Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method

S. Andrade R, El-Hani C. On the origin of mitochondria: a multilayer network approach

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.

Determining a cutoff score for the family burden interview schedule using three statistical methods

Background

While it is widely acknowledged that family burden can be ameliorated with effective psycho-social interventions, how to measure family burden and define a valid cutoff to identify family caregivers in need of such interventions remains a key question. The purpose of the present study was to determine a statistically valid cutoff score for the Family Burden Interview Schedule (FBIS), using the cutoff scores of the Patient Health Questionnaire (PHQ-9) and the Generalized Anxiety Disorder Scale (GAD-7) as the reference.

Methods

The FBIS, PHQ-9, and GAD-7 were administered to a representative community sample of 327 family caregivers of schizophrenia patients. A FBIS cutoff score was determined using three different statistical methods: tree-based modeling, K-means clustering technique and linear regression. Contingency analysis was conducted to compare the FBIS cutoff with depression and anxiety scale scores.

Results

Findings proposed a cutoff score of 23 for the FBIS, with sensitivity being 76% for PHQ-9 and 74% for GAD-7, specificity being 68% for PHQ-9 and 67% for GAD-7.

Conclusion

This cutoff score would enable health care providers to assess family caregivers at risk and provide necessary interventions to improve their quality of life.

Electronic supplementary material

The online version of this article (10.1186/s12874-019-0734-8) contains supplementary material, which is available to authorized users.

Integrating Phylogenetic and Network Approaches to Study Gene Family Evolution: The Case of the AGAMOUS Family of Floral Genes

The study of gene family evolution has benefited from the use of phylogenetic tools, which can greatly inform studies of both relationships within gene families and functional divergence. Here, we propose the use of a network-based approach that in combination with phylogenetic methods can provide additional support for models of gene family evolution. We dissect the contributions of each method to the improved understanding of relationships and functions within the well-characterized family of AGAMOUS floral development genes. The results obtained with the two methods largely agreed with one another. In particular, we show how network approaches can provide improved interpretations of branches with low support in a conventional gene tree. The network approach used here may also better reflect known and suspected patterns of functional divergence relative to phylogenetic methods. Overall, we believe that the combined use of phylogenetic and network tools provide a more robust assessment of gene family evolution.