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Robust Method for Detecting Convergent Shifts in Evolutionary Rates

Partha, Raghavendran, Kowalczyk, Amanda, Clark, Nathan L, Chikina, Maria·2019·Molecular Biology and Evolution
DOI 10.1093/molbev/msz107

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Abstract

Identifying genomic elements underlying phenotypic adaptations is an important problem in evolutionary biology. Comparative analyses learning from convergent evolution of traits are gaining momentum in accurately detecting such elements. We previously developed a method for predicting phenotypic associations of genetic elements by contrasting patterns of sequence evolution in species showing a phenotype with those that do not. Using this method, we successfully demonstrated convergent evolutionary rate shifts in genetic elements associated with two phenotypic adaptations, namely the independent subterranean and marine transitions of terrestrial mammalian lineages. Our original method calculates gene-specific rates of evolution on branches of phylogenetic trees using linear regression. These rates represent the extent of sequence divergence on a branch after removing the expected divergence on the branch due to background factors. The rates calculated using this regression analysis exhibit an important statistical limitation, namely heteroscedasticity. We observe that the rates on branches that are longer on average show higher variance, and describe how this problem adversely affects the confidence with which we can make inferences about rate shifts. Using a combination of data transformation and weighted regression, we have developed an updated method that corrects this heteroscedasticity in the rates. We additionally illustrate the improved performance offered by the updated method at robust detection of convergent rate shifts in phylogenetic trees of protein-coding genes across mammals, as well as using simulated tree data sets. Overall, we present an important extension to our evolutionary-rates-based method that performs more robustly and consistently at detecting convergent shifts in evolutionary rates.

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  • Trait loss may occur when a change in the environment of a lineage makes a trait redundant, or when a change in development has the side effect of causing a trait to no longer form.

    “Trait loss may occur when a change in the environment of a lineage makes a trait redundant (Partha et al. 2019), or when a change in development has the side effect of causing a trait to no longer form (Womack et al. 2018; Pereira and Kohlsdorf 2023; Womack and Hoke 2023).”

    From From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions (2025) · cites this paper as Partha et al. 2019

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Metadata

Authors
Partha, R., Kowalczyk, A., Clark, N. L., & Chikina, M.
Affiliations
Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA
ORCID
Partha, Raghavendran
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2019-05-11
Volume
36
Issue
8
Pages
1817-1830
ISSN
  • 0737-4038
  • 1537-1719
DOI
10.1093/molbev/msz107
Cited by
60
References
3
Language
en
Licence
academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
Funders
  • NIH (R01 HG009299-01A1, T32 EB009403)
  • HHMI-NIBIB

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