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Abstract Understanding phenotypic disparity across the tree of life requires identifying where and when evolutionary rates change on phylogeny. A primary methodological challenge in macroevolution is therefore to develop methods for accurate inference of among-lineage variation in rates of phenotypic evolution. Here, we describe a method for inferring among-lineage evolutionary rate heterogeneity in both continuous and discrete traits. The method assumes that the present-day distribution of a trait is shaped by a variable-rate process arising from a mixture of constant-rate processes and uses a single-pass tree traversal algorithm to estimate branch-specific evolutionary rates. By employing dynamic programming optimization techniques and approximate maximum likelihood estimators where appropriate, our method permits rapid exploration of the tempo and mode of phenotypic evolution. Simulations indicate that the method reconstructs rates of trait evolution with high accuracy. Application of the method to data sets on squamate reptile reproduction and turtle body size recovers patterns of rate heterogeneity identified by previous studies but with computational costs reduced by many orders of magnitude. Our results expand the set of tools available for detecting macroevolutionary rate heterogeneity and point to the utility of fast, approximate methods for studying large-scale biodiversity dynamics. [Brownian motion; continuous characters; discrete characters; macroevolution; Markov process; rate heterogeneity.]
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This content will become publicly available on February 1, 2026
Evidence for Macroevolution
The teaching and learning of macroevolutionary processes have received limited attention in the evolution education literature despite their importance in evolution acceptance and evolution understanding. This necessitates the development of pedagogical content knowledge, including best practices in curriculum and instruction, on macroevolutionary processes that support student understanding and acceptance of macroevolution. One promising approach is to consider macroevolution at the microbiological level by teaching endosymbiotic theory while capitalizing on pre-existing pedagogical content knowledge of tree thinking and bioinformatics. Here, we present a computational laboratory activity that guides students through the construction of a phylogeny based on the universal small subunit ribosomal RNA gene. The resulting phylogenetic tree demonstrates that the photosynthetic organelles of the protist Paulinella chromatophora evolved independently of the chloroplasts of plants and algae. This not only addresses the need for pedagogical content knowledge in macroevolution in an interdisciplinary and integrative fashion, but also serves as a foundation for future research into the teaching of endosymbiosis. This activity is designed for a 15–20 student introductory/intermediate biology laboratory.
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- Award ID(s):
- 2119963
- PAR ID:
- 10594795
- Publisher / Repository:
- The American Biology Teacher
- Date Published:
- Journal Name:
- The American Biology Teacher
- Volume:
- 87
- Issue:
- 2
- ISSN:
- 0002-7685
- Page Range / eLocation ID:
- 93 to 102
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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