Application on Biological Data

As a first application, we used our branch-and-bound algorithm to infer an ancestral gene order for a pair of human and rat olfactory TAGs clusters. The results are shown in Figure 4. We see that this dataset is compatible with an optimal DLIS history containing only one inversion event, that occurred before the human-rat speciation.

The human cluster is located on [email protected] and the rat cluster on [email protected] Protein sequences and gene orders were obtained from the HORDE database (CLIC #35) [1]. The sequences were aligned with ClustalW [30] and the gene tree generated with MrBayes [14], using the Jones-Taylor-Thornton substitution matrix [19] and performing 1,000,000 MCMC iterations.

Fig. 4. The ordered reconciled tree obtained for the pair of olfactory receptor TAGs clusters, and the inferred ancestral gene order at the time of human-rat speciation. Transcriptional orientations are indicated by signs. The unique inversion occurred before human-rat speciation and is indicated by a black contour. The rightmost gene in the ancestral TAGs cluster (dashed contour) has its unique descendant in the rat TAGs cluster, indicating a gene loss in the human lineage after the speciation.

Fig. 4. The ordered reconciled tree obtained for the pair of olfactory receptor TAGs clusters, and the inferred ancestral gene order at the time of human-rat speciation. Transcriptional orientations are indicated by signs. The unique inversion occurred before human-rat speciation and is indicated by a black contour. The rightmost gene in the ancestral TAGs cluster (dashed contour) has its unique descendant in the rat TAGs cluster, indicating a gene loss in the human lineage after the speciation.

This first "simple" application only aims to give an example of a TAGs cluster which is very likely to have evolved in agreement with our model of evolution restricted to simple duplications and inversions, demonstrating its validity.

Was this article helpful?

0 0

Post a comment