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.

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DOG1-imposed dormancy mediates germination responses to temperature cues
Murphey, M. ; Kovach, K. ; Elnacash, T. ; He, H. ; Bentsink, L. ; Donohue, K. - \ 2015
Environmental and Experimental Botany 112 (2015). - ISSN 0098-8472 - p. 33 - 43.
seed-maturation environment - quantitative trait locus - recent climate-change - arabidopsis-thaliana - life-history - ectopic expression - niche construction - natural-selection - dog1-like genes - dog1
Seed dormancy and environment-dependent germination requirements interact to determine the timing of germination in natural environments. This study tested the contribution of the dormancy gene Delay Of Germination 1 (DOG1) to primary and secondary dormancy induction in response to environmental cues, and evaluated how DOG1-mediated dormancy influenced germination responses to different temperature cues. We verified that DOG1 is involved in the induction of primary dormancy in response to cool seed-maturation temperature experienced by maternal plants, and we found that it is also involved in secondary dormancy in response to warm and prolonged cold stratification experienced by seeds during imbibition. DOG1-imposed dormancy can also mediate germination responses to environmental conditions, including cold stratification and germination temperatures experienced by imbibing seeds. Specifically, germination responsiveness to temperature cues is most apparent when seeds exhibit an intermediate degree of dormancy. However, DOG1 itself does not seem to directly regulate the response to cold stratification nor does it determine the function of temperature-dependent germination, since DOG1 mutants were capable of exhibiting increased germination after cold stratification as well as temperature-dependent germination. Instead, DOG1 has major effects on germination behavior primarily by exposing or masking underlying environmental sensitivity, and thereby strongly influences how environmentally responsive germination can be, and when during a season, it is likely to exhibit environmental sensitivity.
Testing the Generalist-Specialist Dilemma: The Role of Pyrrolizidine Alkaloids in Resistance to Invertebrate Herbivores in Jacobaea Species
Wei, X. ; Vrieling, K. ; Mulder, P.P.J. ; Klinkhamer, P.G.L. - \ 2015
Journal of Chemical Ecology 41 (2015). - ISSN 0098-0331 - p. 159 - 167.
longitarsus flea beetles - senecio-jacobaea - secondary metabolites - natural-selection - chemical defense - ipomopsis-aggregata - plant defense - scarlet-gilia - host plants - hybridization
Plants produce a diversity of secondary metabolites (SMs) to protect them from generalist herbivores. On the other hand, specialist herbivores use SMs for host plant recognition, feeding and oviposition cues, and even sequester SMs for their own defense. Therefore, plants are assumed to face an evolutionary dilemma stemming from the contrasting effects of generalist and specialist herbivores on SMs. To test this hypothesis, bioassays were performed with F2 hybrids from Jacobaea species segregating for their pyrrolizidine alkaloids (PAs), using a specialist flea beetle (Longitarsus jacobaeae) and a generalist slug (Deroceras invadens). Our study demonstrated that while slug feeding damage was negatively correlated with the concentration of total PAs and that of senecionine-like PAs, flea beetle feeding damage was not affected by PAs. It was positively correlated though, with leaf fresh weight. The generalist slug was deterred by senecionine-like PAs but the specialist flea beetle was adapted to PAs in its host plant. Testing other herbivores in the same plant system, it was observed that the egg number of the specialist cinnabar moth was positively correlated with jacobine-like PAs, while the silver damage of generalist thrips was negatively correlated with senecionine- and jacobine-like PAs, and the pupae number of generalist leaf miner was negatively correlated with otosenine-like PAs. Therefore, while the specialist herbivores showed no correlation whatsoever with PA concentration, the generalist herbivores all showed a negative correlation with at least one type of PA. We concluded that the generalist herbivores were deterred by different structural groups of PAs while the specialist herbivores were attracted or adapted to PAs in its host plants.
Empirical fitness landscapes and the predictability of evolution
Visser, J.A.G.M. de; Krug, J. - \ 2014
Nature Reviews Genetics 15 (2014). - ISSN 1471-0056 - p. 480 - 490.
escherichia-coli population - beneficial mutations - deleterious mutations - antibiotic-resistance - adaptive trajectories - natural-selection - sequence space - sign epistasis - adaptation - model
The genotype–fitness map (that is, the fitness landscape) is a key determinant of evolution, yet it has mostly been used as a superficial metaphor because we know little about its structure. This is now changing, as real fitness landscapes are being analysed by constructing genotypes with all possible combinations of small sets of mutations observed in phylogenies or in evolution experiments. In turn, these first glimpses of empirical fitness landscapes inspire theoretical analyses of the predictability of evolution. Here, we review these recent empirical and theoretical developments, identify methodological issues and organizing principles, and discuss possibilities to develop more realistic fitness landscape models.
Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci
Andre, C. ; Larsson, L.C. ; Laikre, L. ; Bekkevold, D. ; Brigham, J. ; Carvalho, G.R. ; Dahlgren, T.G. ; Hutchinson, W.F. ; Mariani, S. ; Mudde, C.M. ; Ruzzante, D.E. ; Ryman, N. - \ 2011
Heredity 106 (2011)2. - ISSN 0018-067X - p. 270 - 280.
cod gadus-morhua - salmon salmo-salar - histocompatibility class-i - mitochondrial-dna - north-sea - molecular markers - balancing selection - statistical power - natural-selection - computer-program
In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species. Heredity (2011) 106, 270-280; doi:10.1038/hdy.2010.71; published online 16 June 2010
The effects of herbivore-induced plant volatiles on interactions between plants and flower-visiting insects
Lucas Gomes Marques Barbosa, D. ; Loon, J.J.A. van; Dicke, M. - \ 2011
Phytochemistry 72 (2011)13. - ISSN 0031-9422 - p. 1647 - 1654.
floral scent - leaf herbivory - multitrophic interactions - nicotiana-attenuata - natural-selection - indirect defenses - isomeris-arborea - parasitic wasps - cotton plants - wild radish
Plants are faced with a trade-off between on the one hand growth, development and reproduction and on the other hand defence against environmental stresses. Yet, research on insect–plant interactions has addressed plant–pollinator interactions and plant–attacker interactions separately. Plants have evolved a high diversity of constitutive and induced responses to attack, including the systemic emission of herbivore-induced plant volatiles (HIPVs). The effect of HIPVs on the behaviour of carnivorous insects has received ample attention for leaf-feeding (folivorous) species and their parasitoids and predators. Here, we review whether and to what extent HIPVs affect the interaction of plants in the flowering stage with mutualistic and antagonistic insects. Whereas the role of flower volatiles in the interactions between plants and insect pollinators has received increased attention over the last decade, studies addressing both HIPVs and pollinator behaviour are rare, despite the fact that in a number of plant species herbivory is known to affect flower traits, including size, nectar secretion and composition. In addition, folivory and florivory can also result in significant changes in flower volatile emission and in most systems investigated, pollinator visitation decreased, although exceptions have been found. Negative effects of HIPVs on pollinator visitation rates likely exert negative selection pressure on HIPV emission. The systemic nature of herbivore-induced plant responses and the behavioural responses of antagonistic and mutualistic insects, requires the study of volatile emission of entire plants in the flowering stage. We conclude that approaches to integrate the study of plant defences and pollination are essential to advance plant biology, in particular in the context of the trade-off between defence and growth/reproduction
Varying disease-mediated selection at different life-history stages of Atlantic salmon in fresh water
Eyto, E. de; McGinnity, P. ; Huisman, J. ; Coughlan, J. ; Consuegra, S. ; Megens, H.J.W.C. - \ 2011
Evolutionary Applications 4 (2011)6. - ISSN 1752-4563 - p. 749 - 762.
major histocompatibility complex - class-i locus - salar l. - genetic-variation - pathogen resistance - balancing selection - natural-selection - wild populations - local adaptation - climate-change
Laboratory studies on associations between disease resistance and susceptibility and major histocompatibility (MH) genes in Atlantic salmon Salmo salar have shown the importance of immunogenetics in understanding the capacity of populations to fight specific diseases. However, the occurrence and virulence of pathogens may vary spatially and temporally in the wild, making it more complicated to predict the overall effect that MH genes exert on fitness of natural populations and over several life-history stages. Here we show that MH variability is a significant determinant of salmon survival in fresh water, by comparing observed and expected genotype frequencies at MH and control microsatellite loci at parr and migrant stages in the wild. We found that additive allelic effects at immunogenetic loci were more likely to determine survival than dominance deviation, and that selection on certain MH alleles varied with life stage, possibly owing to varying pathogen prevalence and/or virulence over time. Our results highlight the importance of preserving genetic diversity (particularly at MH loci) in wild populations, so that they have the best chance of adapting to new and increased disease challenges as a result of projected climate warming and increasing aquaculture
DOG1 expression is predicted by the seed-maturation envornment and contributes to geographical variation in germination in Arabidopsis thaliana
Chiang, G.C.K. ; Bartsch, M. ; Barua, D. ; Nakabayashi, K. ; Debieu, M. ; Kronholm, I. ; Koornneef, M. ; Soppe, W.J.J. ; Donohue, K. ; Meaux, J. De - \ 2011
Molecular Ecology 20 (2011)16. - ISSN 0962-1083 - p. 3336 - 3349.
flowering time gene - natural-selection - dormancy - brassicaceae - evolution - field - diversification - adaptation - characters - plasticity
Seasonal germination timing of Arabidopsis thaliana strongly influences overall life history expression and is the target of intense natural selection. This seasonal germination timing depends strongly on the interaction between genetics and seasonal environments both before and after seed dispersal. DELAY OF GERMINATION 1 (DOG1) is the first gene that has been identified to be associated with natural variation in primary dormancy in A. thaliana. Here, we report interaccession variation in DOG1 expression and document that DOG1 expression is associated with seed-maturation temperature effects on germination; DOG1 expression increased when seeds were matured at low temperature, and this increased expression was associated with increased dormancy of those seeds. Variation in DOG1 expression suggests a geographical structure such that southern accessions, which are more dormant, tend to initiate DOG1 expression earlier during seed maturation and achieved higher expression levels at the end of silique development than did northern accessions. Although elimination of the synthesis of phytohormone abscisic acid (ABA) results in the elimination of maternal temperature effects on dormancy, DOG1 expression predicted dormancy better than expression of genes involved in ABA metabolism
The potential of a population genomics approach to analyse geographic mosaics of plant–insect coevolution
Vermeer, K.M.C.A. ; Dicke, M. ; Jong, P.W. de - \ 2011
Evolutionary Ecology 25 (2011)5. - ISSN 0269-7653 - p. 977 - 992.
ecologically important traits - beetle phyllotreta-nemorum - bebbianae leaf beetles - barbarea-vulgaris - host-plant - genetic differentiation - flea beetle - natural-selection - lodgepole pine - diffuse coevolution
A central issue in the evolutionary ecology of species interactions is coevolution, which involves the reciprocal selection between individuals of interacting species. Understanding the importance of coevolution in shaping species interactions requires the consideration of spatial variation in their strength. This is exactly what the, recently developed, geographic mosaic theory of coevolution addresses. Another major development in the study of population ecology is the introduction of the population genomics approach in this field of research. This approach addresses spatial processes through molecular methods. It is of particular interest that population genomics is especially applicable to natural populations of non-model species. We describe how population genomics can be used in the context of the geographic mosaic of coevolution, specifically to identify coevolutionary hot-spots, and to attribute genetic variation found at specific loci to processes of selection versus trait remixing. The proposed integration of the population genomics approach with the conceptual framework of the geographic mosaic of coevolution is illustrated with a few selected, particularly demonstrative, examples from the realm of insect–plant interactions.
Genetic differences among populations in sexual dimorphism: evidence for selection on males in a dioecious plant
Yu, Q. ; Ellen, E.D. ; Wade, M.J. ; Delph, L.F. - \ 2011
Journal of Evolutionary Biology 24 (2011)5. - ISSN 1010-061X - p. 1120 - 1127.
silene-latifolia caryophyllaceae - quantitative genetics - size dimorphism - artificial selection - phenotypic evolution - natural-selection - chloroplast dna - g-matrix - adaptation - traits
Genetic variation among populations in the degree of sexual dimorphism may be a consequence of selection on one or both sexes. We analysed genetic parameters from crosses involving three populations of the dioecious plant Silene latifolia, which exhibits sexual dimorphism in flower size, to determine whether population differentiation was a result of selection on one or both sexes. We took the novel approach of comparing the ratio of population differentiation of a quantitative trait (QST) to that of neutral genetic markers (FST) for males vs. females. We attributed 72.6% of calyx width variation in males to differences among populations vs. only 6.9% in females. The QST/FST ratio was 4.2 for males vs. 0.4 for females, suggesting that selection on males is responsible for differentiation among populations in calyx width and its degree of sexual dimorphism. This selection may be indirect via genetic correlations with other morphological and physiological traits
The role of constraints and limitation in driving individual variation in immune response
Ardia, D.R. ; Parmentier, H.K. ; Vogel, L.A. - \ 2011
Functional Ecology 25 (2011)1. - ISSN 0269-8463 - p. 61 - 73.
red-blood-cells - major histocompatibility complex - primary antibody-response - quantitative trait loci - regulatory t-cells - sheep erythrocytes - natural-selection - drosophila-melanogaster - evolutionary ecology - divergent selection
1. Life history theory predicts that immunity should be plastic and reflect environmental contexts. However, individual variation in immune investment may arise not just because of individual adjustment, but because of developmental, physiological, genetic or immunological constraints which lead to non-adaptive responses by limiting or eliminating flexibility in immune investment. Constraints can arise because organisms are single integrated units with interconnected and interacting components, in which physiological and genetic control mechanisms may limit or constrain immunity. We review some of the key underlying genetic and physiological factors that may constrain the occurrence and intensity of immune responses. 2. A major part of individual variability may rest on variation in genetic background. Genetic-based constraints can limit or influence immune responses, particularly through pleiotropy and epistatic interactions. In addition, genetic variation, an important driver of variation in antigen recognition and immune system polarization, can be constrained through linkage disequilibrium and genetic drift. Epigenetic changes can also constrain or limit immune responses in future generations based on individual experience. 3. The immune system itself can influence individual flexibility in immune investment. Throughout development individuals face tradeoffs within the immune system that favour the expression of one trait at the expense of another. Ontogenetic differences can cause juveniles and adults to produce entirely different immune responses to the same pathogen. T-helper 1 (Th1)/T-helper 1 (Th2) polarization during infection also imposes constraints upon an individual’s immune responsiveness, with the consequence that hosts cannot simultaneously mount strong responses using both Th1 and Th2 cells. In addition, evidence suggests that flexibility in immune responses becomes constrained with age through accumulation of memory cells at the expense of naïve cells, decreased function of cells involved in adaptive and innate immunity, and programming of HPA-immune interactions. 4. In summary, selection on a particular immune trait can have effects on other immune components or phenotypic characters, as revealed by artificial selection studies. In particular selection for increased investment in compartments of the immune system leads to decreased investment in other competing life history functions and/or marked changes in other immune components. The role of past experience, even the past experience of parents, may limit and constrain immune responses through influencing the ontogeny of immunity, as well as through epigenetic influences.
Phenotypic selection on leaf ecophysiological traits in Helianthus
Donovan, L.A. ; Ludwig, F. ; Rosenthal, D.R. ; Rieseberg, L.H. ; Dudley, S.A. - \ 2009
New Phytologist 183 (2009)3. - ISSN 0028-646X - p. 868 - 879.
carbon-isotope discrimination - water-use efficiency - plant physiological traits - natural-selection - impatiens-capensis - genetic-variation - polygonum-arenastrum - differing selection - variable selection - functional traits
Habitats that differ in soil resource availability are expected to differ for selection on resource-related plant traits. Here, we examined spatial and temporal variation in phenotypic selection on leaf ecophysiological traits for 10 Helianthus populations, including two species of hybrid origin, Helianthus anomalus and Helianthus deserticola, and artificial hybrids of their ancestral parents. Leaf traits assessed were leaf size, succulence, nitrogen (N) concentration and water-use efficiency (WUE). Biomass and leaf traits of artificial hybrids indicate that the actively moving dune habitat of H. anomalus was more growth limiting, with lower N availability but higher relative water availability than the stabilized dune habitat of H. deserticola. Habitats differed for direct selection on leaf N and WUE, but not size or succulence, for the artificial hybrids. However, within the H. anomalus habitat, direct selection on WUE also differed among populations. Across years, direct selection on leaf traits did not differ. Leaf N was the only trait for which direct selection differed between habitats but not within the H. anomalus habitat, suggesting that nutrient limitation is an important selective force driving adaptation of H. anomalus to the active dune habitat
Characterization of a major histocompatibility class II A gene (Clha-DAA) with an embedded microsatellite marker in Atlantic herring (Clupea harengus L.)
Stet, R.J.M. ; Mudde, K. ; Wynne, J.W. ; Nooijen, A. ; Dahlgren, T.G. ; Ruzzante, D.E. ; Andre, C. - \ 2008
Journal of Fish Biology 73 (2008)2. - ISSN 0022-1112 - p. 367 - 381.
salmon salmo-salar - mhc class-ii - chain-encoding genes - complex class-ii - population-structure - barbus-intermedius - natural-selection - alpha-chain - danio-rerio - polymorphism
An Atlantic herring major histocompatibility class II A (Clha-DAA) cDNA sequence has been characterized and was shown to encode a leader peptide, alpha-1 domain, alpha-2 domain, connecting peptide, transmembrane and cytoplasmic region. The Clha-DAA protein sequence has all the characteristics of a teleost class II A protein with conserved cysteines in both the alpha-1 and the alpha-2 domains and two potential N-linked glycosylation sites. Exon 2 sequences encoding the polymorphic alpha-1 domain from different individuals were analysed and revealed the presence of at least two loci. The Clha-DAA gene consists of four exons and three short introns. Four unique intron 3 sequences from multiple individuals were obtained and were shown to contain a (TG)(n) microsatellite sequence. Primers were optimized such that only a single microsatellite locus designated Clha-DAA-INTR3 was amplified. Four herring populations from the North Sea and the Baltic Sea were genotyped for Clha-DAA-INTR3. In total, 16 Clha-DAA-INTR3 alleles were detected; the distribution of the alleles showed no deviation from Hardy-Weinberg expectation. Levels of genetic differentiation among samples were of similar magnitude as have been reported earlier for neutral microsatellite loci between northern North Sea and Baltic Sea herring populations. (C) 2008 The Authors Journal compilation (C) 2008 The Fisheries Society of the British Isles.
Coevolution of Human Speech and Trade
Horan, R.D. ; Bulte, E.H. ; Shogren, J.F. - \ 2008
Journal of Economic Growth 13 (2008)4. - ISSN 1381-4338 - p. 293 - 313.
evolutionary game - natural-selection - red-queen - neanderthals - dynamics - brain - equilibrium - extinction - emergence - exclusion
We propose a paleoeconomic coevolutionary explanation for the origin of speech in modern humans. The coevolutionary process, in which trade facilitates speech and speech facilitates trade, gives rise to multiple stable trajectories. While a `trade-speech¿ equilibrium is not an inevitable outcome for modern humans, we find it is a relatively likely scenario given our species evolved in Africa under climatic conditions supporting relatively high population densities. The origin of human speech is not independent of economic institutions¿the economics of early human trade can provide additional insight to help explain the physiological emergence of human speech.
The joint effects of kin, multilevel selection and indirect genetic effects on response to genetic selection
Bijma, P. ; Wade, M.J. - \ 2008
Journal of Evolutionary Biology 21 (2008)5. - ISSN 1010-061X - p. 1175 - 1188.
polygenic behavioral trait - social interactions - natural-selection - incorporating interaction - interacting phenotypes - evolutionary process - model - parameters - individuals - cooperation
Kin and levels-of-selection models are common approaches for modelling social evolution. Indirect genetic effect (IGE) models represent a different approach, specifying social effects on trait values rather than fitness. We investigate the joint effect of relatedness, multilevel selection and IGEs on response to selection. We present a measure for the degree of multilevel selection, which is the natural partner of relatedness in expressions for response. Response depends on both relatedness and the degree of multilevel selection, rather than only one or the other factor. Moreover, response is symmetric in relatedness and the degree of multilevel selection, indicating that both factors have exactly the same effect. Without IGEs, the key parameter is the product of relatedness and the degree of multilevel selection. With IGEs, however, multilevel selection without relatedness can explain evolution of social traits. Thus, next to relatedness and multilevel selection, IGEs are a key element in the genetical theory of social evolution.
Parental effort and reproductive skew in coalitions of brood rearing female common eiders
Ost, M. ; Clark, C.W. ; Kilpi, M. ; Ydenberg, R.C. - \ 2007
American Naturalist 169 (2007)1. - ISSN 0003-0147 - p. 73 - 86.
somateria-mollissima - body condition - group-size - natural-selection - antarctic petrel - sexual conflict - care - vigilance - behavior - costs
Members of breeding groups face conflicts over parental effort when balancing antipredatory vigilance and feeding. Empirical evidence has shown disparate responses to manipulations of parental effort. We develop a model in which we determine the evolutionarily stable effort of partners given their body conditions, allowing the benefits of shared care to be unevenly divided, and we test this model's predictions with data on common eiders (Somateria mollissima). Eiders show uniparental female care; females may share brood rearing, or they may tend alone, and their body condition at hatching of the young shows large environmentally induced variation. The model predicts that parental effort (vigilance) in a coalition is lower than when tending alone, controlling for parental condition; this prediction is supported by the data. The parental effort in a coalition should be positively correlated with body condition, and this prediction is also supported. Finally, parental effort should increase when partner condition decreases and vice versa; this prediction is partially supported. The Nash bargaining game may provide promising avenues by which to determine the precise settlement of reproductive skew and effort between coalition partners in the future.
The evolution of sex: empirical insights into the roles of epistasis and drift
Visser, J.A.G.M. de; Elena, S.F. - \ 2007
Nature Reviews Genetics 8 (2007). - ISSN 1471-0056 - p. 139 - 149.
yeast saccharomyces-cerevisiae - polygenes controlling viability - deleterious mutations - drosophila-melanogaster - caenorhabditis-elegans - beneficial mutations - synergistic epistasis - natural-selection - escherichia-coli - mullers ratchet
Despite many years of theoretical and experimental work, the explanation for why sex is so common as a reproductive strategy continues to resist understanding. Recent empirical work has addressed key questions in this field, especially regarding rates of mutation accumulation in sexual and asexual organisms, and the roles of negative epistasis and drift as sources of adaptive constraint in asexually reproducing organisms. At the same time, new ideas about the evolution of sexual recombination are being tested, including intriguing suggestions of an important interplay between sex and genetic architecture, which indicate that sex and recombination could have affected their own evolution
Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa)
Chen, K. ; Baxter, T. ; Muir, W.M. ; Groenen, M.A.M. ; Schook, L.B. - \ 2007
International Journal of Biological Sciences 3 (2007)3. - ISSN 1449-2288 - p. 153 - 165.
mitochondrial-dna sequence - increased ovulation rate - radiation hybrid panel - pre-messenger-rna - microsatellite markers - natural-selection - phylogenetic-relationships - chromosome evolution - haplotype structure - mammalian genomes
The pig, a representative of the artiodactyla clade, is one of the first animals domesticated, and has become an important agriculture animal as one of the major human nutritional sources of animal based protein. The pig is also a valuable biomedical model organism for human health. The pig's importance to human health and nutrition is reflected in the decision to sequence its genome (3X). As an animal species with its wild ancestors present in the world, the pig provides a unique opportunity for tracing mammalian evolutionary history and defining signatures of selection resulting from both domestication and natural selection. Completion of the pig genome sequencing project will have significant impacts on both agriculture and human health. Following the pig whole genome sequence drafts, along with large-scale polymorphism data, it will be possible to conduct genome sweeps using association mapping, and identify signatures of selection. Here, we provide a description of the pig genome sequencing project and perspectives on utilizing genomic technologies to exploit pig genome evolution and the molecular basis for phenotypic traits for improving pig production and health.
Multilevel selection 2: Estimating the genetic parameters determing inheritance and response to selection
Bijma, P. ; Muir, W.M. ; Ellen, E.D. ; Wolf, J.B. ; Arendonk, J.A.M. van - \ 2007
Genetics 175 (2007). - ISSN 0016-6731 - p. 289 - 299.
multiple-hen cages - biological groups - natural-selection - incorporating interaction - social interactions - behavioral ecology - body-weight - evolution - survival - size
Interactions among individuals are universal, both in animals and in plants and in natural as well as domestic populations. Understanding the consequences of these interactions for the evolution of populations by either natural or artificial selection requires knowledge of the heritable components underlying them. Here we present statistical methodology to estimate the genetic parameters determining response to multilevel selection of traits affected by interactions among individuals in general populations. We apply these methods to obtain estimates of genetic parameters for survival days in a population of layer chickens with high mortality due to pecking behavior. We find that heritable variation is threefold greater than that obtained from classical analyses, meaning that two-thirds of the full heritable variation is hidden to classical analysis due to social interactions. As a consequence, predicted responses to multilevel selection applied to this population are threefold greater than classical predictions. This work, combined with the quantitative genetic theory for response to multilevel selection presented in an accompanying article in this issue, enables the design of selection programs to effectively reduce competitive interactions in livestock and plants and the prediction of the effects of social interactions on evolution in natural populations undergoing multilevel selection
Multilevel selection 1: Quantitative genetics of inheritance and response to selection
Bijma, P. ; Muir, W.M. ; Arendonk, J.A.M. van - \ 2007
Genetics 175 (2007). - ISSN 0016-6731 - p. 277 - 288.
kin-selection - natural-selection - biological groups - incorporating interaction - behavioral ecology - evolution - altruism - populations - cooperation - competition
Interaction among individuals is universal, both in animals and in plants, and substantially affects evolution of natural populations and responses to artificial selection in agriculture. Although quantitative genetics has successfully been applied to many traits, it does not provide a general theory accounting for interaction among individuals and selection acting on multiple levels. Consequently, current quantitative genetic theory fails to explain why some traits do not respond to selection among individuals, but respond greatly to selection among groups. Understanding the full impacts of heritable interactions on the outcomes of selection requires a quantitative genetic framework including all levels of selection and relatedness. Here we present such a framework and provide expressions for the response to selection. Results show that interaction among individuals may create substantial heritable variation, which is hidden to classical analyses. Selection acting on higher levels of organization captures this hidden variation and therefore always yields positive response, whereas individual selection may yield response in the opposite direction. Our work provides testable predictions of response to multilevel selection and reduces to classical theory in the absence of interaction. Statistical methodology provided elsewhere enables empirical application of our work to both natural and domestic populations
Selection on leaf ecophysiological traits in a hybrid Helianthus species and early generation hybrids in a desert dune habitat
Ludwig, F. ; Rosenthal, D.R. ; Johnston, J.A. ; Ryan, N. ; Gross, B.L. ; Lexer, C. ; Dudley, S.A. ; Rieseberg, L.H. ; Donovan, L.A. - \ 2004
Evolution 58 (2004)12. - ISSN 0014-3820 - p. 2682 - 2692.
water-use efficiency - natural-selection - annual plant - polygonum-arenastrum - genetic-variation - evolution - photosynthesis - sunflower - nitrogen - adaptation
Leaf ecophysiological traits related to carbon gain and resource use are expected to be under strong selection in desert annuals. We used comparative and phenotypic selection approaches to investigate the importance of leaf ecophysiological traits for Helianthus anomalus, a diploid annual sunflower species of hybrid origin that is endemic to active desert dunes. Comparisons were made within and among five genotypic classes: H. anomalus, its ancestral parent species (H. annuus and H. petiolaris), and two backcrossed populations of the parental species (designated BC2ann and BC2pet) representing putative ancestors of H. anomalus. Seedlings were transplanted into H. anomalus habitat at Little Sahara Dunes, Utah, and followed through a summer growing season for leaf ecophysiological traits, phenology, and fitness estimated as vegetative biomass. Helianthus anomalus had a unique combination of traits when compared to its ancestral parent species, suggesting that lower leaf nitrogen and greater leaf succulence might be adaptive. However, selection on leaf traits in H. anomalus favored larger leaf area and greater nitrogen, which was not consistent with the extreme traits of H. anomalus relative to its ancestral parents. Also contrary to expectation, current selection on the leaf traits in the backcross populations was not consistently similar to, or resulting in evolution toward, the current H. anomalus phenotype. Only the selection for greater leaf succulence in BC2ann and greater water-use efficiency in BC2pet would result in evolution toward the current H. anomalus phenotype. It was surprising that the action of phenotypic selection depended greatly on the genotypic class for these closely related sunflower hybrids grown in a common environment. We speculate that this may be due to either phenotypic correlations between measured and unmeasured but functionally related traits or due to the three genotypic classes experiencing the environment differently as a result of their differing morphology.
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