Institute of Molecular
Evolutionary Genetics


FALL 2004
Previous IMEG Seminars and Abstracts:
Fall 2009

Spring 2009

Fall 2008 Spring 2008

Fall 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

Speaker: Dr. Zhi-Chun Lai - Department of Biology
Title: Notch Regulation and Cell Fate Control
Abstract: Cellular signaling activities must be tightly regulated for proper cell fate control and tissue morphogenesis.  We have previously  shown that the Drosophila leucine-rich repeat (LRR) transmembrane glycoprotein Gp150 plays a critical role in regulating Notch signaling in the developing eye and other tissues.   Gp150 is co-localized with Delta, a ligand of the Notch receptor, in intracellular vesicles.  More recently, gp150 is shown to synergistically interact with scabrous (sca) to regulate Notch signaling.   Genetic analysis indicated that gp150 and sca function in a common pathway and gp150 is required for all activities of sca.  Immunostaining experiments revealed that Gp150 concentrated Sca protein in late endosomes.  A model is proposed in which endosomal Sca and Gp150 promote Notch activation in response to Delta.

Li, Y., Fetchko, M., Lai, Z.-C. and Baker, N. E. "Scabrous and Gp150 are endosomal proteins that regulate Notch activity," Development, 130: 2819-2827, 2003.
Fetchko, M., Huang, W., Li, Y. and Lai, Z.-C. "Drosophila Gp150 is Required for Early Ommatidial Development through Modulation of Notch Signaling," The EMBO Journal,21: 1074-1083, 2002.

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 09/15/04 Speaker: Dr. Jan Klein - Department of Biology
Title: The Place of the Human Species in Nature
Abstract: The belief that humans are special and hence that they have special rights, which include domination and mastery of nature, is widespread. It is based on three illusions (physical, psychological, and biological) people have about their position in nature. The consequences of this belief are unrestrained growth of human population, disproportionate usurpation of territory by our species, uncurbed exploitation of Earth' resources, befouling of our planet, and unrestrained extermination of other species. I will argue that molecular evolutionary biology provides no justification for the view that we are special and  that a large gap separates our species from our nearest relative. I will discuss rules of rational ethical behavior  which follow from the study of evolution.
Klein, J. 2002. Where do we come from? New York, Springer-Verlag.

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 09/22/04 Speaker: Liying Cui - Department of Biology
Title: Estimating gene number from cDNA libraries of developing flowers
Abstract: The flowering plants are the most successful group of land plants with unique reproductive organs -- flowers. Molecular phylogeny studies elucidate the group of the most early branching flowering plants, or basal angiosperms, including water lilies (Nuphar and Nymphea ), Amborella (a shrub from New Caledonia) and several other woody plants. The Floral Genome Project (FGP) aims at sequencing 10,000 ESTs from cDNA libraries of young flower buds from selected species of basal angiosperms . Several questions arise in EST sequencing. We would like to know how many genes are expressed in a underlying cDNA library with a few thousand EST sequences. We also want to predict the sequence redundancy in future EST sequencing. The statistical model of cDNA libraries was developed to address these questions. I present a simple estimate based on log ratio plots described by Mao and Lindsay.  A web-based software, ESTstat, is developed to correct EST clustering errors and to estimate the number of genes in a given cDNA library. 
Wang, J. P., B. G. Lindsay, J. Leebens-Mack, L. Cui, K. Wall, W. C. Miller, and C. W. DePamphilis. 2004. EST clustering error evaluation and correction. Bioinformatics.

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 09/29/04 Speaker: Dr. Hongzhi Kong - Department of Biology
Title: Rapid Birth-and-Death Evolution in the SKP1 Gene Family
Abstract: Skp1 (S-phase kinase-associated protein 1) is a core component of SCF ubiquitin ligases and mediates protein degradation, thereby regulates eukaryotic fundamental processes such as cell cycle progression, transcriptional regulation, and signal transduction. Among the four components of the SCF complexes, Rbx1 and Cullin form a core catalytic complex, F-box protein acts as a receptor for target proteins, and Skp1 serves as an adaptor that links one of the variable F-box proteins to Cullin. Whereas protists, fungi and some vertebrates have a single SKP1 gene, many animal and plant species possess multiple SKP1 homologs which have evolved at highly heterogeneous rates. The slowly evolving members are relatively conserved in structure and expressed widely and/or at high levels and serve the most fundamental function(s), while the rapidly evolving ones are structurally more diverse and usually expressed at low levels, in specific tissues, or possibly under specific conditions, suggesting that they may have lost their original function(s) and/or acquired new function(s). In addition, the relationships of the most slowly evolving Skp1 proteins from different species tend to follow the organismal phylogeny, but the moderately and rapidly evolving genes appear to be members of species-specific clades. Orthologous relationships could not be easily observed even when SKP1 genes from the closely related species were compared. dN/dS analysis further indicated that the vast majority of the moderately and rapidly evolving SKP1 genes have evolved under relaxed or altered constraint. All this suggests that the SKP1 gene family has experienced a rapid birth-and-death process.

Kong H., Leebens-Mack J., Ni W., dePamphilis C. W., Ma H., 2004.
Highly heterogeneous rates of evolution in the SKP1 gene family in plants and animals: Functional and evolutionary implications. Molecular Biology and Evolution 21: 117-128

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 10/06/04 Speaker: Richard Meisel - Department of Biology
Title: Reexamining a Classic Genetic System: What can laboratory crosses tell us about the maintenance of paracentric inversions in natural populations of Drosophila pseudoobscura?
Drosophila pseudoobscura is polymorphic for over 30 different arrangements of the third chromosome distinguished by single paracentric inversions.  Surveys of natural populations, experimental studies, and sequence analysis (Schaeffer et al. 2003) all suggest that natural selection plays a role in maintaining this polymorphism.  It is hypothesized that suppressed recombination between karyotypes maintains coadapted alleles within inversions so that favorable combinations are held in cis.  Early studies (e.g., Dobzhansky and Epling 1948) confirm that recombination is highly suppressed in inversion heterozygotes, but the data suggest a possible meiotic drive mechanism that has been overlooked in the literature for over a half of a century.  Due to the paucity of markers used in these early studies it is difficult to quantify the degree that recombination is suppressed by inversions.  Also, these studies relied on phenotypic markers that may cause decreased fitness of certain phenotypic classes.  To gain a more fine scale understanding of recombination in inversion heterozygotes and to overcome the problems associated with phenotypic markers in studying meiotic drive, we propose using microsatellite markers to study both of these phenomena.
Dobzhansky, T., and C. Epling. 1948. The suppression of crossing over in inversionheterozygotes of Drosophila pseudoobscura. Proc. Natl. Acad. Sci. USA 34:137-141.
Schaeffer, S. W., M. P. Goetting-Minesky, M. Kovacevic, J. R. Peoples, J. L. Graybill, J. M. Miller, K. Kim, J. G. Nelson, and W. W. Anderson. 2003. Evolutionary genomics of inversions in Drosophila pseudoobscura: evidence for epistasis. Proc. Natl. Acad. Sci. USA 100:8319-8324.

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 10/13/04 Speaker: Dietmar Schwarz - Department of Biology
Title: Speciation via hybridization in a specialist insect is triggered by the shift to a new host
Hybridization has long been regarded as an important source of evolutionary novelty in plants. Zoologists, in contrast, have regarded hybridization merely as an artifact of incomplete reproductive isolation. Especially the formation of new animal species via hybridization has been deemed highly unlikely (unless it results in parthenogenetic, polyploid taxa). Here I present the first case of hybridization in an insect that has resulted in an isolated, diploid and bisexually reproducing population. I discovered the infestation of invasive honeysuckle, Lonicera spp., by flies belonging to the R. pomonella species complex (Diptera: Tephritidae). Because all members of this species complex are native to North America, the infestation of Lonicera has to be the result of a recent host shift. Multilocus nuclear genotypes and mitochondrial DNA sequences suggested that the Lonicera Fly originated via hybridization between the blueberry maggot R. mendax and the snowberry maggot R. zephyria. I tested a hybrid origin of the Lonicera Fly against the competing hypotheses of a single species host shift and incomplete lineage sorting. The same data also provide indirect evidence for the reproductive isolation of the Lonicera Fly from its parent taxa.This unique combination of host shift and hybridization suggests sympatric speciation via host shift as the mechanism by which the hybrid Lonicera Fly formed. I discuss how the increased phenotypic variability of hybrid origin populations could facilitate adaptive speciation. Based on the example of the Lonicera Fly I propose the concept “biological metaspecies,” that describes a group of sibling species that are connected by some degree of hybridization. While under most circumstances gene flow between the taxa of the metaspecies is of little consequence, hybridization can provide novel genetic variation to adapt to a change in the environment, such as the introduction of a new host plant.
Vie, S. 2001. Sympatric speciation in animals: the ugly duckling grows up. Trends Ecol. Evol.16:381-390.

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 10/20/04 Speaker: Dr. Claude dePamphilis - Department of Biology
Title: Origin and diversification of the floral regulators in the earliest angiospersms
Abstract: The
sudden appearance of flowers in the fossil record about 100 million years ago represents a great mystery that has long puzzled evolutionary biologists.   Among the many key questions surrounding the origin diversification of flowers include: Did the ancestral flower possess the full complement of genetic information needed to assemble a modern flower?   Are there genes that have conserved functions throughout much of flowering plant history?  What components of genetic diversity cause the important variation in flower diversity that we see today?  Recent studies in plant developmental genetics and genomics have identified more than 100 genes with specific roles in flower development in Arabidopsis and other model organisms, and any other genes with critical roles may remain undiscovered, largely because of functional redundancy or lethality of loss of function mutations.
The Floral Genome Project ( was initiated to address these questions by identifying the origin and studying the evolutionary diversification of floral regulators throughout the major lineages of flowering plants.  Our study was designed to capture large numbers of genes expressed during early flower development in phylogenetically critical lineages of flowering plants and gymnosperms, and to determine their expression patterns at several levels of resolution.  We then link the sequences and expression patterns through phylogenetic analysis to infer the gene sets and expression patterns that may have been present in the earliest angiosperm lineages.   This talk will summarize some of the results coming from over 70,000 EST sequences that tag homologs of most genes known to be important in flower development.  Among our observations to date:  1) The floral transcriptome is similarly large, and estimated to contain over 10,000 expressed genes, in basal as well as more derived dicot and monocot model organisms.   2) Most key genes playing known roles flower development have homologs present in basal angiosperm lineages and may be inferred to be part of the ancestral floral transcriptome.   3) genome doubling (polyploidy) appears to be a common process in plant genomes, including these most basal lineages, meaning that uniquely orthologous genes may be relatively uncommon, 4) consistent with the above, specific genes of known function are often the product of one or more gene duplications that separate basal lineages from more derived eudicot and grass models.
I will illustrate these findings with a summary of several case studies involving MADS box genes, which are critical regulators of flower form, as well as several other gene families with genes important in flower development.
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.  Response:  Missing links: the genetic architecture of flower and floral diversification.  Trends in Plant Science 7: 31-33.

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 10/27/04 Speaker: Jongmin Nam - Department of Biology
Title: Evolution of homeobox gene family controlling fundamental processes of animal development.
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.
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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 11/03/04 Speaker: Indrani Halder - Department of Biology
Title: Analyzing individual BioGeographical ancestry and Admixture structure in human
Understanding genetic variation in populations and how this variation contributes to differences in disease risk among populations is an important area of research. We have typed a panel of 11,555 SNP markers in three resident US populations, (African Americans, Puerto Ricans and European Americans) in an effort to analyze patterns of genetic variability. The first two are considered admixed populations with varying levels of BioGeographical ancestry (BGA), while the European Americans are assumed to be more homogeneous. Putative ancestral populations were chosen from among a panel of twelve world populations typed for the same markers. Using a maximum likelihood based method and a separate Bayesian method we show that individual BGA estimates vary within all groups. Assuming a trihybrid model of admixture between Europeans, West Africans and Native Americans we observed large variations in individual BGA levels in both the African-American and Puerto Rican samples, while the European Americans are more tightly clustered. Additional simulation studies were done to check the reliability of the estimates under the specified model. Simulations further indicate that the choice of ancestral population and its sample size both affect individual BGA estimates. To test for stratification within the population samples we have used the Individual Ancestry Correlation (IAC) test, where markers are split into two non-overlapping subsets and ancestry is estimated separately with both sets. Correlation between estimates obtained with the different marker sets indicates presence of genetic structure. While both the African-American and the Puerto Rican samples show admixture stratification as expected, we also detected evidence for stratification within the European-American sample. Additional simulations showed that individual BGA estimates differed when only a subset of informative markers was used as opposed to including all markers.
Bonilla C, Shriver MD, Parra EJ, Jones A, Fernandez JR. Ancestral proportions and their association with skin pigmentation and bone mineral density in Puerto Rican women from New York City. 
Hum Genet. 2004 Jun;115(1):57-68.
Hoggart CJ, Shriver MD, Kittles RA, Clayton DG, McKeigue PM. Design and analysis of admixture mapping studies.   Am J Hum Genet. 2004 May;74(5):965-78.
Halder I; Shriver M.D. Measuring and using admixture to study the genetics of complex diseases.  Human Genomics, November 2003, vol. 1, no. 1, pp. 52-62(11).

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 11/10/04 Speaker: Dr. Kazuhiko Kawasaki - Department of Anthropology
Title: Molecular evolution of vertebrate mineralized skeleton.
Abstract: Mineralized skeleton is a critical innovation for the adaptive evolution of vertebrates.  Paleozoic jawless fish developed extensive body armor consisting of three tissue layers: surface enameloid (enamel-like hard tissue), dentin, and basal bone.  Three similar tissues are seen in mammalian teeth, suggesting their ancient origin.  We have revealed that eight mammalian genes for enamel, dentin, and bone matrix proteins arose by gene duplication from an ancestral gene, SPARC.  In addition, mammalian milk caseins, salivary proteins, and an avian eggshell protein are also the relatives of these proteins, and all form the secretory calcium-binding phosphoprotein (SCPP) family.  Notably, our analysis suggested that most SCPPs arose during the evolution of the lobe-finned fish.  This suggests that the mechanism of tissue mineralization was considerably modified by parallel functional specialization of duplicated SCPP genes facilitating adaptive evolution in our lineage after the divergence of rayfins and lobefins.
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.
Kawasaki, K., Suzuki, T., and Weiss, K. M. 2004. Genetic basis for the evolution of vertebrate mineralized tissue.  Proc. Natl. Acad. Sci. USA. 101: 11356-11361.

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 11/17/04 Speaker: Dimitra Chalkia - Department of Biology
Title: Phylogenetic Analysis of the Formin Homology 2 Domain in Metazoa
Abstract: Formins are multidomain proteins which are implicated in a wide range of actin-based processes, including cell polarization, cytokinesis, and embryonic development in all eukaryotic species studied so far. The most conserved segment of formins is the formin homology-2 (FH2) domain, which is crucial for actin nucleation. FH2 domain can be divided in five subdomains, namely lasso, linker, knob, coiled-coil, and post. Athough, six different formin protein subfamilies have been so far described, there is no comprehensive understanding of the actual number of genes encoding for the FH2 domains in different metazoan genomes. Here, we describe several novel proteins containing FH2 domains from 13 metazoan species and investigate their evolutionary relationships.
Our results show that metazoan formins can be classified into eight monophyletic groups. Two novel groups, form4 and form5, were identified, which are chordate-specific and nematode-specific, respectively. All the metazoan formins evolved sequentially from a common ancestor following the model of divergent evolution. Post subdomain is highly conserved, while linker is the least conserved region both within and between the eight formin groups. Amino acid residues that directly or indirectly have been implicated in the function of formins are conserved in all groups, suggesting that all proteins most likely function in a similar manner. The remaining residues show group-specific conservation, which could imply functional specificity. Our analyses predict that metazoan formins should share the same mechanism of function and furthermore that the different groups might show functional specificity.  The latter could also be true for some of the paralogous sequences.
Wallar, B. J., and Alberts, A. S. 2003. The formins: active scaffolds that remodel the cytoskeleton. Trends Cell Biol. 13, 435-446.
Xu, Y. Moseley, G. B., Sagot, I., Poy, F., Pellman, D., Goode, B. L., and Eck, M. J. 2004. Crystal structures of a formin homology-2 domain reveal a tethered dimer architecture. Cell 116, 711-723.
Zigmond, S. H. 2003. Fomin-induced nucleation of actin filaments. Curr.  Opin. Cell Biol. 16, 1-7.

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 12/01/04 Speaker: Dr. Nikolas Nikolaidis - Department of Biology
Origin and evolution of the Ig-like domains present in mammalian leukocyte receptors.
In mammals many natural killer (NK) cell receptors encoded by the leukocyte receptor complex (LRC) regulate the cytotoxic activity of NK cells and provide protection against virus-infected and tumor cells. To investigate the origin of the Ig-like domains encoded by the LRC genes, a subset of C2-type Ig-like domain sequences was compiled from mammals, birds, amphibians, and fish. Phylogenetic analysis of these sequences generated several monophyletic groups. Two main conclusions can be drawn from the phylogenetic relationships between the major groups. First, the two groups of mammalian LRC sequences must diverged before the separation of the avian and mammalian lineages. Second, the mammalian LRC sequences are most closely related to the Fc receptor sequences and these two groups diverged before the separation of birds and mammals.
Dennis G Jr, Kubagawa H, Cooper MD (2000) Paired Ig-like receptor homologs in birds and mammals share a common ancestor with mammalian Fc receptors. Proc Natl Acad Sci U S A 97:13245-13250
Hao L, Nei M (2004) Rapid expansion of Killer Cell Immunoglobulin-like Receptor genes in primates and their coevolution with MHC Class I genes. Gene
in press.
Hughes AL, Nei M (1988) Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 355:167-170.
Martin AM, Kulski JK, Witt C, Pontarotti P, Christiansen FT (2002) Leukocyte Ig-like receptor complex (LRC) in mice and men. Trends Immunol 23:81-88

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 12/08/04 Speaker: Jill Ricker - Department of Biology
Strong evidence for expression pattern shifts driving the maintenance of duplicated regulatory genes in Arabidopsis thaliana
Whole genome duplication is common in flowering plants, with at least one detectable genome duplication in 50-70% of species. This study examines the frequency of expression pattern shifts representing subfunctionalization and/or neofunctionalization in maintained duplicated regulatory genes.  280 paralogous pairs in Arabidopsis were identified using phylogenetic trees of Arabidopsis and rice amino acid sequences for 91 regulatory gene families.  A two-way ANOVA was performed to identify significance of gene, tissue, and gene by tissue interaction effects within each paralogous pair using microarray data from six wild-type tissues.  Results indicate that 85% of paralogous pairs have statistically significant gene by tissue interactions; this is indicative of subfunctionalization and/or neofunctionalization.  Ka/Ks analyses for global protein constraint indicate that there is no relationship between the Ka/Ks ratio and a significant gene by tissue interaction. We conclude that expression pattern shifts drive maintenance of duplicated genes in Arabidopsis regulatory gene families.
Force, A., Lynch, M., Pickett, F. B., Amores, A., Yan, Y.  L. & Postlethwait, J. (1999) Genetics 151, 1531-1545.
Blanc, G. & Wolfe, K. H. (2004) Plant Cell 16, 1679-1691.
Makova, K. D. & Li, W. H. (2003) Genome Research 13, 1638-1645.

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