An Integrated Model of Phenotypic Trait Changes and Site-Specific Sequence Evolution

Eli Levy Karin, Susann Wicke, Tal Pupko, Itay Mayrose

Research output: Contribution to journalArticlepeer-review


Recent years have seen a constant rise in the availability of trait data, including morphological features, ecological preferences, and life history characteristics. These phenotypic data provide means to associate genomic regions with phenotypic attributes, thus allowing the identification of phenotypic traits associated with the rate of genome and sequence evolution. However, inference methodologies that analyze sequence and phenotypic data in a unified statistical framework are still scarce. Here, we present TraitRateProp, a probabilistic method that allows testing whether the rate of sequence evolution is associated with a binary phenotypic character trait. The method further allows the detection of specific sequence sites whose evolutionary rate is most noticeably affected following the character transition, suggesting a shift in functional/structural constraints. TraitRateProp is first evaluated in simulations and then applied to study the evolutionary process of plastid plant genomes upon a transition to a heterotrophic lifestyle. To this end,we analyze 20 plastid genes across 85 orchid species, spanning different lifestyles and representing different genera in this large family of flowering plants. Our results indicate higher evolutionary rates following repeated transitions to a heterotrophic lifestyle in all but four of the loci analyzed.

Original languageEnglish
Pages (from-to)917-933
Number of pages17
JournalSystematic Biology
Issue number6
StatePublished - 1 Nov 2017


  • Evolutionary models
  • Evolutionary rate
  • Genotype-phenotype
  • Orchids
  • Plastome
  • Rate shift

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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