Can we infer the duplication of BRANCHED1 gene at the base of Solanaceae clade?

We retrieved sequences of the “ancestral” form of the gene for outgroup species Arabidopsis, Ricinus, Populus and Vitis, annotated as BRC01. And both (here called BRC1l and BRC2) supposed forms of the gene for Solanaceae including 9 tomatoes and 1 potato.

We grouped the sequences according as this:

• All together, BRC01, BRC1l and BRC2: brc01-1l-2.fasta

1. Download the sequence.
2. Compute a neighbour-joining tree.
3. Define the best evolutionary model.
4. Compute accurate distances.
5. Find the maximum parsimony topology.
6. Find the best tree by maximum likelihood.
7. Compute statistical support for each bipartition of the tree.

Are you able to rebuild the phylogeny of BRANCHED1-like genes, and on top of that can you ensure that form 1l and 2 are true paralogs? If not which form would be orthologous BRANCHED1 genes of outgroup species?

Answer