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An Evolving View of Character Macroevolution.

Carrie M Tribble1,2, Jesús Martínez Gómez3,4, Carl J Rothfels5

  • 1Department of Biology, University of Washington, Seattle, WA 98195, USA.

Systematic Biology
|April 12, 2026
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Summary
This summary is machine-generated.

This study introduces a new paradigm in character evolution, advocating for joint inference of evolutionary patterns with phylogenetic trees. This approach integrates character evolution with diversification processes for a more holistic understanding of macroevolution.

Keywords:
Alignment inferenceBayesian inferenceBrownian motionSSE modelsancestral-state estimationhidden-state modelsindel modelsjoint inferencephylogenetic comparative methodsstochastic character mapsstructured Markov modelsthreshold modeltotal-evidence dating

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Area of Science:

  • Evolutionary Biology
  • Phylogenetics
  • Comparative Genomics

Background:

  • Phenotypes are crucial for understanding organism-environment interactions but require accounting for phylogenetic non-independence in comparative analyses.
  • Phylogenetic comparative methods (PCMs) traditionally correct for non-independence on pre-existing phylogenies.

Purpose of the Study:

  • To propose a paradigm shift towards jointly inferring character evolution and phylogenetic trees.
  • To review historical and recent advances in character macroevolution, emphasizing joint inference.

Main Methods:

  • Review of historical milestones in macroevolutionary studies.
  • Discussion of conceptual and methodological advances in joint inference.
  • Primers on specific applications of joint inference in evolutionary studies.

Main Results:

  • Joint inference integrates character evolution with diversification processes, moving beyond two-step analyses.
  • Highlights opportunities in state-dependent speciation/extinction, modeling discrete/continuous characters, and accounting for hidden variation.
  • Demonstrates effectiveness in divergence-time estimation, ancestral state reconstruction, and alignment inference.

Conclusions:

  • Joint inference offers a more integrated perspective on macroevolution.
  • Future research should focus on the interconnectedness of character evolution and broader biological processes.
  • This paradigm shift enhances our understanding of evolutionary patterns and diversification.