Chung-I Wu

Sr. Fellow,
- Professor at the Chinese Academy of Science
- Professor at the Department of Ecology and Evolution

Contact Information

Beijing Institute of Genomics
&
The University of Chicago
Zoology Building, room 201A
1101 East 57th Street
Chicago, IL 60637

Phone: 773-702-2565
Fax: 773-702-9740
Email: .(JavaScript must be enabled to view this email address)
Email: .(JavaScript must be enabled to view this email address)

Research

I. Molecular genetics of species differentiation - The main interest is in the genetic and molecular basis of species differences. (You can think of human vs. chimpanzee, if you wish. How many genetic differences delineate us from them?) We use sibling species of Drosophila to get to the answers (see Wu, C.-I and C.-T. Ting 2004 Genes and speciation. Nature Review Genetics 5: 114-122). Among the traits of special interest are hybrid incompatibility and sexual behavior divergence. These traits are what define species.

Current approaches
In the past, we took a gene-by-gene approach and have successfully cloned two speciation genes (see the list below, or Wu and Ting 2004). In the beginning of this new century, there is a need and an opportunity to take a system-wide approach in order to identify the majority of genes involved in a particular process of speciation. We shall study the divergence in mating behaviors between the Z (for Zimbabwe) and M (cosmopolitan) behavioral races of Drosophila melanogaster (Wu et al. 1995; Hollocher et al. 1997a, b; Ting et al. 2001). These two races are at the very nascent stage of species formation.

We wish to understand the genetic and transcriptional bases of phenotypic divergence at this early stage of speciation. As shown in the figure above, the studies will be at 3 different levels - genotype, transcriptome and phenotype. The scope will be genomic and the tools will include genotyping tiling array, expression microarrays, large-scale sequencing, behavioral QTL mapping and, finally, precise gene replacement.

Aim 1 – At the genotypic level, we will identify nucleotide sites that are strongly differentiated between the Z and M races in a whole-genome scan of expressed genes. These race-differentiating sites will anchor genetic mapping of transcription and phenotypic divergence. We will construct multiply recombined (MR) lines between the Z- and M-races for such mapping.

Aim 2 – At the transcriptional level, we shall study the expression profiles of the MR lines (in heads and reproductive organs of the two sexes) and correlate these profiles with their underlying genotypes. The regulation of transcription is important in linking phenotype and genotype.

Aim 3 – At the phenotypic level, we shall first attempt to find the transcriptional basis of the phenotypic divergence (behavioral isolation), using the MR lines. We shall also link phenotypic divergence to genotypic changes directly. Genotyping will be done by whole-genome tiling array. We expect to identify most candidate “speciation genes” between the Z- and M- races and will carry out precise gene replacement (Rong and Golic 2000; Greenberg et al. 2003; Sun et al. 2004) to confirm their effects on the mating behavior.

II. Genomics and population genetics -The torrent of genomic data by DNA sequencing and expression microarrays have provided unprecedented opportunities for analyzing natural selection and adaptation. Speciation is the consequence of natural selection driving populations to adapt to different environments. It is also a genome-scale phenomenon.

Current approaches -We continue to carry out data analysis as done in the papers cited below. The data were often obtained from the public domain and we have been developing theoretical tools to analyze these data. At the same time, we also carry out large-scale data collection in collaboration with various sequencing centers in several countries. An example is our organization of an international consortium that sequenced 10,000 full-length transcripts from the macaque brain and testis (see Wang et al. in review). This effort will be the foundation of a comparative primate genome database. We also collaborate with these centers on many other fronts (see He et al. 2004 and Song et al. 2005 for the analysis of SARS evolution).


Research Papers