Simon Ho's Honours Research Project Opportunities

Project 1: Rates of molecular evolution in insects

Supervisor: Simon Ho

The molecular clock hypothesis, which was proposed in the early 1960s, states that the rate of molecular evolution is constant among organisms. Although it is now widely known that evolutionary rates show significant variation, the patterns of variation have not been characterised in detail in insects.

Over the past year, large amounts of DNA sequence data from the mitochondrial and nuclear genomes has been produced from insects. The release of this information provides an excellent opportunity for characterising the patterns of rate variation within an extremely important group of animals. Some particularly interesting questions include:

  1. How much rate variation exists among orders of insects?
  2. Do mitochondrial and nuclear genomes show similar patterns of rates?
  3. To what extent does natural selection affect the patterns of rate variation in coding genes compared with non-coding DNA?
  4. Do rates of evolution appear to be higher over short timeframes because natural selection has not yet weeded out the ‘slightly deleterious’ mutations?

In this project, the student will collect DNA sequence data from online databases and published studies. Evolutionary rates will be estimated using current phylogenetic methods. The student will have the opportunity to develop bioinformatic skills and will gain a broad appreciation of statistical and computational techniques in evolutionary biology.

Project 2: Phylogenetic relationships and evolutionary timescale of carnivores: Testing the properties of data supermatrices

Supervisor: Simon Ho

The mammalian order Carnivora includes significant animals such as cats, seals, bears, dogs, and weasels. The phylogenetic relationships among carnivore groups have been examined in a number of recent studies. As a result, DNA sequences are available for all 261 extant species. These data will form the basis for an investigation into some of the properties of large data sets.

With the rapid growth in online databases, researchers have been able to construct huge data sets comprising DNA sequences from large numbers of genes and species. One approach that has been gaining in popularity involves the use of ‘data supermatrices’. The aim of a data supermatrix is to maximise the number of species and/or genes in a data set. This comes at the cost of including incompletely sequenced species, which introduces ‘missing data’ into the analysis. There has been recent debate over the impact of missing data on phylogenetic analysis, but few studies have examined the effects of missing data on estimates of evolutionary timescales.

In this project, the student will assemble a data supermatrix using DNA sequences available on public databases. This data set will be used to examine the impact of missing data on estimation of the phylogeny and timescales of carnivores. The student will have the opportunity to develop bioinformatic skills and will gain a broad appreciation of statistical and computational techniques in evolutionary biology. The results of this research will have wide implications for phylogenetic analyses of large data sets.

Project 3: Understanding the evolutionary history of ribosomal protein gene copy number in plant genomes

Supervisors: Mary Byrne and Simon Ho

In Eukaryotes, the cytoplasmic 80S ribosome is a multimeric complex comprising a large and a small subunit with around 80 distinct ribosomal proteins contributing to these two subunits. In animals, most ribosomal proteins are encoded by single copy genes. In contrast, all ribosomal proteins in Arabidopsis are encoded by small gene families, of two to five genes. Other sequenced plant genomes also appear to have multiple genes for each ribosomal protein. One possible explanation for the presence of multiple genes for each ribosomal protein in plants is that ribosomal protein genes are retained following genome duplication in order to maintain stoichiometric ratios of the ribosomal proteins that make up the multi-protein complex of the ribosome. However, this hypothesis has not been tested. The available Arabidopsis thaliana genome sequence and recent release of the genome sequence of the closely related species Arabidopsis lyrata, allows for comparative analysis of ribosomal protein retention post whole genome duplication in the Arabidopsis lineage.

In this Honours project the student will carry out comparative sequence analysis, and compare amino acid sequence, genome location and rates of sequence divergence for ribosomal protein genes in A. thaliana and A. lyrata. Gene families with divergent members will be further characterized through expression analysis. The student will have the opportunity to use bioinformatics and available genome resources and molecular biology to make further comparison with other closely related species. This project will allow the student to develop skills and expertise in bioinformatics, phylogenetic and gene evolution analysis, and in molecular biology techniques for gene amplification, sequencing and expression studies. The student will have the benefit of developing a broad knowledge and skill base through the complementary expertise provided by members of the Byrne and Ho labs. The student will also have opportunities for advancing their communication skills through regular lab meetings and presentations within the Biological Sciences.