Projects

Graduate Research


Recombination in the C. reinhardtii MT locus and consequences for selection efficacy
Recombination in the C. reinhardtii MT locus and consequences for selection efficacy

‘Sex’ in C. reinhardtii is determined by a dimorphic, crossover-suppressed mating type locus, which encodes an individual as either MT+ or MT-. C. reinhardtii is isogamous (equal sized gametes) which means there are no sex differences; hence the term ‘mating type’. The two alleles of the MT locus can be thought of as ‘X and Y chromosomes’, except that each individual only carries one and that the alleles are genetically very similar.

Unexpectedly similar, that is. Work has shown that the two MT alleles of C. reinhardtii are hardly differentiated from one another. Meanwhile, its multicellular, anisogamous relative Volvox carteri has shown over 100x more differentiation between its own MT alleles (Ferris 2010). Later work showed evidence for gene conversion, a form of noncrossover recombination, in two C. reinhardtii genes that had copies in both MT alleles, suggesting that genetic exchange was preventing the two alleles from diverging.

For this project, we estimate levels of genetic exchange across the MT locus of C. reinhardtii, and undertake a population genetic analysis to find out whether gene conversion is sufficient to avoid the differentiation and degeneration that is often seen in sex determining loci, asking the questions:

  1. What are the spatial patterns of LD across MT?
  2. Do patterns of polymorphism or divergence between MT alleles reflect the strength of LD?
  3. Do shared and MT-limited regions show evidence for differences in selection efficacy?
  4. Do patterns of inter-chromosomal LD between mating type alleles and organelle genomes suggest leaky uniparental inheritance?
 
Recombination rate variation and infrequent sex influence genetic diversity in C. reinhardtii
Recombination rate variation and infrequent sex influence genetic diversity in C. reinhardtii

Recombination confers a major evolutionary advantage by breaking up linkage disequilibrium (LD) between harmful and beneficial mutations,thereby facilitating selection. However, in species that are only periodically sexual, such as many microbial eukaryotes, the realized rate of recombination is also affected by the frequency of sex, meaning that infrequent sex can increase the effects of selection at linked sites despite high recombination rates. Despite this, the rate of sex of most facultatively sexual species is unknown. In this project, I am using population genomic data from natural populations of C. reinhardtii to examine fine-scale variation in the population recombination rate across the genome. Specifically, I hope to answer the following questions:

  1. What is the landscape of recombination rate variation across the genome of C. reinhardtii?
  2. What genomic features predict recombination rate variation in the genome?
  3. What is the rate of sex in natural populations of C. reinhardtii?
  4. How does recombination rate affect patterns of neutral diversity?
 

Undergraduate Research


Endophytes as biocontrols for the Côte d’Ivoire Lethal Yellowing (CILY) disease
Endophytes as biocontrols for the Côte d’Ivoire Lethal Yellowing (CILY) disease

As part of my undergraduate research work, I attempted to identify endophytic microbes that may potentially be used as biocontrols against the Côte d’Ivoire Lethal Yellowing (CILY) disease, which had previously destroyed approximately 350 ha of coconut trees in the West African country. This was done by creating profiles of the microbial communities present within both infected and uninfected trees. A ‘dilution-to-extinction’ method of high-throughput culturing was used in order to cultivate both bacterial and fungal endophytes directly from samples collected from the town of Grand-Lahou, followed by molecular analyses for strain identification. Our results identified Trichoderma, Penicillium, Bacillus, and Pseudomonas as endophytes present within coconut palms. Several of these endophytes have historically been used as part of microbial biocontrol consortia against other plant pathogens such as Fusarium, and show promise as potential biocontrols to be tested for use against CILY in field studies.

Related publication: Morales-Lizcano et al. (2017) Microbial diversity in leaves, trunk and rhizosphere of coconut palms (Cocos nucifera L.) associated with the coconut lethal yellowing phytoplasma in Grand-Lahou, Côte d’Ivoire. Available online.

Bonus: Here’s a fun and largely jargon-free one-minute video summary of the project that I made.