About

Michael Barker is an Associate Professor and the Director of the Bioinformatics Degree Program at the University of Arizona, where he has been a faculty member since 2011 and an associate professor since 2018. His research interests focus on the origins of biological diversity, particularly how abrupt genomic events such as polyploidy, chromosomal change, and hybridization have contributed to the evolution and diversity of life. Barker's research program integrates computational and evolutionary genomic tools with traditional approaches like molecular evolution, population genetics, phylogenetics, and experimental work to understand how changes in genome organization impact biological diversity. His lab utilizes publicly available genomic data and generates new data through collaborations, studying systems including crops in the genus Brassica, local resurrection lycophytes in Selaginella, and macroevolutionary analyses across eukaryotes. Barker aims to connect patterns of genome evolution across different time scales by studying microevolutionary processes to inform macroevolutionary patterns. His contributions include advancing understanding of genome duplications, polyploidy, and their roles in plant and eukaryotic evolution.

Research topics

• Evolutionary biology
• Genetics
• Biology
• Botany
• Ecology

Selected publications

• The Genomic Legacy of Ancient Polyploidy in Crop Domestication

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-11

  articleOpen accessSenior author

  Abstract Species that have an ancestry of whole-genome duplications (WGDs) are more likely to be domesticated, but the underlying mechanisms remain unclear. We tested whether paleologs—genes duplicated during ancient WGDs—are enriched in candidate domestication lists across 22 crop species spanning 17 genera. Paleologs were significantly enriched in 14 species, with single-copy paleologs showing the most consistent overrepresentation. In contrast, genes from small-scale duplications were consistently underrepresented among domestication candidates. This enrichment was independent of WGD age and degree of gene loss, indicating that constraint on copy number does not preclude selection on gene function. Several non-mutually exclusive processes could explain this pattern, including accumulated genetic diversity becoming available upon return to single-copy, selection to maintain essential functions, and greater selection efficiency on unmasked loci. Ancient WGDs thus provide a persistent genomic substrate for crop evolution millions of years later.

  PublisherOA PDFDOI

• Phylogenomic synteny reveals paleohexaploid-derived genomic blocks across Asteraceae

  Proceedings of the National Academy of Sciences · 2026-02-10

  articleOpen access

  The Asteraceae (Compositae) is the largest flowering plant family, ubiquitous in most terrestrial communities, and morphologically diverse. A two-step, ancient whole genome triplication (paleohexaploidization) occurred at approximately the same time as the evolutionary innovation and adaptive radiation of the family during the middle Eocene. Despite its importance, the consequences of this triplication have yet to be tracked in context of the Asteraceae genome evolution. To do so, we applied a synteny oriented phylogenomic analysis of 23 Asterales genomes. We identified 16 genomic groups that date back to the common diploid ancestor of all Asteraceae. Each group underwent triplication, resulting in 48 genomic blocks (16 × 3) that collectively represent the ancestral Asteraceae genome, excluding the early-diverging lineages which do not share the second step. We then analyzed the evolutionary dynamics of the 48 genomic blocks across the Asteraceae phylogeny. We found that modern Asteraceae genomes are genetic mosaics of three progenitor genomes, shaped by genomic exchanges, chromosomal rearrangements, and gene fractionation. One hundred fifty-seven genes retained three paleohexaploid-derived syntenic paralogs across most Asteraceae species. Transcription factors and auxin-related genes are significantly overrepresented in these triplets, and expression of the paleohexaploidy paralogs is spatiotemporally differentiated. These genes are involved in the development of floral capitula, a remarkable morphological innovation of the family. The discovery of the 157 triplicated genes can direct further study to understand the evolutionary innovation, and the synteny-phylogenomic framework provides a comparative framework to characterize newly sequenced Asteraceae genomes.

  PublisherOA PDFDOI

• Phylogenomic synteny analysis tracks conserved ancient polyploid-derived triplicated genomic blocks across Asteraceae genomes

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-11 · 3 citations

  preprintOpen access

  Abstract The Asteraceae (Compositae) is the largest flowering plant family, ubiquitous in most terrestrial communities, and morphologically hyper-diverse. An ancient whole genome triplication (paleo-hexaploidization) occurred at approximately the same time as the evolutionary innovation and adaptive radiation of the family during the middle Eocene. Despite its importance, the genomic contents arising from this triplication have yet to be tracked in context of the Asteraceae genome evolution. We applied a synteny oriented phylogenomic analysis of 21 Asterales genomes and to study the paleo-hexaploidization and its consequences to gene, trait, and genome evolution. We identified 15 ancestral linkage groups (ALGs) that date back to the common diploid ancestor of all Asteraceae. Each of these groups was triplicated, resulting in 45 genomic blocks (3×15), which serve as the foundation for cross-family analyses. We demonstrate the complex evolutionary dynamics of the 45 genomic blocks across the Asteraceae phylogeny. We found that modern genomes are genetic mosaics of three progenitor genomes by extensive genomic exchange, chromosomal shuffling and gene fractionation. 157 genes retained three paleo-hexaploid derived syntenic paralogs across most Asteraceae species. Transcription factors (TFs) and auxin-related genes are significantly overrepresented in the conserved triplets, and expression of the paleo-hexaploidy paralogs is spatiotemporally differentiated. These genes are involved in the development of floral capitulum, a remarkable morphological innovation of the family. The discovery of conserved triplicated genes can direct further study to understand the evolutionary innovation, and the synteny-phylogenomic framework and ALGs provide a comparative framework to characterize newly sequenced Asteraceae genomes.

  PublisherDOI

• The Role of Meiotic Drive in Chromosome Number Disparity Between Heterosporous and Homosporous Plants

  Molecular Ecology · 2025-04-07 · 3 citations

  articleOpen accessSenior author

  In vascular plants, heterosporous lineages typically have fewer chromosomes than homosporous lineages. The underlying mechanism causing this disparity has been debated for over half a century. Although reproductive mode has been identified as critical to these patterns, the symmetry of meiosis during sporogenesis has been overlooked as a potential cause of the difference in chromosome numbers. In most heterosporous plants, meiosis during megasporogenesis is asymmetric, meaning one of the four meiotic products survives to become the egg. Comparatively, meiosis is symmetric in homosporous megasporogenesis and all meiotic products survive. The symmetry of meiosis is important because asymmetric meiosis enables meiotic drive and associated genomic changes, while symmetric meiosis cannot lead to meiotic drive. Meiotic drive is a deviation from Mendelian inheritance where genetic elements are preferentially inherited by the surviving egg cell, and can profoundly impact chromosome (and genome) size, structure, and number. Here we review how meiotic drive impacts chromosome number evolution in heterosporous plants, how the lack of meiotic drive in homosporous plants impacts their genomes, and explore future approaches to understand the role of meiotic drive on chromosome number across land plants.

  PublisherOA PDFDOI

• Bistable Mutation-Selection Equilibria and Violations of Fisher’s Theorem in Tetraploids: Insights from Nonlinear Dynamics

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-01

  preprintOpen access

  Polyploidy and whole genome duplication (WGD) are widespread biological phenomena with substantial cellular, meiotic, and genetic effects. Despite their prevalence and significance across the tree of life, population genetics theory for polyploids is not well developed. The lack of theoretical models limits our understanding of polyploid evolution and restricts our ability to harness polyploidy for crop improvement amidst increasing environmental stress. To address this gap, we developed and analyzed deterministic models of mutation-selection balance for tetraploids under polysomic (autotetraploid) and disomic (allotetraploid) inheritance patterns and arbitrary dominance relationships. We also introduced a new mathematical framework based on ordinary differential equations and nonlinear dynamics for analyzing the models. We find that autotetraploids approach Hardy-Weinberg Equilibrium 33% faster than allotetraploids, but the different tetraploid inheritance models show little differences in mutation load and allele frequency at mutation-selection balance. Our model also reveals two bistable points of mutation-selection balance for dominant alleles with biased mutation rates over a wide range of selection coefficients in the tetraploid models compared to bistability in only a narrow range for diploids. Finally, using discrete time simulations, we explore the temporal dynamics of allele frequency and fitness change and compare these dynamics to the predictions of Fisher's Fundamental Theorem of Natural Selection. While Fisher's predictions generally hold, we show that the bistable dynamics for dominant mutations fundamentally alter the associated temporal dynamics. Overall, this work develops foundational theoretical models that will facilitate the development of population genetic models and methodologies to study evolution in empirical tetraploid populations.

  PublisherOA PDFDOI

• Doubling down on polyploid discoveries: Global advances in genomics and ecological impacts of polyploidy

  American Journal of Botany · 2024-08-01 · 7 citations

  articleOpen access1st authorCorresponding

  All flowering plants are now recognized as diploidized paleopolyploids (Jiao et al., 2011; One Thousand Plant Transcriptomes Initiative, 2019), and polyploid species comprise approximately 30% of contemporary plant species (Wood et al., 2009; Barker et al., 2016a). A major implication of these discoveries is that, to appreciate the evolution of plant diversity, we need to understand the fundamental biology of polyploids and diploidization. This need is broadly recognized by our community as there is a continued, growing interest in polyploidy as a research topic. Over the past 25 years, the sequencing and analysis of plant genomes has revolutionized our understanding of the importance of polyploid speciation to the evolution of land plants.

  PublisherOA PDFDOI

• Species‐tree topology impacts the inference of ancient whole‐genome duplications across the angiosperm phylogeny

  American Journal of Botany · 2024-07-22 · 14 citations

  articleOpen accessSenior author

  PREMISE: The history of angiosperms is marked by repeated rounds of ancient whole-genome duplications (WGDs). Here we used state-of-the-art methods to provide an up-to-date view of the distribution of WGDs in the history of angiosperms that considers both uncertainty introduced by different WGD inference methods and different underlying species-tree hypotheses. METHODS: ) of paralogs and orthologs from transcriptomic and genomic data to infer and place WGDs across two hypothesized angiosperm phylogenies. We further tested these WGD hypotheses with syntenic inferences and Bayesian models of duplicate gene gain and loss. RESULTS: -based methods often yield alternative hypothesized WGD placements due to variation in substitution rates among lineages. Phylogenetic models of duplicate gene gain and loss are more robust to topological variation. However, errors in species-tree inference can still produce spurious WGD hypotheses, regardless of method used. CONCLUSIONS: Here we showed that different WGD inference methods largely agree on an average of 3.5 WGD in the history of individual angiosperm species. However, the precise placement of WGDs on the phylogeny is subject to the WGD inference method and tree topology. As researchers continue to test hypotheses regarding the impacts ancient WGDs have on angiosperm evolution, it is important to consider the uncertainty of the phylogeny as well as WGD inference methods.

  PublisherOA PDFDOI

• Chromosome-scale Reference Genome and RAD-based Genetic Map of Yellow Starthistle ( <i>Centaurea solstitialis</i> ) Reveal Putative Structural Variation and QTL Associated With Invader Traits

  Genome Biology and Evolution · 2024-11-25 · 2 citations

  articleOpen access

  Invasive species offer outstanding opportunities to identify the genomic sources of variation that contribute to rapid adaptation, as well as the genetic mechanisms facilitating invasions. The Eurasian plant yellow starthistle (Centaurea solstitialis) is highly invasive in North and South American grasslands and known to have evolved increased growth and reproduction during invasion. Here, we develop new genomic resources for C. solstitialis and map the genetic basis of invasiveness traits. We present a chromosome-scale (1N = 8) reference genome using PacBio CLR and Dovetail Omni-C technologies, and functional gene annotation using RNAseq. We find repeat structure typical of the family Asteraceae, with over 25% of gene content derived from ancestral whole-genome duplications (paleologs). Using an F2 mapping population derived from a cross between native and invading parents, with a restriction site-associated DNA (RAD)-based genetic map, we validate the assembly and identify 13 quantitative trait loci underpinning size traits that have evolved during invasion. We find evidence that large effects of quantitative trait loci may be associated with structural variants between native and invading genotypes, including a variant with an overdominant and pleiotropic effect on key invader traits. We also find evidence of significant paleolog enrichment under two quantitative trait loci. Our results add to growing evidence of the importance of structural variants in evolution, and to understanding of the rapid evolution of invaders.

  PublisherDOI

• Ancient polyploidy and low rate of chromosome loss explain the high chromosome numbers of homosporous ferns

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-09-25 · 4 citations

  preprintOpen accessSenior author

  Abstract A longstanding question in plant evolution is why ferns have many more chromosomes than angiosperms. The leading hypothesis proposes that ferns have ancient polyploidy without chromosome loss or gene deletion to explain the high chromosome numbers of ferns. Here, we test this hypothesis by estimating ancient polyploidy frequency, chromosome evolution, protein evolution in meiosis genes, and patterns of gene retention in ferns. We found similar rates of paleopolyploidy in ferns and angiosperms from independent phylogenomic and chromosome number evolution analyses, but lower rates of chromosome loss in ferns. We found elevated evolutionary rates in meiosis genes in angiosperms, but not in ferns. Finally, we found some evidence of parallel and biased gene retention in ferns, but this was comparatively weak to patterns in angiosperms. This work provides genomic evidence supporting a decades-old hypothesis on fern genome evolution and provides a foundation for future work on plant genome structure.

  PublisherDOI

• A de novo long-read genome assembly of the sacred datura plant (Datura wrightii) reveals a role of tandem gene duplications in the evolution of herbivore-defense response

  BMC Genomics · 2024-01-02 · 7 citations

  articleOpen access

  The sacred datura plant (Solanales: Solanaceae: Datura wrightii) has been used to study plant-herbivore interactions for decades. The wealth of information that has resulted leads it to have potential as a model system for studying the ecological and evolutionary genomics of these interactions. We present a de novo Datura wrightii genome assembled using PacBio HiFi long-reads. Our assembly is highly complete and contiguous (N50 = 179Mb, BUSCO Complete = 97.6%). We successfully detected a previously documented ancient whole genome duplication using our assembly and have classified the gene duplication history that generated its coding sequence content. We use it as the basis for a genome-guided differential expression analysis to identify the induced responses of this plant to one of its specialized herbivores (Coleoptera: Chrysomelidae: Lema daturaphila). We find over 3000 differentially expressed genes associated with herbivory and that elevated expression levels of over 200 genes last for several days. We also combined our analyses to determine the role that different gene duplication categories have played in the evolution of Datura-herbivore interactions. We find that tandem duplications have expanded multiple functional groups of herbivore responsive genes with defensive functions, including UGT-glycosyltranserases, oxidoreductase enzymes, and peptidase inhibitors. Overall, our results expand our knowledge of herbivore-induced plant transcriptional responses and the evolutionary history of the underlying herbivore-response genes.

  PublisherOA PDFDOI

Recent grants

• EAGER-NEON: Genomic Plasticity in Response to Variable Environments

  NSF · $300k · 2016–2019

Frequent coauthors

• Loren H. Rieseberg

  University of British Columbia

  45 shared

• Pamela S. Soltis

  Florida Museum of Natural History

  21 shared

• Katrina M. Dlugosch

  University of Arizona

  21 shared

• Michael T. W. McKibben

  University of Arizona

  17 shared

• Gane Ka‐Shu Wong

  University of Alberta

  16 shared

• Hannah E. Marx

  University of New Mexico

  14 shared

• Nolan C. Kane

  University of Colorado Boulder

  14 shared

• J. Chris Pires

  14 shared

Awards & honors

• Emerging Leader Award, Botanical Society of America (2016)
• Young International Scientist Fellow, Chinese Academy of Sci…
• NSERC-BRITE Biodiversity Postdoctoral Fellow, The Biodiversi…
• Margaret Menzel Award, Genetics Section, Botanical Society o…
• Edgar T. Wherry Award, Pteridological Section, Botanical Soc…