Cladogenetic and Anagenetic Models of Chromosome Number Evolution: A Bayesian Model Averaging Approach

William A. Freyman, Sebastian Höhna

Research output: Contribution to journalArticlepeer-review

59 Scopus citations

Abstract

Chromosome number is a key feature of the higher-order organization of the genome, and changes in chromosome number play a fundamental role in evolution. Dysploid gains and losses in chromosome number, as well as polyploidization events, may drive reproductive isolation and lineage diversification. The recent development of probabilistic models of chromosome number evolution in the groundbreaking work by Mayrose et al. (2010, ChromEvol) have enabled the inference of ancestral chromosome numbers over molecular phylogenies and generated new interest in studying the role of chromosome changes in evolution. However, the ChromEvol approach assumes all changes occur anagenetically (along branches), and does not model events that are specifically cladogenetic. Cladogenetic changes may be expected if chromosome changes result in reproductive isolation. Here we present a new class of models of chromosome number evolution (called ChromoSSE) that incorporate both anagenetic and cladogenetic change. The ChromoSSE models allow us to determine the mode of chromosome number evolution; is chromosome evolution occurring primarily within lineages, primarily at lineage splitting, or in clade-specific combinations of both? Furthermore, we can estimate the location and timing of possible chromosome speciation events over the phylogeny. We implemented ChromoSSE in a Bayesian statistical framework, specifically in the software RevBayes, to accommodate uncertainty in parameter estimates while leveraging the full power of likelihood based methods. We tested ChromoSSE's accuracy with simulations and re-examined chromosomal evolution in Aristolochia, Carex section Spirostachyae, Helianthus, Mimulus sensu lato (s.l.), and Primula section Aleuritia, finding evidence for clade-specific combinations of anagenetic and cladogenetic dysploid and polyploid modes of chromosome evolution.

Original languageEnglish (US)
Pages (from-to)195-215
Number of pages21
JournalSystematic Biology
Volume67
Issue number2
DOIs
StatePublished - Mar 1 2018

Bibliographical note

Funding Information:
FUNDING This work was supported by a National Science Foundation Graduate Research Fellowship grant [DGE 1106400 to W.A.F.] and the Miller Institute for basic research in science to S.H. Analyses were computed using XSEDE, which is supported by the National Science Foundation [grant number ACI-1053575], and the Savio computational cluster provided by the Berkeley Research Computing program at the University of California, Berkeley.

Funding Information:
This work was supported by a National Science Foundation Graduate Research Fellowship grant [DGE 1106400 to W.A.F.] and the Miller Institute for basic research in science to S.H. Analyses were computed using XSEDE, which is supported by the National Science Foundation [grant number ACI-1053575], and the Savio computational cluster provided bythe Berkeley Research Computing program at the University of California, Berkeley.

Publisher Copyright:
© 2017 The Author(s).

Keywords

  • Anagenetic
  • Bayes factors
  • chromoSSE
  • chromosome evolution
  • chromosome speciation
  • cladogenetic
  • dysploidy
  • phylogenetic models
  • polyploidy
  • reversible-jump Markov chain Monte Carlo
  • whole genome duplication

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