Identifying parsimonious pathways of accumulation and convergent evolution from binary data
Data files
Jun 29, 2026 version files 2.78 MB
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mt-trans-manual.csv
272.96 KB
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pt-trans-manual.csv
2.51 MB
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README.md
1.39 KB
Abstract
How stereotypical, and hence predictable, are evolutionary and accumulation dynamics? Here we consider processes – from genome evolution to cancer progression – involving the irreversible accumulation of binary features (characters). We seek models of how these characters evolve in the form of transition networks, describing transitions between sets of characters, that reflect the simplest possible sets of character dynamics that can explain all the observations. A transition network supporting a single, deterministic dynamic pathway is maximally simple and lowest cost, and branches (corresponding to different possible “next steps” for evolution) increase cost, particularly if these branches are “deep”, occurring at early stages in the dynamics. In this sense, the optimal description measures how stereotypical the evolutionary or accumulation process is – how predictable are its dynamics in independent samples or lineages. The problem is solvable in polynomial time for cross-sectional observations by building on an existing method due to Gutin, and we provide a polynomial-time estimate in the more general case of pairs of observed states. We use this approach to define a “stereotypy index” reflecting the extent of evolutionary predictability, and to efficiently estimate likely orderings of evolutionary events, common precursor steps, relationships between characters, and pathways of evolution. We demonstrate use cases in the evolution of antimicrobial resistance, organelle evolution, and cancer progression, and provide a software implementation.
https://doi.org/10.5061/dryad.pc866t23t
Description of data
This repository contains two datasets used in the analysis of the "HyperDAGs" method. The codebase for the method can be found in the Software Related Work. The datasets are:
mt-trans-manual.csv -- mtDNA evolutionary transitions inferred from the Giannakis et al. pipeline [1], used as a case study with the HyperDAGS method. Each row is a transition; the binary values in columns describe the presence/absence of each gene in the ancestral (a) and descendant (d) states for that transition.
pt-trans-manual.csv -- ptDNA evolutionary transitions inferred from the Giannakis et al. pipeline [1], used as a case study with the HyperDAGS method. Each row is a transition; the binary values in columns describe the presence/absence of each gene in the ancestral (a) and descendant (d) states for that transition.
hyperDAGs codebase -- repository containing an R implementation of the HyperDAGs codebase (internally documented) (on Zenodo)
Organelle genome data:
[1] Giannakis, K., Arrowsmith, S.J., Richards, L., Gasparini, S., Chustecki, J.M., Røyrvik, E.C. and Johnston, I.G., 2022. Evolutionary inference across eukaryotes identifies universal features shaping organelle gene retention. Cell Systems, 13(11), pp.874-884.
