Heterosis for biomass-related traits in Arabidopsis investigated by quantitative trait loci analysis of the triple testcross design with recombinant inbred lines

Arabidopsis thaliana has emerged as a leading model species in plant genetics and functional genomics including research on the genetic causes of heterosis. We applied a triple testcross (TTC) design and a novel biometrical approach to identify and characterize quantitative trait loci (QTL) for heterosis of five biomass-related traits by (i) estimating the number, genomic positions, and genetic effects of heterotic QTL, (ii) characterizing their mode of gene action, and (iii) testing for presence of epistatic effects by a genomewide scan and marker x marker interactions. In total, 234 recombinant inbred lines (RILs) of Arabidopsis hybrid C24 x Col-0 were crossed to both parental lines and their F1 and analyzed with 110 single-nucleotide polymorphism (SNP) markers. QTL analyses were conducted using linear transformations Z1, Z2, and Z3 calculated from the adjusted entry means of TTC progenies. With Z1, we detected 12 QTL displaying augmented additive effects. With Z2, we mapped six QTL for augmented dominance effects. A one-dimensional genome scan with Z3 revealed two genomic regions with significantly negative dominance x additive epistatic effects. Two-way analyses of variance between marker pairs revealed nine digenic epistatic interactions: six reflecting dominance x dominance effects with variable sign and three reflecting additive x additive effects with positive sign. We conclude that heterosis for biomass-related traits in Arabidopsis has a polygenic basis with overdominance and/or epistasis being presumably the main types of gene action.

High variability and non-neutral evolution of the mammalian avpr1a gene

BACKGROUND: The arginine-vasopressin 1a receptor has been identified as a key determinant for social behaviour in Microtus voles, humans and other mammals. Nevertheless, the genetic bases of complex phenotypic traits like differences in social and mating behaviour among species and individuals remain largely unknown. Contrary to previous studies focusing on differences in the promotor region of the gene, we investigate here the level of functional variation in the coding region (exon 1) of this locus. RESULTS: We detected high sequence diversity between higher mammalian taxa as well as between species of the genus Microtus. This includes length variation and radical amino acid changes, as well as the presence of distinct protein variants within individuals. Additionally, negative selection prevails on most parts of the first exon of the arginine-vasopressin receptor 1a (avpr1a) gene but it contains regions with higher rates of change that harbour positively selected sites. Synonymous and non-synonymous substitution rates in the avpr1a gene are not exceptional compared to other genes, but they exceed those found in related hormone receptors with similar functions. DISCUSSION: These results stress the importance of considering variation in the coding sequence of avpr1a in regards to associations with life history traits (e.g. social behaviour, mating system, habitat requirements) of voles, other mammals and humans in particular.

Simulating the evolution of a clonal trait in plants with sexual and vegetative reproduction

Aims Phenotypic optimality models neglect genetics. However, especially when heterozygous genotypes ire fittest, evolving allele, genotype and phenotype frequencies may not correspond to predicted optima. This was not previously addressed for organisms with complex life histories. Methods Therefore, we modelled the evolution of a fitness-relevant trait of clonal plants, stolon internode length. We explored the likely case of air asymmetric unimodal fitness profile with three model types. In constant selection models (CSMs), which are gametic, but not spatially explicit, evolving allele frequencies in the one-locus and five-loci cases did not correspond to optimum stolon internode length predicted by the spatially explicit, but not gametic, phenotypic model. This deviation was due to the asymmetry of the fitness profile. Gametic, spatially explicit individual-based (SEIB) modeling allowed us relaxing the CSM assumptions of constant selection with exclusively sexual reproduction. Important findings For entirely vegetative or sexual reproduction, predictions. of the gametic SEIB model were close to the ones of spatially explicit CSMs gametic phenotypic models, hut for mixed modes of reproduction they appoximated those of gametic, not spatially explicit CSMs. Thus, in contrast to gametic SEIB models, phenotypic models and, especially for few loci, also CSMs can be very misleading. We conclude that the evolution of trails governed by few quantitative trait loci appears hardly predictable by simple models, that genetic algorithms aiming at technical optimization may actually, miss the optimum and that selection may lead to loci with smaller effects, in derived compared with ancestral lines.

Spatial isolation and genetic differentiation in naturally fragmented plant populations of the Swiss Alps

Aims The effect Of anthropogenic landscape fragmentation on the genetic diversity and adaptive potential of plant populations is a major issue in conservation biology. However, little is known about the partitioning of genetic diversity in alpine species, which occur in naturally fragmented habitats. Here, we, investigate molecular patterns of three alpine plants (Epilobium fleischeri, Geum reptans and Campanula thyrsoides) across Switzerland and ask whether Spatial isolation has led to high levels of populations differentiation, increasing over distance, and a decrease of within-population variability. We further hypothesize that file contrasting potential for long-distance dispersal (LDD) of Seed in these Species will considerably influence and explain diversity partitioning. Methods For each study species, we Sampled 20-23 individuals from each of 20-32 populations across entire Switzerland. We applied Random Amplified Polymorphic Dimorphism markers to assess genetic diversity within (Nei's expected heterozygosity, H-e; percentage of polymorphic hands, P-P) and among (analysis of molecular variance, Phi(st)) populations and correlated population size and altitude with within-populalion diversity. Spatial patterns of genetic relatedness were investigated using Mantel tests and standardized major axis regression as well as unweighted pair group method with arithmetic mean cluster analyses and Monmonier's algorithm. To avoid known biases, We standardized the numbers of populations, individuals and markers using multiple random reductions. We modelled LDD with a high alpine wind data set using the terminal velocity and height of seed release as key parameters. Additionally, we assessed a number of important life-history traits and factors that potentially influence genetic diversity partitioning (e.g. breeding system, longevity and population size). Important findings For all three species, We found a significant isolation-by-distance relationship but only a moderately high differentiation among populations (Phi(st): 22.7, 48 and 16.8%, for E. fleischeri, G. reptans and C. thyrsoides, respectively). Within-population diversity (H-c: 0.19-0.21, P-p: 62-75%) was not reduced in comparison to known results from lowland species and even small populations with < 50 reproductive individuals contained high levels of genetic diversity. We further found no indication that a high long-distance seed dispersal potential enhances genetic connectivity among populations. Gene flow seems to have a strong stochastic component causing large dissimilarity between population pairs irrespective of the spatial distance. Our results suggest that other life-history traits, especially the breeding System, may play an important role in genetic diversity partitioning. We conclude that spatial isolation in the alpine environment has a strong influence on population relatedness but that a number of factors can considerably influence the strength of this relationship.

Adaptive rather than non-adaptive evolution of Mimulus guttatus in its invasive range

Adaptive and non-adaptive evolutionary processes are likely to play important roles in biological invasions but their relative importance has hardly ever been quantified. Moreover, although genetic differences between populations in their native versus invasive ranges may simply reflect different positions along a genetic latitudinal cline, this has rarely been controlled for. To study non-adaptive evolutionary processes in invasion of Mimulus guttatus, we used allozyme analyses on offspring of seven native populations from western North America, and three and four invasive populations from Scotland and New Zealand, respectively. To study quantitative genetic differentiation, we grew 2474 plants representing 17 native populations and the seven invasive populations in a common greenhouse environment under temporarily and permanently wet soil conditions. The absence of allozyme differentiation between the invasive and native range indicates that multiple genotypes had been introduced to Scotland and New Zealand, and suggests that founder effects and genetic drift played small, if any, roles in shaping genetic structure of invasive M. guttatus populations. Plants from the invasive and native range did not differ in phenology, floral traits and sexual and vegetative reproduction, and also not in plastic responses to the watering treatments. However, plants from the invasive range produced twice as many flower-bearing upright side branches than the ones from the native populations. Further, with increasing latitude of collection, vegetative reproduction of our experimental plants increased while sexual reproduction decreased. Plants from the invasive and native range shared these latitudinal clines. Because allozymes showed that the relatedness between native and invasive populations did not depend on latitude, this suggests that plants in the invasive regions have adapted to the local latitude. Overall, our study indicates that quantitative genetic variation of M. guttatus in its two invasive regions is shaped by adaptive evolutionary processes rather than by non-adaptive ones. (C) 2007 Gesellschaft fur Okologie. Published by Elsevier GmbH. All rights reserved.

Molecular phylogenetic analyses identify Alpine differentiation and dysploid chromosome number changes as major forces for the evolution of the European endemic Phyteuma (Campanulaceae)

Phyteuma is a chromosomally and ecologically diverse vascular plant genus and constitutes an excellent system for studying both the role of chromosomal change for species diversification and the evolution of high-mountain biota. This kind of research is, however, hampered by the lack of a sound phylogenetic framework exacerbated by the notoriously low predictive power of traditional taxonomy with respect to phylogenetic relationships in Campanulaceae. Based on a comprehensive taxon sampling and analyses of nuclear and plastid sequence and AFLP fingerprint data, Phyteuma is confirmed as a monophyletic group sister to the monotypic Physoplexis, which is in line with their peculiar flower morphologies. Within Phyteuma two clades, largely corresponding to previously recognized sections, are consistently found. The traditional circumscription of taxonomic series is largely rejected. Whereas distinctness of the currently recognized species is mostly corroborated, some interspecific relationships remain ambiguous due to incongruences between nuclear and plastid data. Major forces for diversification and evolution of Phyteuma are descending dysploidy (i.e., a decrease in chromosome base number) as well as allopatric and ecological differentiation within the Alps, the genus' center of species diversity. (C) 2013 Elsevier Inc. All rights reserved.

Sexual dimorphism dominates divergent host plant use in stick insect trophic morphology

Background: Clear examples of ecological speciation exist, often involving divergence in trophic morphology. However, substantial variation also exists in how far the ecological speciation process proceeds, potentially linked to the number of ecological axes, traits, or genes subject to divergent selection. In addition, recent studies highlight how differentiation might occur between the sexes, rather than between populations. We examine variation in trophic morphology in two host-plant ecotypes of walking-stick insects (Timema cristinae), known to have diverged in morphological traits related to crypsis and predator avoidance, and to have reached an intermediate point in the ecological speciation process. Here we test how host plant use, sex, and rearing environment affect variation in trophic morphology in this species using traditional multivariate, novel kernel density based and Bayesian morphometric analyses. Results: Contrary to expectations, we find limited host-associated divergence in mandible shape. Instead, the main predictor of shape variation is sex, with secondary roles of population of origin and rearing environment. Conclusion: Our results show that trophic morphology does not strongly contribute to host-adapted ecotype divergence in T. cristinae and that traits can respond to complex selection regimes by diverging along different intraspecific lines, thereby impeding progress toward speciation.

The evolution of host associations in the parasitic wasp genus Ichneumon (Hymenoptera: Ichneumonidae): convergent adaptations to host pupation sites

Background: The diversification of organisms with a parasitic lifestyle is often tightly linked to the evolution of their host associations. If a tight host association exists, closely related species tend to attack closely related hosts; host associations are less stable if associations are determined by more plastic traits like parasitoid searching and oviposition behaviour. The pupal-parasitoids of the genus Ichneumon attack a variety of macrolepidopteran hosts.They are either monophagous or polyphagous, and therefore offer a promissing system to investigate the evolution of host associations. Ichneumon was previously divided into two groups based on general body shape; however, a stout shape has been suggested as an adaptation to buried host pupation sites, and might thus not represent a reliable phylogenetic character. Results: We here reconstruct the first molecular phylogeny of the genus Ichneumon using two mitochondrial (CO1 and NADH1) and one nuclear marker (28S). The resulting phylogeny only supports monophyly of Ichneumon when Ichneumon lugens Gravenhorst, 1829 (formerly in Chasmias, stat. rev.) and Ichneumon deliratorius Linnaeus, 1758 (formerly Coelichneumon) are included. Neither parasitoid species that attack hosts belonging to one family nor those attacking butterflies (Rhopalocera) form monophyletic clades. Ancestral state reconstructions suggest multiple transitions between searching for hosts above versus below ground and between a stout versus elongated body shape. A model assuming correlated evolution between the two characters was preferred over independent evolution of host-searching niche and body shape. Conclusions: Host relations, both in terms of phylogeny and ecology, evolved at a high pace in the genus Ichneumon. Numerous switches between hosts of different lepidopteran families have occurred, a pattern that seems to be the rule among idiobiont parasitoids. A stout body and antennal shape in the parasitoid female is confirmed as an ecological adaptation to host pupation sites below ground and has evolved convergently several times. Morphological characters that might be involved in adaptation to hosts should be avoided as diagnostic characters for phylogeny and classification, as they can be expected to show high levels of homoplasy.

Genetic diversity, phenotypic variation and local adaptation in the alpine landscape: case studies with alpine plant species

Plant survival in alpine landscapes is constantly challenged by the harsh and often unpredictable environmental conditions. Steep environmental gradients and patchy distribution of habitats lead to small size and spatial isolation of populations and restrict gene flow. Agricultural land use has further increased the diversity of habitats below and above the treeline. We studied the consequences of the highly structured alpine landscape for evolutionary processes in four study plants: Epilobium fleischeri, Geum reptans, Campanula thyrsoides and Poa alpina. The main questions were: (1) How is genetic diversity distributed within and among populations and is it affected by altitude, population size or land use? (2) Do reproductive traits such as allocation to sexual or vegetative reproduction vary with altitude or land use? Furthermore, we studied if seed weight increases with altitude. Within-population genetic diversity of the four species was high and mostly not related to altitude and population size. Nevertheless, genetic differentiation among populations was pronounced and strongly increasing with distance. In Poa alpina genetic diversity was affected by land use. Results suggest considerable genetic drift among populations of alpine plants. Reproductive allocation was affected by altitude and land use in Poa alpina and by succession in Geum reptans. Seed weight was usually higher in alpine species than in related lowland species. We conclude that the evolutionary potential to respond to global change is mostly intact in alpine plants, even at high altitude. Phenotypic variability is shaped by adaptive as well as by random evolutionary processes; moreover plastic responses to growth conditions seem to be crucial for survival of plants in the alpine landscape.

Does Land-Use Intensification Decrease Plant Phylogenetic Diversity in Local Grasslands?

Phylogenetic diversity (PD) has been successfully used as a complement to classical measures of biological diversity such as species richness or functional diversity. By considering the phylogenetic history of species, PD broadly summarizes the trait space within a community. This covers amongst others complex physiological or biochemical traits that are often not considered in estimates of functional diversity, but may be important for the understanding of community assembly and the relationship between diversity and ecosystem functions. In this study we analyzed the relationship between PD of plant communities and land-use intensification in 150 local grassland plots in three regions in Germany. Specifically we asked whether PD decreases with land-use intensification and if so, whether the relationship is robust across different regions. Overall, we found that species richness decreased along land-use gradients the results however differed for common and rare species assemblages. PD only weakly decreased with increasing land-use intensity. The strength of the relationship thereby varied among regions and PD metrics used. From our results we suggest that there is no general relationship between PD and land-use intensification probably due to lack of phylogenetic conservatism in land- use sensitive traits. Nevertheless, we suggest that depending on specific regional idiosyncrasies the consideration of PD as a complement to other measures of diversity can be useful.

Seasonal Variation in the Capacity for Plant Trait Measures to Predict Grassland Carbon and Water Fluxes

There is a need for accurate predictions of ecosystem carbon (C) and water fluxes in field conditions. Previous research has shown that ecosystem properties can be predicted from community abundance-weighted means (CWM) of plant functional traits and measures of trait variability within a community (FDvar). The capacity for traits to predict carbon (C) and water fluxes, and the seasonal dependency of these trait-function relationships has not been fully explored. Here we measured daytime C and water fluxes over four seasons in grasslands of a range of successional ages in southern England. In a model selection procedure, we related these fluxes to environmental covariates and plant biomass measures before adding CWM and FDvar plant trait measures that were scaled up from measures of individual plants grown in greenhouse conditions. Models describing fluxes in periods of low biological activity contained few predictors, which were usually abiotic factors. In more biologically active periods, models contained more predictors, including plant trait measures. Field-based plant biomass measures were generally better predictors of fluxes than CWM and FDvar traits. However, when these measures were used in combination traits accounted for additional variation. Where traits were significant predictors their identity often reflected seasonal vegetation dynamics. These results suggest that database derived trait measures can improve the prediction of ecosystem C and water fluxes. Controlled studies and those involving more detailed flux measurements are required to validate and explore these findings, a worthwhile effort given the potential for using simple vegetation measures to help predict landscape-scale fluxes.

Plant diversity effects on the water balance of an experimental grassland

In the literature, contrasting effects of plant species richness on the soil water balance are reported. Our objective was to assess the effects of plant species and functional richness and functional identity on soil water contents and water fluxes in the experimental grassland of the Jena Experiment. The Jena Experiment comprises 86 plots on which plant species richness (0, 1, 2, 4, 8, 16, and 60) and functional group composition (zero to four functional groups: legumes, grasses, tall herbs, and small herbs) were manipulated in a factorial design. We recorded meteorological data and soil water contents of the 0·0–0·3 and 0·3–0·7 m soil layers and calculated actual evapotranspiration (ETa), downward flux (DF), and capillary rise with a soil water balance model for the period 2003–2007. Missing water contents were estimated with a Bayesian hierarchical model. Species richness decreased water contents in subsoil during wet soil conditions. Presence of tall herbs increased soil water contents in topsoil during dry conditions and decreased soil water contents in subsoil during wet conditions. Presence of grasses generally decreased water contents in topsoil, particularly during dry phases; increased ETa and decreased DF from topsoil; and decreased ETa from subsoil. Presence of legumes, in contrast, decreased ETa and increased DF from topsoil and increased ETa from subsoil. Species richness probably resulted in complementary water use. Specific functional groups likely affected the water balance via specific root traits (e.g. shallow dense roots of grasses and deep taproots of tall herbs) or specific shading intensity caused by functional group effects on vegetation cover. Copyright © 2013 John Wiley & Sons, Ltd.

Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories

Biodiversity, a multidimensional property of natural systems, is difficult to quantify partly because of the multitude of indices proposed for this purpose. Indices aim to describe general properties of communities that allow us to compare different regions, taxa, and trophic levels. Therefore, they are of fundamental importance for environmental monitoring and conservation, although there is no consensus about which indices are more appropriate and informative. We tested several common diversity indices in a range of simple to complex statistical analyses in order to determine whether some were better suited for certain analyses than others. We used data collected around the focal plant Plantago lanceolata on 60 temperate grassland plots embedded in an agricultural landscape to explore relationships between the common diversity indices of species richness (S), Shannon's diversity (H'), Simpson's diversity (D-1), Simpson's dominance (D-2), Simpson's evenness (E), and Berger-Parker dominance (BP). We calculated each of these indices for herbaceous plants, arbuscular mycorrhizal fungi, aboveground arthropods, belowground insect larvae, and P.lanceolata molecular and chemical diversity. Including these trait-based measures of diversity allowed us to test whether or not they behaved similarly to the better studied species diversity. We used path analysis to determine whether compound indices detected more relationships between diversities of different organisms and traits than more basic indices. In the path models, more paths were significant when using H', even though all models except that with E were equally reliable. This demonstrates that while common diversity indices may appear interchangeable in simple analyses, when considering complex interactions, the choice of index can profoundly alter the interpretation of results. Data mining in order to identify the index producing the most significant results should be avoided, but simultaneously considering analyses using multiple indices can provide greater insight into the interactions in a system.