteria. The extensive sequence data further point out that the primary division within
