Distance metrics for ranked evolutionary trees

Proc Natl Acad Sci U S A. 2020 Nov 17;117(46):28876-28886. doi: 10.1073/pnas.1922851117. Epub 2020 Nov 2.

Abstract

Genealogical tree modeling is essential for estimating evolutionary parameters in population genetics and phylogenetics. Recent mathematical results concerning ranked genealogies without leaf labels unlock opportunities in the analysis of evolutionary trees. In particular, comparisons between ranked genealogies facilitate the study of evolutionary processes of different organisms sampled at multiple time periods. We propose metrics on ranked tree shapes and ranked genealogies for lineages isochronously and heterochronously sampled. Our proposed tree metrics make it possible to conduct statistical analyses of ranked tree shapes and timed ranked tree shapes or ranked genealogies. Such analyses allow us to assess differences in tree distributions, quantify estimation uncertainty, and summarize tree distributions. We show the utility of our metrics via simulations and an application in infectious diseases.

Keywords: coalescent; distance metric; phylogenetics; ranked genealogy; ranked tree shape.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biological Evolution
  • Computer Simulation
  • Genetics, Population / methods*
  • Models, Genetic
  • Pedigree
  • Phylogeny
  • Sequence Analysis, DNA / methods*