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In many species, temperature-sensitive phenotypic plasticity (i.e., an individual's phenotypic response to temperature) displays a positive correlation with latitude, a pattern presumed to reflect local adaptation. This geographical pattern raises two general questions: (a) Do a few large-effect genes contribute to latitudinal variation in a trait? (b) Is the thermal plasticity of different traits regulated pleiotropically? To address the questions, we crossed individuals of Plantago lanceolata derived from northern and southern European populations. Individuals naturally exhibited high and low thermal plasticity in floral reflectance and flowering time. We grew parents and offspring in controlled cool- and warm-temperature environments, mimicking what plants would encounter in nature. We obtained genetic markers via genotype-by-sequencing, produced the first recombination map for this ecologically important nonmodel species, and performed quantitative trait locus (QTL) mapping of thermal plasticity and single-environment values for both traits. We identified a large-effect QTL that largely explained the reflectance plasticity differences between northern and southern populations. We identified multiple smaller-effect QTLs affecting aspects of flowering time, one of which affected flowering time plasticity. The results indicate that the genetic architecture of thermal plasticity in flowering is more complex than for reflectance. One flowering time QTL showed strong cytonuclear interactions under cool temperatures. Reflectance and flowering plasticity QTLs did not colocalize, suggesting little pleiotropic genetic control and freedom for independent trait evolution. Such genetic information about the architecture of plasticity is environmentally important because it informs us about the potential for plasticity to offset negative effects of climate change.

2018-2019 UNCG University Libraries Open Access Publishing Fund Grant Winner. A long-standing debate in evolutionary biology concerns the relative importance of different evolutionary forces in explaining phenotypic diversification at large geographic scales. For example, natural selection is typically assumed to underlie divergence along environmental gradients. However, neutral evolutionary processes can produce similar patterns. We collected molecular genetic data from 14 European populations of Plantago lanceolata to test the contributions of natural selection versus neutral evolution to population divergence in temperature-sensitive phenotypic plasticity of floral reflectance. In P. lanceolata, reflectance plasticity is positively correlated with latitude/altitude. We used population pairwise comparisons between neutral genetic differentiation (FST and Jost's D) and phenotypic differentiation (PST) to assess the contributions of geographic distance and environmental parameters of the reproductive season in driving population divergence. Data are consistent with selection having shaped large-scale geographic patterns in thermal plasticity. The aggregate pattern of PST versus FST was consistent with divergent selection. FST explained thermal plasticity differences only when geographic distance was not included in the model. Differences in the extent of cool reproductive season temperatures, and not overall temperature variation, explained plasticity differences independent of distance. Results are consistent with the hypothesis that thermal plasticity is adaptive where growing seasons are shorter and cooler, that is, at high latitude/altitude.

Costs of reproduction due to resource allocation trade-offs have long been recognized as key forces in life history evolution, but little is known about their functional or genetic basis. Arabidopsis lyrata, a perennial relative of the annual model plant A. thaliana with a wide climatic distribution, has populations that are strongly diverged in resource allocation. In this study, we evaluated the genetic and functional basis for variation in resource allocation in a reciprocal transplant experiment, using four A. lyrata populations and F2 progeny from a cross between North Carolina (NC) and Norway parents, which had the most divergent resource allocation patterns. Local alleles at quantitative trait loci (QTL) at a North Carolina field site increased reproductive output while reducing vegetative growth. These QTL had little overlap with flowering date QTL. Structural equation models incorporating QTL genotypes and traits indicated that resource allocation differences result primarily from QTL effects on early vegetative growth patterns, with cascading effects on later vegetative and reproductive development. At a Norway field site, North Carolina alleles at some of the same QTL regions reduced survival and reproductive output components, but these effects were not associated with resource allocation trade-offs in the Norway environment. Our results indicate that resource allocation in perennial plants may involve important adaptive mechanisms largely independent of flowering time. Moreover, the contributions of resource allocation QTL to local adaptation appear to result from their effects on developmental timing and its interaction with environmental constraints, and not from simple models of reproductive costs.

Selection on quantitative trait loci (QTL) may vary among natural environments due to differences in the genetic architecture of traits, environment-specific allelic effects or changes in the direction and magnitude of selection on specific traits. To dissect the environmental differences in selection on life history QTL across climatic regions, we grew a panel of interconnected recombinant inbred lines (RILs) of Arabidopsis thaliana in four field sites across its native European range. For each environment, we mapped QTL for growth, reproductive timing and development. Several QTL were pleiotropic across environments, three colocalizing with known functional polymorphisms in flowering time genes (CRY2, FRI and MAF2-5), but major QTL differed across field sites, showing conditional neutrality. We used structural equation models to trace selection paths from QTL to lifetime fitness in each environment. Only three QTL directly affected fruit number, measuring fitness. Most QTL had an indirect effect on fitness through their effect on bolting time or leaf length. Influence of life history traits on fitness differed dramatically across sites, resulting in different patterns of selection on reproductive timing and underlying QTL. In two oceanic field sites with high prereproductive mortality, QTL alleles contributing to early reproduction resulted in greater fruit production, conferring selective advantage, whereas alleles contributing to later reproduction resulted in larger size and higher fitness in a continental site. This demonstrates how environmental variation leads to change in both QTL effect sizes and direction of selection on traits, justifying the persistence of allelic polymorphism at life history QTL across the species range.

Understanding how genetic variation at individual loci contributes to adaptation of populations to different local environments is an important topic in modern evolutionary biology. To date, most evidence has pointed to conditionally neutral quantitative trait loci (QTL) showing fitness effects only in some environments, while there has been less evidence for single-locus fitness trade-offs. At QTL underlying local adaptation, alleles from the local population are expected to show a fitness advantage. Cytoplasmic genomes also can have a role in local adaptation, but the role of cytonuclear interactions in adaptive differentiation has remained largely unknown. We mapped genomic regions underlying adaptive differentiation in multiple fitness components and flowering time in diverged populations of a perennial plant Arabidopsis lyrata. Experimental hybrids for this purpose were grown in natural field conditions of the parental populations in Norway and North Carolina (NC), USA, and in the greenhouse. We found QTL where high fitness and early flowering were associated with local alleles, indicating a role of different selection pressures in phenotypic differentiation. At two QTL regions, a fitness component showing local adaptation between the parental populations also showed signs of putative fitness trade-offs. Beneficial dominance effects of conditionally neutral QTL for different fitness components resulted in hybrid vigour at the Norwegian site in the F(2) hybrids. We also found that cytoplasmic genomes contributed to local adaptation and hybrid vigour by interacting with nuclear QTL, but these interactions did not show evidence for cytonuclear coadaptation (high fitness of local alleles combined with the local cytoplasm).

Discovering the mechanisms by which genetic variation influences phenotypes is integral to understanding life-history evolution. Models describing causal relationships among traits in a developmental hierarchy provide a functional basis for understanding the correlations often observed among life-history traits. In this paper, we evaluate a developmental network model of life-history traits based on the perennial herb Arabidopsis lyrata, evaluate phenotypic, genetic, and environmental covariance matrices obtained under different scenarios of quantitative trait locus (QTL) effects in simulated crosses, test the efficacy of structural equation modeling to identify the correct basis for multiple-trait QTL effects, and compare model predictions with field data. We found that the trait network constrained the phenotypic covariance patterns to varying degrees, depending on which traits were directly affected by QTLs. Genetic and environmental covariance matrices were strongly correlated only when direct QTL effects were spread over many traits. Structural equation models that included all simulated traits correctly identified traits directly affected by QTLs, but heuristic search algorithms found several network structures other than the correct one that also fit the data closely. Estimated correlations among a subset of traits in F(2) data from field studies corresponded closely to model predictions when simulated QTLs affected traits known to differ between the parental populations. Our results show that causal trait network models can unify several aspects of quantitative genetic theory with empirical observations on genetic and phenotypic covariance patterns, and that incorporating trait networks into genetic analysis offers promise for elucidating mechanisms of life history evolution.

Selection for local adaptation results in genetic differentiation in ecologically important traits. In a perennial, outcrossing model plant Arabidopsis lyrata, several differentiated phenotypic traits contribute to local adaptation, as demonstrated by fitness advantage of the local population at each site in reciprocal transplant experiments. Here we compared fitness components, hierarchical total fitness and differentiation in putatively ecologically important traits of plants from two diverged parental populations from different continents in the native climate conditions of the populations in Norway and in North Carolina (NC, U.S.A.). Survival and number of fruits per inflorescence indicated local advantage at both sites and aster life-history models provided additional evidence for local adaptation also at the level of hierarchical total fitness. Populations were also differentiated in flowering start date and floral display. We also included reciprocal experimental F1 and F2 hybrids to examine the genetic basis of adaptation. Surprisingly, the F2 hybrids showed heterosis at the study site in Norway, likely because of a combination of beneficial dominance effects from different traits. At the NC site, hybrid fitness was mostly intermediate relative to the parental populations. Local cytoplasmic origin was associated with higher fitness, indicating that cytoplasmic genomes also may contribute to the evolution of local adaptation.

We present a game theoretic model of brood parasitism in the dung beetle Onthophagus taurus. Female O. taurus engage in brood parasitism when they attack a brood ball made by another female, destroy the existing egg and place one of their own eggs to develop within the existing dung ball. Brood parasitism is more costly than other forms of kleptoparasitism because an individual loses the total investment in an offspring. In this paper, we outline the behaviors involved in brood ball production and provide time estimates of those behaviors. The model is then used to predict when it is beneficial to steal the brood ball created by another female and when it is beneficial for a female to create her own. We also investigate how long a female should guard her eggs.

Adaptation to different habitat types across a patchy landscape may either arise independently in each patch or occur due to repeated colonization of each patch by the same specialized genotype. We tested whether open- and closed-canopy forms of Impatiens capensis, an herbaceous annual plant of eastern North America, have evolved repeatedly by comparing hierarchical measures of F(ST) estimated from AFLPs to morphological differentiation measured by Q(ST) for five pairs of populations found in open and closed habitats in five New England regions. Morphological differentiation between habitats (Q(HT)) in elongation traits was greater than marker divergence (F(HT)), suggesting adaptive differentiation. Genotypes from open- and closed-canopy habitats differed in shade avoidance traits in several population pairs, whereas patterns of AFLP differentiation suggest this differentiation does not have a single origin. These results suggest that open- and closed-canopy habitats present different selective pressures, but that the outcome of diversifying selection may differ depending on specific closed- and open-canopy habitats and on starting genetic variation. Hierarchical partitioning of F(ST) and Q(ST) makes it possible to distinguish global stabilizing selection on traits across a landscape from diversifying selection between habitat types within regions.

Mechanisms of reproductive isolation during plant speciation are often unclear because distinct species often experience high levels of gene flow and hybridization. Adaptive radiations such as the Hawaiian silversword alliance (HSA) provide unique opportunities to study the interactions of selection, gene flow and isolating mechanisms during the speciation process. We examined patterns of phenotypic and genetic differentiation in Dubautia arborea and Dubautia ciliolata, two parapatric HSA taxa that show marked morphological divergence but evidence of weak molecular differentiation, in order to estimate genome-wide differentiation and gene flow patterns. We scored 166 amplified fragment length polymorphism markers in a set of 89 plants from two populations each of D. arborea and D. ciliolata and phenotypically D. arborea-like and D. ciliolata-like plants from a natural hybrid zone. Analyses of population subdivision showed low levels of differentiation between the two species (F(ST) = 0.089) and evidence that the phenotypically parental hybrid zone plants were largely of parental species rather than of hybrid origin. A Bayesian analysis of population ancestry identified a number of plants with admixed D. arborea and D. ciliolata ancestry, even in nonhybrid-zone populations. These results suggest that genome-wide low levels of differentiation between D. arborea and D. ciliolata are in part due to gene flow, and favour models of genic speciation and collective evolution in which gene flow has different effects on selected loci vs. nonselected genomic regions. We discuss ecological and climatic factors that may have shaped patterns of differentiation in this species complex.

A new method for working with morphological characters is described and explored in experiments using human participants. The method uses direct comparison and sorting of images to produce hierarchical character-cladograms. A character-cladogram is a graphical representation of a single character that serves as a hypothesis of phylogeny based on that character. Each dichotomy in the character-cladogram represents a character state. Character states are unnamed, thus avoiding problems that arise through the application of verbal labels. Experiments with human participants are used to explore the conditions under which direct comparison produces reliable (consistent from investigator to investigator) and valid (in agreement with an independent estimate of phylogeny) characters. Participants were drawn from students taking a course in plant diversity at UNC Greensboro, and professional plant morphologists attending the Botany 2004 meetings. The students were randomly assigned to trained and untrained groups. Training was carried out using a method that has been shown to change a participant‘s mode of visual processing from analytic (the mode used by visual novices) to holistic (an additional mode only employed by visual experts). Morphologists (no specialists of the taxonomic group) were included in the study to investigate the effects of disciplinary expertise on the ability to describe character-cladograms. They received no additional training beyond that available to them as disciplinary experts. The results suggest an improvement in both reliability and validity after the training regime. We found no support for the idea that the morphologists differed from untrained students in their ability to produce reliable or valid character-cladograms. Disciplinary expertise may not translate into the ability to make reliable and valid assessments of similarity in an unfamiliar visual domain. Based on these results, we suggest a method for creating morphological characters and character states.

The dinoflagellate species originally described as Pfiesteria shumwayae Glasgow et Burkholder, recently transferred to a new genus, Pseudopfiesteria Litaker et al., is reclassified into the redefined genus Pfiesteria Steidinger et Burkholder, as Pfiesteria shumwayae within the order Peridiniales. This change is based upon consideration of a compilation of previous and new morphological analyses and molecular phylogenetic analyses. Morphological analysis with scanning and transmission electron microscopy supports previous findings except in the sulcal area. In the cells examined, the sulcus is partly concealed by the peduncle cover plate (p.c.), which originates at the right side of the sulcus along the left side of the 6c and 5? plates. The fine structure of the p.c. appears similar to that of other thecal plates. The 1? plate can also extend slightly over the sulcus. Transmission electron microscopy revealed that Pfiesteria shumwayae can have at least six sulcal plates; the number remains uncertain and may vary. The sulcal plates of this small, delicately thecate species have not been clearly discerned by scanning electron microscopy of membrane-stripped and/or suture-swollen cells. The Kofoidian thecal plate formula for the genus Pfiesteria is Po, cp, X, 4', la, 5–6?, 6c, p.c., ?s, 5?, 0p, 2?'. The monophyletic grouping of ?pfiesteria-like? taxa within the order Peridiniales, as well as the grouping of Pfiesteria piscicida and Pfiesteria shumwayae within the same genus, is also supported by the preponderance of previous molecular evidence, and by the phylogenetic trees contributed in the present analysis. Pfiesteria appears to be closely related to as-yet informally described cryptoperidiniopsoids and calcareous dinoflagellates such as Thoracosphaera; thus, the family classification requires revision that is beyond the scope of this study.

Perspectives on the role of large-effect quantitative trait loci (QTL) in the evolution of complex traits have shifted back and forth over the past few decades. Different sets of studies have produced contradictory insights on the evolution of genetic architecture. I argue that much of the confusion results from a failure to distinguish mutational and allelic effects, a limitation of using the Fisherian model of adaptive evolution as the lens through which the evolution of adaptive variation is examined. A molecular-based perspective reveals that allelic differences can involve the cumulative effects of many mutations plus intragenic recombination, a model that is supported by extensive empirical evidence. I discuss how different selection regimes could produce very different architectures of allelic effects under a molecular-based model, which may explain conflicting insights on genetic architecture from studies of variation within populations versus between divergently selected populations. I address shortcomings of genome-wide association study (GWAS) practices in light of more suitable models of allelic evolution, and suggest alternate GWAS strategies to generate more valid inferences about genetic architecture. Finally, I discuss how adopting more suitable models of allelic evolution could help redirect research on complex trait evolution toward addressing more meaningful questions in evolutionary biology.

Molecular methods, including conventional PCR, real-time PCR, denaturing gradient gel electrophoresis, fluorescent fragment detection PCR, and fluorescent in situ hybridization, have all been developed for use in identifying and studying the distribution of the toxic dinoflagellates Pfiesteria piscicida and P. shumwayae. Application of the methods has demonstrated a worldwide distribution of both species and provided insight into their environmental tolerance range and temporal changes in distribution. Genetic variability among geographic locations generally appears low in rDNA genes, and detection of the organisms in ballast water is consistent with rapid dispersal or high gene flow among populations, but additional sequence data are needed to verify this hypothesis. The rapid development and application of these tools serves as a model for study of other microbial taxa and provides a basis for future development of tools that can simultaneously detect multiple targets.

Two key characteristics of the neo-Darwinian synthesis in evolutionary biology have been its emphasis on the importance of mutations of small effect (micromutationism) and the view that studies of individual gene function shed relatively little light on evolutionary processes. Recent advances in molecular biology, however, have broken down many of the barriers between functional and evolutionary inquiry, opening the door to detailed studies of the genetic basis of functional trait evolution in plants. In this article, we review the insights into plant evolution that have been provided by molecular methods and address future research needs. Quantitative trait locus (QTL) mapping in crop and model plants has shown that individual loci often have large effects on trait variation, at variance with the micromutationist perspective. Evidence so far indicates that QTLs with large effects are also important in wild populations, underlying interspecific differences as well as intraspecific variation. Isolation of some of these QTLs, in particular for flowering time variation, has revealed a prominent role for regulatory genes known to function in regulation of flowering and exposed the complexity of regulatory processes. Preliminary evidence indicates that plant growth variation may be directly regulated rather than primarily the indirect result of selection on constituent processes. Future research should expand the number of traits that are intensively studied and make greater use of QTL mapping in wild plant taxa, especially those undergoing adaptive radiations, while continuing to draw on insights from model plants. Promising techniques include testing of candidate gene-trait associations in wild populations, genetic mapping in hybrid zones, and microarray analyses of gene expression.

Map-based cloning has been considered problematic for isolating quantitative trait loci (QTLs) due to the confounding phenotypic effects of environment and other QTLs. However, five recent studies, all in plants, have succeeded in cloning QTLs using map-based methods. We review the important features of these studies and evaluate the prospects for broader application of the techniques. Successful map-based cloning requires that QTLs represent single genes that can be isolated in near-isogenic lines, and that genotypes can be unambiguously inferred by progeny testing. In plants or animals for which map-based cloning of genes with discrete phenotypes is feasible, the modified procedures required for QTLs should not be limiting in most cases. The choice between map-based cloning and alternative methods will depend on details of the species and traits being studied.

Association studies based on linkage disequilibrium (LD) can provide high resolution for identifying genes that may contribute to phenotypic variation. We report patterns of local and genome-wide LD in 102 maize inbred lines representing much of the worldwide genetic diversity used in maize breeding, and address its implications for association studies in maize. In a survey of six genes, we found that intragenic LD generally declined rapidly with distance ( r 2 < 0.1 within 1500 bp), but rates of decline were highly variable among genes. This rapid decline probably reflects large effective population sizes in maize during its evolution and high levels of recombination within genes. A set of 47 simple sequence repeat (SSR) loci showed stronger evidence of genome-wide LD than did single-nucleotide polymorphisms (SNPs) in candidate genes. LD was greatly reduced but not eliminated by grouping lines into three empirically determined subpopulations. SSR data also supplied evidence that divergent artificial selection on flowering time may have played a role in generating population structure. Provided the effects of population structure are effectively controlled, this research suggests that association studies show great promise for identifying the genetic basis of important traits in maize with very high resolution.

Inbreeding depression is important in the evolution of plant populations and mating systems. Previous studies have suggested that early-acting inbreeding depression in plants is primarily due to lethal alleles and possibly epistatic interactions. Recent advances in molecular markers now make genetic mapping a powerful tool to study the genetic architecture of inbreeding depression. We describe a genome-wide evaluation of embryonic viability loci in a selfed family of loblolly pine (Pinus taeda L.), using data from AFLP markers from an essentially complete genome map. Locus positions and effects were estimated from segregation ratios using a maximum-likelihood interval mapping procedure. We identified 19 loci showing moderately deleterious to lethal embryonic effects. These loci account for >13 lethal equivalents, greater than the average of 8.5 lethal equivalents reported for loblolly pine. Viability alleles show predominantly recessive action, although potential overdominance occurs at 3 loci. We found no evidence for epistasis in the distribution of pairwise marker correlations or in the regression of fitness on the number of markers linked to deleterious alleles. The predominant role of semilethal alleles in embryonic inbreeding depression has implications for the evolution of isolated populations and for genetic conservation and breeding programs in conifers.

Cinnamyl alcohol dehydrogenase (CAD, E.C. 1.1.1.195) is a monolignol biosynthetic enzyme that catalyzes the final step of lignin subunit biosynthesis in higher plants. Recently, a mutant allele of the cad gene, cad-n1, encoding for the CAD enzyme, was discovered in loblolly pine. By reducing the expression of the cad gene, this mutant has a decreased lignin content and major changes in the lignin composition in wood. In this study, we found that the substitution of a wild-type allele by cad-n1 was associated with a significant effect on 2nd-year shoot elongation in a half-sib family of loblolly pine (designated family 7-1037). The average effect of cad-n1 appeared to increase with tree growth and was greater for stem radial growth than height growth. An increase of 14.1% in de-barked volume in year 4 was associated with cad-n1. Co-segregation analysis indicated that the cad locus itself might represent a gene that governs stem growth in pine. The significance of the mutation cad-n1 for tree growth and wood processing is discussed.

De novo construction of complete genetic linkage maps requires large mapping populations, large numbers of genetic markers, and efficient algorithms for ordering markers and evaluating order confidence. We constructed a complete genetic map of an individual loblolly pine (Pinus taeda L.) using amplified fragment length polymorphism (AFLP) markers segregating in haploid megagametophytes and PGRI mapping software. We generated 521 polymorphic fragments from 21 AFLP primer pairs. A total of 508 fragments mapped to 12 linkage groups, which is equal to the Pinus haploid chromosome number. Bootstrap locus order matrices and recombination matrices generated by PGRI were used to select 184 framework markers that could be ordered confidently. Order support was also evaluated using log likelihood criteria in MAPMAKER. Optimal marker orders from PGRI and MAPMAKER were identical, but the implied reliability of orders differed greatly. The framework map provides nearly complete coverage of the genome, estimated at approximately 1700 cM in length using a modified estimator. This map should provide a useful framework for merging existing loblolly pine maps and adding multiallelic markers as they become available. Map coverage with dominant markers in both linkage phases will make the map useful for subsequent quantitative trait locus mapping in families derived by self-pollination.

The math biology program at UNCG has been running since 2006 when we first received the funding from NSF. Every year, we provided integrated research projects at the interface of biology and mathematics to eight UNCG undergraduate students who worked in interdisciplinary teams. Up to date, our project resulted in 32 peer-reviewed publications and over 200 presentations; this demonstrates the extent to which undergraduate research can produce genuine scientific advancement. Moreover, our program also prepared UNCG students for rigorous interdisciplinary graduate studies and career opportunities and set them on a path toward productive careers as twenty-one century scientists and educators. We hope our experience will motivate and encourage others to pursue similar efforts.

Understanding how genetic variation at individual loci contributes to adaptation of populations to different local environments is an important topic in modern evolutionary biology. To date, most evidence has pointed to conditionally neutral quantitative trait loci (QTL) showing fitness effects only in some environments, while there has been less evidence for single-locus fitness trade-offs. At QTL underlying local adaptation, alleles from the local population are expected to show a fitness advantage. Cytoplasmic genomes also can have a role in local adaptation, but the role of cytonuclear interactions in adaptive differentiation has remained largely unknown. We mapped genomic regions underlying adaptive differentiation in multiple fitness components and flowering time in diverged populations of a perennial plant Arabidopsis lyrata. Experimental hybrids for this purpose were grown in natural field conditions of the parental populations in Norway and North Carolina (NC), USA, and in the greenhouse. We found QTL where high fitness and early flowering were associated with local alleles, indicating a role of different selection pressures in phenotypic differentiation. At two QTL regions, a fitness component showing local adaptation between the parental populations also showed signs of putative fitness trade-offs. Beneficial dominance effects of conditionally neutral QTL for different fitness components resulted in hybrid vigour at the Norwegian site in the F(2) hybrids. We also found that cytoplasmic genomes contributed to local adaptation and hybrid vigour by interacting with nuclear QTL, but these interactions did not show evidence for cytonuclear coadaptation (high fitness of local alleles combined with the local cytoplasm).

The use of high-throughput genomic techniques to map gene expression quantitative trait loci has spurred the development of path analysis approaches for predicting functional networks linking genes and natural trait variation. The goal of this study was to test whether potentially confounding factors, including effects of common environment and genes not included in path models, affect predictions of cause–effect relationships among traits generated by QTL path analyses. Structural equation modeling (SEM) was used to test simple QTL-trait networks under different regulatory scenarios involving direct and indirect effects. SEM identified the correct models under simple scenarios, but when common-environment effects were simulated in conjunction with direct QTL effects on traits, they were poorly distinguished from indirect effects, leading to false support for indirect models. Application of SEM to loblolly pine QTL data provided support for biologically plausible a priori hypotheses of QTL mechanisms affecting height and diameter growth. However, some biologically implausible models were also well supported. The results emphasize the need to include any available functional information, including predictions for genetic and environmental correlations, to develop plausible models if biologically useful trait network predictions are to be made.

Keys are character based tools for plant identification. They are based on the decomposition of the plant into very small, atomistic parts. These parts are described with the technical and often arcane terminology of plant taxonomy. Even the best electronic keys (Delta, Lucid) make use of this terminology. Keys are not based on pattern recognition, the forte of visual experts. Instead they demand that the user look at the plant as if it consisted of a series of isolated parts that are classified by name. Keys would be more effective if they were visually based. They would be easier to use for visual experts because accurate perception is their providence. They would also be easier to use for novices because they would not depend on knowledge of arcane terminology. This paper proposed an innovative image-based key system for species recognition.

The evolutionary pattern of the myc-like anthocyanin regulatory gene antR-Cor was examined in the dwarf dogwood species complex (Cornus Subgenus Arctocrania) that contains two diploid species (C. canadensis and C. suecica), their putative hybrids with intermediate phenotypes, and a tetraploid derivative (C. unalaschkensis). Full-length sequences of this gene ( approximately 4 kb) were sequenced and characterized for 47 dwarf dogwood samples representing all taxa categories from 43 sites in the Pacific Northwest. Analysis of nucleotide diversity indicated departures from neutral evolution, due most likely to local population structure. Neighbor-joining and haplotype network analyses show that sequences from the tetraploid and diploid intermediates are much more strongly diverged from C. suecica than from C. canadensis, and that the intermediate phenotypes may represent an ancestral group to C. canadensis rather than interspecific hybrids. Seven amino acid mutations that are potentially linked to myc-like anthocyanin regulatory gene function correlate with petal colors differences that characterize the divergence between two diploid species and the tetraploid species in this complex. The evidence provides a working hypothesis for testing the role of the gene in speciation and its link to the petal coloration. Sequencing and analysis of additional nuclear genes will be necessary to resolve questions about the evolution of the dwarf dogwood complex.

The complete genomic sequence for Arabidopsis provides the opportunity to combine phylogenetic and genomic approaches to study the evolution of gene families in plants. The Aux/IAA and ARF gene families, consisting of 29 and 23 loci in Arabidopsis, respectively, encode proteins that interact to mediate auxin responses and regulate various aspects of plant morphological development. We developed scenarios for the genomic proliferation of the Aux/IAA and ARF families by combining phylogenetic analysis with information on the relationship between each locus and the previously identified duplicated genomic segments in Arabidopsis. This analysis shows that both gene families date back at least to the origin of land plants and that the major Aux/IAA and ARF lineages originated before the monocot-eudicot divergence. We found that the extant Aux/IAA loci arose primarily through segmental duplication events, in sharp contrast to the ARF family and to the general pattern of gene family proliferation in Arabidopsis. Possible explanations for the unusual mode of Aux/IAA duplication include evolutionary constraints imposed by complex interactions among proteins and pathways, or the presence of long-distance cis-regulatory sequences. The antiquity of the two gene families and the unusual mode of Aux/IAA diversification have a number of potential implications for understanding both the functional and evolutionary roles of these genes.

Accelerated evolution of regulatory genes has been proposed as an explanation for decoupled rates of morphological and molecular evolution. The Hawaiian silversword alliance (Asteraceae-Madiinae) has evolved drastic differences in growth form, including rosette plants, cushion plants, shrubs, and trees, since its origin approximately 6 MYA. We have isolated genes in the DELLA subfamily of putative growth regulators from 13 taxa of Hawaiian and North American Madiinae. The Hawaiian taxa contain two copies of DaGAI that form separate clades within the Madiinae, consistent with an allotetraploid origin for the silversword alliance. DaGAI retains conserved features that have previously been identified in DELLA genes. Selective constraint in the Hawaiian DaGAI copies remains strong in spite of rapid growth form divergence in the silversword alliance, although the constraint was somewhat relaxed in the Hawaiian copies relative to the North American lineages. We failed to detect evidence for positive selection on individual codons. Notably, selective constraint remained especially strong in the gibberellin-responsive DELLA region for which the gene subfamily is named, which is truncated or deleted in all identified dwarf mutants in GAI homologues in different angiosperm species. In contrast with the coding region, however, approximately 900 bp of the upstream flanking region shows variable rates and patterns of evolution, which might reflect positive selection on regulatory regions.

Amplified fragment length polymorphism (AFLP) analysis is currently the most powerful and efficient technique for the generation of large numbers of anonymous DNA markers in plant and animal genomes. We have developed a protocol for high-throughput AFLP analysis that allows up to 70 000 polymorphic marker genotype determinations per week on a single automated DNA sequencer. This throughput is based on multiplexed PCR amplification of AFLP fragments using two different infrared dyelabeled primer combinations. The multiplexed AFLPs are resolved on a two-dye, model 4200 LI-COR® automated DNA sequencer, and the digital images are scored using semi-automated scoring software specifically designed for complex AFLP banding patterns (AFLP-Quantar™). Throughput is enhanced by using high-quality genomic DNA templates obtained by a 96-well DNA isolation procedure.

The AFLP (amplified fragment length polymorphism) technique was adapted to carry out genetic analysis in maritime pine, a species characterized by a large genome size (24 pg/C). A genetic linkage map was constructed for one F1 individual based on 239 AFLP and 127 RAPD (randomly amplified polymorphic DNA) markers. Markers were scored on megagametophytes (1n) from 200 germinated F2 seedlings. Polymorphism rate, labour time and cost of both AFLP and RAPD techniques were compared. The AFLP technique was found to be twice as fast and three-times less costly per marker than the RAPD technique. Thirteen linkage groups were identified with a LOD score =6 covering 1873 cM, which provided 93.4% of genome coverage. Proteins were extracted from needles (2n) of the F2 progeny and revealed by 2-DE (two-dimensional electrophoresis). Thirty one segregating proteins were mapped using a QTL detection strategy based on the quantification of protein accumulation. Two framework maps of the same F1 individual are now available. The first map (Plomion et al. 1996) uses RAPD markers and the second map, presented in this study, uses mostly AFLP markers. Although the total genetic length of both maps was almost identical, differences among homologous groups were observed.

The magnitude of fitness effects at genetic loci causing inbreeding depression at various life stages has been an important question in plant evolution. We used genetic mapping in a selfed family of loblolly pine (Pinus taeda L.) to gain insights on inbreeding depression for early growth and viability. Two quantitative trait loci (QTLs) were identified that explain much of the phenotypic variation in height growth through age 3 and may account for more than 13% inbreeding depression in this family. One of these QTLs maps to the location of cad-nl, a lignin biosynthesis mutation. Both QTLs show evidence of overdominance, although evidence for true versus pseudo-overdominance is inconclusive. Evidence of directional dominance for height growth was noted throughout the genome, suggesting that additional loci may contribute to inbreeding depression. A chlorophyll-deficiency mutation, spf, did not appear to be associated with growth effects, but had significant effects on survival through age 3. Previously identified embryonic viability loci had little or no overall effect on germination, survival, or growth. Our results challenge, at least in part, the prevailing hypothesis that inbreeding depression for growth is due to alleles of small effect. However, our data support predictions that loci affecting inbreeding depression are largely stage specific.

Background Perenniality is best understood in quantitative terms, involving the relationship between production vs. turnover of meristems, biomass, or energy reserves. Previous quantitative trait locus (QTL) studies using divergent populations of the perennial rock cress Arabidopsis lyrata have shown that trade-offs in vegetative growth vs. reproduction are due to cascading effects of differences in early vegetative development, which contribute to local adaptation. However, details of the developmental differences and how they affect perenniality remained unclear. In this study, we investigated in detail the developmental differences in perenniality between populations. A. lyrata from Norway and North Carolina populations, representing contrasting environments and degrees of perenniality, were grown under controlled conditions, and data were collected on plant phenology and shoot-level development. We tested hypotheses that differences in perenniality involve strict allocation of lateral meristems to vegetative vs. reproductive fates, or alternatively quantitative effects of pre-reproductive vegetative development. Results The two populations showed large differences in the degree of vegetative development on individual shoots prior to reproductive transitions. The number of leaves produced on shoots prior to bolting, and not strict meristem allocation or variation in apical dominance, was able to explain variation in the number of inflorescences on individual plants. These results suggested that allocation of time to shoot vegetative vs. reproductive development could be a major factor in resource allocation differences between the populations. Conclusions Based on these results and those of previous QTL studies, we propose a model in which the degree of shoot vegetative development shapes the developmental context for reproduction and subsequent vegetative growth in different environments. Climate-specific effects of shoot development patterns on reproductive output and survival may result in divergent evolutionary trajectories along a perenniality continuum, which may have broader relevance for plant life history evolution.