Hi everyone!
I have a phylogenetic tree obtained using BEAST2 and inferred from two genes (COI and 18S). I would like to use this tree to improve my understanding of the evolution of each of the groups, therefore I thought about a molecular clock.
Unfortunately, I don't have fossils or geologic events that can help me set this molecular clock.
I am working with psyllids (Hemiptera: Psylloidea) and I was wondering if any known (or similar) mutation rate can be applied..
Question within the question, given that my phylogenetic tree was inferred from two genes (having different mutation rates) does this complicate the situation?
Thank you for your time,
Francesco
Dear Francesco,
There are several fossil psyllids you can use to calibrate your clock. Most of them are from Cenozoic, e.g. Middle Eocene (Baltic amber), terminal Eocene (Isle of Wight deposits), Middle Miocene (Dominican amber). No true psyllids are known from the pre-Cenozoic times. Some of fossils are now at various stages of revisionary studies, a few more are to be described soon. There are also a number of biotic and abiotic events influencing the evolutionary history of Psylloidea, i.e. climatic changes, appearance of new habitats, changes in vegetation structure due to changing conditions, etc. Psyllids and host plant relationships should be also taken into consideration, as some psyllids host plants radiated and diversified during the Cenozoic. IMO modern Psylloidea is one of the last diversifying groups among Sternorrhyncha (competition with scale insects and aphids could be important factor), but with evolutionary roots placed very deep in the past. See the results of morphological analysis of Psylloidea presented by Jowita Drohojowska.
all the best,
Jacek
Dear Jacek, thank you very much for your answer!
I probably formulated my question in the wrong way.. What I probably should have specified is that DESPITE having fossils, I DO NOT know how to use them to calibrate a clock. What is the safest way to use fossils as a calibration?
For example, (let's be approximate with the correct dates) fossils belonging to the family Aphalaridae in the Eocene can surely tell me that this family was already present around approx 45 Mya. Similarly, fossils from Triozidae and Psyllidae dating back to Miocene tell me that these were already present less than 20 Mya.
Now, the fact that we do not have fossils older than these for these families would be enough to assume that they are more recent? Or simply that we have not found these fossils yet?
Thank you very much for your time and for your help!
Francesco
Dear Francesco,
I suggest you that before starting any dating/calibration, check that your mtCOI sequences are not saturated (DAMBE5 is a good software for that). If they are, make different partitions or just don't use the third codon position. If you mix all positions, you can get and overestimation, since these positions are evolving at different rate.
On BEAST2 web (https://www.beast2.org/tutorials/) you have a really nice tutorial to get the basics on how to calibrate your tree. And don't forget to run a couple of runs just from the priors to be sure that your results are form your sequences!
Best,
Diego
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