IMEG

Institute of Molecular
Evolutionary Genetics

 
 
 
          
 

IMEG SEMINARS
FALL 2003
 
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
 
 09/03/03

Speaker: Dr. Seogchan Kang, Dept. of Plant Pathology, Penn State Univ.
Title: Plant pathogen database: Cyber-infrastructure to capture and visualize the structure and dynamics of plant pathogens in the context of agroecosystems
Abstract: Crop losses from diseases pose a serious threat to global food/fiber/feed security. Considering the importance of agriculture, concerted efforts should be committed to developing a comprehensive risk management decision support system to effectively deal with any future crop disease outbreaks whether accidental or deliberate. This project aims to achieve the following goals:
(i)  To link pathogen genotypes to their phenotypes
(ii) To develop an integrated set of data analysis and visualization tools to examine complex disease interactions
(iii) To build a cyber-infrastructure linking community research
(iv) To provide rapid, sensitive and accurate diagnostic tools for high-risk pathogens at both the species and population levels
References:
Kang et al. (2002) The Internet-based fungal pathogen database: A proposed model. Phytopathology 92:232-236.

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 09/10/03 Speaker: Dr. Laura Zahn, Dept. of Biology, Penn State Univ.
Title: Comparative analyses of Poppy MADS-box genes expressed during flower development
Abstract: The Type II MIKC MADS-box genes play critical roles in controlling flower development and specifying floral organ identity in plants.  Although homologs of many MADS-box genes have been analyzed from both eudicots and monocots, it is not clear how conserved these genes are among divergent angiosperm lineages, particularly in the basal eudicots.  Studies of the phylogenetic placement and expression of 4 MADS-box genes isolated from a pre-meiotic floral library of the California poppy demonstrate that these genes share homology with genes in Arabidopsis.  The expression patterns of these genes in the basal Eschscholzia are both similar and divergent to their homologs from the more derived Arabidopsis.  Based on this we can hypothesize that ancestral gene function has both been conserved and diverged in these 4 MADS-box genes. 
References:
Ma H., dePamphilis C. (2000) The ABCs of floral evolution. Cell. Mar 31;101:5-8.
Soltis, D. E., Soltis, P. S., Albert, V. A., Oppenheimer, D. G., dePamphilis, C. W., Ma, H., Frohlich, M. W., and Theissen, G. Floral Genome Project Research Group. (2002) Missing links: the genetic architecture of flowers [correction of flower] and floral diversification. Trends in Plant Sciences. Jan;7:22-31.

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 09/17/03 Speaker: Barbara Bliss, Dept. of Biology, Penn State Univ.
Title: Revealing multiple transfers among plant organelle genomes
Abstract: Phylogenetic analysis of vertically transferred (parent to offspring) sequence information illustrates accepted species relationships.  Greater similarity of sequence is presumed to reflects conserved function or a more recent common ancestor.  Horizontal gene transfer (HGT) is also revealed with phylogenetic analysis, in which case the resulting topology differs from the accepted organismal topology.  Historically, putative HGTs  have been uncovered one at a time, using careful hybridization experiments to probe unlikely genomes.  Functional information about a candidate sequence may suggest that it did not arise there independently or be conserved to perform an essential function.  I used a bioinformatics approach to develop a whole genome view of multiple organelles, revealing numerous putative horizontal transfers, large and small.  Experimental evidence from PCR and sequencing reactions confirmed the existence of these sequences, and phylogenetic analyses support the hypothesis that organelle genomes have been extensively invaded by horizontal gene transfer.  Present-day availability of whole, well-annotated genomes and the tools to manipulate them allows rapid identification and analysis of evolutionary events involving multiple genomes.
References:
Lawrence, J. G., and Ochman, H. (1997) Amelioration of bacterial genomes: Rates of change and exchange. Journal of Molecular Evolution 44:383-397.
Woese, C. (1998) The universal ancestor. Proceedings of the National Academy of Sciences of the United States of America 95:6854-6859.
Cummings, M. P., Nugent, J. M., Olmstead, R. G., and Palmer, J. D. (2003) Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in angiosperms. Current Genetics 43:131-138.
Schwartz, S.,  Zhang, A., Frazer, K. A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R., and Miller, W.  (2000) PipMaker - A web server for aligning two genomic DNA sequences.  Genome Research 10:577-586.

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 09/24/03 Speaker: Dr. Ning Zhang, Dept. of Plant Pathology, Penn State Univ.
Title: Discula destructiva, the causal agent of dogwood anthracnose is thought to have been introduced to North America in late 1970s. Two distinct groups of D. destructiva isolates, one from the western U. S. and the other from the eastern U. S., were identified with amplified fragment length polymorphism (AFLP) markers and sequences of several genes. The remarkably low genetic diversity indicated that it is still under intense selection pressure. In another important group of fungi, Fusarium solani species complex, a number of new lineages were identified based on phylogeny of the Elongation Factor 1-alpha gene, suggesting that there are more species in the F. solani complex than previously recognized. In order to apply phylogenetic species concept to the F. solani complex, multiple loci were analyzed for a subset of isolates. The results show support for clades corresponding to known mating populations, in addition to a number of new lineages. Overall, the F. solani complex was found to contain a tremendous amount of phylogenetic diversity.
References:
Zhang, N., and Blackwell, M. (2002) Population structure of dogwood anthracnose fungus. Phytopathology 92: 1276-1283.
O’Donnell, K. (2000) Molecular phylogeny of the Nectria haematococca-Fusarium solani species complex. Mycologia 92: 919-938.

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 10/01/03 Dr. Wojciech Makalowski, Dept. of Biology, Penn State Univ.
Title: Genomic scrap yard: how genomes utilize all that junk
Abstract: Interspersed repetitive sequences are major components of eukaryotic genomes. Repetitive elements comprise over 50% of the mammalian genome. Because the specific function of these elements remains to be defined and because of their unusual  behavior  in the genome, they are often quoted as a selfish or junk DNA. Our view of the entire phenomenon of repetitive elements has to now be revised in light of data on their biology and evolution, especially in the light of what we know about the retroposons. I would like to argue that even if we cannot define the specific functions of these elements, we still can show that they are not useless pieces of the genomes. The repetitive elements interact with the whole genome and influence its evolution. Repetitive elements interact with the surrounding sequences and nearby genes. They may serve as recombination hot spots or acquire specific cellular functions such as RNA transcription control or even become part of protein coding regions. Finally, they provide very eYcient mechanism for genomic shuZing. As such, repetitive elements should be called genomic scrap yard rather than junk DNA.
References:
Makalowski, W. (2000) Genomic scrap yard: how genomes utilize all that junk. Gene  259:61-67.
Brosius, J. (2003) The contribution of RNAs and retroposition to evolutionary novelties. Genetica. 118:99-116.
Makalowski, W. (2003) Not Junk After All. Science 300:1246-1247.

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 10/08/03 Speaker: Dr. Kazuhiko Kawasaki, Dept. of Anthropology, Penn State Univ.
Title: Paralogue after paralogue in teeth and bones
Abstract: Mineralized tissue is a critical innovation in vertebrate evolution.  The mammalian tooth forms in three layers, enamel, dentin, and bone, each of which crystallizes on specific extracellular matrix (ECM) proteins.  We have characterized the secretory calcium-binding phosphoprotein (SCPP) gene family, which arose from a common ancestor by gene duplications, and specialized into enamel or dentin/bone ECM protein genes early in vertebrate evolution.  Later in mammals, an enamel ECM protein gene eventually created milk casein and salivary protein gene clusters by recurrent duplications.  These proteins help grow or maintain teeth and bones.  The SCPP gene sequences are poorly conserved during evolution; hence efforts to identify fish SCPP genes have been largely unsuccessful.  However, by searching the Fugu genome syntenic to the human SCPP gene locus, we found an SCPP gene cluster.  Surprisingly, none of these genes show sequence homology to mammalian genes.  Thus, apparently a different SCPP family developed in Teleosts, suggesting that different sets of paralogous genes organize mammalian and fish mineralized tissues.
References:
Toyosawa, S., O’hUigin, C., Figueroa, F., Tichy, H., and Klein, J. (1998) Identification and characterization of amelogenin genes in nomotremes, reptiles, and amphibians.  Proc. Natl. Acad. Sci. USA. 95:13056-13061.
Kawasaki, K., and Weiss, K. M. (2003) Mineralized tissue and vertebrate evolution: The secretory calcium-binding phosphoprotein gene cluster. Proc. Natl. Acad. Sci. USA. 100:4060-4065.

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 10/15/03 Speaker: Li Hao, Dept. of Biology, Penn State Univ.
Title: Sequence and Phylogenetic Analysis of the Ly49 Gene Cluster in Rats: A Very Rapidly Evolving Gene Family in Rodent Lineage
Abstract:
The natural killer cell receptors play a significant role in innate immunity as the first line of defense against pathogens. Interestingly, primates and rodents use different gene families to perform the equivalent function: killer cell immunoglobulin-like receptors (KIRs) in primates and Ly49s in rodents. However both of these two gene families duplicate at an unexpectedly high rate in either primates or rodents. Here we examined the rapid evolution of Ly49 genes in rats and compare them with mouse Ly49 homologues. More than 20 new Ly49 loci have been characterized in rat chromosome 4. Excluding short gene fragments, a total of 31 Ly49 genes are clustered in a 1.8 Mb genomic region. Compared to the mouse Ly49 cluster, the rat Ly49 cluster is more complicated in terms of gene number and gene arrangement. Sequence analysis also shows the extreme difference between mouse and rat Ly49 genes. Most of the Ly49 genes in these two species form highly divergent and species-specific groups, suggesting that multiple duplications and diversification have been occurring after the mice-rats divergence. The similarity of the evolutionary pattern between KIR genes in primates and Ly49 genes in rodents will be also discussed.
References:
Makrigiannis, A. P., Pau, A. T., Schwartzberg, P. L., McVicar, D. W., Beck, T. W., and Anderson, S. K. (2002) A BAC contig map of the Ly49 gene cluster in 129 mice reveals extensive differences in gene content relative to C57BL/6 mice. Genomics 79:437-444.
Naper, C., Hayashi, S., Kveberg, L., Niemi, E. C., Lanier, L. L., Vaage, J. T., and Ryan, J. C.. (2002a) Ly49-s3 is a promiscuous activating rat NK cell receptor for nonclassical MHC class I-encoded target ligands. J. Immunol. 169:22-30.
Naper, C., Hayashi, S. Joly, E., Butcher, G. W., Rolstad, B., Vaage, J. T., and Ryan, J. C. (2002b) Ly49i2 is an inhibitory rat natural killer cell receptor for an MHC class Ia molecule (RT1-A1c). Eur. J. Immunol. 32:2031-2036.
Wilhelm, B. T., Gagnier, L., and Mager, D. L. (2002) Sequence analysis of the Ly49 cluster in C57BL/6 mice: A rapidly evolving multigene family in the immune system. Genomics 80:646-661.
Smith, H. R. C., Heusel, J. W., Mehta, I. K., Kim, S. Dorner, B. G., Naidenko, O. V., Lizuka, K., Furukawa, H., Beckman, D. L., Pingel, J. T., Scalzo, A. A., Fremont, D. H., and Yokoyama, W. M. (2002) Recognition of a virus-encoded ligand by a natural killer cell activation receptor. Proc. Natl. Acad. Sci. U S A 99:8826-31.

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 10/22/03 Speaker: Jongmin Nam - Department of Biology
Title: Evolution of homeobox gene family controlling fundamental processes of animal development.
Abstract:
Homeobox genes are important transcription factors regulating various processes of animal development. Therefore, study of the evolution of homeobox genes is helpful for understanding the evolutionary changes of morphological and physiological characters. To this end we compiled 1699 homeodomain sequences from 11 completely or almost completely sequenced genomes (humans, rodents, frogs, fishes, tunicates, insects, and nematodes). We then performed a phylogenetic analysis of these sequences and studied the increase and decrease of the number of homeobox genes in the evolutionary process. Our analysis showed that there were at least 71 homeobox genes in the most recent common ancestor (MRCA) of all of the 11 species. Our further phylogenetic analysis suggested that (1) the number of the descendents of these 71 genes increased substantially in the vertebrate lineage, but the increase was moderate in other lineages such as nematode, insects, and tunicate, (2) the gene number increase was most dramatic in the early stage of insect and vertebrate evolution, (3) although the total number of descendents of 71 ancestral genes increased in each genome, a substantial number of genes were lost in all evolutionary lineages, (4) in contrast to the unequal rate of increase of gene number among different evolutionary lineages, the numbers of losses of descendents of the 71 ancestral genes were similar among the 11 species, and (5) at least 20 ~ 30 genes out of 71 ancestral genes were lost in each genome. We also studied the increase and decrease of gene number for different groups of homeobox genes and found that most groups show similar patterns of increase and loss of genes, though there are several exceptions. Biological implication of these evolutionary changes of homeobox genes will be discussed.
References:
Wagner G. P., Amemiya C., Ruddle F. (2003) Hox cluster duplications and the opportunity for evolutionary novelties. Proc. Natl. Acad. Sci. USA. 100(25):14603-6.
Banerjee-Basu S., Baxevanis A. D. (2001) Molecular evolution of the homeodomain family of transcription factors. Nucleic Acids Res. 29(15):3258-69.

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 10/29/03 Speaker: Dr. Yoshihito Niimura, Dept. of Biology, Penn State Univ.
Title: Comparative Evolutionary Analysis of Olfactory Receptor Genes: Humans Lost, Mice Gained
Abstract: Olfactory receptor (OR) genes are the largest known multigene family in mammalian genomes. Previously we reported that the complete human genome contains ~800 OR functional genes and pseudogenes, and 52% of them are pseudogenes. To see the difference in the evolution of OR genes, we detected the entire OR gene family from mouse whole genome sequences. We identified 1,037 potentially functional genes and 354 apparent pseudogenes, and they are distributed in 69 chromosomal locations. The largest genomic cluster contains 267 OR genes, and it occupies a 5-Mb region. By conducting extensive phylogenetic analysis, we showed that the organization of genomic clusters in mice are highly conserved with those in humans, though the number of genes are much larger in mice than humans. We also found that each of >150 human pseudogenes form a phylogenetic clade with mouse functional gene(s), indicating that the human lineage lost many OR genes after the separation of human and mouse lineages. In contrast, most of the mouse OR pseudogenes seem to have generated after the human-mouse divergence. Estimation of the divergence time at each branching point suggests that the mouse lineage gained >300 OR genes by gene duplications after the human-mouse divergence, while the number is ~50 for the human lineage. These observations imply that the difference in OR gene family between humans and mice has been formed by two major processes: the human lineage lost many OR genes by pseudogenizations, and the mouse lineage gained hundreds of OR genes by tandem gene duplications.
References:
Niimura, Y., and Nei, M. (2003) Evolution of olfactory receptor genes in the human genome. Proc. Natl. Acad. Sci. USA 14:12235-12240.
Young, J. M. et al. (2002) Different evolutionary processes shaped the mouse and human olfactory receptor gene families. Hum. Mol. Genet. 11:535-546.
Zhang, X., and Firestein, S. (2002) The olfactory receptor gene superfamily of the mouse. Nat. Neurosci. 5:124-133.

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 11/05/03 Speaker: Dr. Hiroshi Akashi, Dept. of Biology, Penn State Univ.
Title: Metabolic economics and the Yeast proteome
Abstract: The notion of "functional constraint" in protein evolution considers mainly the relationship between the primary structure of a protein and its function.  Here, I test whether selection for efficient synthesis acts as a global pressure on the amino acid composition and sizes of proteins.  The Saccharomyces cerevisiae genome sequence, DNA microarray expression data, tRNA gene numbers, and functional categorizations of proteins are employed to determine whether the amino acid composition of peptides reflects natural selection to optimize the speed and accuracy of translation.  Strong relationships between synonymous codon usage bias and estimates of transcript abundance suggest that DNA array data serve as adequate predictors of translation rates.  Amino acid usage also shows striking relationships with expression levels.  Stronger correlations between tRNA concentrations and amino acid abundances among highly expressed than among less abundant proteins supports adaptation of both tRNA abundances and amino acid usage to enhance the speed and accuracy of protein synthesis.  Natural selection for efficient synthesis appears to also favor shorter proteins as a function of their expression levels.  Comparisons restricted to proteins within functional classes are employed to control for differences in amino acid composition and protein size that reflect differences in the functional requirements of proteins expressed at different levels.
References:
Akashi, H. (2001) Gene expression and molecular evolution. Curr. Opin. Genet. Dev. 11:660-666.
Akashi, H. (2003) Translational selection and yeast proteome evolution. Genetics 164:1291-1303.
Baudouin-Cornu, P., Surdin-Kerjan, Y., Marliere, P., and Thomas, D. (2001) Molecular evolution of protein atomic composition. Science 293:297-300.
Ikemura, T. (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2:13-34.

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 11/12/03 Speaker: Dimitra Chalkia, Dept. of Biology, Penn State Univ.
Title:
Phylogenetic analysis of formin homology proteins in Arabidopsis thaliana and Oryza sativa
Abstract: The plant cell cytoskeleton plays an important role in many cellular processes, including cell polarity establishment and cytokinesis. Proteins that regulate cytoskeletal assembly are likely to be a part of the signaling cascade that governs plant cell morphogenesis. Formins are members of a large protein family that is defined by the presence of the highly conserved Formin Homology II (FH2) domain. In a wide range of organisms, including vertebrates, arthropods, nematodes and fungi, formins have been implicated in the regulation of cytoskeletal assembly and in the control of cytokinesis and cell polarity establishment and maintenance. The genomes of Arabidopsis thaliana and Oryza sativa contain putative formin-like proteins based on the presence of an FH2 domain. Arabidopsis thaliana formins have been tentatively sub-divided into two clades: Type I and Type II, based on the FH2 domain alignment. We have extended this analysis to cover both Arabidopsis and rice and have provided an evolutionary context for these plant formin families. Our phylogenetic analysis shows that formins are divided in two distinct clades in plants. This phylogenetic clustering is also supported by the structural features of these proteins. This division of plant formins in two distinctive groups seems to predate the split of monocots/eudicots. The detailed evolutionary relationships of plant formins remain unclear. The placement of fungi formins at the basal position of the tree is in accordance with the most recent proposed phylogenetic scheme for eukaryotes. Animal and plant formins cluster together, and split into two major groups. This clustering may suggest that their last common ancestor had already at least two different types of formins.
References:
Cvrckova, F. (2000) Are plant formins integral membrane proteins? Genome Biology; 1(1) research 001.1-001.7.
Deeks, M. J., Hussey, P. J., and Davies, B. (2002) Formins: intermediates in signal-transduction cascades that affect cytoskeletal reorganization. Trends Plant Sci 7 13:492-498.

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 11/19/03 Speaker: Norman Barr, Dept. of Entomology, Penn State Univ.
Title: Phylogenetics of the genus Ceratitis (Tephritidae) based on mtDNA and the nuclear gene period
Abstract:
The genus Ceratitis, native to the Afrotropics, consists of 88 described species in six recognized subgenera. Like other tephritids, Ceratitis species feed on and damage the fruit of host plants. Several species within the genus are polyphagous and pose a threat to agriculture. For example, the Medfly (C. capitata), which attacks over 300 species in almost 70 plant families, is considered one of the world’s worst insect pests. Despite its importance to agriculture, the systematic positions of Ceratitis relative to closely related genera, subgenera within Ceratitis, and species within the Ceratitis subgenera are yet uncertain. I have produced Ceratitis phylogenies using mitochondrial (cytochrome oxidase 1 and NADH dehydrogenase 6) and nuclear (period) genes, to help understand the systematics of this important group.
References:
De Meyer, M. (1999) Phylogeny of the genus Ceratitis (Dacinae Ceratitidini). In Fruit Flies (Tephritidae) Phylogeny and Evolution of Behavior, M. Aluja and A. Norrbom (eds), CRC Press, Boca Raton, FLorida.

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 11/26/03 Thanksgiving Holiday

 12/03/03 Speaker: Dr. Kateryna Makova, Dept. of Biology, Penn State Univ.
Title: Divergence in the spatial pattern of gene expression between human duplicate genes
Abstract: Microarray gene expression data provide a wealth of information for elucidating the mode and tempo of molecular evolution. In the present study, we analyze the spatial expression pattern of human duplicate gene pairs by using oligonucleotide microarray data, and study the relationship between coding sequence divergence and expression divergence. First, we find a strong positive correlation between the proportion of duplicate gene pairs with divergent expression (as presence or absence of expression in a tissue) and both synonymous (K(S)) and nonsynonymous divergence (K(A)). The divergence of gene expression between human duplicate genes is rapid, probably faster than that between yeast duplicates in terms of generations. Second, we compute the correlation coefficient (R) between the expression levels of duplicate genes in different tissues and find a significant negative correlation between R and K(S). There is also a negative correlation between R and K(A), when K(A) <or=0.2. These results indicate that protein sequence divergence and divergence of spatial expression pattern are initially coupled. Finally, we compare the functions of those duplicate genes that show rapid divergence in spatial expression pattern with the functions of those duplicate genes that show no or little divergence in spatial expression.
References:
Makova, K. D., and Li, W. H. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res. 2003 Jul;13(7):1638-45.

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 12/10/03 Speaker: Dr. Vamshi Veeramachaneni, Dept. of Biology, Penn State Univ.
Title: Database of Evolutionary Distances
Abstract: A large database of homologous sequence alignments with good estimates of evolutionary distances can be a valuable resource for molecular evolutionary studies and phylogenetic research in particular. We recently created a prototype database containing 69,000 genes from human, mouse and rat species. Approximately 17,000 homology groups were identified with the help of Ensembl homology evidence.  At the macro-level the database allows us to answer questions of the form:

  1. "What is the average k-distance between 5'UTRs of human and mouse?"
  2. "List the 10 groups with the highest Ka/Ks ratio between mouse and rat"
  3. "List all identical proteins between human and rat"

Researchers interested in specific proteins can use a simple web-interface to retrieve the homology groups of interest, examine all pair-wise distances between members of the group, and study the exon-intron gene structures using graphical interface.

Current data, access to the database, and proposed extensions will be discussed.

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