Biology Reference
In-Depth Information
between bacterial and protist globins remains an uncertain goal, the clarifi-
cation of the relations between the protist globins and the globins of higher
eukaryotes represents a more attainable objective. In examining the phylog-
eny of protist globins, it must be kept in mind that one can only examine the
evolution of globin lineages that belong to the same globin subfamily.
A major roadblock in globin phylogeny is the unacceptably poor statistics
found in support of phylogenetic trees, irrespective of the alignments
employed, the type of trees (Bayesian inference, ML or NJ) and the evolu-
tionary models used. On the one hand, the globin sequences are relatively
short, and on the other, the low identities found in pairwise alignments of
protist and higher eukaryote globins result in the masking of phylogenetic
signals coded within the sequences. Figure 9.4 shows a Bayesian tree of a
MAFFT alignment of the protist SDgbs and FHb globin domains. It is evi-
dent that the node support probabilities are unacceptably low, even though
the sequences being compared are from the same family. Nevertheless, this
result provides useful information. First of all, it is apparent that the FHb
globin domains cluster apart from the SDgbs and related domains in chime-
ric proteins, in agreement with their having completely separate phyloge-
nies. It is likely that the diversification of ancient bacterial globins into
the eight subfamilies observed in extant bacteria would have occurred in
the bacterial precursors to LECA, predating the two endosymbiotic events,
that resulted in the emergence of mitochondria and chloroplastids and per-
mitted the transfer of bacterial globin genes representing some of the eight
bacterial subfamilies to LECA ( Vinogradov et al., 2007 ). Furthermore, the
tree assists in the assignment of protist globins. For example, it shows the
Albugo laibachi FHb globin domain (red arrow) to cluster with the SDgbs,
as do the chimeric globins of Leishmanias. Although the former was assigned
based on FUGUE search results, it appears to be missing the C-terminal,
NADP-binding module (PDB:1cqx3). Such truncated FHbs also occur
widely among the fungi and bacteria ( Hoogewijs, Dewilde, et al., 2012 )
and were mentioned earlier, and may thus represent a third subfamily in
the FHb family. The same can be said of the Ectocarpus siliculosus chimeric
FHb (blue arrow); in both cases, the globin domains belong to the SDgb
lineage and should not be considered as degraded FHbs.
Very low probabilities of node support are also evident in a Bayesian tree
of all the TrHb1s and TrHb1 domains of P. tetraurelia , T. thermophila and
P. marinus , shown in Fig. 9.5 , underlining the sequence divergence within
one globin subfamily, the likely result of more than a billion years of ciliate
evolution, accompanied by genome duplications and reductions. It is
Search WWH ::




Custom Search