About

Our lab studies how and why new species form in nature (“the speciation process”). We focus on the evolution of divergence and reproductive isolation at multiple biological levels. To do this, we use an interdisciplinary approach that leverages genomic sequencing techniques and integrates field collections, museum specimens, and laboratory experiments in hybridizing species of birds and fish.

Research topics

• Computer Science
• Zoology
• Biology
• Genetics
• Pedagogy
• Demographic economics
• Mathematics education
• Medicine
• Evolutionary biology
• Psychology

Selected publications

• Strong selection maintains a narrow, stable tension zone between grosbeak species in the Great Plains

  Evolution · 2025-09-05 · 3 citations

  articleOpen accessSenior author

  When genetically divergent and geographically isolated lineages come back into contact, their interactions allow us to observe reproductive isolating barriers in action. The avian contact zone between Pheucticus melanocephalus and P. ludovicianus in the North American Great Plains has been studied for more than 60 years, but never with the aid of genomic data. Here, we generate reduced-representation genome sequence data from a transect in South Dakota spanning pure P. melanocephalus to pure P. ludovicianus. While the presence of recent-generation hybrids and backcrosses confirms the ongoing production of fertile F1 offspring, the narrow (48-61 km) and concordant geographic transitions in nuclear ancestry, mitochondrial ancestry, and male plumage phenotypes are hallmarks of a "tension zone," where selection against hybrids is balanced by immigration of parental individuals. Additionally, the bimodal distribution of genomic ancestry in the heart of the contact zone and the highly significant association between genomic and mitochondrial ancestry both suggest a role for intrinsic genetic incompatibilities in the maintenance of this species boundary. Overall, we infer that strong selection maintains a narrow region of geographic contact between P. melanocephalus and P. ludovicianus in the Great Plains despite ongoing hybridization and introgression.

  PublisherOA PDFDOI

• Pervasive gene flow despite strong and varied reproductive barriers in swordtails

  Nature Ecology & Evolution · 2025-03-26 · 11 citations

  articleOpen access1st authorCorresponding

  Abstract The evolution of reproductive barriers leads to the formation of new species. However, recent research has demonstrated that hybridization has been pervasive across the tree of life even in the presence of strong barriers. Using swordtail fishes (genus Xiphophorus ), an emerging model system, we document overlapping mechanisms that act as barriers to gene flow between Xiphophorus birchmanni and Xiphophorus cortezi by combining genomic sequencing from natural hybrid populations, experimental laboratory crosses, behavioural assays, sperm measures and developmental studies. We show that assortative mating plays a role in maintaining subpopulations with distinct ancestry within natural hybrid populations. Using F 2 hybrids we identify several genomic regions that strongly impact hybrid viability. Strikingly, two of these regions underlie genetic incompatibilities in hybrids between X. birchmanni and its sister species Xiphophorus malinche . Our results demonstrate that ancient hybridization has played a role in the origin of this shared genetic incompatibility. Moreover, ancestry mismatch at these incompatible regions has remarkably similar consequences for phenotypes and hybrid survival in X. cortezi × X. birchmanni hybrids as in X. malinche × X. birchmanni hybrids. Our findings identify varied reproductive barriers that shape genetic exchange between naturally hybridizing species and highlight the complex evolutionary outcomes of hybridization.

  PublisherOA PDFDOI

• AvianLexiconAtlas: A database of descriptive categories of English-language bird names around the world

  PLoS ONE · 2025-06-11 · 1 citations

  articleOpen accessCorresponding

  Common names of species are important for communicating with the general public. In principle, these names should provide an accessible way to engage with and identify species. The common names of species have historically been labile without standard guidelines, even within a language. Currently, there is no systematic assessment of how often common names communicate identifiable and biologically relevant characteristics about species. This is a salient issue in ornithology, where common names are used more often than scientific names for species of birds in written and spoken English, even by professional researchers. To gain a better understanding of the types of terminology used in the English-language common names of bird species, a group of 85 professional ornithologists and non-professional contributors classified unique descriptors in the common names of all recognized species of birds. In the AvianLexiconAtlas database produced by this work, each species' common name is assigned to one of ten categories associated with aspects of avian biology, ecology, or human culture. Across 10,906 species of birds, 89% have names describing the biology of the species, while the remaining 11% of species have names derived from human cultural references, human names, or local non-English languages. Species with common names based on features of avian biology are more likely to be related to each other or be from the same geographic region. The crowdsourced data collection also revealed that many common names contain specialized or historic terminology unknown to many of the data collectors, and we include these terms in a glossary and gazetteer alongside the dataset. The AvianLexiconAtlas can be used as a quantitative resource to assess the state of terminology in English-language common names of birds. Future research using the database can shed light on historical approaches to nomenclature and how people engage with species through their names.

  PublisherDOI

• Pervasive gene flow despite strong and varied reproductive barriers in swordtails

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-04-20 · 6 citations

  preprintOpen access1st authorCorresponding

  Abstract One of the mechanisms that can lead to the formation of new species occurs through the evolution of reproductive barriers. However, recent research has demonstrated that hybridization has been pervasive across the tree of life even in the presence of strong barriers. Swordtail fishes (genus Xiphophorus ) are an emerging model system for studying the interface between these barriers and hybridization. We document overlapping mechanisms that act as barriers between closely related species, X. birchmanni and X. cortezi , by combining genomic sequencing from natural hybrid populations, artificial crosses, behavioral assays, sperm performance, and developmental studies. We show that strong assortative mating plays a key role in maintaining subpopulations with distinct ancestry in natural hybrid populations. Lab experiments demonstrate that artificial F 1 crosses experience dysfunction: crosses with X. birchmanni females were largely inviable and crosses with X. cortezi females had a heavily skewed sex ratio. Using F 2 hybrids we identify several genomic regions that strongly impact hybrid viability. Strikingly, two of these regions underlie genetic incompatibilities in hybrids between X. birchmanni and its sister species X. malinche . Our results demonstrate that ancient hybridization has played a role in the origin of this shared genetic incompatibility. Moreover, ancestry mismatch at these incompatible regions has remarkably similar consequences for phenotypes and hybrid survival in X. cortezi Ô X. birchmanni hybrids as in X. malinche Ô X. birchmanni hybrids. Our findings identify varied reproductive barriers that shape genetic exchange between naturally hybridizing species and highlight the complex evolutionary outcomes of hybridization. Significance Statement Biologists are fascinated by how the diverse species we see on Earth have arisen and been maintained. One driver of this process is the evolution of reproductive barriers between species. Despite the commonality of these barriers, many species still exchange genes through a process called hybridization. Here, we show that related species can have a striking array of reproductive barriers—from genetic interactions that harm hybrids to mate preferences that reduce hybridization in the first place. However, we also find that genetic exchange between these species is very common, and may itself play an important role in the evolution of reproductive barriers. Together, our work highlights the complex web of interactions that impact the origin and persistence of distinct species.

  PublisherOA PDFDOI

• Swordtail fish hybrids reveal that genome evolution is surprisingly predictable after initial hybridization

  PLoS Biology · 2024-08-26 · 20 citations

  articleOpen accessCorresponding

  Over the past 2 decades, biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common-not just in particular lineages but in taxonomic groups across the tree of life. As a result, the genomes of many modern species harbor regions inherited from related species. This observation has raised fundamental questions about the degree to which the genomic outcomes of hybridization are repeatable and the degree to which natural selection drives such repeatability. However, a lack of appropriate systems to answer these questions has limited empirical progress in this area. Here, we leverage independently formed hybrid populations between the swordtail fish Xiphophorus birchmanni and X. cortezi to address this fundamental question. We find that local ancestry in one hybrid population is remarkably predictive of local ancestry in another, demographically independent hybrid population. Applying newly developed methods, we can attribute much of this repeatability to strong selection in the earliest generations after initial hybridization. We complement these analyses with time-series data that demonstrates that ancestry at regions under selection has remained stable over the past approximately 40 generations of evolution. Finally, we compare our results to the well-studied X. birchmanni × X. malinche hybrid populations and conclude that deeper evolutionary divergence has resulted in stronger selection and higher repeatability in patterns of local ancestry in hybrids between X. birchmanni and X. cortezi.

  PublisherDOI

• On the brink of explosion? Identifying the source and potential spread of introduced Zosterops white-eyes in North America

  Biological Invasions · 2024-03-02 · 5 citations

  articleOpen access
  PublisherOA PDFDOI

• Structural genomic variation and behavioral interactions underpin a balanced sexual mimicry polymorphism

  Current Biology · 2024-09-25 · 14 citations

  articleOpen access

  How phenotypic diversity originates and persists within populations are classic puzzles in evolutionary biology. While balanced polymorphisms segregate within many species, it remains rare for both the genetic basis and the selective forces to be known, leading to an incomplete understanding of many classes of traits under balancing selection. Here, we uncover the genetic architecture of a balanced sexual mimicry polymorphism and identify behavioral mechanisms that may be involved in its maintenance in the swordtail fish Xiphophorus birchmanni. We find that ∼40% of X. birchmanni males develop a "false gravid spot," a melanic pigmentation pattern that mimics the "pregnancy spot" associated with sexual maturity in female live-bearing fish. Using genome-wide association mapping, we detect a single intergenic region associated with variation in the false gravid spot phenotype, which is upstream of kitlga, a melanophore patterning gene. By performing long-read sequencing within and across populations, we identify complex structural rearrangements between alternate alleles at this locus. The false gravid spot haplotype drives increased allele-specific expression of kitlga, which provides a mechanistic explanation for the increased melanophore abundance that causes the spot. By studying social interactions in the laboratory and in nature, we find that males with the false gravid spot experience less aggression; however, they also receive increased attention from other males and are disdained by females. These behavioral interactions may contribute to the maintenance of this phenotypic polymorphism in natural populations. We speculate that structural variants affecting gene regulation may be an underappreciated driver of balanced polymorphisms across diverse species.

  PublisherDOI

• Complex structural variation and behavioral interactions underpin a balanced sexual mimicry polymorphism

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-05-14 · 2 citations

  preprintOpen access

  Summary How phenotypic diversity originates and persists within populations are classic puzzles in evolutionary biology. While polymorphisms hypothesized to be under balancing selection segregate within many species, it remains rare for the genetic basis and the selective forces to both be known for the same trait, leading to an incomplete understanding of many classes of polymorphisms. Here, we uncover the genetic architecture of a balanced sexual mimicry polymorphism and identify behavioral mechanisms that may be involved in its maintenance in the swordtail fish Xiphophorus birchmanni . We find that ∼40% of X. birchmanni males develop a “false gravid spot”, a melanic pigmentation pattern that mimics the “pregnancy spot” associated with sexual maturity in female live-bearing fish. Using genome-wide association mapping, we detect a single intergenic region associated with variation in the false gravid spot, which is upstream of kitlga , a gene involved in melanophore patterning. By performing long-read sequencing within and across populations, we identify complex structural rearrangements between alternate alleles at this locus. The false gravid spot haplotype drives increased allele-specific expression of kitlga , which provides a mechanistic explanation for the increased melanophore abundance that causes the spot. By studying social interactions in the laboratory and in nature, we find that males with the false gravid spot experience less aggression; however, they also receive increased attention from other males and are disdained by females. These behavioral interactions may play a role in maintaining this phenotypic polymorphism in natural populations. We speculate that structural variants affecting gene regulation may be an underappreciated driver of balanced polymorphisms across diverse species.

  PublisherOA PDFDOI

• AvianLexiconAtlas: A database of descriptive categories of English-language bird names around the world

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-09-16 · 1 citations

  preprintOpen access

  Abstract Common names of species are important for communicating with the general public. In principle, these names should provide an accessible way to engage with and identify species. The common names of species have historically been labile without standard guidelines, even within a language. Currently, there is no systematic assessment of how often common names communicate identifiable and biologically relevant characteristics about species. This is a salient issue in ornithology, where common names are used more often than scientific names for species of birds in written and spoken English, even by professional researchers. To gain a better understanding of the types of terminology used in the English-language common names of bird species, a group of 85 professional ornithologists and non-professional contributors classified unique descriptors in the common names of all recognized species of birds. In the AvianLexiconAtlas database produced by this work, each species’ common name is assigned to one of ten categories associated with aspects of avian biology, ecology, or human culture. Across 10,906 species of birds, 89% have names describing the biology of the species, while the remaining 11% of species have names derived from human cultural references, human names, or local non-English languages. Species with common names based on features of avian biology are more likely to be related to each other or be from the same geographic region. The crowdsourced data collection also revealed that many common names contain specialized or historic terminology unknown to many of the data collectors, and we include these terms in a glossary and gazetteer alongside the dataset. The AvianLexiconAtlas can be used as a quantitative resource to assess the state of terminology in English-language common names of birds. Future research using the database can shed light on historical approaches to nomenclature and how people engage with species through their names.

  PublisherOA PDFDOI

• Community-sourced sightings of atypical birds can be used to understand the evolution of plumage color and pattern

  The Auk · 2023-06-16 · 10 citations

  articleOpen access1st authorCorresponding

  Abstract Birds are known for their brilliant colors and extraordinary patterns. Sightings of individuals with atypical plumage often cause considerable excitement in the birding public, but receive little attention beyond reporting one-off sightings by the scientific community. In this Perspective, we argue that sightings of individuals with atypical plumage submitted to community science platforms hold the potential to further our understanding of the evolution of plumage color and patterning in birds. As a demonstration, we outline two examples using sightings of leucistic individuals—those that lack melanin across the body or in certain feather patches. First, we discuss the potential for understanding carotenoid pigmentation with these sightings. Leucism influences melanins, but not carotenoids, and so the extent and distribution of carotenoids across the body are unmasked. In a leucistic individual, carotenoids may or may not be more extensive than what is typically visible and this could help to understand the energetic costs and constraints involved in obtaining, processing, and depositing carotenoids in different species. Second, we discuss how partial leucism could provide insights into plumage pattern evolution. We demonstrate that one can use the many observations present on community science platforms to identify repeated patterns in different partially leucistic individuals of the same species, and match these to patches present in related species. These patterns could be the result of shared underlying genetic variation that controls plumage patterning in birds over long evolutionary timescales. With these examples, we outline a few potential lines of inquiry possible with atypical sightings submitted to community science platforms and note that other plumage aberrations provide additional opportunities. We encourage researchers to take full advantage of these chance sightings when they occur and database managers to make it possible to more easily tag photos of individuals with atypical plumage or other traits.

  PublisherOA PDFDOI

Frequent coauthors

• Molly Schumer

  Stanford University

  37 shared

• Daniel L. Powell

  Stanford University

  31 shared

• Quinn K. Langdon

  Gladstone Institutes

  24 shared

• Manfred Schartl

  Texas State University

  17 shared

• Alexandra Donny

  Centro de Investigaciones Cientifícas de las Huastecas 'Aguazarca'

  16 shared

• Tristram O. Dodge

  Centro de Investigaciones Cientifícas de las Huastecas 'Aguazarca'

  16 shared

• Theresa R. Gunn

  Stanford University

  16 shared

• Shreya M. Banerjee

  Stanford University

  14 shared

Labs

• Aguillon LabPI

Education

• PhD, Ecology and Evolutionary Biology

  Cornell University

  2021

• Master of Science, Ecology and Evolutionary Biology

  University of Arizona

  2014

• Bachelor of Science, Ecology and Evolutionary Biology

  University of Arizona

  2013