Mauricio Publications

The Genetics of Adaptation (R. Mauricio, editor). Springer, Dordrecht (2005)

An enduring controversy in evolutionary biology is the genetic basis of adaptation. Darwin emphasized “many slight differences” as the ultimate source of variation to be acted upon by natural selection. In the early 1900’s, this view was opposed by “Mendelian geneticists”, who emphasized the importance of “macromutations” in evolution. The Modern Synthesis resolved this controversy, concluding that mutations in genes of very small effect were responsible for adaptive evolution. A decade ago, Allen Orr and Jerry Coyne reexamined the evidence for this neo-Darwinian view and found that both the theoretical and empirical basis for it were weak. Orr and Coyne encouraged evolutionary biologists to reexamine this neglected question: what is the genetic basis of adaptive evolution? In this volume, a new generation of biologists have taken up this challenge. Using advances in both molecular genetic and statistical techniques, evolutionary geneticists have made considerable progress in this emerging field. In this volume, a diversity of examples from plant and animal studies provides valuable information for those interested in the genetics and evolution of complex traits.

ONTOGENETICS OF QTL: THE GENETIC ARCHITECTURE OF TRICHOME DENSITY OVER TIME IN ARABIDOPSIS THALIANA

R. Mauricio
Genetica 123: 72-82 (2005)

Although much is known about the molecular genetic basis of trichome development in Arabidopsis thaliana, less is known about the underlying genetic basis of continuous variation in a trait known to be of adaptive importance: trichome density. The density of leaf trichomes is known to be a major determinant of herbivore damage in natural populations of A. thaliana and herbivores are a significant selective force on genetic variation for trichome density. A number of developmental changes occur during ontogeny in A. thaliana, including changes in trichome density. I used multiple interval mapping (MIM) analysis to identify QTL responsible for trichome density on both juvenile leaves and adult leaves in replicate, independent trials and asked whether those QTL changed with ontogeny. In both juvenile and adult leaves, I detected a single major QTL on chromosome 2 that explained much of the genetic variance. Although additional QTL were detected, there were no consistent differences in the genetic architecture of trichome density measured on juvenile and adult leaves. The finding of a single QTL of major effect for a trait of known adaptive importance suggests that genes of major effect may play an important role in adaptation.

EPISTASIS FOR FITNESS-RELATED QUANTITATIVE TRAITS IN ARABIDOPSIS THALIANA GROWN IN THE FIELD AND IN THE GREENHOUSE

R. L. Malmberg, S. Held, A. Waits and R. Mauricio

Genetics 171: 2013-2027 (2005)

The extent to which epistasis contributes to adaptation, population differentiation, and speciation is a long-standing and important problem in evolutionary genetics. Using recombinant inbred (RI) lines of Arabidopsis thaliana grown under natural field conditions, we have examined the genetic architecture of fitness-correlated traits with respect to epistasis; we identified both single-locus additive and two-locus epistatic QTL for natural variation in fruit number, germination, and seed length and width. For fruit number, we found seven significant epistatic interactions, but only two additive QTL. For seed germination, length, and width, there were from two to four additive QTL and from five to eight epistatic interactions. The epistatic interactions were both positive and negative. In each case, the magnitude of the epistatic effects was roughly double that of the effects of the additive QTL, varying from -41% to +129% for fruit number and from -5% to +4% for seed germination, length, and width. A number of the QTL that we describe participate in more than one epistatic interaction, and some loci identified as additive also may participate in an epistatic interaction; the genetic architecture for fitness traits may be a network of additive and epistatic effects.We compared the map positions of the additive and epistatic QTL for germination, seed width, and seed length from plants grown in both the field and the greenhouse. While the total number of significant additive and epistatic QTL was similar under the two growth conditions, the map locations were largely different. We found a small number of significant epistatic QTL x environment effects when we tested directly for them. Our results support the idea that epistatic interactions are an important part of natural genetic variation and reinforce the need for caution in comparing results from greenhouse-grown and field-grown plants.

QTL-BASED EVIDENCE FOR THE ROLE OF EPISTASIS IN EVOLUTION

The extent to which epistasis contributes to adaptation and speciation has been a controversial topic in evolutionary genetics. One experimental approach to study epistasis is based on quantitative trait locus (QTL) mapping using molecular markers. Comparisons can be made among all possible pair-wise combinations of the markers, irrespective of whether an additive QTL is associated with a marker; several software packages have been developed that facilitate this. We review several examples of using this approach to identify epistatic QTLs for traits of evolutionary or ecological interest. While there is variability in the results, the number of epistatic QTL interactions is often greater than or equal to the number of additive QTLs. The magnitude of epistatic effects can be larger than the additive effects. Thus, epistatic interactions seem to be an important part of natural genetic variation. Future studies of epistatic QTLs could lead to descriptions of the genetic networks underlying variation for fitness-related traits.

HYBRIDIZATION AS A SOURCE OF EVOLUTIONARY NOVELTY: LEAF SHAPE IN A HAWAIIAN COMPOSITE

S. Jørgensen and R. Mauricio

Genetica 123: 164-172 (2005)

Hybridization is increasingly recognized as a significant creative force in evolution. Interbreeding among species can lead to the creation of novel genotypes and morphologies that lead to adaptation. On the Hawaiian island of O‘ahu, populations of two species of plants in the endemic genus Lipochaeta grow at similar elevations in the northern Wai‘anae Mountains. These two species represent extremes of the phenotypic distribution of leaf shape: the leaves of Lipochaeta tenuifolia individuals are compound and highly dissected while leaves of L. tenuis are simple. Based primarily on leaf shape morphology, a putative hybrid population of Lipochaeta located at Pu‘u Kawiwi was identified. Individuals in this population exhibit a range of leaf shapes intermediate in varying degrees between the leaf shapes of the putative parental species. We analyzed individuals from pure populations of L. tenuifolia, L. tenuis and the putative hybrids using 133 AFLP markers. Genetic analysis of these neutral markers provided support for the hybrid origin of this population. The correlation between genetic background and leaf morphology in the hybrids suggested that the genome of the parental species with simple leaves might have significantly contributed to the evolution of a novel, compound leaf morphology.

CAN ECOLOGY HELP GENOMICS: THE GENOME AS ECOSYSTEM

Ecologists study the rules that govern processes influencing the distribution and abundance of organisms, particularly with respect to the interactions of organisms with their biotic and abiotic environments. Over the past decades, using a combination of sophisticated mathematical models and rigorous experiments, ecologists have made considerable progress in understanding the complex web of interactions that constitute an ecosystem. The field of genomics runs on a path parallel to ecology. Like ecology, genomicists seek to understand how each gene in the genome interacts with every other gene and how each gene interacts with multiple, environmental factors. Gene networks connect genes as complex as the “webs” that connect the species in an ecosystem. In fact, genes exist in an ecosystem we call the genome. The genome as ecosystem is more than a metaphor – it serves as the conceptual foundation for an interdisciplinary approach to the study of complex systems characteristic of both genomics and ecology. Through the infusion of genomics into ecology and ecology into genomics both fields will gain fresh insight into the outstanding major questions of their disciplines.

THE ‘BRICOLAGE’ OF THE GENOME ELUCIDATED THROUGH EVOLUTIONARY GENOMICS

Geneticists are fond of referring to a genome as a ‘book of life’. A genome contains all the information needed to create life: genes, the words of the book, are strung out on chromosomes, like ‘beads on a string’. Although most would agree that this view of genomes is too simplistic, the fact remains that it has been a powerful metaphor. Recent discoveries, however, highlight just how unlike a book a genome seems to be, or at least how incredibly sloppy the publisher is: the book of life has many ostensibly extraneous letters, sections of duplicate paragraphs, and pages that simply do not seem to open.

UNEXPECTEDLY HIGH CLONAL DIVERSITY OF TWO SALT MARSH PERENNIALS ACROSS A SEVERE ENVIRONMENTAL GRADIENT

C. L. Richards, J. L. Hamrick, L. A. Donovan and R. Mauricio

Ecology Letters 7: 1155-1162 (2004)

In salt marsh habitats, noted for their extreme environments, a widely held assumption is that a few large clones dominate plant populations. Using a large number of polymorphic genetic markers, we were able to test this assumption for two salt marsh plants known to span extreme salinity gradients. For both species, clonal diversity was surprisingly high across populations: Simpson's diversity indices were 0.96 and 0.99. Although clonal diversity was high, there was no pattern of association between specific clones or alleles with salt microhabitat. Our findings suggest that sexual reproduction and recruitment from seeds may have been generally underappreciated as an important ecological force in the salt marsh. Furthermore, clonal diversity has implications for conservation and restoration of these critical coastal habitats, particularly with regard to buffering environmental change or disease. Recent studies also suggest that high levels of intraspecific diversity can affect a variety of community and ecosystem processes.

NEUTRAL GENETIC VARIATION AMONG WILD NORTH AMERICAN POPULATIONS OF THE WEEDY PLANT ARABIDOPSIS THALIANA IS NOT GEOGRAPHICALLY STRUCTURED

We investigated neutral genetic variation within and among 53 wild-collected populations of the weedy, annual plant Arabidopsis thaliana in North America, using amplified fragment length polymorphism (AFLP) markers. Arabidopsis thaliana is thought to have been introduced to North America from Eurasia by humans; such an introduction might be expected to leave a clear geographic signal in the genetic data. To detect such patterns, we sampled populations at several hierarchical geographic levels. We collected individuals from populations in two areas of the Southeast and one in the Midwest, as well as individuals from populations in the Pacific Northwest and Northeast. To estimate within population variation, we sampled eight individuals from each of six populations in the Southeast and Midwest. Among all 95 individuals analyzed, we detected 131 polymorphic AFLP fragments. We found no evidence for continental or regional diversification. Individuals sampled from Midwestern and Southeastern populations intermingled in a neighbor-joining tree, and Mantel tests conducted within the Midwestern and Southeastern regions as well as the full data set failed to detect any significant relationship between geographic and genetic distance. These results mirror those found for most global surveys of neutral genetic variability in A. thaliana. Surprisingly, we detected substantial amounts of neutral genetic variability within populations. The levels of genetic variation within populations, coupled with the non-geographical nature of divergence among populations, are consistent with contemporary gene flow and point to a complex and dynamic population history of A. thaliana in North America.

FITNESS COSTS AND BENEFITS OF NOVEL HERBICIDE TOLERANCE IN A NOXIOUS WEED

R. S. Baucom and R. Mauricio

Proceedings of the National Academy of Sciences, USA 101: 13386-13390 (2004) [see accompanying commentary: Roy, B.A. 2004. Rounding up the costs and benefits of herbicde use. PNAS 101: 13974-13975]

Glyphosate, the active ingredient in the herbicide RoundUp, has increased dramatically in use over the past decade and constitutes a potent anthropogenic source of selection. In the southeastern United States, weedy morning glories have begun to develop tolerance to glyphosate, representing a unique opportunity to examine the evolutionary genetics of a novel trait. We found genetic variation for tolerance, indicating the potential for the population to respond to selection by glyphosate. However, the following significant evolutionary constraint exists: in the absence of glyphosate, tolerant genotypes produced fewer seeds than susceptible genotypes. The combination of strong positive directional selection in the presence of glyphosate and strong negative directional selection in its absence may indicate that the selective landscape of land use could drive the evolutionary trajectory of glyphosate tolerance. Understanding these evolutionary forces is imperative for devising comprehensive management strategies to help slow the rate of the evolution of tolerance.

NATURAL SELECTION FOR POLYMORPHISM IN THE DISEASE RESISTANCE GENE RPS2 OF ARABIDOPSIS THALIANA

R. Mauricio, E. A. Stahl, T. Korves, D. Tian, M. Kreitman and J. Bergelson

Genetics 163: 735-746 (2003)

Pathogen resistance is an ecologically important phenotype increasingly well understood at the molecular genetic level. In this paper, we examine levels of avrRpt2-dependent resistance and Rps2 locus DNA sequence variability in a worldwide sample of 27 accessions of Arabidopsis thaliana. The rooted parsimony tree of Rps2 sequences drawn from a diverse set of ecotypes includes a deep bifurcation separating major resistance and susceptibility clades of alleles. We find evidence for selection maintaining these alleles and identify the 5’ part of the leucine rich repeat region as a probable target of selection. Additional protein variants are found within the two major clades and correlate well with measurable differences among ecotypes in resistance to the avirulence gene avrRpt2 of the pathogen Pseudomonas syringae. Long-lived polymorphisms have been observed for other resistance genes of A. thaliana; the Rps2 data suggest that the long-term maintenance of phenotypic variation in resistance genes may be a general phenomenon, and are consistent with diversifying selection acting in concert with selection acting to maintain variation.

TESTING FOR ENVIRONMENTALLY INDUCED BIAS IN PHENOTYPIC ESTIMATES OF NATURAL SELECTION: THEORY AND PRACTICE

J.R. Stinchcombe, M. T. Rutter, D. S. Burdick, P. Tiffin, M. D. Rausher, and R. Mauricio

American Naturalist 160: 511-523 (2002)

Measuring natural selection has been a fundamental goal of evolutionary biology for more than a century, and techniques developed in the last 20 yr have provided relatively simple means for biologists to do so. Many of these techniques, however, share a common limitation: when applied to phenotypic data, environmentally induced covariances between traits and fitness can lead to biased estimates of selection and misleading predictions about evolutionary change. Utilizing estimates of breeding values instead of phenotypic data with these methods can eliminate environmentally induced bias, although this approach is more difficult to implement. Despite this potential limitation to phenotypic methods and the availability of a potential solution, little empirical evidence exists on the extent of environmentally induced bias in phenotypic estimates of selection. In this article, we present a method for detecting bias in phenotypic estimates of selection and demonstrate its use with three independent data sets. Nearly 25% of the phenotypic selection gradients estimated from our data are biased by environmental covariances.We find that bias caused by environmental covariances appears mainly to affect quantitative estimates of the strength of selection based on phenotypic data and that the magnitude of these biases is large. As our estimates of selection are based on data from spatially replicated field experiments, we suggest that our findings on the prevalence of bias caused by environmental covariances are likely to be conservative.

MAPPING QUANTITATIVE TRAIT LOCI IN PLANTS: USES AND CAVEATS FOR EVOLUTIONARY BIOLOGY

Although Gregor Mendel was either clever or lucky enough to study traits of simple inheritance in his pea plants, many plant characters of interest to modern geneticists are decidedly complex. Understanding the genetic basis of such complex, or quantitative, traits requires a combination of modern molecular genetic techniques and powerful statistical methods. These approaches have begun to give us insight into understanding the evolution of complex traits in both crops and in wild plants.

AN ECOLOGICAL GENETIC APPROACH TO THE STUDY OF COEVOLUTION

Almost forty years ago, Ehrlich and Raven (1964) hypothesized that the great diversity of plants and the herbivores that feed on them arose from a process of coevolution. Plants do possess an amazing diversity of traits that are easily imagined as having arisen from an antagonistic interaction between plants and herbivores. Two basic assumptions lie at the root of most theories of coevolution between plants and their herbivores. First, herbivores are agents of natural selection on plant resistance traits. Second, plants incur a significant fitness cost for possessing these resistance traits. An ecological genetic approach can provide rigorous evidence for these coevolutionary assumptions. In this paper, I present new experimental work on the subject of costs of resistance and review and discuss my own previous work bearing directly on these questions. Using both field experiments on natural populations of the mouse-ear cress (Arabidopsis thaliana) and laboratory experiments using genetically modified plants, I demonstrate that herbivores are exerting selection on both a chemical and physical resistance trait and that there are significant fitness costs to possessing these two traits. These results provide direct confirmation that our current models of the evolution of plant defenses are appropriate.

NATURAL SELECTION AND THE JOINT EVOLUTION OF TOLERANCE AND RESISTANCE AS PLANT DEFENSES

Plants can defend themselves against the damaging effects of herbivory in at least two ways. Resistant plants avoid or deter herbivores and are therefore fed upon less than susceptible plants. Tolerant plants are not eaten less than plants with little tolerance, but the effects of herbivore damage are not so detrimental to a tolerant plant as they are to a less tolerant plant. Biologists have suggested that these two strategies might represent two alternative and redundant defenses against herbivory since they appear to serve the same function for plants. I explore the relationship between resistance and tolerance, particularly with regards to how the joint evolution of these two traits will influence the evolution of plant defense. Although I briefly review some of the contributions of theory to the study of tolerance, I concentrate on an empirical, ecological genetic approach to the study of the evolution of these characters and the coevolution of tolerance and herbivores. In order to understand the evolution of any trait, we must understand the evolutionary forces acting on the trait. Specifically, we must understand how natural selection acts on tolerance. I review several studies that have specifically measured the form of selection acting on tolerance and tested the hypothesis that resistance and tolerance are alternative strategies. I also present a statistical analysis that does not support the hypothesis that herbivores are selective agents on tolerance. Finally, I consider a variety of constraints that possibly restrict the evolution of tolerance.

DYNAMICS OF DISEASE RESISTANCE POLYMORPHISM AT THE RPM1 LOCUS OF ARABIDOPSIS

E. A. Stahl, G. Dwyer, R. Mauricio, M. Kreitman and J. Bergelson

Nature 400: 667-671 (1999)

The co-evolutionary "arms race" is a widely accepted model for the evolution of host-pathogen interactions. This model predicts that variation for disease resistance will be transient, and that host populations generally will be monomorphic at disease-resistance (R-gene) loci. However, plant populations show considerable polymorphism at R-gene loci involved in pathogen recognition. Here we have tested the arms-race model in Arabidopsis thaliana by analysing sequences flanking Rpm1, a gene conferring the ability to recognize Pseudomonas pathogens carrying AvrRpm1 or AvrB. We reject the arms-race hypothesis: resistance and susceptibility alleles at this locus have co-existed for millions of years. To account for the age of alleles and the relative levels of polymorphism within allelic classes, we use coalescence theory to model the long-term accumulation of nucleotide polymorphism in the context of the short-term ecological dynamics of disease resistance. This analysis supports a "trench warfare" hypothesis, in which advances and retreats of resistance-allele frequency maintain variation for disease resistance as a dynamic polymorphism.

COSTS OF RESISTANCE TO NATURAL ENEMIES IN FIELD POPULATIONS OF THE ANNUAL PLANT, ARABIDOPSIS THALIANA

The annual plant, Arabidopsis thaliana, is widely used as a model system in molecular genetics, but little is known about populations in the field. In this experimental field study of natural populations of Arabidopsis, I tested the assumption that plant resistance has fitness costs. Models of the evolution of resistance assume a cost, envisioned as a reduction in fitness in the absence of natural enemies, such as insect herbivores and pathogens. The presumed basis of this cost is the diversion of limiting resources away from present and future growth and reproduction. Recent failures to detect allocation costs of resistance to herbivores have raised questions about whether costs exist, and thus, about the appropriateness of theories that postulate such costs. I found genetic variation for two traits commonly thought to function as resistance characters: trichome density and total glucosinolate concentration. Under field conditions, these characters both reduced damage by the natural assemblage of herbivores and exhibited significant fitness costs.

REDUCING BIAS IN THE MEASUREMENT OF SELECTION

Selection on quantitative characters is commonly measured in natural populations using regression techniques based on phenotypic covariances between traits and fitness. However, such methods do not give an accurate view of the causal relationship between the phenotype and fitness if environmental factors also contribute to covariances between traits and fitness. A recently developed method for estimating selection eliminates the problem of bias resulting from environmental covariances. This underappreciated method represents a significant addition to the toolbox of the evolutionary ecologist.

EXPERIMENTAL MANIPULATION OF PUTATIVE SELECTIVE AGENTS PROVIDES EVIDENCE FOR THE ROLE OF NATURAL ENEMIES IN THE EVOLUTION OF PLANT DEFENSE

R. Mauricio and M. D. Rausher

Evolution 51: 1435-1444 (1997)

Although biologists have long assumed that plant resistance characters evolved under selection exerted by such natural enemies as herbivores and pathogens, experimental evidence for this assumption is sparse. We present evidence that natural enemies exert selection on particular plant resistance characters. Specifically, we demonstrate that elimination of natural enemies from an experimental field population of Arabidopsis thaliana alters the pattern of selection on genetic variation in two characters that have been shown to reduce herbivore damage in the field: total glucosinolate concentration and trichome density. The change in pattern of selection reveals that natural enemies imposed selection favoring increased glucosinolate concentrations and increased trichome density, and thus, supports one of the major assumptions of the coevolution hypothesis. We also demonstrate that a pattern of stabilizing selection on glucosinolate concentration results from a balance between the costs and benefits associated with increasing levels of this resistance character. This result provides direct confirmation of the appropriateness of cost-benefit models for characterizing the evolution of plant defenses.

VARIATION ON THE DEFENSE STRATEGIES OF PLANTS: ARE RESISTANCE AND TOLERANCE MUTUALLY EXCLUSIVE?

R. Mauricio, M. D. Rausher and D. S. Burdick

Ecology 78: 1301-1310 (1997)

Plants can employ two general strategies to defend themselves against herbivory: they can either reduce the amount of damage they experience (resistance), or they can tolerate herbivore damage. Theoretical considerations suggest that, in many cases, tolerance and resistance are redundant strategies, and may therefore be mutually exclusive adaptations. In this investigation of natural populations of the annual plant, Arabidopsis thaliana, we examine whether the pattern of selection acting on resistance and tolerance favors the evolution of one defense strategy, or the other, but not both. We found that the joint pattern of selection acting on tolerance and two resistance traits, trichome density and total glucosinolate concentration, indicated that there were not alternate peaks in the fitness landscape favoring either resistance or tolerance. Rather, selection favored the retention of both tolerance and resistance. One reason for the absence of mutually exclusive alternative resistance/tolerance strategies is the absence of a negative genetic correlation between resistance and tolerance. An unexpected result is the detection of disruptive selection acting on tolerance, which seems to result from a non-linear relationship between tolerance and its costs.

PATTERN OF LEAF DAMAGE AFFECTS FITNESS OF THE ANNUAL PLANT RAPHANUS SATIVUS (BRASSICACEAE)

R. Mauricio, M. D. Bowers and F. A. Bazzaz

Ecology 74: 2066-2071 (1993)

We investigated how the pattern of leaf damage influences reproduction, growth, and allocation in the wild radish, Raphanus sativus (Brassicaceae). We removed an equivalent leaf area from plants with four leaves in five treatments ranging from concentrated to dispersed damage: one entire mature leaf removed, one entire new leaf removed, 50% of two mature leaves removed, 50% of two new leaves removed, and 25% of all four leaves removed. Plants in a control group were undamaged. Reproduction, growth, and allocation were not affected by the age of the damaged leaf. However, the pattern of leaf damage significantly affected our three measures of plant fitness: the number of flowers produced, the reproductive biomass, and the total biomass. Plants in the treatment in which the damage was most dispersed had significantly higher flower number, reproductive biomass, and total biomass than an intermediate damage treatment and significantly more reproductive biomass than the concentrated damage treatment. There were no significant differences between the concentrated and intermediate damage treatments and no differences between the dispersed damage treatment and the undamaged control. Our data indicate that more dispersed damage is less detrimental to the plant than more concentrated damage. Therefore, the pattern of leaf damage must be considered in determining the impact of herbivores on plant performance.

DO CATERPILLARS DISPERSE THEIR DAMAGE?: LARVAL FORAGING BEHAVIOR OF 2 SPECIALIST HERBIVORES, EUPHYDRYAS PHAETON (NYMPHALIDAE) AND PIERIS RAPAE (PIERIDAE)

R. Mauricio and M. D. Bowers

Ecological Entomology 15: 153-161 (1990)

To examine ecological and evolutionary aspects of caterpillar foraging behaviour, this study focused on observation of the individual foraging behaviour of two lepidopteran species, Pieris rapae L. and Euphydryas phaeton (Drury), on their respective host plants. Periodic observations over the course of a day showed that the larvae move considerable distances, forage on the upper surfaces of leaves, and often immediately leave areas from which they have fed, leaving a pattern of dispersed herbivory. Differences in foraging behaviour were not found between the two species, even though one species is aposematic and the other is cryptically coloured, but there were significant differences in the foraging patterns of P. rapae on the two host plants, broccoli and radish.