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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    Scots pine trees react to drought by increasing xylem and phloem conductivities
    Kiorapostolou, Natasa ; Camarero, J.J. ; Carrer, Marco ; Sterck, Frank ; Brigita, Brigita ; Sangüesa-Barreda, Gabriel ; Petit, Giai - \ 2020
    Tree Physiology 40 (2020)6. - ISSN 0829-318X - p. 774 - 781.
    Pinus sylvestris - forest dieback - hydraulic failure - phenotypic plasticity - phloem - tree mortality - wood anatomy - xylem

    Drought limits the long-distance transport of water in the xylem due to the reduced leaf-to-soil water potential difference and possible embolism-related losses of conductance and of sugars in the phloem due to the higher viscosity of the dehydrated sugary solution. This condition can have cascading effects in water and carbon (C) fluxes that may ultimately cause tree death. We hypothesize that the maintenance of xylem and phloem conductances is fundamental for survival also under reduced resource availability, when trees may produce effective and low C cost anatomical adjustments in the xylem and phloem close to the treetop where most of the hydraulic resistance is concentrated. We analyzed the treetop xylem and phloem anatomical characteristics in coexisting Scots pine trees, symptomatic and non-symptomatic of drought-induced dieback. We selected the topmost 55 cm of the main stem and selected several sampling positions at different distances from the stem apex to test for differences in the axial patterns between the two groups of trees. We measured the annual ring area, the tracheid hydraulic diameter (Dh) and cell wall thickness (CWT), the conductive phloem area and the average lumen diameter of the 20 largest phloem sieve cells (Dph). Declining trees grew less than the non-declining ones, and despite the similar axial scaling of anatomical traits, had larger Dh and lower CWT. Moreover, declining trees had wider Dph. Our results demonstrate that even under drought stress, maintenance of xylem and phloem efficiencies is of primary importance for survival, even if producing fewer larger tracheids may lead to a xylem more vulnerable to embolism formation.

    Testing sensory drive speciation in cichlid fish: Linking light conditions to opsin expression, opsin genotype and female mate preference
    Wright, Daniel Shane ; Eijk, Roel van; Schuart, Lisa ; Seehausen, Ole ; Groothuis, Ton G.G. ; Maan, Martine E. - \ 2020
    Journal of Evolutionary Biology 33 (2020)4. - ISSN 1010-061X - p. 422 - 434.
    ecological speciation - Haplochromine - LWS - phenotypic plasticity - Pundamilia - visual pigment

    Ecological speciation is facilitated when divergent adaptation has direct effects on selective mating. Divergent sensory adaptation could generate such direct effects, by mediating both ecological performance and mate selection. In aquatic environments, light attenuation creates distinct photic environments, generating divergent selection on visual systems. Consequently, divergent sensory drive has been implicated in the diversification of several fish species. Here, we experimentally test whether divergent visual adaptation explains the divergence of mate preferences in Haplochromine cichlids. Blue and red Pundamilia co-occur across south-eastern Lake Victoria. They inhabit different photic conditions and have distinct visual system properties. Previously, we documented that rearing fish under different light conditions influences female preference for blue versus red males. Here, we examine to what extent variation in female mate preference can be explained by variation in visual system properties, testing the causal link between visual perception and preference. We find that our experimental light manipulations influence opsin expression, suggesting a potential role for phenotypic plasticity in optimizing visual performance. However, variation in opsin expression does not explain species differences in female preference. Instead, female preference covaries with allelic variation in the long-wavelength-sensitive opsin gene (LWS), when assessed under broad-spectrum light. Taken together, our study presents evidence for environmental plasticity in opsin expression and confirms the important role of colour perception in shaping female mate preferences in Pundamilia. However, it does not constitute unequivocal evidence for the direct effects of visual adaptation on assortative mating.

    The effect of temporal environmental autocorrelation on eco-evolutionary dynamics across life histories
    Postuma, Maarten ; Schmid, Max ; Guillaume, Frédéric ; Ozgul, Arpat ; Paniw, Maria - \ 2020
    Ecosphere 11 (2020)2. - ISSN 2150-8925
    eco-evolutionary dynamics - individual-based modeling - life history - phenotypic plasticity - population dynamics - temporal autocorrelation

    One of the largest causes of fluctuations in the size and structure of populations is changes in the environment. In nature, these changes are often temporally autocorrelated and the strength and direction of the autocorrelation can affect population dynamics. These effects are mediated by complex, simultaneously occurring ecological and evolutionary processes, such as phenotypic plasticity and selection. Determining how these processes interact to affect responses of different life histories to autocorrelated environmental fluctuations is of paramount importance to infer which taxa are likely to go extinct or become invasive under global change. Here, we assessed the effect of autocorrelation in environmental states on the trait and population dynamics of different life histories using an evolutionary explicit individual-based modeling approach. We found that, in general, higher positive temporal autocorrelation caused more variation in population size. Fast life histories were more affected than slow ones as they were able to adapt more quickly to varying environmental optima and therefore experienced larger initial decreases in population size when optima changed. Including adaptive phenotypic plasticity buffered the effects of autocorrelation on population dynamics while nonadaptive plasticity amplified them, especially for slow life histories, which recovered less from maladaptation. This study highlights that integration of phenotypic plasticity, selection, and population dynamics is important to improve our understanding of how different life histories deal with autocorrelated climate variability.

    Quantifying individual variation in reaction norms: Mind the residual
    Ramakers, Jip J.C. ; Visser, Marcel E. ; Gienapp, Phillip - \ 2020
    Journal of Evolutionary Biology 33 (2020)3. - ISSN 1010-061X - p. 352 - 366.
    heteroscedasticity - mixed models - phenotypic plasticity - random regression - random slope

    Phenotypic plasticity is a central topic in ecology and evolution. Individuals may differ in the degree of plasticity (individual-by-environment interaction (I × E)), which has implications for the capacity of populations to respond to selection. Random regression models (RRMs) are a popular tool to study I × E in behavioural or life-history traits, yet evidence for I × E is mixed, differing between species, populations, and even between studies on the same population. One important source of discrepancies between studies is the treatment of heterogeneity in residual variance (heteroscedasticity). To date, there seems to be no collective awareness among ecologists of its influence on the estimation of I × E or a consensus on how to best model it. We performed RRMs with differing residual variance structures on simulated data with varying degrees of heteroscedasticity and plasticity, sample size and environmental variability to test how RRMs would perform under each scenario. The residual structure in the RRMs affected the precision of estimates of simulated I × E as well as statistical power, with substantial lack of precision and high false-positive rates when sample size, environmental variability and plasticity were small. We show that model comparison using information criteria can be used to choose among residual structures and reinforce this point by analysis of real data of two study populations of great tits (Parus major). We provide guidelines that can be used by biologists studying I × E that, ultimately, should lead to a reduction in bias in the literature concerning the statistical evidence and the reported magnitude of variation in plasticity.

    ATLANTIC BIRD TRAITS: a data set of bird morphological traits from the Atlantic forests of South America
    Rodrigues, Rodolpho Credo ; Hasui, Érica ; Assis, Julia Camara ; Pena, João Carlos Castro ; Muylaert, Renata L. ; Tonetti, Vinicius Rodrigues ; Martello, Felipe ; Regolin, André Luis ; Vernaschi Vieira da Costa, Thiago ; Pichorim, Mauro ; Carrano, Eduardo ; Lopes, Leonardo Esteves ; Vasconcelos, Marcelo Ferreira de; Fontana, Carla Suertegaray ; Roos, Andrei Langeloh ; Gonçalves, Fernando ; Banks-Leite, Cristina ; Cavarzere, Vagner ; Efe, Marcio Amorim ; Alves, Maria Alice S. ; Uezu, Alexandre ; Metzger, Jean Paul ; Tarso Zuquim de Antas, Paulo de; Paschoaletto Micchi de Barros Ferraz, Katia Maria de; Calsavara, Larissa Corsini ; Bispo, Arthur Angelo ; Araujo, Helder F.P. ; Duca, Charles ; Piratelli, Augusto João ; Naka, Luciano N. ; Dias, Rafael Antunes ; Gatto, Cassiano A.F.R. ; Villegas Vallejos, Marcelo Alejandro ; Reis Menezes, Gregório dos; Bugoni, Leandro ; Rajão, Henrique ; Zocche, Jairo José ; Willrich, Guilherme ; Silva, Elsimar Silveira da; Manica, Lilian Tonelli ; Camargo Guaraldo, André de; Althmann, Giulyana ; Serafini, Patricia Pereira ; Francisco, Mercival Roberto ; Lugarini, Camile ; Machado, Caio Graco ; Marques-Santos, Fernando ; Bobato, Rafaela ; Souza, Elivan Arantes de; Donatelli, Reginaldo José ; Ferreira, Carolina Demetrio ; Morante-Filho, José Carlos ; Paes-Macarrão, Natalia Dantas ; Macarrão, Arthur ; Lima, Marcos Robalinho ; Jacoboski, Lucilene Inês ; Candia-Gallardo, Carlos ; Alegre, Vanesa Bejarano ; Jahn, Alex E. ; Camargo Barbosa, Karlla Vanessa de; Cestari, Cesar ; Silva, José Nilton da; Silveira, Natalia Stefanini da; Vara Crestani, Ana Cristina ; Petronetto, Adeliane Peterle ; Abreu Bovo, Alex Augusto ; Viana, Anderson Durão ; Araujo, Andrea Cardoso ; Santos, Andressa Hartuiq dos; Araújo do Amaral, Andreza Clarinda ; Ferreira, Ariane ; Vieira-Filho, Arnaldo Honorato ; Ribeiro, Bianca Costa ; Missagia, Caio C.C. ; Bosenbecker, Camila ; Bronzato Medolago, Cesar Augusto ; Rodriguez Espínola, Cid Rodrigo ; Faxina, Claudenice ; Campodonio Nunes, Cristiane Estrela ; Prates, Cristine ; Apolinario da Luz, Daniela Tomasio ; Moreno, Daniele Janina ; Mariz, Daniele ; Faria, Deborah ; Meyer, Douglas ; Doná, Eder Afonso ; Alexandrino, Eduardo Roberto ; Fischer, Erich ; Girardi, Fabiane ; Giese, Felipe Borba ; Santos Shibuya, Felipe Leonardo ; Faria, Fernando Azevedo ; Bittencourt de Farias, Fernando ; Lima Favaro, Fernando de; Ferneda Freitas, Fernando José ; Chaves, Flávia G. ; Guedes Las-Casas, Flor Maria ; Rosa, Gabriel L.M. ; Massaccesi de laTorre, Gabriel ; Bochio, Gabriela Menezes ; Bonetti, Giselle Evelise ; Kohler, Glauco ; Toledo-Lima, Guilherme Santos ; Plucenio, Gustavo Piletti ; Menezes, Ícaro ; Denóbile Torres, Ingrid Maria ; Carvalho Provinciato, Ivan Celso ; Viana, Ivan Réus ; Roper, James Joseph ; Persegona, Jaqueline Evelyn ; Barcik, Jean Júnior ; Martins-Silva, Jimi ; Gava Just, João Paulo ; Tavares-Damasceno, João Paulo ; Almeida Ferreira, João Ricardo de; Rodrigues Rosoni, Jonas Rafael ; Teixeira Falcon, José Eduardo ; Schaedler, Laura Maria ; Mathias, Leonardo Brioschi ; Deconto, Leonardo Rafael ; Cruz Rodrigues, Licléia da; Meyer, Marcela Afonso P. ; Repenning, Márcio ; Melo, Marcos Antônio ; Santos de Carvalho, Maria Amélia ; Rodrigues, Marcos ; Conti Nunes, Maria Flavia ; Ogrzewalska, Maria Halina ; Lopes Gonçalves, Mariana ; Vecchi, Maurício B. ; Bettio, Maurício ; Matta Baptista, Michelle Noronha da; Arantes, Murilo Sérgio ; Ruiz, Nicolás Luciano ; Bisetto de Andrade, Paulo Guilherme ; Lima Ribeiro, Pedro Henrique ; Galetti Junior, Pedro Manoel ; Macario, Phoeve ; Oliveira Fratoni, Rafael de; Meurer, Rafael ; Saint-Clair, Rafael S. ; Romagna, Rafael Spilere ; Alves Lacerda, Raquel Caroline ; Serpa Cerboncini, Ricardo Augusto ; Lyra, Ricardo Brioschi ; Lau, Ricardo ; Rodrigues, Roberta Costa ; Faria, Rogério Rodrigues ; Laps, Rudi Ricardo ; Althoff, Sérgio Luiz ; Jesus, Shayana de; Namba, Sumiko ; Braga, Talita Vieira ; Molin, Tamara ; França Câmara, Thanyria P. ; Enedino, Thayz Rodrigues ; Wischhoff, Uschi ; Oliveira, Vanessa Cristina de; Leandro-Silva, Victor ; Araújo-Lima, Vitor ; Oliveira Lunardi, Vitor de; Gusmão, Reginaldo Farias de; Souza Correia, Jozélia Maria de; Gaspar, Lucas P. ; Batista Fonseca, Renata Cristina ; Fonseca Pires Neto, Paulo Affonso ; Medeiros Morato de Aquino, Ana Carla ; Camargo, Bruna Betagni de; Cezila, Beatriz Azevedo ; Costa, Leonardo Marques ; Paolino, Roberta Montanheiro ; Kanda, Claudia Zukeran ; Monteiro, Erison C.S. ; Oshima, Júlia Emi F. ; Alves-Eigenheer, Milene ; Pizo, Marco Aurelio ; Silveira, Luís F. ; Galetti, Mauro ; Ribeiro, Milton Cezar - \ 2019
    Ecology 100 (2019)6. - ISSN 0012-9658
    body size - functional diversity - individual variation - interspecific variation - phenotypic plasticity - phylogenetic diversity - rapid evolution - tropical forest

    Scientists have long been trying to understand why the Neotropical region holds the highest diversity of birds on Earth. Recently, there has been increased interest in morphological variation between and within species, and in how climate, topography, and anthropogenic pressures may explain and affect phenotypic variation. Because morphological data are not always available for many species at the local or regional scale, we are limited in our understanding of intra- and interspecies spatial morphological variation. Here, we present the ATLANTIC BIRD TRAITS, a data set that includes measurements of up to 44 morphological traits in 67,197 bird records from 2,790 populations distributed throughout the Atlantic forests of South America. This data set comprises information, compiled over two centuries (1820–2018), for 711 bird species, which represent 80% of all known bird diversity in the Atlantic Forest. Among the most commonly reported traits are sex (n = 65,717), age (n = 63,852), body mass (n = 58,768), flight molt presence (n = 44,941), molt presence (n = 44,847), body molt presence (n = 44,606), tail length (n = 43,005), reproductive stage (n = 42,588), bill length (n = 37,409), body length (n = 28,394), right wing length (n = 21,950), tarsus length (n = 20,342), and wing length (n = 18,071). The most frequently recorded species are Chiroxiphia caudata (n = 1,837), Turdus albicollis (n = 1,658), Trichothraupis melanops (n = 1,468), Turdus leucomelas (n = 1,436), and Basileuterus culicivorus (n = 1,384). The species recorded in the greatest number of sampling localities are Basileuterus culicivorus (n = 243), Trichothraupis melanops (n = 242), Chiroxiphia caudata (n = 210), Platyrinchus mystaceus (n = 208), and Turdus rufiventris (n = 191). ATLANTIC BIRD TRAITS (ABT) is the most comprehensive data set on measurements of bird morphological traits found in a biodiversity hotspot; it provides data for basic and applied research at multiple scales, from individual to community, and from the local to the macroecological perspectives. No copyright or proprietary restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications or teaching and educational activities.

    Rapid plastic breeding response to rain matches peak prey abundance in a tropical savanna bird
    Hidalgo Aranzamendi, Nataly ; Hall, Michelle L. ; Kingma, Sjouke A. ; Pol, Martijn van de; Peters, Anne - \ 2019
    Journal of Animal Ecology 88 (2019)11. - ISSN 0021-8790 - p. 1799 - 1811.
    annual cycle - avian life-history - phenology - phenotypic plasticity - timing of reproduction - trophic interactions - tropics - unpredictable environment

    Changes in climate are shifting the timing of life cycle events in the natural world. Compared to northern temperate areas, these effects are relatively poorly understood in tropical and southern regions, where there is limited information on how timing of breeding and food availability are affected by climatic factors, and where patterns of breeding activity are more unpredictable within and between years. Combining a new statistical modelling approach with 5 years of continuous individual-based monitoring of a monsoonal tropical insectivorous bird, we quantified (a) the proximate climatic drivers at two trophic levels: timing of breeding and abundance of arthropod prey; (b) the effect of climate variation on reproductive output and (c) the role of individual plasticity. Rainfall was identified as the main determinant of phenology at both trophic levels. Throughout the year, likelihood of egg laying increased very rapidly in response to even small amounts of rain during the preceding 0–3 weeks. Adult body mass and male sperm storage also increased rapidly after rain, suggesting high breeding preparedness. Additionally, females were flexible, since they were more likely to nest whether their previous attempt was longer ago and unsuccessful. Arthropod abundance also increased after rainfall, but more slowly, with a peak around 10 weeks. Therefore, the peak food availability coincided with the presence of dependent fledglings. Fitness benefits of nesting after more rain appeared to be linked to offspring quantity rather than quality: nest attempts following higher rainfall produced larger clutches, but showed no improvement in nestling mass or relative fledging success. The response of clutch size to rainfall was plastic, since repeated sampling showed that individual females laid larger clutches after more rain, possibly mediated by improved body mass. Rapid, individually flexible breeding in response to rainfall and slower increase in arthropod abundance also as a response to rainfall, might buffer insectivorous species living in tropical seasonal environments from climate change-induced phenological trophic mismatches.

    Ecology of Plastic Flowers
    Rusman, Quint ; Lucas-Barbosa, Dani ; Poelman, Erik H. ; Dicke, Marcel - \ 2019
    Trends in Plant Science 24 (2019)6. - ISSN 1360-1385 - p. 725 - 740.
    flower traits - flower visitors - herbivore-induced plant responses - phenotypic plasticity - plant defense - specificity

    Plant phenotypic plasticity in response to herbivore attack includes changes in flower traits. Such herbivore-induced changes in flower traits have consequences for interactions with flower visitors. We synthesize here current knowledge on the specificity of herbivore-induced changes in flower traits, the underlying molecular mechanisms, and the ecological consequences for flower-associated communities. Herbivore-induced changes in flower traits seem to be largely herbivore species-specific. The extensive plasticity observed in flowers influences a highly connected web of interactions within the flower-associated community. We argue that the adaptive value of herbivore-induced plant responses and flower plasticity can be fully understood only from a community perspective rather than from pairwise interactions.

    Floral plasticity: Herbivore-species-specific-induced changes in flower traits with contrasting effects on pollinator visitation
    Rusman, Quint ; Poelman, Erik H. ; Nowrin, Farzana ; Polder, Gerrit ; Lucas-Barbosa, Dani - \ 2019
    Plant, Cell & Environment 42 (2019)6. - ISSN 0140-7791 - p. 1882 - 1896.
    Brassica nigra (black mustard) - flower colour - flower morphology - flower rewards - flower volatiles - herbivore-induced plant responses - phenotypic plasticity - plant defence - plant-mediated interactions - specificity

    Plant phenotypic plasticity in response to antagonists can affect other community members such as mutualists, conferring potential ecological costs associated with inducible plant defence. For flowering plants, induction of defences to deal with herbivores can lead to disruption of plant–pollinator interactions. Current knowledge on the full extent of herbivore-induced changes in flower traits is limited, and we know little about specificity of induction of flower traits and specificity of effect on flower visitors. We exposed flowering Brassica nigra plants to six insect herbivore species and recorded changes in flower traits (flower abundance, morphology, colour, volatile emission, nectar quantity, and pollen quantity and size) and the behaviour of two pollinating insects. Our results show that herbivory can affect multiple flower traits and pollinator behaviour. Most plastic floral traits were flower morphology, colour, the composition of the volatile blend, and nectar production. Herbivore-induced changes in flower traits resulted in positive, negative, or neutral effects on pollinator behaviour. Effects on flower traits and pollinator behaviour were herbivore species-specific. Flowers show extensive plasticity in response to antagonist herbivores, with contrasting effects on mutualist pollinators. Antagonists can potentially act as agents of selection on flower traits and plant reproduction via plant-mediated interactions with mutualists.

    Adaptation to developmental diet influences the response to selection on age at reproduction in the fruit fly
    May, Christina M. ; Heuvel, Joost van den; Doroszuk, Agnieszka ; Hoedjes, Katja M. ; Flatt, Thomas ; Zwaan, Bas J. - \ 2019
    Journal of Evolutionary Biology 32 (2019)5. - ISSN 1010-061X - p. 425 - 437.
    ageing - experimental evolution - life-history evolution - phenotypic plasticity

    Experimental evolution (EE) is a powerful tool for addressing how environmental factors influence life-history evolution. While in nature different selection pressures experienced across the lifespan shape life histories, EE studies typically apply selection pressures one at a time. Here, we assess the consequences of adaptation to three different developmental diets in combination with classical selection for early or late reproduction in the fruit fly Drosophila melanogaster. We find that the response to each selection pressure is similar to that observed when they are applied independently, but the overall magnitude of the response depends on the selection regime experienced in the other life stage. For example, adaptation to increased age at reproduction increased lifespan across all diets; however, the extent of the increase was dependent on the dietary selection regime. Similarly, adaptation to a lower calorie developmental diet led to faster development and decreased adult weight, but the magnitude of the response was dependent on the age-at-reproduction selection regime. Given that multiple selection pressures are prevalent in nature, our findings suggest that trade-offs should be considered not only among traits within an organism, but also among adaptive responses to different—sometimes conflicting—selection pressures, including across life stages.

    Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen
    Pais, Marina ; Yoshida, Kentaro ; Giannakopoulou, Artemis ; Pel, M. ; Cano, Liliana M. ; Oliva, Ricardo F. ; Witek, Kamil ; Lindqvist-Kreuze, Hannele ; Vleeshouwers, V.G.A.A. ; Kamoun, Sophien - \ 2018
    The Sainsbury Laboratory
    asexual reproduction - clonal lineage - Phytophthora infestans - emergent pathogen - evolution - immunity - phenotypic plasticity - expression polymorphism - structural variation - copy number variation - loss of heterozygosity
    Background Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186–194, 2012; Kupferschmidt K, Science 337:636–638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335–345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591–11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans. Results Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081–1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375–380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265–271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. Conclusions Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes.
    Pervasive gene expression responses to a fluctuating diet in Drosophila melanogaster : The importance of measuring multiple traits to decouple potential mediators of life span and reproduction
    Zandveld, Jelle ; Heuvel, Joost van den; Mulder, Maarten ; Brakefield, Paul M. ; Kirkwood, Thomas B.L. ; Shanley, Daryl P. ; Zwaan, Bas J. - \ 2017
    Evolution 71 (2017)11. - ISSN 0014-3820 - p. 2572 - 2583.
    Fecundity - gene regulatory networks - life span regulation - phenotypic plasticity - trade-offs
    Phenotypic plasticity is an important concept in life-history evolution, and most organisms, including Drosophila melanogaster, show a plastic life-history response to diet. However, little is known about how these life-history responses are mediated. In this study, we compared adult female flies fed an alternating diet (yoyo flies) with flies fed a constant low (CL) or high (CH) diet and tested how whole genome expression was affected by these diet regimes and how the transcriptional responses related to different life-history traits. We showed that flies were able to respond quickly to diet fluctuations throughout life span by drastically changing their transcription. Importantly, by measuring the response of multiple life-history traits we were able to decouple groups of genes associated with life span or reproduction, life-history traits that often covary with a diet change. A coexpression network analysis uncovered which genes underpin the separate and shared regulation of these life-history traits. Our study provides essential insights to help unravel the genetic architecture mediating life-history responses to diet, and it shows that the flies’ whole genome transcription response is highly plastic.
    The island rule of body size demonstrated on individual hosts : phytophagous click beetle species grow larger and predators smaller on phylogenetically isolated trees
    Molleman, Freerk ; Depoilly, Alexandre ; Vernon, Philippe ; Müller, Jörg ; Bailey, Richard ; Jarzabek-Müller, Andrea ; Prinzing, Andreas - \ 2016
    Journal of Biogeography 43 (2016)7. - ISSN 0305-0270 - p. 1388 - 1399.
    community ecology - dispersal selection - Elateridae - forest - island biogeography - local adaptation - microevolution - phenotypic plasticity - plant–animal interactions - vegetation diversity

    Aim: Under spatial isolation on oceanic islands, species tend to show extreme body sizes. From the point of view of many colonizers, individual hosts surrounded by phylogenetically distant neighbours are phylogenetically isolated. This study addresses for the first time how phylogenetic isolation of individual hosts affects body size of colonizers, and whether effects on body size reflect selection among colonizers established on host individuals rather than selection among colonizers dispersing toward trees or phenotypic plasticity of colonizers. Location: Rennes National Forest, Western France. Methods: We sampled click beetles (Elateridae) on individual oak trees varying in phylogenetic isolation from their neighbours and in age. We measured body size and fluctuating asymmetry (which we found to correlate to reduced body size) and related both to phylogenetic isolation and age of trees. We compared these relationships among species of different larval trophic position and adult body size, using meta-analytical approaches. Results: Within species, body size changes with phylogenetic isolation of individual host trees: root feeders tend to become larger, predators smaller. Effects were independent of mean body-size, disappeared with tree age, and were inconsistent with patterns of fluctuating asymmetry. Main conclusions: Our results are consistent with body-size selection among colonizers established on individual trees, rather than selection among colonizers dispersing toward trees or phenotypic plasticity. Overall, phenotype patterns of animals across islands in the ocean may resemble those across host individuals in a phylogenetically distant neighbourhood, suggesting micro-evolution of colonizers in response to the macro-evolutionary structure of the host community.

    Community structure and abundance of insects in response to early-season aphid infestation in wild cabbage populations
    Li, Yehua ; Stam, Jeltje M. ; Poelman, Erik H. ; Dicke, Marcel ; Gols, Rieta - \ 2016
    Ecological Entomology 41 (2016)4. - ISSN 0307-6946 - p. 378 - 388.
    Aphid infestation - Brassica oleracea - early-season herbivory - genotypic variation - insect community - phenotypic plasticity - 016-3964

    Changes in the arthropod community structure can be attributed to differences in constitutively expressed plant traits or those that change depending on environmental conditions such as herbivory. Early-season herbivory may have community-wide effects on successive insect colonisation of host plants and the identity of the initially inducing insect may determine the direction and strength of the effects on the dynamics and composition of the associated insect community. 2. Previous studies have addressed the effect of early infestation with a chewing herbivore. In the present study, the effect of early infestation was investigated with a phloem-feeding aphid [Brevicoryne brassicae L. (Hemiptera, Aphididae)] on the insect community associated with three wild cabbage (Brassica oleracea L.) populations, which are known to differ in defence chemistry, throughout the season in field experiments. 3. Aphid infestation had asymmetric effects on the associated insect community and only influenced the abundance of the natural enemies of aphids, but not that of chewing herbivores and their natural enemies. The effect size of aphid infestation further depended on the cabbage population. 4. Aphid feeding has been previously reported to promote host-plant quality for chewing herbivores, which has been attributed to antagonism between the two major defence signalling pathways controlled by the hormones salicylic acid (SA) and jasmonic acid (JA), respectively. Our results show no effects of early infestation by aphids on chewing herbivores, suggesting the absence of long-term JA–SA antagonism. 5. Investigating the effects of the identity of an early-season coloniser and genotypic variation among plant populations on insect community dynamics are important in understanding insect–plant community ecology.

    The epigenetic footprint of poleward range-expanding plants in apomictic dandelions
    Preite, V. ; Snoek, L.B. ; Oplaat, C. ; Biere, A. ; Putten, W.H. van der; Verhoeven, K.J.F. - \ 2015
    Molecular Ecology 24 (2015)17. - ISSN 0962-1083 - p. 4406 - 4418.
    dna methylation polymorphism - arabidopsis-thaliana - geographic parthenogenesis - ecological epigenetics - phenotypic plasticity - cytosine methylation - population-structure - japanese knotweed - common dandelion - taraxacum
    Epigenetic modifications, such as DNA methylation variation, can generate heritable phenotypic variation independent of the underlying genetic code. However, epigenetic variation in natural plant populations is poorly documented and little understood. Here, we test if northward range expansion of obligate apomicts of the common dandelion (Taraxacum officinale) is associated with DNA methylation variation. We characterized and compared patterns of genetic and DNA-methylation variation in greenhouse-reared offspring of T. officinale that were collected along a latitudinal transect of northward range expansion in Europe. Genetic AFLP and epigenetic MS-AFLP markers revealed high levels of local diversity and modest but significant heritable differentiation between sampling locations and between the Southern, Central and Northern regions of the transect. Patterns of genetic and epigenetic variation were significantly correlated, reflecting the genetic control over epigenetic variation and/or the accumulation of lineage-specific spontaneous epimutations, which may be selectively neutral. In addition, we identified a small component of DNA methylation differentiation along the transect that is independent of genetic variation. This epigenetic differentiation might reflect environment-specific induction or, in case the DNA methylation variation affects relevant traits and fitness, selection of heritable DNA methylation variants. Such generated epigenetic variants might contribute to the adaptive capacity of individual asexual lineages under changing environments. Our results highlight the potential of heritable DNA methylation variation to contribute to population differentiation along ecological gradients. Further studies are needed using higher-resolution methods to understand the functional significance of such natural occurring epigenetic differentiation.
    Interplay of robustness and plasticity of life history traits in habitats with different thermal regimes
    Liefting, M. ; Grunsven, R.H.A. van; Morrissey, M.B.M. ; Timmermans, M. ; Ellers, J. - \ 2015
    Journal of Evolutionary Biology 28 (2015)5. - ISSN 1010-061X - p. 1057 - 1066.
    orchesella-cincta collembola - wild bird population - phenotypic plasticity - reaction norms - genetic-structure - environmental canalization - drosophila-melanogaster - indeterminate growth - soil arthropod - evolution
    Phenotypic plasticity describes the ability of an individual to alter its phenotype in response to the environment and is potentially adaptive when dealing with environmental variation. However, robustness in the face of a changing environment may often be beneficial for traits that are tightly linked to fitness. We hypothesized that robustness of some traits may depend on specific patterns of plasticity within and among other traits. We used a reaction norm approach to study robustness and phenotypic plasticity of three life-history traits of the collembolan Orchesella cincta in environments with different thermal regimes. We measured adult mass, age at maturity and growth rate of males and females from heath and forest habitats at two temperatures (12 and 22 °C). We found evidence for ecotype-specific robustness of female adult mass to temperature, with a higher level of robustness in the heath ecotype. This robustness is facilitated by plastic adjustments of growth rate and age at maturity. Furthermore, female fecundity is strongly influenced by female adult mass, explaining the importance of realizing a high mass across temperatures for females. These findings indicate that different predicted outcomes of life-history theory can be combined within one species' ontogeny and that models describing life-history strategies should not assume that traits like growth rate are maximized under all conditions. On a methodological note, we report a systematic inflation of variation when standard deviations and correlation coefficients are calculated from family means as opposed to individual data within a family structure.
    Combined biotic and abiotic stress resistance in tomato
    Kissoudis, C. ; Chowdhury, R. ; Heusden, A.W. van; Wiel, C.C.M. van de; Finkers, H.J. ; Visser, R.G.F. ; Bai, Y. ; Linden, C.G. van der - \ 2015
    Euphytica 202 (2015)2. - ISSN 0014-2336 - p. 317 - 332.
    salt tolerance - oidium-neolycopersici - salinity tolerance - botrytis-cinerea - powdery mildew - abscisic-acid - plant-disease - phenotypic plasticity - solanum-lycopersicon - climate-change
    Abiotic and biotic stress factors are the major constrains for the realization of crop yield potential. As climate change progresses, the spread and intensity of abiotic as well as biotic stressors is expected to increase, with increased probability of crops being exposed to both types of stress. Shielding crops from combinatorial stress requires a better understanding of the plant’s response and its genetic architecture. In this study, we evaluated resistance to salt stress, powdery mildew and to both stresses combined in tomato, using the Solanum habrochaites LYC4 introgression line (IL) population. The IL population segregated for both salt stress tolerance and powdery mildew resistance. Using SNP array marker data, QTLs were identified for salt tolerance as well as Na+ and Cl- accumulation. Salt stress increased the susceptibility of the population to powdery mildew in an additive manner. Phenotypic variation for disease resistance was reduced under combined stress as indicated by the coefficient of variation. No correlation was found between disease resistance and Na+ and Cl- accumulation under combined stress Most genetic loci were specific for either salt stress tolerance or powdery mildew resistance. These findings increase our understanding of the genetic regulation of responses to abiotic and biotic stress combinations and can provide leads to more efficiently breeding tomatoes and other crops with a high level of disease resistance while maintaining their performance in combination with abiotic stress.
    On selection for flowering time plasticity in response to density
    Vermeulen, P.J. - \ 2015
    New Phytologist 205 (2015)1. - ISSN 0028-646X - p. 429 - 439.
    arabidopsis-thaliana - phenotypic plasticity - shade-avoidance - adaptive plasticity - impatiens-capensis - dependent selection - plant-populations - genetic-variation - local adaptation - life-history
    Different genotypes often exhibit opposite plastic responses in the timing of the onset of flowering with increasing plant density. In experimental studies, selection for accelerated flowering is generally found. By contrast, game theoretical studies predict that there should be selection for delayed flowering when competition increases. Combining different optimality criteria, the conditions under which accelerated or delayed flowering in response to density would be selected for are analysed with a logistic growth simulation model. To maximize seed production at the whole-stand level (simple optimization), selection should lead to accelerated flowering at high plant density, unless very short growing seasons select for similar onset of flowering at all densities. By contrast, selection of relative individual fitness will lead to delayed flowering when season length is long and/or growth rates are high. These different results give a potential explanation for the observed differences in direction of the plastic responses within and between species, including homeostasis, as a result of the effect of the variation in season length on the benefits of delayed flowering. This suggests that limited plasticity can evolve without the costs and limits that are currently thought to constrain the evolution of plasticity.
    Data from: The plastic fly: the effect of sustained fluctuations in adult food supply on life history traits
    Heuvel, Joost van den; Zandveld, Jelle ; Mulder, M. ; Brakefield, P.M. ; Kirkwood, T.B.L. ; Shanley, D.P. ; Zwaan, Bas - \ 2014
    Wageningen University & Research
    ageing - resource allocation - lifespan - life history - phenotypic plasticity - weight - diet - drosophila melanogaster - reproduction
    Many adult traits in Drosophila melanogaster show phenotypic plasticity, and the effects of diet on traits such as lifespan and reproduction are well explored. Although plasticity in response to food is still present in older flies, it is unknown how sustained environmental variation affects life-history traits. Here, we explore how such life-long fluctuations of food supply affect weight and survival in groups of flies and affect weight, survival and reproduction in individual flies. In both experiments, we kept adults on constant high or low food and compared these to flies that experienced fluctuations of food either once or twice a week. For these ‘yoyo’ groups, the initial food level and the duration of the dietary variation differed during adulthood, creating four ‘yoyo’ fly groups. In groups of flies, survival and weight were affected by adult food. However, for individuals, survival and reproduction, but not weight, were affected by adult food, indicating that single and group housing of female flies affects life-history trajectories. Remarkably, both the manner and extent to which life-history traits varied in relation to food depended on whether flies initially experienced high or low food after eclosion. We therefore conclude that the expression of life-history traits in adult life is affected not only by adult plasticity, but also by early adult life experiences. This is an important but often overlooked factor in studies of life-history evolution and may explain variation in life-history experiments.
    Ecdysteroid hormones link the juvenile environment to alternative adult life histories in a seasonal insect
    Oostra, V. ; Mateus, A.R.A. ; Burg, K.R.L. van den; Piessens, T. ; Eijk, M. van; Brakefield, P.M. ; Beldade, P. ; Zwaan, B.J. - \ 2014
    Wageningen UR
    development - endocrinology - evolution - life history - aging - phenotypic plasticity - physiology - seasonal adaptation - ecdysone
    Four datasets from: Ecdysteroid hormones link the juvenile environment to alternative adult life histories in a seasonal insect; by Oostra, Vicencio; Mateus, Ana Rita A.; Van der Burg, Karin R.L.; Piessens,Thomas; Van Eijk, Marleen; Brakefield, Paul M.; Beldade, Patrícia; Zwaan, Bas; as published in American Naturalist 2014. This ZIP archive contains four csv data files: 1) experiment1.csv; 2) experiment2_dataset1.csv; 3) experiment2_dataset2.csv; 4) experiment2_dataset3.csv. See readme.txt for details.
    On the fate of seasonally plastic traits in a rainforest butterfly under relaxed selection
    Oostra, V. ; Brakefield, P.M. ; Hiltemann, Y. ; Zwaan, B.J. ; Brattström, O. - \ 2014
    Ecology and Evolution 4 (2014)13. - ISSN 2045-7758 - p. 2654 - 2667.
    sexual size dimorphism - bicyclus-anynana - phenotypic plasticity - reaction norms - life-history - evolutionary significance - artificial selection - geographic-variation - resource-allocation - thermal plasticity
    Many organisms display phenotypic plasticity as adaptation to seasonal environmental fluctuations. Often, such seasonal responses entails plasticity of a whole suite of morphological and life-history traits that together contribute to the adaptive phenotypes in the alternative environments. While phenotypic plasticity in general is a well-studied phenomenon, little is known about the evolutionary fate of plastic responses if natural selection on plasticity is relaxed. Here, we study whether the presumed ancestral seasonal plasticity of the rainforest butterfly Bicyclus sanaos (Fabricius, 1793) is still retained despite the fact that this species inhabits an environmentally stable habitat. Being exposed to an atypical range of temperatures in the laboratory revealed hidden reaction norms for several traits, including wing pattern. In contrast, reproductive body allocation has lost the plastic response. In the savannah butterfly, B. anynana (Butler, 1879), these traits show strong developmental plasticity as an adaptation to the contrasting environments of its seasonal habitat and they are coordinated via a common developmental hormonal system. Our results for B. sanaos indicate that such integration of plastic traits – as a result of past selection on expressing a coordinated environmental response – can be broken when the optimal reaction norms for those traits diverge in a new environment
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