If your individual gene trees show congruence, then you can concatenate the datasets and then do the calibration. Another good way would be to see whether the dates (node ages, 95% HPD) you observe from calibration of the different datasets agree or not.

Hi Tilottama,

Each of the different gene trees showing different tree topologies and I am not sure if it's appropriate to concatenate such datasets?

Even if the topologies are identical you cannot both concatenate and date and then expect the result to be a 'correct' phylogeny. The state-of-the-art approach in this case would be to estimate the species tree under the multispecies coalescent model using alignments for the genes mentioned, while putting a calibration on the species tree (i.e. not on the concatenated gene trees). I recommend the *BEAST function in BEAST for this, which allows you to take into account also the different effective population sizes of the three genomes. There are numerous tutorials and manuals available on the internet. Good luck!

BEAST software should be useful for you. It considers each gene information (seperate clock models, substituon model etc.) at the same time and it also handle with incongruence among gene trees.