Wen-Ya Ko, Ph.D.

Postdoctoral Fellow Department of Genetics School of Medicine University of Pennsylvania 426 Clinical Research Building 415 Curie Boulevard Philadelphia, PA 19104-6145 215-746-2315

Research Interests Education Awards Professional Experience Conference Presentations Publications Academic Service Professional Affiliations Service to Biology Department

Research Interests

My research interests in Dr. Sarah Tishkoff’s lab focus on studying erythrocyte-specific glycoproteins, which interact with Plasmodium falciparum ligands.  Since these receptor-genes may play a role in resistance to malaria, detecting signatures of natural selection at these genes could help identify functionally significant variants, which will advance our understanding of the underlying invasive mechanisms of P. faclciparum infection.

Before joining Sarah’s lab, my doctoral studies with Dr. Hiroshi Akashi at Penn State University focused on molecular phylogeny and evolution of Drosophila melanogaster and its closely related species (D. simulans, teissieri, yakuba, erecta, and orena).  Although the phylogeny among these species was thought well established, we found strong molecular evidence supporting an alternative tree topology (Ko et al. 2003).  We also studied patterns and rates of molecular evolution among these lineages and the underlying evolutionary forces.  We inferred nucleotide changes on the tree branches among these species and found prevalence of non-stationary nucleotide evolution and weak selection at synonymous sites (Akashi et al. 2006).  We also identified striking regional heterogeneity in patterns and rates of base composition evolution in D. yakuba and orena (Ko et al. 2006).  These results illustrate that temporal (on a gene tree) and spatial (near telemetric chromosomal regions) fluctuations in evolution parameters may be frequent even among closely related species, and imply that stationarity assumptions in modeling DNA evolution for phylogenetic reconstruction or in detecting footprints of natural selection (e.g., dN/dS test) may be often violated.

Figure 1: A maximum likelihood tree of species in the Drosophila melanogaster group inferred from a concatenated sequence of Adh + Adhr + Gld + ry genes (7164 bp).  Bootstrap values (1000 replicates) on each node are shown and represent, from top to bottom: Maximum likelihood (ML), neighbor-joining distance (NJ), and maximum parsimony (MP) values. “ * ” indicates identical bootstrap values for ML, NJ, and MP (see Ko, David, and Akashi 2003).

Education

Awards

Biology Graduate Student Research Excellence Awards, Pennsylvania State University, 2006

Professional Experience:

Postdoctoral Researcher, Department of Genetics, University of Pennsylvania School of Medicine

Research Associate, Department of Biology, University of Maryland

Teaching Assistant, Department of Biology, Pennsylvania State University

• Population Genetics, in 2003, 2005, and 2006 (lectured by Dr. Hiroshi Akashi)
• Molecular Evolution, in 2002 and 2005 (lectured by Dr. Stephen Schaeffer and by Dr. Kateryna Makova, respectively)
• Genetics, in 2002 (lectured by Drs. Stephen Schaeffer and Mitch Price)
• Biology of Molecules and Cell, in 2006 (lectured by Dr. Graham Thomas)

Research Assistant, Section of Integrative Biology, University of Texas at Austin, July 1999 - May 2000

• Molecular phylogeny of fireflies in North America (worked with Dr. Kathrin Stanger-Hall at Dr. David Hillis's Lab)

Research Assistant, Department of Biology, Tunghai University, Taiwan, January - June 1999

• Species investigation of bats in Taiwan
• Dynamics of species compositions of small mammals in Ta-Ta-Jia,Yu- Shan National Park, Taiwan

Research Assistant, Molecular Oncology Laboratory, Department of Education and Research, Taichung Veterans General Hospital, Taichung, Taiwan, 1997 - 1998

• Apoptosis in neuroblastoma cells induced by hydrogen peroxide

Research Assistant, Wildlife Ecology Laboratory, Forestry Department, National Pintung University of Science and Technology, 1993 - 1995

• Species diversity survey of Ruei-Jan stream Nature Reserve, Nantou County, Taiwan
• Species diversity survey after forest fire in Ta-Ta-Jia, Yu-Shan National Park, Taiwan
• Assessment of survival and rehabilitation of Formosa Flying Fox, Pteropus dasymallus formosus, Green Island, Taiwan

Conference Presentations

Ko, W.-Y., K. Kaercher, and S. A. Tishkoff, Population genetic analysis of erythrocyte surface glycoproteins in malaria-endemic human populations of Africa. 

Poster presentations:

58^th Annual meeting of the American Society of Human Genetics, Philadelphia, Pennsylvania, Nov 11 - 15, 2008

Ecology and Evolution of Infectious Disease PI Meeting, Albuquerque, New Mexico, Dec 02 - 05, 2007

Ko, W.-Y., K. Kaercher, and S. A. Tishkoff (2007) Population genetic analysis of erythrocyte surface glycoproteins in malaria-endemic human populations of Africa. Poster presentation at Ecology and Evolution of Infectious Disease PI Meeting, Albuquerque, New Mexico, Dec 02 - 05, 2007

Ko, W.-Y., S. Piao, and H. Akashi, Strong regional heterogeneity in base composition evolution on the Drosophila X chromosome.

Poster presentations:

Evolution 2006, the join annual meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN) at Stony Brook University, Stony Brook, NY, June 23 - 27 2006

Genomes, Evolution, and Bioinformatics, the annual meeting for the Society for Molecular Biology and Evolution at Arizona State University, Tempe, AZ, May 24 - 28 2006

47th Annual Drosophila Research Conference, Houston, TX, March 29 - April 2 2006

The Comparative and Functional Genomics of Summer Symposium at Pennsylvania State University, University Park, PA, July 20 - 23 2005

Oral presentations:

Northeast Ecology and Evolution Conference (NEEC) at Pennsylvania State University, University Park, PA, March 18 - 20 2005

Ko, W.-Y., R. David, J. Anoop, C.-F. Lin, S. Piao, and H. Akashi (2004) Lineage-specific molecular evolution in the Drosophila melanogaster species subgroup.  Poster presentation at Genome and Evolution conference for the Society for Molecular Biology and Evolution at Pennsylvania State University, University Park, PA, June 17 - 20 2004

Ko, W.-Y., R. David, and H. Akashi, Molecular phylogeny of the Drosophila melanogaster species subgroup. 

Poster presentations:

Eastern Great Lake Molecular Evolution Meeting (EGLME VIII) at Cornell University, Ithaca, NY, April 24 2004

The annual conference for the Society of Molecular Biology and Evolution (SMBE), Newport Beach, CA, June 26 - 29 2003

Publications

Ko, W.-Y., S. Piao, and H. Akashi (2008) With- and between-species sequence variation in Drosophila teissieri and Drosophila yakuba: evolutionary mechanisms of Codon Bias and protein Evolution. (in preparation for submission to Genetics)

Iida, K., D. L. Cox-Foster, X. Yang, W.-Y. Ko, D. R. Cavener (2007) Expansion and evolution of insect GMC oxidoreductases. BMC Evolutionary Biology 7:75

Ko, W.-Y.,  S. Piao, and H. Akashi (2006) Strong regional heterogeneity in base composition evolution on the Drosophila X chromosome. Genetics 174:349-362

Akashi, H., W.-Y. Ko, S. Piao, A. John, P. Goel, C. F. Lin, and A. Vitins (2006) Molecular evolution in the Drosophila melanogaster species subgroup: Frequent parameter fluctuations on the time-scale  of molecular divergence. Genetics 172:1711-1726

Ko, W.-Y., R. David, and H. Akashi (2003) Molecular phylogeny of the Drosophila melanogaster species subgroup.  J. Mol. Evol. 57:562-573

Ko, W.-Y., A Note on the Playing-Dead Behavior of Pipistrellus abramus. Notes of Wildlifers and Newsletter of Wildlifers 4(2):10 (in Chinese)

Ko, W.-Y. (1995) Reproductive cycle of the house bat, Pipistrellus abramus, in South Taiwan. A Tunghai University Publication (Master's thesis, in English).

Academic Service:

Manuscripts reviewed:

• BMC Evolutionary Biology (with Dr. H. Akashi)
• Journal of Molecular Evolution (with Dr. H. Akashi)
• Molecular Biology and Evolution

Professional Affiliations:

• Genetics Society of America
• Society for Molecular Biology and Evolution
• Society for the Study of Evolution

Service To Biology Department:

Graduate Affairs Committee of Biology Department, Pennsylvania State University, 2006