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1.
Figure 5

Figure 5. From: The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms.

Plots of use and reuse of FFs in proteomes. The sum of multiple occurrences of FFs was plotted against the number of distinct FFs for each of 420 proteomes of free-living organisms, including 48 Archaea (red circles), 239 Bacteria (blue circles), and 133 Eukarya (gray circles). Both axes are in logarithmic scale.

Kyung Mo Kim, et al. BMC Evol Biol. 2012;12:13-13.
2.
Figure 3

Figure 3. From: The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms.

Emergence and evolution of molecular functions along the timeline. The cumulative frequency distribution plot illustrates the accumulation of FFs associated with the seven major functional categories of SUPERFAMILY. Dotted lines indicate the first appearance of FFs associated with one of the 49 minor functional categories.

Kyung Mo Kim, et al. BMC Evol Biol. 2012;12:13-13.
3.
Figure 6

Figure 6. From: The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms.

Model of protein domain and proteome diversification. Venn diagrams show the evolutionary accumulation of FFs in superkingdoms as these distribute in the five phases of the timeline. The tree diagram in the top describes major dichotomies in the organismal world and shows how reductive evolution and diversification has tailored proteome evolution in the three cellular superkingdoms. The model was assembled directly from phylogenomic data.

Kyung Mo Kim, et al. BMC Evol Biol. 2012;12:13-13.
4.
Figure 1

Figure 1. From: The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms.

Phylogenomic tree reconstruction at the FF level of structural classification. The SCOP database classifies protein domains into a hierarchy of fold families (FFs), fold superfamilies and folds. In this study, we counted multiple occurrences of individual FFs in proteomes to build data matrices. Matrices of genomic abundances are normalized in a scale of '0' to '9' and 'A' to 'N' and their columns and rows can be transposed to generate both trees of proteomes and trees of FFs.

Kyung Mo Kim, et al. BMC Evol Biol. 2012;12:13-13.
5.
Figure 4

Figure 4. From: The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms.

Species trees reconstructed using phase-specific FFs in 420 proteomes of free-living organisms. (A) Tree of proteomes reconstructed from the 76 FFs of phase I (tree length = 12,829 steps; CI = 0.065, RI = 0.727; g1 = -0.116). (B) Tree of proteomes reconstructed from the 232 FFs of phase II (tree length = 28,447 steps; CI = 0.056, RI = 0.708; g1 = -0.242). (C) Tree of proteomes reconstructed from the 331 FFs of phase III (tree length = 13,773 steps; CI = 0.082, RI = 0.783; g1 = -0.212). (D) Tree of proteomes reconstructed from the 1,008 FFs of phase IV (tree length = 21,804 steps; CI = 0.153, RI = 0.614; g1 = -0.356). (E) Tree of proteomes reconstructed from the 750 FFs of phase V (tree length = 47,213 steps; CI = 0.136, RI = 0.828; g1 = -0.284). Terminal leaves of Archaea, Bacteria, and Eukarya were labeled in red, blue, and gray. Venn diagrams show the distribution of FFs in the three superkingdoms for the FFs of each phase. The green arrow indicates the root position of a given tree of proteomes.

Kyung Mo Kim, et al. BMC Evol Biol. 2012;12:13-13.
6.
Figure 2

Figure 2. From: The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms.

A timeline of domain appearance in the protein world. (A) Phylogenomic tree of FF domain structures (tree length = 177,864; CI = 0.030; RI = 0.749; g1 = -0.070) reconstructed from a genomic census of 2,397 FFs in 420 proteomes of free-living organisms (all 420 characters were parsimoniously informative). Terminal leaves are not labeled because they would not be legible. The Venn diagram shows diversity of FFs in the three superkingdoms. (B) Five phases in the evolutionary timeline of appearance of FFs in all three superkingdoms (top), and in Archaea, Bacteria, and Eukarya. Individual plots show the relationships of f (distribution index) and nd values (age of FFs). (C) The seven horizontal bars indicate nd ranges for taxonomic groups of FFs that are unique to individual superkingdoms (A, B, E) or shared by two (AB, BE, AE) or all (ABE) superkingdoms. The total number of FFs emerging in each phase is indicated in parentheses. The numbers labeled above bars indicate diversity of FFs belonging to taxonomic groups in each phase. (D) Cumulative frequency distribution of FFs along the timeline of domain structures.

Kyung Mo Kim, et al. BMC Evol Biol. 2012;12:13-13.

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