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The genomes of the livebearing fish species Poeciliopsis retropinna and Poeciliopsis turrubarensis reflect their different reproductive strategies
No full textThe evolution of a placenta is predicted to be accompanied by rapid evolution of genes involved in processes that regulate mother–offspring interactions during pregnancy, such as placenta formation, embryonic development, and nutrient transfer to offspring. However, these predictions have only been tested in mammalian species, where only a single instance of placenta evolution has occurred. In this light, the genus Poeciliopsis is a particularly interesting model for placenta evolution, because in this genus a placenta has evolved independently from the mammalian placenta. Here, we present and compare genome assemblies of two species of the livebearing fish genus Poeciliopsis (family Poeciliidae) that differ in their reproductive strategy: Poeciliopsis retropinna which has a well-developed complex placenta and P. turrubarensis which lacks a placenta. We applied different assembly strategies for each species: PacBio sequencing for P. retropinna (622-Mb assembly, scaffold N50 of 21.6 Mb) and 10 Genomics Chromium technology for P. turrubarensis (597-Mb assembly, scaffold N50 of 4.2 Mb). Using the high contiguity of these genome assemblies and near-completeness of gene annotations to our advantage, we searched for gene duplications and performed a genome-wide scan for genes evolving under positive selection.We find rapid evolution inmajor parts of severalmolecular pathways involved in parent–offspring interaction in P. retropinna, both in the form of gene duplications as well as positive selection. We conclude that the evolution of the placenta in the genus Poeciliopsis is accompanied by rapid evolution of genes involved in similar genomic pathways as found in mammals
The Impact of Non-additive Effects on the Genetic Correlation Between Populations
No full textAverage effects of alleles can show considerable differences between populations. The magnitude of these differences can be measured by the additive genetic correlation between populations ([Formula: see text]). This [Formula: see text] can be lower than one due to the presence of non-additive genetic effects together with differences in allele frequencies between populations. However, the relationship between the nature of non-additive effects, differences in allele frequencies, and the value of [Formula: see text] remains unclear, and was therefore the focus of this study. We simulated genotype data of two populations that have diverged under drift only, or under drift and selection, and we simulated traits where the genetic model and magnitude of non-additive effects were varied. Results showed that larger differences in allele frequencies and larger non-additive effects resulted in lower values of [Formula: see text] In addition, we found that with epistasis, [Formula: see text] decreases with an increase of the number of interactions per locus. For both dominance and epistasis, we found that, when non-additive effects became extremely large, [Formula: see text] had a lower bound that was determined by the type of inter-allelic interaction, and the difference in allele frequencies between populations. Given that dominance variance is usually small, our results show that it is unlikely that true [Formula: see text] values lower than 0.80 are due to dominance effects alone. With realistic levels of epistasis, [Formula: see text] dropped as low as 0.45. These results may contribute to the understanding of differences in genetic expression of complex traits between populations, and may help in explaining the inefficiency of genomic trait prediction across populations
Effect of non‐migrating bars on dune dynamics in a lowland river
No full textAs dunes and larger scale bed forms such as bars coexist in rivers, the question arises whether dune dynamics are influenced by interaction with the underlying bed topography. The present study aims to establish the degree in which dune characteristics in two and three dimensions are influenced by an underlying topography dominated by non‐migrating bars. As a case study, a 20km stretch in the Waal River in the Netherlands is selected, which represents a sand‐bed lowland river. At this location, longitudinal training dams (LTDs) have recently been constructed to ensure sufficient navigation depth during periods with low water levels, and to reduce flood risk. By using data covering two‐year‐long periods before and after LTD construction, the robustness of the results is investigated. Before LTD construction, dune characteristics show large variability both spatially and temporally, with dunes being longer, lower, less steep and having a lower lee side angle when they are located on bar tops. The correlation between dune characteristics and the underlying bed topography is disrupted by unsteady conditions for which the dunes are in a state of transition. The bar pattern causes tilting of dune crest lines, which may result from a transverse gradient in bed load sediment transport. As a result of LTD construction, the hydraulic and morphological conditions have changed significantly. Despite this, the main conclusions still hold, which strengthens the validity of the results
Statistical modeling of phenotypic, pedigree and genomic information for improved genetic evaluation in modern plant breeding: a case study with sorghum
No full textThe increasing global food demand in the context of climate change is a major concern of the 21st century. Developing crop varieties with improved adaptability to variable environmental conditions might be crucial to ensure food supply. Sorghum [Sorghum bicolor (L.) Moench] is a staple cereal crop in semi-arid regions of the world and is also grown worldwide as feed and bioenergy crop. Its drought-tolerance ability makes it a strategic crop for sustainable grain production. Modern approaches to quantitative genetics and statistical models such as genomic-assisted breeding techniques offer new opportunities for further improvements in crop productivity and adaptability. Compared to other major cereal crops such as maize and wheat, the application of these approaches remains largely unexplored for grain sorghum. The motivation of this thesis is to implement statistical models that exploit information from phenotypic, pedigree and genomic data for improving genetic evaluation and selection in sorghum breeding. Chapter 2 assessed the performance of a novel method for spatial analysis of plant breeding field experiments based on two-dimensional smoothing with P-splines. This method was evaluated in comparison with the conventional spatial models by considering the improvement in precision and predictions of genetic effects in early generation sorghum breeding trials. The Chapter shows that both spatial methods produced equivalent performance. Differences in model parameterization as well as the advantages of the new spatial approach for routine application are discussed. In Chapter 3, the impact of using pedigree and genomic information on prediction quality was explored for different traits in sorghum. For this, the Chapter proposes to use BLUP models fitting weighted combinations of pedigree and genomic relationship matrices, where the best-predictive combination is identified empirically in each prediction scenario. Results showed that the use of a merged pedigree–genomic matrix always improved predictive ability and unbiasedness of prediction relative to conventional G-BLUP, mainly for the traits with lower heritabilities. Based on these outcomes, the inclusion of pedigree information in genomic models is recommended to optimize predictions when the additive variation is not fully explained by markers. Chapter 4 presents an extension of the study in Chapter 3 to the context of multi-trait genomic prediction. Specifically, we assessed the capacity of multi-trait models to improve genomic prediction for grain yield and stay-green in sorghum by using information from correlated auxiliary traits. In general, results showed that genomic prediction for both target traits can be enhanced by combining information from specific sets of traits. Predictions from conventional multi-trait G-BLUP were also optimized by combining pedigree and genomic information. Chapter 5 investigated the effect of modelling genotype-by-environment interaction (G×E) on genomic prediction for grain yield in drought-stress and non-stress environments. Results indicated that accommodating G×E in genomic models was beneficial to improve the quality of prediction for specific adaptation as well as for broad adaptation to both types of environments. This Chapter also tested if better genomic predictions can be obtained by accounting for heterogeneous variances of marker effects. We found that weighting individual markers based on estimated locus-specific variances produced important improvements in predictive performance of genomic models, even for a largely polygenic trait such as grain yield. To conclude, this thesis deals with different challenging aspects that may affect genetic evaluation in modern sorghum breeding. Specifically, several statistical modeling strategies making use of different sources of information have been proposed and assessed. The findings presented in this thesis are expected to contribute to increase the efficiency of selection schemes not only for sorghum but for crops in general
Land tenure security, migration and farm performance in rural China
No full textLand tenure security and migration play vital roles in rural development and livelihood security of rural households. Farm performance benefits not only a nation’s food security, but also sustainable agricultural development. However, a full picture of the linkages is lacking. Hence, the overall objective of this thesis is to conduct a joint analysis of land tenure, migration and farm performance in China. Based on the household and village data collected from four regions in China, the following main conclusions could be drawn. Village democracy and households’ knowledge of policy have a positive impact on migration through encouraging land reallocations in villages where land rental market is less developed. Actual land tenure security has a positive impact on migration through perceived land tenure security, but a negative impact on migration through other channels in villages where the land rental market is less-developed. Through influencing households’ migration decisions, actual land tenure security has a positive impact on farm performance, while perceived land tenure security has a negative impact on farm performance, given the level of actual land tenure security
Assessing countrywide soil organic carbon stock using hybrid machine learning modelling and legacy soil data in Cameroon
No full textCountrywide estimates of soil organic carbon stock (SOCS) are useful to set up national strategies for sustainable land use management as well as to enhance the accuracy of global SOCS inventories. We appraised the spatial distribution of SOCS at five depth layers (0–15 cm, 15–30 cm, 30–100 cm, 0–30 cm and 0–100 cm) in Cameroon at 100 m spatial resolution, using a national harmonized legacy soil database (Camsodat 0.1) with 1432 georeferenced soil profiles. We assessed the prediction performances of random forest (RF) and generalized boosted regression (GBR), combined with two hybridization approaches of spatial interpolation of the residuals using ordinary kriging (OK) and inverse distance weighting (IDW). The estimates were compared to two global estimates derived from the Harmonized World Soil Database (HWSD) and SoilGrids250m. The SOCS distribution across the country showed a moderate spatial heterogeneity at all depth layers with coefficients of variation between 35% and 47%, and values ranging from 6 to 108 Mg C ha−1 at 0–15 cm, from 4 to 107 Mg C ha−1 at 15–30 cm, from 10 to 276 Mg C ha−1 at 30–100 cm, from 11 to 210 Mg C ha−1 at 0–30 cm and from 21 to 468 Mg C ha−1 at the 0–100 cm layer. Of the selected environmental covariates, terrain and climate attributes were the most relevant to predict the SOCS spatial distribution at country level. The RF model outperformed the GBR model, with about 10% improvement on prediction performance (R2) for most soil depths. The hybridization further slightly improved performance. However, OK was only slightly better than IDW in the overall assessment. Compared to national estimates, SoilGrids overestimated the SOCS by 15% at 0–30 cm depth, while HWSD underestimated SOCS by 26% at the same depth. Overall, about 5.7 Pg C are stored in the top 1 m of soils in Cameroon, with about 50% of that in the top 30 cm. The national distribution of SOCS is consistent with the pattern of agro-ecological zones. Our assessment provides baseline information for sustainable land management and climate change mitigation, as well as for improving the understanding of the spatial distribution of SOCS in Cameroon.</p
Sediment toxicity of the fungicide fludioxonil to benthic macroinvertebrates -evaluation of the tiered effect assessment procedure
No full text28-Day sediment-spiked laboratory toxicity tests with eight benthic macroinvertebrates and the lipophilic fungicide fludioxonil were conducted to verify the proposed tiered sediment effect assessment procedure as recommended by the European Food Safety Authority (EFSA). The test species were the oligochaetes Lumbriculus variegatus and Tubifex tubifex, the insects Chironomus riparius and Caenis horaria, the crustaceans Hyalella azteca and Asellus aquaticus and the bivalves Corbicula fluminalis and Pisidium amnicum. Toxicity estimates were expressed in terms of total concentration of dry sediment as well as in pore water concentration. Field-collected sediment, also used in a previously performed sediment-spiked microcosm experiment, was used in tests with all species. L. variegatus and C. riparius had similar lowest 28d-L(E)C10 values when expressed in terms of total sediment concentration, but in terms of pore water concentration L. variegatus was more sensitive. Three of the six additional benthic test species (A. aquaticus, C. horaria, C. fluminalis) had 28d-EC10 values a factor of 2–6 lower than that of L. variegatus. Comparing different effect assessment tiers for sediment organisms, i.e. Tier-0 (Modified Equilibrium Partitioning approach), Tier-1 (Standard Test Species approach), Tier-2 (Species Sensitivity Distribution (SSD) approach) and Tier-3 (Model Ecosystem approach), it is concluded that the tiers based on sediment-spiked laboratory toxicity tests provide sufficient protection when compared with the Tier-3 Regulatory Acceptable Concentration (RAC). Differences between Tier-1 and Tier-2 RACs, however, appear to be relatively small and not always consistent, irrespective of expressing the RAC in terms of total sediment or pore water concentration. Derivation of RACs by means of the SSD approach may be a challenge, because it is difficult obtaining a sufficient number of valid chronic EC10 values with appropriate 95% confidence bands for sediment-dwelling macroinvertebrates. Therefore, this paper proposes a Tier-2 Weight-of-Evidence approach to be used in case an insufficient number of valid additional toxicity data is made available. Similar studies with pesticides that differ in fate properties and toxic mode-of-action are necessary for further validation of the tiered effect assessment approach for sediment organisms.</p
Beaver effects on macroinvertebrate assemblages in two streams with contrasting morphology
No full textBeaver populations are increasing throughout Europe and especially in Switzerland. Beaver are major ecological engineers of fluvial systems, dramatically influencing river morphology, ecohydrology and, consequently, aquatic and terrestrial biota. This study compared macroinvertebrate assemblages and trophic structure at two beaver complexes with contrasting topography in Switzerland over an annual cycle. One complex (Marthalen) was in a low gradient open basin, whereas the other complex (Flaach) flowed through a higher gradient ravine-like basin. Both complexes were embedded in an overall agricultural landscape matrix. Water physico-chemistry differed between the two complexes with nitrogen, phosphorus, and DOC being higher at Marthalen than at Flaach. Both complexes showed strong seasonality in physico-chemistry, but retention of nutrients (N, P) was highest in summer and only at Marthalen. Both complexes also showed strong seasonality in macroinvertebrate assemblages, although assemblages differed substantially between complexes. At Marthalen, macroinvertebrate assemblages were predominantly lentic in character at ‘pool’ sites within the complex. At Flaach, lotic macroinvertebrate assemblages were common at most sites with some lentic taxa also being present. Dietary shifts based on carbon/nitrogen stable isotopes occurred in spring and summer among sites at both complexes (autochthonous resource use increasing over allochthonous resource use downstream), although being most pronounced at Marthalen. In contrast, similar resource use across sites occurred in winter within both complexes. Although beaver significantly influenced fluvial dynamics and macroinvertebrate assemblage structure at both complexes, this influence was most pronounced at Marthalen where beaver caused the system to become more wetland in character, e.g., via higher hydraulic residence time, than at Flaach. We conclude that topography can shape beaver effects on fluvial systems and resident biota.</p
Predation risk shapes the degree of placentation in natural populations of live-bearing fish
No full textThe placenta is a complex life-history trait that is ubiquitous across the tree of life. Theory proposes that the placenta evolves in response to high performance-demanding conditions by shifting maternal investment from pre- to post-fertilisation, thereby reducing a female’s reproductive burden during pregnancy. We test this hypothesis by studying populations of the fish species Poeciliopsis retropinna in Costa Rica. We found substantial variation in the degree of placentation among natural populations associated with predation risk: females from high predation populations had significantly higher degrees of placentation compared to low predation females, while number, size and quality of offspring at birth remained unaffected. Moreover, a higher degree of placentation correlated with a lower reproductive burden and hence likely an improved swimming performance during pregnancy. Our study advances an adaptive explanation for why the placenta evolves by arguing that an increased degree of placentation offers a selective advantage in high predation environments.</p
Integrated Pest Management Methods and Considerations Concerning Implementation in Greenhouses
No full textWe consider IPM as a combination of durable, environmentally, toxicologically and economically justifiable farming practices which prevent pest damage primarily through the use of natural factors limiting pest population growth and disease development, and which resort only if needed to other, preferably non-chemical, measures. IPM is not simply a combination of various control methods. We give an overview of IPM measures used in greenhouses and refer to specific chapters in this book for examples. In IPM, each practical situation dictates a number of special aspects for consideration, and IPM methods need continuous adaptation, making IPM knowledge intensive and interactive. Successful IPM programmes for greenhouse crops have a number of characteristics in common: (a) their use was promoted only after a complete IPM programme had been developed, (b) intensive support by the extension service was essential during initial implementation, (c) the costs of crop protection with IPM should not be higher than those of a chemical control programme, and (d) non-chemical management methods, such as biocontrol agents and resistant plant material, should be as easily available, as reliable, and as constant in quality, as chemical agents. IPM research and implementation in greenhouses during the past 50 years has taught us the lesson that the development of an IPM programme needs to be discussed in a very early stage with all stakeholders, including growers, pest management specialists, extension services and researchers. Such a meeting often results in a pragmatic design of a draft, very pragmatic IPM programme, which is continuously adapted during later meetings, based on growers’ experience and new research results