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Genetic Architecture (genetic + architecture)
Selected AbstractsWATER STRESS ALTERS THE GENETIC ARCHITECTURE OF FUNCTIONAL TRAITS ASSOCIATED WITH DROUGHT ADAPTATION IN AVENA BARBATAEVOLUTION, Issue 3 2009Mark E. Sherrard Environmental stress can alter genetic variation and covariation underlying functional traits, and thus affect adaptive evolution in response to natural selection. However, the genetic basis of functional traits is rarely examined in contrasting resource environments, and consequently, there is no consensus regarding whether environmental stress constrains or facilitates adaptive evolution. We tested whether resource availability affects genetic variation for and covariation among seven physiological traits and seven morphological/performance traits by growing the annual grass Avena barbata in dry and well-watered treatments. We found that differences in the overall genetic variance,covariance (G) matrix between environments were driven by physiological traits rather than morphology and performance traits. More physiological traits were heritable in the dry treatment than the well-watered treatment and many of the genetic correlations among physiological traits were environment dependent. In contrast, genetic variation and covariation among the morphological and performance traits did not differ across treatments. Furthermore, genetic correlations between physiology and performance were stronger in the dry treatment, which contributed to differences in the overall G -matrix. Our results therefore suggest that physiological adaptation would be constrained by low heritable variation in resource-rich environments, but facilitated by higher heritable variation and stronger genetic correlations with performance traits in resource-poor environments. [source] EVOLUTION OF GENETIC ARCHITECTURE UNDER DIRECTIONAL SELECTIONEVOLUTION, Issue 8 2006Thomas F. Hansen Abstract We investigate the multilinear epistatic model under mutation-limited directional selection. We confirm previous results that only directional epistasis, in which genes on average reinforce or diminish each other's effects, contribute to the initial evolution of mutational effects. Thus, either canalization or decanalization can occur under directional selection, depending on whether positive or negative epistasis is prevalent. We then focus on the evolution of the epistatic coefficients themselves. In the absence of higher-order epistasis, positive pairwise epistasis will tend to weaken relative to additive effects, while negative pairwise epistasis will tend to become strengthened. Positive third-order epistasis will counteract these effects, while negative third-order epistasis will reinforce them. More generally, gene interactions of all orders have an inherent tendency for negative changes under directional selection, which can only be modified by higher-order directional epistasis. We identify three types of nonadditive quasi-equilibrium architectures that, although not strictly stable, can be maintained for an extended time: (1) nondirectional epistatic architectures; (2) canalized architectures with strong epistasis; and (3) near-additive architectures in which additive effects keep increasing relative to epistasis. [source] THE EVOLUTION OF GENETIC ARCHITECTURE UNDER FREQUENCY-DEPENDENT DISRUPTIVE SELECTIONEVOLUTION, Issue 8 2006Michael Kopp Abstract We propose a model to analyze a quantitative trait under frequency-dependent disruptive selection. Selection on the trait is a combination of stabilizing selection and intraspecific competition, where competition is maximal between individuals with equal phenotypes. In addition, there is a density-dependent component induced by population regulation. The trait is determined additively by a number of biallelic loci, which can have different effects on the trait value. In contrast to most previous models, we assume that the allelic effects at the loci can evolve due to epistatic interactions with the genetic background. Using a modifier approach, we derive analytical results under the assumption of weak selection and constant population size, and we investigate the full model by numerical simulations. We find that frequency-dependent disruptive selection favors the evolution of a highly asymmetric genetic architecture, where most of the genetic variation is concentrated on a small number of loci. We show that the evolution of genetic architecture can be understood in terms of the ecological niches created by competition. The phenotypic distribution of a population with an adapted genetic architecture closely matches this niche structure. Thus, evolution of the genetic architecture seems to be a plausible way for populations to adapt to regimes of frequency-dependent disruptive selection. As such, it should be seen as a potential evolutionary pathway to discrete polymorphisms and as a potential alternative to other evolutionary responses, such as the evolution of sexual dimorphism or assortative mating. [source] SEXUAL SELECTION, GENETIC ARCHITECTURE, AND THE CONDITION DEPENDENCE OF BODY SHAPE IN THE SEXUALLY DIMORPHIC FLY PROCHYLIZA XANTHOSTOMA (PIOPHILIDAE)EVOLUTION, Issue 1 2005Russell Bonduriansky Abstract The hypothesis that sexual selection drives the evolution of condition dependence is not firmly supported by empirical evidence, and the process remains poorly understood. First, even though sexual competition typically involves multiple traits, studies usually compare a single sexual trait with a single "control" trait, ignoring variation among sexual traits and raising the possibility of sampling bias. Second, few studies have addressed the genetic basis of condition dependence. Third, even though condition dependence is thought to result from a form of sex-specific epistasis, the evolution of condition dependence has never been considered in relation to intralocus sexual conflict. We argue that condition dependence may weaken intersexual genetic correlations and facilitate the evolution of sexual dimorphism. To address these questions, we manipulated an environmental factor affecting condition (larval diet) and examined its effects on four sexual and four nonsexual traits in Prochyliza xanthostoma adults. As predicted by theory, the strength of condition dependence increased with degree of exaggeration among male traits. Body shape was more condition dependent in males than in females and, perhaps as a result, genetic and environmental effects on body shape were congruent in males, but not in females. However, of the four male sexual traits, only head length was significantly larger in high-condition males after controlling for body size. Strong condition dependence was associated with reduced intersexual genetic correlation. However, homologous male and female traits exhibited correlated responses to condition, suggesting an intersexual genetic correlation for condition dependence itself. Our findings support the role of sexual selection in the evolution of condition dependence, but reveal considerable variation in condition dependence among sexual traits. It is not clear whether the evolution of condition dependence has mitigated or exacerbated intralocus sexual conflict in this species. [source] Genetic Architecture of Idiopathic Generalized Epilepsy: Clinical Genetic Analysis of 55 Multiplex FamiliesEPILEPSIA, Issue 5 2004Carla Marini Summary: Purpose: In families with idiopathic generalized epilepsy (IGE), multiple IGE subsyndromes may occur. We performed a genetic study of IGE families to clarify the genetic relation of the IGE subsyndromes and to improve understanding of the mode(s) of inheritance. Methods: Clinical and genealogic data were obtained on probands with IGE and family members with a history of seizures. Families were grouped according to the probands' IGE subsyndrome: childhood absence epilepsy (CAE), juvenile absence epilepsy (JAE), juvenile myoclonic epilepsy (JME), and IGE with tonic,clonic seizures only (IGE-TCS). The subsyndromes in the relatives were analyzed. Mutations in genes encoding ,1 and ,2 ,-aminobutyric acid (GABA)-receptor subunits, ,1 and ,1 sodium channel subunits, and the chloride channel CLC-2 were sought. Results: Fifty-five families were studied. 122 (13%) of 937 first- and second-degree relatives had seizures. Phenotypic concordance within families of CAE and JME probands was 28 and 27%, respectively. JAE and IGE-TCS families had a much lower concordance (10 and 13%), and in the JAE group, 31% of relatives had CAE. JME was rare among affected relatives of CAE and JAE probands and vice versa. Mothers were more frequently affected than fathers. No GABA-receptor or sodium or chloride channel gene mutations were identified. Conclusions: The clinical genetic analysis of this set of families suggests that CAE and JAE share a close genetic relation, whereas JME is a more distinct entity. Febrile seizures and epilepsy with unclassified tonic,clonic seizures were frequent in affected relatives of all IGE individuals, perhaps representing a nonspecific susceptibility to seizures. A maternal effect also was seen. Our findings are consistent with an oligogenic model of inheritance. [source] Genetic architecture of population differences in oviposition behaviour of the seed beetle Callosobruchus maculatusJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 5 2004C. W. Fox Abstract Few studies have examined the genetic architecture of population differences in behaviour and its implications for population differentiation and adaptation. Even fewer have examined whether differences in genetic architecture depend on the environment in which organisms are reared or tested. We examined the genetic basis of differences in oviposition preference and egg dispersion between Asian (SI) and African (BF) populations of the seed beetle, Callosobruchus maculatus. We reared and tested females on each of two host legumes (cowpea and mung bean). The two populations differed in mean oviposition preference (BF females preferred cowpea seeds more strongly than did SI females) and egg dispersion (SI females distributed eggs more uniformly among seeds than did BF females). Observations of hybrid and backcross individuals indicated that only the population difference in oviposition preference could be explained by complete additivity, whereas substantial dominance and epistasis contributed to the differences in egg dispersion. Both rearing host and test host affected the relative magnitude of population differences in egg dispersion and the composite genetic effects. Our results thus demonstrate that the relative influence of epistasis and dominance on the behaviour of hybrids depends on the behaviour measured and that different aspects of insect oviposition are under different genetic control. In addition, the observed effect of rearing host and oviposition host on the relative importance of dominance and epistasis indicates that the genetic basis of population differences depends on the environment in which genes are expressed. [source] Genetic architecture for normal and novel host-plant use in two local populations of the herbivorous ladybird beetle, Epilachna pustulosaJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 5 2003H. Ueno Abstract Trade-offs in host-plant use are thought to promote the evolution of host specificity. However, usually either positive or no genetic correlations have been found. Whereas factors enhancing variation in overall viability have been claimed to mask negative genetic correlations, alternative hypotheses emphasize the sequential changes in genetic correlation in the course of host-range evolution. In this study, the genetic architectures of performances on different hosts were compared in two populations of the herbivorous ladybird beetle, Epilachna pustulosa, using three host plants, one being normal for both, one novel for only one population, and the other novel for both populations. The genetic correlations between larval periods on normal hosts were significantly positive whereas those between normal and novel hosts were not different from zero. There was no evidence for reduced genetic variation on the normal host-plants. These results suggest that the host-range is not restricted by the antagonistic genetic associations among exploitation abilities on different plant species, but rather that selection of different host-plants may improve the coordination between genes responsible for the use of different plants. [source] TOWARD THE EVOLUTIONARY GENOMICS OF GAMETOPHYTIC DIVERGENCE: PATTERNS OF TRANSMISSION RATIO DISTORTION IN MONKEYFLOWER (MIMULUS) HYBRIDS REVEAL A COMPLEX GENETIC BASIS FOR CONSPECIFIC POLLEN PRECEDENCEEVOLUTION, Issue 12 2008Lila Fishman Conspecific pollen precedence (CPP) is a major component of reproductive isolation between many flowering plant taxa and may reveal mechanisms of gametophytic evolution within species, but little is known about the genetic basis and evolutionary history of CPP. We systematically investigated the genetic architecture of CPP using patterns of transmission ratio distortion (TRD) in F2 and backcross hybrids between closely related species of Mimulus (Phrymaceae) with divergent mating systems. We found that CPP in Mimulus hybrids was polygenic and was the majority source of interspecific TRD genome-wide, with at least eight genomic regions contributing to the transmission advantage of M. guttatus pollen grains on M. guttatus styles. In aggregate, these male-specific transmission ratio distorting loci (TRDLs) were more than sufficient to account for the 100% precedence of pure M. guttatus pollen over M. nasutus pollen in mixed pollinations of M. guttatus. All but one of these pollen TRDLs were style-dependent; that is, we observed pollen TRD in F1 and/or M. guttatus styles, but not in M. nasutus styles. These findings suggest that species-specific differences in pollen tube performance accumulate gradually and may have been driven by coevolution between pollen and style in the predominantly outcrossing M. guttatus. [source] UNDERSTANDING THE EVOLUTION AND STABILITY OF THE G-MATRIXEVOLUTION, Issue 10 2008Stevan J. Arnold The G -matrix summarizes the inheritance of multiple, phenotypic traits. The stability and evolution of this matrix are important issues because they affect our ability to predict how the phenotypic traits evolve by selection and drift. Despite the centrality of these issues, comparative, experimental, and analytical approaches to understanding the stability and evolution of the G -matrix have met with limited success. Nevertheless, empirical studies often find that certain structural features of the matrix are remarkably constant, suggesting that persistent selection regimes or other factors promote stability. On the theoretical side, no one has been able to derive equations that would relate stability of the G -matrix to selection regimes, population size, migration, or to the details of genetic architecture. Recent simulation studies of evolving G -matrices offer solutions to some of these problems, as well as a deeper, synthetic understanding of both the G -matrix and adaptive radiations. [source] POPULATION DIFFERENTIATION IN THE BEETLE TRIBOLIUM CASTANEUM.EVOLUTION, Issue 3 2007We used joint-scaling analyses in conjunction with rearing temperature variation to investigate the contributions of additive, non-additive, and environmental effects to genetic divergence and incipient speciation among 12 populations of the red flour beetle, Tribolium castaneum, with small levels of pairwise nuclear genetic divergence (0.033 < Nei's D < 0.125). For 15 population pairs we created a full spectrum of line crosses (two parental, two reciprocal F1's, four F2's, and eight backcrosses), reared them at multiple temperatures, and analyzed the numbers and developmental defects of offspring. We assayed a total of 219,388 offspring from 5147 families. Failed crosses occurred predominately in F2's, giving evidence of F2 breakdown within this species. In all cases where a significant model could be fit to the data on offspring number, we observed at least one type of digenic epistasis. We also found maternal and cytoplasmic effects to be common components of divergence among T. castaneum populations. In some cases, the most complex model tested (additive, dominance, epistatic, maternal, and cytoplasmic effects) did not provide a significant fit to the data, suggesting that linkage or higher order epistasis is involved in differentiation between some populations. For the limb deformity data, we observed significant genotype-by-environment interaction in most crosses and pure parent crosses tended to have fewer deformities than hybrid crosses. Complexity of genetic architecture was not correlated with either geographic distance or genetic distance. Our results support the view that genetic incompatibilities responsible for postzygotic isolation, an important component of speciation, may be a natural but serendipitous consequence of nonadditive genetic effects and structured populations. [source] THE CONDITIONS FOR SPECIATION THROUGH INTRASPECIFIC COMPETITIONEVOLUTION, Issue 11 2006Reinhard Bürger Abstract It has been shown theoretically that sympatric speciation can occur if intraspecific competition is strong enough to induce disruptive selection. However, the plausibility of the involved processes is under debate, and many questions on the conditions for speciation remain unresolved. For instance, is strong disruptive selection sufficient for speciation? Which roles do genetic architecture and initial composition of the population play? How strong must assortative mating be before a population can split in two? These are some of the issues we address here. We investigate a diploid multilocus model of a quantitative trait that is under frequency-dependent selection caused by a balance of intraspecific competition and frequency-independent stabilizing selection. This trait also acts as mating character for assortment. It has been established previously that speciation can occur only if competition is strong enough to induce disruptive selection. We find that speciation becomes more difficult for very strong competition, because then extremely strong assortment is required. Thus, speciation is most likely for intermediate strengths of competition, where it requires strong, but not extremely strong, assortment. For this range of parameters, however, it is not obvious how assortment can evolve from low to high levels, because with moderately strong assortment less genetic variation is maintained than under weak or strong assortment sometimes none at all. In addition to the strength of frequency-dependent competition and assortative mating, the roles of the number of loci, the distribution of allelic effects, the initial conditions, costs to being choosy, the strength of stabilizing selection, and the particular choice of the fitness function are explored. A multitude of possible evolutionary outcomes is observed, including loss of all genetic variation, splitting in two to five species, as well as very short and extremely long stable limit cycles. On the methodological side, we propose quantitative measures for deciding whether a given distribution reflects two (or more) reproductively isolated clusters. [source] THE EVOLUTION OF GENETIC ARCHITECTURE UNDER FREQUENCY-DEPENDENT DISRUPTIVE SELECTIONEVOLUTION, Issue 8 2006Michael Kopp Abstract We propose a model to analyze a quantitative trait under frequency-dependent disruptive selection. Selection on the trait is a combination of stabilizing selection and intraspecific competition, where competition is maximal between individuals with equal phenotypes. In addition, there is a density-dependent component induced by population regulation. The trait is determined additively by a number of biallelic loci, which can have different effects on the trait value. In contrast to most previous models, we assume that the allelic effects at the loci can evolve due to epistatic interactions with the genetic background. Using a modifier approach, we derive analytical results under the assumption of weak selection and constant population size, and we investigate the full model by numerical simulations. We find that frequency-dependent disruptive selection favors the evolution of a highly asymmetric genetic architecture, where most of the genetic variation is concentrated on a small number of loci. We show that the evolution of genetic architecture can be understood in terms of the ecological niches created by competition. The phenotypic distribution of a population with an adapted genetic architecture closely matches this niche structure. Thus, evolution of the genetic architecture seems to be a plausible way for populations to adapt to regimes of frequency-dependent disruptive selection. As such, it should be seen as a potential evolutionary pathway to discrete polymorphisms and as a potential alternative to other evolutionary responses, such as the evolution of sexual dimorphism or assortative mating. [source] EVOLUTION OF MIGRATION UNDER KIN SELECTION AND LOCAL ADAPTATIONEVOLUTION, Issue 1 2005Sylvain Billiard Abstract We present here a stochastic two-locus, two-habitat model for the evolution of migration with local adaptation and kin selection. One locus determines the migration rate while the other causes local adaptation. We show that the opposing forces of kin competition and local adaptation can lead to the existence of one or two convergence stable migration rates, notably depending on the recombination rate between the two loci. We show that linkage between migration and local adaptation loci has two antagonist effects: when linkage is tight, cost of local adaptation increases, leading to smaller equilibrium migration rates. However, when linkage is tighter, the population structure at the migration locus tends to be very high because of the indirect selection, and thus equilibrium migration rates increases. This result, qualitatively different from results obtained with other models of migration evolution, indicates that ignoring drift or the detail of the genetic architecture may lead to incorrect conclusions. [source] EVOLUTION AND STABILITY OF THE G-MATRIX ON A LANDSCAPE WITH A MOVING OPTIMUMEVOLUTION, Issue 8 2004Adam G. Jones Abstract In quantitative genetics, the genetic architecture of traits, described in terms of variances and covariances, plays a major role in determining the trajectory of evolutionary change. Hence, the genetic variance-covariance matrix (G-matrix) is a critical component of modern quantitative genetics theory. Considerable debate has surrounded the issue of G-matrix constancy because unstable G-matrices provide major difficulties for evolutionary inference. Empirical studies and analytical theory have not resolved the debate. Here we present the results of stochastic models of G-matrix evolution in a population responding to an adaptive landscape with an optimum that moves at a constant rate. This study builds on the previous results of stochastic simulations of G-matrix stability under stabilizing selection arising from a stationary optimum. The addition of a moving optimum leads to several important new insights. First, evolution along genetic lines of least resistance increases stability of the orientation of the G-matrix relative to stabilizing selection alone. Evolution across genetic lines of least resistance decreases G-matrix stability. Second, evolution in response to a continuously changing optimum can produce persistent maladaptation for a correlated trait, even if its optimum does not change. Third, the retrospective analysis of selection performs very well when the mean G-matrix (,) is known with certainty, indicating that covariance between G and the directional selection gradient (3 is usually small enough in magnitude that it introduces only a small bias in estimates of the net selection gradient. Our results also show, however, that the contemporary ,-matrix only serves as a rough guide to ,. The most promising approach for the estimation of G is probably through comparative phylogenetic analysis. Overall, our results show that directional selection actually can increase stability of the G-matrix and that retrospective analysis of selection is inherently feasible. One ?riajor remaining challenge is to gain a sufficient understanding of the G-matrix to allow the confident estimation of ,. [source] PERSPECTIVE: MODELS OF SPECIATION: WHAT HAVE WE LEARNED IN 40 YEARS?EVOLUTION, Issue 10 2003Sergey Gavrilets Abstract Theoretical studies of speciation have been dominated by numerical simulations aiming to demonstrate that speciation in a certain scenario may occur. What is needed now is a shift in focus to identifying more general rules and patterns in the dynamics of speciation. The crucial step in achieving this goal is the development of simple and general dynamical models that can be studied not only numerically but analytically as well. I review some of the existing analytical results on speciation. I first show why the classical theories of speciation by peak shifts across adaptive valleys driven by random genetic drift run into trouble (and into what kind of trouble). Then I describe the Bateson-Dobzhansky-Muller (BDM) model of speciation that does not require overcoming selection. I describe exactly how the probability of speciation, the average waiting time to speciation, and the average duration of speciation depend on the mutation and migration rates, population size, and selection for local adaptation. The BDM model postulates a rather specific genetic architecture of reproductive isolation. I then show exactly why the genetic architecture required by the BDM model should be common in general. Next I consider the multilocus generalizations of the BDM model again concentrating on the qualitative characteristics of speciation such as the average waiting time to speciation and the average duration of speciation. Finally, I consider two models of sympatric speciation in which the conditions for sympatric speciation were found analytically. A number of important conclusions have emerged from analytical studies. Unless the population size is small and the adaptive valley is shallow, the waiting time to a stochastic transition between the adaptive peaks is extremely long. However, if transition does happen, it is very quick. Speciation can occur by mutation and random drift alone with no contribution from selection as different populations accumulate incompatible genes. The importance of mutations and drift in speciation is augmented by the general structure of adaptive landscapes. Speciation can be understood as the divergence along nearly neutral networks and holey adaptive landscapes (driven by mutation, drift, and selection for adaptation to a local biotic and/or abiotic environment) accompanied by the accumulation of reproductive isolation as a by-product. The waiting time to speciation driven by mutation and drift is typically very long. Selection for local adaptation (either acting directly on the loci underlying reproductive isolation via their pleiotropic effects or acting indirectly via establishing a genetic barrier to gene flow) can significantly decrease the waiting time to speciation. In the parapatric case the average actual duration of speciation is much shorter than the average waiting time to speciation. Speciation is expected to be triggered by changes in the environment. Once genetic changes underlying speciation start, they go to completion very rapidly. Sympatric speciation is possible if disruptive selection and/or assortativeness in mating are strong enough. Sympatric speciation is promoted if costs of being choosy are small (or absent) and if linkage between the loci experiencing disruptive selection and those controlling assortative mating is strong. [source] Genetic variation for dorsal,ventral patterning of the Drosophila melanogaster eggshellEVOLUTION AND DEVELOPMENT, Issue 2 2005Lisa M. Goering Summary Patterning of the insect eggshell is an excellent system for exploring the molecular basis of phenotypic variation. In Drosophila melanogaster, two dorsal,anterior respiratory appendages are produced in response to signaling through the Epidermal growth factor receptor (Egfr). Previous work implicates Egfr pathway function in both intraspecific variation for dorsal appendage spacing (DAS) on the eggshell, as well as interspecific differences in dorsal appendage number and location. To test the hypothesis that genetic variation in Egfr contributes to variation in eggshell patterning, we have made use of naturally occurring intraspecific variation for DAS as a model quantitative trait. We found that there is substantial segregating genetic variation for DAS in D. melanogaster, and have tested for associations with 289 common polymorphisms in the Egfr locus. A marginal association was seen with two polymorphic sites in Egfr; however, we failed to replicate these findings in a second population, or in a modified quantitative complementation test designed to specifically test the effects of the putative polymorphisms. Therefore, we conclude that the polymorphisms we have identified in Egfr do not contribute to variation in DAS, and further work is required to understand the genetic architecture of this trait. [source] Chromosomal loci that influence oral nicotine consumption in C57BL/6J × C3H/HeJ F2 intercross miceGENES, BRAIN AND BEHAVIOR, Issue 5 2007X. C. Li Several studies have demonstrated that there are genetic influences on free-choice oral nicotine consumption in mice. In order to establish the genetic architecture that underlies individual differences in free-choice nicotine consumption, quantitative trait loci (QTL) mapping was used to identify chromosomal regions that influence free-choice nicotine consumption in male and female F2 mice derived from a cross between C57BL/6J and C3H/HeJ mice. These two mouse strains were chosen not only because they differ significantly for oral nicotine consumption, but also because they are at or near phenotypic extremes for all measures of nicotine sensitivity that have been reported. A four-bottle choice paradigm was used to assess nicotine consumption over an 8-day period. The four bottles contained water or water supplemented with 25, 50 or 100 ,g/ml of nicotine base. Using micrograms of nicotine consumed per milliliter of total fluid consumed per day as the nicotine consumption phenotype, four significant QTL were identified. The QTL with the largest LOD score was located on distal chromosome 1 (peak LOD score = 15.7). Other chromosomes with significant QTL include central chromosome 4 (peak LOD score = 4.1), proximal chromosome 7 (peak LOD score = 6.1) and distal chromosome 15 (peak LOD score = 4.8). These four QTL appear to be responsible for up to 62% of the phenotypic variance in oral nicotine consumption. [source] Gene, region and pathway level analyses in whole-genome studiesGENETIC EPIDEMIOLOGY, Issue 3 2010Omar De la Cruz Abstract In the setting of genome-wide association studies, we propose a method for assigning a measure of significance to pre-defined sets of markers in the genome. The sets can be genes, conserved regions, or groups of genes such as pathways. Using the proposed methods and algorithms, evidence for association between a particular functional unit and a disease status can be obtained not just by the presence of a strong signal from a SNP within it, but also by the combination of several simultaneous weaker signals that are not strongly correlated. This approach has several advantages. First, moderately strong signals from different SNPs are combined to obtain a much stronger signal for the set, therefore increasing power. Second, in combination with methods that provide information on untyped markers, it leads to results that can be readily combined across studies and platforms that might use different SNPs. Third, the results are easy to interpret, since they refer to functional sets of markers that are likely to behave as a unit in their phenotypic effect. Finally, the availability of gene-level P -values for association is the first step in developing methods that integrate information from pathways and networks with genome-wide association data, and these can lead to a better understanding of the complex traits genetic architecture. The power of the approach is investigated in simulated and real datasets. Novel Crohn's disease associations are found using the WTCCC data. Genet. Epidemiol. 34: 222,231, 2010. © 2009 Wiley-Liss, Inc. [source] Evolution of the innate immune system: the worm perspectiveIMMUNOLOGICAL REVIEWS, Issue 1 2004Hinrich Schulenburg Summary:, Simple model organisms that are amenable to comprehensive experimental analysis can be used to elucidate the molecular genetic architecture of complex traits. They can thereby enhance our understanding of these traits in other organisms, including humans. Here, we describe the use of the nematode Caenorhabditis elegans as a tractable model system to study innate immunity. We detail our current understanding of the worm's immune system, which seems to be characterized by four main signaling cascades: a p38 mitogen-activated protein kinase, a transforming growth factor-,-like, a programed cell death, and an insulin-like receptor pathway. Many details, especially regarding pathogen recognition and immune effectors, are only poorly characterized and clearly warrant further investigation. We additionally speculate on the evolution of the C. elegans immune system, taking into special consideration the relationship between immunity, stress responses and digestion, the diversification of the different parts of the immune system in response to multiple and/or coevolving pathogens, and the trade-off between immunity and host life history traits. Using C. elegans to address these different facets of host,pathogen interactions provides a fresh perspective on our understanding of the structure and complexity of innate immune systems in animals and plants. [source] Genetic structure of two populations of the Namibian giraffe, Giraffa camelopardalis angolensisAFRICAN JOURNAL OF ECOLOGY, Issue 4 2009Rick A. Brenneman Abstract Two geographically distinct populations of giraffe (Giraffa camelopardalis) were sampled for this study, the northern Namib Desert and Etosha National Park. Population genetic parameters and relationships within subpopulations were estimated to better understand the genetic architecture of this isolated subspecies. Gene flow between the geographically separated populations can be attributed to recent translocation of giraffe between the two populations. Inbreeding estimates in the six subpopulations studied were low though we found evidence that genetic drift may be affecting the genetic diversity of the isolated populations in northern Namibia. Population dynamics of the sampling locations was inferred with relationship coefficient analyses. Recent molecular systematics of the Namibian giraffe populations indicates that they are distinct from the subspecies Giraffa camelopardalis giraffa and classified as G. c. angolensis. Based on genetic analyses, these giraffe populations of northern Namibia, the desert-dwelling giraffe and those protected in Etosha National Park, are a distinct subspecies from that previously assumed; thus we add data on G. c. angolensis to our scientific knowledge of this giraffe of southern Africa. Résumé Deux populations de girafes (Giraffa camelopardalis) distinctes sur le plan géographique ont servi d'échantillons pour cette étude, celle du nord du Désert du Namib et celle du Parc National d'Etosha. Nous avons estimé les paramètres génétiques des populations et les relations au sein des sous-populations pour mieux comprendre l'architecture génétique de cette sous-espèce isolée. Les flux génétiques entre les populations séparées géographiquement peuvent être attribués à la récente translocation de girafes entre ces deux populations. L'inbreeding estimé dans les six sous-populations étudiées était faible, encore que nous ayons découvert des preuves que la dérive génétique pourrait bien affecter la diversité génétique des populations isolées dans le nord de la Namibie. La dynamique des populations des endroits où furent faits les échantillonnages fut déduite en fonction de l'analyse des coefficients. La nouvelle systématique moléculaire des populations de girafes de Namibie indique qu'elles sont distinctes de la sous-espèce Giraffa camelopardalis giraffa et classées comme G.c. angolensis. Selon les analyses génétiques, ces populations de girafes du nord de la Namibie, les girafes qui vivent dans le désert et celles qui sont protégées dans le Parc National d'Etosha sont une sous-espèce distincte de celle que l'on croyait auparavant, et nous ajoutons ainsi des données sur G.c. angolensisà la connaissance scientifique de cette girafe d'Afrique australe. [source] Genetic basis of differential opsin gene expression in cichlid fishesJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2010K. L. CARLETON Abstract Visual sensitivity can be tuned by differential expression of opsin genes. Among African cichlid fishes, seven cone opsin genes are expressed in different combinations to produce diverse visual sensitivities. To determine the genetic architecture controlling these adaptive differences, we analysed genetic crosses between species expressing different complements of opsin genes. Quantitative genetic analyses suggest that expression is controlled by only a few loci with correlations among some genes. Genetic mapping identifies clear evidence of trans-acting factors in two chromosomal regions that contribute to differences in opsin expression as well as one cis-regulatory region. Therefore, both cis and trans regulation are important. The simple genetic architecture suggested by these results may explain why opsin gene expression is evolutionarily labile, and why similar patterns of expression have evolved repeatedly in different lineages. [source] Resource specialization in a phytophagous insect: no evidence for genetically based performance trade-offs across hosts in the field or laboratoryJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2009S. J. AGOSTA Abstract We present a field test of the genetically based performance trade-off hypothesis for resource specialization in a population of the moth Rothschildia lebeau whose larvae primarily feed on three host plant species. Pairwise correlations between growth vs. growth, survival vs. survival and growth vs. survival across the different hosts were calculated, using families (sibships) as the units of analysis. Of 15 pairwise correlations, 14 were positive, 5 significantly so and none were negative. The same pattern was found using complementary growth and survival data from the laboratory. Overall, we found no evidence of negative genetic correlations in cross-host performance that would be indicative of performance trade-offs in this population. Rather, variation among families in performance appears to reflect ,general vigour' whereby families that perform well on one host perform well across multiple hosts. We discuss the implications of positive genetic correlations in cross-host performance in terms of the ecology and evolution of host range. We argue that this genetic architecture facilitates colonization of novel hosts and recolonization of historical hosts, therefore contributing to host shifts, host range expansions, biological invasions and introductions, and host ranges that are regionally broad but locally narrow. [source] Fluctuating asymmetry and developmental instability in evolutionary biology: past, present and futureJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 6 2006S. V. DONGEN Abstract The role of developmental instability (DI), as measured by fluctuating asymmetry (FA), in evolutionary biology has been the focus of a wealth of research for more than half a century. In spite of this long period and many published papers, our current state of knowledge reviewed here only allows us to conclude that patterns are heterogeneous and that very little is known about the underlying causes of this heterogeneity. In addition, the statistical properties of FA as a measure of DI are only poorly grasped because of a general lack of understanding of the underlying mechanisms that drive DI. If we want to avoid that this area of research becomes abandoned, more efforts should be made to understand the observed heterogeneity, and attempts should be made to develop a unifying statistical protocol. More specifically, and perhaps most importantly, it is argued here that more attention should be paid to the usefulness of FA as a measure of DI since many factors might blur this relationship. Furthermore, the genetic architecture, associations with fitness and the importance of compensatory growth should be investigated under a variety of stress situations. In addition, more focus should be directed to the underlying mechanisms of DI as well as how these processes map to the observable phenotype. These insights could yield more efficient statistical models and a unified approach to the analysis of patterns in FA and DI. The study of both DI and canalization is indispensable to obtain better insights in their possible common origin, especially because both have been suggested to play a role in both micro- and macro-evolutionary processes. [source] Maternal genetic effects on adaptive divergence between anadromous and resident brook charr during early life historyJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 5 2005G. M. L. PERRY Abstract The importance of directional selection relative to neutral evolution may be determined by comparing quantitative genetic variation in phenotype (QST) to variation at neutral molecular markers (FST). Quantitative divergence between salmonid life history types is often considerable, but ontogenetic changes in the significance of major sources of genetic variance during post-hatch development suggest that selective differentiation varies by developmental stage. In this study, we tested the hypothesis that maternal genetic differentiation between anadromous and resident brook charr (Salvelinus fontinalis Mitchill) populations for early quantitative traits (embryonic size/growth, survival, egg number and developmental time) would be greater than neutral genetic differentiation, but that the maternal genetic basis for differentiation would be higher for pre-resorption traits than post-resorption traits. Quantitative genetic divergence between anadromous (seawater migratory) and resident Laval River (Québec) brook charr based on maternal genetic variance was high (QST > 0.4) for embryonic length, yolk sac volume, embryonic growth rate and time to first response to feeding relative to neutral genetic differentiation [FST = 0.153 (0.071,0.214)], with anadromous females having positive genetic coefficients for all of the above characters. However, QST was essentially zero for all traits post-resorption of the yolk sac. Our results indicate that the observed divergence between resident and anadromous brook charr has been driven by directional selection, and may therefore be adaptive. Moreover, they provide among the first evidence that the relative importance of selective differentiation may be highly context-specific, and varies by genetic contributions to phenotype by parental sex at specific points in offspring ontogeny. This in turn suggests that interpretations of QST - FST comparisons may be improved by considering the structure of quantitative genetic architecture by age category and the sex of the parent used in estimation. [source] How do natural and sexual selection contribute to sympatric speciation?JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 6 2004S. Gourbiere Abstract I use explicit genetic models to investigate the importance of natural and sexual selection during sympatric speciation and to sort out how genetic architecture influences these processes. Assortative mating alone can lead to speciation, but rare phenotypes' disadvantage in finding mates and intermediate phenotypes' advantage due to stabilizing selection strongly impede speciation. Any increase in the number of loci also decreases the likelihood of speciation. Sympatric speciation is then harder to achieve than previously demonstrated by many theoretical studies which assume no mating disadvantage for rare phenotypes and consider a small number of loci. However, when a high level of assortative mating evolves, sexual selection might allow populations to split into dimorphic distributions with peaks corresponding to nearly extreme phenotypes. Competition then works against speciation by favouring intermediate phenotypes and preventing further divergence. The interplay between natural and sexual selection during speciation is then more complex than previously explained. [source] Genetic architecture of population differences in oviposition behaviour of the seed beetle Callosobruchus maculatusJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 5 2004C. W. Fox Abstract Few studies have examined the genetic architecture of population differences in behaviour and its implications for population differentiation and adaptation. Even fewer have examined whether differences in genetic architecture depend on the environment in which organisms are reared or tested. We examined the genetic basis of differences in oviposition preference and egg dispersion between Asian (SI) and African (BF) populations of the seed beetle, Callosobruchus maculatus. We reared and tested females on each of two host legumes (cowpea and mung bean). The two populations differed in mean oviposition preference (BF females preferred cowpea seeds more strongly than did SI females) and egg dispersion (SI females distributed eggs more uniformly among seeds than did BF females). Observations of hybrid and backcross individuals indicated that only the population difference in oviposition preference could be explained by complete additivity, whereas substantial dominance and epistasis contributed to the differences in egg dispersion. Both rearing host and test host affected the relative magnitude of population differences in egg dispersion and the composite genetic effects. Our results thus demonstrate that the relative influence of epistasis and dominance on the behaviour of hybrids depends on the behaviour measured and that different aspects of insect oviposition are under different genetic control. In addition, the observed effect of rearing host and oviposition host on the relative importance of dominance and epistasis indicates that the genetic basis of population differences depends on the environment in which genes are expressed. [source] Allochronic differentiation among Daphnia species, hybrids and backcrosses: the importance of sexual reproduction for population dynamics and genetic architectureJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 2 2004T. Jankowski Abstract Seasonal dynamics of the abundance, sexual reproduction and genetic architecture in a Daphnia hyalina-galeata hybrid complex were studied in the large and deep Lake Constance. We found evidence for the occurrence of first and second order hybridization. Our study revealed strong differences between the parental species not only regarding their seasonal dynamics, genetic architecture and diversity, but also their sexual reproductive behaviour. The overwintering D. hyalina showed low genetic diversity, no genetic differentiation during the season, and reproduced sexually in autumn, whereas D. galeata reached higher levels of genetic diversity, reproduced sexually in early summer, and exhibited changes in genetic structure during the season, but was only present from spring to autumn. However, in both species sexual reproduction was a rare event, and daphnids, including hybrids, reproduced predominantly asexually. This allows long-term persistence of hybrids as well without continuing hybridization events. Within all variables studied, F1 and F2 hybrids showed an intermediate pattern, whereas proposed backcross hybrids were more similar to their respective parentals. These differences in phenotype as well as significant differences in pairwise Fst values between parentals suggest that gene flow seems to be relatively low in the Lake Constance hybrid system. We found evidence for unidirectional introgression by backcrossing from D. galeata to D. hyalina and found a decrease in at least one of the proposed introgressed alleles in the hyalina -backcross while the season progressed. Our findings suggest allochronic differentiation within this hybrid population and different microevolutionary trajectories of the parental species, which will be discussed in the light of the ongoing reoligotrophication process of Lake Constance. [source] Selection experiments and the study of phenotypic plasticity,JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 6 2002S. M. Scheiner Abstract Laboratory selection experiments are powerful tools for establishing evolutionary potentials. Such experiments provide two types of information, knowledge about genetic architecture and insight into evolutionary dynamics. They can be roughly classified into two types: (1) artificial selection in which the experimenter selects on a focal trait or trait index, and (2) quasi-natural selection in which the experimenter establishes a set of environmental conditions and then allows the population to evolve. Both approaches have been used in the study of phenotypic plasticity. Artificial selection experiments have taken various forms including: selection directly on a reaction norm, selection on a trait in multiple environments, and selection on a trait in a single environment. In the latter experiments, evolution of phenotypic plasticity is investigated as a correlated response. Quasi-natural selection experiments have examined the effects of both spatial and temporal variation. I describe how to carry out such experiments, summarize past efforts, and suggest further avenues of research. [source] An analysis of G matrix variation in two closely related cricket species, Gryllus firmus and G. pennsylvanicusJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 1 2001M. Bégin An important issue in evolutionary biology is understanding the pattern of G matrix variation in natural populations. We estimated four G matrices based on the morphological traits of two cricket species, Gryllus firmus and G. pennsylvanicus, each reared in two environments. We used three matrix comparison approaches, including the Flury hierarchy, to improve our ability to perceive all aspects of matrix variation. Our results demonstrate that different methods perceive different aspects of the matrices, which suggests that, until more is known about these methods, future studies should use several different statistical approaches. We also found that the differences in G matrices within a species can be larger than the differences between species. We conclude that the expression of the genetic architecture can vary with the environment and that future studies should compare G matrices across several environments. We also conclude that G matrices can be conserved at the level of closely related species. [source] Sculpin hybrid zones: natural laboratories for the early stages of speciationMOLECULAR ECOLOGY, Issue 12 2009ANDREA SWEIGART Firmly rooted as we are in the genomic era, it can seem incredible that as recently as 1974, Lewontin declared, ,we know virtually nothing about the genetic changes that occur in species formation'. To the contrary, we now know the genetic architecture of phenotypic differences and reproductive isolation between species for many diverse groups of plants, animals, and fungi. In recent years, detailed genetic analyses have produced a small but growing list of genes that cause reproductive isolation, several of which appear to have diverged by natural selection. Yet, a full accounting of the speciation process requires that we understand the reproductive and ecological properties of natural populations as they begin to diverge genetically, as well as the dynamics of newly evolved barriers to gene flow. One promising approach to this problem is the study of natural hybrid zones, where gene exchange between divergent populations can produce recombinant genotypes in situ. In such individuals, genomic variation might be shaped by introgression at universally adaptive or neutral loci, even as regions associated with local adaptation or reproductive isolation remain divergent. In Nolte et al. (2009), the authors take advantage of two independent, recently formed hybrid zones between sculpin species to investigate genome-wide patterns of reproductive isolation. Using a recently developed genomic clines method, the authors identify marker loci that are associated with isolation, and those that show evidence for adaptive introgression. Remarkably, Nolte et al. (2009) find little similarity between the two hybrid zones in patterns of introgression, a fact that might reflect genetic variation within species or heterogeneous natural selection. In either case, their study system has the potential to provide insight into the early stages of speciation. [source] | ||||||||||||||||||||||||||||