About

Michael Alfaro is a Professor and Chair in the Department of Ecology and Evolutionary Biology at UCLA. His research program aims to understand the factors that govern the evolutionary dynamics of organismal diversification. He investigates how to explain the uneven patterns of species richness and morphological diversity across the Tree of Life, focusing on the adequacy of macroevolutionary theory in explaining diversity patterns and the relationship between morphological diversity and ecological or functional diversity. Alfaro works on two main systems: coral reef fishes and neotropical primates, employing an interdisciplinary and quantitative approach that crosses traditional boundaries among molecular phylogenetics, evolutionary morphology, and theoretical evolution. His research involves constructing evolutionary trees using phylogenomic approaches, testing evolutionary hypotheses with phylogenetic statistical methods, and exploring form-function dynamics through models of trait evolution. His contributions include advancing understanding of organismal diversification and evolutionary patterns in marine and terrestrial species.

Research topics

• Biology
• Evolutionary biology
• Paleontology
• Zoology
• Ecology
• Genetics
• Anatomy

Selected publications

• Unlocking a flexible set of phylogenetic models for discrete and continuous trait evolution using discretized stochastic diffusion

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-21

  articleOpen access

  Abstract The practical utility of many modern phylogenetic comparative methods can depend on how accurately mathematical models capture the evolutionary process of traits. Boucher and Démery (2016) described a new quantitative trait model, Brownian motion with reflective limits, that they anticipated might be of use in testing hypotheses about a particular sort of constraint on phenotypic character evolution. Since their analytic solution for the probability function under this bounded evolutionary scenario was not practical to evaluate for reasonably-sized trees, Boucher and Démery (2016) also identified a creative technique for computing the likelihood of their model. The basis of this methodology derives from the convergence of an equal-rates, symmetric, ordered Markov chain and continuous stochastic diffusion in the limit as the number of steps in our chain goes to ∞ (or, alternatively, as their widths decrease towards zero). We refer to this convergence in the limit as the discretized diffusion approximation or (more compactly) the discrete approximation. We realized that this discrete approximation of Boucher and Démery (2016) unlocked a number of additional models for the phylogenetic comparative analysis of discrete and continuous trait data, and we explore several of these in the present article. Specifically, we examine application of this discretized diffusion approximation to the threshold model from evolutionary quantitative genetics, to a new “semi-threshold” trait evolution model, to a joint model of discrete and continuous traits in which the discrete trait influences the rate of evolution of our continuous character, as well as a model where precisely the converse is true, and to a discrete character dependent multi-trend trended continuous trait evolution model. We conclude with some context for the origins of our article and discussion of other possible applications of this powerful approach.

  PublisherDOI

• shawntz/charisma: charisma v1.1.0

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-10

  otherOpen accessSenior author

  What's Changed Add CLI warning when charisma() runs in non-interactive mode in https://github.com/shawntz/charisma/pull/37 Full Changelog: https://github.com/shawntz/charisma/compare/v1.0.0...v1.1.0

  PublisherDOI

• shawntz/charisma: charisma v1.1.0

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-10

  otherOpen accessSenior author

  What's Changed Add CLI warning when charisma() runs in non-interactive mode in https://github.com/shawntz/charisma/pull/37 Full Changelog: https://github.com/shawntz/charisma/compare/v1.0.0...v1.1.0

  PublisherDOI

• charisma: An R package to perform reproducible colour characterization of digital images for biological studies

  Methods in Ecology and Evolution · 2026-04-27

  articleOpen accessSenior author

  Abstract Advances in digital imaging and software tools have provided increasingly accessible datasets and methods for analysing colour evolution. Despite the variety of computational packages available, most rely on colour classification before running analyses. Previous methods to characterize colour limit the ability to analyse large‐scale image databases and are not always representative of biologically relevant colour classes, which decrease the accuracy of downstream analyses. Here, we present charisma , an R package designed to characterize the distribution of distinct colour classes in images suitable for large‐scale studies of biological organisms. We demonstrate the utility of our package through an analysis of colour evolution in a sample of diverse and charismatic birds, tanagers, in the subfamily Thraupinae. We show that charisma can quickly and accurately classify every pixel in an image and validate these results using pre‐identified, canonical colour swatches. We find that charisma colour classifications are consistent with those made by colour pattern experts in the field. Applying charisma to tanager colour evolution, we find that charisma outputs seamlessly integrate with downstream evolutionary analyses. Our results demonstrate that using charisma to manually curate and characterize colours in images provides a standardized, reliable and reproducible framework for high‐throughput colour classification.

  PublisherDOI

• charisma: An R package to perform reproducible color characterization of digital images for biological studies

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-27

  preprintOpen accessSenior author

  1. Advances in digital imaging and software tools have provided increasingly accessible datasets and methods for analyzing color evolution. Despite the variety of computational packages available, most rely on color classification before running analyses. Previous methods to characterize color limit the ability to analyze large-scale image databases and are not always representative of biologically relevant color classes, which decrease the accuracy of downstream analyses. 2. Here, we present charisma, an R package designed to characterize the distribution of distinct color classes in images suitable for large-scale studies of biological organisms. Here, we demonstrate the utility of our package through an analysis of color evolution in a sample of diverse and charismatic birds, tanagers, in the subfamily Thraupinae. 3. We show that charisma can quickly and accurately classify every pixel in an image and validate these results using pre-identified, canonical color swatches. We find that charisma color classifications are consistent with those made by color-pattern experts in the field. Applying charisma to tanager color evolution, we find that charisma outputs seamlessly integrate with downstream evolutionary analyses. 4. Our results demonstrate that using charisma to manually curate and characterize colors in images provides a standardized, reliable, and reproducible framework for high-throughput color classification.

  PublisherDOI

• Integrating Genomic Tools to Predict Climate Adaptation and Vulnerability across a Latitudinal Gradient in a Brazilian Atlantic Forest Treefrog (Dendropsophus elegans)

  Research Square · 2025-10-27

  preprintOpen accessSenior author
  PublisherOA PDFDOI

• Explosion of goby fish diversity at the Eocene-Oligocene transition

  Molecular Phylogenetics and Evolution · 2025-03-26 · 7 citations

  articleOpen accessSenior author

  • Phylogenomic resolution of Gobiiformes with UCE sequences from 121 species including all gobioid families and goby lineages. • Phylogenetic analysis using concatenated-partitioned and gene tree-species tree strategies. • Node dating with fossil outgroup- and relaxed molecular clock-based approaches. • Gobies are young and exceptionally diverse. A rapid drop of sea level at the Eocene-Oligocene transition (EOT; 34–33 Ma) triggered a marine mass extinction event and the turnover of terrestrial fauna, but its influence on the diversification of nearshore marine fish communities is unclear. Goby fishes ( Acanthomorpha : Percomorpha : Gobiiformes ) provide an ideal system to investigate the hypothesis that ecological opportunity at the EOT triggered the proliferation of coastal marine fishes. However, despite more than 30 years of molecular evolutionary research, divergence time estimates for gobies are widely variable, incomplete with respect to sampling of taxonomic families and sub-familial lineages, and far older than evident by the modest fossil record. Here we use 1,314 ultraconserved element (UCE) sequences sampled from 121 species, including all gobiiform families and sub-familial goby lineages, to infer phylogeny and node ages under species tree and relaxed molecular clock models. Our time-calibrated phylogenomic hypothesis reconciles molecular clock- and fossil-based estimates for gobiiform diversification, dating the origin of Apogonidae and Gobioidei to the uppermost Late Cretaceous, with lower to middle Paleogene divergence of the gobioid backbone and an explosion of goby lineages at the EOT. Our results support a remarkably recent evolutionary origin of goby families and stimulate new questions on the seemingly exceptional diversity of the group.

  PublisherDOI

• Explosion of Goby Fish Diversity at the Eocene-Oligocene Transition

  SSRN Electronic Journal · 2024-01-01 · 1 citations

  preprintOpen accessSenior author
  PublisherDOI

• Eyespot function in butterflyfishes (Chaetodontidae): comparing evidence for aposematism, automimicry, and predator mimicry

  Biological Journal of the Linnean Society · 2024-12-11 · 2 citations

  articleSenior author

  Abstract Many species of butterflyfish display false eyespots, but factors underlying eyespot diversity remain poorly understood. Eyespots are thought to function in predator avoidance, but there are multiple ways in which this might occur. An eyespot can function as deflection when distracting predators away from the true eye of the fish by mimicking it elsewhere on the body (automimicry). It can also function as intimidation, either by mimicking the appearance of predator eyes (predator mimicry) or by serving as a conspicuous warning to predators that the fish is spiny (warning coloration). Colour patterns that conceal the eye are common among butterflyfishes. Eye concealment is predicted under automimicry and can also occur in predator mimicry but is not predicted under warning coloration. Long median fin spines and deep bodies can make many species of butterflyfishes unpalatable, as predicted under intimidation. We adopt a comparative approach to examine relationships between eyespot presence, conspicuousness, and position on the body with eye coverage and physical defences, in order to evaluate evidence under the deflection vs. intimidation hypotheses within different trait complexes. Our results suggest that eyespots and eye coverage have evolved in conjunction with traits that facilitate predator evasion. We did not find evidence to support eyespots functioning as warning coloration for physical defences.

  PublisherDOI

• A highly contiguous genome assembly for the Yellow Warbler ( <i>Setophaga petechia</i> )

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-01-11

  preprintOpen access

  Abstract The Yellow Warbler ( Setophaga petechia ) is a small songbird in the New World Warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California’s riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation and can inform conservation management of this charismatic bird species.

  PublisherOA PDFDOI

Recent grants

• Systematics and Influence of Coral Reefs on Diversification in Tetraodontiform Fishes

  NSF · $450k · 2009–2013

• DISSERTATION RESEARCH: Testing macroevolutionary predictions of diversity and disparity in the ray-finned fishes

  NSF · $20k · 2016–2019

• Collaborative Research: Tempo and Mode of Diversification In Vertebrates

  NSF · $265k · 2009–2013

Frequent coauthors

• Luke J. Harmon

  University of Idaho

  147 shared

• Brant C. Faircloth

  Louisiana State University

  142 shared

• Thomas J. Near

  Yale Peabody Museum

  122 shared

• Matt Friedman

  University of Michigan–Ann Arbor

  114 shared

• James S. Albert

  University of Louisiana at Lafayette

  108 shared

• Brian C. O’Meara

  105 shared

• Liam J. Revell

  103 shared

• Samantha A. Price

  103 shared

Education

• PhD, Committee on Evolutionary Biology

  University of Chicago

  2000