Lawton-Rauh Laboratory:

Molecular Population Genetics & Evolutionary Genomics 

Department of Genetics & Biochemistry

101 & 102 Jordan Hall

Clemson University

Clemson, SC 29634-0318

WELCOME!  

WILLKOMMEN!   BIENVENUE!   BENVENUTO!   BOA VINDA!  

Major research areas:

Evolutionary Dynamics of Agroecosystems (red rice, Palmer amaranth)

Evolutionary Genetics in the Amaranthus genus (~ 50 cultivated and wild species)

The Role of Linkage Disequilibrium in Speciation & Adaptation (Hawaiian Silversword Alliance)

Demographic Factors Shaping Genetic Variation in Arabidopsis petraea and Arabidopsis arenosa

The Lawton-Rauh lab studies mechanisms shaping genetic variation at the population and species level. In particular, we investigate the interplay of effective population size, allele sharing among populations and species, and linkage disequilibrium by taking an empirical approach in plants. How these factors shape genetic variation at individual loci, as well as the association among loci, indicate the impact of demographic history on genome evolution. The relationships among alleles (i.e. linkage disequilibrium and haplotype diversity) and effective population size reflect demographic history and the potential impact of selection on genetic variation at the population level. This tight interaction suggests that the partitioning of genetic variation attributable to demographic forces versus natural selection is difficult, but necessary, to unwind in order to understand the mechanisms underlying genetic variation and the role of natural and speciation.  Our research also helps us understand how strong directional selection is on population differentiation in species that greatly impact agroecosystems such as weedy, invasive species like weedy rice and amaranth.  Our work on molecular evolution and phylogenetic relationships in the genus Amaranthus also informs us regarding the impact of various selection pressures on cultivated and wild species because Amaranth is an important grain and leaf crop for many cultures.

To empirically investigate the relationships among linkage disequilibrium, demographic forces, and natural selection in shaping genetic variation, our work includes several systems: the edaphically-restricted species Arabidopsis lyrata (and other close relatives in Brassicaceae) with alternative post-glacial distributions among populations, the Hawaiian Silversword Alliance insular plant adaptive radiation, and weedy red rice introgression with cultivated rice.  Our work in the Hawaiian silversword alliance involves collaborations with a number of labs specializing on different facets of adaptive evolution and dynamics.  For more information, please see our Hawaiian silversword alliance group web portal (www.silverswordalliance.org) which also contains links to the group Wiki and GoogleGroup sites.  Our work in weedy red rice is a recently-funded USDA grant in collaboration with Nilda Burgos (University of Arkansas) and Albert Fischer (UC-Davis) and investigates the evolutionary dynamics of weedy red rice in the context of alternative management strategies and ecozones in the United States.  We also collaborate with the Burgos and Norsworthy labs at University of Arkansas to investigate the interactions between strong directional selection and demography in several amaranth populations and are developing a more extensive research program probing the cultivation, distribution, and evolution of cultivated and wild species in the Amaranthus genus (we are excited about this project... stay tuned for more information!).

Other research interests and directions in our lab include: empirical null distributions for hypothesis testing, extension of model system-based experimental and analytical techniques to non-model species, molecular evolution and population dynamics of duplicated genes and genomes, divergence population genetics in other plant lineages, and evolutionary dynamics of genes in different gene classes (at the population level and among closely-related species). The Lawton-Rauh lab also conducts collaborative research, both nationally and internationally with researchers in China, Germany, and Switzerland. 

FURTHER RESEARCH INFORMATION:

The Lawton-Rauh Laboratory investigates mechanisms that maintain and shape genetic variation at two levels of genome organization:  

        gene/locus-specific &

        genome-wide patterns

We use nucleotide sequence data to investigate the relationship between neutral-equilibrium (stasis) factors shaping genetic variation in the entire genome and natural selection factors in shaping genetic variation in specific genes or loci. Often these particular loci (i.e. genes of 'favorite' functions) are involved in adaptive evolution and are located in defined genomic regions, thus our lab focuses on factors within short gene regions.  We look at loci all over the genome and estimate average indices of various factors that change genetic variation in short regions.  Such factors include:

1) 'hitch-hiking' within genome regions via linkage disequilibrium and effective recombination between genes under natural selection and genes in the surrounding genomic neighborhood 

as well as 

2) demographic factors that change effective population size (eg. population substructure, admixture, bottleneck, etc.) which lead to similar patterns of nucleotide sequence (DNA) polymorphism but affect a larger proportion of the genome than gene-specific natural selection. 

By addressing the interplay and relative effects of these processes, we aim to gain insight into mechanisms shaping the effectiveness of natural selection, evolutionary diversification of lineages, and general genome dynamics. Our laboratory currently focuses on plant taxa, but the processes we study are relevant to most living organisms and is especially pertinent to trait association and mapping in cultivated species and humans (including the detection of markers associated with disease presence).  

MEMBERS OF THE LAWTON-RAUH LAB

Amy Lawton-Rauh

Ph.D., Principal Investigator, amylr"at"clemson.edu

Kristin Beard

Clemson, Ph.D. Genetics student, kebeard"at"clemson.edu

Molecular evolution of resistance genes in genus Amaranthus

Cindy Climer

Clemson, Ph.D. Genetics candidate, cclimer"at"clemson.edu

Impact of recombination, population structure, and gene flow on genetic variation in Arabidopsis petraea

Molecular population genetics of weedy red rice in the U.S. (with collaborator N. Burgos, Uni. Arkansas)

Amanda Allison^{^}, Sarah Barfield*, Jessica Gancar^{^}, Kyle Gettler^{#^}, Mary Jones^#

Academic year 2009-10 Clemson Genetics and Biochemistry, Undergraduate Research Assistants

^#Calhoun Honors Departmental Grant, ^SCLife/HHMI Research Grant recipients

*Sarah is continuing her project this year as a high school service learning student

Brad Rauh

M.S., Research Associate, brauh"at"clemson.edu

Lewis Bradley Lawton Rauh

Newest permanent member since 18.May 2008, resident "scientist-in-training"

Former researchers of the Lawton-Rauh lab:

Sarah Barfield (SPRI/HHMI Research Intern from Daniels High School, Summer 2009)

Margaret Beaudrot (Honors HHMI/SCLife Undergraduate Research Intern 2006-07; now medical student, MUSC)

Paige Catotti (S.C. Governor's School for Science and Math, SPRI Research Intern 2007; now Clemson Genetics undergrad student)

Christina Hawbaker (Willamette University, NSF-REU Research Intern Summer 2008; now M.S. Genetic Counseling student, U. Utah)

Katie Horton (Seneca High School, Service Learning Intern Fall 2006; current Honors Chemistry undergrad)

Devleena Kole (SPRI/HHMI Research Intern from Daniels High School, Summer 2009)

Meredith O'Toole (EUREKA! Honors Research Intern, Summer 2009)

Chelsea Reighard (SCLife/HHMI & Calhoun Honors Research Intern 2007-08, now Teach for America faculty & Rhodes Scholar nominee)

Alanna Slack (EUREKA! Honors Research Intern, Summer 2009)

Jennifer Smith (Francis Marion University, NSF-REU Research Intern Summer 2007; now PhD student)

Steven Vensko (HHMI/SCLife Intern 2008-09, Research Assistant Summer 2009; now PhD student NCSU Genetics)

Sarah Walker (HHMI/SCLife Undergraduate Research Intern 2006-07; now Physicians Assistant student, MUSC)

Sarah Walker                          Margaret Beaudrot                 Jennifer Smith                 Chelsea Reighard                      

CU Graduate May 2007        CU Graduate Dec. 2007         Francis Marion Uni.       CU Graduate May 2008             

B.S. Genetics                          Honors B.S. Biochemistry   NSF-REU Intern              Honors B.S. Genetics                                                                                                                                                             

PLANT PICTURES

Grow-room pictures

  Arabidopsis petraea                 A. petraea flower        Arabidopsis arenosa

PUBLICATIONS

(pubmed search for updated 'Lawton-Rauh' list) 

Lawton-Rauh A.L., Climer C.R., B.L. Rauh.  (2009, in press). Comparative and evolutionary genomics.  in  Principles and practices of plant genomics, Volume 3 Advanced genomics.  Eds. C. Kole and A.G. Abbott (book chapter).

Jiménez, S., Lawton-Rauh, A.L., Reighard, G.L., Abbott, A.G., and D.G. Bielenberg (2009). Phylogenetic analysis and molecular evolution of the dormancy associated MADS-box genes from peach. BMC PLANT BIOLOGY   Vol: 9 Art: 81.

Lawton-Rauh, A.  (2008).  Demographic processes shaping genetic variation.  (2008). Current Opinion in Plant Biology 11(2):103-9. 

Lawton-Rauh, A., Friar, E., and D.L. Remington. (2007).  Collective evolution processes and the tempo of lineage divergence in the Hawaiian silversword alliance adaptive radiation (Heliantheae, Asteraceae).  Molecular Ecology 16(19): 3993-3994.

Lawton-Rauh, A., Robichaux, R.H., and M.D. Purugganan. (2007).  Diversity and divergence patterns in regulatory genes suggest differential gene flow in recently-derived species of the Hawaiian silversword alliance adaptive radiation (Asteraceae).  Molecular Ecology 16(19):3995-4013, Cover Photo, News & Views coverage.

Schranz, M.E. , Windsor,  A.J., Song, B-H, Lawton-Rauh, A. and T. Mitchell-Olds.  (2007).  Comparative genetic mapping in Boechera stricta (Brassicaceae).  Plant Physiology 144:286-298.

Lawton-Rauh, A. (2003) Evolutionary dynamics of duplicated genes in plants. Molecular Phylogenetics and Evolution. 29(3):396-409. Review.  

Lawton-Rauh, A., Robichaux, R.H., and M.D. Purugganan (2003) Patterns of nucleotide variation in homoeologous regulatory genes in the allotetraploid Hawaiian silversword alliance (Asteraceae). Molecular Ecology 12(5):1301-13. Cover photo. 

Lawton-Rauh, A., Alvarez-Buylla, E., and M.D. Purugganan (2000) Molecular Evolution of Flower Development. Trends in Ecology and Evolution. 15(4):144-149. 

Lawton-Rauh, A., Buckler, E.S., and M.D. Purugganan (1999) Patterns of molecular evolution among paralogous floral homeotic genes. Molecular Biology and Evolution. 16(8):1037-45.

Other publications directly involving the Lawton-Rauh Lab:

(pubmed search for publications by Brad Rauh)

Karve, A., Rauh, B.L., Xia, X., Kandasamy, M., Meagher, R.B., Sheen, J., and B.D. Moore (2008).  Expression and evolutionary features of the hexokinase gene family in Arabidopsis.  Planta.  228(3):411-25. Epub 2008 May 15.

Rauh, B.L., Basten, C., and E.S. Buckler (2002). Quantitative trait loci of growth response to varying nitrogen sources in Arabidopsis thaliana. 104:743-750.

(pubmed search for publications by Cindy Climer)

Manfre, A.J., LaHatte, G.A., Climer, C.R., and W.R. Marcotte Jr (2009). Seed dehydration and the establishment of desiccation tolerance during seed maturation is altered in Arabidopsis thaliana mutant atem6-1.  Plant and Cell Physiology. 50(2):243-253.

OPPORTUNITIES
Our lab warmly invites and is currently accepting postdoctoral researchers, Ph.D. graduate students, and undergraduate research students.  Students and researchers requesting preparation support for extramural funding and fellowships to directly or indirectly investigate research objectives of the Lawton-Rauh lab should contact the principal investigator directly and read the following information:

Information for prospective postdoctoral researchers and visiting scholars:

In addition to the projects listed above, there are a number of other potential research scopes (among many!) to consider developing and exploring in our lab, such as:  

Test alternative hypotheses of population structure, historical divergence patterns, and pattern of species  divergence in a particular organismal group (taxonomic lineage).

Utilize molecular evolutionary analysis tools to understand and infer the potential evolutionary relationships and historical genome dynamics of gene regions, gene families or particular functionally important loci. 

There are a number of relevant sources for extramural funding of postdoctoral researchers, for international scholars and U.S. citizens.  Please contact the P.I. (Amy Lawton-Rauh) directly for further information.

Information for prospective graduate students:

Interested prospective graduate students must formally apply and be accepted into the Clemson University Department of Genetics & Biochemistry. Information about the deadlines, required exams and required documents can be found here: GenBiochem Graduate Program website.  All prospective students (especially international students) are strongly encouraged to contact Amy Lawton-Rauh directly via email to discuss research project scopes and the graduate program coordinator (via email: gbhelp"at"clemson.edu) to discuss the application process.  Please pay careful attention to the application deadlines and the program requirements.  Additionally, potential students (especially international students) greatly benefit from applying for external graduate fellowship funding.  

Information for prospective undergraduate research interns:

Our lab is happy to host undergraduate and high school research interns, both during the summer and during the academic year.  Clemson University undergraduates that are interested in completing their 491 research internship in our lab are encouraged to apply for several fellowships on campus which further enhance your experience and your professional portfolio, especially in preparation for your post-graduate plans.   Undergraduate students from other campuses are encouraged to apply for an NSF-REU research internship in our departmental 'Molecular Genetics and Biochemistry' NSF-REU program.  For more information about the NSF-REU program, please see the following link:  Clemson Molecular Genetics and Biochemistry NSF-REU Program.  Rising honors undergraduate freshman at Clemson University are encouraged to apply for a EUREKA! fellowship during the summer prior to starting undergraduate work.  

Prospective graduate students, postdoctoral researchers, and undergraduate students are encouraged to contact Amy Lawton-Rauh directly to discuss potential research project scopes and to consider possible funding sources (amylr"at"clemson.edu).

Special note for prospective '491' undergraduate research interns:  The Lawton-Rauh laboratory typically hosts 2-3 students per academic year for this internship and projects require preparation before your internship begins.  Thus you are strongly encouraged to apply for a position and make arrangements for your '491' internship at least 1 full semester before the start of your internship.  This permits more effective project development and makes it possible to subsequently apply for on and off-campus fellowships as well as opens possibilities for attending scientific meetings.  

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Last updated: 20.October 2009
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