Estimating Placoderms Origination Environment via ancThresh Model




Assistant Professor of Earth and Environmental Science

Project Summary

The goal of this project was to determine what benthic assemblage (BA) zone Plaocdermi likely originated in and later migrated from. In order to achieve this I had to complete a series of tasks. First, I took three different phylogenetic trees published since 2015 and composed a matrix representation by parsimony (MRP) matrix of them in Mesquite. Following this, I ran this MRP matrix through MrBayes, through 5000000 generations sampled every 100, and waited for the average standard deviation to fall below 0.10 to demonstrate convergence. Then I imported 12,500 of the sampled generations and made a majority consensus tree of them. Next I collected data on 175 occurrences of Placoderms that were in this tree, including likely BA zone, fauna, and range of the occurrence date (within 5ma). I then converted my data into a PCM file containing each occurrence, its fauna, and a probability distribution of the BA zones it was in. Running this PCM file as well as my majority consensus tree through the “Equals” method by Graeme T. Lloyd, based on the Brusatte et al. (2008) method allowed me to timescale the whole tree merely based on tip ages. Now I was ready to run ancThresh, a method developed in R by Liam Revell, the author of the Phytools kit. I ran ancThresh 3 different times with 3 different models: BM, OU, and Lambda, to see which one was the best fit. Each time the OU model was superior. Continuing forward I ran the OU model for 1000000 generations in ancThresh to find the best parameters of the model, and generated plots with these parameters to articulate where the likely origination of Placodermi was and where they expanded to as they diversified. In another test, I added 0.05 to all PCM zones which originally were 0.00 since this can help to account for sampling issues and see if it has a major impact on my results. This must be done because it is possible some potential fossils or occurrences have simply never been found yet.

Overall our results found that Placoderms very likely began in BA zones 0 and 1, and then expanded away from the shore as they diversified. This parallels our previous findings that jawless fish seemed to follow the same pattern of diversification.

Estimating Placoderms Origination Environment via ancThresh Model