Faculty & Research
Center for Genomics & Bioinformatics
Indiana Molecular Biology Institute
- Contact Information
- Contact Jeffrey Palmer by jpalmer [at] indiana [dot] edu
- By telephone: 812-855-8892
- By fax: 812-855-6705
- JH 235C / JH 229/235 (lab)
- Evolution, Ecology & Behavior
- Research Areas
- Genomics and Bioinformatics
- Plant Molecular Biology
Ph.D., Stanford University, 1981
Postdoctoral Fellow, Duke University, 1983-1984
Postdoctoral Fellow, Carnegie Institution of Washington, 1981-1983
Member, National Academy of Sciences
Fellow, American Academy of Arts & Sciences
David Starr Jordan Prize
Wilhelmine E. Key Award, American Genetics Association
Merit Award, Botanical Society of America
We use approaches of comparative molecular biology, genomics, phylogenetics, and bioinformatics to study various major issues in the evolution of genes and genomes. Current studies fall into four areas:
Horizontal Gene Transfer in Plants - Horizontal gene transfer (HGT) is now recognized as a major evolutionary genetic force driving genomic and phenotypic change in prokaryotes and many unicellular eukaryotes. In contrast, there is little published evidence that HGT is common or important in the major groups of multicellular eukaryotes (animals, plants, and fungi). We recently discovered that HGT of mitochondrial genes in plants is both widespread and recent and have now expanded this work in several directions. Our efforts focus on plant mitochondrial genomes because their evident propensity for HGT and certain other attributes make them a model system for investigating HGT in eukaryotes. These studies assess rates, patterns, extents, chimeric consequences, directionality, donor/recipient relationships, functionality, and mechanistic aspects of HGT across many lineages of plant mitochondrial genomes. Our recent work has provided insight into mechanisms of HGT (it frequently occurs by direct physical contract between parasitic plants and their host plants) and has identified a plant whose mitochondrial genome has been radically shaped by HGT (it contains numerous genes acquired by HGT, and from a wide variety of donors, from other flowering plants to mosses).
Transfer of Mitochondrial Genes to the Nucleus - We are using flowering plants as a model "system" to study the evolutionary transfer of mitochondrial genes to nucleus. This process occurred on a massive scale early in mitochondrial evolution, and is therefore of fundamental importance to all eukaryotes, but continues to a significant extent only in plants. We have identified a number of very recent cases of gene transfer, which we are studying to elucidate underlying mechanisms and to characterize intermediates in the gene transfer process, e.g., plants which contain and express the same gene in both the organelle and the nucleus. We are also asking why some genes are transferred surprisingly frequently, hundreds of times during plant evolution, why certain lineages of plants transfer genes at highly elevated rates, and whether nuclear genes of mitochondrial origin are ever recaptured by the mitochondrial genome.
Accelerated Evolution of Mitochondrial Genes - We have discovered two separate lineages of plants whose mitochondrial genes are evolving at a highly accelerated rate, up to 4,000 times faster than in other plants. In each group, multiple major increases in the mutation rate have occurred, in some cases followed by major decreases. Current efforts seek to elucidate the molecular bases of these unprecedented changes in the fundamental mutation rate and to investigate whether such exceptionally high mutation rates have had any secondary effects on mitochondrial genome evolution and function.
Molecular Phylogeny - Although elucidating organismal phylogeny is no longer a primary goal of our research, a phylogenetic perspective necessarily informs almost all of our molecular evolutionary studies. As a consequence, valuable insights into important phylogenetic issues are often an unexpected bonus of our work. Our recent phylogenetic studies have identified what may be the earliest eukaryotes, land plants, and flowering plants, and have radically revised our concepts of seed plant evolution.
Sloan, D. B., Alverson, A. J., Chuckalovcak , J. P., Wu, M., McCauley, D. E., Palmer, J. D., and Taylor, D. R. 2012. Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biol. vol. 10, issue 1, e1001241 (17 pp)
Sloan, D. B., Alverson, A. J., Wu, M., Palmer, J. D., and Taylor, D. R. 2012. Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence in the angiosperm genus Silene. Genome Biol. Evol. 4:294-306.
Sanchez-Puerta, M. V., Abbona, C. C., Zhuo, S., Tepe, E., Bohs, L., Olmstead, R., and Palmer, J. D. 2011. Multiple recent horizontal transfers of the cox1 intron in Solanaceae and extended co-conversion of flanking exons. BMC Evol. Biol. 11:277 (15 pages).
- Alverson, A. J., Rice, D. W., Dickinson, S., Barry, K., and Palmer, J. D. 2011. Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber (Cucumis sativus). Plant Cell 23:2499-2513.
- Mower, J. P., Stefanović , S., Hao, W., Gummow, J., Jain, K., Ahmed, D., Palmer, J. D. 2010. Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes. BMC Biol. 8:150 (16 pages).
- Hao, W., Richardson, A. O., Zheng, Y., and Palmer, J. D. 2010. Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. Proc. Natl. Acad. Sci. USA 107:21576-21581.
- Hao, W. and Palmer, J. D. 2009. Fine-scale mergers of chloroplast and mitochondrial genes create functional, trans-compartmentally chimeric mitochondrial genes. Proc. Natl. Acad. Sci. USA106:16728-16733.
- Keeling, P. J., and Palmer, J. D. 2008. Horizontal gene transfer in eukaryotic evolution. Nature Reviews Genetics 9:605-618.
- Sanchez-Puerta, M. V., Cho, Y., Mower, J. P., Alverson, A. J., and Palmer, J. D. 2008. Frequent, phylogenetically local horizontal transfer of the cox1 group I intron in flowering plant mitochondria. Mol. Biol. Evol. 25:1762-1777.
- Mower, J. P., Touzet, P., Gummow, J. S., Delph, L. F., and Palmer, J. D. 2007. Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evol. Biol. 7:135 (14 pages).
- Richardson A. O., and Palmer, J. D. 2007. Horizontal gene transfer in plants. J. Exp. Botany, 58:1-9.
- Rice, D. W. and Palmer, J. D. 2006. An exceptional horizontal gene transfer in plastids: Gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters. BMC Biology 4:31 (15 pages).
- Parkinson, C. L., Mower, J. P., Qiu, Y.-L., Shirk, A., Song, K., Young, N. D., dePamphilis, C. W., and Palmer, J.D. 2005. Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae. BMC Evol. Biol. 5:73 (12 pages)
- Bergthorsson, U., Richardson, A., Young, G. J., Goertzen, L., and Palmer, J. D. 2004. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. Proc. Natl. Acad. Sci. USA 101:17747-17752.
- Mower, J. P., Stefanovic, S., Young, G. J., and Palmer, J. D. 2004. Gene transfer from parasitic to host plants. Nature 432:165-166.
- Cho, Y., Mower, J. P., Qiu, Y.-L., and Palmer, J. D. 2004. Mitochondrial substitution rates are extraordinarily elevated and variable within a genus of flowering plants. Proc. Natl. Acad. Sci. USA 101:17741-17746.
- Bergthorsson, U., Adams, K. L., Thomason, B., and Palmer, J. D. 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424:197-201.