Ahn, D., You, K.H., and Kim, C.H. (2012) Evolution of the Tbx6/16 Subfamily Genes in Vertebrates: Insights from Zebrafish. Mol. Biol. Evol.. 29(12):3959-3983.
In any comparative studies striving to understand the similarities and differences of the living organisms at the molecular
genetic level, the crucial first step is to establish the homology (orthology and paralogy) of genes between different organisms.
Determination of the homology of genes becomes complicated when the genes have undergone a rapid divergence in sequence or
when the involved genes are members of a gene family that has experienced a differential gain or loss of its constituents
in different taxonomic groups. Organisms with duplicated genomes such as teleost fishes might have been especially prone to
these problems since the functional redundancies provided by the duplicate copies of genes would have allowed a rapid divergence
or loss of genes during evolution. In this study, we will demonstrate that much of the ambiguities in the determination of
the homology between fish and tetrapod genes resulting from the problems like these can be eliminated by complementing the
sequence-based phylogenies with non-sequence information, such as the exon-intron structure of a gene or the composition of
a gene’s genomic neighbors. We will use the Tbx6/16 sub-family genes of zebrafish (tbx6, tbx16, tbx24, and mga genes) as an illustrative example, which have been well-known for the ambiguity of their evolutionary relationships to the
Tbx6/16 sub-family genes of tetrapods. We will show that, in spite of the similarity of sequence and expression to the tetrapod Tbx6 genes, zebrafish tbx6 gene is actually a novel T-box gene more closely related to the tetrapod Tbx16 genes, while the zebrafish tbx24 gene, hitherto considered to be a novel gene due to the high level of sequence divergence, is actually an ortholog of tetrapod
Tbx6 genes. We will also show that, after their initial appearance by the multiplication of a common ancestral gene at the beginning
of vertebrate evolution, the Tbx6/16 sub-family of vertebrate T-box genes might have experienced differential losses of member genes in different vertebrate groups
and gradual pooling of member gene’s functions in surviving members, which might have prevented the revelation of the true
identity of member genes by way of the comparison of sequence and function.