Posted: November 24th, 2014

Statement of Research Interests and Goals for Graduate Admission

Statement of Research Interests and Goals for Graduate Admission

Project description
This statement does not tie you to a specific research project. We use it to identify students who have a mature sense of the type of research they want to pursue in graduate school. We look for students who can think critically and write clearly about a research problem.
Be sure to mention the faculty members you might like to work with and the types of specific projects that interest you. Hint: Dont begin your statement with, Ever since I was a child…
Here is the website of the professor I want to work with during my PhD years. https://sites.google.com/site/mwilsonsayres/home
I am working in her lab right now. My project is about Investigating sex determination mechanisms and sex chromosome evolution in squamates.
The program I intend to apply is focused on Biology and Evolutionary. Here is the outline of my current project:
Squamate sex determination and sex chromosome evolution
The sex chromosomes of mammals, birds, worms, and flies lead to some interested expectations for general sex chromosome evolution. Several genes appear to be conserved in the sex determination pathway of mammals. The specific sex-determining loci in many other vertebrates is unknown. The first goal of this project is to analyze patterns of evolution of genes involved in the sex determining pathway in mammals (and birds)

Project goals:
1.Collect the list of genes involved in sex-determination
a.Mammals
b.Birds
c.Other vertebrates (frogs, fish, reptiles)
2.Download the multiple alignment for each gene
a.Identify the NM accession number of the longest transcript in humans
b.Use this NM accession to download multiple alignment from UCSC genome browser
c.Nucleotide sequences
d.Protein sequences
e.Versions
i.Original (with NM ids)
ii.Genome_build_names
iii.Common_names
3.Quality control on the multiple sequence alignments
a.Ensuring a triplet number of nucleotides for the nucleotide sequences
b.Mask out internal stop codons (TAA, TAG, TGA)
c.FASTA format (default)
d.Convert to phylip format
4.Compute substitution rates in these genes
a.Phyml (http://atgc.lirmm.fr/phyml/)
b.Codeml (part of PAML: http://abacus.gene.ucl.ac.uk/software/paml.html)
c.Use a fixed topology (relationship between the species).
5.Assess diversity in sex-determining genes
a.Human (1000genomes data)
b.Great Ape Genome Diversity
c.Mouse, and maybe others
6.Summary of the project
a.Methods, results discussion
b.Prepare powerpoint
c.Share for lab meeting
And another outline for my up coming project
Comparative Fertility
A comparative study of rates of evolution in the gene SEMG2, known to be involved in semen coagulation, showed a strong positive correlation between rates of molecular evolution and the level of sperm competition in the species. However, this study was limited to primates only, and it is unknown whether SEMG2 shows a correlation with sperm competition outside of primates. Further, such a comparative study between rates of evolution and levels of sperm competition (both within primates and across mammals) might provide a set of candidate fertility genes.

1.Collect information on sperm competition across animals
a.Make a table of available animal genomes available in the 100-way alignment.
b.Collect information on mating patterns
i.Monogamous
ii.Polygynous
iii.Polyandrous
iv.Polygynandrous
c.Collect levels of sperm competition for each species with a genome sequence.
i.Testes-to-body mass ratio
2.Assemble a set of candidate fertility genes
a.From a literature search, assemble set of candidate fertility genes.
b.Download multiple-way alignments for these candidate genes.
c.Curate set of candidate genes for quality.
3.Compute substitution rates and correlate
a.Compute substitution rates for each gene (e.g. phyml)
b.Compute phylogenetically corrected correlations (BayesTraits) between substitution rates and levels of sperm competition.
4.Write up results
a.Methods, results discussion
5.Prepare presentation to share results

Alternative approach:
1.Download alignments for all genes.
2.Quality control alignments.
3.Collect data on life history traits for all species.
4.Conduct substitution rate analysis of all genes.
5.Conduct BayesTraits correlation between each gene and each life history trait (TBR, Lifespan, BMR).
6.Rank genes by positive correlation between T-B-R and substitution rate to identify candidate genes for those involved in sexual selection.

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