We used a fixed model, cpREV+I+Γ, estimated specifically for phylogenetic estimation of plastid-encoded proteins [ 66].
Molak, M., Lorenzen, E. D., Shapiro, B. & Ho, S. Y. Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages.
Wang, L.S. et al. The impact of multiple protein sequence alignment on phylogenetic estimation. in IEEE/ACM Transactions on Computational Biology and Bioinformatics (IEEE Computer Society, 2009) 〈http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.68〉.org/10.1109/TCBB.2009.68〉
First, Bayesian phylogenetic estimation in BEAST with substantial within-subspecies samplijng (cinereum, n = 27; fraseri, n = 8; littorale, n = 83) revealed monophyly for cinereum, but paraphyly for littorale and fraseri (posterior probabilities of monophyly: cinereum = 1, littorale/fraseri = 1).
Other than that, this appendix is an excellent introduction to some basic methods in phylogenetic estimation.
We predict that as more genomic sequences become available for other Rickettsia spp., the four clades defined herein using phylogenetic estimation (AG, TG, TRG, SFG) will remain strongly supported, and that R. australis and other rickettsiae with either recent host switches or the presence of plasmids, will likely fall within the AG and TRG rickettsiae.
Garnering support for either evolutionary model requires the evaluation of each plasmid gene through phylogenetic estimation and comparative analysis with other organisms that may likely have contributed to the structure and composition of pRF via vertical (phylogenetic) and horizontal (e.g., conjugative) gene transfer (HGT).
In general, estimates of the time to the most recent common ancestor are less sensitive to reductions in the historical signal in mtDNA sequence data than phylogenetic estimation [33], a result consistent with our ability to recover similar coalescence times but not the changes in Nef seen when comparing the coding vs. HVRI+II skyline plots.
Recombination can mislead phylogenetic estimation and positive selection analysis.
Well-aligned sites were chosen manually prior to phylogenetic estimation.
In this section we briefly review phylogenetic estimation.
