Research

Whole Genome Duplication

Whole genome duplication is when additional copies of all chromosomes occur. Instead of having 2 copies of each chromosome (like humans), polyploids may have 3 or more copies of each chromosome. Our research mostly focuses on autopolyploidy; this is when the extra set of chromosomes can be inherited from the same individual or two closely related individuals. Alternatively, hybridization can lead to extra sets of chromosomes—this is known as allopolyploidy. The term cytotype refers to a group of organisms that have the same ploidal level.

Polyploidy is known to play an important role in the evolution and diversification of vascular plants. So far, most research has shown that whole genome duplication alone does not lead to a single set of expectations (other than maybe the nucleotypic effect), instead there are dynamic ecological or evolutionary consequences. The search for general patterns or trends associated with polyploidy events still remains – and this is a particularly interesting and fun topic to pursue.

Identifying Polyploids

Identifying ploidal diversity is a crucial first step to understanding the impact of whole genome duplication on patterns of biodiversity. We focus on identifying polyploids both in the present and in the past based on genetic and genomic data. Currently, genomic approaches do not replace flow cytometry and chromosome squashes. If you are interested in learning either, please reach out for a google drive full of material to aid in ploidal estimation via flow cytometry (named `FlowHullabaloo`).

In the present, we use sequence-based ploidal predictions to assign ploidy level to organisms. To address shortcomings of available ploidal level inference methods based on sequence data, we developed the easy-to-use R package nQuack. To hear more about this project, check out the second half of my 2024 Polyploidy Webinar. We are currently developing nQuack-AI, a data based approach to predicting ploidal level based on >10,000 samples from over 70 collaborators.

In the past, we often use gene-divergence methods to identify whole genome duplication events. We have identified that current approaches are reliant on gene-copies and fail to capture allele-copies. Find out more in our 2026 preprint.

Understanding Mixed-Cytotype Coexistence

We are fascinated by the coexistence of multiple cytotypes. Historically, it was believed that a tetraploid had to outcompete its diploid progenitor to persist. The idea was that a tetraploid formed, spread, and caused the diploid to be geographically restricted and rare (Stebbins, 1947, 1971). We now know that closely related polyploids and their diploid progenitors can both remain extant.

Much of our research focuses understanding coexistence of multiple cytotypes both in nature and theory. In theory, coexistence may require reproductive isolation, reproductive assurance, and recurrent formation - however, in nature, we often find mixed-cytotypes lacking reproductive isolation, including our focal species!

Galax urceolata (Diapensiaceae). Herbarium Specimen: FLAS275422.

Much of our population-level work has focused on autopolyploid Galax urceolata (Diapensiaceae), which includes diploid, triploid, and tetraploid cytotypes co-occurring throughout the Southern Appalachians - cytotypes lack reproductive isolation! We also collaborate on other systems, including Larrea tridentata (Zygophyllaceae), and are open to developing projects on other species and systems.

Ecological Consequences: Could ecological differentiation help support cytotype coexistence when gene flow is ongoing? We investigated the cytogeography of G. urceolata in relation to stomatal cell size, soil chemistry, soil fungal and bacterial community composition, and broad-scale climate. We found that cytotypes of G. urceolata have little to no ecological differences that would enable coexistence.

To understand stability of coexisting cytotypes with ongoing gene flow and without ecological niche differentiation, we designed a new matrix population model with demographic and environmental stochasticity. Here, we identified that stable coexistence is very probable among mixed-cytotypes, even when reproductive isolation and ecological niche differentiation are absent. See Gaynor et al. 2025 and our R package, AutoPop. To find out more about this project, check out my 2024 Polyploidy Webinar.

Population Genomics: The genetic consequences of mixed-cytotype populations with ongoing gene flow are mostly unknown. Tools are currently lacking to understand the evolutionary history of mixed-cytotype populations and this has been a focus of our ongoing research!

Ongoing collaborations with Drs. Trevor Faske and Alyssa Phillips have identified limitations of current approaches for quantifying population structure of mixed-cytotypes. To begin to address these limitations and build new approaches, we must first develop frameworks for autotetraploids; in collaboration with Drs. John Wakeley and Justin Conover we are extending coalescence based-approaches to be conditional on the population pedigree.

Ongoing biological studies include the population genomics of Galax urceolata and Larrea tridentata. To hear more about the current work on Galax urceolata, check out my talk at Evolution 2024.

Phylogenetics, Macroevolution, and Beyond

To understand the long-term consequences of whole genome duplication on ecological and community dynamics, phylogenetic-scale analyses are necessary. Along with microevolutionary processes, we are interested in large-scale trends regarding whole-genome duplication.

For example, at a community level, the effects of genome duplication remains unclear. One way to investigate this is with a community phylogenetic approach where we can explore (1) whether polyploid species are more distantly related to diploids within the same community than co-occurring diploids are to one another and (2) whether polyploid species tend to exhibit greater ecological success than diploid species. In Gaynor et al. 2018, we did not find a consistent pattern, suggesting whole genome duplication impact on community structure may not be very black and white.