Nicholas VanKuren

Motivation                                                            

"The fact that two independent measures of functional importance—evolutionary conservation over 500 million years and requirement for normal phenotype—are correlated has significant implications. For example, it argues that functionally essential genes are not organism specific, nor are their functions protected by gene duplication." (Ashburner et al., 1999, Genetics)



Research:

My research interests are varied, but centered around understanding how species-specific genetic variation causes evolution on short time scales. Until recently, identifying within-species variation was difficult, and actually testing the fitness of such variation was near impossible. However, whole-genome sequencing and improved methods for sequence analysis and variant detection.

My thesis work focused on three main questions: 

1. What are the fitness effects of genes found specifically in Drosophila melanogaster?

I showed that ~30% of fixed species-specific genes (less than ~1.5 million years old) are essential for proper fly development: constitutive knockdown of species-specific gene expression results in fly death before adulthood. Furthermore, many species-specific genes reside in recent and strong selective sweeps, suggesting that natural selection plays a large role in the early stages of their evolution. Even though most new genes are formed by tandem duplication, it is unlikely that many gene pairs are functionally redundant because they have divergent gene structures and expression patterns that arose concurrent with or shortly after they formed. 

New genes can clearly rapidly become essential. 

2. How can species-specific genes be essential?

I am investigating in depth the functions and phenotypic effects of one essential D. melanogaster-specific gene and its parent (the gene from which it was formed by tandem duplication) using the CRISPR/Cas9 system and traditional genetics.

3. What are the evolutionary forces acting on and phenotypic effects of novel genes segregating within D. melanogaster populations?

To understand the earliest stages of new gene evolution and put my previous results into context, I am also investigating the evolution and fitness effects novel genes segregating within fly populations. I have used population genomic data and population genetic analyses to identify candidate novel genes segregating in D. melanogaster that appear to be being swept to fixation. In one case study, I am simulating the formation and early stages of a new gene's evolution by inserting one such novel gene (found in ~50% of D. melanogaster) into a line that does not carry it. What happens when we put this new gene into a line that does not carry it? Probably nothing, but stay tuned!

 

Contact:

Nicholas W. VanKuren
Ph.D. Candidate
Committee on Genetics, Genomics, and Systems Biology
Department of Ecology and Evolution
Long Lab, 303 Zoology
1101 E. 57th Street 
Chicago, IL 60637  

Email: nvankuren@uchicago.edu, nwvankuren@gmail.com
Lab Phone: (773) 834-3567

CV:

  

Publications:

9. VanKuren NW and Long M. A pair of species-specific duplicate genes are both essential. in prep (7-18-2016).

8. VanKuren NW and Long M. Drosophila melanogaster-specific genes rapidly became essential for fly development. under review (7-18-2016).

7. Toomer KH, Chen X, Naito M, Mondo SJ, den Bakker HC, VanKuren NW, Lekberg Y, Morton JB, and Pawlowska TE. 2015. Molecular evolution patterns reveal life history features of mycoplasma-related endobacteria associated with arbuscular mycorrhizal fungi. Molecular Ecology. 24(13):3485-500.

6. Gao G, Vibranovski MD, Zhang L, Li Z, Liu M, Zhang YE, Li X, Zhang W, Fan Q, VanKuren NW, Long M, Wei L. 2014. A long-term demasculinization of X-linked noncoding RNAs in Drosophila melanogaster. Genome Research. 24(4):629-38.

5. VanKuren NW & Vibranovski MD. 2013. A novel dataset for sex-biased gene identification in Drosophila. Journal of Genomics 2: 64-7.

4. Long M, VanKuren NW, Chen S, & Vibranovski MD. 2013. New gene evolution: Little did we know. Annual Review of Genetics 47:325-51.

3. VanKuren NW, den Bakker HC, Morton JB, & Pawlowska TE. 2013. Ribosomal RNA gene diversity, effective population size, and evolutionary longevity in asexual Glomeromycota. Evolution 67(1):207-24.

2. Vibranovski MD, Zhang YE, Kemkemer C, VanKuren NW, Lopes HF, Karr TL, Long M. 2012. Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophila retrogenes. BMC Evolutionary Biology 12, 169

1.  den Bakker HC*, VanKuren NW*, Morton JB, & Pawlowska TE. 2010. Clonality and recombination in the life history of an asexual arbuscular mycorrhizal fungus. Molecular Biology and Evolution 27(11):2474-2486. *Contributed equally. 

 

Potentially useful perl scripts:

Coming relatively soon?