Institute of Molecular
Evolutionary Genetics











Spring 2006


Previous IMEG Seminars and Abstracts:

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

Spring 2002




Speaker: Dr. David Geiser

Title: "Fusarium infections of humans: who are the culprits?"

Abstract: . As cytotoxic therapies are increasingly used to treat a variety of disease syndromes,  opportunistic fungal infections are becoming more common.  Fusarium, a genus of fungi that is most often associated with plant diseases, often causes superficial or subcutaneous infections that become disseminated in heavily immunocompromised individuals, frequently causing death.  Certain morphological species of Fusarium tend to be more commonly associated with human infections than others, particularly F. solani and F. oxysporum.  However, Fusarium species defined morphologically have proven generally to be diverse species complexes, raising the question of whether specific species lineages within them are associated with human infections.  Multilocus phylogenetic analyses of over 400 members of two of the major complexes, the F. oxysporum complex and F. solani complex, indicated that diverse isolates within each complex are associated with human infections, with certain specific clones and lineages showing the greatest association.  Some of these lineages are associated with specific diseases of plants and other animals.  We conclude that the major agents of infection are those fusaria that are most common in the environment, including the indoor environment of hospitals.  Certain groups of Fusarium also exhibit a predilection toward both human and plant disease, a unique characteristic among the fungi.  Human Fusarium infections are thus likely to be truly opportunistic, caused by a diverse set of competent pathogens that are commonly encountered by humans.



O'Donnell K, Sutton DA, Rinaldi MG, et al.
Genetic diversity of human pathogenic members of the Fusarium oxysporum complex inferred from multilocus DNA sequence data and amplified fragment length polymorphism analyses: Evidence for the recent dispersion of a geographically widespread clonal lineage and nosocomial origin 


Speaker: Dr. Christipher House - Department of Geosciences

Title: "Linking Taxonomy with Environmental Geochemsitry:  the Anaerobic Oxidation of Methane in Cold Seeps & deeply Buried Marine Sediments."

Abstract: The linking of molecular taxonomy (including 16s rRNA) to environmental geochemistry is a powerful way to work out the interactions, metabolic activities, and food webs of microorganisms in their natural setting, whether it is sediment, soil, or a water column.  To this end, we developed a method for coupling an extant microorganism’s genetic information with geochemical data derived from the direct analysis of its cell. FISH–SIMS combines fluorescent in-situ hybridization (FISH) with secondary ion mass spectrometry (SIMS).  FISH is a culture-independent technique used to visually identify naturally occurring microorganisms by staining their ribosomal RNA.  Secondary ion mass spectrometry (SIMS) is a method by which geochemical information can be obtained from microsamples.  Using FISH-SIMS, a researcher can measure a target cell’s isotopic or elemental composition in a mixed environment.

    The identification and study of methane-consuming microorganisms is an important step toward understanding the methane cycle and microbial response to methane release. The recent identification of two distinct Archaea capable of anaerobic methane oxidation was in part accomplished using FISH-SIMS.  Because natural methane is highly depleted in 13C, FISH-SIMS is particularly powerful at determining if a particular cell, collected from the environment, consumed methane as a substrate for its cell carbon. This research demonstrated that both the ANME-1 and ANME–2 Archaea from the Eel River Methane Seep are highly depleted in 13C due to growth on methane.  Most recently, we have aimed to track the activity of cells in the cell cluster by monitoring both their natural carbon isotopic composition and their incorporation of isotopically-labeled ammonium.

    The deep marine biosphere is thought to contain abundant microbial inhabitants, estimated to be a tenth of the Earth’s total biomass. Sediments from this environment were recovered during Ocean Drilling Program (ODP) Leg 201, and were analyzed by both molecular biological and organic geochemical techniques. Of particular interest in these sediments were four sulfate/methane transition zones seen at ODP Sites 1227, 1229 and 1230, two of which coincided with strongly elevated cell counts. Archaeal cells in these zones were analyzed for abundance and d13C composition by whole cell analysis (FISH-SIMS) and intact membrane lipids (HPLC-ESI-MSn). Cell counts showed greater archaeal abundance than bacterial, which was reflected by intact membrane lipid abundance. Isotopic compositions by both techniques (often around -20‰) suggest that methane is not an important carbon source for these cells. Autotrophic carbon fixation appears to be an unlikely metabolism given the relationship between the isotopic composition of DIC and archaeal biomass. The isotopic evidence suggests that the bulk archaeal community is heterotrophic, possibly mediating the oxidation of methane without consuming it as a carbon source.

    The importance of these techniques is that the cells targeted for study can be environmental species that cannot currently be grown in the laboratory.  These techniques promises to become critical for working out the interactions, metabolic activities, and food webs of microorganisms in their natural setting, whether it is sediment, soil, or a water column.


Orphan, V. J., Ussler III, W., Naehr, T., House,  C.H., Hinrichs, K. U. and Paull,  C. K., 2004.  Geological, Geochemical, and Microbiological Heterogeneity of the Seafloor Around Methane Vents in the Eel River Basin, offshore California.  Chemical Geology, 205:  265-289. 


Speaker: Dr. Kenneth Weiss -Department of Anthropology and Genetics

Title: "Searching for olfactory receptor regulators."

Abstract: .Olfactory receptors are the largest class of vertebrate genes and evolve by a history of gene gain, loss, and translocation.  These 1000 genes are dispersed across the mammalian genome. Yet, only one gene (and only from one homolog) is expressed in each of the millions of olfactory neurons.  I'm reporting on work in progress that I began last summer in a sabbatical leave in England, to try to identify regulatory sequence signals that could begin to explain this phenomenon.  There are various kinds of orderliness in the system, and some precedents from other genes in various organisms.  But it is not yet clear what kinds of signal we should be looking for, or how to look.



Speaker: Dr. Wojciech Makalowski -Department of Biology


Title: "The comparative genomics of honeybee spliceosomal RNAs."


Abstract: We have examined the number and distribution of putative snRNA genes in the Apis mellifera genome and used this as a basis for an analysis of the pattern of conservation of snRNA genes among insect genomes (Tribolium castaneum, Bombyx mori, Anopheles gambiae, Aedes aegypti and six Drosophila species).   Small nuclear RNA sequence variants within a species, including those observed to previously observed to show regulated expression in Drosophila melanogaster, are not conserved between species.  Instead, the pattern of sequence variation is more suggestive of neutral variation than functional differentiation. Promoters for different snRNAs within each insect species share similar sequence motifs that are likely to correspond to the binding sites of snRNA-specific transcription factors such as SNAPc.  In striking contrast, there is little conservation of these promoter elements between different insect species.  Those snRNAs that are specific for the minor spliceosome (U11, U12, U4atac and U6atac) accumulate fixed nucleotide differences at a much higher rate than do snRNAs found in the major spliceosome.  In addition, the genus Drosophila is characterized by both a loss of U12 introns and rapid evolution (or loss) of components of the minor spliceosome.



Hastings, M.L. and A.R. Krainer, Pre-mRNA splicing in the new millennium. Curr Opin Cell Biol, 2001. 13(3): p. 302-9., Eddy, S.R. and R. Durbin, RNA sequence analysis using covariance models. Nucleic Acids Res, 1994. 22(11): p. 2079-88., Schneider, C., C.L. Will, J. Brosius, M.J. Frilander, and R. Luhrmann, Identification of an evolutionarily divergent U11 small nuclear ribonucleoprotein particle in Drosophila. PNAS, 2004. 101(26): p. 9584-9589.



Speaker: Dr. Webb Miller -Department of Computer Science

Title: "Three on-going projects."

Abstract: The talk will sketch three "works in progress":
1. Computational reconstruction of the boreoeutherian ancestral genome.
Blanchette et al. (2004)
Reconstructing large regions of an ancestral mammalian genome in silico.
Genome Research 14, 2412-2423.
2. A set of programs to search annotation, sequences, and alignments downloaded
from UCSC's Genome Browser for rare genomic changes that suggest or confirm a
phylogenetic tree topology.
Rokas and Holland (2000)
Rare genomic changes as a tool for phylogenetics.
Trends Ecol. Evol. 15, 454-459.
3. Sequencing the mammoth genome.
Poinar et al. (2006)
Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA.
Science 311, 392-394.

References: Blanchette et al. (2004)
Reconstructing large regions of an ancestral mammalian genome in silico. Genome Research 14, 2412-2423., Rokas and Holland (2000) Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15, 454-459., Poinar et al. (2006)
Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311, 392-394.



Speaker: Dr.  Kai Meuller -Department of Biology

Title: "Phylogenetic reconstructions in carnivorous and weedy plants and insights on encoding microstructural changes and bootstrapping given large taxon samplings."

Abstract: The talk will cover ongoing projects on

  1. reconstructing the phylogeny of the carnivorous plant-family Lentibulariaceae and related plants,  and analyses of extreme substitutional rate shifts
  2. reconstructing the phylogeny of Amaranthaceae, the food of the Aztecs,  with insights on  the evolution of highly derived, unique pollen features
  3. a set of software tools and thoughts about methods to deal with a) estimating node support when analyzing a great number of taxa, b) encoding microstructural changes, in particular in cpDNA evolving at high length-mutational rates

References: Müller K (2005) Incorporating information from length-mutational events into phylogenetic analysis. Molecular Phylogenetics and Evolution, doi:10.1016/j.ympev.2005.07.011 Müller K (2005) The efficiency of different search strategies in estimating parsimony jackknife, bootstrap, and Bremer support. BMC Evolutionary Biology, 5, 58. Müller K, Borsch T (2005) Phylogenetics of Amaranthaceae based on matK/trnK sequence data - evidence from parsimony, likelihood, and Bayesian analyses. Annals of the Missouri Botanical Garden, 92, 66-102 Müller K, Borsch T (2005) Phylogenetics of Utricularia (Lentibulariaceae) and molecular evolution of the trnK intron in a lineage with high substitutional rates. Plant Systematics and Evolution, 250, 39-67.


Speaker: Dr. Kateryna Makova -Department of Biology

Title: "Mammalian male mutation bias: impacts of genereation time and regional variation in substitution rates."


Abstract: In mammals, males undergo a greater number of germline cell divisions 

compared with females. Thus, the male germline accumulates more DNA 

replication errors, which result in male mutation bias ­ the  higher 

mutation rate for males than for females. The phenomenon of male 

mutation bias has been investigated mostly for rodents and primates, 

however, it has not been studied in detail for other mammalian 

orders. Here we sequenced and analyzed five introns of three genes 

(DBX/DBY, UTX/UTY, and ZFX/ZFY) homologous between X and Y 

chromosomes in several species of perissodactyls (horses and rhinos) 

and of primates. Male mutation bias was evident: substitution rate 

was higher for a Y chromosome intron than for its X chromosome 

homolog for all five intron pairs studied. Substitution rates varied 

regionally among introns sequenced on the same chromosome and this 

variation influenced male mutation bias inferred from each intron 

pair. Interestingly, we observed a positive correlation in 

substitution rates between homologous X vs. Y introns as well as 

between orthologous primate and perissodactyl introns. The male-to- female mutation rate ratio estimated from concatenated sequences of 

five perissodactyl introns was 3.88 (95% CI = 2.90-6.07). Using the 

data generated here and estimates available in the literature, we 

compared male mutation bias among several mammalian orders. We 

conclude that male mutation bias is significantly higher for 

organisms with long generation times (primates, perissodactyls, and 

felids) than for organisms with short generation times (e.g., 

rodents) since the former undergo a greater number of male germline 

cell divisions.   


References: Li, W.-H., S. Yi, and K. D. Makova. 2002. Current Opinions in 

Genetics and Development. Male-driven evolution 12: 650-656.




Speaker: Matt Heinicke -Department of Biology


Title: "Systematics and biogeography of the genus Eleutherodactylus."


Abstract: The neotropical frog genus Eleutherodactylus is the largest among terrestrial vertebrates, with greater than 700 described species.  Eleutherodactylus species dominate the amphibian faunas of the West Indies and northern Andes, and are also well-represented in Central America and other parts of South America.  Phylogenetic relationships within the genus have proven difficult to resolve through traditional morphology-based systematics.  However, molecular data have proven more useful.  We used sequences of 12S and 16S ribosomal RNA genes to infer relationships within Eleutherodactylus.  Our data indicate that the West Indian species stem from a single, ancient radiation and that many South American species belong to a second large radiation centered on the Andes.


References: Crawford, A.J. and E.N. Smith. 2005. Cenozoic biogeography and evolution in direct-developing frogs of Central America (Leptodactylidae: Eleutherodactylus) as inferred from a phylogenetic analysis of nuclear and mitochondrial genes. Molecular Phylogenetics and Evolution 35 (3), 536-555.     


Speaker: Dr. Claude dePamphilis -Department of Biology

Title:  "Genome evolution in parasitic plants:  new genomes, surprising findings."

Abstract: Although most species of flowering plants are free-living and fully photosynthetic about 1% of plant species are direct parasites on photosynthetic plants, and as a result lead partly to fully heterotrophic lifestyles.  How parasitism originated  and how their genomes evolve under dramatically altered evolutionary constraints are fundamental problems.  The first parasitic plant studied in any detail was Epifagus virginiana, a nonphotosynthetic plant that retains greatly reduced, but evidently functional plastid genomes that encode a small number of genes for nonphotosynthetic function.  The insights gained from studying the Epifagus plastid genome were wide-ranging and provide a starting point for this lecture.  We have recently completed new plastid genome sequences in a number of parasitic species that represent independent origins of parasitism within the flowering plants.   These new plastid genomes provide many surprising findings, including examples of unexpected retention of photosynthetic genes and pathways in some entirely heterotrophic species and almost perfect parallel reduction in gene content in others.  There is even the possibility that some nonphotosynthetic plants have entirely lost their plastid genomes entirely.  While plastid and mitochondrial genomes are now the focus of intensive study in parasitic plants, the nuclear genome of parasites remains nearly unexplored.  I will conclude with a few unexpected observations about the nuclear genomes of parasites.

References: Bunggard, Ralph A.  2004.  Photosynthetic evolution in parasitic plants:  Insight from the chloroplast genome.  BioEssays 26: 235-247., Cui, L, N. Veeraraghavan, A. Richter, K. Wall, R. K. Jansen, J. Leebens-Mack, I. Makalowska, and C. W. dePamphilis. ChloroplastDB: the chloroplast genome database. Nucleic Acids Research, 2006, vol. 34, Database issue, D692-D696., dePamphilis, C.W., and Palmer, J.D. Loss of photosynthetic and chlororespiratory genes from the plastid genome of a nonphotosynthetic plant. Nature 1990, 348:337-339., Leebens-Mack, J.H. and C.W. dePamphilis. Power analysis of tests for loss of selective constraint in cave crayfish and nonphotosynthetic plant lineages. Molecular Biology and Evolution 2002, 19:1292-1302., McNeal, J.R., J.H. Leebens-Mack, C.W. dePamphilis. Utilization of fosmid partial genomic libraries for sequencing complete organellar genomes. Submitted to Biotechniques. Under review.,
Mower JP, Stefanovic S, Young GJ, Palmer JD (2004) Gene transfer from parasitic to host plants.  Nature 432: 165-166., Wolfe H, Morden CW, Palmer JD (1992) Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc. Natl. Acad. Sci. USA 89: 10648-10652., Young, N.D. and C.W. dePamphilis. Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function. BMC Evolutionary Biology 2005, 5:16.


Speaker: Dr. Anton Nekrutenko -Department of Biochemistry and Molecular Biology



Wen-Yu Chung1

Jianbin He1

Anton Nekrutenko1

Radek Szklarczyk2

Samir Wadhawan1


1Center for Comparative Genomics and Bioinformatics, Penn State 

University, University Park, PA, USA

2Dept. of Computer Science, Faculty of Sciences, Vrije Universiteit, 

Amsterdam, The Netherlands

Genes with overlapping reading frames (dual coding) are frequently 

found in viral genomes but though to be non-existent in eukaryotes. 

However, three known cases (XBP1, p16INK4A and XLaS) have been 

studied in mammals so far and show a remarkable pattern of co- evolution between the two frames. Are there more of these unexpected 

cases in the human genome? A new comparative approach designed in our 

laboratory yielded a number of additional candidates based on high 

stringency criteria including conservation in other species (mouse, 

rat and/or dog), the overlap length, and the results of the position- specific transition-transversion ratio test. Most of the candidate 

genes are expressed in the nervous system. Why do human genome 

contain such genes? Here we attempt to answer this question.


1:  Nekrutenko A, Wadhawan S, Goetting-Minesky P, Makova KD.

 Oscillating Evolution of a Mammalian Locus with Overlapping Reading 

Frames: An

XLalphas/ALEX Relay.

PLoS Genet. 2005 Aug 12;1(2):e18 [Epub ahead of print]

PMID: 16110341 [PubMed - as supplied by publisher]


Speaker: Xin Ye -Department of Biology


Title: "Evolutionary Analysis of Mob Gene Superfamily."


Abstract: Intercollege Program in Genetics, Institute of Molecular Evolutionary Genetics Department of Biology


A main cause of tumor development is mutations in tumor-suppressor genes, which normally function as negative regulators of cell proliferation or positive regulators of apoptosis. We have newly identified a tumor-suppressor gene named mats (mob as tumor suppressor) whose loss-of-function mutation was shown to be able to induce tumors in Drosophila. The protein encoded by mats is highly conserved both in amino acid sequence and biological function between human and Drosophila. To investigate more about this conserved gene family, we carried out a series of evolutionary studies. An exhaustive database search identified Mob genes present in a variety of eukaryotes from the primitive Giardia to animals and plants. Phylogenetic analysis classifies Mob genes into four major groups (Group I-IV). Interestingly, Mob’s from species like Giardia and slime mold are present in almost all groups, suggesting that the major duplications that gave rise to the members of the Mob family should have occurred very early in evolution. Each major Mob group contains only one gene from invertebrates but some groups have more than two genes from vertebrates, suggesting that additional duplication events have resulted in the different gene repertoire of the vertebrates. The observed branching pattern suggests that orthologous Mob proteins could accommodate similar functions. This pattern coincides with the functional study which demonstrated that a human Mats ortholog of group I (Mats group) could rescue the tumor phenotype of Drosophila mats mutant. We also looked at the transcripts levels of human Mob genes which displayed the ubiquitous expression pattern in most tissues throughout development. Moreover, protein sequences alignments showed high conservation level among four Mob groups, which might indicate their important function. In addition, we have identified and mapped the conserved amino acid changes to the simulated 3-dimensional structure of Mob proteins, to gain an insight into the putative functional divergence between the paralogous Mob genes.


 References: Lai, Z. C. et al. (2005). Control of cell proliferation and apoptosis by mob as tumor suppressor, mats. Cell 120, 675-685. Luca, F.C et al. (1998). MOB1, an essential yeast gene required for completion of mitosis and maintenance of ploidy. Mol. Biol. Cell 9, 29–46. Bichsel, S J. et al. (2004). Mechanism of activation of NDR (Nuclear Dbf2-related) protein kinase by the hMOB1 protein. J. Biol. Chem. 279, 35228–35235. Stavridi, E S. et al. (2003). Crystal structure of a human Mob1 protein: toward understanding Mob-regulated cell cycle pathways. Structure 11, 1163–1170.


Speaker: Marc Bouchet -Department of Biology - Cancelled





Speaker:  Jill Daurte -Department of Biology

Title: "Evolutionary dynamics of single copy nuclear genes in flowering plants."


authors: Duarte, J. M., Beckmann, K., Wall, P. K., Leebens-Mack, J., Ma., H., dePamphilis, C.W.

Abstract: Although all major lineages of angiosperms now appear to have undergone repeated rounds of ancient genome duplication and most genes belong to multigene familes, there are numerous nuclear genes that persist as single copies.  In order to understand the molecular evolution of these single copy genes, we have undertaken a bioinformatic analysis of ~1500 nuclear genes that are single copy in both Arabidopsis and rice as well as a detailed phylogenetic analysis for twenty of these genes.  Results indicate these genes have distinct sequence characteristics and functional affiliations, and are likely subject to selection to maintain low copy number.


Chapman, B.A., J.E. Bowers, F.A. Feltus, and A.H. Paterson. 2006. Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. PNAS 103: 2730-2735.

Cui, L., P.K. Wall, J. Leebens-Mack, B.G. Lindsay, D.E. Soltis, J.J. Doyle, P.S. Soltis, J. Carlson, A. Arumuganathan, A. Barakat, V. Albert, H. Ma, and C.W. dePamphilis. 2006. Widespread genome duplications throughout the history of flowering plants. Genome Research in press.

Duarte, J.M., L. Cui, P.K. Wall, Q. Zhang, X. Zhang, J. Leebens-Mack, H. Ma, N. Altman, and C.W. dePamphilis. 2006. Expression Pattern Shifts Following Duplication Indicative of Subfunctionalization and Neofunctionalization in Regulatory Genes of Arabidopsis. Mol. Biol. Evol. 23: 469-478.





Speaker: Chungoo Park -Department of Biology



Abstract: Mechanisms to coordinately control gene expression over large genomic distances are complex and must involve, at some level, the underlying DNA sequence. Mammalian X chromosome inactivation represents one of the most fascinating examples of such mechanisms in action. Indeed, most genes on one X chromosome are silenced, while ~15% of X-linked genes escape inactivation and yet another ~10% exhibit variable patterns of inactivation among individuals (Carrel and Willard 2005). However, what drives such differences in expression among X-linked genes is not well understood. One family of repetitive elements, LINE-1 (L1), has been proposed to play a role in the chromosomal control of X inactivation. Namely, since the X chromosome is enriched in L1s as compared with autosomes, these elements were hypothesized to represent “way stations” for spreading the X inactivation signal (Lyon 1998). In agreement with this hypothesis, an L1 density gradient was found along a recently sequenced human X: regions with a higher density of L1s, which are usually located in more ancient evolutionary strata, harbor larger numbers of X-inactivated genes than other regions (Ross et al. 2005). It is not clear, however, whether L1s accumulated there due to their importance in X inactivation or simply because such regions had more time to do so as compared with the younger strata.

          Here we utilized an experimentally derived comprehensive inactivation profile of the whole human X chromosome (Carrel and Willard 2005) and developed a rigorous bioinformatic and statistical framework to identify candidate sequences that potentially determine inactivation status of human X chromosome genes. We focused our analysis on the nonpseudoautosomal portion of Xp22 that possesses the youngest evolutionary strata on X. Inactive X expression patterns in Xp22 are striking; approximately half of the genes tested in Xp22 escape X inactivation, in contrast with only 10% of genes outside of Xp22.  Additionally, Xp22 genes that escape inactivation map to large clusters, providing compelling support for regional models of gene control. Interestingly, Xp22 is depleted of L1s compared with the rest of X chromosome.

           We subdivided Xp22 into two subgenomes: Inactivated (I) and Escaping (E) inactivation. Each subgenome consisted of clusters of neighboring genes with the same (either I or E) expression status. The two subgenomes were searched for overrepresented oligomers (8- to 24-mers). Significance of overrepresentation was assessed by a permutation test. Using oligomers that were significantly enriched in the I vs. E Xp22 subgenome (or vice versa) as classification features, and data from the Xp22 region as training sets, we performed Linear Discriminant Analysis (LDA). Cross-validation within the training data showed success rates of 80-90% in predicting the expression status of Xp22 genes, and we obtained promising results also when predicting the expression status of X chromosome genes outside of Xp22. Interestingly, almost all oligomers significantly overrepresented in the I subgenome of Xp22 are located within L1 elements, even though L1 frequencies are similar in the I and E subgenomes of Xp22. This supports the importance of L1 elements in X chromosome inactivation. Our results suggest that the chromatin microenvironment which is composed of multiple genomic sequence elements contributes to the expression patterns found on the X chromosome.

References:  (1) Carrel and Willard. X-inactivation profile reveals extensive variability in X-linked gene expression in females. 2005. Nature 2005 434 400-404 (2) Chow et al. Silencing of the Mammalian X Chromosome. 2005 Annu. Rev. Genomics Hum. Genet. 6:69-92.