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known that P . tetraurelia has undergone three successive whole genome
duplications ( Aury et al., 2006 ). Interestingly, some of the P. tetraurelia glo-
bins cluster with T. thermophila globins (boxes A and B in Fig. 9.5 ), similarly
to what has been observed with cytochrome P450 genes ( Fu, Xiong, &
Miao, 2009 ). The tree in Fig. 9.5 is consonant with the shared ancestry
of the three ciliate genomes.
Despite the inherent weaknesses of molecular reconstruction of globin
phylogenies, we believe that useful results can be obtained by repeated ana-
lyses with different globin sequences representing the same bacterial subfam-
ilies. The Bayesian tree of protist, plant and bacterial TrHb2s, shown in
Fig. 9.6 , provides results that agree with the proposed close phylogenetic
relationship of plant and chlorophyte TrHb2s with each other and with
the bacterial Chloroflexi TrHb2s, inferred earlier, suggesting the possibility
of an ancient horizontal gene transfer (HGT) of TrHb2 genes form an ances-
tor of Chloroflexi to the last common ancestor of the TrHb2 containing
protists ( Vinogradov, Fernandez, Hoogewijs, & Arredondo-Peter, 2011;
Vinogradov, Hoogewijs, & Arredondo-Peter, 2011 ).
Figure 9.7 shows a Bayesian tree of a MAFFT alignment of 37 protist,
and 30 vertebrate SDgbs and 7 plant globins, with the two bacterial non-
haem globin-like sequences as outgroups. Each sequence is identified by
the first three letters of the binomial, the number of residues, the first three
or four letters of the taxon and the identification number. Although the
node probabilities are low, the tree reproduces the phylogeny of the major
vertebrate globin lineages established by Storz and Hoffmann ( Hoffmann,
Opazo, Hoogewijs, et al., 2012; Hoffmann, Opazo, & Storz, 2012; Storz,
Opazo, & Hoffmann, 2013 ). Although as expected, there is a clear separa-
tion of the microbial eukaryote groups from the vertebrate sequences, it also
suggests a close phylogenetic relationship between vertebrate Ngbs and plant
symbiotic and non-symbiotic Hbs, on one hand, and with choanoflagellate
as well as chlorophyte and haptophyte SDgbs on the other. Note the rela-
tively short phylogenetic distances (marked in red) between the three
groups. It is appropriate to point out that robust molecular phylogenies sup-
port the monophyly of choanoflagellates ( Carr, Leadbeater, Hassan,
Nelson, & Baldauf, 2008; Shalchian-Tabrizi et al., 2008 ). Furthermore, they
appear to be among the closest sister groups to the metazoans, and likely
share a common marine protistan ancestor ( Carr et al., 2008 ). Interestingly,
cadherin and integrin genes, considered to be the hallmark of multicellular
animals, are present in the choanoflagellate M. brevicollis , C. owczarzaki
( Nichols, Roberts, Richter, Fairclough, & King, 2012 ) and other protists
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