Institute of Molecular
Evolutionary Genetics


spring 2002
Previous IMEG Seminars and Abstracts:
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

Spring 2002

Fall 2001

Spring 2001

Fall 2000

Fall 1999

Spring 1998

Fall 1997

 Date Speaker and title of seminar

Dr. Mark Shriver
, Dept. of Anthropology, Penn State Univ.
Title & Abstract:
1)  Update work on estimating ancestry and the relationships between ancestry and skin pigmentation in three population samples
2)  Provide a review of the idea of "population genomics"
Black et al. 2001 Ann. Rev. Entomol. 46:441-469 and show data on our initial efforts at a study of human population genomics using the SNP Consortium data.

 01/23/02 Dr. Yoshiyuki Suzuki, Dept. of Biology, Penn State Univ.
Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites
Abstract: Inferring positive selection at single amino acid sites is of biological and medical importance.  The parsimony-based methods have been developed for this purpose, but the reliabilities of these methods are not well understood.  Since the evolutionary models assumed in these methods are only rough approximations to reality, it is desirable that the methods are not very sensitive to violation of the assumptions made.  Here we show by computer simulation that the parsimony-based method is generally conservative, whereas the likelihood-based method is sensitive to violation of assumptions under certain conditions and produces many false-positive results.  These observations, together with those from previous real data analysis, suggest that the parsimony-based method is generally more reliable than the likelihood-based method.

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 01/30/02 Dr. Stephen Schaeffer, Dept. of Biology, Penn State Univ.
Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura
Abstract:    Two hypotheses have been suggested for how natural selection acts on intron length in natural populations of Drosophila.  Carvalho and Clark (Nature 401:344) have suggested that introns that are either too large or small are selected against more efficiently in regions of high recombination, while Comeron and Kreitman (Genetics 156:1175-1190) have suggested that natural selection favors long introns in regions of low recombination to enhance genetic exchange. A 3.5 kilobase segment of the Adh region that includes the Adh and Adh-related genes was sequenced in 139 D. pseudoobscura strains collected from 13 populations.  Insertion and deletion variation in the Adh region was used to determine if sequence variation departs from an equilibrium neutral model for a gene in a high recombination region.  A total of 38 deletion and 46 insertion polymorphisms are segregating within D. pseudoobscura populations.  The Tajima test fails to reject a neutral model for insertion polymorphisms, but an excess of rare frequency deletions leads to a rejection of a neutral model of deletions.  Insertions and deletions were classified as repetitive sequences if the added or missing bases were similar to flanking sequences.  The insertions events had a higher frequency of repetitive polymorphisms than the deletion events (68% repetitive insertions versus 41% repetitive deletions).  Deletions are nonuniformly distributed among the noncoding regions, while insertions do not depart from a uniform distribution.  These results suggest that introns in regions of high recombination will tend to increase in size because purifying selection acts against deletions, but not insertions.  The nonuniform distribution on deletions is likely to result from selective constraints for intron sequences necessary for proper splicing.  The source of new information for insertions tends to be sequences that flank the insertion site.

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 02/06/02 Dr. Malia Fullerton, Depts. of Anthropology and Biology, Penn State Univ.
Title: Population Genetic Variation at the Type 2 Diabetes Candidate Locus Calpain-10
Previous research has suggested that haplotypes at the calpain-10 locus (CAPN10) are associated with increased risk of type 2 or non-insulin dependent diabetes mellitus (NIDDM) in Mexican-Americans, Finns, and Germans (Horikawa et al. 2000).  To inform the original mapping results and look for evidence of the action of natural selection on CAPN10, we undertook a population-based genotyping survey of the candidate susceptibility variants.  First, we genotyped sites 43, 19, and 63 (the haplotype-defining variants proposed by Horikawa et al.) and 4 closely-linked SNPs, in 561 individuals drawn from 11 populations from five continents, and examined the linkage disequilibrium (LD) among them.  We then examined the ancestral state of these sites by sequencing orthologous portions of CAPN10 in chimpanzee and orangutan.  Our survey identified larger-than-expected differences in the distribution of CAPN10 susceptibility variants between African and non-African populations, with common, derived haplotypes in European and Asian samples (including one of two proposed risk haplotypes) being rare or absent within Africa. These results suggest a history of positive natural selection at the locus resulting in significant geographic differences in polymorphism frequencies, with possible implications for disease risk.
Fullerton et al. (in press) "Geographic and haplotype structure of candidate type 2 diabetes susceptibility variants at the calpain-10 locus"  American Journal of Human Genetics.
Horikawa et al. (2000) "Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus." Nature Genetics, 26:163-75.

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 02/13/02 Dr. Claude dePamphilis, Dept. of Biology, Penn State Univ.
THE FLORAL GENOME PROJECT: An evolutionary genomic approach to understanding the origin and diversification of floral architecture
Abstract: The sudden appearance of flowers in the fossil record about 100 million years ago represents a longstanding mystery that has long puzzled evolutionary biologists.   Among the many key questions surrounding the origin of flowers include: Did the ancestral flower possess the full complement of genetic information needed to assemble a modern flower?   How did the flower (an inherently bisexual structure) evolve from ancestors that had inherently unisexual reproductive parts?  What components of genetic diversity causes the important variation in flower diversity that we see today?  Recent studies in plant developmental genetics and genomics have identified dozens of genes with specific roles in flower development in Arabidopsis and other model organisms.  Despite this rapid progress, many (if not most) genes with critical roles remain undiscovered, largely because of functional redundancy.   Furthermore, it is still very unclear the extent to which one or even a few intensely studied models will lead to general understanding of the floral developmental process.  In this talk, I will describe Floral Genome Project (FGP), a newly funded study involving multiple collaborators at Penn State and other universities, that will address these and other questions about flower origins and diversification.   Because this project has only begun within the last few months, I will focus on the project goals, basic design features of our genomic experiments, and how genomic scale data can be used to address evolutionary hypotheses.
Albert, V.A., Gustafsson, H.G., and DiLaurenzio, L.  1998.  Ontogenetic systematics, molecular developmental genetics, and the angiosperm petal.  In Soltis, D. E., Soltis, P.S., Doyle, J. J. (eds).  Molecular Systematics of Plants II, pp 349-374.  Kluwer, Norwell, MA.
Barkman, T. J., G. Chenery, J. R. McNeal, J. Lyons-Weiler, W. J. Elisens, G. Moore, A. D. Wolfe, and C. W. dePamphilis.  2000.  Independent and combined  analyses of sequences from all three genomic comparments converge on the root of flowering plant phylogeny.
Proceedings of the
National Academy of Sciences 97:13166-13171.
Ma, H. and C. W. dePamphilis.  2000.  The ABCs of flower evolution.  Cell 101:5-8.
The Floral Genome Project Research Group.  2002.  Missing Links:  The genetic architecture of the flower and flower diversification.  Trends In Plant Science 7:22-31.
Baum, D. A., J. Doebley, V. F. Irish, E. M. Kramer.  2002.  Resonse:  Missing links: the genetic architecture of flower and floral diversification.  Trends in Plant Science 7: 31-33. 

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 02/20/02 Open

 02/27/02 Xi Wang, Depts. of Biochemistry and Mol. Biol., Penn State Univ.
Title: Molecular and evolutionary aspect of self incompatibility in flowering plants
Abstract: In flowering plants, self-incompatibility (SI) is a widespread mechanism that prevents self fertilization and promotes outcrossing.  In the simplest case, SI response is genetically controlled by one multi-allelic loci, and relies on a series of complex cellular interactions between self-incompatible pollen and pistil.  This multi-alleic SI locus is one of the most highly polymorphic loci known and has long interested geneticist and evolutionist.  The talk will describe the recent progress made in molecular study with several plant species and discuss the implications in evolutionary aspect.
McCubbin AG, Kao T. (2000) Molecular recognition and response in pollen and pistil interactions.  Annu Rev Cell Dev Biol. 16:333-64.
Hughes A.L. (1999) Adaptive evolution of genes and genomes.  New York : Oxford University Press, p110-115.
Matton, D.P., Luu, D.T., Qin, X., Laublin, G., O'Broem, M., Maes, O., Morse, D., and Cappadocia, M. (1999).
Production of an S RNase with dual specificity suggests a novel hypothesis for the generation of new S alleles.  Plant Cell 11, 2087-2097.
Wang X., Hughes A.L., Tshkamoto T., Ando, T., and Kao T.H, (2001) Evidence that Intragenic Recombination Contributes to Allelic Diversity of the S-RNase Gene.  Plant Physiology 125: 1012-1022.

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 03/06/02 Spring Break

 03/13/02 Dr. Hiroshi Akashi, Dept. of Biology, Penn State Univ.
Gene expression and amino acid composition in the Saccharomyces cerevisiae proteome
Abstract: Although translational selection at silent sites is well established, the role of metabolic constraints on protein structure remains unclear.  The yeast proteome was investigated to determine whether highly expressed genes preferentially encode translationally superior amino acids.  Both oligo DNA array data and major codon usage were employed to estimate the translation rates of gene.  The usage of a number of amino acids appears to be strongly dependent on gene expression levels.  Relationships between expression and amino acid usage remain strong both within protein functional categories and when simple amino acid sequences are removed.  Amino acids that are used preferentially in highly expressed genes tend to be recognized by relatively abundant tRNA isoacceptors and/or relatively inexpensive to synthesize.  The base composition of introns does not show a relationship with transcription rates, suggesting that transcription-dependent mutational processes do not account for these patterns.  In S. cerevisiae, both synonymous codon usage and the amino acid composition of proteins appear to reflect natural selection to enhance the translational or metabolic efficiency of cells.

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 03/20/02 Brian Lazzaro, Dept. of Biology, Penn State Univ.
Is Selection Acting on Antibacterial Peptide Genes in Drosophila?
Abstract: Drosophila kill bacterial pathogens with an array of potent antibacterial peptides.  Because these peptides bind directly to pathogens, they may be targets of host-pathogen co-evolution.  I have sequenced the coding region and 1-2 kb upstream sequence of 6 antibacterial peptide genes from 12 naturally occuring D. melanogaster chromosomes.  The genes are very short, limiting power for many evolutionary analsyses.  Nevertheless, there are several indications that natural selection may be acting on the loci.  The inferred selective history is not compatible with two simple models of host-pathogen co-evolutionary genetics, evolutionary arms race and overdomininant/diverisfying selection.

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 03/27/02 Joel McNeal, Dept. of Biology, Penn State Univ.Use it or Lose it: Chloroplast Genome Evolution of the Parasitic Plant Genus Cuscuta
Title: Use it or Lose it: Chloroplast Genome Evolution of the Parasitic Plant Genus Cuscuta
Abstract: Since the appearance of the first autotrophic life on earth, the transition to heterotrophy has occurred independently many times with profound repercussions.  The multiple origins of parasitism in angiosperms serve as an excellent system to study molecular evolution of photosynthetic genes that may be under relaxed functional constraint.  The parasitic plant genus Cuscuta contains well over 100 species that show considerable variation in pigmentation and chloroplast structure.   Study of chloroplast gene structure and apparent levels of selection across the taxonomic range of Cuscuta should provide insight into which genes are most likely to be lost, which Cuscuta species may still perform residual photosynthesis, and which chloroplast genes may be under selection for functions other than photosynthesis.  Comparison with other independently evolved parasitic lineages will eventually lead to a better understanding of the similarities in molecular evolution of genes that are under relaxed selection.
dePamphilis, C. W. 1995. “Genes and genomes.” pp. 177-205 in Parasitic Plants.  M. C Press and J. D Graves eds. Chapman and Hall, London.
Hibberd, J. M., R. A. Bungard, M. C. Press, W. D. Jeschke, J. D. Scholes, and W. P. Quick. 1998. “Localization of photosynthetic metabolism in the parasitic angiosperm Cuscuta reflexa.” Planta 205: 506-513.
Machado, M. A. and  K. Zetsche. 1990. “A structural, functional, and molecular analysis of plastids of the holoparasites Cuscuta reflexa and Cuscuta europaea.” Planta 181: 91-96.
Nickrent, D. L., A. E. Colwell, A. D. Wolfe, N. D. Young, K. E. Steiner, and C. W. dePamphilis. 1998. “Molecular phylogeny and evolutionary studies of parasitic plants.” pp. 211-241 in Molecular Systematics of Plants II: DNA Sequencing. D. Soltis, P. Soltis, and J. Doyle eds. Kluwer Academic Publishers, Boston. 
van der Kooij, T.A., K. Krause, I. Dorr, and K. Krupinska. 2000. Molecular, functional, and ultrastructural characteriza
tion of plastids from six species of the parasitic flowering plan genus Cuscuta.” Planta 210: 701-707.

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 04/03/02 Open

 04/10/02 Dr. Mark Batzer, Louisiana State Univ.Alu elements and human genomic variation
Alu Elements and Human Genomic Variation
Abstract: Alu elements have amplified within primate genomes over 65 million years through a RNA-dependent mechanism, termed retroposition.  The amplification of Alu repeats within the human genome has resulted in the generation of the largest family of mobile elements within the human genome with greater than 1,100,000 copies.  Even though there are 1.1 million Alu copies in the human genome, only a limited number of Alu elements have been capable of mobilization and have given rise to a series of distinct subfamilies of Alu repeats that are different genetic ages.  Several thousand Alu elements have integrated and been fixed within the human genome after the divergence of humans and African apes. The insertion of Alu elements within the human genome has resulted in a number of new detrimental mutations.  Most of the newly integrated Alu insertions serve as an innocuous source of genetic variation with a subset of identical-by-descent Alu insertion polymorphisms that are useful for the study of human population relationships.  Post integration recombination events between Alu elements have acted as a means to create human genetic diversity and generated a variety of human genetic disorders.   The sequence structure of Alu elements that have integrated within the human genome has also undergone extensive gene conversion events that impact the accumulation of single nucleotide polymorphisms within the human genome.  Alu elements are also one of the primary sources of microsatellite sequences in the human genome.  Thus, Alu repeats contribute to human genomic diversity in a number of different ways.
Deininger, P. L. and M. A. Batzer  (1993)  Evolution of Retroposons.  In "Evolutionary Biology, Volume 27", M. Hect, R. J. MacIntyre and M. Clegg (Eds), Plenum Publishing Corporation, New York, pp. 157-196.
Deininger, P. L. and M. A. Batzer  (1999) Alu repeats and human disease.  Molecular Genetics and Metabolism  67:  183-193.
Stoneking, M., J. J. Fontius, S. Clifford, H. Soodyall, S. S. Arcot, N. Saha, T. Jenkins, M. A. Tahir, P. L. Deininger and M. A. Batzer  (1997)  Alu insertion polymorphisms and human evolution:  evidence for a larger population size in Africa.   Genome Research  7:  1061-1071.
Roy, A. M. , M. L. Carroll , S. V. Nguyen, M. Oldridge, A.-H. Salem, A. O. Wilkie, M. A. Batzer and P. L. Deininger (2000)  Potential gene conversion and source genes for recently integrated Alu elements.  Genome Research 10:  1485-1495.
Roy-Engel, A. M. , M. L. Carroll, E. Vogel, R. K. Garber, S. V. Nguyen, A.-H. Salem, M. A. Batzer and P. L. Deininger (2001)  Alu insertion polymorphisms for the study of human genomic diversity.  Genetics  159:  279-290.
Carroll, M. L., A. M. Roy-Engel, S. V. Nguyen, A.-H. Salem, E. Vogel, B. Vincent, J. Myers, Z. Ahmad, L. Nguyen, M. Sammarco, W. S. Watkins, J. Henke, W. Makalowski, L. B. Jorde, P. L. Deininger, and M. A. Batzer  (2001)  Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity.  Journal of Molecular Biology  311:  17-40.
Roy-Engel, A. M. , M. L. Carroll, M. El-Sawy, A.-H. Salem, R. K. Garber, S. V. Nguyen, P. L. Deininger, and M. A. Batzer (In Press)  Non-traditional Alu evolution and primate genomic diversity.  Journal of Molecular Biology

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 04/17/02 Wen-Ya Ko, Dept. of Biology, Penn State Univ.
Title: Molecular Phylogeny of The Drosophila melanogaster  Species Subgroup
Abstract: Both molecular and phenotypic evolution have been extensively studied in the melanogaster species subgroup. However, phylogenetic relationships within the subgroup remain unresolved. In particular the D. yakuba - D. teissieri species pair and D. erecta - D. orena species pair in relation to the D. melanogaster, D. simulans, D. mauritiana, and D. sechellia  species complex remains unclear. Recent molecular studies do not converge on a single topology. The purpose of our study  was to reconstruct the molecular phylogeny of the melanogaster species subgroup using multiple nuclear genes.  We have developed a strategy employing “vectoerette PCR” to efficiently sequence orthologous genes from even distantly related species. Regions of the Adh, Adhr, Gld, and ry genes (totally ~7221 bp) from 6 melanogaster subgroup species (D. melanogaster, D. simulans, D. teissieri, D. yakuba,  D. erecta , and D. orena ) and 3 of their sister species (D. eugracilis, D. mimetic, and D. lutescens) were sequenced for phylogenetic reconstruction. Phylogenetic analyses employed maximum parsimony, neighbor-joining, and maximum likelihood methods. Our results reject the currently favored tree topology and strongly support (with high bootstrap scores) the topology that groups yakuba -teissieri closest to erecta -orena pair.  Although stationarity of base composition was rejected in our data, violation of this assumption had no impact on the analysis; the same tree topology is supported by simple (Jukes-Cantor) and more complex (non-stationary base composition) models.
Lachaise, D., M. L. Cariou, J. R. David, F. Lemeunier, L. Tsacas et al., 1988 Historical Biogeography of the Drosophila-Melanogaster Species Subgroup. Evolutionary Biology 22: 159-225.
Powell, J. R., 1997 Progress and prospects in evolutionary biology : the Drosophila model. Oxford University Press, New York.

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 04/24/02 Kristi Montooth, Dept. of Biology, Penn State Univ.
Relating genetic and biochemical variation in metabolic pathways to physiological performance in Drosophila.
Abstract: Great strides have been made in understanding the relationship between flux through metabolic pathways and metabolic performance in both bacteria and yeast (e.g. Hartl 1989; Edwards and Palsson 2000; Cornish-Bowden and Cardenas 2001; Zaslavskaia et al. 2001).  However, in multicellular organisms, it remains unclear how variation in the components of energy metabolism relates to variation in complex whole organism physiological performance.  The network of genes underlying energy metabolism is well characterized in Drosophila, and this knowledge enables a pathway approach to dissecting the genetic architecture of physiological performance.  I will present results from two studies quantifying and modeling genetic and biochemical variation within metabolic pathways.  First, a quantitative genetic analysis, involving quantitative trait loci (QTL) mapping, of the complex pathway underlying glycolytic metabolism reveals the importance of trans-regulatory variation within the metabolic pathways.  It also sheds light on the relationship between metabolism and flight. 
Second, I am quantifying biochemical variation at all three steps in the ethanol and acetic acid metabolic pathway. Ethanol and acetic acid are relevant environmental stresses for species of Drosophila that inhabit rotting fruit, and natural selection for increased tolerance to both ethanol and acetic acid could allow species of Drosophila to exploit new habitat niches, as appears to be the case for D. melanogaster (McKenzie and Parsons 1972; McKenzie and McKechnie 1979).  Thus, the simple linear pathway underlying ethanol and acetic acid detoxification in Drosophila offers a unique system to study the genetic response of a pathway to selection.  Kinetic models of variation in alcohol dehydrogenase (ADH), aldehyde dehydrogenase (ALDH) and acetyl-CoA synthetase (AcCoAS) enzyme activity may better predict ethanol and acetic acid tolerance in Drosophila than simple unitary relationships between any single enzyme and tolerance.
Cornish-Bowden, A., and M. L. Cardenas.  2001.  Silent genes given voice. Nature 409:571-572.
Edwards, J. S., and B. O. Palsson.  2000.  The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci U S A 97:5528-33.
Hartl, D. L.  1989.  The physiology of weak selection. Genome 31:183-9.
McKenzie, J. A., and S. W. McKechnie.  1979.  A comparative study of resource utilization in natural populations of Drosophila melanogaster and D. simulans. Oecologia 40:299-309.
Zaslavskaia, L. A., J. C. Lippmeier, C. Shih, D. Ehrhardt, A. R. Grossman, and K. E. Apt.  2001.  Trophic conversion of an obligate photoautotrophic organism through metabolic engineering. Science 292:2073-5.

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