The phylogenetic tree is the estimate of the evolutionary history of branching order (sequence of bifurcations) and sister group relationships that evolved during the history of the protein. And using Phyml with a properly optimized model of sequence evolution adds branch lengths which further describes the evolutionary history by quantifying the amount of evolution (number of substitutions) along each branch in the tree. So that is the answer to question 1.

Question 2 asks whether the common ancestry of each branch represents a duplication event (say) within a population or species (paralogs) or is associated with species event or population level event that separated the proteins onto independent evolutionary trajectories. And it is here that the biology becomes especially interesting and more complicated. Work is ongoing on doing so in a reliable manner.

Here you wish to separate gene trees from species trees. I attach a few newish papers that discuss the topic and suggest analysis methods. Please let me know if you have any questions from reading these works.

thank you sir for your kind response

in response to question 1, you said branch length describes the evolutionary history, so do I need to quantify the number of substitutions or branch length is enough to explain the same. .

regards

juhi

The evolutionary history of the divergence events (e.g. speciation) is described by the pattern of bifurcations across the tree. Reading the history back from the tips is the best way to study the series of common ancestries that gave rise to the tip organisms.

The phyml tree is generally a phylogram in which the tips are not necessarily aligned. Some branch lengths from the most recent common ancestor are longer than others. These branches have accumulated more substitutions along the tree than the shorter ones. This is quantified by the branch length labels on the phyml tree.

Note that phyml gives two different and valuable branch label options. One is similar to but better than a bootstrap value and is called the aLRT (approximate likelihood ratio test) and provides a measure of the support for the clade that emanates from that branch. The other option quantifies the number of substitutions. You will see that, if you choose to show branch lengths, these numbers are smaller for the short branches and larger for the longer ones.

See the contrasting information in the attached pdfs.

All off the information about the evolutionary history of these species is confined in the divergence pattern and the branch lengths. The confidence that you have in the estimated tree and branch lengths is contained in the tree labelled with the aLRTs.

Please let me know if you have further questions or if I have failed to answer your questions.