Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Ghost Introgression: Spooky Gene Flow in the Distant Past
    Ottenburghs, Jente - \ 2020
    Bioessays 42 (2020)6. - ISSN 0265-9247
    adaptation - demographic modelling - hybridization - macroevolution - phylogenetic networks - reproductive isolation - speciation

    Evolution is a continuous trial and error process in which most lineages go extinct without leaving fossil remains. Many of these lineages would be closely related and occasionally hybridized with lineages that gave rise to extant species. Hence, it is likely that one can find genetic signatures of these ancient introgression events in present-day genomes, so-called ghost introgression. The increasing availability of high-quality genome assemblies for non-model organisms and the development of more sophisticated methods for detecting introgression will undoubtedly reveal more cases of ghost introgression, indicating that the Tree of Life is even more reticulated than assumed. The presence of ghost introgression has important consequences for the study of numerous evolutionary processes, including adaptation, speciation, and macroevolutionary patterns. In addition, detailed studies of introgressed regions could provide insights into the morphology of the extinct lineage, providing an unexpected link between genomics and the fossil record. Hence, new methods that take into account ghost introgression will need to be developed.

    Limited mass-independent individual variation in resting metabolic rate in a wild population of snow voles (Chionomys nivalis)
    Hagmayer, Andres ; Camenisch, Glauco ; Canale, Cindy ; Postma, Erik ; Bonnet, Timothée - \ 2020
    Journal of Evolutionary Biology 33 (2020)5. - ISSN 1010-061X - p. 608 - 618.
    adaptation - constraints - measurement error - metabolism - mixed model - repeatability - rodent

    Resting metabolic rate (RMR) is a potentially important axis of physiological adaptation to the thermal environment. However, our understanding of the causes and consequences of individual variation in RMR in the wild is hampered by a lack of data, as well as analytical challenges. RMR measurements in the wild are generally characterized by large measurement errors and a strong dependency on mass. The latter is problematic when assessing the ability of RMR to evolve independently of mass. Mixed models provide a powerful and flexible tool to tackle these challenges, but they have rarely been used to estimate repeatability of mass-independent RMR from field data. We used respirometry to obtain repeated measurements of RMR in a long-term study population of snow voles (Chionomys nivalis) inhabiting an environment subject to large circadian and seasonal fluctuations in temperature. Using both uni- and bivariate mixed models, we quantify individual repeatability in RMR and decompose repeatability into mass-dependent and mass-independent components, while accounting for measurement error. RMR varies among individuals, that is, is repeatable (R =.46) and strongly co-varies with BM. Indeed, much of the repeatability of RMR is attributable to individual variation in BM, and the repeatability of mass-independent RMR is reduced by 41% to R =.27. These empirical results suggest that the evolutionary potential of RMR independent of mass may be severely constrained. This study illustrates how to leverage bivariate mixed models to model field data for metabolic traits, correct for measurement error and decompose the relative importance of mass-dependent and mass-independent physiological variation.

    From QTLs to Adaptation Landscapes: Using Genotype-To-Phenotype Models to Characterize G×E Over Time
    Bustos-Korts, Daniela ; Malosetti, Marcos ; Chenu, Karine ; Chapman, Scott ; Boer, Martin P. ; Zheng, Bangyou ; Eeuwijk, Fred A. van - \ 2019
    Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
    adaptation - APSIM model - crop growth model - G×E interaction - QTL (quantitative trait loci) - reaction norm - wheat

    Genotype by environment interaction (G×E) for the target trait, e.g. yield, is an emerging property of agricultural systems and results from the interplay between a hierarchy of secondary traits involving the capture and allocation of environmental resources during the growing season. This hierarchy of secondary traits ranges from basic traits that correspond to response mechanisms/sensitivities, to intermediate traits that integrate a larger number of processes over time and therefore show a larger amount of G×E. Traits underlying yield differ in their contribution to adaptation across environmental conditions and have different levels of G×E. Here, we provide a framework to study the performance of genotype to phenotype (G2P) modeling approaches. We generate and analyze response surfaces, or adaptation landscapes, for yield and yield related traits, emphasizing the organization of the traits in a hierarchy and their development and interactions over time. We use the crop growth model APSIM-wheat with genotype-dependent parameters as a tool to simulate non-linear trait responses over time with complex trait dependencies and apply it to wheat crops in Australia. For biological realism, APSIM parameters were given a genetic basis of 300 QTLs sampled from a gamma distribution whose shape and rate parameters were estimated from real wheat data. In the simulations, the hierarchical organization of the traits and their interactions over time cause G×E for yield even when underlying traits do not show G×E. Insight into how G×E arises during growth and development helps to improve the accuracy of phenotype predictions within and across environments and to optimize trial networks. We produced a tangible simulated adaptation landscape for yield that we first investigated for its biological credibility by statistical models for G×E that incorporate genotypic and environmental covariables. Subsequently, the simulated trait data were used to evaluate statistical genotype-to-phenotype models for multiple traits and environments and to characterize relationships between traits over time and across environments, as a way to identify traits that could be useful to select for specific adaptation. Designed appropriately, these types of simulated landscapes might also serve as a basis to train other, more deep learning methodologies in order to transfer such network models to real-world situations.

    Pigs Ferment Enzymatically Digestible Starch when it Is Substituted for Resistant Starch
    Erp, Rik J.J. van; Vries, Sonja de; Kempen, Theo A.T.G. van; Gerrits, Walter J.J. - \ 2019
    The Journal of Nutrition 149 (2019)8. - ISSN 0022-3166 - p. 1346 - 1353.
    adaptation - feed intake - feeding behavior - nutrient digestibility - resistant starch

    BACKGROUND: Feeding behavior is controlled by satiety mechanisms, which are affected by the extent of starch digestion, and thus resistant starch (RS) intake. Alterations in feeding behavior to changes in RS intake may depend on the adaptation of processes involved when shifting from starch digestion to fermentation or vice versa. OBJECTIVES: The aim of this study was to investigate how growing pigs adapt their feeding behavior in response to increasing and decreasing dietary RS concentrations. METHODS: Thirty-six groups of 6 pigs (25.4 ± 2.8 kg; Hypor Libra × Hypor Maxter; male:female, 1:1) were fed diets containing 50% high-amylose maize starch (high RS; HRS) or waxy maize starch (low RS; LRS). Over 28 d, diets were exchanged following a 5-step titration (25% per step) that was executed in the upward (LH) or downward direction (HL). Twelve groups received a control diet to correct for changes over time. Individual feeding behavior and total tract starch digestion and fermentation were evaluated. The response in each parameter to increasing dietary HRS inclusion was estimated through the use of linear regression procedures, and tested for titration direction and sex effects. RESULTS: Complete substitution of LRS with HRS increased the proportion of starch fermented, which was greater in LH pigs than in HL pigs (17.6% compared with 8.18%; P < 0.001), and decreased the feed intake (106 g/d; P = 0.021) and meal size (12.6 g; P < 0.001) of LH pigs, but not of HL pigs. In LH pigs, the size of the starch fermentation response positively correlated with the size of the feed intake response (r = 0.90, P < 0.001). CONCLUSIONS: The attenuated response in starch fermentation in HL pigs indicates that pigs adapt more slowly to dietary supply of digestible starch than to RS, consequently resulting in fermentation of enzymatically digestible starch. Feed intake and feeding behavior only changed in pigs poorly adapting to RS, indicating that adequacy of adaptation, rather than RS itself, drives feed intake. These findings stress the importance of diet history for nutrient digestion and feeding behavior.

    Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley
    Bustos-Korts, Daniela ; Dawson, Ian K. ; Russell, Joanne ; Tondelli, Alessandro ; Guerra, Davide ; Ferrandi, Chiara ; Strozzi, Francesco ; Nicolazzi, Ezequiel L. ; Molnar-Lang, Marta ; Ozkan, Hakan ; Megyeri, Maria ; Miko, Peter ; Çakır, Esra ; Yakışır, Enes ; Trabanco, Noemi ; Delbono, Stefano ; Kyriakidis, Stylianos ; Booth, Allan ; Cammarano, Davide ; Mascher, Martin ; Werner, Peter ; Cattivelli, Luigi ; Rossini, Laura ; Stein, Nils ; Kilian, Benjamin ; Waugh, Robbie ; Eeuwijk, Fred A. van - \ 2019
    The Plant Journal 99 (2019)6. - ISSN 0960-7412 - p. 1172 - 1191.
    adaptation - barley - common garden trials - exome sequence haplotypes - genetic diversity - genotype-by-environment interactions - H. vulgare ssp. vulgare

    Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi-environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype-by-environment (G×E) modelling. Sub-populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock-related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large-effect alleles. Our analysis supports a gene-level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses.

    Costs and benefits of climate change in Switzerland
    Vöhringer, Frank ; Vielle, Marc ; Thalmann, Philippe ; Frehner, Anita ; Knoke, Wolfgang ; Stocker, Dario ; Thurm, Boris - \ 2019
    Climate Change Economics 10 (2019)2. - ISSN 2010-0078
    adaptation - Climate change impacts - computable general equilibrium model - Switzerland

    Understanding the economic magnitude of climate change (CC) impacts is a prerequisite for developing adequate adaptation strategies. In Switzerland, despite new climate scenarios and impact studies, only few impacts have been monetized. Our objective is to assess costs and opportunities of CC for Switzerland by 2060, while enhancing the assessment methods. Using inputs from bottom-up impact studies, we simulate the economic consequences of climate scenarios in a computable general equilibrium (CGE) framework. We cover health, buildings/infrastructure, energy, water, agriculture, tourism, the spill-overs to other sectors, and international effects. Due to data constraints, significant impacts have not been quantified, e.g., for heat waves and droughts more extreme than the 2060 average climate. For the considered impacts, welfare decreases by 0.37% to 1.37% in 2060 relative to a reference without CC. Higher summer temperatures increase mortality and decrease productivity. Contrariwise, tourism benefits from extended summer seasons. Regarding energy, increased demand for cooling is overcompensated by savings in heating.

    Bioinformatic evidence of widespread priming in type I and II CRISPR-Cas systems
    Nicholson, Thomas J. ; Jackson, Simon A. ; Croft, Bradley I. ; Staals, Raymond H.J. ; Fineran, Peter C. ; Brown, Chris M. - \ 2019
    RNA Biology 16 (2019)4. - ISSN 1547-6286 - p. 566 - 576.
    adaptation - adaptive immunity - CRISPR-Cas - primed - priming - spacer acquisition

    CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against invading genetic elements, such as plasmids, bacteriophages and archaeal viruses. They consist of cas genes and CRISPR loci, which store genetic memories of previously encountered invaders as short sequences termed spacers. Spacers determine the specificity of CRISPR-Cas defence and immunity can be gained or updated by the addition of new spacers into CRISPR loci. There are two main routes to spacer acquisition, which are known as naïve and primed CRISPR adaptation. Naïve CRISPR adaptation involves the de novo formation of immunity, independent of pre-existing spacers. In contrast, primed CRISPR adaptation (priming) uses existing spacers to enhance the acquisition of new spacers. Priming typically results in spacer acquisition from locations near the site of target recognition by the existing (priming) spacer. Primed CRISPR adaptation has been observed in several type I CRISPR-Cas systems and it is potentially widespread. However, experimental evidence is unavailable for some subtypes, and for most systems, priming has only been shown in a small number of hosts. There is also no current evidence of priming by other CRISPR-Cas types. Here, we used a bioinformatic approach to search for evidence of priming in diverse CRISPR-Cas systems. By analysing the clustering of spacers acquired from phages, prophages and archaeal viruses, including strand and directional biases between subsequently acquired spacers, we demonstrate that two patterns of primed CRISPR adaptation dominate in type I systems. In addition, we find evidence of a priming-like pathway in type II CRISPR-Cas systems.

    Exploring the hybrid speciation continuum in birds
    Ottenburghs, Jente - \ 2018
    Ecology and Evolution 8 (2018)24. - ISSN 2045-7758 - p. 13027 - 13034.
    adaptation - admixture - genomics - introgression - mito-nuclear discordance - reproductive isolation

    Hybridization is increasingly recognized as a creative evolutionary force contributing to adaptation and speciation. Homoploid hybrid speciation—the process in which hybridization results in a stable, fertile, and reproductively isolated hybrid lineage where there is no change in ploidy—has been documented in several taxa. Hybridization can directly contribute to reproductive isolation or reinforce it at a later stage. Alternatively, hybridization might not be related to the evolution of reproductive isolation. To account for these different scenarios, I propose to discriminate between two types of hybrid speciation: type I where reproductive isolation is a direct consequence of hybridization and type II where it is the by-product of other processes. I illustrate the applicability of this classification scheme with avian examples. To my knowledge, seven hybrid bird species have been proposed: Italian sparrow, Audubon's warbler, Genovesa mockingbird, Hawaiian duck, red-breasted goose, golden-crowned manakin, and a recent lineage of Darwin's finches on the island of Daphne Major (“Big Bird”). All studies provide convincing evidence for hybridization, but do not always confidently discriminate between scenarios of hybrid speciation and recurrent introgressive hybridization. The build-up of reproductive isolation between the hybrid species and their parental taxa is mainly driven by premating isolation mechanisms and comparable to classical speciation events. One hybrid species can be classified as type I (“Big Bird”) while three species constitute type II hybrid species (Italian sparrow, Audubon's warbler, and golden-crowned manakin). The diversity in hybrid bird species across a range of divergence times also provides an excellent opportunity to study the evolution of hybrid genomes in terms of genome stabilization and adaptation.

    Limiting the high impacts of Amazon forest dieback with no-regrets science and policy action
    Lapola, David M. ; Pinho, Patricia ; Quesada, Carlos A. ; Strassburg, Bernardo B.N. ; Rammig, Anja ; Kruijt, Bart ; Brown, Foster ; Ometto, Jean P.H.B. ; Premebida, Adriano ; Marengo, José A. ; Vergara, Walter ; Nobre, Carlos A. - \ 2018
    Proceedings of the National Academy of Sciences of the United States of America 115 (2018)46. - ISSN 0027-8424 - p. 11671 - 11679.
    adaptation - agriculture - ecosystem services - hydroelectricity generation - migration

    Large uncertainties still dominate the hypothesis of an abrupt large-scale shift of the Amazon forest caused by climate change [Amazonian forest dieback (AFD)] even though observational evidence shows the forest and regional climate changing. Here, we assess whether mitigation or adaptation action should be taken now, later, or not at all in light of such uncertainties. No action/later action would result in major social impacts that may influence migration to large Amazonian cities through a causal chain of climate change and forest degradation leading to lower river-water levels that affect transportation, food security, and health. Net-present value socioeconomic damage over a 30-year period after AFD is estimated between US dollar (USD) $957 billion (×109) and $3,589 billion (compared with Gross Brazilian Amazon Product of USD $150 billion per year), arising primarily from changes in the provision of ecosystem services. Costs of acting now would be one to two orders of magnitude lower than economic damages. However, while AFD mitigation alternatives-e.g., curbing deforestation-are attainable (USD $64 billion), their efficacy in achieving a forest resilience that prevents AFD is uncertain. Concurrently, a proposed set of 20 adaptation measures is also attainable (USD $122 billion) and could bring benefits even if AFD never occurs. An interdisciplinary research agenda to fill lingering knowledge gaps and constrain the risk of AFD should focus on developing sound experimental and modeling evidence regarding its likelihood, integrated with socioeconomic assessments to anticipate its impacts and evaluate the feasibility and efficacy of mitigation/adaptation options.

    Data from: A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour
    Kim, J.M. ; Santure, Anna W. ; Barton, H.J. ; Quinn, John L. ; Cole, Ella F. ; Visser, M.E. ; Sheldon, B.C. ; Groenen, M. ; Oers, K. van; Slate, J. - \ 2018
    University of Sheffield
    adaptation - ecological genetics - genomics/proteomics - natural selection and contemporary evolution - population genetics - empirical - quantitative genetics
    High density SNP microarrays (‘SNP chips’) are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this paper we describe the development and application of a high density Affymetrix Axiom chip with around 500 000 SNPs, designed to perform genomics studies of great tit (Parus major) populations. We demonstrate that the per-SNP genotype error rate is well below 1% and that the chip can also be used to identify structural or copy number variation (CNVs). The chip is used to explore the genetic architecture of exploration behaviour (EB), a personality trait that has been widely studied in great tits and other species. No SNPs reached genome-wide significance, including at DRD4, a candidate gene. However, EB is heritable and appears to have a polygenic architecture. Researchers developing similar SNP chips may note: (i) SNPs previously typed on alternative platforms are more likely to be converted to working assays, (ii) detecting SNPs by more than one pipeline, and in independent datasets, ensures a high proportion of working assays, (iii) allele frequency ascertainment bias is minimised by performing SNP discovery in individuals from multiple populations and (iv) samples with the lowest call rates tend to also have the greatest genotyping error rates.
    Ramial wood amendments (Piliostigma reticulatum) mitigate degradation of tropical soils but do not replenish nutrient exports
    Félix, Georges F. ; Clermont-Dauphin, Cathy ; Hien, Edmond ; Groot, Jeroen C.J. ; Penche, Aurélien ; Barthès, Bernard G. ; Manlay, Raphaël J. ; Tittonell, Pablo ; Cournac, Laurent - \ 2018
    Land Degradation and Development 29 (2018)8. - ISSN 1085-3278 - p. 2694 - 2706.
    adaptation - farmer innovation - Sahel - shrub material - termites

    Restoring degraded soils to support food production is a major challenge for West African smallholders who have developed local innovations to counter further degradation. The objective of this study was to evaluate a local farmer's technique that uses ramial wood (RW) as soil amendment (Piliostigma reticulatum shrub). Three treatments were applied in an experimental plot in Burkina Faso: control (no amendment), low RW (3 Mg fresh mass·ha−1·yr−1), and high RW (12 Mg fresh mass·ha−1·yr−1). RW was chipped to <5-cm pieces and either buried or mulched. Topsoil carbon (C), nitrogen (N), and phosphorus (P) in control and low-RW treatments declined after 7 years of continuous sorghum cultivation. Use of high-RW amendment stabilized soil C content while N and P declined, thus not replenishing nutrient exports. Net contribution to soil C in the layer measuring 0–15 cm was 15% of the applied C in the high-RW amendments. Although biomass and grain yields were higher in high-RW treatments, crop productivity declined throughout the experiment for all treatments. Termite casts on RW treatments evidenced the potential role of wood-foraging termites in diluting the impact of RW on soil fertility build-up and soil water content. We conclude that mitigating soil degradation under semiarid conditions in Burkina Faso would require large amounts of woody amendments, particularly if the level of termite activity is high. Additional nutrient sources would be needed to compensate for removal in exported products so that biomass and grain production can be stabilized or increased.

    Comparing impacts of climate change and mitigation on global agriculture by 2050
    Meijl, Hans van; Havlik, Petr ; Lotze-Campen, Hermann ; Stehfest, Elke ; Witzke, Peter ; Domínguez, Ignacio P. ; Bodirsky, Benjamin L. ; Dijk, Michiel van; Doelman, Jonathan ; Fellmann, Thomas ; Humpenöder, Florian ; Koopman, Jason F.L. ; Müller, Christoph ; Popp, Alexander ; Tabeau, Andrzej ; Valin, Hugo ; Zeist, Willem J. van - \ 2018
    Environmental Research Letters 13 (2018)6. - ISSN 1748-9318
    adaptation - agriculture - climate change - economic models - mitigation - shared socioeconomic pathways

    Systematic model inter-comparison helps to narrow discrepancies in the analysis of the future impact of climate change on agricultural production. This paper presents a set of alternative scenarios by five global climate and agro-economic models. Covering integrated assessment (IMAGE), partial equilibrium (CAPRI, GLOBIOM, MAgPIE) and computable general equilibrium (MAGNET) models ensures a good coverage of biophysical and economic agricultural features. These models are harmonized with respect to basic model drivers, to assess the range of potential impacts of climate change on the agricultural sector by 2050. Moreover, they quantify the economic consequences of stringent global emission mitigation efforts, such as non-CO2 emission taxes and land-based mitigation options, to stabilize global warming at 2 °C by the end of the century under different Shared Socioeconomic Pathways. A key contribution of the paper is a vis-à-vis comparison of climate change impacts relative to the impact of mitigation measures. In addition, our scenario design allows assessing the impact of the residual climate change on the mitigation challenge. From a global perspective, the impact of climate change on agricultural production by mid-century is negative but small. A larger negative effect on agricultural production, most pronounced for ruminant meat production, is observed when emission mitigation measures compliant with a 2 °C target are put in place. Our results indicate that a mitigation strategy that embeds residual climate change effects (RCP2.6) has a negative impact on global agricultural production relative to a no-mitigation strategy with stronger climate impacts (RCP6.0). However, this is partially due to the limited impact of the climate change scenarios by 2050. The magnitude of price changes is different amongst models due to methodological differences. Further research to achieve a better harmonization is needed, especially regarding endogenous food and feed demand, including substitution across individual commodities, and endogenous technological change.

    Neutral and functionally important genes shed light on phylogeography and the history of high-altitude colonization in a widespread New World duck
    Lozano-Jaramillo, Maria ; McCracken, Kevin G. ; Cadena, Carlos Daniel - \ 2018
    Ecology and Evolution 8 (2018)13. - ISSN 2045-7758 - p. 6515 - 6528.
    adaptation - hypoxia - migration - natural selection

    Phylogeographic studies often infer historical demographic processes underlying species distributions based on patterns of neutral genetic variation, but spatial variation in functionally important genes can provide additional insights about biogeographic history allowing for inferences about the potential role of adaptation in geographic range evolution. Integrating data from neutral markers and genes involved in oxygen (O2)-transport physiology, we test historical hypotheses about colonization and gene flow across low- and high-altitude regions in the Ruddy Duck (Oxyura jamaicensis), a widely distributed species in the New World. Using multilocus analyses that for the first time include populations from the Colombian Andes, we also examined the hypothesis that Ruddy Duck populations from northern South America are of hybrid origin. We found that neutral and functional genes appear to have moved into the Colombian Andes from both North America and southern South America, and that high-altitude Colombian populations do not exhibit evidence of adaptation to hypoxia in hemoglobin genes. Therefore, the biogeographic history of Ruddy Ducks is likely more complex than previously inferred. Our new data raise questions about the hypothesis that adaptation via natural selection to high-altitude conditions through amino acid replacements in the hemoglobin protein allowed Ruddy Ducks to disperse south along the high Andes into southern South America. The existence of shared genetic variation with populations from both North America and southern South America as well as private alleles suggests that the Colombian population of Ruddy Ducks may be of old hybrid origin. This study illustrates the breadth of inferences one can make by combining data from nuclear and functionally important loci in phylogeography, and underscores the importance of complete range-wide sampling to study species history in complex landscapes.

    Maternal Effects in a Wild Songbird Are Environmentally Plastic but Only Marginally Alter the Rate of Adaptation
    Ramakers, Jip J.C. ; Cobben, Marleen M.P. ; Bijma, Piter ; Reed, Thomas E. ; Visser, Marcel E. ; Gienapp, Phillip - \ 2018
    American Naturalist 191 (2018)5. - ISSN 0003-0147 - p. E000 - E000.
    adaptation - environmental shift - evolutionary dynamics - maternal inheritance - plastic maternal effect - quantitative genetics
    Despite ample evidence for the presence of maternal effects (MEs) in a variety of traits and strong theoretical indications for their evolutionary consequences, empirical evidence to what extent MEs can influence evolutionary responses to selection remains ambiguous. We tested the degree to which MEs can alter the rate of adaptation of a key life-history trait, clutch size, using an individual-based model approach parameterized with experimental data from a long-term study of great tits (Parus major). We modeled two types of MEs: (i) an environmentally plastic ME, in which the relationship between maternal and offspring clutch size depended on the maternal environment via offspring condition, and (ii) a fixed ME, in which this relationship was constant. Although both types of ME affected the rate of adaptation following an abrupt environmental shift, the overall effects were small. We conclude that evolutionary consequences of MEs are modest at best in our study system, at least for the trait and the particular type of ME we considered here. A closer link between theoretical and empirical work on MEs would hence be useful to obtain accurate predictions about the evolutionary consequences of MEs more generally.
    Data from: Recent natural selection causes adaptive evolution of an avian polygenic trait
    Bosse, M. ; Spurgin, Lewis G. ; Laine, Veronika N. ; Cole, Ella F. ; Firth, Josh A. ; Gienapp, Phillip ; Gosler, Andrew G. ; McMahon, Keith ; Poissant, Jocelyn ; Verhagen, I.C. ; Groenen, M. ; Oers, C.H.J. ; Sheldon, Ben C. ; Visser, M.E. ; Slate, Jon - \ 2017
    Wageningen University & Research
    adaptation - evolution - genomics - natural selection - bill length - birds - Parus major
    We used extensive data from a long-term study of great tits (Parus major) in the United Kingdom and Netherlands to better understand how genetic signatures of selection translate into variation in fitness and phenotypes. We found that genomic regions under differential selection contained candidate genes for bill morphology and used genetic architecture analyses to confirm that these genes, especially the collagen gene COL4A5, explained variation in bill length. COL4A5 variation was associated with reproductive success, which, combined with spatiotemporal patterns of bill length, suggested ongoing selection for longer bills in the United Kingdom. Last, bill length and COL4A5 variation were associated with usage of feeders, suggesting that longer bills may have evolved in the United Kingdom as a response to supplementary feeding.
    Data from: Maternal effects in a wild songbird are environmentally plastic but only marginally alter the rate of adaptation
    Ramakers, J.J.C. ; Cobben, M.M.P. ; Bijma, P. ; Reed, T.E. ; Visser, M.E. ; Gienapp, P. - \ 2017
    Wageningen University & Research
    adaptation - bird - evolution - experimental - fitness - genetics - quantative - maternal effects
    Despite ample evidence for the presence of maternal effects (MEs) in a variety of traits and strong theoretical indications for their evolutionary consequences, empirical evidence to what extent MEs can influence evolutionary responses to selection remains ambiguous. We tested the degree to which MEs can alter the rate of adaptation of a key life-history trait, clutch size, using an individual-based model approach parameterized with experimental data from a long-term study of great tits (Parus major). We modeled two types of MEs: (i) an environmentally plastic ME, in which the relationship between maternal and offspring clutch size depended on the maternal environment via offspring condition, and (ii) a fixed ME, in which this relationship was constant. Although both types of ME affected the rate of adaptation following an abrupt environmental shift, the overall effects were small. We conclude that evolutionary consequences of MEs are modest at best in our study system, at least for the trait and the particular type of ME we considered here. A closer link between theoretical and empirical work on MEs would hence be useful to obtain accurate predictions about the evolutionary consequences of MEs more generally.
    Reproductive adaptations to reduce locomotor costs in viviparous fish (Poeciliidae)
    Fleuren, Mike - \ 2017
    Wageningen University. Promotor(en): J.L. van Leeuwen, co-promotor(en): B.J.A. Pollux. - Wageningen : Wageningen University - ISBN 9789463438025 - 204
    fishes - poeciliidae - reproduction - adaptation - vivipary - locomotion - biomechanics - zoology - vissen - poeciliidae - voortplanting - adaptatie - levendbarend - voortbeweging - biomechanica - zoölogie

    Viviparity, a live-bearing mode of reproduction, has evolved over 100 times independently in vertebrate animals. Despite its frequent evolution, viviparity has a number of hypothesised disadvantages compared to the ancestral mode of reproduction, oviparity (egg-laying). One of these disadvantages is a reduction in locomotor performance during pregnancy, the period of internal development of the embryos. Adaptations to a live-bearing reproductive mode could have evolved to reduce these locomotor costs. In this thesis, I aim to find whether matrotrophy, post-fertilization nutrient provisioning (e.g. through a placental structure), and superfetation, the presence of multiple broods of different developmental stages, reduce the locomotor performance decline during pregnancy in the Poeciliidae, live-bearing fishes.

    In Chapter 2, we review the literature on the effects of pregnancy on morphology, performance and fitness. The biomechanics of each mode of locomotion (walking, swimming or flying) are distinct, and are affected differently by the added mass and volume of pregnancy. Furthermore, we list the possible adaptations that have evolved to reduce the locomotor costs of pregnancy, and divide them into three different categories: adaptations that reduce the locomotor costs of live-bearing, adaptations with which the locomotor costs of live-bearing are avoided, and adaptations to the life history of the animal. Lastly, we discuss hiatuses in the literature and experimental procedures to quantify the hypothesised benefit of adaptations.

    In Chapter 3, we compare the morphological changes during pregnancy in two closely-related species of live-bearing fish: Poeciliopsis turneri and Poeciliopsis gracilis. These species mainly differ in their mode of nutrient provisioning: P. gracilis is lecithotrophic and P. turneri is an extensive matrotroph. We tracked the morphological changes in 3D using a non-invasive method that creates three-dimensional body models. We find that P. turneri is more slender during the early stages of pregnancy, but increase in size more rapidly. This is in line with the locomotor costs hypothesis, which predicts that matrotrophic fish are more slender during the early stages of pregnancy, but that the difference between the body shapes of lecithotrophic and matrotrophic fish diminishes as pregnancy progresses. Our results indicate that matrotrophy could indeed provide a morphological advantage during pregnancy.

    Fast-start performance, a manoeuvre fish deploy to escape predatory strikes, is important for individual survival. In Chapter 4, we use state-of-the-art biomechanical methods to, for the first time, quantify this manoeuvre in three-dimensional space in adult fish (Heterandria formosa). We show that fish can orient their escapes in up- and downwards direction, and that this is correlated with a change in pitch angle of the body. Changes in roll angle of the body were not correlated with orientation of the fish. We furthermore demonstrate that stage 1 of the fast start, often described as a preparatory stage, can already contribute to propulsion. The results from Chapter 4 indicate that three-dimensional measurements of fast-start manoeuvres provide novel insights that were often overlooked.

    Measuring fast starts in three-dimensional space is relevant in determining the adverse effects of pregnancy on locomotor performance. We did this by comparing three species of live-bearing fish: P. turneri, H. formosa and Phalloptychus januarius. In Chapter 5, we show that pregnancy-induced changes in abdominal width are correlated with a reduction in performance in the horizontal plane (maximal horizontal speed, change in yaw angle), but less so in the vertical plane (maximal vertical speed, change in pitch angle). Furthermore, we demonstrate that an increase in abdominal width is correlated with a decrease in abdominal curvature and, for some species, in a decrease in maximal curvature rate in the abdomen. Lastly, we show that the pregnancy-induced morphological changes depend on the level of superfetation: species with a high level of superfetation experience higher frequency, but smaller amplitude changes in the shape of the abdomen. Whether superfetation actually results in a more slender body shape, as predicted by the locomotor costs hypothesis, depends on the level of reproductive investment.

    In this thesis, I show that pregnancy induces changes in morphology which comes with a cost in fast-start performance. Both matrotrophy and superfetation affect how body shape changes due to pregnancy, but whether the latter provides beneficial changes depends on the level of reproductive investment. Furthermore, I reveal that fast starts can have a substantial three-dimensional component which is relevant both to biomechanicists that aim to understand the physical and physiological mechanisms underlying this manoeuvre and to evolutionary biologists that strive to answer performance-related questions.

    Sensitivity analysis methodologies for analysing emergence using agent-based models
    Broeke, Guus ten - \ 2017
    Wageningen University. Promotor(en): J. Molenaar, co-promotor(en): G.A.K. van Voorn; A. Ligtenberg. - Wageningen : Wageningen University - ISBN 9789463436991 - 211
    mathematics - computational mathematics - mathematical models - dynamic modeling - sensitivity analysis - adaptation - methodology - simulation - wiskunde - computerwiskunde - wiskundige modellen - dynamisch modelleren - gevoeligheidsanalyse - adaptatie - methodologie - simulatie

    Many human and natural systems are highly complex, because they consist of many interacting parts. Such systems are known as complex adaptive systems (CAS). Understanding CAS is possible only by studying the interactions between constituent parts, rather than focussing only on the properties of the parts in isolation. Often, the possibilities for systematically studying these interactions in real-life systems are limited. Simulation models can then be an important tool for testing what properties may emerge, given various assumptions on the interactions in the system. Agent-based models (ABMs) are particularly useful for studying CAS, because ABMs explicitly model interactions between autonomous agents and their environment.

    Currently, the utility of ABMs is limited by a lack of available methodologies for analysing their results. The main tool for analysing CAS models is sensitivity analysis. Yet, standard methods of sensitivity analysis are not well-suited to deal with the complexity of ABMs. Thus, there is a need for sensitivity analysis methodologies that are specifically developed for analysing ABMs. The objective of this thesis is to contribute such methodologies. Specifically, we propose methodologies for (1) detecting tipping points, (2) analysing the effects of agent adaptation, and (3) analysing resilience of ABMs.

    Chapter 2 introduces traditional methods of sensitivity analysis. These methods are demonstrated by applying them to rank the most influential parameters of an ODE model of predator-prey interaction. Furthermore, the role of sensitivity analysis in model validation is discussed.

    In Chapter 3 we investigate the use of sensitivity analysis for detecting tipping points. Whereas bifurcation analysis methods are available for detecting tipping points in ODE models, these methods are not applicable to ABMs. Therefore, we use an ODE model to verify the results from sensitivity analysis against those of bifurcation analysis. We conclude that one-factor-at-a-time sensitivity analysis (OFAT) is a helpful method for detecting tipping points. However, OFAT is a local method that considers only changes in individual parameters. It is therefore recommended to supplement OFAT with a global method to investigate interaction effects. For this purpose, we recommend all-but-one-at-a-time sensitivity analysis (ABOS) as a graphical sensitivity analysis method that takes into account parameter interactions and can help with the detection of tipping points.

    In Chapter 4 we introduce a basic ABM model of agents competing in a spatial environment for a renewable resource. This basic model will be extended in the subsequent chapters, and will serve as a testing case for various sensitivity analysis methods. In Chapter 4, it is used to assess the utility of existing sensitivity analysis methods for ABMs. The results show that traditional methods of sensitivity are not sufficient to analyse the ABM, due to the presence of tipping points and other strong non-linearities in the model output. In contrast, OFAT is found to be helpful for detecting tipping points, as was suggested in Chapter 3. Based on these outcomes, OFAT is recommended as a starting point for sensitivity analysis of ABMs, preferably supplemented by a global method to investigate interaction effects.

    In Chapter 5 we extend the ABM of Chapter 4 by adding agent adaptation in the form of a mechanism of natural selection. On short time-scales, the model behaviour appears to be similar to the non-adaptive model version. On longer time-scales, the agent adaptation causes the state of the model to gradually change as agents continue to adapt to their surroundings. We propose a sensitivity analysis method to measure the effects of this adaptation. This method is based on a quantification of the difference between probability density functions of model version with and without adaptation. Using this method, we show that this adaptation increases the resilience of the system by giving it the flexibility needed to respond to pressures.

    In Chapter 6 we further extend the test-case by giving agents the option to harvest either cooperatively or individually. Cooperation increases the potential yields, but introduces the risk of defection of the interaction partner. It is shown that ecological factors, which are usually not considered in models on cooperation, strongly affect the level of cooperation in the system. For example, low levels of cooperation lead to a decreased population size, and causes the formation of small groups of agents with a higher level of cooperation. As a result, cooperation persists even without any mechanisms to promote it. Nevertheless, the inclusion of such mechanisms in the form of indirect reciprocity does further increase the level of cooperation. Furthermore, we show that the resulting high levels of cooperation, depending on the circumstances, can increase the resilience of the agent population against shocks.

    To conclude, in this thesis several methodologies have been proposed to help with ABM analysis. Specifically, OFAT and ABOS are recommended for detecting tipping points in ABMs, and in Chapter 5 a protocol is introduced for quantifying the effects of adaptation. By suggesting these methodologies, this thesis aims to contribute to the utility of ABMs, especially for studying CAS.

    Marine complex adaptive systems : theory, legislation and management practices
    Bigagli, Emanuele - \ 2017
    Wageningen University. Promotor(en): Arnold Bregt, co-promotor(en): M. Craglia. - Wageningen : Wageningen University - ISBN 9789463431255 - 160
    marine areas - marine environment - adaptation - environmental management - oceans - climate - environmental legislation - global warming - climatic change - mariene gebieden - marien milieu - adaptatie - milieubeheer - oceanen - klimaat - milieuwetgeving - opwarming van de aarde - klimaatverandering

    Anthropogenic and climate-related stressors challenge the health of nearly every part of the global oceans. They affect the capacity of oceans to regulate global weather and climate, as well as ocean productivity and food services, and result in the loss or degradation of marine habitats and biodiversity. Moreover, they have a negative impact on maritime economic sectors and on the social welfare of dependent coastal populations. In order to overcome the deficiencies of traditional single-sector management, in the recent decades several scientific approaches emerged, based on the view of marine systems as Complex Adaptive Systems (CAS), i.e. systems where components interact in non-linear, path dependent ways, with lock-in and feedback loop mechanisms, and unpredictable effects also across scales. These approaches have been introduced into the texts of several international agreements related to marine CAS, and related management practices, with contrasting results in relation to effectiveness and integration of governance.

    This thesis evaluates for the first time the current international and European legal frameworks from the perspective of marine CAS. To accomplish this objective, four research objectives are formulated: (1) Develop a framework for marine CAS assessment and management; (2) Evaluate the entire European Union (EU) legal framework against the framework developed; (3) Evaluate the international legal framework for the assessment and management of the global oceans against the framework developed; and (4) Evaluate the implementation of the EU and global legal frameworks into practice.

    Chapter 2 develops a framework for marine CAS, based on the combination of two promising theoretical approaches: Adaptive Management (AM) and Transition Management (TM). The framework is based on the idea that AM and TM have the potential to overcome each other’s limitations, which are related to the insufficient attention to micro-level socio-economic components, and to the limited incorporation of environmental aspects into socio-technical assessments, respectively. More into detail, the proposed framework is articulated into three components. First, the two sets of marine social-ecological systems and connected socio-technical systems (e.g. fisheries, maritime transportation, coastal tourism and energy) must be clearly identified, and the complex interactions and influences between socio-economic patterns of production and consumption, and ecological components must be assessed. Second, the achievement of ecological resilience of a marine social-ecological system should be performed in coordination with transitions of unsustainable connected socio-technical systems. This implies that sustainability should be evaluated in relation to the pressures socio-technical systems generate on the ecological resilience of connected social-ecological systems, and related impacts. Third, the implementation of the two approaches should be articulated into iterative, learning- and science-based policy cycles, with mechanisms to foster coordination between the policy cycles of social-ecological and socio-technical systems. The benefits of this framework are threefold. First, the assessment of the two sets of social-ecological and socio-technical systems, taken together, allows to overcome current AM limitations and include micro-level socio-economic components into the assessment of ecological resilience. Second, by linking AM managers with established transition arenas, it is possible to overcome TM limitations and streamline the consideration of ecological aspects into the TM process. Third, by linking AM and TM policy cycles, it is possible to reduce the current legal and policy fragmentation.

    Chapters 3 and 4 apply the framework proposed in Chapter 2 to evaluate the EU and global legal frameworks for the assessment and management of marine CAS. Chapter 3 presents the first comprehensive review ever realised of the entire EU legal framework, composed of more than 12,000 EU legal acts, from the perspective of marine CAS assessment and management. It concludes that the EU legislation does not provide a fully coherent framework for the assessment and management of EU marine CAS. Although the Marine Strategy Framework Directive (MSFD; 2008/56/EC) is a major step towards this purpose, the present research highlights three major limitations: (1) the limited capacity of the MSFD to support the coordination between Member States sharing the same marine region or sub-region; (2) the insufficient characterisation of marine ecological resilience, in particular in relation to socio-economic elements, ecosystem services, human benefits and cross-scale interactions; and (3) the limited capacity of the MSFD to tackle the fragmentation of the EU legal framework and integrate ecological resilience into the objectives of sector-based laws and policies.

    Chapter 4 reviews 500 multilateral agreements, evaluated for the first time from the perspective of marine CAS. It shows that there is no international agreement aiming at the ecological resilience of the global oceans social-ecological system. Instead, the international legal framework is fragmented along two dimensions. On the one side, global agreements focus on specific objectives for determined socio-economic activities, ecological features or anthropogenic pressures. On the other side, regional agreements are in place for 18 ocean regions of the world, with a varying level of inclusion of elements of marine CAS assessment and management. The need is highlighted for a reformed global ocean governance framework, which should be based on a bio-geographical approach to the ecological resilience of the global oceans, and build on iteration, learning, and science-based advice to policy and management.

    Chapter 5 evaluates the implementation of the EU and global legal frameworks into the practice of assessment and management of a case-study area, the Adriatic Sea. It shows the importance of the MSFD as the first policy trying to deliver a CAS approach to marine assessment and management. However, the case-study investigation confirms the three limitations of the MSFD, laying in: 1) an insufficient geographical approach, where implementation is driven at national level and the requirement of cross-border cooperation is weak; 2) the vagueness of legal requirements, and the limited capacity to include socio-economic aspects into the required assessment; and 3) an insufficient capacity to coordinate with other laws, policies and programmes at various levels of governance. Based on the identified limitations, suggestions are advanced on how to strengthen the implementation of the MSFD, both at Adriatic and EU level. These suggestions are further advanced in Chapter 6, which includes detailed proposals on how to foster integrated large-scale marine monitoring in the EU, in order to contribute to the implementation of the MSFD in an efficient and effective way, also in relation to costs.

    Chapter 7 synthesizes the major findings of this thesis and evaluates the capacity of the framework to deliver a CAS approach to marine systems. It concludes that AM and TM, although holding different visions on sustainability and referring to different principles, have the potential to be put in synergy at the practical level. Further scientific research and management practices should focus on the need for AM and TM to overcome the relative isolation and foster synergies across sector-based management, in order to integrate environmental considerations into economic sectors. Suggestions are advanced to improve legal frameworks and policy practices at the global and EU level. They focus on the need: (i) to fill the gaps in the geographical scope of legal texts and to foster international cooperation at the right social-ecological scale; (ii) to increase guidance in translating complex scientific requirements into clear management objectives, and improve related data collection and sharing; and (iii) to reduce current legal and policy fragmentation through targeted, ecological resilience-based marine environmental impact assessments and maritime spatial planning. Lines for further scientific research are suggested, focusing on: (i) improving the evidence-base through additional case-studies; (ii) analysing legal frameworks and governance regimes in place for other marine social-ecological systems, like e.g. the United States of America, Canada, Australia and China; (iii) improving existing tools, or creating new ones for marine ecological resilience assessment; and (iv) developing innovative instruments and mechanisms to strengthen global oceans governance.

    Climate change adaptation planning for Global South megacities: The case of Dhaka
    Araos, Malcolm ; Ford, James D. ; Berrang-Ford, L. ; Biesbroek, G.R. ; Moser, S. - \ 2017
    Journal of Environmental Policy and Planning 19 (2017)6. - ISSN 1523-908X - p. 682 - 696.
    Climate change - adaptation - adaptation readiness - cities - Global South - environmental planning
    Megacities in low- and middle-income countries face unique threats from climate change as vulnerable populations and infrastructure are concentrated in high-risk areas. This paper develops a theoretical framework to characterize adaptation readiness in Global South cities and applies the framework to Dhaka, Bangladesh, a city with acute exposure and projected impacts from flooding and extreme heat. To gather case evidence from Dhaka we draw upon interviews with national and municipal government officials and a review of planning documents and peer-reviewed literature. We find: (1) national-level plans propose a number of adaptation strategies, but urban concerns compete with priorities such as protection of coastal assets and agricultural production; (2) municipal plans focus on identifying vulnerability and impacts rather than adaptation strategies; (3) interviewees suggest that lack of coordination among local government (LG) organizations and lack of transparency act as barriers for municipal adaptation planning, with national plans driving policy where LGs have limited human and financial resources; and (4) we found limited evidence that national urban adaptation directives trickle down to municipal government. The framework developed offers a systematic and standardized means to assess and monitor the status of adaptation planning in Global South cities, and identify adaptation constraints and opportunities.
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