b o t a n y a n d p l a n t p a t h o l o g y
p u r d u e u n i v e r s i t y
Overview: We are interested in multiple aspects and scales of evolutionary biology. Our first long-term interest is to identify evolutionary processes that shape diversity in genetic pathways. A second long-term focus is to determine the genetic structure of ecological communities. Some of our projects include:
Evolution of Developmental Genetic Pathways (Evo-Devo): Gene and genome duplications together with mutation accumulation are processes that play an important role in the diversification of genetic pathways. What is the frequency with which gene duplications occur and what are the evolutionary changes that occur in duplicate genes - especially over long evolutionary time scales? To address this and similar questions,
we are investigating the rates of changes in MADS-box genes. MADS-box genes represent a class of transcription factors that play an important role in regulating plant development. We use phylogenetic inferences to understand the origin of gene duplicates as well as the nucleotide substitutions that have
occurred in coding DNA and “non-coding” putative cis-regulatory elements across angiosperms. We are testing the functional changes associated with gene duplications using both grass systems and Arabidopsis.
Evolutionary and Ecological Diversification of North American Wild Rice (Zizania sp) and Rice Cutgrass ( Leersia sp): Population level extinction (extirpation) and subsequent loss of genetic diversity are major factors in the overall decline of global biodiversity and ecosystem structure. The complexity of long-term population persistence involves the interaction of genetic variation and phenotypic response to environmental variables. We are examining the evolutionary genetics of North American Wild Rice, Zizania, and Rice Cutgrass, Leersia, species across their geographic range. Zizania and Leersia are closely related to domesticated rice, Oryza sp. We are investigating multiple aspects of Zizania sp. and Leersia sp. biology including speciation, evo-devo and eco-devo, evolutionary ecology of reproductive strategies, adaptation to abiotic stressors, and hybridization barries. One area we are espescially excited about is understanding molecular evolutionary dynamics of genes that regulate ecologically important morphological and physiological traits. We are conducting experiments, greenhouse and field, that test for relationships between patterns of molecular evolution and ecological variables.
Evolutionary and Ecological Genomics of Aquatic Communities: The goal of this project is to examine patterns of genetic diversity across species at the community scale. This research is evaluating the spatial and temporal distribution of genetic diversity across interacting aquatic plant and insect species that span 400 million years of evolutionary diversification. Although a number of conceptual models exist that explain how interacting species may co-evolve, much remains to be learned about which concpetual model best fits "natural" communitites. We have identified a set of insect and plant species with interesting and varied ecological relationships, providing an opportunity to address a number of questions about the patterns and consequences of genetic variation at the community scale. For example, what are the rates of gene flow between aquatic communities across taxonomic scales. Levels of gene flow are important for shaping local adaptation and evolution of populations. In order to address this question as well as others, we are using species of aquatic plants and aquatic insects as well as a combination of coalescent and phylogenetic approaches and second generation sequencing.
Computational and Theory Based Research: Phylogenetic trees are a widely used as statistical estimates of evolutionary relationships in the biological sciences. However, much work remains in understanding the powers and pitfalls in applying phylogenetic methodologies to diverse data sets. We have several projects that involve the use of phylogenetics towards understanding and linking genome evolution to biodiversity:
- Sindhu, A, Chintamanai, S, Brandt, AS, Zanis, MJ, Scofield, SR, Johal, GS. 2008. Guardian of Grasses: Specific Origin and Conservation of a Unique Disease Resistance Gene in the Grass Lineage. PNAS. 105: 1762-1767.
- Zanis, MJ 2007. Grass spikelet genetics and duplicate gene comparisons. International Journal of Plant Sciences. 168:93-110
- Whipple, CJ, Zanis, MJ, Kellogg, EA, Schmidt, RJ. 2007. Conservation of B class gene expression in the second whorl of a basal grass and outgroups links the origin of lodicules and petals. PNAS. 104: 1081-1086.
- Qiu YL, Dombrovska O, Lee J, Li LB, Whitlock BA, Bernasconi-Quadroni F, Rest JS, Davis CC, Borsch T, Hilu KW, Renner SS, Soltis DE, Soltis PS, Zanis MJ, Cannone JJ, Gutell RR, Powell M, Savolainen V, Chatrou LW, Chase MW 2005. Phylogenetic analyses of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes. International Journal of Plant Sciences. 166: 815-842.
- Kim S, Soltis DE, Soltis PS, Zanis, MJ, Suh Y. 2004. Phylogenetic relationships among early-diverging eudicots based on four genes: were the eudicots ancestrally woody? Mol Phylogenet Evol. 1:16-30.
- Soltis, DE, Senters, AE, Zanis, MJ, Kim, S, Thompson, JD, Soltis, PS, De Craene, LPR, Endress, PK, and Farris, JS. 2003. Gunnerales are sister to other core eudicots: Implications for the evolution of pentamery. American Journal of Botany 90: 461-470
- Zanis, MJ, Soltis DE, Soltis PS, Qiu Y-L, Zimmer EA. 2003. Phylogenetic analyses and perianth evolution in basal angiosperms. Annals of the Missouri Botanical Garden 90: 129-150
- Nickrent, DL, Blarer, A, Qiu, Y-L, Soltis, DE, Soltis, PS, Zanis, MJ: 2002 Molecular data place Hydnoraceae with Aristolochiaceae. American Journal of Botany 89: 1809-1817
- Soltis, DE, Soltis PE, Zanis, MJ: 2002 Phylogeny of seed plants based on evidence from eight genes. American Journal of Botany 89: 1670-1681
- Zanis, MJ, Soltis DE, Soltis PS, Mathews S, Donoghue MJ: 2002 The root of the angiosperms revisited. PNAS 99: 6848-6853
- Soltis, DE, Kuzoff, RK, Mort, ME, Zanis, MJ, Fishbein, M, Hufford, L, Koontz, J, Arroyo, MK: 2001 Elucidating deep-level phylogenetic relationships in Saxifragaceae using sequences for six chloroplastic and nuclear DNA regions Annals of the Missouri Botanical Garden, 88: 669-693
- Qiu Y-L, Lee J, Bernasconi-Quadroni F, Soltis DE, Soltis PS, Zanis, MJ, Zimmer EA, Chen Z, Savolainen V, Chase MW. 2000. Phylogeny of basal angiosperms: Analysis of five genes from three genomes. International Journal of Plant Science; 161:S3-S27.
- Soltis DE, Soltis PS, Chase MW, Mort ME, Albach DC, Zanis, MJ, Savolainen V, Hahn WH, Hoot SB, Fay MF, Axtell M, Swensen SM, Prince LM, Kress WJ, Nixon KC, Farris JS. 2000. Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Botanical Journal of the Linnean Society; 133:381-461.
- Soltis PS, Soltis DE, Zanis, MJ, Kim S: Basal Lineages of Angiosperms: Relationships and Implications for Floral Evolution. International Journal of Plant Science 2000; 161:S97-S107.
- Qiu Y-L, Lee J, Bernasconi-Quadroni F, Soltis DE, Soltis PS, Zanis, MJ, Zimmer EA, Chen Z, Savolainen V, Chase MW. 1999. Evidence of the Earliest angiosperms from mitochondrial, plastid and nuclear genomes. Nature; 402:404-407.
- Les DH, Schneider EL, Padgett DJ, Soltis PS, Soltis DE, Zanis, MJ. 1999. Phylogeny, classification and floral evolution of water lilies (Nymphaeaceae; Nymphaeales): A synthesis of non-molecular, rbcL, matK, and 18S rDNA data. Systematic Botany; 24:28-46.
- Introduction to Plant Science (Botany 210) : This class introduces students to basic aspects of plant biology such as plant morphology, ecology, evolution, genetics, metabolism, photosynthesis, and physiology.
- Phylogenetics (Botany 590z) : This is a graduate class that I teach from a statistical point of view. We examine a wide range of topics including phylogenetic inference, character evolution, molecular evolution and I also introduce coalescent based methods of inference of population gene histories.
- Plant Evolution : This class is developed and ready to go, but will not be taught until a future date - Spring of 2011.
- Z.E.N. journal club : This journal club is organized by the Zanis, Emery, and Nichols labs here at Purdue. We meet at resource limiting intervals (i.e., the amount of other course work everyone is juggling). This journal club is inspired by EEGR at Washington State University. We read journal articles that include at leaset two of the following topics: Evolution, Ecology, and/or Genetics.
- Philip Morton , Ph.D. (Post-Doctoral Fellow): Community Genetics and Genomics, Phylogenetics and Molecular Evolution
- Rebecca Tucker , graduate student,(co-advised with Dr. Kevin Gibson): Zizania aquatica population and conservation genetics
- Joseph Walker , undergraduate student: Zizania aquatica and Leersia sp. population genetics
- Sheryl Walker , graduate student: Evo-Devo and Eco-Devo in aquatic grass species
- Renate Wuersig , graduate student: Evo-Devo of C and D class MADS-box genes
- Michael Zanis , PI