Figure 1.
Diversification dates for Amoebozoa based on a 6-protein data set.
The two trees shown are superimposed chronograms of Amoebozoa based on analyses of a 6-protein concatenated data set using BEAST [35], with the WAG model of substitution and calibrated either with two opistokont fossils (grey tree) or two opisthokont and two plant fossils (black tree). Taxonomic circumscription is indicated on the right where Myxo stands for Myxogastria and Dicty for Dictyostelia. The geological time-scale is depicted at the bottom; acronyms within the Phanerozoic are C for Cambriam, O for Ordovician, S for Silurian, De for Devonian, Car for Carboniferous, Pe for Permian, T for Triassic, Jur for Jurassic, Cret for Cretaceous and Ter for Tertiary. Bootstrap support (BS) values are indicated by black circles (BS>95%), black squares (BS>85) and black triangle (BS>75).
Figure 2.
Diversification rate shifts in Amoebozoa based on an 18S rDNA chronogram.
The tree shown was derived and dated using BEAST [35] with the HKY substitution model. Colored branches indicate significant rate shifts detected by the birth-death model of MEDUSA [37]: red branches, green triangle (arcellinids) and blue triangle (Myxogastria) indicate faster rates and an orange branch indicates a single terminal clade with slower rates (Acanthamoeba). Alternative coding of the number of species for each terminal is indicated with a slash (see section 2.2). Violet vertical bar indicates the time span between the initial colonization of land by plants to the origin of the terrestrial ecosystems [50]. Bootstrap support (BS) values obtained from a maximum likelihood analysis using RAxML v 7.04 [27] are indicated by black circles (BS>95%), black squares (BS>75) black triangles (BS>50).
Figure 3.
Reconstructed node ages and their 95% HPD distribution based on a 6-protein phylogeny.
Reconstructed ages and 95% highest posterior density (HPD) from a 6-protein data set under different fossil constraints (four or two fossil -580-400 myr), models (WAG, with or without a gamma rate correction) and programs (BEAST or MCMCtree) for the following nodes: A) crown Amoebozoa B) crown Mycetozoa C) crown Dictyostelia and D) stem Arcellinida. Note the different scales among the plots. The exact values for nodes and HPDs are given in Table 1.