McEvoy, Susan - Gymnosperm genomics: evolution, diversity and adaptation

Research

A woman wearing a white t-shirt, a blue cap and black gloves stainding in front of a tree in a forest on a sunny day.Photo: Vidya Vuruputoor

My research group studies genetic diversity and adaptation within conifer species. Genetic diversity is what provides the foundation for adaptation to a changing environment. Compared to many angiosperm plants, gymnosperm species such as conifers are relatively slow growing organisms that can take many years to reproduce. This means a slower rate of adaptation for the many populations now facing a number of challenges that are only expected to increase as climate change progresses. These challenges can be complex; for example, the increasing prevalence of drought stress has led to an increased susceptibility to other stressors such as pests and pathogens, and this trend has been reported in many plant species world-wide. Given the timing, magnitude, and nature of future environmental changes, integrating genetics into our understanding and decision-making regarding forest trees is essential to support resilient forest ecosystems and resources long into the future.

While the genetics of economically important conifer species has been studied for a long time, it is only recently that we have been able to do this more broadly at the molecular level using DNA, RNA, and epigenomic data.  Conifer genomes are vastly larger than many other plant and animal genomes, requiring a lot of data generation, but recent advances in sequencing technologies and bioinformatic algorithms have made conifer genomics more feasible. There are many aspects to genomics that are not yet well understood, even in more tractable model species, regarding the origin, extent, and effect of genomic differences, and the dynamic of this diversity across populations. In addition to delving into differences in genome biology and how they may relate to traits, I am also interested in using comparisons to study evolutionary biology, as understanding evolutionary strategies of the past may help shed light on what to expect from future adaptation. To examine these issues, I apply approaches drawn from comparative genomics and population genetics.

Phylogeny-based comparative genomics

Though conifer species such as Norway spruce and Scots pine are very important to Nordic forests, much can be learned by comparing their genomes to other lineages throughout the gymnosperm clade to better understand the ways different genomic features and phenotypic traits have evolved. There are many features within a genome that can be compared in this way.  For protein-coding genes, we can study the dynamics of similar gene families across species to see if they are expanding or contracting, absent, or unique and novel to a species. Conifer genomes contain extensive intergenic content outside of these protein-coding regions, which contributes to their giant genome size. This includes transposable elements, which are mobile elements that move or copy themselves throughout the genome, sometimes taking parts of genes or regulatory elements with them. Their activity can result in structural variants, which are interesting to compare across genomes, particularly in regard to traits of interest such as disease resistance, as they can be mechanisms of adaptation. The expression of genes and transposable elements is often regulated by DNA modifications and the interaction of other non-protein-coding genes, resulting in complex, interactive networks. Comparisons of these mechanisms from an evolutionary perspective can also lead to very interesting foundational science in the understanding of genome biology and phylogenomics.

Population based metrics

Population genomics provides many methods for assessing genetic diversity that take into consideration evolutionary forces that operate at the population level, such as drift, selection, and gene flow. Rather than focusing on specific genes or other genomic features, variants can be identified across the genome to estimate a wide range of metrics depending on the research question.  One example involves estimating the proportion and effect of deleterious versus beneficial mutations on a species “fitness”, meaning their ability to survive and reproduce. Other approaches include the identification of local adaptation, which is when a population adapts based on natural selection to its local environment, and then examination of strategies of local adaptation across species. One important question going forward is how we can use these metrics in an applied way to help inform resource management policy and planning with regard to conservation.

The overarching goal of these approaches is to build a clearer picture of how genetic complexity contributes to the adaptability and long-term sustainability of forest species in a rapidly changing world.

Key Publications

  • McEvoy, S. L., Grady, P. G. S., Pauloski, N. Wegrzyn, J., (2024). Profiling genome-wide methylation in two maples: fine-scale approaches to detection with nanopore technology. Evolutionary Applications; 17(4) e13669.
  • McEvoy, S. L., Meyer, R. S., Hasenstab-Lehman, K. E., Guilliams, C. M. (2024). The reference genome of an endangered Asteraceae, Deinandra increscens subsp. villosa, endemic to the Central Coast of California. G3; 14(8), jkae117.
  • Vuruputoor, V. S., Monyak, D., Fetter, K. C., Webster, C., Zaman, S., Bhattarai, A., Bennett, J., McEvoy, S. L., Shrestha, B., Caballero, M., & Wegrzyn, J. (2023). Welcome to the big leaves: best practices for improving genome annotation in non-model plant genomes. Applications in Plant Sciences; 11(4), e11533.
  • McEvoy, S. L., Lustenhouwer, N., Melen, M. K., Nguyen, Oanh, Marimutha, M. P. A., Chumchim, N., Beraut, E., Parker, I. M., Meyer, R. S. (2023). Chromosome-level reference genome of stinkwort, Dittrichia graveolens (L.) Greuter: a resource for studies on invasion, range expansion, and evolutionary adaptation under global change. Journal of Heredity; 114(5), esad033.
  • McEvoy, S. L., Sezen, U. U., Trouern-Trend, A., McMahon, S. M., Schaberg, P. G., Yang, J., Wegrzyn, J., & Swenson, N. G. (2021). Strategies of tolerance reflected in two North American maple genomes. The Plant Journal; 109(6), 1591-1613.
  • Caballero, M., Lauer, E., Bennett, J., Zaman, S., McEvoy, S., Acosta, J., Jackson, C., Townsend, L., Eckert, A., Whetten, R.W. and Loopstra, C., Holliday, J., Mandal, M., Wegrzyn, J., & Isik, F. (2021). Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome. Applications in Plant Sciences; 9(6), e11439.
  • Howe, G. T., Jayawickrama, K., Kolpak, S. E., Kling, J., Trappe, M., Hipkins, V., Ye, T., Guida, S. Cronn, R., Cushman, S., & McEvoy, S. (2020). An Axiom SNP genotyping array for Douglas-fir. BMC genomics; 21(9), 1-17.