Population Genetics of Polyploids
The explosion in DNA sequencing technologies has led to impressive insights about various evolutionary phenomenon at the population level, including patterns of introgression, mechanisms of speciation, and the inference of demographic histories. However, many aspects of population genetics rely on the assumption that the species of interest is diploid - that is, it has two sets of chromosomes with strict pairing at meiosis. Polyploids violate these assumptions, which has unknown effects on the predictions of how natural selection operates. Additionally, there are various biological processes that are unique to polyploids (e.g. recombination between homoeologous subgenomes, doubled reduction, and homoeologous gene conversion) that make population genetic inferences especially difficult to make in polyploids.
During my dissertation, I discovered that mutations at phylogenetically well-conserved sites (and, therefore, presumably deleterious) accumulate faster in allopolyploid than diploid cottons. I recently was awarded a NSF Postdoctoral Research Fellowship in Biology (PRFB) to further explore this phenomenon using Brassica crops (turnip, cauliflower, canola) as a model system. As a part of this work, I will explore how the distribution of fitness effects (a fundamental concept in all of population genetics) differs between diploid and polyploid populations and how this distribution changes through the process of diploidization and genome fractionation (i.e. the process by which polyploids return to a diploid-like state).
Paper of Interest (Publications Page):
16. Conover and Wendel, 2022. MBE. Deleterious Mutations Accumulate Faster in Allopolyploid than Diploid Cotton (Gossypium) and Unequally Between Subgenomes. (Image at right from here).
DNA is localized in three different cellular compartments in plant cells - the nucleus, plastids, and mitochondria. The cellular functions of the plastids and mitochondria are highly dependent on co-evolutionary forces between genes encoded in these organelles with genes that are encoded in the nucleus and subsequently transported to the plastids and mitochondria. Upon allopolyploid formation (resulting from interspecific hybridization), both nuclear genomes are inherited, but only one set of genomes in the mitochondria and plastid. This sets up the potential for evolutionary mismatches which the allopolyploid must overcome in order to successfully survive and reproduce.
This work is highly collaborative with the labs of Drs. Dan Sloan at Colorado State University and Joel Sharbrough at the New Mexico Institute of Mining and Technology.
Papers of Interest (Publications Page):
18. Sharbrough and Conover et al., 2022. Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms.
15. Gyorfy et al., 2021. Plant J. Nuclear-Cytoplasmic Balance: Whole Genome Duplications Induce Elevated Organellar Genome Copy Number.
1. Sharbrough, et al., 2017. AJB. Cytonuclear Responses to Genome Doubling. (Image at left from here).
Comparative Genomics and Ancient Polyploidy Events in Malvaceae
One of the most important insights in plant evolution during the genomics era is the ubiquity of ancient whole genome duplication events in the angiosperms. All angiosperms share a polyploidy event that occurred before the first flower evolved, and many taxa have experienced repeated, cyclical episodes of genome duplication followed by genome downsizing and fractionation. The Mallow Family (Malvaceae) has one of the most complicated and unresolved duplication histories in the angiosperms, with some subfamilies having experienced a 5-6X multiplication event. Additionally, identifying orthologs between polyploids and their diploid relatives is a challenging for traditional ortholog detection tools, so I've developed a method (pSONIC) that combines synteny with sequence similarity to identify a high-confidence set of genome-wide orthologs despite any difference in ploidy between the species of interest.
Papers of Interest (Publications Page):
14. Conover et al., 2021, G3. pSONIC: Ploidy-aware Syntenic Orthologous Networks identified via Collinearity.
7. Conover and Karimi et al., 2019, A Malvaceae Mystery: A Mallow Maelstrom of Genome Multiplications and Maybe Misleading Methods?. (Image at left from here).