20th-banner-rev.png

Albany 2019: 20th Conversation - Abstracts

category image Albany 2019
Conversation 20
June 11-15 2019
Adenine Press (2019)

A ‘Double Tale’ of Evolutionary Accretion in the Structure of Biological Networks

The evolution of structure in biology is driven by accretion and change (Caetano-Anollés et al. 2018). Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Networks describe how parts associate with each other to form integrated systems. Here we explain the structure of biological networks with a biphasic (bow-tie) theory of module creation embodied in a ‘double tale’ of evolutionary accretion (Mittenthal et al. 2012). In a first phase, parts are weakly linked and associate variously. As they diversify, they compete with each other and are selected for performance. The emerging interactions constrain their structure and associations. This causes parts to self-organize into modules with tight linkage. In a second phase, variants of the modules evolve and become new parts for a new generative cycle of higher-level organization. The paradigm predicts the rise of hierarchical modularity in evolving networks at different timescales and complexity levels, which we confirm with phylogenomic and molecular simulation data. Analyses of evolving networks describing the emergence of metabolism, the rise and diversification of the proteome, the evolution of the ribosome, and nanosecond-level change in protein loop dynamics consistently reveal an increase of hierarchical modularity and scale-free behavior as networks unfold in evolutionary time (e.g. Figure 1). As expected, evolutionary constraints on network structure are stronger at lower levels of biological organization. Remarkably, the phylogenomic data-driven ‘double tale’ of evolutionary accretion was already recounted in P. Strasb. Gr. Inv. 1665-6, a ~2,000-year-old papyrus roll from the ancient city of Panopolis in Upper Egypt attributed to Empedocles and archived at Strasbourg’s National University Library (Janko 2004).

gustavo-fig.gif

Fig. 1. Log-log plots of the clustering coefficient C(k) as a function of the number of links k for enzyme and subnetwork projections of metabolic enzyme-subnetwork bipartite networks as they grow in evolutionary time, billions of years ago (Gya). The scaling is the hallmark of hierarchical modularity. It increases in evolution and is stronger at lower levels of metabolic organization.

This research has been supported by USDA NIFA award H-1014249 and several Blue Waters supercomputer allocations.

References

    Caetano-Anollés, G., Caetano-Anollés, K. & Caetano-Anollés, D. (2018) Evolution of macromolecular structure: a ‘double tale’ of biological accretion and diversification. Sci. Prog. 101, 360-383.

    Mittenthal, J.E., Caetano-Anollés, D. & Caetano-Anollés, G. (2012) Biphasic patterns of diversification and the emergence of modules. Front. Genet. 3, 147.

    Janko, R. (2004) Empedocles, On nature I 233–364: A new reconstruction of P. Strasb. Gr. Inv. 1665–6. Zeitschrift Papyrologie Epigraphik 150, 1-26.

Gustavo Caetano-Anollés
Fizza Mughal
M. Fayez Aziz

Department of Crop Sciences and Illinois Informatics Institute
University of Illinois
Urbana, IL 61801

Ph: (217) 333-8172
Fx: (217) 333-8046
E-mail: gca@illinois.edu