Galled Perfect Transfer Networks

2024-09-05

RECOMB Comparative Genomics Satellite Conference

AI Summary

Horizontal gene transfer (HGT) inference faces challenges in modeling evolutionary histories that are approximately tree-like yet exhibit topological conflicts. Method: We propose galled perfect transfer networks (galled PTNs)—a novel model integrating biological interpretability with computational tractability—by incorporating galled tree structure into perfect transfer networks (PTNs). Galled PTNs enforce single acquisition, rare loss, and允许多次 lateral transfers per character. We define galled compatibility and devise polynomial-time algorithms to decide whether a given species tree can be extended into a galled PTN and whether a character matrix is galled-compatible. Results: Empirical evaluation on bacterial species trees and KEGG functional data reveals that most functional characters violate galled compatibility, indicating their evolutionary histories exceed the galled constraint’s complexity limits. This establishes a theoretical boundary for simplified HGT modeling and points toward new frameworks balancing parsimony with biological realism.

Technology Category

• Knowledge Representation and Reasoning: Computational Complexity of Reasoning
• Game Theory and Economic Paradigms: Imperfect Information
• Search and Optimization: Evolutionary Computation

Application Category

• Web Mining and Content Analysis: Models for Web evolution
• Graph Algorithms and Modeling for the Web: Graph neural networks and deep learning approaches for Web-related graphs
• Semantics and Knowledge: Methods, algorithms and applications for the development of semantic models, knowledge graphs and other forms of structured data models with machine-interpretable semantics

Abstract

Predicting horizontal gene transfers often requires comparative sequence data, but recent work has shown that character-based approaches could also be useful for this task. Notably, perfect transfer networks (PTN) explain the character diversity of a set of taxa for traits that are gained once, rarely lost, but that can be transferred laterally. Characterizing the structure of such characters is an important step towards understanding more complex characters. Although efficient algorithms can infer such networks from character data, they can sometimes predict overly complicated transfer histories. With the goal of recovering the simplest possible scenarios in this model, we introduce galled perfect transfer networks, which are PTNs that are galled trees. Such networks are useful for characters that are incompatible in terms of tree-like evolution, but that do fit in an almost-tree scenario. We provide polynomial-time algorithms for two problems: deciding whether one can add transfer edges to a tree to transform it into a galled PTN, and deciding whether a set of characters are galled-compatible, that is, they can be explained by some galled PTN. We also analyze a real dataset comprising of a bacterial species trees and KEGG functions as characters, and derive several conclusions on the difficulty of explaining characters in a galled tree, which provide several directions for future research.

Problem

• Predict horizontal gene transfers using character-based approaches
• Simplify transfer histories with galled perfect transfer networks
• Analyze bacterial species trees and KEGG functions compatibility

Innovation

• Introducing galled perfect transfer networks for simplicity
• Polynomial-time algorithms for galled PTN compatibility
• Analyzing bacterial species trees with KEGG functions