Abstract
Evolution is a historical process, unfolding across the spectra of space and time. This historical nature has long rendered evolutionary biology an exercise in retrospection: paleontologists reconstruct the past through the fossil remnants of species which once flourished, and neontologists conduct historical inference through the partial or complete genome sequences of extant taxa, and, from time to time, combine both approaches. However, when Stephen Jay Gould published Wonderful Life in 1987, biologists began to look at this retrospective exercise differently: they began to ask if evolution contained predictable elements amidst its innumerable historical contingencies. Since Gould’s narration of the Burgess Shale fauna and its ultimate decimation, phenotypic convergence between species has arisen as a powerful means in investigating the divergence and confluence between distantly related species that have independently evolved similar features. Still, our hierarchical understanding of convergence remains incomplete— we know relatively little about the contexts in which ecological, phenotypic, and molecular convergence generally co-occur, or the circumstances under which they are decoupled. As such, in this dissertation, I sought to examine the process and consequences of convergent adaptation, linking macroevolutionary inference and molecular evolution. In Chapter 2, I review and conceptually reorganize the study of a major class of adaptations— key innovations. In Chapter 3, through the development of a new approach of examining the signatures of key innovation evolution across molecular phylogenies, I demonstrate that the repeated evolution of a key innovation—adhesive toepads in arboreal lizards—can confer similar deep time macroevolutionary consequences among convergent lineages. In Chapter 4, I sequence short-read whole genomes for nearly all 435 different Anolis lizard species, which I use to infer and resolve a complete tree of life for this iconic group, recovering total support for subgenus monophyly, parallel adaptive radiation, and the extensive phenotypic convergence of Greater Antillean anoles. In Chapter 5, I conduct a test of Gould’s grand question on the relative roles of chance and fate in evolution by examining the genomic basis of phenotypic convergence in anoles. I find that anoles exhibit signatures of hierarchical convergence across ecological, phenotypic, and molecular scales, observing excessive parallel positive selection across anole radiations, ecomorph-associated selective regimes at loci regulating limb development, and remarkable residue-level parallel evolution in a transcription factor central to vertebrate morphogenesis.
Committee Chair
Jonathan Losos
Committee Members
Allan Larson; Anthony Geneva; Jonathan Losos; Kenneth Olsen; Michael Landis
Degree
Doctor of Philosophy (PhD)
Author's Department
Biology & Biomedical Sciences (Evolution, Ecology & Population Biology)
Document Type
Dissertation
Date of Award
3-25-2026
Language
English (en)
DOI
https://doi.org/10.7936/d6s3-m370
Author's ORCID
https://orcid.org/0000-0002-5031-3991
Recommended Citation
Miller, Aryeh Hershel, "Macroevolutionary Innovation and the Genomic Basis of Convergent Adaptation in Anolis Lizards" (2026). Arts & Sciences Theses and Dissertations. 3723.
The definitive version is available at https://doi.org/10.7936/d6s3-m370