Joanna Rifkin, EEB Postdoctoral Fellow

Department of Ecology & Evolutionary Biology
University of Toronto
25 Willcocks Street
Toronto, Ontario, Canada
M5S 3B2

Office: Earth Science Building 2047
Twitter: @joanna.rifkin


B. A.                             Biology and Classical Studies, cum laude, with distinction (2009)
                                     Amherst College, Amherst, U.S.A. 

Ph. D.                           University Program in Genetics and Genomics (2017)
                                     Duke University, Durham, U.S.A. 

Current Position

EEB Postdoctoral Fellow, Department of Ecology & Evolutionary Biology, University of Toronto

Project: Comparative genomics of the evolution of sex chromosomes in Rumex

Co-supervised by Spencer C.H. Barrett and Stephen I. Wright

Research Interests

I am interested in the relationships between reproductive behavior, trait evolution, and genome structure in plants. Before coming to the University of Toronto, I investigated how the evolutionary transition from mixed mating to predominant self-pollination affected trait and genome evolution in pitted morning glory (Ipomoea lacunosa) and its sister species tievine (I. cordatotriloba). My current research focuses on two major questions in the evolution of sex chromosomes: 1) the reason for the spread of recombination suppression, and 2) the causes and consequences of Y chromosome degeneration.

To address these questions, I use comparative genomics approaches in the sorrels and docks (genus Rumex). Although most of the approximately 200 species in the genus are hermaphroditic, two lineages have acquired dioecy and sex chromosomes, and one species (heartwing dock, R. hastatulus) exhibits a sex chromosome polymorphism. In this system, therefore, it is possible to compare sex chromosomes of different age. To facilitate these comparisons, I am improving our genomic resources in several ways, including scaffolding the R. hastatulus genome onto linkage maps, generating a new genome assembly for the hermaphroditic species willow dock (R. salicifolius), and collecting sequence data from diverse species across the genus.

Recombination suppression on sex chromosomes is widely believed to result from sexually antagonistic selection pairing sex-specific alleles with sex-determining loci. However, recombination can also be lost in the apparent absence of such selection. To determine whether sexual antagonism is a driving force in recombination suppression and gene position across Rumex sex chromosomes, I identify genes exhibiting genomic signatures of sexually antagonistic selection and compare their position and function both between sex chromosomes and autosomes within dioecious species and across species.

The spread of recombination suppression on heterogametic chromosomes (Y or W) is often stepwise, leading to marked “strata” of recombination suppression. Using this structure, it is possible to compare older and newer strata and determine which elements of the genome are preserved and which are lost in the course of Y chromosome degeneration. For example, pollen- and pollen tube-expressed genes are likely highly conserved even in degenerated regions because of their expression in the haploid phase of the lifecycle; conversely, the suppression and removal of transposable elements is likely to be less efficient.


Ostevik, K. L., Rifkin, J.L., Xia, H. & Rausher, M.D. (2021). Morning glory species co‐occurrence is associated with asymmetrically decreased and cascading reproductive isolation. Evolution Letters 5: 75-85.

Rifkin, J.L., Beaudry, F.E.G., Humphries, Z., Choudhury, B.I., Barrett S.C.H. & Wright, S.I. (2021). Widespread recombination suppression facilitates plant sex chromosome evolution. Molecular Biology and Evolution 38: 1018-1030.

Beaudry, F.E.G., Rifkin, J.L., Barrett, S.C.H. & Wright S.I. (2020). Evolutionary genomics of plant gametophytic selection. Plant Communications 1: 100115.

Rifkin J. L., Liao I. T., Castillo A. C. & M. D. Rausher. (2019). Multiple aspects of the selfing syndrome of the morning glory Ipomoea lacunosa evolved in response to selection: A Qst-Fst comparison. Ecology and Evolution 9: 7712-7725.

Rifkin J. L., Castillo A. C., Liao I. T. & M. D. Rausher. (2019). Gene flow, divergent selection and resistance to introgression in two species of morning glories (Ipomoea). Molecular Ecology 28: 1709–1729. Highlighted in Molecular Ecology Perspectives, David Field:

Rifkin J. L., Nunn C. L. & Garamszegi L.Z. (2012). Do animals living in larger groups experience greater parasitism? A meta-analysis. The American Naturalist180: 70–82.

Temeles, E. J., Miller, J. S. & Rifkin, J. L. (2010). Evolution of sexual dimorphism in bill size and shape of hermit hummingbirds (Phaethornithinae): a role for ecological causation. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences365: 1053–63.