Reliable confidence intervals in quantitative genetics: narrow-sense heritability

Many quantitative genetic statistics are functions of variance components, for which a large number of replicates is needed for precise estimates and reliable measures of uncertainty, on which sound interpretation depends. Moreover, in large experiments the deaths of some individuals can occur, so methods for analysing such data need to be robust to missing values. We show how confidence intervals for narrow-sense heritability can be calculated in a nested full-sib/half-sib breeding design (males crossed with several females) in the presence of missing values. Simulations indicate that the method provides accurate results, and that estimator uncertainty is lowest for sampling designs with many males relative to the number of females per male, and with more females per male than progenies per female. Missing data generally had little influence on estimator accuracy, thus suggesting that the overall number of observations should be increased even if this results in unbalanced data. We also suggest the use of parametrically simulated data for prior investigation of the accuracy of planned experiments. Together with the proposed confidence intervals an informed decision on the optimal sampling design is possible, which allows efficient allocation of resource

PestiRed: A Swiss on-farm approach to reduce pesticide use in arable crops

Das Konzept des integrierten Pflanzenschutzes (IPM) hat sich erfolgreich bewährt. Allerdings ist es immer noch eine Herausforderung IPM Strategien erfolgreich umzusetzen. Darüber hinaus fehlen umfassende Untersuchungen zu Effekten und Wechselwirkungen kombinierter Verfahren im Verlauf gesamter Fruchtfolgen. Im Rahmen der Bemühungen den Einsatz von Pflanzenschutzmitteln (PSM) in der Schweizer Landwirtschaft zu reduzieren, wird der integrierte Pflanzenschutz im Ackerbau in einem mehrjährigen on-farm Projekt weiterentwickelt. Projektbeginn ist Herbst 2019. Ziel ist es, den PSM Einsatz um 75 % zu reduzieren, bei einem maximalen Ertragsverlust von 10 %. Es werden vorbeugende und alternative Maßnahmen umgesetzt, die vor allem natürliche Regulationsmechanismen von Schadorganismen (Pathogene, Schädlinge, Unkräuter) ausnutzen. Maßnahmen wie Zwischenfrüchte, Mischkulturen, Blühstreifen und biologische Bekämpfungsmittel werden in unterschiedlichen 6-jährigen Fruchtfolgen in einem Netzwerk von 75 landwirtschaftlichen Betrieben untersucht und umgesetzt. Es handelt sich um einen co-innovativen Ansatz, an dem Wissenschaftler, Landwirte und landwirtschaftliche Beratungsdienste in unterschiedlichen Regionen der Schweiz beteiligt sind. Die Wirksamkeit der Methoden auf Unkräuter, Krankheiten, Schädlinge und Nützlinge wird über alle Fruchtfolgen beobachtet und beurteilt.The concept of integrated pest management (IPM) has proven successful, however challenges in implementing IPM strategies remain. Furthermore, detailed investigations are needed to elucidate the performance and trade-offs of combined practices along entire crop rotations. In the framework of efforts to reduce the use of pesticides in Swiss agriculture, IPM in arable crops will be further developed in an on-farm project starting in autumn 2019. The overall aim of the project is to reduce pesticide use by 75% with a maximum yield loss of 10%. Preventive and alternative practices supporting natural control of noxious organisms (pathogens, pests, weeds) such as cover crops, intercropping, flower strips and biological control agents will be implemented and investigated in different 6-year crop rotations in a network involving 75 farms. The project involves scientists, farmers and extension services in a co-innovation process in five regions of the Swiss plateau. Effectiveness of the practices on weeds, diseases, pests and beneficials will be closely monitored and evaluated along the entire crop rotation

Mit kleinen Flächen die Produktion verbessern

Der Streifenanbau ist eine Umstellung der Bewirtschaftung von ganzen Schlägen auf Streifen mit einer wählbaren Vielfachen der gängigen Arbeitsbreiten. Im Gemüsebau ist dies schon lange bekannt. Im Ackerbau ist diese Bewirtschaftung vergleichsweise neu, mittlerweile durch die präzise Wiederfindung der Streifen mit dem GPS auf dem Traktor aber machbar

Predicting adaptive evolution under elevated atmospheric CO₂ in the perennial grass <i>Bromus erectus</i>

Increasing concentrations of CO₂ in the atmosphere are likely to affect the ecological dynamics of plant populations and communities worldwide, yet little is known about potential evolutionary consequences of high CO₂. We employed a quantitative genetic framework to examine how the expression of genetic variation and covariation in fitness-related traits, and thus, the evolutionary potential of a species, is influenced by CO₂. In two field experiments, genotypes of the dominant grassland perennial Bromus erectus were grown for several years in plots maintained at present-day or at elevated CO₂ levels. Under noncompetitive conditions (experiment 1), elevated CO₂ had little impact on plant survival, growth, and reproduction. Under competitive conditions in plots with diverse plant communities (experiment 2), performance of B. erectus was reduced by elevated CO₂. This suggests that the effect of CO₂ was largely indirect, intensifying competitive interactions. Elevated CO₂ had significant effects on the expression of genetic variation in both the competitive and noncompetitive environment, but the effects were in opposite direction. Heritability of plant size was generally higher at elevated than at ambient CO₂ in the noncompetitive environment, but lower in the competitive environment. Selection analysis revealed a positive genotypic selection differential for plant size at ambient CO₂, indicating selection favoring genotypes with high growth rate. At elevated CO₂, the corresponding selection differential was nonsignificant and slightly negative. This suggests that elevated CO₂ is unlikely to stimulate the evolution of high biomass productivity in this species

Reliable confidence intervals in quantitative genetics: narrow-sense heritability

Many quantitative genetic statistics are functions of variance components, for which a large number of replicates is needed for precise estimates and reliable measures of uncertainty, on which sound interpretation depends. Moreover, in large experiments the deaths of some individuals can occur, so methods for analysing such data need to be robust to missing values. We show how confidence intervals for narrow-sense heritability can be calculated in a nested full-sib/half-sib breeding design (males crossed with several females) in the presence of missing values. Simulations indicate that the method provides accurate results, and that estimator uncertainty is lowest for sampling designs with many males relative to the number of females per male, and with more females per male than progenies per female. Missing data generally had little influence on estimator accuracy, thus suggesting that the overall number of observations should be increased even if this results in unbalanced data. We also suggest the use of parametrically simulated data for prior investigation of the accuracy of planned experiments. Together with the proposed confidence intervals an informed decision on the optimal sampling design is possible, which allows efficient allocation of resources

Evolution in invasive plants: implications for biological control

Evidence is increasing that invasive plants can undergo rapid adaptive evolution during the process of range expansion. Here, we argue that evolutionary change during invasions will also affect plant–antagonist inter-actions and, thus, will have important implications for biological control programmes targeted at invasive plants. We explore how altered selection in the new range might influence the evolution of plant defence (resistance and tolerance) and life history. The degree to which such evolutionary processes might affect biological control efficacy is largely unexplored. We hope that, by testing the hypotheses that we propose here, a closer link can be established between biological control and evolutionary biology, to the benefit of both disciplines

Seed provenance matters — Effects on germination of four plant species used for ecological restoration

The use of local seed provenances is often recommended in restoration and habitat creation because they are thought to be better adapted to local habitat conditions. However, spatial scales and the degree of population differentiation are not well known and germination is often not included in comparisons between provenances. We analysed germination as a key trait of plant development in five provenances of four species used for ecological restoration on arable land (wildflower strips). Germination was tested under different conditions in growth chambers (early vs. late spring) and in the field (non-competition vs. competition). We also examined the contribution of non-genetic (maternal) effects to population differentiation.Large differences in germination traits were found between the provenances in growth chambers and in the field. The ranking was species-specific, but largely consistent across all tested environments. Local provenances did not generally exhibit higher germination percentages in the field relative to non-local provenances. Due to the high stability of germination traits across various environments, growth chamber tests provided a reliable prediction for provenance differences in the field. The differences among provenances seemed to be largely genetically determined as the inclusion of seed mass in the analysis to control for maternal effects did not decrease the degree differences between-provenance differences. In one species, however, non-genetic contributions to population differentiation were found by comparing F1 seeds grown under homogeneous conditions and original seed material. We conclude that potentially large between-provenance differences in germination traits need to be considered in ecological restoration projects, particularly in non-permanent systems where they may determine vegetation development

Testing the Evolution of Increased Competitive Ability (EICA) hypothesis in a novel framework

The “evolution of increased competitive ability” (EICA) hypothesis proposes that escape from natural enemies, e.g., after transcontinental introductions, alters the selection regime because costly defenses no longer enhance fitness. Such an evolutionary loss of defenses enables resources to be directed toward growth or other traits improving performance. We tested the EICA hypothesis in a novel framework in which the natural enemy is the traveler that follows its widespread host by accidental or deliberate (biocontrol) introductions. In a greenhouse experiment we used populations of Senecio vulgaris from North America, Europe, and Australia that differ in the history of exposure to the rust fungus Puccinia lagenophorae. Contrary to what is predicted by EICA, we found no evidence for increased levels of resistance to the rust fungus in plant populations with a longer history of rust exposure (Australia). Similarly, there was no evidence for reduced fecundity in these populations, although vegetative vigor, measured as secondary branching and growth rate, was lower. The maintenance of high rust resistance in populations with no (North America) or only a short history (Europe) of rust exposure is surprising given that resistance seems to incur considerable fitness costs, as indicated by the negative association between family mean resistance and fitness in the absence of disease observed for all three continents. The comparison of population differentiation in quantitative traits with estimates of differentiation in amplified fragment length polymorphic (AFLP) markers suggests that a number of fitness-related traits are under divergent selection among the studied populations. The proposed framework to test changes in the evolutionary trajectory underlying EICA can be employed in an expanded range of systems. These may include investigations on a cosmopolitan weed or crop when an antagonist is expanding its geographic range (such as our study), studies along a chronosequence of introduction time with expected increasing accumulation of natural enemies over time, or comparisons between introduced plant populations that differ in exposure time to biocontrol organisms