Molecular Genetics and Ecology of Plant Adaptation Abstracts

Molecular Genetics and Ecology of Plant Adaptation
December 11-13, 2002
an international workshop sponsored by the ubc botanical garden and centre for plant research

Speakers:

Philip Awadalla (University of California, Davis)
Jörg Bohlmann (UBC)
Justin Borevitz (Salk Institutue)
Amy Bouck (University of Georgia)
Toby Bradshaw (University of Washington)
Quentin Cronk (UBC)
Mitchell Cruzan (Portland State University)
Carl Douglas (UBC)
Elizabeth Elle (Simon Fraser University)
Sara Good-Avila (Acadia University)
Scott Hodges (University of California, Santa Barbara)
Brian Husband (University of Guelph)
Donald Levin (University of Texas)
Barbara Mable (University of Guelph)
Sarah Mathews (University of Missouri)
Heather McKhaan (Centre National de Recherche en Génomique)
Rebecca Montgomery (University of Wisconsin, Madison)
Leonie Moyle (University of California, Davis)
Michael Purugganan (North Carolina State University)
Nishanta Rajakaruna (UBC)
Mark Rausher (Duke University)
Jennifer Rhode (Portland State University)
Kermit Ritland (UBC)
Doug Schemske (Michigan State University)
Carl Schlichting (University of Connecticut)
Dolph Schluter (UBC)
Suhua Shi (Zhongshan University)
D. Lee Taylor (Institute of Arctic Biology, University of Alaska Fairbanks)
Peter Tiffin (University of Minnesota)
Jeannette Whitton (UBC)
John H. Willis (Duke University)

Poster Presenters

Diane Byers (Illinois State University)
Amy Breen Carroll (University of Alaska Fairbanks)
Charles Chen (UBC)
Daniel Fulop (Harvard University)
Matthew Hahn (Duke University)
Xin-sheng Hu (UBC)
Anshuman Kumar (UBC)
Matthew S. Olson (University of Alaska Fairbanks)
Risa Sargent (UBC)
Stacey Thompson (UBC)
Erica J. Wheeler (University of Victoria)

Talk Abstracts (listed alphabetically by speaker)

Speaker	Abstract
Awadalla, Philip	The Genomic Significance of Recombination to Adaptation in Plants The evolutionary significance of recombination has been subject to much theoretical examination. To address this issue using genome data, and in order to make use of completed genomes and genome-wide polymorphism data to identify regions under selection, we must have a reliable means of estimating the recombination rate such that model-based approaches to detect selection can be employed. We have used two approaches to study how recombination contributes to adaptation at the intra- and inter-specific level in plants. First, we used a composite likelihood method to estimate recombination rates from SNP data so that we can examine how recombination contributes to the evolution of important loci under strong selection. Using this approach, we observed that recombination and gene conversion are significant evolutionary forces at self-incompatibility and plant defense loci. Second, using genetic map data, we examined how recombination evolves at the interspecific level by performing a comparative survey among angiosperms. This analysis revealed that genome-wide recombination rates vary only 14-fold (in contrast to the 1900 fold variation in genome size) and do not correlate with genome sizes - similar to observations made for mutation (Drake’s Rule). Furthermore, gene density is positively correlated with per base recombination rates along chromosomes in A. thaliana as well as many other genomes. These observations suggest that recombination releases sites (including regulatory regions) subject to selection from the inhibiting effects of Hill-Robertson interference. Finally recombination, like mutation, may be maintained at some 'equilibrium' through interactions of a number of important population genetic parameters.
Bohlmann, Jörg	Terpenoid Synthases: A large gene family for ecological plant interactions Terpenoids are the largest known group of natural products, historically referred to as secondary metabolites. These or other natural products have essential functions in all plants, which rely, as sessile organisms, to a large extend on natural product special chemistry for a plethora of ecological interactions with their biotic and abiotic environment. In the last five to ten years tremendous progress has been made in deciphering biochemical and molecular processes of terpenoid natural product formation under constitutive and stress-response conditions. Based on recent biochemical, molecular genetic, and genomic analyses of plant terpene synthases (TPS) in a suite of plant species, it is likely that all plants contain natural product tps genes, the expression of which can be as subtle as in plant-insect tritrophic defenses or as obvious as in the context of floral scent emission. I will present examples for functions of new tps genes from Arabidopsis, poplar, snapdragon flowers and conifers.
Borevitz, Justin	Molecular basis of Natural Variation: Arrays to the rescue We use the model plant Arabidopsis thaliana to investigate the genetic determinants of variation in plant light response. A survey of 140 accessions, or ecotypes, identified heritable genetic variation that is correlated with latitude as well as a natural variant in the PHYTOCHROME A photoreceptor. Quantitative Trait Locus (QTL) mapping identified 12 loci important for light response between the Ler and Cvi accessions. A major QTL, LIGHT1, maps to a novel locus, whereas a second major QTL maps to the PHYTOCHROME B (PHYB) locus. Both QTL are associated with light response across Arabidopsis ecotypes. In addition, the pattern of sequence variation at PHYB is suggestive of balancing selection. If QTL are determined by gene expression variation, the LIGHT1 gene may be detected using global transcription analysis using oligo-nucleotide arrays. We profiled three day old seedlings of the LIGHT1 NIL and parental Ler and Cvi lines. Significant transcription variation, mapping to the LIGHT1 interval, was identified. We then developed a highly parallel genotyping method to identify more than 8000 Single Feature Polymorphisms (SFPs) via DNA hybridization to oligo-nucleotide arrays. Bulk segregant analysis using these SFPs was used to map a mutation. Candidate genes in QTL regions were also identified that contain single or multiple feature polymorphisms. This method was used to identify a flowering time QTL as Flowering Locus M. Linkage Disequilibrium (LD) mapping may also be effective in fine mapping QTL. To this end we are generating a high resolution LD map by SFP genotyping 100s of Arabidopsis accessions. This will allow genome wide association mapping to be performed. Oligo-nucleotide array technology is being used to identify candidates via transcriptional profiling and/or as containing feature polymorphisms, and to map mutations via traditional or LD mapping. The molecular basis of natural variation can now be investigated at an incredibly detailed level.
Bouck, Amy and Edward Kentner, Ryan Peeler, Michael L. Arnold and Susan R. Wessler	Genetic mapping of reproductive isolation in Louisiana Irises Understanding the evolution of traits involved in adaptation and speciation requires knowledge of their genetic basis. Genetic and QTL mapping are means of investigating the genetic architecture of such traits. Our work aims to characterize the genetic underpinnings of reproductive isolation between Iris fulva and I. brevicaulis. We have constructed a linkage map of I. fulva by mapping approximately 215 retrotransposon display markers in 120 backcross 1 hybrids. Our map covers approximately 2000 Kosambi cM on 25 linkage groups. Sixteen percent of mapped loci exhibit segregation distortion (a < 0.05). The number, distribution, and degree of distortion of these loci reveal genomic areas of negative and -- less frequently -- positive selection acting on the introgression of I. fulva alleles into the I. brevicaulis genetic background. Future work will involve QTL mapping of floral traits that specialize I. fulva to hummingbird pollination, allowing us to compare the genetic architecture of a prezygotic isolating mechanism to that of the postzygotic isolating mechanism presented here.
Bradshaw, Toby and Doug Schemske	The genetics of adaptation in natural plant populations The genetic architecture of adaptive evolution remains unknown for wild plant populations. How many mutations are required for adaptation to a new environment? How large a phenotypic effect does each mutation have? Are the same genes mutated during independent instances of adaptation to the same environment, or is adaptive evolution purely a contingent process? We address questions such as these using a combination of QTL mapping and cloning, candidate gene identification, and extensive field experimentation with natural plant populations in their native ranges. Examples of such work include the genetic basis of pollinator-mediated reproductive isolation in Mimulus lewisii and M. cardinalis, adaptation to climate along an elevational transect in M. lewisii and M. cardinalis, and adaptation to serpentine soils in Linanthus parviflorus and L. bicolor.
Constabel, Peter	The Adaptive Nature of Herbivore Defenses in Populus Plant defense against insect herbivores is a very active process, and involves rapid transcription of defense and signaling genes. Using differential screening approaches and EST sequencing and other approaches, we have identified a series of wound and herbivore-induced genes. These include genes encoding trypsin inhibitors and polyphenol oxidase, commonly observed defense proteins, as well as genes with less well-defined defensive functions. Comparisons of hybrid poplar with trembling aspen indicate that there are significant differences in how different species of Populus respond to herbivory. Trypsin inhibitor genes and proteins appear to be redundant and very variable in Populus, and we have begun comparing TIs from different poplar species and hybrids. The ultimate aim of this work is to understand the extent to which defense responses vary among Populus species and genotypes in the context of their ecological adaptations.
Cronk, Quentin	Genomes in time and space: the new science of adaptation Evolution varies strongly in tempo. Some lineages such as Ginkgo and Lingula have varied little (at least in morphology) for hundreds of millions of years. What is not yet clear is the balance between ecological stability and genomic constraint (developmental canalisation) in maintaining such stasis. Alternatively, evolution, as in rapid radiations, may proceed at an astonishing rate. Again this fast tempo may be genomic in origin, due to heritable developmental lability for key traits, or ecological because the environment is permissive to phenotypic extremes and selects strongly on these extremes. Between the genome and the ecosystem is developmental biology, the unfolding of the phenotype, which in plants involves continuous feedback between the environment and the genome. Using examples from floral morphology I will examine the expected limits to evolution from (1) labile versus constrained development and (2) permissive versus difficult fitness landscapes. New understanding of the genomic features of development (such as epistasis, epigenetics, heterotopy and heterochrony) and variation (such as cis-regulatory changes, genetic capacitance, epimutation), can now provide numerous hypotheses for testing in an adaptationist framework. Furthermore, new tools (e.g. whole genome sequences, EST databases, SNP detection, TILLING, microarrays, real time PCR, and RNA in situ hybridisation) provide the means to test these hypotheses. This "ecomolecular synthesis" (connecting specific nucleotide changes, developmental biology and ecology) has the potential to extend radically the "modern synthesis" (with its classical treatment of "black box" alleles in populations).
Cruzan, Mitchell and Jennifer Rhode	Hybridization and Adaptive Variation in the Piriqueta Complex Hybridization between divergent plant taxa can be a creative evolutionary process. The Piriqueta (Turneraceae) complex in central Florida provides an interesting example of a broad (300 km), dynamic plant hybrid zone that has persisted for ~5000 years. Greenhouse crosses indicate that fitness among cross types is variable, but some backcrossed types have vegetative and sexual fitness coefficients equal to or greater than parentals. These patterns are maintained in field transplants. Fitness of natural hybrids is affected by vegetative morphology and genetic composition, as well as these factors' interactions with environmental conditions and cytonuclear backgrounds. Continued introgression into northern populations could change the adaptive fitness landscape across this hybrid zone.
Douglas, Carl	Phenylpropanoid metabolism and plant adaptation. Phenylpropanoid compounds played a key role in plant adaptation to the terrestrial environment, for example by providing efficient UV sunscreens (flavonoids and phenolic acid conjugates) and structural support/water transport (lignin). Evolution of phenylpropanoid pathways in land plants has continued subsequently, as evidenced by the diversity of phenylpropanoid compounds and the proliferation of gene family members encoding phenylpropanoid enzymes. Diverse phenylpropanoid compounds also play adaptive roles in defense against herbivores and pathogens, and appear to play roles in controlling plant development, though these are poorly understood. Completion of the Arabidopsis genome has revealed the full extent of the gene families encoding structural genes for phenylpropanoid biosynthesis in this plant. Surprisingly, in addition to duplicated genes encoding enzymes of known function, the genome contains numerous families of genes encoding enzymes that share similarity to known enzymes, but that are of unknown function. Reverse genetics, expression profiling, and metabolic profiling can be used evaluate the potential adaptive significance of such super-gene family members and their metabolic products, and we are using these approaches with regards the Arabidopsis 4-coumarate-coenzyme A ligase (4CL) super gene family, as well as selected other gene families. Comparative and genomics approaches across taxa and functional genomics approaches within new taxa can be used to evaluate the evolution of related gene families in different lineages, and to evaluate their potential adaptive significance in these lineages. Populus (poplar) species are known to be very rich in phenolic and phenylpropanoid compounds. We will use information from the poplar genome sequence, from large poplar EST collections, and from poplar gene expression profiling, as well as information from other sequenced plant genomes, to investigate these questions.
Elle, Elizabeth	Floral adaptations and biotic and abiotic selection pressures Explanations for the evolution of floral phenotypes have historically focussed on pollinator choice. Yet, phenotypes may also reflect adaptation to abiotic selection pressures. Populations of Collinsia parviflora vary significantly in floral phenotype, specifically corolla size and relative sex allocation. Traditional explanations for this variation (pollinator choice and the reproductive assurance benefit of selfing) may explain some of the phenotypic variation observed. However, genetic correlations between corolla size and development time suggest that an abiotic factor, annual precipitation, may be an important agent of selection as well. Rapidly developing populations of C. parviflora have small flowers and are found in drier, more ephemeral, ecological settings, where time to grow large and build large flowers is limited. Molecular data from model systems like Arabidopsis and Antirrhinum has elucidated the genetic basis of phase change in plants, and some studies have linked development time with flower size. I will use my data as a springboard to ask questions about the study of floral adaptation, specifically whether, and how, we might integrate ecological studies of adaptation with emerging mechanistic molecular information.
Good-Avila, Sara and Valeria Souza, Amanda Castillo, Brandon G. Gaut, Luis E. Eguiarte	*Evidence of a recent origin and high levels of speciation in the Agave* genus.** In this study we aim to understand the phylogenetic limits and time of the origin of the family Agavaceae, a family that includes more than 300 species, to clarify the phylogenetic relationship among its 8 genera, and to explore the possibility that there has been an adaptive radiation in its most speciose genus, Agave sensu lato. To this end, we present an original analysis of the phylogenetic relationship of the monocots using 334 sequences of rbcL obtained from genebank, and 24 dicot and one gymnosperm sequence to help with rooting the tree. We generate a phylogenetic tree using maximum parsimony and estimate the branch lengths on the tree using maximum likelihood. The tree and branch length information is used to estimate the age of all internal nodes using penalized maximum likelihood and a smoothing parameter using the age of the gymnosperm/ angiosperm split (132 MYA) to calibrate rates. This method allows different molecular clock analyses across the tree. Next we combine some original and genebank sequences for both nuclear (ITS intergenic region) and chloroplast (two intergenic spacers) genes to resolve the phylogenetic relationship among the 8 genera in the Agavaceae. Lastly, we use the information about the rate of evolution of the Agavaceae derived from the methods above to examine rates of speciation in the highly diverse group, Agave sensu lato, that includes more than 200 species. These analyses indicate that the Agavaceae is a very young family (~10 MY), and that rates of speciation in Agave sensu lato are similar to those found in the Hawaiian silversword alliance. Possible evolutionary forces driving these high rates of speciation are discussed.
Hodges, Scott	*The genetics of reproductive isolation between Aquilegia formosa* and A. pubescens.** In plants, reproductive isolation can be affected multiple factors at several life history stages including flowering time, pollination, pollen-tube growth, zygote viability and seedling establishment. We have been investigating the genetic architecture for several of these factors in order to establish the number of genetic factors, the sizes of their effects, and their distributions in the genome. In particular, we have conducted a QTL analysis to determine the genetic architecture of floral differences, which affect pollinator behavior and pollen transfer between Aquilegia formosa and A. pubescens. In addition, our experiments reveal that segregation distortion can affect the outcome of hybridization and influence reproductive isolation. Because of the extremely rapid evolution of species in Aquilegia genetic markers are readily transferable within this genus and therefore offer the opportunity for understanding general patterns in the evolution of reproductive isolation.
Husband, Brian	*Role of genome duplication as an instrument of adaptation along an altitudinal gradient in fireweed (Chamerion angustifolium)* Genome duplications (polyploidy) are prevalent in flowering plants and are frequently associated with shifts in the geographical and ecological range of species; however it's relative contribution to adaptation along ecological gradients is poorly understood . Fireweed (Chamerion angustifolium) occurs over a wide range of latitudes and altitudes, and genome duplication (polyploidy) may provide a significant source of variation in flowering time, which is related to fitness. The genetic basis for variation in fllowering time in fireweed remains to be explored; however, our research indicates that extant diploids flower earlier than tetraploids, a pattern that corresponds to differences in their respective habitats. The importance of genome duplication in flowering time evolution is suggested by several lines of evidence: 1) the rate of polyploid mutation is high relative to most genic mutations; and 2) newly formed polyploids exhibit a qualitatively similar flowering time as extant polyploids. In addition, variation among several diploid and tetraploid populations indicates that most variation in flowering time is attributable to genome size variation, with relatively little variation within ploidies. These preliminary results suggest that genome duplications may provide a rapid and dramatic response to selection on flowering time, but may also impose additional constraints on any subsequent responses to selection.
Levin, Donald	The Cytoplasmic Factor in Plant Speciation The role of nucleocytoplasmic interactions in the genesis of post-zygotic isolation has been given little attention by plant evolutionists. I present evidence from reciprocal crosses, cytoplasmic substitution lines, and cell fusion lines that hybrid weakness and sterility often arise from interactions between the nuclear genome and the chloroplast and mitochondrial genomes. These interactions are much more important in the origin and isolation of species than we appreciate. The strength of the post-zygotic barriers tends to be a function of cytoplasmic divergence. I also review evidence indicating that the properties and evolutionary potential of allopolyploids and diploid hybrid derivatives may be influenced by cytoplasmic factors.
Mable, Barbara K.	Molecular genetics of sporophytic self-incompatibility in diploid and tetraploid populations of the Arabidopsis lyrata species group. Recently, Arabidopsis lyrata has been proposed as a new model plant "species" because it is an outcrossing relative of the selfing species Arabidopsis thaliana. The taxonomy of A. lyrata is confused at best, but former classifications have been based predominantly on geographic distribution. The current suggestion to synonymize populations from Europe, North America, and Asia into a single species runs the risk of overlooking potentially interesting variation in morphology, development, mating systems, and genomic restructuring that could be related to habitat types or environmental differences among localities. We have been studying the strength of sporophytic self-incompatibility (SSI) and ploidy variation in populations sampled from Europe (A. lyrata petraea: Iceland, Scotland, Austria), North America (A. lyrata lyrata: Michigan, North Carolina, Ontario), and Asia (A. lyrata kawasakiana: Japan). Contrary to suggestions in the recent literature, not all populations are diploid and populations of both diploid and tetraploids have been found that show a complete breakdown in the self-incompatibility system. Recent surveys of variation in DNA content and the strength of SSI will be discussed in relation to the habitats in which the plants grow.
Mathews, Sarah	Rapid evolution in the photoreceptor phytochrome A of early-diverging flowering plants Insights from recent phylogenetic analyses of flowering plants suggest that members of the earliest diverging lines may have had the capacity to initiate seedling development in shaded environments or under water. The origin of flowering plants was followed by the decline of previously dominant plant groups, and angiosperm diversity now far exceeds the combined diversity of all other plant groups. We are exploring the hypothesis that evolution in a phytochrome photoreceptor may have played a role in their initial establishment. The control of plant development by ambient light conditions is mediated by phytochromes, which absorb red light and far-red light, and by distinct blue- and ultraviolet-absorbing receptors. Phytochrome null mutants of Arabidopsis and rice demonstrate that phytochrome A (phyA) is the primary photoreceptor for two photosensory functions that are unique to angiosperms or that are poorly developed outside of flowering plants. Angiosperm phyA allows dark-imbibed seeds to germinate in response to millisecond pulses of light and allows etiolated seedlings to initiate development in deep shade, two responses that might have been crucial to colonizing the understory of ferns and gymnosperms. Results will be presented from tests for selection and functional divergence in phyA sequences from early-diverging angiosperms, and strategies will be discussed for determining whether these responses are found in early-diverging species, work that is just getting underway in our lab. Finally, approaches will be discussed for further investigating the functional significance of sites identified in tests for selection and for determining the fitness attributes of phyA using null mutants.
McKhann, Heather I.	Arabidopsis natural genetic variation: a nested core collection of genotypes Natural genetic variation can be exploited to identify quantitative trait loci (QTL), to perform genotype/phenotype association studies and to explore ecological and evolutionary relations. To study natural variation in Arabidopsis thaliana, we have defined a nested core collection of accessions. Ten gene fragments of ca. 600 bp (introns and exons), distributed throughout the genome, were sequenced on 95 or ca. 240 Arabidopsis accessions from the different stock centers. Single nucleotide polymorphism (SNP) detection was performed using Genalys software, and the core collections chosen based on these results using the program MSTRAT. The collections, 8 to 48 accessions, aim to maximize the diversity present. This nested core collection is to be used for SNP discovery, following which the entire collection of Arabidopsis accessions will be genotyped for selected SNPs. The nested nature of the core collection allows the investigator to balance the cost of sequencing and experimentation vs. the need to capture more rare alleles by allowing him to chose a smaller or large core respectively. The level of variation present in the core collections was then checked on a set of morphological data. It was shown that the molecular information succeeded in capturing variation on a priori adaptive traits. This set of core collections will be available to the scientific community and thus provides an important resource for the study of natural genetic variation in Arabidopsis.
Montgomery, Rebecca and Thomas Givnish	Putting the "adaptive" into "adaptive radiation": divergence in light regime and photosynthetic adaptations in the Hawaiian lobeliads The Hawaiian lobeliads are considered to be one of the most spectacular cases of adaptive radiation in plants. From a single colonist, they have invaded habitats ranging from open alpine bogs to densely shaded rain-forest interiors, and evolved a striking diversity in leaf morphology. Yet very little has been known about their ecology or - indeed - whether they have undergone an adaptive radiation in photosynthetic traits related to life in sun vs. shade. To address this question, we conducted a series of field and common-garden experiments on 11 species representing each Hawaiian sublineage. In field populations of each species, average light levels vary from 3.0 to 24.2 mol day-1 and Amax varies from 3.1 to 13.5 g CO2 g-1 s-1. Across species, variation in SLA, leaf longevity, carboxylation efficiency, and the compensation point, saturation point, and convexity of the static photosynthetic light response correlate significantly with light levels in the expected directions. To analyze the extent to which these differences are genetic (rather than merely being induced by the different light regimes inhabited by different species), we studied the photosynthetic responses and growth of plants at 6.5, 14, 33, and 80% full sunlight. Within a given light regime and across species, maximum photosynthetic rate and several other parameters varied as expected with native irradiance, with genetic differences among species for Amax apparently accounting for roughly 50% of the variance observed in the field. Species differed in their plastic responses to light regime, with one species outperforming all others at 6.5% sunlight; another species best at 14 and 30% sunlight; and a third species best at 80% sunlight. The sequence of these species corresponds to the range of irradiances they occupy in the field, as expected. This study is apparently the first to provide evidence of adaptive divergence in photosynthetic light responses, reaction norms, and associated leaf traits in relation to differences in the light habitats invaded by members of an adaptive radiation.
Moyle, Leonie	The evolution of incipient isolation in Silene rotundifolia: comparative divergence in molecules, morphology and reproductive incompatibility Although Darwin famously championed the view that differences between species are merely intraspecific differences writ large, our understanding of the evolutionary mechanisms responsible for transitions from population- to species-level differentiation remains rudimentary. To examine differentiation processes that lead to speciation, I have characterised patterns of intraspecific divergence in quantitative genetic traits, non-coding DNA, and inter-population crossability, between 9 natural populations of an herbaceous plant species (Silene rotundifolia); inter-population distances range from 0.05 km to 150km. By simultaneously examining differentiation in multiple trait classes, one goal of this work is to distinguish patterns of reproductive divergence due to random processes (e.g. genetic drift) from those due to the action of divergent adaptive selection in isolated populations. I will discuss evidence of differentiation among study populations in all classes of traits examined. In particular, crosses between distant populations show evidence of partial reproductive barriers; multi-correlation 'path' analyses indicate that this reproductive incompatibility is most closely associated with divergence in non-coding molecular genetic traits. This finding is consistent with reproductive barriers resulting from the gradual accumulation of divergent alleles between isolated populations, rather than isolation being associated with one or more morphological traits that are diverging via selection. Using this case study, I will discuss the utility of such path analyses for investigating the relative roles of different evolutionary forces in the generation of species barriers, particularly in non-model organisms.
Purugganan, Michael	*The molecular evolutionary genetics of Arabidopsis* shoot architecture** Understanding the evolution of developmental systems will require understanding the evolution of genes and genetic pathways that underlie morphological development. Levels and patterning of molecular variation provides insights into the evolutionary forces that act on developmental genes. An analysis of the evolution of 6 inflorescence and floral regulatory loci indicate that positive selection is associated with early acting genes in the developmental pathway. Moreover, balancing selection has been detected at the TFL1 inflorescence architecture gene and the CLAVATA2 meristem regulatory locus. QTL mapping analysis also reveals genetic correlations between flowering time and inflorescence architecture, suggesting pleiotropic effects of genes that regulate the floral transition.
Rajakaruna, Nishanta and Jeannette Whitton	Building a case for the parallel evolution of edaphic races in Lasthenia californica sensu lato (Asteraceae:Heliantheae) The independent and recurrent evolution of adaptive traits in closely related lineages is best explained by the action of natural selection. Thus, case studies of parallel evolution have the power to uncover the role of ecological selection in speciation. Lasthenia californica s.l., the common goldfields of California, provides an ideal case for the study of parallel evolution driven by edaphic forces. Two edaphic races (A, C) exist in two cryptic species within L. californica s.l. The two races, characterized by their flavonoid pigments, are physiologically differentiated to deal with key variables that are associated with their distinct edaphic habitats. Race A plants have greater tolerance to sodium and magnesium, ions that predominate in their habitats. Race C plants are better able to tolerate drought, a feature that is common to their habitats. Both races achieve greater fitness under conditions that best match their natural environment, strongly suggesting adaptive differentiation. Phylogenetic analysis suggests that race C has risen independently in each of the two cryptic species, suggesting that adaptations to drier, ionically-benign habitats may have resulted in loss of tolerance to potentially toxic ions such as sodium and magnesium. The races are also reproductively isolated via flowering time differences and pollen incompatibility reactions. Taken together, these data make this one of the best examples for the study of parallel evolution in plants.
Rausher, Mark	The Genes Evolution Uses: Genetic Constraint vs. Evolutionary Opportunism in Flower Color Evolution In producing phenotypic adaptation, evolution often has a choice among different genes to modify. A largely unanswered question in evolutionary biology is what determines which of a set of alternative genes natural selection targets to produce a particular phenotype. One extreme possibility is that novel alleles at different loci differ in the magnitude of deleterious pleiotropic effects, such that some genes are more constrained and thus less likely to be used by natural selection (Differential Constraint hypothesis). At the other extreme, a particular phenotypic change may be so adaptive that the beneficial effects of any mutation producing it outweigh associated detrimental pleiotropic effects. In this case, evolution will be opportunistic, chosing whichever locus first mutates to produce the adaptive phenotype (Evolutionary Opportunism hypothesis). I describe our lab¹s ongoing efforts to distinguish between these two hypotheses using flower-color evolution in Ipomoea (morning glories) as a model system. The genus Ipomoea consists of approximately 1000 described species. Within the genus there are numerous (probably > 20) evolutionarily independent cases of the evolution of white flowers from pigmented flowers. Work on petunias, snapdragons, and maize indicates that knockouts of any of at least eight different genes of the anthocyanin pigment pathway can produce white flowers. Preliminary evidence indicates that knockout mutations of these genes differ in the magnitude of associated deleterious pleiotropy. In addition, sequence evolution in upstream structural genes is more constrained than sequence evolution of downstream genes, indicating differential constraint. These two types of evidence indicate that a necessary condition for Differential Constraint hypothesis is met. We are currently examining a number of species in which white flowers have evolved independently to determine which anthocyanin genes have been altered to produce the white phenotype. This information should allow us to determine whether participating genes are chosen at random in different lineages (Evolutionary Opportunism) or certain genes are chosen preferentially for pigment inactivation (Differential Constraint).
Ritland, Kermit	Prospects in Plant Population Genomics The pattern of variation along chromosomes adds another dimension to the diversity of a population, and the patterns of divergence for a population of genes add another dimension to the diversity of species. Here I discuss some approaches to exploring these dimensions of "population genomics", and note how plants provide unique opportunities. Within populations, the correlation of heterozygosity and the linkage disequilibria between linked loci are quantities both affected by various evolutionary forces, and the dynamics of these quantities are described. We are currently implementing a procedure termed "diversity mapping", which maps diversity along linkage groups with progeny arrays, and are implementing it in lodgepole pine, to the end of detecting selective sweeps and/or enhanced drift due to migrational bottlenecks. Between species, evolutionary comparisons of populations of genes can give information about population-level processes: sequence comparisons among taxa allow estimates of the deleterious mutation rate, and when combined with knowledge of nucleotide heterozygosities within taxa, allow inferences about adaptive genetic divergence. Examples will be given with regard to cDNA sequences from spruce, pine and Arabidopsis, and from complete chloroplast sequences.
Schlichting, Carl	The role of hidden reaction norms in plant evolution The hidden reaction norm is the set of plastic responses that are elicited in reaction to novel environmental cues. Although hidden reaction norms are largely unexplored, a number of studies indicate that there is a surprising amount of genetic variability hidden by regulatory systems. This variation is released when environmental parameters exceed the boundaries within which the canalization system operates. I will evaluate evidence for the extent of hidden reaction norms, and discuss the potential role and mechanisms by which this variation may influence evolutionary processes, including the possibility that the maintenance of hidden variability has itself been favored.
Schluter, Dolph	Mechanisms of adaptive radiation in plants compared with animals Adaptive radiation was thought by the early naturalists ultimately to be caused by divergent natural selection stemming from features of environment, especially resources and resource competition. This is a stronger claim than merely that different species are adapted to exploiting their preferred resources, which by itself does not imply population differences are directly favored. I review methods for testing divergent natural selection on phenotypic traits, and conclusions that may be drawn from them in plants versus animals. I draw attention to phenotypic traits contributing to reproductive isolation, which indicate possible links between divergent selection and the origin of species in adaptive radiation. I highlight the contribution that genetic studies of traits have made and may yet make to our understanding of divergence and speciation.
Shi, Suhua and Yelin Huang, Fewngxiao Tan and Yang Zhong	*Molecular adaptation in mangroves: evidences from cpDNA rbcL, mtDNA matR and nrDNA 18S genes* The harsh conditions of the intertidal zone have led to some remarkable adaptations in mangroves. The phylogenetic relationships among 35 mangrove species representing 19 families were reconstructed based on the sequences of cpDNA rbcL, mtDNA matR and nrDNA 18S genes. Likelihood ratio tests (LRT) of the three genes showed that the global molecular clock was clearly violated for each data set. Maximum-likelihood models of codon substitution were used to analyze the two protein-coding genes rbcL and matR. The variations of nonsynonymous / synonymous rate ratio among the lineages or sites were detected, providing a strong support for variable selection intensity among the amino acid sites, however, suggesting significant variations among lineages of the rbcL tree but no significant variations among lineages of the matR tree. Neutral model was rejected in favor of the operation of positive selection in matR but negative-selection in rbcL genes. Branch-site model analysis did not show significant deviation from background selection existing on the "eumangrove" clade. In addition, the evolutionary relationships between the major adaptive characters such as vivipary were also investigated in this paper.
Taylor, D. Lee	Adaptation belowground: Evidence for mycorrhizal host-races in two non-photosynthetic orchids. Evidence is accumulating for specialized yet evolutionarily dynamic associations between orchids and their mycorrhizal fungi. However, the phylogenetic scales of changes in specificity in orchids are largely unexplored. In other words, do changes occur close to speciation (evidenced by differences in specificity in sister species or genotypes)? Or, in contrast, do changes accumulate during the course of divergence long after speciation (evidenced by differences in specificity among families or genera, but not among sister species)? We address these questions in two genera of non-photosynthetic orchids which appear to parasitize their mycorrhizal fungal associates. In the Hexalectris spicata complex, we find that different floral variants in the southwest associate with different, but closely related jelly fungi in the Sebacinaceae. In the Corallorhiza maculata complex, we find that different genotypes (distinguished via putatively neutral molecular markers) associate with closely related but distinct mushroom-forming clades within the Russulaceae. In both orchid genera, the differently specialized variants or genotypes are frequently sympatric, and maintain their distinct mycorrhizal specificity in sympatry. Hence, these orchid genotypes appear analogous to host-races in phytophagous insects. Host-race formation can drive speciation, especially when host-choice is related to mate-choice. It is unclear how specialization on different fungi could promote reproductive isolation between orchids, but differences in flowering phenology have been noted among some of these variants.
Tiffin, Peter	*Molecular evolution of defense genes in the genus Zea* and family Poaceae** The majority of research into the evolution of defense traits has examined selection occurring in contemporary populations. In contrast, relatively little is known about the long-term evolution of plant defense. In order to gain insight into these long-term dynamics I investigated the molecular evolution of several genes that code for two classes of pathogenesis-related (PR) proteins, proteins that have direct negative impacts on parasite growth and reproduction. Specifically, I examined sequence diversity of protease inhibitor and chitinase genes in two Zea species (Z. mays subsp. parviglumis and Z. diploperennis) and the divergence of these genes among several genera within the grass family. Statistical analyses were used to test for non-neutral evolution and evidence of past selective sweeps or balancing selection as predicted by arms-race and balanced polymorphism models of host-parasite interactions, respectively. The results from these analyses will be compared to the evolutionary history of other defense genes that have been investigated in Zea and Arabidopsis.
Whitton, Jeannette and Nishanta Rajakaruna	Adaptation Underground: Incorporating edaphic influences in plant evolutionary studies Sister taxa rarely occur in sympatry. This observation alone suggests that habitat differentiation is likely a key factor in diversification. The overwhelming emphasis of evolutionary QTL studies in plants to date has been on features believed to contribute directly to reproductive isolation (e.g. on floral traits related to pollinator preferences, chromosomal sterility barriers, etc.). While we will continue to learn a great deal from such emphasis, the importance of differential edaphic adaptation has been underplayed, yet is likely to be central to speciation in many groups, including some of those which serve as models for the study of reproductive isolation. Case studies of adaptation to extreme soils such as serpentine and other substrates rich in heavy metals provide a solid foundation for the action of natural selection in local adaptation to soil features. Many less dramatic examples also suggest that edaphic factors are potent agents of natural selection. Using examples from the literature and our own work, we aim to point out promising approaches for the study of edaphic differentiation, and suggest avenues for incorporating the study of edaphic factors into existing research programs.
Willis, John and Lila Fishman	The evolution of selfing and its consequences for speciation The genetic basis of species differences provides insight into past evolutionary change and has long been a subject of contention among evolutionary biologists. Most traits that differentiate strains or species do not show simple Mendelian inheritance, but vary continuously in segregating hybrid populations. In this study, we investigate the genetic architecture of phenotypic differences and reproductive isolation between two flowering plant species with highly divergent mating systems: Mimulus guttatus (outcrossing) and M. nasutus (selfing). In order to characterize the nature of this floral divergence at the level of individual loci, we constructed a framework linkage map of a large F2 mapping population (N = 524) based on 174 microsatellites, AFLPs, and gene-based markers. We identified a total of 24 quantitative trait loci (QTLs) underlying seven floral traits associated with the divergent mating systems. Variation in each floral trait was caused by at least 11 QTLs, and almost all QTLs affected more than one floral trait. Nearly all of the QTLs had very small effects. We also use this map to investigate the genetic basis of partial reproductive isolating barriers. We identified 11 QTLs responsible for segregation distortion in the F2, 9 of which cause an excess of M. guttatus alleles. A detailed genetic analysis of the most distorted region reveals that the distortion is caused by true meiotic drive during female but not male meioses. In addition, we found evidence of both Dobzhansky-Muller incompatibilities and nucleo-cytoplasmic interactions responsible for partial male and female hybrid sterility. These investigations provide an unusually detailed view of the complex genetic changes that occurred during the evolution of self-fertilization and reproductive isolation, and set the stage for future investigations into the molecular genetic basis of these traits.

Poster Abstracts (listed in alphabetical order of first author)

Presenter	Abstract
Byers, Diane L.	Phenotypic Selection in Heterogeneous Nutrient Environments Genetic diversity is critical for adaptation, particularly in our changing environments. Selection is expected to eliminate diversity, especially in fitness-related traits. The goal of this research is to experimentally test theoretical models that have suggested selection in heterogeneous environments as a potential mechanism for the maintenance of genetic variation. For heterogeneous environments to contribute to the maintenance of genetic variation, phenotypic selection must be environmentally dependent. Furthermore, differences in the extent of heritable variation and the genetic correlations between the traits may contribute to the maintenance of genetic variation. These issues were addressed by growing half-sib lines of rapid cycling Brassica rapa in six nutrient environments. Analysis revealed that the extent of heritable variation and the strength of genetic correlations were environmentally dependent. Exploratory path analysis was used to develop a model of the relationships among the traits, and with fitness, for each environment. To determine if selection differed in the other environments, these path models were then tested using the data from the other environments. The results reveal that the most extreme environments have more complex relationships among the traits. This experiment demonstrated that the expression of genetic variation, genetic correlations and phenotypic selection are environmentally dependent and may constrain evolutionary responses in heterogeneous environments. Further work includes a phenotypic selection experiment to experimentally determine if selection in different nutrient environments has the potential to maintain genetic diversity.
Carroll, Amy Breen and Matthew S. Olson	Toward an understanding of balsam poplar's evolutionary history in Alaska, U.S.A. Quaternary ice ages induced large-scale population migrations, resulting in population extinction, dispersal to new locations, or survival in refugia. These processes shaped the present day genetic structure of plant populations in the Arctic. We have begun a comprehensive study of population genetic structure and adaptation to climate in balsam poplar, Populus balsamifera subsp. balsamifera in Alaska, U.S.A. Balsam poplar is a common tree throughout Alaska, but it also occurs in isolated stands in the otherwise treeless Alaskan Arctic. The occurrence of these trees in the Arctic has puzzled ecologists since they were first described in the literature over twenty years ago. Contrasting hypotheses suggest Arctic populations either 1) migrated from the east, based on the fossil record, during the interval of 11,000 to 9,000 years ago, or 2) persist from an earlier late-glacial Arctic landscape. In addition, anecdotal evidence suggests this species may be expanding in the Arctic in response to recent climate warming. We have collected genetic material from 20 individuals from 15 populations across a latitudinal gradient from the Arctic Ocean to the Kenai Peninsula in Alaska. We will use these samples to identify the levels of population structure associated with neutral genetic markers to assess the overall levels of population structure in both the nuclear and maternally inherited chloroplast regions. We will contrast the population structure of these neutral genes with the population structure of candidate genes putatively associated with spring bud flush, a trait known to vary with latitude and of importance for adaptation to local climate. Collectively, this work will aid in reconstruction of the recent Quaternary history, and understanding adaptation to climate change, of balsam poplar in Alaska.
Chen, Charles and Kermit Ritland	The required explanation for adaptationist, is selection the primary cause of phenotypic diversification? The ability of natural selection to produce exquisite diversity of phenotypes continues to enthrall us since Darwin's age. Its fascination on species differentiation has been extensively discussed, however, phenotypic differentiation between species sometimes appear to be non-adaptive. We begin to validate Darwin's claim by using a three species QTL phylogeny. To argue the importance of directional selection in species divergence, we adopt Orr (1998) sign test where the null hypothesis of neutral phenotypic evolution would be determined. Thus, if a trait has a continuous history of directional selection, QTLs along a phylogenetic lineage should be mostly in the same direction. In contrast, QTLs with opposing or antagonistic effects should be common. Knowledge from the phylogenetic comparison of QTLs would help to reveal the plausibility of selection, the central role of evolution.
Fulop, Daniel	*Evolution of flower sexual dimorphism in Catasetum* L.C. Rich. (Orchidaceae)** Flowers of the Neotropical orchid genus Catasetum are sexually dimorphic, with pistillate and staminate flowers that are distinctly different in morphology and coloration. Staminate flowers of different (even closely related) species are also quite dissimilar. In contrast, pistillate flowers of different species are quite similar. Plants of Catasetum are monoecious, yet are thought of as functionally dioecious because a given individual will typically only produce either pistillate or staminate inflorescences in one flowering season (i.e., gender diphasy). Flower gender seems to be largely determined by light environment, and size of the individual plant; large individuals exposed to a lot of direct sunlight typically produce pistillate flowers, as they can bear the metabolic cost of producing seed. I am working on a molecular species level phylogeny of Catasetum in order to understand the patterns of floral morphological evolution and the overall evolutionary history of the genus. There are eight natural Catasetum hybrids reported in the literature, which will be included in the phylogeny. Patterns of reticulation will be examined in order to assess whether the species recognized by taxonomists as the hybrid parentals are truly so. Gender diphasy in Catasetum allows the cultivation of clonal plants under different conditions, such that one clone will produce pistillate flowers and the other clone will produce staminate flowers. This makes Catasetum very amenable to differential expression studies, which I will use to identify candidate developmental regulator genes involved in producing staminate and pistillate specific floral morphologies. Flowers of Catasetum are pollinated by fragrance-collecting male euglossine bees, and some authors posit that these pollinators played an important role in the evolution of sexual dimorphism in this genus. To study the effect of the intricate pollination ecology on the evolution of sexual dimorphism, I am developing an evolutionary population model of Catasetum and its euglossine pollinators to find conditions under which dimorphism would evolved and fixate. I hope to derive predictions from this model that I can test in the field. Further characterization of both the pollination ecology of Catasetum and the developmental genetics of their sexual dimorphism could inform such a model to make it more realistic. In this manner, I hope to study the evolution of Catasetum flowers from both genetical and ecological perspectives.
Hahn, Matthew	The effects of selection against spurious transcription factor binding sites on plant genomes The biological demands on the interacting network of proteins and DNA in plants and other multicellular organisms dictate that transcription of each gene must be regulated in time, level, and place. Transcription factors and other parts of the transcriptional machinery regulate this process in a complicated cellular environment by interacting directly in a sequence-specific manner with short stretches of DNA (generally 6-10 base pair binding sites) surrounding the target gene. Here we show that the frequent creation of new binding sites by mutation introduces a large amount of noise into the efficient functioning of a cell and that natural selection acts throughout the genome to remove such spurious binding sites because of this. Results for 52 whole eubacterial and archaeal genomes are compared with results for the A. thaliana and O. sativa genomes. The two plant genomes show a heterogeneous pattern of selection against spurious binding sites, most likely because of the effects of heterochromatin, gene-rich regions, and different rates of recombination along a chromosome.
Hu, Xin-Sheng	Sex differential and gene invasion via seed and pollen vectors in flowering plants Understanding of the mechanisms that maintain sex differential of dioecious plants in natural populations remains important for insights into the evolutionary process of sexual dimorphism in flowering plants. In the present study I develop a population genetic model of dioecious plants, where gender dimorphism is determined by sex chromosomes (either XX-XY or WZ-ZZ mode) and genetic variation of a diallelic sex-linked gene is present. The model incorporates independent migration of seeds and pollen grains, the selection at both the haploid gametophyte and the diploid sporophyte stages. The analytical relationships between migration rate of seed and pollen and the differential in allele frequency between sexes are explicitly formulated. Impacts of seed and pollen flow on sex differential are evaluated through numerical examples. With the application of the proposed model, the relative selection intensity between the gametophyte and sporophyte stages can be predicted for either male or female populations. As an addition to the preexisting theories, the proposed model provides a new approach to explain the spatial segregation of the sexes (SSS) in natural populations that are formed within a short history.
Kumar, Anshuman and Anthony D.M. Glass	*Regulation of high-affinity NH4+ absorption with respect to altered N status and diurnal irradiance in Rice (Oryza sativa* L.).** Nitrogen is the most important element limiting plant growth, and hence all plant species must adapt to various N stress, in form of either inadequate or excessive soil nitrogen concentrations. In addition, the assimilation of nitrogen requires the availability of carbohydrate generated photosynthetically. Thus N assimilation is intimately impacted by irradiance. Rice is the world's foremost cereal crop and over fifty percent of planet earth's population depends on it as their primary food source. Rice absorbs NH4+ as the preferential N source under field conditions as well as in controlled growth facilities. When N is in abundant supply, rice, like other species, down-regulates high-affinity ammonium uptake, resulting in significant N fertilizer loss through volatilization and other processes. Therefore it is very important to understand the regulation of NH4+ absorption by rice seedlings. In order to understand the regulation of NH4+ absorption by rice seedling roots, we have investigated the expression of three members of AMT1 gene family encoding putative high-affinity NH4+ transporters in rice roots in response to different conditions of N provision along with changes in diurnal irradiance. In this talk we report and discuss changes in NH4+ influx and expression of the three members of AMT1 gene family in rice seedling roots due to altered N status and diurnal irradiance.
Sargent, Risa	Evidence for correlated evolution of pollination syndrome and mating system in flowering plants The functional significance of dichogamy in flowering plants (temporal separation of male and female function) is unclear. Of particular interest is why two seemingly equal strategies, male function before female (protandry) and female function before male (protogyny) have evolved. Several species-level comparative studies have found a correlation between species displaying protandrous flowers and insect pollination. Similarly, the occurrence of protogynous flowers is correlated with wind pollination. One possible problem with the previous correlative studies is that none consider the possibility that phylogenetic relatedness is responsible for the pattern. I mapped the occurrence of protandry/protogyny and insect/wind pollination on to a version of the angiosperm phylogeny. Following Pagel (1994) two models of evolutionary change (one allowing only for independent evolution and the other allowing correlated evolution of the two traits) were fit to the phylogeny. Monte Carlo simulations (N=100) support the dependent model (P = 0.05), suggesting that the pattern is robust to phylogenetic considerations.
Thompson, Stacey	*The transmission of apomixis in a Townsendia* hybrid zone** Because many plant genomes are mosaics in their permeability to the introgression of genetic material from other species, hybrid zones grant an opportunity to examine the reticulate transmission of both neutral and adaptive traits. The transmission of apomixis has implications for the fixation of adaptive gene combinations and the avoidance of the cost of sex: all things being equal, apomicts are twice as fit. Recent experimental work has demonstrated that the genes for apomixis can be spread artificially between species by diploid pollen "carriers". My research investigates the lateral transmission of apomixis via interspecific gene flow within a Townsendia hybrid zone. Studies of pollen viability have demonstrated that Townsendia exscapa is predominantly sexual, while T. hookeri is an obligate apomict in this part of the range. Both chloroplast microsatellite and AFLP markers are being used to assess the extent and direction of gene flow between T. hookeri and T. exscapa. Apomixis is being characterized within the hybrid zone in two ways: first, by examining genetic variation in progeny collected from maternal families across the hybrid zone, using ALFPs, and second, by microscopic examination of cleared ovules from field-collected buds. The presence of apomixis in T. exscapa will be correlated with the introgression of molecular markers from T. hookeri. This study will be the first attempt to document the horizontal transmission of apomixis across species boundaries in nature.
Wheeler, Erica	*Does apomixis have adaptive significance along a latitudinal gradient in the slim-leaf onion (Allium amplectens)?* Apomixis (asexual seed production) in triploids has historically been considered an escape from infertility, conferring no specific environmental adaptive advantage. However, recent work suggests that within agamic complexes, triploid apomicts may be more fit than their sexual conspecifics in some environments. For example, it is often reported that apomictic forms are more successful at higher latitudes. The adaptive significance of this trend is not well understood. One possible explanation is that apomicts are able to set seed under ecological conditions at higher latitudes to which the sexual form may not be adapted (i.e. lack of suitable pollinators, shorter growing season, colder winters etc.). The slim-leaf onion (Allium amplectens) occurs as a diploid, a triploid and a tetraploid in California and Oregon, but only as an apomictic triploid in British Columbia, at the northern extreme of its range. The current distribution of the genetic forms of this species is potentially the result of at least three processes: the fitness advantage of the apomictic triploid in the north, historic bottleneck effects, historic vicariance events. I propose to measure the genetic variation in the three genetic forms of A. amplectens across the species range using AFLP markers in order to assess the relative importance of these three hypotheses.

Organizers: Quentin Cronk (UBC), Iain Taylor (UBC), Jeannette Whitton (UBC)
Coordinator: Hailey Pappin (UBC)