Driven progressive evolution of genome sequence complexity in Cyanobacteria

Abstract

Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they encode the historical information of a species' biotic and environmental interactions. As a case study, we have measured genome sequence complexity in the ancient phylum Cyanobacteria. To arrive at an appropriate measure of genome sequence complexity, we have chosen metrics that do not decipher biological functionality but that show strong phylogenetic signal. Using a ridge regression of those metrics against root-to-tip distance, we detected positive trends towards higher complexity in three of them. Lastly, we applied three standard tests to detect if progressive evolution is passive or driven-the minimum, ancestor-descendant, and sub-clade tests. These results provide evidence for driven progressive evolution at the genome-level in the phylum Cyanobacteria.

Figure 1

Phylogeny of Cyanobacteria with the metrics of sequence complexity and genome parameters for each chosen genome. The values of metrics and parameters are proportional to circle size. The colored species correspond to four monophyletic sub-clades that were used to test evidence of a driven trend for each sub-clade (see also Fig. S2).

Figure 2

Phylogenetic trends of genomic complexity metrics (a) and standard genome parameters (b). The estimated genomic value for each tip (red circles) or node (white circles) in the phylogenetic tree is regressed against its evolutionary age (i.e., distance from the root). The statistical significance of the regression is tested against 10,000 slopes obtained under simulated Brownian evolution. The slopes and their P values are shown in Table S2.

Figure 3

Distribution of metrics and parameters according to root-to-tip distance. The interior dashed line corresponds to the value of the basal clade, x_b. The histograms that appear above each figure correspond to the number of accumulated values of metrics and parameters (regardless of the age) ranging from lower (left) to higher (right) values than x_b.

Figure 4

Mapping of the SCC complexity metric on the Cyanobacteria tree.