IMEG

Institute of Molecular
Evolutionary Genetics

 

 

 

 

 

 

  

 

 

 

IMEG SEMINARS
Fall 2007

 

Previous IMEG Seminars and Abstracts:

Fall 2013

Spring 2013

Fall 2012

 

Spring 2012

Fall 2011

Fall 2010

 

Spring 2010
Fall 2009

Spring 2009

Fall 2008

Spring 2008

Fall 2007
Spring 2007
Fall 2006

Spring 2006
Fall 2005
Spring 2005

Fall 2004

Spring 2004

Fall 2003

Spring 2003
Fall 2002

Date

Speaker

 09/05/07

Speaker: Dr. Ross Hardison- Department of Biochemistry & Molecular Biology

Title: ENCODE and Evolution: What signatures of selection are associated with functional genomic regions?

 

Abstract: The ENCODE project is a consortium supported by the National Human Genome Research Institute that has as its goal to build an ENCyclopedia Of functional DNA Elements. The aim is to identify all the functional DNA sequences in the human genome, and a new MOD-ENCODE has recently begun for model organisms. In the pilot phase of ENCODE, a large number of high through-put biochemical assays were run on 1% of the human genome (30 Mb in 44 different regions). These included extensive transcript mapping, chromatin modifications, and binding by transcription factors and components of transcription complexes. Hybridization to high density microarrays of DNA enriched for these various “functions” was a major technology employed. In parallel, regions orthologous to the human ENCODE pilot regions were sequenced (or extracted from existing sequences) for 28 species; these were mostly mammals but they included vertebrates as distant as fish. The sequences were aligned and evaluated for evidence of constraint. Comparing the functional DNA segments (defined by the biochemical assays) and the constrained DNAs led to these conclusions, which I plan to discuss:
- About 60% of the “constrained bases” are associated with a known function.
- Although functional regions tend to overlap with constrained segments, not all the bases in the functional regions are under constraint.
- “Surprisingly, many functional elements are seemingly unconstrained across mammalian evolution. This suggests the possibility of a large pool of neutral elements that are biochemically active but provide no specific benefit to the organism. This pool may serve as a ‘warehouse’ for natural selection, potentially acting as the source of lineage-specfic elements and functionally conserved but non-orthologous elements between species.” 


References:

The ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816
Full text available from
http://www.nature.com/nature/journal/v447/n7146/full/nature05874.html
 
David C. King, James Taylor, Ying Zhang, Yong Cheng, Heather A. Lawson, Joel Martin, ENCODE groups for Transcriptional Regulation and Multispecies Alignment, Francesca Chiaromonte, Webb Miller, and Ross C. Hardison (2007) Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. Genome Research 17 : 775-786.
Full text available from
http://www.genome.org/cgi/content/full/17/6/775
 

 09/12/07

Speaker: Dr. Masafumi Nozawa- Department of Biology

Title: Genomic drift and copy number variation of sensory receptor genes in humans


Abstract: The number of sensory receptor genes varies extensively among different mammalian species. This variation is believed to be caused partly by physiological requirements of animals and partly by genomic drift due to random duplication and deletion of genes. If the contribution of genomic drift is substantial, each species should contain a significant amount of copy number variation (CNV). We therefore investigated CNVs in sensory receptor genes among 270 human individuals by using published CNV (i.e., relatively large insertion and deletion) data. The results indicated that olfactory receptor (OR), taste receptor type 2, and vomeronasal receptor type 1 genes show a much larger extent of CNVs than the average for all annotated genes. However, there was no significant difference between functional and nonfunctional OR genes in the extent of CNVs. If OR pseudogenes have evolved in a neutral fashion, this suggests that functional OR genes also have evolved in a similar manner with respect to copy number change in humans. In addition, we found that the ratio of interspecific copy number divergence to intraspecific copy number polymorphism is much higher than the corresponding ratio for human populations, indicating that copy number difference has increased with time. We therefore conclude that genomic drift is an important factor for generating intra- and interspecific CNVs.


References: Gilad Y et al. (2004) Loss of olfactory receptor genes coincides with the acquisition of full trichromatic vision in primates. PLoS Biol 2: e5.

Redon R, et al. (2006) Global variation in copy number in the human genome. Nature 444: 444-454.

Niimura Y, and Nei M (2007) Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS One 2: e708.

 09/19/07

Speaker: Dr. Sabyasachi Das- Department of Biology

Title: Evolution of immunoglobulin VH multigene families in vertebrates


Abstract: Immunoglobulin heavy chains are polypeptides encoded by four gene segments: variable region (VH), joining (JH ), diversity (D), and constant (CH) gene segments. The number of VH gene segments varies from species to species. To understand the evolution of the VH multigene families, we identified and analyzed the VH sequences from sixteen vertebrate species. The results show that the numbers of functional and nonfunctional VH are highly correlated among different species. The number of VH gene segments is relatively stable in teleosts, but the intragenomic sequence variation is generally higher in teleosts than in tetrapods. The VH gene segments in tetrapods can be classified into three phylogenetic groups (I, II, and III). The group III and/or II gene segments are relatively abundant, whereas group I gene segments exist in small numbers or are absent in most species. The genomic organization of group I, II, and III VH gene segments varies considerable among species, but the entire VH region seems to be conserved in the subtelomeric or near-centromeric region of chromosome. The presence or absence of specific VH group members and the lineage-specific expansion and contraction of VH gene segments indicate that the VH region continues to evolve in a species-specific manner. Our results suggest that the evolution of VH gene segments is more complex than previously thought and that several factors may act synergistically for the development of antibody repertoire.


References:

 09/26/07

Speaker: Eleca Dunham- Department of Biology - CANCELLED

Title: Molecular evolution and population demography of the swine H1N1 influenza A viruses


Abstract: A comparative analysis of the classical swine H1N1 and European swine H1N1 influenza A viruses reveals both convergent evolution and differential population dynamics. Our analyses of the European swine virus indicate that the classical H1N1 lineage suffered substantial population bottlenecking during its introduction into Europe in the late 1970s. Coalescent models confirm that the European swine lineage arose from a Eurasian avian ancestor in the late 1970s and that the diversity of the virus population is increasing over time. The classical swine lineage arose sometime in the 1920s in North America from the 1918 Spanish H1N1 influenza A pandemic strain. Analysis of the amino acid profiles of both lineages (classical and European) indicate similarities, but the genomes of these two lineages are evolving differently. In line with previous studies, we find that antigenic drift is much more pronounced in the European swine lineage than it is in the classical swine lineage.


References: Brown, I, et al. (1997) Antigenic and genetic analysis of H1N1 influenza A viruses from European pigs. J. Gen. Virol. 78: 553-562.
Schultz, U, et al. (1991) Evolution of pig influenza viruses. Virol. 183: 61-73
.
 

10/03/07

Speaker: Zhenguo Lin- Department of Biology

Title: The sound of silence: non-neutral evolution at synonymous sites in mammalian Hox genes

 

Abstract: The discovery of the Hox gene cluster uncovered a general universal principle of genetic control of development. Hox genes encode homeodomain-containing transcription factors which determine the body plan along anterior-posterior axis in bilaterian animal. Hox genes are arranged on the chromosomes in the same order as they are expressed along the anterior-posterior axis in developing embryo.  In this study, we found some mysterious phenomena about the evolutionary dynamics of so call silent mutation, synonymous mutation.  The levels of synonymous mutation in Hox genes have strong correlation with their position on the cluster in mammals. Furthermore, many ultraconserved coding regions were identified with completely depleted synonymous substitution over 100 million years. Evolutionary analysis indicates that the selection forces are mainly specific to placental mammals. Our study suggests that these synonymous sites in Hox genes may play active roles during mammalian embryo development.

 

References: McGinnis, W., and Krumlauf, R. (1992). Homeobox genes and axial patterning. Cell 68, 283-302.

Zhang, J., and Nei, M. (1996). Evolution of Antennapedia-class homeobox genes. Genetics 142, 295-303.

 10/10/07

Speaker: Fabia Battistuzzi- Department of Biology

Title: Prokaryote evolution and a terrestrial ancestry for most species


Abstract: 
 The relationships and timescale of prokaryote evolution are unresolved. The poor fossil record of these organisms does not provide sufficient information to outline their evolutionary history. Hence, phylogenetic and molecular clock methods are fundamental to clarifying their evolution and relating that to events in early Earth history. This study uses genomic sequence data to reconstruct the phylogeny of prokaryotes and estimate the divergence times of major groups. Multiple methods and data sets are applied and compared to gain a more general and robust result compared with previous studies that were narrower in scope. The timeline of prokaryotes obtained was used to infer evolutionary patterns in types of metabolism, such as the origin of phototrophy, and the colonization of land. In general, a more robust phylogeny of prokaryotes is established, with high-level groups previously unrecognized. Archaebacteria and Eubacteria are found to have rapidly evolved in the mid- to late-Archean (3.3-2.6 billion years ago) in relation to the colonization of new environments such as mesophilic photic zones and terrestrial habitats. We also traced a terrestrial ancestry for most prokaryote species.


References: Ciccarelli, F.D. et al. Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283-1287 (2006).

 10/15/07

 

Speaker: Dr. Sean Carroll - Professor of Molecular Biology and Genetics University of Wisconsin- Marker       

                  Lecture 5:30 PM 112 Kern Bldg.

Title: The Making of the Fittest: DNA and Evolution in Action


Abstract: Every change or new trait, from the gaudy colors of tropical birds to our color vision through which we admire nature's diversity. is due to changes in DNA that biologists can now trace in exquisite detail. We can now see not just that the fittest survive, but how they are made. n this lecture, Dr. Carroll will examine the massive DNA record of evolution and what that tells us about how some fascinating creatures have adapted to life on a changing planet.

 10/16/07

 

Speaker: Dr. Sean Carroll - Professor of Molecular Biology and Genetics University of Wisconsin- Marker       

                  Lecture 4:00 PM Berg Auditorium, Life Science Bldg.

Title: Endless Flies Most Beautiful: The Role of cis-Regulatory Sequences in the Evolution of Animal Diversity

 

Abstract: Changes in animal form arise through changes in development, but for a very long time biologists  have wanted to understand just how new structures and patterns arise?  Contrary to expectations, the evolution of new genes has played a much lesser role in the evolution of form than has the evolution of gene regulatory sequences.  In this lecture, Dr. Carroll will examine the role of cis-regulatory sequences in the evolution of animal form.

 10/24/07

Speaker: Dr. Claude dePamphilis - Department of Biology
Title: Palaeopolyploidy and the genomes of the flowering plants

 

Abstract: This talk will review several completed and current plant genome sequencing projects.   While Arabidopsis thaliana was selected for genome sequencing in part because of its small diploid genome, the Arabidopsis genome proved to include large amounts segmental duplication tracing to at least two distinct time points, suggesting at least two rounds of ancient genome duplication ["paleopolyploidy]' in Arabidopsis' history.   The rice and poplar genomes also show evidence of likely ancient polyploidy.   Although complete genome sequences are in progress for many plant species, smaller scale studies of the relative age distribution of duplicate genes suggest that most if not all flowering plant lineages have a likely polyploid history.  Surprisingly, the recently published genome of Vitis [grapevine] shows no such evidence, which helps to identify the likely dates of genome scale duplication events in angiosperms.  Here, I will compare some of the evidence for polyploid events in the history of flowering plants and attempt to summarize the current state of our understanding.  Numerous current and and future genome sequencing projects will address a host of questions about the implications of these genome-wide events.
 

Reference Arabidopsis Genome Initiative (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.


 Simillion, C., Vandepoele, K., Van Montagu, M., Zabeau, M. & Van de Peer, Y. (2002). The hidden duplication past of Arabidopsis thaliana. Proceedings of the National Academy of Science of the USA 99: 13627-13632.


 Paterson, A.H., Bowers, J. E., Van de Peer, Y. & Vandepoele, K. (2005). Ancient duplication of cereal genomes. New Phytologist 165: 658-661.


 Cui, L., P.K. Wall, J.H. Leebens-Mack, B.G. Lindsay, D.E. Soltis, J.J. Doyle, P.S. Soltis, J.E. Carlson, K. Arumuganathan, A. Barakat, V.A. Albert, H. Ma, and C.W. dePamphilis. 2006. Widespread genome duplications throughout the history of flowering plants. Genome Research 16: 738-749. (cover)


 Tuskan, G.A. and many others (including PSU group K. Wall, J. Leebens-Mack, J. Carlson, and C.W. dePamphilis). 2006. The genome of black cottonwood, Populus trichcarpa (Torr. & Gray ex Brayshaw). Science, 313:1596-1604.


 Jaillon, O. and many others [2007].  The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463-46.

 10/31/07

Speaker: Dr. Daniel Cosgrove - Department of Biology

                                             &

                  Dr. Nikolas Nikolaidis - Department of Biology

Title: Expansin diversions: plant, pollen and plant pathogens

 

Abstract: Expansins are plant cell wall loosening proteins that function in plant cell enlargement, fruit softening, abscission and various other developmental processes. Land plants possess 30-60 or more genes, which are readily divided into two large families (EXPA and EXPB), with ~20% identity at the protein sequence level. Sequence-based phylogenetic analysis was combined with microsynteny analysis to reconstruct the history of gene births and deaths in this family since the divergence of the rice/Arabidopsis lineages. The EXPB family has grown considerably, perhaps because of coincidence changes in cell wall structure in grasses. One subset of the EXPB family in grasses gave rise to two novel classes of noxious pollen allergens. We have begun to reconstruct the evoution of this pollen allergen clade. Crystal structure of the maize EXPB pollen allergen has not only revealed aspects of the protein structure and its likelly mechanism of interaction with the cell wall, but also focussed interest on a group of distantly related bacterial proteins. These have only 5-15% amino acid identity with plant expansins, but their protein structures superimpose on each other amazingly well, indicating homology. We will present our ideas on the possible origin and function of the bacterial homologs.
 

References: Yennawar,N.H., Li, L-C., Dudsinski,D.M., Tabuchi,A., Cosgrove, D.J. (2006). Crystal structure and activities of EXPB1 (Zea m 1), a {beta}-expansin and group-1 pollen allergen from maize.  PNAS 103:14664-14671.
 
J. Sampedro and D. J. Cosgrove. The expansin superfamily. Genome Biol. 6 (12):242, 2005.
 
http://www.bio.psu.edu/expansins/

 11/07/07

Speaker: Dr. Chris House - Department of Geosciences

Title: Genome-wide Gene Order Distances Support a United Gram-Positive Bacteria

 

Abstract:The pair-wise distance between 143 prokaryotic genomes was determined using a simple monte carlo method to estimate the conservation of gene order.  The method was based on repeatedly selecting six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order.  The raw distances were then corrected for gene order convergence using an adaptation of the Jukes-Cantor model.  We have compared the distances found to those of ortholog gene content and small subunit ribosomal RNA (rRNA).  The
gene order distances are reasonably well correlated with the divergence of rRNA (R2 = 0.24), especially at rRNA Jukes-Cantor distances of less than 0.2 (R2 = 0.52).  Overall, gene content is only
weakly correlated with rRNA divergence (R2 = 0.04), however, it is especially strongly correlated at rRNA Jukes-Cantor distances of less than 0.1 (R2 = 0.67).  Using the gene order distances, the relations of prokaryotes (tree of life) were studied using neighbor joining, agreement subtrees, and a new proposed hierarchical tree building strategy that relies on the fact that shorter distances are known with higher confidence than longer distances.  Consistently, our trees show the Actinobacteria as a sister group to the bulk of the Firmicutes. In fact, the level of gene order support was found to be considerably greater for uniting these two phyla than for uniting any of the proteobacterial classes together.  The results are supportive of the idea that the Actinobacteria and Firmicutes are a monophyletic group, which in turn implies a single origin for the gram-positive cell.

 

References: NO REFERNCES

 11/14/07

Speaker: Yogeshwar Kelkar - Department of Biology

Title: The Genome-Wide Determinants of Human and Chimpanzee Microsatellite Evolution


Abstract: Mutation rates of microsatellites vary greatly among loci. The causes of this heterogeneity remain largely enigmatic, yet are crucial for understanding numerous human neurological diseases and genetic instability in cancer. In this first genome-wide study, the relative contributions of intrinsic features and regional genomic factors to the variation in mutability among orthologous human-chimpanzee microsatellites are investigated with resampling and regression techniques. As a result, we uncover the intricacies of microsatellite mutagenesis as follows. First, intrinsic features (repeat number, length, and motif size), which all influence the probability and rate of slippage, are the strongest predictors of mutability. Second, mutability increases non-uniformly with length, suggesting that processes additional to slippage, such as faulty repair, contribute to mutations. Third, mutability varies among microsatellites with different motif composition likely due to dissimilarities in secondary DNA structure formed by their slippage intermediates. Fourth, mutability of mononucleotide microsatellites is impacted by their location on sex chromosomes vs. autosomes and inside vs. outside of Alu repeats, the former confirming the importance of replication and the latter suggesting a role for gene conversion. Fifth, transcription status and location in a particular isochore do not influence microsatellite mutability. Sixth, compared to intrinsic features, regional genomic factors have only minor effects. Finally, our regression models explain ~90% of variation in microsatellite mutability and can generate useful predictions for the studies of human diseases, forensics, and conservation genetics.

References: Ellegren, H. 2000. Heterogeneous mutation processes in human microsatellite DNA sequences. Nat Genet 24: 400-402.

Ellegren, H. 2004. Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5: 435-445.

Lai, Y. and F. Sun. 2003. The relationship between microsatellite slippage mutation rate and the number of repeat units. Mol Biol Evol 20: 2123-2131.

Pearson, C.E., K. Nichol Edamura, and J.D. Cleary. 2005. Repeat instability: mechanisms of dynamic mutations. Nat Rev Genet 6: 729-742.

Webster, M.T., N.G. Smith, and H. Ellegren. 2002. Microsatellite evolution inferred from human-chimpanzee genomic sequence alignments. Proc Natl Acad Sci U S A 99: 8748-8753.

 11/21/07

NO IMEG SEMINAR~ THANKSGIVING HOLIDAY


 

11/28/07

Speaker: Dimitra Chalkia - Department of Biology

Title: "Origin and evolution of the Formin gene family"

 

Abstract: Molecular innovations of eukaryotes are fundamental for understanding the dramatic changes that have contributed to the advent of the eukaryotic cell. Actin, one of the principal components of the cytoskeleton, was classified as a molecular innovation of eukaryotes, but recent studies have revealed that it is not a genuine eukaryotic innovation, since actin homologs have been identified in prokaryotes. On the other hand, eukaryotes possess four actin-filament assembly factors, but whether these factors have precursor molecules in prokaryotes remains unknown. In this study we focused on formin, one of the known actin-filament assembly factors, and addressed the question of formin origin and evolution. Our results showed that formin constitutes an authentic and ancient eukaryotic innovation. Formin multi-gene family has followed a gene birth-and-death mode of evolution and has experienced multiple lineage-specific gene rearrangement events that led to domain gain and/or loss. Moreover, our analyses showed that formin proteins from deeply diverged eukaryotes possess similar motifs, which can be attributed to independent amino acid replacement events. Thus, this study provides insights into how eukaryote-specific molecular regulators of the cytoskeleton diversified, which may be beneficial for understanding not only the eukaryotic scaffolding apparatus, but also the eukaryotic phylogenetic patterns and the functional attributes of early eukaryotes.
 

References: Goode, B.L., and Eck, M.J. (2007). Mechanism and function of formins in the control of actin assembly. Ann. Rev. Biochem 76: 32.1-32.35.
 
Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J., and Gray, M.W. (2005). The tree of eukaryotes. Trends Ecol. Evol 20: 670-676.

 12/05/07

Speaker: Dr. Sarah Melissa Witiak - Department of Plant Pathology

Title: Insect galls as fruits and seeds ? was Darwin right again?

 

Abstract: Galls have long captured the curiosity of scientists, including Darwin who noted their morphological resemblance to fruits. Produced only in response to an insect stimulus, galls are highly varied and complex structures with distinct tissues. Insect galls typically contain specialized nutritive inner tissue that accumulates carbohydrates and seed-specific proteins, and outer tissue with high levels of secondary metabolites analogous to many fruits and seeds. In conjunction with studies on the evolution of galling systems and floral organs, these observations led us to hypothesize that the same genetic pathway that controls normal fruit and seed development is also induced by galling insects during gall development. To test this hypothesis, we examined
the hormonal characteristics and the expression of fruit and seed developmental genes in the galls of an aphid-like insect, phylloxera, and of a cecidomyiid fly elicited on wild grapevine leaves. We found that a specific subset of plant genes involved in normal floral, furit, and seed development is also expressed in gall tissues, supporting the hypothesis that insect galls are developmentally related to fruits and seeds. These results raise interesting questions about the relationships between the evolution of galling insects, their plant hosts, and gall structure and complexity
.
References: NO REFERENCES

 12/12/07

Speaker: Rubing Chen - Department of Biology

Title: Molecular Evolution of Influenza Viruses


Abstract: Influenza viruses have three types (A, B, C).  Influenza A viruses infect a variety of hosts, including birds, human and other mammals, and are responsible for the vast majority of disease in humans, including all three major pandemics in the twentieth century.  Some subtypes (H5 and H7) of avian influenza virus can also cause epidemics when introduced to poultry.  However, despite the intensive study of human influenza A viruses and H5N1 avian influenza viruses, many aspects of their evolution are not clearly understood.  In particular, it is not clear how influenza A viruses evolve, persist and spread in their nature reservoir, wild aquatic birds. To address this question we utilized an expansive data set of complete genome sequence data to examine the evolutionary pattern, global distribution and transmission of avian influenza virus in wild birds.  Our research reveals a rapid rate of evolutionary change in avian influenza virus (running counter to the theory of ‘evolutionary stasis’), with some evidence for positive selection in the HA, NA and NS genes.  We also found frequent reassortment events, which play an important role in the maintenance of genetic diversity in avian influenza virus.  Interestingly, although there are few genetic exchanges between birds resident in the North American and Eurasian/Australian flyways, both contain most of the subtypes detected so far.  In the second part of my seminar I will consider influenza B virus.  Although type B virus shares great similarities with type A virus both genomically and phylogentically, it only causes milder respiratory disease and local epidemics in humans. To investigate the underlying mechanism and driving force of influenza B evolution, we traced its evolutionary history using complete genome sequence data.  This led us to propose a model in which the shift of dominant viral strains through time is the result of changes in herd immunity, with reassortment continuously generating novel genetic variation.  Finally, we suggest that the interaction with influenza A virus may be central in shaping the evolutionary dynamics of influenza B virus.


References: Chen R & Holmes EC (2006) Avian influenza virus exhibits rapid evolutionary dynamics. Mol Biol Evol 23: 2336-2341.
Olsen B, Munster VJ, Wallensten A, Waldenstro¨m J, Osterhaus ADME, Fouchier RAM (2006) Global Patterns of Influenza A Virus in Wild Birds. Science 312:384-388.