9th EAI International Conference on Bio-inspired Information and Communications Technologies (formerly BIONETICS)

Research Article

Quantifying Reticulation in Phylogenetic Complexes Using Homology

  • @INPROCEEDINGS{10.4108/eai.3-12-2015.2262454,
        author={Kevin Emmett and Raul Rabadan},
        title={Quantifying Reticulation in Phylogenetic Complexes Using Homology},
        proceedings={9th EAI International Conference on Bio-inspired Information and Communications Technologies (formerly BIONETICS)},
        publisher={ACM},
        proceedings_a={BICT},
        year={2016},
        month={5},
        keywords={topological data analysis reticulate evolution},
        doi={10.4108/eai.3-12-2015.2262454}
    }
    
  • Kevin Emmett
    Raul Rabadan
    Year: 2016
    Quantifying Reticulation in Phylogenetic Complexes Using Homology
    BICT
    EAI
    DOI: 10.4108/eai.3-12-2015.2262454
Kevin Emmett1,*, Raul Rabadan1
  • 1: Columbia University
*Contact email: kje2109@columbia.edu

Abstract

Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we demonstrate the correspondence between nontrivial higher homology and reticulate evolution. We discuss the sensitivity of the standard filtration and show cases where reticulate evolution can fail to be detected. We introduce an extension of the standard framework and define the median complex as a construction to recover signal of the frequency and scale of reticulate evolution by inferring and imputing putative ancestral states. Finally, we apply our methods to two datasets from phylogenetics. Our work expands on earlier ideas of using topology to extract important evolutionary features from genomic data.