Institute of Molecular
Evolutionary Genetics


















Previous IMEG Seminars and Abstracts:

Fall 2013

Spring 2013

Fall 2012


Spring 2012

Fall 2011

Fall 2010


Spring 2010
Fall 2009

Spring 2009

Fall 2008

Spring 2008

Fall 2007
Spring 2007
Fall 2006

Spring 2006
Fall 2005
Spring 2005

Fall 2004

Spring 2004

Fall 2003

Spring 2003
Fall 2002





12:10 PM

317 Mueller Lab.

Speaker: Dr. David Liberles - University of Wyoming - Department of Molecular Biology


Title: Computational Approaches for Linking Comparative Genomics to Biochemistry and Evolution


Abstract: Standard bioinformatics pipelines for comparative genomic data analysis typically include steps like multiple sequence alignment, phylogenetic tree reconstruction, calculation of the ratio of rates of nonsynonymous to synonymous nucleotide substitution (dN/dS), and gene tree-species tree reconciliation. Models for amino acid substitution used in these processes assume that each site evolves independently according to average properties in the absence of a protein structural or functional context. Models for duplicate gene retention assume that the process is evolutionarily neutral and do not consider functional or mechanistic underpinnings. A model for duplicate gene retention that would allow for mechanistic differentiation between nonfunctionalization, neofunctionalization, subfunctionalization, and dosage balance based upon differences in expected time-dependent retention profiles is presented. Two characterizations of amino acid substitution are also presented. One approach extends a population genetic model to inter-specific genomic data and a second approach evaluates the effects of selection for protein folding and protein-protein interaction on sequence evolution.  These approaches reflect an in progress strategy for increasing biochemical and evolutionary realism in bioinformatics.




8 Mueller Lab

Speaker: Dr. Helen Salz - Case Western University- Department of Genetics


Title: Sex Determiniation in Drosophila: a binary decision controlled by RNA binding proteins


Abstract:The gene regulatory networks that control sex determination vary between species. Despite these differences, comparative studies in insects have found that alternative splicing is reiteratively used in evolution to control expression of the key sex-determining genes. Sex determination is best understood inDrosophila melanogaster where activation of the RNA binding protein-encoding gene Sex-lethal (Sxl) is the central female-determining event. Sex is determined in early embryogenesis when the X-chromosome number is relayed through regulatory proteins such that Sxl is activated only in XX animals. X-chromosome counting functions only transiently and female identity is maintained by a self-sustaining feedback loop in which the Sxl protein controls its own splicing to yield protein-encoding mRNAs only in females. Without Sxl protein, as in males, the mRNAs include the 3rdexon, resulting in the insertion of several premature stop codons into the open reading frame and the production of truncated non-functional protein products. Current studies suggest that while the spliceosome begins to assemble on the 3rd exon in both males and females, in females the Sxl protein prevents the reaction from finishing by forming a dead-end complex with these spliceosomal proteins. Sxl-mediated splicing inhibition is co-transcriptional and emerging data suggests that communication between chromatin and the splicing regulatory complexes is also important.



Johnson, M L, Nagengast, A A, and Salz, H K (2010) PPS, a large multidomain protein, functions with Sex-lethal to regulate alternative splicing in Drosophila. PLoS Genet. 6:e1000872.

Salz, H. K. (2011) Sex Determination in insects: a binary decision based on alternative splicing. Current Opinion in Genetics & Development. 4:395-400.



4:00 PM

100 Life Sci. Bldg.


Speaker: Dr. Mariana Wolfner - Cornell University - Department of Molecular Biology and Genetics

Title: Battles and ballets: interactions between males, females and their molecules during reproduction in Drosophilia





317 Mueller Lab


Speaker: Yazhou Sun - Penn State University - Department of Biology (Ma Lab)


Title: HapSearch, a fast and accurate haplogroup identification system based on 7985 human mitochondrial genomes


Abstract: With the increased efficiency of the latest sequencing technologies, more and more complete human mitochondrial genomes have been generated at an increasingly faster speed. Although mitochondrial haplogroups, and their classification and identification were widely used in human evolution and population studies, the current tools could not fully take advantage of the rapidly growing number of new mitochondrial genomes. An updated mitochondrial haplogroup classification system was thus developed with evolutionary models that incorporate mitochondrial genomic variations within the human population. These variations have not been considered by previous methods, which could lead to incorrectly classified haplogroups. The variation parameters, including the whole-genome substitution rate (0.013 - 0.1 substitutions per generation), the rate heterogeneity among sites (Gamma distribution shape parameter α = 0.7078) and the percentage of invariant sites (64%), were estimated based on 7985 full-length human mitochondrial genome sequences. Haplogroups were then classified based on the corrected genetic distance estimation. The resulting haplogroups were then modeled with position specific matrices (PSM). A new haplogroup identification system was developed based on these inferred matrices and the maximum-likelihood estimation (MLE) method, permitting fast and accurate haplogroup assignment for both known and new mitochondrial genomes. The entire system is available through the HapSearch web application (