Research Interests:
Plant evolutionary genomics; speciation; domestication; invasiveness; Compositae genomics

The Rieseberg lab integrates high-throughput genomic methods, bioinformatics, ecological experiments, and evolutionary theory to study the origin and evolution of species, domesticated plants, and weeds. Some of the problems we are currently working on are described below:

1. Speciation

Our primary research interest concerns how new plant species arise (Science 317:910-914) – one of the most fundamental questions in biology. Much of this work focuses on members of the sunflower genus Helianthus, but we also analyze patterns of variation in other plant and animal groups to make more general conclusions about speciation. Problems that have attracted our attention recently include, the nature of species (Nature 440:524-527), the importance of advantageous alleles in holding species together (Molecular Ecology 13:1341-1356), the evolutionary forces underlying phenotypic diversification (PNAS 99:12242-12245), the frequency of polyploid speciation (PNAS 106:13875-13879), the role of hybridization in evolution (ARES 28:359-389), and the contribution of chromosomal rearrangements to speciation (TREE 16:351-358).

In Helianthus, our goals are to identify and order the genetic changes responsible for the origin of species in this group and to understand how the new species survive, evolve, and interact after they are formed. Specific phenomena that appear to be critical for speciation in this group include hybridization, ecological divergence, and chromosomal rearrangements.

1.2. The genetics of ecological divergence.
Speciation in Helianthus appears to have been driven by habitat differentiation. Even hybrid species are strongly divergent ecologically from their parental species. We are employing a combination of ecophysiological studies, QTL analyses, field experiments, association mapping, candidate gene analyses, and hitchhiking mapping to identify the traits, genes, and mutations responsible for habitat divergence in this group (Molecular Ecology 12:1225-1235; Genetics 175:1803–1812). We are particularly interested in the molecular and ecological bases of variability in flowering time, salt adaptation, and drought tolerance. For example, we have recently shown that a latitudinal cline in flowering time in common sunflower (Fig. 2) results from changes at multiple hierarchical levels in multiple genetic pathways, including paralog-specific changes in FT homolog expression and tissue-specific changes in SOC1 homolog expression (B. Blackman et al. unpublished).

1.3. The role of chromosomal rearrangements in speciation.
Chromosomal rearrangements contribute to speciation in two main ways. First, some types of rearrangements such as inversions may suppress recombination locally, thereby facilitating the accumulation of hybrid incompatibilities or other species’ differences (ARES 39:21-42). Other kinds of rearrangements such as translocations can cause sterility in hybrids heterozygous for the rearrangement. A major unsolved mystery is why such “under-dominant” rearrangements are much more frequent in plants than in animals.

We are investigating the establishment of chromosomal rearrangements in wild sunflowers and their role in speciation. We have previously shown that (1) sunflowers have the highest rate of karyotypic evolution in either plants or animals (Genetics 167:449-457), (2) many of the rearrangements are strongly under-dominant (Genetics 171:291-303), and (3) rates of interspecific gene flow are reduced near chromosomal breakpoints (Molecular Biology and Evolution 26:1341-1355). Current studies employ a combination of genome sequencing and bioinformatic approaches to ask whether the greater redundancy of plant genomes might account for differences in rates and patterns of karyotypic evolution between plants and animals. Genetic redundancy due to whole genome and/or segmental duplication should reduce the initial under-dominance of chromosomal rearrangements, thereby facilitating their establishment.

2. Domestication

Current work includes a large-scale search for associations between sequence variation at candidate genes and domestication traits, genome scans using next generation sequencing approaches to search for regions of the genome that have undergone selective sweeps during domestication and improvement, and further analyses of the FT/TFL1 family to identify the causative mutations underlying flowering time QTLs. Other projects focus on the domestication and improvement of Noug and Yacon, which are indigenous Compositae crops from Ethiopia and South America, respectively.

3. Invasiveness

Invasive plants represent a major threat to the economy and environment, with annual economic costs to North America of $35-40 billion. In collaboration with laboratories at UBC (S. Otto, J. Whitton, and K. Adams) and Indiana University (Z. Lao, Jim Bever, and K. Clay), we are using common garden experiments, microarray analyses (Genetics 179:1881-1890), and hitchhiking and association mapping with next generation sequence data to identify specific genetic changes associated with invasiveness. By targeting Compositae weeds for this work – diffuse knapweed, starthistle, Canada thistle, ragweed, and common sunflower – we can exploit the genomic tools and resources developed by the Compositae Genome Project (see below).

Individuals from weedy or invasive populations of many plant species grow larger and faster than individuals from native populations, an observation that we have confirmed for several Compositae weeds. Explanations for this pattern typically involve life history trade-offs, in which investment in costly defense or abiotic tolerance traits is reallocated to growth and reproduction. We are asking whether similar molecular genetic mechanisms underlie these trade-offs in different Compositae weeds.

We also are exploring the role of hybridization in weed evolution. Many plant invasions are associated with hybridization, so it might be that the increased vigor observed in some invasive plants results from residual heterosis rather than life history trade-offs. We have found evidence of past hybridization in invasive starthistle populations (K. Dlugosch et al. unpublished), and will explore this possibility in other Compositae weeds.

4. Compositae genomics

In collaboration with groups at UC Davis (R. Michelmore & K. Bradford), U. Georgia (S. Knapp & J. Burke), U. Massachusetts (R. Kesseli), Indiana University (Z. Lai), and Cal Poly Pomona (D. Still), we are developing genomic resources and tools for the Compositae, one of the largest and most ecologically diverse families of flowering plants (http://cgpdb.ucdavis.edu/). These resources include ~1 million Sanger ESTs for crops and weeds in the family, detailed genetic linkage maps, QTL populations, functional maps, and NimbleGen and/or Affymetrix gene chips for key species. These tools and resources underlie many of the projects described above. In addition, the large sequence and expression data sets generated by the Compositae Genome Project (CGP) are being used to answer more general questions about genomic and phenotypic evolution across the family. For example, analyses of the age distribution of duplicate genes in 18 species from across the Compositae family revealed at least three ancient whole genome duplications. These include a paleopolyploidization shared by all analyzed taxa and placed near the origin of the family just prior to the rapid radiation of its tribes, and independent genome duplications near the base of the tribes Mutisieae and Heliantheae (Molecular Biology and Evolution 25:2445-2455). We also showed that contrary to Arabidopsis, genes annotated to structural components or cellular organization GO categories were significantly enriched among paleologs, whereas genes associated with transcription and other regulatory functions were significantly underrepresented (Fig. 6).

Ongoing work includes the sequencing of gene space for lettuce, sunflower, and safflower, transcriptome sequencing of an additional 25 genotypes from across the Compositae, analyses of copy number variation within and among Compositae species, and comparative analyses of domestication traits and the genes that underlie them. In addition, we are collaborating with researchers at INRA (P. Vincourt), U. Georgia (S. Knapp & J. Burke), and UBC (N. Kane & E. Marden) to sequence the sunflower genome and to determine the genetic basis of wood development in drought tolerant, wood-forming, wild sunflower species.

Fig. 6. GO annotations of Compositae whole transcriptome and paleologs. The left-most column displays the pooled Compositae transcriptome of 18 species, whereas the remaining columns represent paleologs retained in each tribe from the basal Compositae genome duplication and the basal Heliantheae genome duplication. Colors represent % of transcriptome a particular GO category composes. Superscripts indicate significantly different groups as determined by Chi-square tests (p < 0.05). GO categories that are significantly enriched or reduced among paleologs relative to non-paleologs in at least three comparisons are indicated with +/- signs. (from Barker et al. 2009; Molecular Biology and Evolution 25:2445-2455).

Blackman, B.K., J.L. Strasburg, S.D. Michaels, and L.H. Rieseberg. 2010. The role of recently derived FT paralogs in sunflower domestication. Current Biology 20:629–635.

Wood, T.E., N. Takebayashi, M.S. Barker, I. Mayrose, P.B. Greenspoon, L.H. Rieseberg. 2009. The frequency of polyploid speciation in vascular plants. Proceedings of the National Academy of Sciences USA 106:13875-13879.

Rieseberg, L.H., and J.H. Willis. Plant speciation. 2007. Science 317:910-914.

Rieseberg, L.H., T.E. Wood, and E. Baack. 2006. The nature of plant species. Nature 440:524-527.

Harter, A.V., K.A. Gardner, D. Falush, D.L. Lentz, R. Bye, L.H. Rieseberg. 2004. Origin of extant domesticated sunflowers in eastern North America. Nature 430:201-205.

Burke, J.M., and L.H. Rieseberg. 2003. The fitness effects of transgenic disease resistance in wild sunflowers. Science 300:1250.

Rieseberg, L.H., O. Raymond, D.M. Rosenthal, Z. Lai, K. Livingstone, T. Nakazato, J.L. Durphy, A.E. Schwarzbach, L.A. Donovan, and C. Lexer. 2003. Major ecological transitions in annual sunflowers facilitated by hybridization. Science 301:1211-1216.