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Spatiotemporal reconstruction of ancient road networks through sequential cost-benefit analysis.

ABSTRACT: The construction of ancient road networks spanned generations and exhibits temporal path dependence that is not fully captured by established network formation models that are used to support archaeological reasoning. We introduce an evolutionary model that captures explicitly the sequential nature of road network formation: A central feature is that connections are added successively and according to an optimal cost-benefit trade-off with respect to existing connections. In this model, the network topology emerges rapidly from early decisions, a trait that makes it possible to identify plausible road construction orders in practice. Based on this observation we develop a method to compress the search space of path-dependent optimization problems. We use this method to show that the model's assumptions on ancient decision-making allow the reconstruction of partially known road networks from the Roman era in good detail and from sparse archaeological evidence. In particular, we identify missing links in the major road network of ancient Sardinia that are in good agreement with expert predictions.

SUBMITTER: Stahlberg MJ

PROVIDER: S-EPMC9944230 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

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Spatiotemporal reconstruction of ancient road networks through sequential cost-benefit analysis.

Stahlberg Maximilian J MJ Sagnol Guillaume G Ducke Benjamin B Klimm Max M

PNAS nexus 20230119 2

The construction of ancient road networks spanned generations and exhibits temporal path dependence that is not fully captured by established network formation models that are used to support archaeological reasoning. We introduce an evolutionary model that captures explicitly the sequential nature of road network formation: A central feature is that connections are added successively and according to an optimal cost-benefit trade-off with respect to existing connections. In this model, the netw ...[more]

PMID: 36845350

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Project description:Cellular functions are based on the complex interplay of proteins, therefore the structure and dynamics of these protein-protein interaction (PPI) networks are the key to the functional understanding of cells. In the last years, large-scale PPI networks of several model organisms were investigated. A number of theoretical models have been developed to explain both the network formation and the current structure. Favored are models based on duplication and divergence of genes, as they most closely represent the biological foundation of network evolution. However, studies are often based on simulated instead of empirical data or they cover only single organisms. Methodological improvements now allow the analysis of PPI networks of multiple organisms simultaneously as well as the direct modeling of ancestral networks. This provides the opportunity to challenge existing assumptions on network evolution. We utilized present-day PPI networks from integrated datasets of seven model organisms and developed a theoretical and bioinformatic framework for studying the evolutionary dynamics of PPI networks. A novel filtering approach using percolation analysis was developed to remove low confidence interactions based on topological constraints. We then reconstructed the ancient PPI networks of different ancestors, for which the ancestral proteomes, as well as the ancestral interactions, were inferred. Ancestral proteins were reconstructed using orthologous groups on different evolutionary levels. A stochastic approach, using the duplication-divergence model, was developed for estimating the probabilities of ancient interactions from today's PPI networks. The growth rates for nodes, edges, sizes and modularities of the networks indicate multiplicative growth and are consistent with the results from independent static analysis. Our results support the duplication-divergence model of evolution and indicate fractality and multiplicative growth as general properties of the PPI network structure and dynamics.

Dataset Information

Spatiotemporal reconstruction of ancient road networks through sequential cost-benefit analysis.

Publications

Spatiotemporal reconstruction of ancient road networks through sequential cost-benefit analysis.

Similar Datasets

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