About

Our lab aims to understand evolutionary processes at the molecular level. We are particularly focused on studies that link genetic mechanisms to evolution in natural populations. Current research in our lab explores the genetic basis of adaptation, mechanisms of genome evolution, and consequences of hybridization.

Research topics

• Evolutionary biology
• Biology
• Genetics
• Fishery
• Zoology

Selected publications

• Tables S1-10 and Figures S1-12 from Sensitivity of genome-wide tests for mitonuclear genetic incompatibilities

  Open MIND · 2026-01-01

  article

  Descriptive tables of gene lists, population summary statistics, statistical tests, and more. Additionally, Supplementary figures for placement of incompatibility genes in CALL, CHAF, and HUEX-STAC distributions and a permutation test for HUEX-STAC.

  DOI

• Sensitivity of genome-wide tests for mitonuclear genetic incompatibilities

  Philosophical Transactions of the Royal Society B Biological Sciences · 2026-04-02

  articleOpen access

  Mismatches between interacting mitochondrial and nuclear gene products in hybrids have been proposed to disproportionately contribute to early species boundaries. Under this model, genetic incompatibilities emerge when mitochondrial haplotypes are in a cellular context without their coevolved nuclear-encoded mitochondrial (n-mt) proteins. Some case studies have shown that such disruptions in mitonuclear coevolution can contribute to reproductive isolation, but whether mitonuclear incompatibilities generate selection that impacts multiple n-mt loci and/or causes broad, genome-wide contributions to speciation is unclear. Here, we leverage a system with several hybridizing species pairs (Xiphophorus fishes) that have known mitonuclear incompatibilities of large effect. We divided nuclear-encoded genes into three classes based on level of interaction with mitochondrial gene products. We found only inconsistent statistical support for a difference between these classes in the degree of positive covariation in mitonuclear ancestry. We discuss evidence that these analyses are sensitive to the amount of non-synonymous divergence between parent species in interacting n-mt genes or the age of the hybridization event. Overall, our results imply that genome-wide scans focused on enrichment of broad functional gene classes may often be insufficient for detecting a history of mitonuclear coevolution, even when strong selection is acting on mitonuclear incompatibilities at multiple loci. This article is part of the theme issue 'Evolutionary genetics of mitochondria: on diverse and common evolutionary constraints across eukarya'.

  PublisherDOI

• Recent evolution of large offspring size and post-fertilization nutrient provisioning in swordtails

  Proceedings of the Royal Society B Biological Sciences · 2026-02-11

  articleOpen accessSenior author

  Organisms have evolved diverse reproductive strategies that impact the probability that their offspring survive to adulthood. Using morphological measurements in embryos and fry, gene expression analysis and hybrid crosses, we describe divergence in reproductive strategy between two closely related species of swordtail fish (Xiphophorus), which have internal fertilization and give birth to free-swimming fry. We find that one species, Xiphophorus malinche, has evolved larger offspring than its closest relative Xiphophorus birchmanni and dwarfs the offspring size of other species in the genus. The fry of X. malinche are more resilient to starvation than X. birchmanni, hinting that the evolution of large offspring size could be an adaptation to the challenging environments in which X. malinche are born. We also find evidence that X. malinche mothers provision nutrients to their offspring during embryonic development, the first time this process has been documented in the Xiphophorus genus. Moreover, in the ovary, we observe differential regulation of genes associated with maternal nutrient provisioning in other groups that use this reproductive strategy. Finally, we generated hybrid crosses between X. malinche and X. birchmanni to explore the impact of genetics and maternal environment on offspring size, finding that offspring size is at least in part genetically determined. Intriguingly, we find a low rate of survival in one cross direction and investigate the links between reproductive strategy and this asymmetric hybrid incompatibility.

  PublisherDOI

• Tables S1-10 and Figures S1-12 from Sensitivity of genome-wide tests for mitonuclear genetic incompatibilities

  Figshare · 2026-01-01

  articleOpen access

  Descriptive tables of gene lists, population summary statistics, statistical tests, and more. Additionally, Supplementary figures for placement of incompatibility genes in CALL, CHAF, and HUEX-STAC distributions and a permutation test for HUEX-STAC.

  PublisherDOI

• Insertion of an invading retrovirus regulates a novel color trait in swordtail fish

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

  preprintOpen accessSenior author

  Abstract For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable within and between species and can serve as an important window into the mechanisms of adaptation. Here, we map the genetic basis of a newly described iridescence trait in swordtail fish to a single locus. Individuals with this trait appear to sparkle as they move through the water. We find that the trait is driven by the recent endogenization of a retrovirus that inserted near the gene alkal2a . This insertion is associated with changes in the chromatin landscape, upregulation of alkal2a , and accumulation of iridescent cells that adhere to the scales. Rather than causing diseases, our results demonstrate that invading endogenous retroviruses can also regulate novel trait variation in the host. Moreover, we find that this coloration trait may act as an important signal in interactions between fish and their predators in the natural environment.

  PublisherDOI

• Increased rates of hybridization in swordtails are associated with water pollution

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-26 · 4 citations

  preprintOpen accessCorresponding

  Summary The nature of reproductive barriers that separate species is a fundamental question in evolutionary biology. Such barriers may be sensitive to environmental conditions, and recent research has documented an increasing number of cases where anthropogenic environmental disturbance is associated with new hybrid populations. However, few studies have been able to quantitatively compare potential environmental drivers and test possible mechanisms connecting interspecific hybridization to anthropogenic disturbance. Here, we combine genomic and chemical surveys to explore the loss of reproductive isolation between the sister species Xiphophorus malinche and X. birchmanni , fishes whose riverine habitat in the Sierra Madre Oriental of Mexico is increasingly impacted by human-mediated disturbance. By inferring genome-wide ancestry in thousands of fish, we characterize the landscape of hybridization between these species in four distinct streams. Ancestry structure varied dramatically across streams, ranging from stable coexistence to clinal hybrid zones, hinting that the dynamics of hybridization in this system may be environmentally dependent. In one stream, a sudden shift in hybridization patterns coincides with the stream’s passage through an urbanized area, with upstream sites showing distinct ancestry clusters and downstream sites showing a swarm of hybrids with variable ancestry. By sequencing mothers and embryos, we show that assortative mating by ancestry is weakened downstream of this urbanized area. We hypothesize that the hybrid swarm downstream of the town is driven by chemical disruption of olfaction that impacts mating preferences. Water chemistry measurements show that water quality changes significantly across this area, including in parameters known to disrupt fish olfaction and mating. We identify alterations of the olfactory epithelium between sites upstream and downstream of the urbanized area that are consistent with differential effects of water quality. Taken together, our work illuminates potential mechanisms linking anthropogenic disturbance to the breakdown of reproductive isolation in these hybridizing species.

  PublisherOA PDFDOI

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

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

  articleOpen accessSenior 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

• Data for Sensitivity of genome-wide tests for mitonuclear genetic incompatibilities Manuscript

  Figshare · 2025-01-01

  otherOpen access

  This repository contains the data from the manuscript titled "Sensitivity of genome-wide tests for mitonuclear genetic incompatibilities", submitted June 2024. <br> It includes the ancestry informative markers (AIMs) for fish from the CALL, CHAF, and HUEX-STAC populations investigated in this manuscript. LD values and allele frequencies for the applicable populations are also uploaded here. Informational tables may also be found here. <br> Code used to analyze these datasets for the manuscript can be found on Shady Kuster's github: https://github.com/sakuster/sensitivity-of-genome-wide-mtnuc

  PublisherDOI

• The molecular evolutionary basis of species formation revisited

  2025-04-09 · 4 citations

  preprintOpen accessSenior author

  How do new species arise? This is among the most fundamental questions in evolutionary biology. The first genetic model for how reproductive barriers leads to the origin of new species was proposed nearly 90 years ago. However, empirical evidence for the genetic mechanisms that cause reproductive barriers took many decades to accumulate. In 2010, Presgraves presented a comprehensive review of the literature on known “speciation genes” and the possible evolutionary mechanisms through which they arose. Fifteen years later, with an explosion of studies that include both non-model and model organisms, the number of known incompatibility genes has increased ~7 fold. Here, we synthesize previous and new empirical examples to investigate the genetic mechanisms through which intrinsic incompatibilities arise and highlight current gaps in our understanding.

  PublisherOA PDFDOI

• Non-synonymous Substitution Data

  Figshare · 2025-01-01

  datasetOpen access

  The aim of this analysis was to identify whether gene classes' (interacting n-mts, non-interacting n-mts, and non-n-mts) mitonuclear linkage disequilibrium metrics were mitigated by the number of non-synonymous substitutions in a gene. In other words, we wanted to know whether the relationship between gene class and mitonuclear LD differed in genes with more non-synonymous substitutions. Substitution data was provided by Molly Schumer and used to identify whether an AIM represented a non-synonymous or synonymous, species-specific variant. Of all the substitutions identified between hybridizing Xiphophorus species, substitutions included in this analysis must still be an AIM (or be able to be used for identifying species-specific ancestry in a hybrid swordtail fish). Xbirchmanni10xgenome_addmito_ancestry_informative_sites_filterF1 is the substitution data used for CALL and CHAF hybrids. xbir_xcor_10x_genomes_identify_pairwise_dxy was used for HUEX-STAC hybrids. All other files here are outputs of the analysis (either files that have AIMs' substitution identifications and relevant info or files that show statistical testing outputs). <br>'goodDat' files have information for each AIM<br>'quantDat' files have only relevant information from goodDat with the addition of mitonuclear LD values<br>'summary-stat' files have summary statistics for each grouping variable for each population'ANOVA-III' files are the type III ANOVA results for all mitonuclear LD stats for that population<br>'summary' files are the output of the summary() command in R comparing the non-n-mt class to each of the n-mt classes to identify differences in slopes for each level of the gene class variable in the model<br><br>please see the 09_dNAnalysis in the GitHub repo for scripts used to generate and make use of these files: https://github.com/sakuster/sensitivity-of-genome-wide-mtnuc/tree/main/09_dNAnalysis

  PublisherDOI

Recent grants

• The population genomics of hybridization: from genetic incompatibilities to genome evolution

  NIH · $2.9M · 2019–2029

Frequent coauthors

• Daniel L. Powell

  Stanford University

  193 shared

• Gil G. Rosenthal

  University of Padua

  111 shared

• Shreya M. Banerjee

  Stanford University

  91 shared

• Cheyenne Payne

  Stanford University

  84 shared

• Manfred Schartl

  Texas State University

  69 shared

• Quinn K. Langdon

  Gladstone Institutes

  62 shared

• Theresa R. Gunn

  Stanford University

  61 shared

• Rongfeng Cui

  Sun Yat-sen University

  55 shared

Labs

• Schumer labPI

Education

• PhD

  Princeton University

  2016

Awards & honors

• Junior Fellow, Harvard Society of Fellows
• Hanna H. Gray Fellow at Harvard Medical School