Applying Machine Learning to Classify the Origins of Gene Duplications

Michael T.W. McKibben, Michael S. Barker

Research output: Chapter in Book/Report/Conference proceedingChapter


Nearly all lineages of land plants have experienced at least one whole-genome duplication (WGD) in their history. The legacy of these ancient WGDs is still observable in the diploidized genomes of extant plants. Genes originating from WGD—paleologs—can be maintained in diploidized genomes for millions of years. These paleologs have the potential to shape plant evolution through sub- and neofunctionalization, increased genetic diversity, and reciprocal gene loss among lineages. Current methods for classifying paleologs often rely on only a subset of potential genomic features, have varying levels of accuracy, and often require significant data and/or computational time. Here, we developed a supervised machine learning approach to classify paleologs from a target WGD in diploidized genomes across a broad range of different duplication histories. We collected empirical data on syntenic block sizes and other genomic features from 27 plant species each with a different history of paleopolyploidy. Features from these genomes were used to develop simulations of syntenic blocks and paleologs to train a gradient boosted decision tree. Using this approach, Frackify (Fractionation Classify), we were able to accurately identify and classify paleologs across a broad range of parameter space, including cases with multiple overlapping WGDs. We then compared Frackify with other paleolog inference approaches in six species with paleotetraploid and paleohexaploid ancestries. Frackify provides a way to combine multiple genomic features to quickly classify paleologs while providing a high degree of consistency with existing approaches.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages29
StatePublished - 2023

Publication series

NameMethods in Molecular Biology


  • Fractionation
  • Ks
  • Machine learning
  • Ohnologs
  • Paleologs
  • Polyploidy
  • Synteny
  • Whole-genome duplication

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


Dive into the research topics of 'Applying Machine Learning to Classify the Origins of Gene Duplications'. Together they form a unique fingerprint.

Cite this