IMEG

Institute of Molecular
Evolutionary Genetics

 

 

 

 

 

 

  

 

 

 

IMEG SEMINARS
Spring 2010

 

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

 01/27/10

Speaker: Dr. Ross Hardison - Dept of Biochem/Mol Biol

Title: Genomics of Erythroid Gene Regulation

 

Abstract: Cells in a particular lineage are derived from multipotential progenitor cells by the processes of commitment, differentiation and maturation.  These processes result from induction of lineage-specific genes and repression of other genes that are not part of the lineage. Regulation of gene expression involves occupancy of cis-regulatory modules (CRMs) by transcription factors, recruitment of co-activators and co-repressors and modifications of the chromatin structure. However, a full picture of these epigenomic features and how they result in induction and repression of specific genes is not yet available. We explore these questions in a mouse cell line model of late erythroid maturation. G1E cells are derived from mouse ES cells with a knockout of the gene Gata1, which encodes a transcription factor required for erythroid maturation. We restore GATA1 in an estradiol-inducible manner by expressing a GATA1-ER hybrid protein in the G1E-ER4 subline. After activation of GATA1-ER, the cells progress from proerythroblast to mature erythroblasts, making abundant hemoglobin and changing morphology dramatically. We have measured comprehensively changes in gene expression during this GATA1-dependent maturation and concomitantly, genome-wide occupancy by the transcription factors GATA1, GATA2, TAL1, and CTCF, as well as chromatin accessibility (DNase hypersensitive sites) and histone modifications in the chromatin (activating marks H3K4me1 and H3K4me3 and the repressing Polycomb mark H3K27me3), using Illumina sequencing technology for ChIP-seq. The data are being analyzed to determine globally the changes of protein occupancy and histone modification levels after restoration of active GATA1. Further, we are searching for features that can account for the expression patterns of the genes and their differential response to GATA1. Suprisingly, we find that only limited changes in histone modification status accompany the substantial changes in gene expression, and rather than altering chromatin structure upon restoration, GATA1 binds to genomic sites that already have activating histone modifications. The occupancy of CRMs by transcription factors does correlate in many respects with reponses in gene expression. In particular, induced genes tend to have GATA1 binding relatively close to the transcription start site (within 10kb), many induced genes show co-occupancy with GATA1 and TAL1, and some repressed genes show a loss of TAL1 upon restoration of GATA1. Several lines of evidence suggest that induction of gene expression is under stronger evolutionary constraint than is repression.


References:

Cheng, Y., King, D.C., Dore, L.C., Zhang, X., Zhou, Y., Zhang, Y., Dorman, C., Abebe, D., Kumar, S.A., Chiaromonte, F. et al. 2008. Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with     evolutionary constraint on the binding site motif. Genome Res 18: 1896-1905.

Cheng, Y., Wu, W., Kumar, S.A., Yu, D., Deng, W., Tripic, T., King, D.C., Chen, K.-B., Zhang, Y., Drautz, D. et al. 2009. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone         modifications and mRNA expression. Genome Res 19: 2172-2184.

 02/03/10

Speaker: Dr. Jim Marden - Dept of Biology

Title: Context-dependent selection and balanced polymorphism in succinate dehyrdrogenase d: ecologically important variation at the heart of aerobic metabolism

 

Abstract: Succinate dehyrogenase (mitochondrial respiratory complex II) has a central role in aerobic metabolism; it is the only enzyme involved in both the TCA cycle and electron transport. Four unique nuclear genes encode SDH subunits. Mutations at these loci have potent effects on the hypoxia inducible pathway, triggering changes in vascular morphogenesis and oxygen delivery to tissues.  Hence, one might expect to find quantitative variation in SDH function, tissue oxygenation, aerobic metabolic performance, and ecological function, but to date this possibility has not been examined.  In a metapopulation of the Glanville fritillary butterfly in the Aland islands of Finland, we have found that Sdhd allele frequencies are significantly different between new and old populations.  The allele associated with greater flight endurance is more abundant in newly founded populations (i.e. where the founding female made a dispersal flight).  Another Sdhd allele is associated with greater longevity and a slower rate of oogenesis; it is more frequent in old, established populations (<5 yrs).  Allele frequencies at Sdhd and another polymorphic metabolic enzyme locus (Pgi) associated with flight and oogenesis phenotypes are strongly related to the year-to-year growth of populations, in a context-dependent manner involving patch size.  The combination of allele frequencies changing in response to ecological dynamics, and demographics varying in response to allele frequencies, indicate that ecological and evolutionary dynamics are strongly coupled in this system.  We are presently examining the physiological consequences of Sdhd polymorphism in butterflies, particularly the way that differences in SDH enzyme affect the hypoxia inducible pathway and tracheal morphogenesis.  In humans, Sdha shows a strong signature of long-term balancing selection, with a Tajima’s D value higher than all but one of 282 polymorphic genes in African Americans (Baysal et al., 2007).  Together, these results indicate that SDH enzyme may frequently be involved in ecologically important phenotypic variation and balanced polymorphism.

References:
Wheat CW, Haag CR, Marden JH, Hanski I, Frilander MJ. 2010. Nucleotide polymorphism at a gene (Pgi) under balancing selection in a butterfly metapopulation. Mol Biol Evol. 27:267-81.

Niitepõld K, Smith AD, Osborne JL, Reynolds DR, Carreck NL, Martin AP, Marden JH, Ovaskainen O, Hanski I. 2009. Flight metabolic rate and Pgi genotype influence butterfly dispersal rate in the field. Ecology 90:2223-32.

 Baysal BE, Lawrence EC, Ferrell RE. 2007. Sequence variation in human succinate dehydrogenase genes: evidence for long-term balancing selection on SDHA. BMC Biol. 5:12.

 02/10/10

Speaker: Sayaka Miura - Dept of Biology

(Nei Lab)

Title: Evolution of Target Sites of MicroRNAs, MiR-iab-4 and MiR-iab-4as, in the Hox Gene Clusters of Insects

Abstract:MicroRNAs (miRNAs) are noncoding RNAs that regulate gene expression at the post-transcriptional level. In animals, the target sites of miRNAs generally reside in the 3’ UTRs of mRNAs. However, whether or how target sites have changed during evolution is largely unknown. This problem can be studied by using miR-iab-4 and miR-iab-4as, because they are known to have target sites in Hox genes, Abd-A and Ubx. This study may also provide some insights into the evolution of Hox gene clusters, which encode transcription factors that are involved in the specification of body segmentation. We have therefore examined the evolutionary changes of the target sites of these miRNAs in insect species. Our homology search identified a single copy of each of the miRNA genes in 12 Drosophila species, mosquito, silkworm, red flour beetle, and honeybee. In addition, these miRNA genes are encoded at the same location in the Hox gene cluster. The nucleotide sequences of mature miRNA regions in the genes have also been perfectly conserved among the species. By contrast, the number of target sites in the Abd-A and Ubx 3’ UTRs varied considerably among the species. Although we found three conserved target sites for each Hox gene among 12 Drosophila species, many target sites were lineage specific. In fact, frequent gains and losses of target sites were observed during Drosophila evolution. These results suggest that the target sites have changed more dynamically than the miRNA genes in the Hox gene clusters.

References: Chen, K., Rajewsky, N. 2007. The evolution of gene regulation by transcription factors and microRNAs. NATURE REVIEWS GENETICS 8: 93-103.

 02/17/10

Speaker: Song Li - Dept of Biology

(Assmann Lab)

Title: High Kurtosis is an Essential Feature of Gene Expression in Multi-cellular Organisms


Abstract:
Understanding gene expression patterns of multi-cellular organisms at the transcriptome level is a major step towards revealing organizing principles of many complex biological systems. One unique feature of multi-cellular organisms is that multiple somatic cell types harboring the same genome perform drastically different functions; therefore, the importance of the same gene can vary in different cell types. High-throughput transcriptome profiling and computational approaches have been employed to collect tissue-specific gene expression data (Birnbaum et al., 2003; Su et al., 2004; Schmid et al., 2005; Jiao et al., 2009) , and to identify “tissue specific genes” in several multi-cellular organisms. However, the genes are designated as “tissue specific” vary from one method to another, because the definition is intrinsically vague: a tissue specific gene could be a gene that is exclusively expressed in one tissue type, but a gene that was expressed in only, e.g., two out of 50 different tissue types could also be said to exhibit specificity of gene expression.

    This ambiguity in the definition of tissue-specificity motivated us to study gene expression in multi-cellular organisms from a fundamentally different perspective: examining the distributional features of gene expression across multiple tissues. We found that highly kurtotic expression of a gene across multiple tissue types is a unifying principle of four disparate multi-cellular organisms: human, mouse, rice and Arabidopsis. After identifying genes with kurtotic expression patterns, we constructed gene-tissue associations for these genes based on the extent to which a gene’s expression in a given tissue affected the gene expression kurtosis of the same gene in all tissues. Gene-tissue associations from human and Arabidopsis were then used to construct gene-centric tissue networks, by connecting tissues pairs within an organism if they shared a significant number of commonly associated genes with high kurtosis. We found that the resulting tissue networks of these evolutionarily distant organisms exhibit similar features of connectivity, modularity and node size (number of high kurtosis genes associated with each tissue). We discovered that connected tissues within each species’ network are often developmentally related and modules in both tissue networks represent well-defined groups of tissues with similar physiologies. For many genes without functional annotation, we are able to predict their functions in tissues these genes are associated with. Using a particular plant cell type, guard cells, as an example, we validated our predictions of novel functional associations between four genes and guard cells. Finally, we found that multi-tissue association and multi-level expression patterns underlie the observed leptokurtic distributions and represent a high dimension extension to the genome expansion theory of multi-cellular organisms (Kaiser, 2001) .        

References: Birnbaum, K., Shasha, D.E., Wang, J.Y., Jung, J.W., Lambert, G.M., Galbraith, D.W., and Benfey, P.N. (2003). A gene expression map of the Arabidopsis root. Science 302, 1956-1960.

Jiao, Y., Tausta, S.L., Gandotra, N., Sun, N., Liu, T., Clay, N.K., Ceserani, T., Chen, M., Ma, L., Holford, M., Zhang, H.Y., Zhao, H., Deng, X.W., and Nelson, T. (2009). A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet 41, 258-263.

Kaiser, D. (2001). Building a multicellular organism. Annu Rev Genet 35, 103-123.

Schmid, M., Davison, T.S., Henz, S.R., Pape, U.J., Demar, M., Vingron, M., Scholkopf, B., Weigel, D., and Lohmann, J.U. (2005). A gene expression map of Arabidopsis thaliana development. Nat Genet 37, 501-506.

Su, A.I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K.A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., Cooke, M.P., Walker, J.R., and Hogenesch, J.B. (2004). A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101, 6062-6067.

02/24/10

Speaker: Guru Anada - Dept of Integrative BioSci

(Nekruntenko Lab)

Title: Multivariate Analysis of Rate Co-Variation for Different Types of Mutations in Their Genomic Context

 

Abstract: While the abundance of completely sequenced genomes has greatly facilitated our understanding of regional heterogeneity in rates of individual mutation types, the co-variation in rates of multiple mutation types has remained largely unexplored, hindering a deeper understanding of mutagenesis. In this study, we used linear and non-linear multivariate analysis tools to explore rate co-variation among four mutation types, and associate it to multiple genomic features simultaneously. We observed a concordant and largely linear co-variation among rates of nucleotide substitutions, small insertions and small deletions. In contrast, microsatellite mutability did not display co-variation with any of the other three rates studied. GC content, distance to telomere, and local recombination rates were found to be significant predictors of mutation rate co-variation, corroborating the role of these features as predictors of mutagenesis. Our analysis also uncovered the significance of novel genomic predictors of mutation rate co-variation; namely, nuclear lamina binding regions and methylated non-CpG sites. Thus, co-variation in the rates of different mutation rates might be explained by shared local genomic landscapes. Interestingly, we observed strong non-linearities among the genomic predictors explaining co-variation in mutation rates. The genomic loci driving these non-linear behaviors are located either on chromosome X or at a certain distance to telomeres, suggesting unique environments in these portions of the genome. Based on the role of various genomic predictors, we speculate about the importance of different molecular mechanisms (e.g., replication and recombination) in generating mutations. Importantly, our multivariate analysis approach can provide improved background corrections for computational methods that identify potentially functional regions of a genome – these corrections would employ composite scores, encompassing rates of multiple mutation types simultaneously. 

 

References: Chiaromonte F., Yang S., Elnitski L., Bing Yap V., Miller W. and Hardison R. Association between divergence and interspersed repeats in mammalian noncoding genomic DNA.  Proc. Natl. Acad. Sci.2001, 98(25), 14503-14508.

 

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

 

Gaffney DJ, Keightley PD: The scale of mutational variation in the murid genome. Genome Res 2005, 15:1086-1094.

Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O’Connor M, Kolbe D et al.: Covariation in frequencies of substitution, deletion, transposition, and
recombination during eutherian evolution. Genome Res 2003,13:13-26.

 

Kelkar YD, Tyekucheva S, Chiaromonte F, Makova K: The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Res. 2008 18: 30-38.

 

Kvikstad EM, Tyekucheva S, Chiaromonte F, Makova KD: A macaque's-eye view of human insertions and deletions: dif- ferences in mechanisms. PLoS Comput Biol 2007, 3:1772-1782.

Lunter G, Ponting CP, Hein J: Genome-wide identification of human functional DNA using a neutral indel model. PLoS Comput Biol 2006, 2: e5.

Taylor J, Tyekucheva S, Zody M, Chiaromonte F, Makova K: Strong and Weak Male Mutation Bias at Different Sites in the Primate Genomes: Insights from the Human-Chimpanzee Comparison. Molecular Biology and Evolution 2006 23(3):565-573.

Tian D, Wang Q, Zhang P, Araki H, Yang S, Kreitman M, Nagylaki T, Hudson R, Bergelson J, Chen JQ. Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. Nature 2008, 455:105–108.

Tyekucheva S, Makova KD, Karro JE, Hardison RC, Miller W, Chiaromonte F: Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biology 2008, 9:R76.

Webster MT, Smith NG, and Ellegren H. Microsatellite evolution inferred from human-chimpanzee genomic sequence alignments. Proc. Natl. Acad. Sci. 2002, 99: 8748–8753.

Wolfe KH, Sharp PM, Li WH: Mutation rates differ among regions of the mammalian genome. Nature 1989, 337:283-285.

03/03/10

Speaker: Dr. Paula McSteen - Dept of Biology

Title: The biosynthesis and transport of the hormone auxin regulates vegetative and reproductive development in maize
Abstract: 
The plant growth hormone auxin regulates many aspects of cell expansion, cell division and tissue outgrowth in plants.  Auxin is synthesized locally and transported long distances for proper plant development.  Multiple pathways for auxin biosynthesis have been proposed, but until recently few genes functioning in these predicted pathways had been identified.
We have recently cloned the vanishing tassel2 (vt2) locus of maize using a positional cloning approach.  Phylogenetic analyses indicate that vt2 is co-orthologous to the tryptophan aminotransferase (TAA) genes of Arabidopsis, which function in the indole-3-pyruvic acid (IPA) pathway of auxin biosynthesis.  Unlike the TAA mutants which have subtle defects, a single vt2 knock-out results in strong vegetative and reproductive defects.  vt2 mutants have severely reduced plant height due to the production of fewer leaves, as well as significant reductions in reproductive structures compared to normal.  A similar phenotype to vt2 is seen in the maize sparse inflorescence1 (spi1) mutant.  spi1  encodes a monocot-specific member of the YUCCA gene family functioning in the tryptamine auxin biosynthesis pathway.  Furthermore, unlike the YUCCA mutants in Arabidopsis where quadruple knockouts are required for strong defects, a single spi1 knock-out results in severe vegetative and reproductive defects.  Therefore, even though both spi1 and vt2 are members of genes families, these genes exhibit less redundancy in function in maize than Arabidopsis.
                Both vt2 and spi1 show very localized patterns of expression, indicating that local auxin biosynthesis plays a critical role in maize development.  The synergistic interaction between vt2 or spi1 and the auxin transport mutant barren inflorescence2 (bif2) has revealed that auxin synthesized by these pathways must be transported for proper vegetative and reproductive development.  Therefore, auxin transport and auxin biosynthesis have overlapping roles in maize development.

 

References:

K. Phillips, A. Skirpan, S. Malcomber, T. Slewinski, C. Hudson, S. Barazesh, P. McSteen. vanishing tassel2 encodes a grass-specific tryptophan aminotransferase functioning in vegetative and reproductive development in maize. In preparation.


A. Skirpan, A. Hendrickson Culler, A. Gallavotti, D. Jackson, J.D. Cohen and P. McSteen (2009) BARren inflorescence2 interaction with ZmPIN1a suggests a role in auxin transport during maize inflorescence development.  Plant & Cell Physiology, 50: 652-657.


A. Gallavotti, S. Barazesh, S. Malcomber, D. Hall, D. Jackson, R.J. Schmidt, P. McSteen (2008) sparse inflorescence1 encodes a monocot-specific YUCCA-like gene required for vegetative and reproductive development in maize.  Proceedings of the National Academy of Sciences USA, 105:15196-15201.


P. McSteen, S. Malcomber, A. Skirpan, C. Lunde, X. Wu, E. Kellogg and S. Hake (2007) barren inflorescence2 encodes a co-ortholog of the PINOID serine/threonine kinase and is required for organogenesis during inflorescence and vegetative development in maize. Plant Physiology, 144:1000-1011.

03/10/10

 

~~~ NO SEMINAR ~~~ SPRING BREAK ~~~

03/17/10

 

Speaker: Dr. Hielim Kim - Dept of Biology

(Nei Lab)

Title: Population genetic analysis of ASAH1 gene associated with mental activity in humans
Abstract:
To understand the evolution of human mental activity, we performed population genetic analyses of nucleotide sequences (~ 11 kb) from a world-wide sample of 60 chromosomes of the N-acylsphingosine amidohydrolase(ASAH1) gene. ASAH1 hydrolyzes ceramides and regulates neuronal development, and its deficiency often results in mental retardation. In the region (~ 4.4 kb) encompassing exons 3 and 4 of this gene, there are two distinct lineages (V and M) that have been segregating in the human population for 2.4 ± 0.4 million years (my). The persistence of these two lineages is attributed to ancient population structure of humans in Africa. However, all haplotypes belonging to the V lineage exhibit strong linkage disequilibrium, a high frequency (62%), and small nucleotide diversity (π = 0.05%). These features indicate a signature of positive Darwinian selection for the V lineage. Compared with the orthologs in mammals and birds, it is only Val at amino acid site 72 that is found exclusively in the V lineage in humans, suggesting that this Val is a likely target of positive selection. Computer simulation confirms that demographic models of modern humans except for the ancient population structure cannot explain the presence of two distinct lineages, and neutrality is incompatible with the observed small genetic variation of the V lineage at ASAH1. Based on the above observations, it is argued that positive selection is possibly operating on ASAH1 in the modern human population.

 

References:

HL Kim and Y Satta. 2008. Population genetic analysis of the N-Acylsphingosine amidohydrolase gene associated with mental activity in Humans. Genetics, 178: 1505-1515.  


HL Kim, T Igawa, A Kawashima, Y Satta, and N Takahata. Divergence, demography and gene loss along the Human lineage. Phil. Trans. R. Soc. B. in press.

 03/24/10

Speaker: Dr. Norm Wickett - Dept of Biology

(dePamphilis Lab)
Title: 
Uncovering the causes and consequences of parasitism in the plant family Orobanchaceae using next-generation transcriptome sequencing

Abstract: The Orobanchaceae comprises 84 genera and >2000 species that span the continuum of parasitism from facultative hemiparasites to fully non-photosynthetic holoparasites. With an independent genome sequencing project underway for a closely related, non-parasite, Mimulus, there exists a phylogenetic framework to test hypotheses of genome evolution associated with the transitions between completely autotrophic plants and parasites, as well as between parasites with varying degrees of host reliance. The goal of the Parasitic Plant Genome project is to compare transcriptomes across both the diversity of these parasites represented by Triphysaria (facultative hemiparasite), Striga (obligate hemiparasite), and Orobanche (obligate holoparasite), as well as between and among stage-specific sequenced cDNA. Ultimately, these data will be used to investigate the role of specific genes in specific parasite functions, with particular emphasis on the organ that forms the bridge between parasite and host – the haustorium. Here we present evidence from both 454 and Illumina sequencing projects that examine the loss, and surprising retention, of specific genes and pathways in these parasitic plants.

 

Reference:

Westwood JH et al. 2010. The evolution of parasitism in plants. Trends in Plant Science. doi:10.1016/j.tplants.2010.01.004

03/31/10

Speaker: Xinwei Han - Dept of Genetics

(Ma Lab)

Title: Uncovering crossovers and gene conversions in single meiosis of Arabidopsis by next generation sequencing

Abstract: Crossover (CO) and gene conversion (NCO) are two major types of genetic recombination in meiosis. They not only provide physical connections between homologous chromosomes to ensure synapsis and segregation, but also serve as crucial forces in evolution. Although they have been broadly studied within some potential hotspots or in terms of impacts on allele frequencies, the genome-wide frequency and locations of COs and NCOs in a specific meiosis have not been explored in multicellular organisms. Here, we employed two ecotypes of the model plant Arabidopsis thaliana, Columbia (Col) and Landsberg erecta (Ler), to investigate the overall meiotic recombination events by sequencing and comparing the genomic sequence directly. We first identified 349,171 SNPs between Col and Ler. Then we utilized these SNPs as molecular markers to detect meiotic recombination events. In either replicate, nine crossover were uncovered, at least one in each chromosome. In the first meiosis sample, we found and experimentally confirmed three gene conversion events in SNP-dense region, suggesting a substantial number of gene conversions in single meiosis.

 

References:

Qi J, Wijeratne AJ, Tomsho LP, Hu Y, Schuster SC, Ma H, Characterization of meiotic crossovers and gene conversion by whole-genome sequencing in Saccharomyces cerevisiae, BMC Genomics, 2009 Oct 15;10:475.


Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM, High-resolution mapping of meiotic crossovers and non-crossovers in yeast, Nature, 2008 Jul 24;454(7203):479-85.

 04/07/10

Speaker: Dr. Mike Purugganan- Dept of Biology, New York University

http://biology.as.nyu.edu/object/MichaelPurugganan

Title: Molecular evolution of development: Genes and phenotypes

 Abstract: Several major plant adaptations arise through evolutionary change in developmental programs, resulting in morphological or life history diversification within and between species.  Over the last century, there have been major attempts to unify the study of development and evolution, a synthesis that has resulted in the emergence of the field colloquially referred to as EvoDevo.  Unlike most research on plant EvoDevo, we work at examining the evolution of developmental genes and pathways at the micro-level, using the model genetic system Arabidopsis thaliana to inform our analyses of evolutionary change.  Using examples largely of flowering time variation, a key developmental and life history transition in the plant’s life, we discuss the lessons we have learned about the study of the molecular basis of plant evolution.

 

References:

Flowers, J., Hanzawa, Y., Hall, M., Moore, R.C. and M.D. Purugganan (2009). Population genomics of the Arabidopsis thaliana flowering time genetic network. Mol. Biol. Evol. 26:2475-2486.

Ehrenreich, I., Hanzawa, Y., Chou, L., Roe, J.L., Kover, P.X. and M.D. Purugganan (2009). Candidate gene association mapping of Arabidopsis flowering time. Genetics 183:325-335.

Caicedo, A.L., Stinchcombe, J.R., Olsen, K.M., Schmitt J., and Purugganan, M.D. (2004). Epistatic Interaction Between Arabidopsis FRI and FLC Flowering Time Genes Generates a Latitudinal Cline in a Life History Trait. Proceedings of the National Academy of Sciences USA. 101: 15670-15675.

Older but pertinent reviews:

Purugganan, M.D. (2000). Molecular population genetics of regulatory genes. Mol. Ecol. 9: 1451 - 1461.

Purugganan, M.D. (1998). The molecular evolution of development. BioEssays 20: 700 - 711

 04/14/10

Speaker: Dr. Iliana Baums - Dept of Biology

Title: The transcriptome of the threatened elkhorn coral, Acropora palmata.

Abstract:  Reef- building corals face a multitude of environmental stressors and Caribbean populations have declined precipitously as a consequence. Still, it is expected that standing genetic variation includes genotypes pre-adapted to stressful conditions, specifically increased sea-surface temperatures. Expressed sequence tag (EST) libraries provide a first glimpse of the transcriptional response of corals to temperature stress. Using 454 titanium sequencing technology, we obtained 967,530 high quality reads with an average length of 411 nucleotides. The reads assembled to 32379 contigs of ~34M bp and 49841 singletons of 18Mbp. There are 19161 ISO groups which can be thought of as genes. The transcriptome contains previously identified genes involved in stress responses as well as in calcification. We compared the A. palmata transcriptome to that of its Pacific congener, A. millepora. In line with previous analysis, trinucleotides are the most common microsatellite motifs in the A. palmata transcriptome. Ultimately, a comprehensive microarray will be designed based on the transcriptome to interrogate the temperature response of elkhorn coral larvae. A similar approach but using a much smaller microarray (4000 features) provided preliminary evidence for site adaptation in another common Caribbean coral, Montastraea faveolata. Data generated here will be critical for predicting the response of coral communities to rising sea surface temperatures


References:

Baums IB (2008) A restoration genetics guide for coral reef conservation. Molecular Ecology 17:2796-2811.


Meyer E, Aglyamova G, Wang S, Buchanan-Carter J, Abrego D, Colbourne J, Willis B, Matz M (2009) Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. Bmc Genomics 10:219.


O'Connor MI, Bruno JF, Gaines SD, Halpern BS, Lester SE, Kinlan BP, Weiss JM (2007) Temperature control of larval dispersal and the implications for marine ecology, evolution, and conservation. Proceedings of the National Academy of Sciences of the United States of America 104:1266-1271.

 04/21/10

Speaker: Melissa Wilson- Dept of Integrative BioSci

(Makova Lab)

Title: Life history traits affect the magnitude of male mutation bias across 32 mammalian genomes

Abstract: 
Male mutation bias theory predicts that the mutation rate in males is often higher than in females because male gametes, sperm, undergo significantly more rounds of replication than female gametes, eggs. Male mutation bias has been observed in mammals, birds, fish, and even plants. Curiously, however, estimates of the magnitude of male mutation bias vary substantially across species, and even within the same species. There are two explanations for this. First, differences between estimates from the same species can be explained by regional variation in genome architecture. Not all nucleotide substitutions are affected equally by errors in replication (e.g. CpG vs. nonCpG sites). Furthermore, many genomic factors (e.g. repetitive elements, GC content, recombination rate) influence mutation rates regionally across the genome and, when not accounted for, can skew estimates of male mutation bias. Second, variations observed across species may be influenced by differences in life history traits, specifically metabolic rate, sexual selection, and generation time. Male mutation bias is expected to be influenced by metabolic rate because sperm not only live in a more reactive oxygen species rich environment, they are also more susceptible to mutations through oxidative stress than eggs. Male mutation bias might become elevated with stronger post-copulatory sexual selection; males in species where sperm from multiple males compete to fertilize eggs produce more sperm, potentially at the expense of a higher mutation rate, than males in species without competition. Additionally, species with shorter generation times might experience less male mutation bias because their sperm undergo fewer rounds of replication before conception.


Few studies have investigated the factors that influence variation in the magnitude of male mutation bias across multiple species using more than a subset of any genome. Utilizing the 32 eutherian mammal genome sequences we are able to investigate male mutation bias on a genome-wide scale across mammalian taxa with diverse life history traits. We ask which life history traits affect the magnitude of male mutation bias observed in mammals. To answer this question we collected literature on life history traits for all 32 mammals, filtered whole-genome alignments of factors known to influence substitution rates regionally, and computed global and context-dependent substitution rates. Then, after accounting for phylogenetic dependence, we developed a model to define how variations in life history traits affect variations in the magnitude of male mutation bias. We found that representatives of three major life history traits (metabolic rate, generation time, and sexual selection) all affect the magnitude of male mutation bias, explaining at least 70% of the variation in the magnitude of male mutation bias observed across these diverse mammals. Our results corroborate and expand upon years of previous research, and support the significant effect of life history traits on genome evolution.


References: N/A

Speaker: Dr. David Geiser & Seogchan Kang- Dept of Plant Pathology

Title: DNA sequence databases for fungal pathogen identification

Abstract:  We have been using multilocus phylogenetics as a tool for recognizing species boundaries in fungi since the 1990s, and a great deal of diagnostic DNA sequence data has accumulated in that time. Because fungal species recognized using mating compatibility and phylogenetics tend to be morphologically cryptic, molecular data are often the only useful means for identification. As a result, clinical plant, animal and medical microbiologists are challenged with the need to implement molecular identification in order to accurately identify fungi to the species level. This has necessitated the development of cyberinfrastructural resources that provide genotypic and phenotypic information about fungi to users who are not necessarily well-trained in molecular biology and phylogenetics. In this talk I will outline our efforts to provide resources for two important genera, /Fusarium/ and /Phytophthora/, and discuss some of the successes and pitfalls of the approach.
 

References: RPark, J. and 28 co-authors. 2008. Phytophthora database: A forensic database supporting the identification and monitoring of Phytophthora. Plant Dis. 92: 966-972.
Geiser, D.M., Jiménez-Gasco, M., Kang, S., Makalowska, I., Veerarahavan, N., Ward, T.J. Zhang, N., Kuldau, G.A., and O’Donnell, K. 2004. FUSARIUM-ID v.1.0: A DNA sequence database for identifying Fusarium. European Journal of Plant Pathology 110: 473-479.