On the origin of mitochondria: a multilayer network approach

Abstract

Backgound: The endosymbiotic theory is widely accepted to explain the origin of mitochondria from a bacterial ancestor. While ample evidence supports the intimate connection of Alphaproteobacteria to the mitochondrial ancestor, pinpointing its closest relative within sampled Alphaproteobacteria is still an open evolutionary debate. Many different phylogenetic methods and approaches have been used to answer this challenging question, further compounded by the heterogeneity of sampled taxa, varying evolutionary rates of mitochondrial proteins, and the inherent biases in each method, all factors that can produce phylogenetic artifacts. By harnessing the simplicity and interpretability of protein similarity networks, herein we re-evaluated the origin of mitochondria within an enhanced multilayer framework, which is an extension and improvement of a previously developed method.

Methods: We used a dataset of eight proteins found in mitochondria (N = 6 organisms) and bacteria (N = 80 organisms). The sequences were aligned and resulting identity matrices were combined to generate an eight-layer multiplex network. Each layer corresponded to a protein network, where nodes represented organisms and edges were placed following mutual sequence identity. The Multi-Newman-Girvan algorithm was applied to evaluate community structure, and bifurcation events linked to network partition allowed to trace patterns of divergence between studied taxa.

Results: In our network-based analysis, we first examined the topology of the 8-layer multiplex when mitochondrial sequences disconnected from the main alphaproteobacterial cluster. The resulting topology lent firm support toward an Alphaproteobacteria-sister placement for mitochondria, reinforcing the hypothesis that mitochondria diverged from the common ancestor of all Alphaproteobacteria. Additionally, we observed that the divergence of Rickettsiales was an early event in the evolutionary history of alphaproteobacterial clades.

Conclusion: By leveraging complex networks methods to the challenging question of circumscribing mitochondrial origin, we suggest that the entire Alphaproteobacteria clade is the closest relative to mitochondria (Alphaproteobacterial-sister hypothesis), echoing recent findings based on different datasets and methodologies.

Keywords: Complex networks; Evolution; Mitochondria.

Figure 1. Flowchart of the used frame based on the MultiNG algorithm to multiplex networks.

Sequence of steps required to obtain a dendrogram and community structure within the used approach. After the selection of organisms and protein orthologs, identity matrices are obtained from protein alignments (pair-wise or global) which allow for obtaining similarity networks. Dissimilarity measure δ(σ,σ + Δσ) is used to evaluate threshold values σ_th for each ortholog, leading to the multiplex. Communities are identified using MultiNG and resulting dendrogram.

Figure 2. Dissimilarity graph for the networks of the eight included orthologues.

Dissimilarity graph for the networks of the eight included orthologues. Arrows indicate the values of σ_th used to obtain the dendrograms in Fig. 3 (Cob: 64%; Cox2: 51%; Cox3: 59%; Nad1: 69%; Nad4: 55%; Nad5: 53%; Nad6: 50%; Nad9: 59%) and in Fig. 1 of the Supplemental Material (Cob: 70%; Cox2: 61%; Cox3: 67%; Nad1: 72%; Nad4: 68%; Nad5: 67%; Nad6: 67%; Nad9: 66%).

Figure 3. Dendrogram obtained by the application of the MultiNG algorithm to the weighted multiplex network.

The dendrogram obtained by the application of the MultiNG algorithm to the weighted multiplex network depicts the three retrieved communities (C1, C2, and C3). Higher-order taxonomic information is indicated in the upper left legend. Q = 0.383 is the highest modularity value (blue-dotted line in lower panel) before the subsequent divergence within community C3 (blue-dotted line in the dendrogram).

Figure 4. Summary of bootstrap results for the dendrogram in Fig. 3.

Summary of bootstrap results for the dendrogram in Fig. 3, showing the values for clade, alphaproteobacteria, mitochondria and external group. A total of 1,000 bootstraps were used.