Inferring Temporally Consistent Migration Histories

Mrinmoy Saha Roddur, Sagi Snir, Mohammed El-Kebir

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Not only do many biological populations undergo evolution, but population members may also migrate from one location to another. For example, tumor cells may migrate from the primary tumor and seed a new metastasis, and pathogens may migrate from one host to another. One may represent a population's migration history by labeling the vertices of a given phylogeny T with locations such that an edge incident to vertices with distinct locations represents a migration. Additionally, in some biological populations, taxa from distinct lineages may comigrate from one location to another in a single event, a phenomenon known as a comigration. Here, we show that a previous problem statement for inferring migration histories that are parsimonious in terms of migrations and comigrations may lead to temporally inconsistent solutions. To remedy this deficiency, we introduce precise definitions of temporal consistency of comigrations in a phylogeny, leading to three successive problems. First, we formulate the Temporally Consistent Comigrations (TCC) problem to check if a set of comigrations is temporally consistent and provide a linear time algorithm for solving this problem. Second, we formulate the Parsimonious Consistent Comigration (PCC) problem, which aims to find comigrations given a location labeling of a phylogeny. We show that PCC is NP-hard. Third, we formulate the Parsimonious Consistent Comigration History (PCCH) problem, which infers the migration history given a phylogeny and locations of its extant vertices only. We show that PCCH is NP-hard as well. On the positive side, we propose integer linear programming models to solve the PCC and PCCH problems. We apply our approach to real and simulated data.

Original languageAmerican English
Title of host publication23rd International Workshop on Algorithms in Bioinformatics, WABI 2023
EditorsDjamal Belazzougui, A�da Ouangraoua
PublisherSchloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
ISBN (Electronic)9783959772945
DOIs
StatePublished - Aug 2023
Event23rd International Workshop on Algorithms in Bioinformatics, WABI 2023 - Houston, United States
Duration: 4 Sep 20236 Sep 2023

Publication series

NameLeibniz International Proceedings in Informatics, LIPIcs
Volume273

Conference

Conference23rd International Workshop on Algorithms in Bioinformatics, WABI 2023
Country/TerritoryUnited States
CityHouston
Period4/09/236/09/23

Keywords

  • Integer Linear Programming
  • Maximum parsimony
  • Metastasis
  • Migration

All Science Journal Classification (ASJC) codes

  • Software

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