Matuszewski, Sebastian; Hermisson, Joachim; Kopp, Michael
Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Of these, two complementary modeling approaches have emerged: While so-called adaptive-walk models consider adaptation from the successive fixation of de novo mutations only, quantitative genetic models assume that adaptation proceeds exclusively from preexisting standing genetic variation. The latter approach, however, has focused on short-term evolution of population means and variances rather than on the statistical properties of adaptive substitutions. Our aim is to combine these two approaches by describing the ecological and genetic factors that determine the genetic basis of adaptation from standing genetic variation in terms of the effect-size distribution of individual alleles. Specifically, we consider the evolution of a quantitative trait to a gradually changing environment. By means of analytical approximations, we derive the distribution of adaptive substitutions from standing genetic variation, that is, the distribution of the phenotypic effects of those alleles from the standing variation that become fixed during adaptation. Our results are checked against individual-based simulations. We find that, compared to adaptation from de novo mutations, (i) adaptation from standing variation proceeds by the fixation of more alleles of small effect and (ii) populations that adapt from standing genetic variation can traverse larger distances in phenotype space and, thus, have a higher potential for adaptation if the rate of environmental change is fast rather than slow.
Scheiner, Samuel M
Confronted with variable environments, species adapt in several ways, including genetic differentiation, a jack-of-all-trades strategy, or phenotypic plasticity. Adaptive habitat choice favors genetic differentiation and local adaptation over a generalist, jack-of-all-trades strategy. Models predict that, absent plasticity costs, variable environments generally favor phenotypic plasticity over genetic differentiation and being a jack-of-all-trades generalist. It is unknown how habitat choice might affect the evolution of plasticity. Using an individual-based simulation model, I explored the interaction of choice and plasticity. With only spatial variation, habitat choice promotes genetic differentiation over a jack-of-all-trades strategy or phenotypic plasticity. In the absence of plasticity, temporal variation favors a jack-of-all-trades strategy over choice-mediated genetic differentiation; when plasticity is an option, it is favored. This occurs because habitat choice creates a feedback between genetic differentiation and dispersal rates. As demes become better adapted to their local environments, the effective dispersal rate decreases, because more individuals have very high fitness and so choose not to disperse, reinforcing local stabilizing selection and negating selection for plasticity. Temporal variation breaks that feedback. These results point to a potential data paradox: systems with habitat choice may have the lowest actual movement rates. The potential for adaptive habitat choice may be very common, but its existence may reduce observed dispersal rates enough that we do not recognize systems where it may be present, warranting further exploration of likely systems.
Renaut, Sébastien; Nolte, Arne W; Rogers, Sean M; Derome, Nicolas; Bernatchez, Louis
As populations adapt to novel environments, divergent selection will promote heterogeneous genomic differentiation via reductions in gene flow for loci underlying adaptive traits. Using a data set of over 100 SNP markers, genome scans were performed to investigate the effect of natural selection maintaining differentiation in five lakes harbouring sympatric pairs of normal and dwarf lake whitefish (Coregonus clupeaformis). A variable proportion of SNPs (between 0% and 12%) was identified as outliers, which corroborated the predicted intensity of competitive interactions unique to each lake. Moreover, strong reduction in heterozygosity was typically observed for outlier loci in dwarf but not in normal whitefish, indicating that directional selection has been acting on standing genetic variation more intensively in dwarf whitefish. SNP associations in backcross hybrid progeny identified 16 genes exhibiting genotype-phenotype associations for four adaptive traits (growth, swimming activity, gill rakers and condition factor). However, neither simple relationship between elevated levels of genetic differentiation with adaptive phenotype nor conspicuous genetic signatures for parallelism at outlier loci were detected, which underscores the importance of independent evolution among lakes. The integration of phenotypic, transcriptomic and functional genomic information identified two candidate genes (sodium potassium ATPase and triosephosphate isomerase) involved in the recent ecological divergence of lake whitefish. Finally, the identification of several markers under divergent selection suggests that many genes, in an environment-specific manner, are recruited by selection and ultimately contributed to the repeated ecological speciation of a dwarf phenotype.
Myers, Steven A; Donnellan, Stephen; Kleindorfer, Sonia
Identifying environmentally driven changes in traits that serve an ecological function is essential for predicting evolutionary outcomes of climate change. We examined population genetic structure, sex-specific dispersal patterns, and morphology in relation to rainfall patterns across an island and three peninsulas in South Australia. The study system was the New Holland Honeyeater (Phylidonyris novaehollandiae), a nectarivorous passerine that is a key pollinator species. We predicted that rainfall-related mechanisms would be driving local adaptation of morphological traits, such that in areas of lower rainfall, where nectar is less available, more insectivorous traits – shorter, deeper bills, longer tarsi, and longer wings – would be favored. The study populations differed in phenotype across the Eyre, Yorke, and Fleurieu Peninsulas and Kangaroo Island despite high gene flow (single continuous population) and sex-biased dispersal (males were philopatric and females dispersed). We tested the role of rainfall in shaping the observed phenotypic differences, and found strong support for our predicted relationships: birds in areas of higher rainfall had higher condition indices, as well as longer bill-head length, deeper bills, and shorter tarsi. Bill depth in males in high-rainfall sites showed signals of stabilizing selection, suggesting local adaptation. In addition to these local indications of selection, a global pattern of directional selection toward larger size for bill-head length, bill-nostril length, and wing length was also observed. We suggest this pattern may reflect an adaptive response to the relatively dry conditions that South Australia has experienced over the last decade. We conclude that rainfall has shaped aspects of phenology in P. novaehollandiae, both locally, with different patterns of stabilizing and directional selection, and globally, with evidence of adaptive divergence at a landscape scale. PMID:23145327
Myers, Steven A; Donnellan, Stephen; Kleindorfer, Sonia
Identifying environmentally driven changes in traits that serve an ecological function is essential for predicting evolutionary outcomes of climate change. We examined population genetic structure, sex-specific dispersal patterns, and morphology in relation to rainfall patterns across an island and three peninsulas in South Australia. The study system was the New Holland Honeyeater (Phylidonyris novaehollandiae), a nectarivorous passerine that is a key pollinator species. We predicted that rainfall-related mechanisms would be driving local adaptation of morphological traits, such that in areas of lower rainfall, where nectar is less available, more insectivorous traits - shorter, deeper bills, longer tarsi, and longer wings - would be favored. The study populations differed in phenotype across the Eyre, Yorke, and Fleurieu Peninsulas and Kangaroo Island despite high gene flow (single continuous population) and sex-biased dispersal (males were philopatric and females dispersed). We tested the role of rainfall in shaping the observed phenotypic differences, and found strong support for our predicted relationships: birds in areas of higher rainfall had higher condition indices, as well as longer bill-head length, deeper bills, and shorter tarsi. Bill depth in males in high-rainfall sites showed signals of stabilizing selection, suggesting local adaptation. In addition to these local indications of selection, a global pattern of directional selection toward larger size for bill-head length, bill-nostril length, and wing length was also observed. We suggest this pattern may reflect an adaptive response to the relatively dry conditions that South Australia has experienced over the last decade. We conclude that rainfall has shaped aspects of phenology in P. novaehollandiae, both locally, with different patterns of stabilizing and directional selection, and globally, with evidence of adaptive divergence at a landscape scale.
Held, Torsten; Nourmohammad, Armita; Lässig, Michael
Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak.
Thompson, E; Pembrey, M; Graham, J M
A mother and son are reported with chronic dacrocystitis, cup shaped ears, hearing loss, abnormal teeth, and poor formation of saliva and tears. They are similar to previously reported cases of lacrimo-auriculo-dento-digital (LADD) syndrome. The variability of expression of this autosomal dominant syndrome is discussed, and it is suggested that poor saliva and tear formation be added to the phenotype. Images PMID:4078868
Kelly, Scott A; Panhuis, Tami M; Stoehr, Andrew M
Phenotypic plasticity can be broadly defined as the ability of one genotype to produce more than one phenotype when exposed to different environments, as the modification of developmental events by the environment, or as the ability of an individual organism to alter its phenotype in response to changes in environmental conditions. Not surprisingly, the study of phenotypic plasticity is innately interdisciplinary and encompasses aspects of behavior, development, ecology, evolution, genetics, genomics, and multiple physiological systems at various levels of biological organization. From an ecological and evolutionary perspective, phenotypic plasticity may be a powerful means of adaptation and dramatic examples of phenotypic plasticity include predator avoidance, insect wing polymorphisms, the timing of metamorphosis in amphibians, osmoregulation in fishes, and alternative reproductive tactics in male vertebrates. From a human health perspective, documented examples of plasticity most commonly include the results of exercise, training, and/or dieting on human morphology and physiology. Regardless of the discipline, phenotypic plasticity has increasingly become the target of a plethora of investigations with the methodological approaches utilized ranging from the molecular to whole organsimal. In this article, we provide a brief historical outlook on phenotypic plasticity; examine its potential adaptive significance; emphasize recent molecular approaches that provide novel insight into underlying mechanisms, and highlight examples in fishes and insects. Finally, we highlight examples of phenotypic plasticity from a human health perspective and underscore the use of mouse models as a powerful tool in understanding the genetic architecture of phenotypic plasticity.
Evans, Suzanna M; Sinclair, Elizabeth A; Poore, Alistair G B; Bain, Keryn F; Vergés, Adriana
. However, the strong link between genotypic and phenotypic variation suggests that a range of genotypes is still the best case scenario for adaptation to and recovery from predicted environmental change.
Sinclair, Elizabeth A.; Poore, Alistair G.B.; Bain, Keryn F.; Vergés, Adriana
. However, the strong link between genotypic and phenotypic variation suggests that a range of genotypes is still the best case scenario for adaptation to and recovery from predicted environmental change. PMID:26925313
Riis, Tenna; Lambertini, Carla; Olesen, Birgit; Clayton, John S.; Brix, Hans; Sorrell, Brian K.
Background and Aims The successful spread of invasive plants in new environments is often linked to multiple introductions and a diverse gene pool that facilitates local adaptation to variable environmental conditions. For clonal plants, however, phenotypic plasticity may be equally important. Here the primary adaptive strategy in three non-native, clonally reproducing macrophytes (Egeria densa, Elodea canadensis and Lagarosiphon major) in New Zealand freshwaters were examined and an attempt was made to link observed differences in plant morphology to local variation in habitat conditions. Methods Field populations with a large phenotypic variety were sampled in a range of lakes and streams with different chemical and physical properties. The phenotypic plasticity of the species before and after cultivation was studied in a common garden growth experiment, and the genetic diversity of these same populations was also quantified. Key Results For all three species, greater variation in plant characteristics was found before they were grown in standardized conditions. Moreover, field populations displayed remarkably little genetic variation and there was little interaction between habitat conditions and plant morphological characteristics. Conclusions The results indicate that at the current stage of spread into New Zealand, the primary adaptive strategy of these three invasive macrophytes is phenotypic plasticity. However, while limited, the possibility that genetic diversity between populations may facilitate ecotypic differentiation in the future cannot be excluded. These results thus indicate that invasive clonal aquatic plants adapt to new introduced areas by phenotypic plasticity. Inorganic carbon, nitrogen and phosphorous were important in controlling plant size of E. canadensis and L. major, but no other relationships between plant characteristics and habitat conditions were apparent. This implies that within-species differences in plant size can be explained
While phenotypic plasticity -the capability to respond to the environment- is vital to organisms, tests of its adaptation have remained indecisive because constraints and selection in variable environments are unknown and entangled. We show that one can determine the phenotype-fitness landscape that specifies selection on plasticity, by uncoupling the environmental cue and stress in a genetically engineered microbial system. Evolutionary trajectories revealed genetic constraints in a regulatory protein, which imposed cross-environment trade-offs that favored specialization. However, depending on the synchronicity and amplitude of the applied cue and stress variations, adaptation could break constraints, resolve trade-offs, and evolve optimal phenotypes that exhibit qualitatively altered (inverse) responses to the cue. Our results provide a first step to explain the adaptive origins of complex behavior in heterogeneous environments.
Chen, Guangbo; Rubinstein, Boris; Li, Rong
Despite its wide existence, the adaptive role of aneuploidy (the abnormal state of having unequal number of different chromosomes) has been a subject of debate. Cellular aneuploidy has been associated with enhanced resistance to stress, whereas on the organismal level it is detrimental to multi-cellular species. Certain aneuploid karyotypes are deleterious for specific environments, but karyotype diversity in a population potentiates adaptive evolution. To reconcile these paradoxical observations, this review distinguishes the role of aneuploidy in cellular versus organismal evolution. Further, it proposes a population genetics perspective to examine the behavior of aneuploidy on a populational versus individual level. By altering the copy number of a significant portion of the genome, aneuploidy introduces large phenotypic leap that enables small cell populations to explore a wide phenotypic landscape, from which adaptive traits can be selected. The production of chromosome number variation can be further increased by stress- or mutation-induced chromosomal instability, fueling rapid cellular adaptation. PMID:22926916
Morimoto, Naoki; Ponce de León, Marcia S.; Zollikofer, Christoph P. E.
Studies comparing phenotypic variation with neutral genetic variation in modern humans have shown that genetic drift is a main factor of evolutionary diversification among populations. The genetic population history of our closest living relatives, the chimpanzees and bonobos, is now equally well documented, but phenotypic variation among these taxa remains relatively unexplored, and phenotype-genotype correlations are not yet documented. Also, while the adult phenotype is typically used as a reference, it remains to be investigated how phenotype-genotye correlations change during development. Here we address these questions by analyzing phenotypic evolutionary and developmental diversification in the species and subspecies of the genus Pan. Our analyses focus on the morphology of the femoral diaphysis, which represents a functionally constrained element of the locomotor system. Results show that during infancy phenotypic distances between taxa are largely congruent with non-coding (neutral) genotypic distances. Later during ontogeny, however, phenotypic distances deviate from genotypic distances, mainly as an effect of heterochronic shifts between taxon-specific developmental programs. Early phenotypic differences between Pan taxa are thus likely brought about by genetic drift while late differences reflect taxon-specific adaptations. PMID:25013970
Dayan, David I; Crawford, Douglas L; Oleksiak, Marjorie F
We examine the interaction between phenotypic plasticity and evolutionary adaptation using muscle gene expression levels among populations of the fish Fundulus heteroclitus acclimated to three temperatures. Our analysis reveals shared patterns of phenotypic plasticity due to thermal acclimation as well as non-neutral patterns of variation among populations adapted to different thermal environments. For the majority of significant differences in gene expression levels, phenotypic plasticity and adaptation operate on different suites of genes. The subset of genes that demonstrate both adaptive differences and phenotypic plasticity, however, exhibit countergradient variation of expression. Thus, expression differences among populations counteract environmental effects, reducing the phenotypic differentiation between populations. Finally, gene-by-environment interactions among genes with non-neutral patterns of expression suggest that the penetrance of adaptive variation depends on the environmental conditions experienced by the individual.
Araus, Jose L.; Serret, María D.; Edmeades, Gregory O.
The need of a better adaptation of crops to drought is an issue of increasing urgency. However, enhancing the tolerance of maize has, therefore, proved to be somewhat elusive in terms of plant breeding. In that context, proper phenotyping remains as one of the main factors limiting breeding advance. Topics covered by this review include the conceptual framework for identifying secondary traits associated with yield response to drought and how to measure these secondary traits in practice. PMID:22934056
Pfab, Ferdinand; Gabriel, Wilfried; Utz, Margarete
We introduce a novel model for continuous reversible phenotypic plasticity. The model includes a one-dimensional environmental gradient, and we describe performance of an organism as a function of the environmental state by a Gaussian tolerance curve. Organisms are assumed to adapt their tolerance curve after a change of the environmental state. We present a general framework for calculating the genotype fitness if such adaptations happen in a continuous manner and apply the model to a periodically changing environment. Significant differences of our model with previous models for plasticity are the continuity of adaptation, the presence of intermediate phenotypes, that the duration of transformations depends on their extent, fewer restrictions on the distribution of the environment, and a higher robustness with respect to assumptions about environmental fluctuations. Further, we show that continuous reversible plasticity is beneficial mainly when environmental changes occur slow enough so that fully developed phenotypes can be exhibited. Finally we discuss how the model framework can be generalized to a wide variety of biological scenarios from areas that include population dynamics, evolution of environmental tolerance and physiology.
Campbell, Michael C; Tishkoff, Sarah A
Africa is the birthplace of modern humans, and is the source of the geographic expansion of ancestral populations into other regions of the world. Indigenous Africans are characterized by high levels of genetic diversity within and between populations. The pattern of genetic variation in these populations has been shaped by demographic events occurring over the last 200,000 years. The dramatic variation in climate, diet, and exposure to infectious disease across the continent has also resulted in novel genetic and phenotypic adaptations in extant Africans. This review summarizes some recent advances in our understanding of the demographic history and selective pressures that have influenced levels and patterns of diversity in African populations.
Yampolsky, Lev Y; Schaer, Tobias M M; Ebert, Dieter
Many organisms have geographical distributions extending from the tropics to near polar regions or can experience up to 30°C temperature variation within the lifespan of an individual. Two forms of evolutionary adaptation to such wide ranges in ambient temperatures are frequently discussed: local adaptation and phenotypic plasticity. The freshwater planktonic crustacean Daphnia magna, whose range extends from South Africa to near arctic sites, shows strong phenotypic and genotypic variation in response to temperature. In this study, we use D. magna clones from 22 populations (one clone per population) ranging from latitude 0° (Kenya) to 66° North (White Sea) to explore the contributions of phenotypic plasticity and local adaptation to high temperature tolerance. Temperature tolerance was studied as knockout time (time until immobilization, T(imm)) at 37°C in clones acclimatized to either 20°C or 28°C. Acclimatization to 28°C strongly increased T(imm), testifying to adaptive phenotypic plasticity. At the same time, Timm significantly correlated with average high temperature at the clones' sites of origin, suggesting local adaptation. As earlier studies have found that haemoglobin expression contributes to temperature tolerance, we also quantified haemoglobin concentration in experimental animals and found that both acclimatization temperature (AccT) and temperature at the site of origin are positively correlated with haemoglobin concentration. Furthermore, Daphnia from warmer climates upregulate haemoglobin much more strongly in response to AccT, suggesting local adaptation for plasticity in haemoglobin expression. Our results show that both local adaptation and phenotypic plasticity contribute to temperature tolerance, and elucidate a possible role of haemoglobin in mediating these effects that differs along a cold-warm gradient.
Hall, Anthony E.
Methods for phenotyping cowpeas for adaptation to drought are reviewed. Key factors involve achieving optimal time of flowering and cycle length, and appropriate morphology for different types of cultivars as they relate to their utilization for dry grain, hay, and fresh pea production. Strong resistance to vegetative-stage drought is available and should be incorporated. The extreme ability of extra-early erect cowpea cultivars to escape terminal drought should be exploited in zones with very short rainfall seasons. In zones with the possibility of limited rainfall in the middle of the growing season, resistance to mid-season drought, and the delayed-leaf-senescence trait can be valuable. Breeding for water-use efficiency, deeper rooting, and heat tolerance are discussed. Diseases and pests that influence adaptation to drought are considered. Resistance to the organism causing ashy stem blight disease should be incorporated because this disease can destroy cowpea seedlings under hot, dry soil conditions. The value of varietal intercrops with contrasting types of cowpea cultivars in enhancing adaptation to drought is described. Implications of cowpea/cereal rotations for cowpea breeding are discussed. Breeding strategies for enhancing cowpea adaptation to drought are described. PMID:22654769
Hall, Anthony E
Methods for phenotyping cowpeas for adaptation to drought are reviewed. Key factors involve achieving optimal time of flowering and cycle length, and appropriate morphology for different types of cultivars as they relate to their utilization for dry grain, hay, and fresh pea production. Strong resistance to vegetative-stage drought is available and should be incorporated. The extreme ability of extra-early erect cowpea cultivars to escape terminal drought should be exploited in zones with very short rainfall seasons. In zones with the possibility of limited rainfall in the middle of the growing season, resistance to mid-season drought, and the delayed-leaf-senescence trait can be valuable. Breeding for water-use efficiency, deeper rooting, and heat tolerance are discussed. Diseases and pests that influence adaptation to drought are considered. Resistance to the organism causing ashy stem blight disease should be incorporated because this disease can destroy cowpea seedlings under hot, dry soil conditions. The value of varietal intercrops with contrasting types of cowpea cultivars in enhancing adaptation to drought is described. Implications of cowpea/cereal rotations for cowpea breeding are discussed. Breeding strategies for enhancing cowpea adaptation to drought are described.
Scheiner, Samuel M; Holt, Robert D
Despite the apparent advantages of adaptive plasticity, it is not common. We examined the effects of variation and uncertainty on selection for plasticity using an individual-based computer simulation model. In the model, the environment consisted of a linear gradient of 50 demes with dispersal occurring either before or after selection. Individuals consisted of multiple loci whose phenotypic expression either are affected (plastic) or are not affected (nonplastic) by the environment. Typically, evolution occurred first as genetic differentiation, which was then replaced by the evolution of adaptive plasticity, opposite to the evolutionary trend that is often assumed. Increasing dispersal rates selected for plasticity, if selection occurred before dispersal. If selection occurred after dispersal, the highest plasticity was at intermediate dispersal rates. Temporal variation in the environment occurring after development, but before selection, favored the evolution of plasticity. With dispersal before selection, such temporal variation resulted in hyperplasticity, with a reaction norm much steeper than the optimum. This effect was enhanced with negative temporal autocorrelation and can be interpreted as representing a form of bet hedging. As the number of nonplastic loci increased, plasticity was disfavored due to an increase in the uncertainty of the genomic environment. This effect was reversed with temporal variation. Thus, variation and uncertainty affect whether or not plasticity is favored with different sources of variation—arising from the amount and timing of dispersal, from temporal variation, and even from the genetic architecture underlying the phenotype—having contrasting, interacting, and at times unexpected effects. PMID:22837824
Mérot, Claire; Le Poul, Yann; Théry, Marc; Joron, Mathieu
Müllerian mimicry between chemically defended preys is a textbook example of natural selection favouring phenotypic convergence onto a shared warning signal. Studies of mimicry have concentrated on deciphering the ecological and genetic underpinnings of dramatic switches in mimicry association, producing a well-known mosaic distribution of mimicry patterns across geography. However, little is known about the accuracy of resemblance between natural comimics when the local phenotypic optimum varies. In this study, using analyses of wing shape, pattern and hue, we quantify multimodal phenotypic similarity between butterfly comimics sharing the so-called postman pattern in different localities with varying species composition. We show that subtle but consistent variation between populations of the localized species, Heliconius timareta thelxinoe, enhance resemblance to the abundant comimics which drive the mimicry in each locality. Those results suggest that rarer comimics track the changes in the phenotypic optimum caused by gradual changes in the composition of the mimicry community, providing insights into the process by which intraspecific diversity of mimetic pattern may arise. Furthermore, our results suggest a multimodal evolution of similarity, with coordinated convergence in different features of the phenotype such as wing outline, pattern and hue. Finally, multilocus genotyping allows estimating local hybridization rates between H. timareta and comimic H. melpomene in different populations, raising the hypothesis that mimicry refinement between closely related comimics may be enhanced by adaptive introgression at loci modifying the accuracy of resemblance.
Beebe, Stephen E.; Rao, Idupulapati M.; Blair, Matthew W.; Acosta-Gallegos, Jorge A.
Common beans (Phaseolus vulgaris L.) originated in the New World and are the grain legume of greatest production for direct human consumption. Common bean production is subject to frequent droughts in highland Mexico, in the Pacific coast of Central America, in northeast Brazil, and in eastern and southern Africa from Ethiopia to South Africa. This article reviews efforts to improve common bean for drought tolerance, referring to genetic diversity for drought response, the physiology of drought tolerance mechanisms, and breeding strategies. Different races of common bean respond differently to drought, with race Durango of highland Mexico being a major source of genes. Sister species of P. vulgaris likewise have unique traits, especially P. acutifolius which is well adapted to dryland conditions. Diverse sources of tolerance may have different mechanisms of plant response, implying the need for different methods of phenotyping to recognize the relevant traits. Practical considerations of field management are discussed including: trial planning; water management; and field preparation. PMID:23507928
Hollander, J; Galindo, J; Butlin, R K
A fundamental issue in speciation research is to evaluate phenotypic variation and the genomics driving the evolution of reproductive isolation between sister taxa. Above all, hybrid zones are excellent study systems for researchers to examine the association of genetic differentiation, phenotypic variation and the strength of selection. We investigated two contact zones in the marine gastropod Littorina saxatilis and utilized landmark-based geometric morphometric analysis together with amplified fragment length polymorphism (AFLP) markers to assess phenotypic and genomic divergence between ecotypes under divergent selection. From genetic markers, we calculated the cline width, linkage disequilibrium and the average effective selection on a locus. Additionally, we conducted an association analysis linking the outlier loci and phenotypic variation between ecotypes and show that a proportion of outlier loci are associated with key adaptive phenotypic traits.
Gonçalves-Souza, Thiago; Diniz-Filho, José Alexandre Felizola; Romero, Gustavo Quevedo
An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhabitat scale, although phylogenic signal is present in both scales. Taken together, these results suggest that whereas at the habitat scale selective colonization affect spider body size and shape, at fine scales both selective colonization and adaptive evolution determine spider body shape. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape. We also discussed the relevance in considering multiple scales when studying phylogenetic community structure.
Ritz, Kathryn R; Noor, Mohamed A F; Singh, Nadia D
Rates of meiotic recombination are widely variable both within and among species. However, the functional significance of this variation remains largely unknown. Is the observed within-species variation in recombination rate adaptive? Recent work has revealed new insight into the scale and scope of population-level variation in recombination rate. These data indicate that the magnitude of within-population variation in recombination is similar among taxa. The apparent similarity of the variance in recombination rate among individuals between distantly related species suggests that the relative costs and benefits of recombination that establish the upper and lower bounds may be similar across species. Here we review the current data on intraspecific variation in recombination rate and discuss the molecular and evolutionary costs and benefits of recombination frequency. We place this variation in the context of adaptation and highlight the need for more empirical studies focused on the adaptive value of variation in recombination rate.
Song, Jaeil; Yang, Seungji; Kim, Cheonseog; Nam, Jaeho; Hong, Jin-Woo; Ro, Yong Man
As color is more widely used to carry visual information in the multimedia content, ability to perceive color plays a crucial role in getting visual information. Regardless of color vision variations, one should have visual information equally. This paper proposes the adaptation technique for color vision variations in the MPEG-21 Digital Item Adaptation (DIA). DIA is performed respectively for severe color vision deficiency (dichromats) and for mild color vision deficiency (anomalous trichromats), according to the description of user characteristics about color vision variations. Adapted images are tested by simulation program for color vision variations so as to recognize the appearance of the adapted images in the color deficient vision. Experimental result shows that proposed adaptation technique works well in the MPEG-21 framework.
Holliday, Jason A; Wang, Tongli; Aitken, Sally
Climate is the primary driver of the distribution of tree species worldwide, and the potential for adaptive evolution will be an important factor determining the response of forests to anthropogenic climate change. Although association mapping has the potential to improve our understanding of the genomic underpinnings of climatically relevant traits, the utility of adaptive polymorphisms uncovered by such studies would be greatly enhanced by the development of integrated models that account for the phenotypic effects of multiple single-nucleotide polymorphisms (SNPs) and their interactions simultaneously. We previously reported the results of association mapping in the widespread conifer Sitka spruce (Picea sitchensis). In the current study we used the recursive partitioning algorithm 'Random Forest' to identify optimized combinations of SNPs to predict adaptive phenotypes. After adjusting for population structure, we were able to explain 37% and 30% of the phenotypic variation, respectively, in two locally adaptive traits--autumn budset timing and cold hardiness. For each trait, the leading five SNPs captured much of the phenotypic variation. To determine the role of epistasis in shaping these phenotypes, we also used a novel approach to quantify the strength and direction of pairwise interactions between SNPs and found such interactions to be common. Our results demonstrate the power of Random Forest to identify subsets of markers that are most important to climatic adaptation, and suggest that interactions among these loci may be widespread.
Bell, Rayna C.; Mason, Nicholas A.
Almost 30 y ago, the field of intraspecific phylogeography laid the foundation for spatially explicit and genealogically informed studies of population divergence. With new methods and markers, the focus in phylogeography shifted to previously unrecognized geographic genetic variation, thus reducing the attention paid to phenotypic variation in those same diverging lineages. Although phenotypic differences among lineages once provided the main data for studies of evolutionary change, the mechanisms shaping phenotypic differentiation and their integration with intraspecific genetic structure have been underexplored in phylogeographic studies. However, phenotypes are targets of selection and play important roles in species performance, recognition, and diversification. Here, we focus on three questions. First, how can phenotypes elucidate mechanisms underlying concordant or idiosyncratic responses of vertebrate species evolving in shared landscapes? Second, what mechanisms underlie the concordance or discordance of phenotypic and phylogeographic differentiation? Third, how can phylogeography contribute to our understanding of functional phenotypic evolution? We demonstrate that the integration of phenotypic data extends the reach of phylogeography to explain the origin and maintenance of biodiversity. Finally, we stress the importance of natural history collections as sources of high-quality phenotypic data that span temporal and spatial axes. PMID:27432983
Monty, Arnaud; Bizoux, Jean-Philippe; Escarré, José; Mahy, Grégory
When exotic species spread over novel environments, their phenotype will depend on a combination of different processes, including phenotypic plasticity (PP), local adaptation (LA), environmental maternal effects (EME) and genetic drift (GD). Few attempts have been made to simultaneously address the importance of those processes in plant invasion. The present study uses the well-documented invasion history of Senecio inaequidens (Asteraceae) in southern France, where it was introduced at a single wool-processing site. It gradually invaded the Mediterranean coast and the Pyrenean Mountains, which have noticeably different climates. We used seeds from Pyrenean and Mediterranean populations, as well as populations from the first introduction area, to explore the phenotypic variation related to climatic variation. A reciprocal sowing experiment was performed with gardens under Mediterranean and Pyrenean climates. We analyzed climatic phenotypic variation in germination, growth, reproduction, leaf physiology and survival. Genetic structure in the studied invasion area was characterized using AFLP. We found consistent genetic differentiation in growth traits but no home-site advantage, so weak support for LA to climate. In contrast, genetic differentiation showed a relationship with colonization history. PP in response to climate was observed for most traits, and it played an important role in leaf trait variation. EME mediated by seed mass influenced all but leaf traits in a Pyrenean climate. Heavier, earlier-germinating seeds produced larger individuals that produced more flower heads throughout the growing season. However, in the Mediterranean garden, seed mass only influenced the germination rate. The results show that phenotypic variation in response to climate depends on various ecological and evolutionary processes associated with geographical zone and life history traits. Seeing the relative importance of EME and GD, we argue that a “local adaptation vs
Monty, Arnaud; Bizoux, Jean-Philippe; Escarré, José; Mahy, Grégory
When exotic species spread over novel environments, their phenotype will depend on a combination of different processes, including phenotypic plasticity (PP), local adaptation (LA), environmental maternal effects (EME) and genetic drift (GD). Few attempts have been made to simultaneously address the importance of those processes in plant invasion. The present study uses the well-documented invasion history of Senecio inaequidens (Asteraceae) in southern France, where it was introduced at a single wool-processing site. It gradually invaded the Mediterranean coast and the Pyrenean Mountains, which have noticeably different climates. We used seeds from Pyrenean and Mediterranean populations, as well as populations from the first introduction area, to explore the phenotypic variation related to climatic variation. A reciprocal sowing experiment was performed with gardens under Mediterranean and Pyrenean climates. We analyzed climatic phenotypic variation in germination, growth, reproduction, leaf physiology and survival. Genetic structure in the studied invasion area was characterized using AFLP. We found consistent genetic differentiation in growth traits but no home-site advantage, so weak support for LA to climate. In contrast, genetic differentiation showed a relationship with colonization history. PP in response to climate was observed for most traits, and it played an important role in leaf trait variation. EME mediated by seed mass influenced all but leaf traits in a Pyrenean climate. Heavier, earlier-germinating seeds produced larger individuals that produced more flower heads throughout the growing season. However, in the Mediterranean garden, seed mass only influenced the germination rate. The results show that phenotypic variation in response to climate depends on various ecological and evolutionary processes associated with geographical zone and life history traits. Seeing the relative importance of EME and GD, we argue that a "local adaptation vs
Zimmermann, Tobias D; Kaiser, Sylvia; Hennessy, Michael B; Sachser, Norbert
Environmental conditions during early life can adaptively shape the phenotype for the prevailing environment. Recently, it has been suggested that adolescence represents an additional temporal window for adaptive developmental plasticity, though supporting evidence is scarce. Previous work has shown that male guinea pigs living in large mixed-sex colonies develop a low-aggressive phenotype as part of a queuing strategy that is adaptive for integrating into large unfamiliar colonies. By contrast, males living in pairs during adolescence become highly aggressive towards strangers. Here, we tested whether the high-aggressive phenotype is adaptive under conditions of low population density, namely when directly competing with a single opponent for access to females. For that purpose, we established groups of one pair-housed male (PM), one colony-housed male (CM) and two females. PMs directed more aggression towards the male competitor and more courtship and mating towards females than did CMs. In consequence, PMs attained the dominant position in most cases and sired significantly more offspring. Moreover, they showed distinctly higher testosterone concentrations and elevated cortisol levels, which probably promoted enhanced aggressiveness while mobilizing necessary energy. Taken together, our results provide the clearest evidence to date for adaptive shaping of the phenotype by environmental influences during adolescence.
Archer, Greg S; Dindot, Scott; Friend, Ted H; Walker, Shawn; Zaunbrecher, Gretchen; Lawhorn, Bruce; Piedrahita, Jorge A
Cloning by somatic cell nuclear transfer can result in the birth of animals with phenotypic and gene expression abnormalities. We compared adult cloned pigs and adult pigs from naturally bred control females using a series of physiological and genetic parameters, including detailed methylation profiles of selected genomic regions. Phenotypic and genetic analyses indicated that there are two classes of traits, one in which the cloned pigs have less variation than controls and another characterized by variation that is equally high in cloned and control pigs. Although cloning creates animals within the normal phenotypic range, it increases the variability associated with some traits. This finding is contrary to the expectation that cloning can be used to reduce the size of groups involved in animal experimentation and to reproduce an animal, including a pet, with a homogenous set of desired traits.
Bouklas, Tejas; Fries, Bettina C
Cryptococcus neoformans, similar to other eukaryotes, undergoes replicative aging. Replicative life spans have been determined for clinical C. neoformans strains, and although they are a reproducible trait, life spans vary considerably among strains. C. neoformans has been proposed as an ideal model organism to investigate the contribution of replicative aging in a fungal pathogen population to emerging phenotypic variation during chronic cryptococcal infections. C. neoformans cells of advanced generational age manifest a distinct phenotype; specifically, a larger cell size, a thicker cell wall, drug resistance, as well as resistance to hydrogen peroxide-mediated killing. Consequently, old cells are selected in the host environment during chronic infection and aging could be an unanticipated mechanism of pathogen adaptation that contributes to persistent disease. Aging as a natural process of phenotypic variation should be further studied as it likely is also relevant for other eukaryotic pathogen populations that undergo asymmetric replicative aging.
Storz, Jay F.; Scott, Graham R.; Cheviron, Zachary A.
High-altitude environments provide ideal testing grounds for investigations of mechanism and process in physiological adaptation. In vertebrates, much of our understanding of the acclimatization response to high-altitude hypoxia derives from studies of animal species that are native to lowland environments. Such studies can indicate whether phenotypic plasticity will generally facilitate or impede adaptation to high altitude. Here, we review general mechanisms of physiological acclimatization and genetic adaptation to high-altitude hypoxia in birds and mammals. We evaluate whether the acclimatization response to environmental hypoxia can be regarded generally as a mechanism of adaptive phenotypic plasticity, or whether it might sometimes represent a misdirected response that acts as a hindrance to genetic adaptation. In cases in which the acclimatization response to hypoxia is maladaptive, selection will favor an attenuation of the induced phenotypic change. This can result in a form of cryptic adaptive evolution in which phenotypic similarity between high- and low-altitude populations is attributable to directional selection on genetically based trait variation that offsets environmentally induced changes. The blunted erythropoietic and pulmonary vasoconstriction responses to hypoxia in Tibetan humans and numerous high-altitude birds and mammals provide possible examples of this phenomenon. When lowland animals colonize high-altitude environments, adaptive phenotypic plasticity can mitigate the costs of selection, thereby enhancing prospects for population establishment and persistence. By contrast, maladaptive plasticity has the opposite effect. Thus, insights into the acclimatization response of lowland animals to high-altitude hypoxia can provide a basis for predicting how altitudinal range limits might shift in response to climate change. PMID:21112992
Perry, George H; Foll, Matthieu; Grenier, Jean-Christophe; Patin, Etienne; Nédélec, Yohann; Pacis, Alain; Barakatt, Maxime; Gravel, Simon; Zhou, Xiang; Nsobya, Sam L; Excoffier, Laurent; Quintana-Murci, Lluis; Dominy, Nathaniel J; Barreiro, Luis B
The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions that are significantly associated with the pygmy phenotype in the Batwa, a rainforest hunter-gatherer population from Uganda (east central Africa). The identified genomic regions have multiple attributes that provide supporting evidence of genuine association with the pygmy phenotype, including enrichments for SNPs previously associated with stature variation in Europeans and for genes with growth hormone receptor and regulation functions. To test adaptive evolutionary hypotheses, we computed the haplotype-based integrated haplotype score (iHS) statistic and the level of population differentiation (FST) between the Batwa and their agricultural neighbors, the Bakiga, for each genomic SNP. Both |iHS| and FST values were significantly higher for SNPs within the Batwa pygmy phenotype-associated regions than the remainder of the genome, a signature of polygenic adaptation. In contrast, when we expanded our analysis to include Baka rainforest hunter-gatherers from Cameroon and Gabon (west central Africa) and Nzebi and Nzime neighboring agriculturalists, we did not observe elevated |iHS| or FST values in these genomic regions. Together, these results suggest adaptive and at least partially convergent origins of the pygmy phenotype even within Africa, supporting the hypothesis that small body size confers a selective advantage for tropical rainforest hunter-gatherers but raising questions about the antiquity of this behavior.
Harrod, Chris; Mallela, Jennie; Kahilainen, Kimmo K
1. The adaptive radiation of fishes into benthic (littoral) and pelagic (lentic) morphs in post-glacial lakes has become an important model system for speciation. Although these systems are well studied, there is little evidence of the existence of morphs that have diverged to utilize resources in the remaining principal lake habitat, the profundal zone. 2. Here, we tested phenotype-environment correlations of three whitefish (Coregonus lavaretus) morphs that have radiated into littoral, pelagic and profundal niches in northern Scandinavian lakes. We hypothesized that morphs in such trimorphic systems would have a morphology adapted to one of the principal lake habitats (littoral, pelagic or profundal niches). Most whitefish populations in the study area are formed by a single (monomorphic) whitefish morph, and we further hypothesized that these populations should display intermediate morphotypes and niche utilization. We used a combination of traditional (stomach content, habitat use, gill raker counts) and more recently developed (stable isotopes, geometric morphometrics) techniques to evaluate phenotype-environment correlations in two lakes with trimorphic and two lakes with monomorphic whitefish. 3. Distinct phenotype-environment correlations were evident for each principal niche in whitefish morphs inhabiting trimorphic lakes. Monomorphic whitefish exploited multiple habitats, had intermediate morphology, displayed increased variance in gillraker-counts, and relied significantly on zooplankton, most likely due to relaxed resource competition. 4. We suggest that the ecological processes acting in the trimorphic lakes are similar to each other, and are driving the adaptive evolution of whitefish morphs, possibly leading to the formation of new species.
Eklöv, Peter; Svanbäck, Richard
Predators can cause a shift in both density and frequency of a prey phenotype that may lead to phenotypic divergence through natural selection. What is less investigated is that predators have a variety of indirect effects on prey that could potentially have large evolutionary responses. We conducted a pond experiment to test whether differences in predation risk in different habitats caused shifts in behavior of prey that, in turn, would affect their morphology. We also tested whether the experimental data could explain the morphological variation of perch in the natural environment. In the experiment, predators caused the prey fish to shift to the habitat with the lower predation risk. The prey specialized on habitat-specific resources, and there was a strong correlation between diet of the prey fish and morphological variation, suggesting that resource specialization ultimately affected the morphology. The lack of differences in competition and mortality suggest that the morphological variation among prey was induced by differences in predation risk among habitats. The field study demonstrated that there are differences in growth related to morphology of perch in two different habitats. Thus, a trade-off between foraging and predator avoidance could be responsible for adaptive morphological variation of young perch.
Grenier, S.; Barre, P.; Litrico, I.
Selection and plasticity are two mechanisms that allow the adaptation of a population to a changing environment. Interaction between these nonexclusive mechanisms must be considered if we are to understand population survival. This review discusses the ways in which plasticity and selection can interact, based on a review of the literature on selection and phenotypic plasticity in the evolution of populations. The link between selection and phenotypic plasticity is analysed at the level of the individual. Plasticity can affect an individual's response to selection and so may modify the end result of genetic diversity evolution at population level. Genetic diversity increases the ability of populations or communities to adapt to new environmental conditions. Adaptive plasticity increases individual fitness. However this effect must be viewed from the perspective of the costs of plasticity, although these are not easy to estimate. It is becoming necessary to engage in new experimental research to demonstrate the combined effects of selection and plasticity for adaptation and their consequences on the evolution of genetic diversity. PMID:27313957
Grenier, S; Barre, P; Litrico, I
Selection and plasticity are two mechanisms that allow the adaptation of a population to a changing environment. Interaction between these nonexclusive mechanisms must be considered if we are to understand population survival. This review discusses the ways in which plasticity and selection can interact, based on a review of the literature on selection and phenotypic plasticity in the evolution of populations. The link between selection and phenotypic plasticity is analysed at the level of the individual. Plasticity can affect an individual's response to selection and so may modify the end result of genetic diversity evolution at population level. Genetic diversity increases the ability of populations or communities to adapt to new environmental conditions. Adaptive plasticity increases individual fitness. However this effect must be viewed from the perspective of the costs of plasticity, although these are not easy to estimate. It is becoming necessary to engage in new experimental research to demonstrate the combined effects of selection and plasticity for adaptation and their consequences on the evolution of genetic diversity.
Shrestha, Ram Kumar; Rosenberg, Tally; Makarovsky, Daria; Eckshtain-Levi, Noam; Zelinger, Einat; Kopelowitz, June; Sikorski, Johannes; Burdman, Saul
Acidovorax citrulli causes bacterial fruit blotch (BFB) of cucurbits, a disease that threatens the cucurbit industry worldwide. Despite the economic importance of BFB, little is known about pathogenicity and fitness strategies of the bacterium. We have observed the phenomenon of phenotypic variation in A. citrulli. Here we report the characterization of phenotypic variants (PVs) of two strains, M6 and 7a1, isolated from melon and watermelon, respectively. Phenotypic variation was observed following growth in rich medium, as well as upon isolation of bacteria from inoculated plants or exposure to several stresses, including heat, salt and acidic conditions. When grown on nutrient agar, all PV colonies possessed a translucent appearance, in contrast to parental strain colonies that were opaque. After 72 h, PV colonies were bigger than parental colonies, and had a fuzzy appearance relative to parental strain colonies that are relatively smooth. A. citrulli colonies are generally surrounded by haloes detectable by the naked eye. These haloes are formed by type IV pilus (T4P)-mediated twitching motility that occurs at the edge of the colony. No twitching haloes could be detected around colonies of both M6 and 7a1 PVs, and microscopy observations confirmed that indeed the PVs did not perform twitching motility. In agreement with these results, transmission electron microscopy revealed that M6 and 7a1 PVs do not produce T4P under tested conditions. PVs also differed from their parental strain in swimming motility and biofilm formation, and interestingly, all assessed variants were less virulent than their corresponding parental strains in seed transmission assays. Slight alterations could be detected in some DNA fingerprinting profiles of 7a1 variants relative to the parental strain, while no differences at all could be seen among M6 variants and parental strain, suggesting that, at least in the latter, phenotypic variation is mediated by slight genetic and/or epigenetic
The evolutionary history of modern humans means much more than their demographic past. It includes the way in which humans have had to genetically adapt to the different environments they have encountered-nutritional, climatic or pathogenic-as well as the different epigenetic responses elicited by such environmental cues. Detecting how natural selection has affected human genome variability has proven to be a powerful tool to delineate genes and biological functions having played a key role in human adaptation, a variation which can also be involved in phenotypes of medical relevance. This article reviews several examples that illustrate well how different environmental pressures, particularly those imposed by pathogens and infectious diseases, have shaped the patterns of genetic and epigenetic variability currently observed in human populations.
Radke, David W; Lee, Charles
Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification.
Hirakawa, Matthew P; Martinez, Diego A; Sakthikumar, Sharadha; Anderson, Matthew Z; Berlin, Aaron; Gujja, Sharvari; Zeng, Qiandong; Zisson, Ethan; Wang, Joshua M; Greenberg, Joshua M; Berman, Judith; Bennett, Richard J; Cuomo, Christina A
Candida albicans is a commensal fungus of the human gastrointestinal tract and a prevalent opportunistic pathogen. To examine diversity within this species, extensive genomic and phenotypic analyses were performed on 21 clinical C. albicans isolates. Genomic variation was evident in the form of polymorphisms, copy number variations, chromosomal inversions, subtelomeric hypervariation, loss of heterozygosity (LOH), and whole or partial chromosome aneuploidies. All 21 strains were diploid, although karyotypic changes were present in eight of the 21 isolates, with multiple strains being trisomic for Chromosome 4 or Chromosome 7. Aneuploid strains exhibited a general fitness defect relative to euploid strains when grown under replete conditions. All strains were also heterozygous, yet multiple, distinct LOH tracts were present in each isolate. Higher overall levels of genome heterozygosity correlated with faster growth rates, consistent with increased overall fitness. Genes with the highest rates of amino acid substitutions included many cell wall proteins, implicating fast evolving changes in cell adhesion and host interactions. One clinical isolate, P94015, presented several striking properties including a novel cellular phenotype, an inability to filament, drug resistance, and decreased virulence. Several of these properties were shown to be due to a homozygous nonsense mutation in the EFG1 gene. Furthermore, loss of EFG1 function resulted in increased fitness of P94015 in a commensal model of infection. Our analysis therefore reveals intra-species genetic and phenotypic differences in C. albicans and delineates a natural mutation that alters the balance between commensalism and pathogenicity.
Hirakawa, Matthew P.; Martinez, Diego A.; Sakthikumar, Sharadha; Anderson, Matthew Z.; Berlin, Aaron; Gujja, Sharvari; Zeng, Qiandong; Zisson, Ethan; Wang, Joshua M.; Greenberg, Joshua M.; Berman, Judith
Candida albicans is a commensal fungus of the human gastrointestinal tract and a prevalent opportunistic pathogen. To examine diversity within this species, extensive genomic and phenotypic analyses were performed on 21 clinical C. albicans isolates. Genomic variation was evident in the form of polymorphisms, copy number variations, chromosomal inversions, subtelomeric hypervariation, loss of heterozygosity (LOH), and whole or partial chromosome aneuploidies. All 21 strains were diploid, although karyotypic changes were present in eight of the 21 isolates, with multiple strains being trisomic for Chromosome 4 or Chromosome 7. Aneuploid strains exhibited a general fitness defect relative to euploid strains when grown under replete conditions. All strains were also heterozygous, yet multiple, distinct LOH tracts were present in each isolate. Higher overall levels of genome heterozygosity correlated with faster growth rates, consistent with increased overall fitness. Genes with the highest rates of amino acid substitutions included many cell wall proteins, implicating fast evolving changes in cell adhesion and host interactions. One clinical isolate, P94015, presented several striking properties including a novel cellular phenotype, an inability to filament, drug resistance, and decreased virulence. Several of these properties were shown to be due to a homozygous nonsense mutation in the EFG1 gene. Furthermore, loss of EFG1 function resulted in increased fitness of P94015 in a commensal model of infection. Our analysis therefore reveals intra-species genetic and phenotypic differences in C. albicans and delineates a natural mutation that alters the balance between commensalism and pathogenicity. PMID:25504520
Chevin, Luis-Miguel; Visser, Marcel E; Tufto, Jarle
Despite considerable interest in temporal and spatial variation of phenotypic selection, very few methods allow quantifying this variation while correctly accounting for the error variance of each individual estimate. Furthermore, the available methods do not estimate the autocorrelation of phenotypic selection, which is a major determinant of eco-evolutionary dynamics in changing environments. We introduce a new method for measuring variable phenotypic selection using random regression. We rely on model selection to assess the support for stabilizing selection, and for a moving optimum that may include a trend plus (possibly autocorrelated) fluctuations. The environmental sensitivity of selection also can be estimated by including an environmental covariate. After testing our method on extensive simulations, we apply it to breeding time in a great tit population in the Netherlands. Our analysis finds support for an optimum that is well predicted by spring temperature, and occurs about 33 days before a peak in food biomass, consistent with what is known from the biology of this species. We also detect autocorrelated fluctuations in the optimum, beyond those caused by temperature and the food peak. Because our approach directly estimates parameters that appear in theoretical models, it should be particularly useful for predicting eco-evolutionary responses to environmental change.
Quezada-García, Roberto; Fuentealba, Álvaro; Bauce, Éric
The effects of nutrition may have subtantial impact on insect evolution by shaping different components of phenotypes. The key to undestanding this evolutionary process is to know how nutritional condition affects additive and non-additive components of the phenotype. However, this is poorly understood in outbreaking insects. We investigated the additive and non-additive variation present in food utilization traits in spruce budworm individuals subjected to chronic nutritional stress. 160 full-sib families of spruce budworm (Choristoneura fumiferana Clem.) were raised under laboratory conditions, feeding on two diets (high and low energy) during three generations. Variables tested were pupal mass, consumption rate (RCR), growth rate (RGR), approximate digestibility (AD), the efficiency of conversion of digested food (ECD) and the efficiency of conversion of ingested food (ECI). Our results show that all traits tested presented a high percentage of non-additive effects that modulate phenotype expression. We found a significant impact of family x diet interaction on pupal mass, RGR and ECD. Furthermore, these traits exhibited the greatest heritability. There was no evidence of presence of maternal effects. The results revealed that food utilization traits may evolve through epigenetics effects, such as phenotypic plasticity. This information can be used by modellers to improve forecast of spruce budworm population dynamics. This article is protected by copyright. All rights reserved.
Du, Leshan; Yang, Beifen; Guan, Wenbin; Li, Junmin
The morphological and anatomical characteristics of stems have been found to be related to drought resistance in plants. Testing the phenotypic selection of water availability on stem anatomical traits would be useful for exploring the evolutionary potential of the stem in response to water availability. To test the phenotypic variation of the stem anatomical traits of an invasive plant in response to water availability, we collected a total of 320 individuals of Alternanthera philoxeroides from 16 populations from terrestrial and aquatic habitats in 8 plots in China and then analyzed the variation, differentiation, plasticity and selection potential of water availability on the stem anatomical traits. We found that except for the thickness of the cortex, all of the examined phenotypic parameters of the A. philoxeroides stem were significantly and positively correlated with soil water availability. The phenotypic differentiation coefficient for all of the anatomical structural parameters indicated that most of the variation existed between habitats within the same plot, whereas there was little variation among plots or among individuals within the same habitat except for variation in the thickness of the cortex. A significant phenotypic plasticity response to water availability was found for all of the anatomical traits of A. philoxeroides stem except for the thickness of the cortex. The associations between fitness and some of the anatomical traits, such as the stem diameter, the cortex area-to-stem area ratio, the pith cavity area-to-stem area ratio and the density of vascular bundles, differed with heterogeneous water availability. In both the aquatic and terrestrial habitats, no significant directional selection gradient was found for the stem diameter, the cortex area-to-stem area ratio or the density of vascular bundles. These results indicated that the anatomical structure of the A. philoxeroides stem may play an important role in the adaptation to changes
Lloyd, John D
Mangrove Cuckoo (Coccyzus minor) exhibits substantial phenotypic variation across its geographic range, but the significance of this variation for taxonomy remains unresolved. Using measurements of bill size and ventral color recorded from 274 museum specimens, I found that variation in these traits was clinal. No named subspecies was reciprocally diagnosable from all others, and none was distinguishable from the nominate form, such that previously recognized subspecific distinctions are invalid. Greatest differences in phenotype occurred between populations in Florida, the Bahamas, and the Greater Antilles--characteristically small-billed--and those in the Lesser Antilles, which had larger bills. Phenotypically intermediate individuals on the geographically intermediate islands of Barbuda and Antigua linked these two extremes. Individuals intermediate in bill size and color also characterized populations from throughout the remainder of the range in northern South America and Middle America. Mechanisms maintaining the fairly pronounced phenotypic differences between nearby populations of Greater and Lesser Antillean birds are unknown, yet the geographic proximity of these populations suggests that they probably persist despite occasional gene flow, and may be adaptive.
Lloyd, John D.
Mangrove Cuckoo (Coccyzus minor) exhibits substantial phenotypic variation across its geographic range, but the significance of this variation for taxonomy remains unresolved. Using measurements of bill size and ventral color recorded from 274 museum specimens, I found that variation in these traits was clinal. No named subspecies was reciprocally diagnosable from all others, and none was distinguishable from the nominate form, such that previously recognized subspecific distinctions are invalid. Greatest differences in phenotype occurred between populations in Florida, the Bahamas, and the Greater Antilles–characteristically small-billed–and those in the Lesser Antilles, which had larger bills. Phenotypically intermediate individuals on the geographically intermediate islands of Barbuda and Antigua linked these two extremes. Individuals intermediate in bill size and color also characterized populations from throughout the remainder of the range in northern South America and Middle America. Mechanisms maintaining the fairly pronounced phenotypic differences between nearby populations of Greater and Lesser Antillean birds are unknown, yet the geographic proximity of these populations suggests that they probably persist despite occasional gene flow, and may be adaptive. PMID:27008380
Jelcick, Austin S.; Yuan, Yang; Leehy, Barrett D.; Cox, Lakeisha C.; Silveira, Alexandra C.; Qiu, Fang; Schenk, Sarah; Sachs, Andrew J.; Morrison, Margaux A.; Nystuen, Arne M.; DeAngelis, Margaret M.; Haider, Neena B.
Variation in genetic background can significantly influence the phenotypic outcome of both disease and non-disease associated traits. Additionally, differences in temporal and strain specific gene expression can also contribute to phenotypes in the mammalian retina. This is the first report of microarray based cross-strain analysis of gene expression in the retina investigating genetic background effects. Microarray analyses were performed on retinas from the following mouse strains: C57BL6/J, AKR/J, CAST/EiJ, and NOD.NON-H2-nb1 at embryonic day 18.5 (E18.5) and postnatal day 30.5 (P30.5). Over 3000 differentially expressed genes were identified between strains and developmental stages. Differential gene expression was confirmed by qRT-PCR, Western blot, and immunohistochemistry. Three major gene networks were identified that function to regulate retinal or photoreceptor development, visual perception, cellular transport, and signal transduction. Many of the genes in these networks are implicated in retinal diseases such as bradyopsia, night-blindness, and cone-rod dystrophy. Our analysis revealed strain specific variations in cone photoreceptor cell patterning and retinal function. This study highlights the substantial impact of genetic background on both development and function of the retina and the level of gene expression differences tolerated for normal retinal function. These strain specific genetic variations may also be present in other tissues. In addition, this study will provide valuable insight for the development of more accurate models for human retinal diseases. PMID:21779340
Jahner, Joshua P.; Kozlovsky, Dovid Y.; Parchman, Thomas L.; Pravosudov, Vladimir V.
Montane habitats are characterized by predictably rapid heterogeneity along elevational gradients and are useful for investigating the consequences of environmental heterogeneity for local adaptation and population genetic structure. Food-caching mountain chickadees inhabit a continuous elevation gradient in the Sierra Nevada, and birds living at harsher, high elevations have better spatial memory ability and exhibit differences in male song structure and female mate preference compared to birds inhabiting milder, low elevations. While high elevation birds breed, on average, two weeks later than low elevation birds, the extent of gene flow between elevations is unknown. Despite phenotypic variation and indirect evidence for local adaptation, population genetic analyses based on 18 073 single nucleotide polymorphisms across three transects of high and low elevation populations provided no evidence for genetic differentiation. Analyses based on individual genotypes revealed no patterns of clustering, pairwise estimates of genetic differentiation (FST, Nei's D) were very low, and AMOVA revealed no evidence for genetic variation structured by transect or by low and high elevation sites within transects. In addition, we found no consistent evidence for strong parallel allele frequency divergence between low and high elevation sites within the three transects. Large elevation-related phenotypic variation may be maintained by strong selection despite gene flow and future work should focus on the mechanisms underlying such variation.
Gomez-Mestre, Ivan; Jovani, Roger
An ongoing new synthesis in evolutionary theory is expanding our view of the sources of heritable variation beyond point mutations of fixed phenotypic effects to include environmentally sensitive changes in gene regulation. This expansion of the paradigm is necessary given ample evidence for a heritable ability to alter gene expression in response to environmental cues. In consequence, single genotypes are often capable of adaptively expressing different phenotypes in different environments, i.e. are adaptively plastic. We present an individual-based heuristic model to compare the adaptive dynamics of populations composed of plastic or non-plastic genotypes under a wide range of scenarios where we modify environmental variation, mutation rate and costs of plasticity. The model shows that adaptive plasticity contributes to the maintenance of genetic variation within populations, reduces bottlenecks when facing rapid environmental changes and confers an overall faster rate of adaptation. In fluctuating environments, plasticity is favoured by selection and maintained in the population. However, if the environment stabilizes and costs of plasticity are high, plasticity is reduced by selection, leading to genetic assimilation, which could result in species diversification. More broadly, our model shows that adaptive plasticity is a common consequence of selection under environmental heterogeneity, and hence a potentially common phenomenon in nature. Thus, taking adaptive plasticity into account substantially extends our view of adaptive evolution.
Moore, Kara A.; Stanton, Maureen L.
Adaptation to novel conditions beyond current range boundaries requires the presence of suitable sites within dispersal range, but may be impeded when emigrants encounter poor habitat and sharply different selection pressures. We investigated fine-scale spatial heterogeneity in ecological dynamics and selection at a local population boundary of the annual plant Gilia tricolor. In two years, we planted G. tricolor seeds in core habitat, margin habitat at the edge of the local range, and exterior habitat in order to measure spatial and temporal variation in habitat quality, opportunity for selection, and selection on phenotypic traits. We found a striking decline in average habitat quality with distance from the population core, yet some migrant seeds were successful in suitable, unoccupied microsites at and beyond the range boundary. Total and direct selection on four out of five measured phenotypic traits varied across habitat zones, as well as between years. Moreover, the margin habitat often exerted unique selection pressures that were not intermediate between core and exterior habitats. This study reveals that a combination of ecological and evolutionary forces, including propagule limitation, variation in habitat quality and spatial heterogeneity in phenotypic selection may reduce opportunities for adaptive range expansion, even across a very local population boundary. PMID:24717472
Lind, Martin I.; Yarlett, Kylie; Reger, Julia; Carter, Mauricio J.; Beckerman, Andrew P.
Phenotypic plasticity is the ability of a genotype to produce more than one phenotype in order to match the environment. Recent theory proposes that the major axis of genetic variation in a phenotypically plastic population can align with the direction of selection. Therefore, theory predicts that plasticity directly aids adaptation by increasing genetic variation in the direction favoured by selection and reflected in plasticity. We evaluated this theory in the freshwater crustacean Daphnia pulex, facing predation risk from two contrasting size-selective predators. We estimated plasticity in several life-history traits, the G matrix of these traits, the selection gradients on reproduction and survival, and the predicted responses to selection. Using these data, we tested whether the genetic lines of least resistance and the predicted response to selection aligned with plasticity. We found predator environment-specific G matrices, but shared genetic architecture across environments resulted in more constraint in the G matrix than in the plasticity of the traits, sometimes preventing alignment of the two. However, as the importance of survival selection increased, the difference between environments in their predicted response to selection increased and resulted in closer alignment between the plasticity and the predicted selection response. Therefore, plasticity may indeed aid adaptation to new environments. PMID:26423845
Lind, Martin I; Yarlett, Kylie; Reger, Julia; Carter, Mauricio J; Beckerman, Andrew P
Phenotypic plasticity is the ability of a genotype to produce more than one phenotype in order to match the environment. Recent theory proposes that the major axis of genetic variation in a phenotypically plastic population can align with the direction of selection. Therefore, theory predicts that plasticity directly aids adaptation by increasing genetic variation in the direction favoured by selection and reflected in plasticity. We evaluated this theory in the freshwater crustacean Daphnia pulex, facing predation risk from two contrasting size-selective predators. We estimated plasticity in several life-history traits, the G matrix of these traits, the selection gradients on reproduction and survival, and the predicted responses to selection. Using these data, we tested whether the genetic lines of least resistance and the predicted response to selection aligned with plasticity. We found predator environment-specific G matrices, but shared genetic architecture across environments resulted in more constraint in the G matrix than in the plasticity of the traits, sometimes preventing alignment of the two. However, as the importance of survival selection increased, the difference between environments in their predicted response to selection increased and resulted in closer alignment between the plasticity and the predicted selection response. Therefore, plasticity may indeed aid adaptation to new environments.
Moore, Kara A; Stanton, Maureen L
Adaptation to novel conditions beyond current range boundaries requires the presence of suitable sites within dispersal range, but may be impeded when emigrants encounter poor habitat and sharply different selection pressures. We investigated fine-scale spatial heterogeneity in ecological dynamics and selection at a local population boundary of the annual plant Gilia tricolor. In two years, we planted G. tricolor seeds in core habitat, margin habitat at the edge of the local range, and exterior habitat in order to measure spatial and temporal variation in habitat quality, opportunity for selection, and selection on phenotypic traits. We found a striking decline in average habitat quality with distance from the population core, yet some migrant seeds were successful in suitable, unoccupied microsites at and beyond the range boundary. Total and direct selection on four out of five measured phenotypic traits varied across habitat zones, as well as between years. Moreover, the margin habitat often exerted unique selection pressures that were not intermediate between core and exterior habitats. This study reveals that a combination of ecological and evolutionary forces, including propagule limitation, variation in habitat quality and spatial heterogeneity in phenotypic selection may reduce opportunities for adaptive range expansion, even across a very local population boundary.
Bedhomme, Stéphanie; Elena, Santiago F
Competition and parasitism are two important selective forces that shape life-histories, migration rates and population dynamics. Recently, it has been shown in various pathosystems that parasites can modify intraspecific competition, thus generating an indirect cost of parasitism. Here, we investigated if this phenomenon was present in a plant-potyvirus system using two viruses of different virulence (Tobacco etch virus and Turnip mosaic virus). Moreover, we asked if parasitism interacted with the shade avoidance syndrome, the plant-specific phenotypic plasticity in response to intraspecific competition. Our results indicate that the modification of intraspecific competition by parasitism is not present in the Nicotiana benthamiana--potyvirus system and suggests that this phenomenon is not universal but depends on the peculiarities of each pathosystem. However, whereas the healthy N. benthamiana presented a clear shade avoidance syndrome, this phenotypic plasticity totally disappeared when the plants were infected with TEV and TuMV, very likely resulting in a fitness loss and being another form of indirect cost of parasitism. This result suggests that the suppression or the alteration of adaptive phenotypic plasticity might be a component of virulence that is often overlooked.
Bedhomme, Stéphanie; Elena, Santiago F.
Competition and parasitism are two important selective forces that shape life-histories, migration rates and population dynamics. Recently, it has been shown in various pathosystems that parasites can modify intraspecific competition, thus generating an indirect cost of parasitism. Here, we investigated if this phenomenon was present in a plant-potyvirus system using two viruses of different virulence (Tobacco etch virus and Turnip mosaic virus). Moreover, we asked if parasitism interacted with the shade avoidance syndrome, the plant-specific phenotypic plasticity in response to intraspecific competition. Our results indicate that the modification of intraspecific competition by parasitism is not present in the Nicotiana benthamiana – potyvirus system and suggests that this phenomenon is not universal but depends on the peculiarities of each pathosystem. However, whereas the healthy N. benthamiana presented a clear shade avoidance syndrome, this phenotypic plasticity totally disappeared when the plants were infected with TEV and TuMV, very likely resulting in a fitness loss and being another form of indirect cost of parasitism. This result suggests that the suppression or the alteration of adaptive phenotypic plasticity might be a component of virulence that is often overlooked. PMID:21359142
Monneveux, Philippe; Jing, Ruilian; Misra, Satish C.
Wheat (Triticum spp) is one of the first domesticated food crops. It represents the first source of calories (after rice) and an important source of proteins in developing countries. As a result of the Green Revolution, wheat yield sharply increased due to the use of improved varieties, irrigation, pesticides, and fertilizers. The rate of increase in world wheat production, however, slowed after 1980, except in China, India, and Pakistan. Being adapted to a wide range of moisture conditions, wheat is grown on more land area worldwide than any other crop, including in drought prone areas. In these marginal rain-fed environments where at least 60 m ha of wheat is grown, amount and distribution of rainfall are the predominant factors influencing yield variability. Intensive work has been carried out in the area of drought adaptation over the last decades. Breeding strategies for drought tolerance improvement include: definition of the target environment, choice and characterization of the testing environment, water stress management and characterization, and use of phenotyping traits with high heritability. The use of integrative traits, facilitated by the development and application of new technologies (thermal imaging, spectral reflectance, stable isotopes) is facilitating high throughput phenotyping and indirect selection, consequently favoring yield improvement in drought prone environments. PMID:23181021
Monneveux, Philippe; Jing, Ruilian; Misra, Satish C
Wheat (Triticum spp) is one of the first domesticated food crops. It represents the first source of calories (after rice) and an important source of proteins in developing countries. As a result of the Green Revolution, wheat yield sharply increased due to the use of improved varieties, irrigation, pesticides, and fertilizers. The rate of increase in world wheat production, however, slowed after 1980, except in China, India, and Pakistan. Being adapted to a wide range of moisture conditions, wheat is grown on more land area worldwide than any other crop, including in drought prone areas. In these marginal rain-fed environments where at least 60 m ha of wheat is grown, amount and distribution of rainfall are the predominant factors influencing yield variability. Intensive work has been carried out in the area of drought adaptation over the last decades. Breeding strategies for drought tolerance improvement include: definition of the target environment, choice and characterization of the testing environment, water stress management and characterization, and use of phenotyping traits with high heritability. The use of integrative traits, facilitated by the development and application of new technologies (thermal imaging, spectral reflectance, stable isotopes) is facilitating high throughput phenotyping and indirect selection, consequently favoring yield improvement in drought prone environments.
Blamires, Sean J; Hasemore, Matthew; Martens, Penny J; Kasumovic, Michael M
The adaptive benefits of extended phenotypic plasticity are imprecisely defined due to a paucity of experiments examining traits that are manipulable and measurable across environments. Spider webs are often used as models to explore the adaptive benefits of variations in extended phenotypes across environments. Nonetheless, our understanding of the adaptive nature of the plastic responses of spider webs is impeded when web architectures and silk physicochemical properties appear to co-vary. An opportunity to examine this co-variation is presented by modifying prey items while measuring web architectures and silk physiochemical properties. Here, we performed two experiments to assess the nature of the association between web architectures and gluey silk properties when the orb web spider Argiope keyserlingi was fed a diet that varied in either mass and energy or prey size and feeding frequency. We found web architectures and gluey silk physicochemical properties to co-vary across treatments in both experiments. Specifically, web capture area co-varied with gluey droplet morphometrics, thread stickiness and salt concentrations when prey mass and energy were manipulated, and spiral spacing co-varied with gluey silk salt concentrations when prey size and feeding frequency were manipulated. We explained our results as A. keyserlingi plastically shifting its foraging strategy as multiple prey parameters simultaneously varied. We confirmed and extended previous work by showing that spiders use a variety of prey cues to concurrently adjust web and silk traits across different feeding regimes.
Tunnicliffe, Verena; St Germain, Candice; Hilário, Ana
We examine the nature of variation in a hot vent tubeworm, Ridgeia piscesae, to determine how phenotypes are maintained and how reproductive potential is dictated by habitat. This foundation species at northeast Pacific hydrothermal sites occupies a wide habitat range in a highly heterogeneous environment. Where fluids supply high levels of dissolved sulphide for symbionts, the worm grows rapidly in a "short-fat" phenotype characterized by lush gill plumes; when plumes are healthy, sperm package capture is higher. This form can mature within months and has a high fecundity with continuous gamete output and a lifespan of about three years in unstable conditions. Other phenotypes occupy low fluid flux habitats that are more stable and individuals grow very slowly; however, they have low reproductive readiness that is hampered further by small, predator cropped branchiae, thus reducing fertilization and metabolite uptake. Although only the largest worms were measured, only 17% of low flux worms were reproductively competent compared to 91% of high flux worms. A model of reproductive readiness illustrates that tube diameter is a good predictor of reproductive output and that few low flux worms reached critical reproductive size. We postulate that most of the propagules for the vent fields originate from the larger tubeworms that live in small, unstable habitat patches. The large expanses of worms in more stable low flux habitat sustain a small, but long-term, reproductive output. Phenotypic variation is an adaptation that fosters both morphological and physiological responses to differences in chemical milieu and predator pressure. This foundation species forms a metapopulation with variable growth characteristics in a heterogeneous environment where a strategy of phenotypic variation bestows an advantage over specialization.
Tunnicliffe, Verena; St. Germain, Candice; Hilário, Ana
We examine the nature of variation in a hot vent tubeworm, Ridgeia piscesae, to determine how phenotypes are maintained and how reproductive potential is dictated by habitat. This foundation species at northeast Pacific hydrothermal sites occupies a wide habitat range in a highly heterogeneous environment. Where fluids supply high levels of dissolved sulphide for symbionts, the worm grows rapidly in a “short-fat” phenotype characterized by lush gill plumes; when plumes are healthy, sperm package capture is higher. This form can mature within months and has a high fecundity with continuous gamete output and a lifespan of about three years in unstable conditions. Other phenotypes occupy low fluid flux habitats that are more stable and individuals grow very slowly; however, they have low reproductive readiness that is hampered further by small, predator cropped branchiae, thus reducing fertilization and metabolite uptake. Although only the largest worms were measured, only 17% of low flux worms were reproductively competent compared to 91% of high flux worms. A model of reproductive readiness illustrates that tube diameter is a good predictor of reproductive output and that few low flux worms reached critical reproductive size. We postulate that most of the propagules for the vent fields originate from the larger tubeworms that live in small, unstable habitat patches. The large expanses of worms in more stable low flux habitat sustain a small, but long-term, reproductive output. Phenotypic variation is an adaptation that fosters both morphological and physiological responses to differences in chemical milieu and predator pressure. This foundation species forms a metapopulation with variable growth characteristics in a heterogeneous environment where a strategy of phenotypic variation bestows an advantage over specialization. PMID:25337895
Perry, George H.; Foll, Matthieu; Grenier, Jean-Christophe; Patin, Etienne; Nédélec, Yohann; Pacis, Alain; Barakatt, Maxime; Gravel, Simon; Zhou, Xiang; Nsobya, Sam L.; Excoffier, Laurent; Quintana-Murci, Lluis; Dominy, Nathaniel J.; Barreiro, Luis B.
The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions that are significantly associated with the pygmy phenotype in the Batwa, a rainforest hunter-gatherer population from Uganda (east central Africa). The identified genomic regions have multiple attributes that provide supporting evidence of genuine association with the pygmy phenotype, including enrichments for SNPs previously associated with stature variation in Europeans and for genes with growth hormone receptor and regulation functions. To test adaptive evolutionary hypotheses, we computed the haplotype-based integrated haplotype score (iHS) statistic and the level of population differentiation (FST) between the Batwa and their agricultural neighbors, the Bakiga, for each genomic SNP. Both |iHS| and FST values were significantly higher for SNPs within the Batwa pygmy phenotype-associated regions than the remainder of the genome, a signature of polygenic adaptation. In contrast, when we expanded our analysis to include Baka rainforest hunter-gatherers from Cameroon and Gabon (west central Africa) and Nzebi and Nzime neighboring agriculturalists, we did not observe elevated |iHS| or FST values in these genomic regions. Together, these results suggest adaptive and at least partially convergent origins of the pygmy phenotype even within Africa, supporting the hypothesis that small body size confers a selective advantage for tropical rainforest hunter-gatherers but raising questions about the antiquity of this behavior. PMID:25136101
Landy, J Alex; Travis, Joseph
Studies of the adaptive significance of variation among conspecific populations often focus on a single ecological factor. However, habitats rarely differ in only a single ecological factor, creating a challenge for identifying the relative importance of the various ecological factors that might be maintaining local adaptation. Here we investigate the ecological factors associated with male body shape variation among nine populations of the poeciliid fish, Heterandria formosa, from three distinct habitats and combine those results with a laboratory study of three of those populations to assess the contributions of genetic and environmental influences to shape variation. Field-collected animals varied principally in three ways: the orientation of the gonopodium, the intromittent organ; the degree of body depth and streamlining; and the shape of the tail musculature. Fish collected in the spring season were larger and had a more anteriorly positioned gonopodium than fish collected in autumn. Fish collected from lotic springs were larger and more streamlined than those collected from lentic ponds or tidal marshes. Some of the variation in male shape among populations within habitats was associated with population-level variation in species richness, adult density, vegetative cover, predation risk, and female standard length. Population-level differences among males in body size, position of the gonopodium, and shape of the tail musculature were maintained among males reared in a common environment. In contrast, population variation in the degree of streamlining was eliminated when males were reared in a common environment. These results illustrate the complicated construction of multivariate phenotypic variation and suggest that different agents of selection have acted on different components of shape.
Hedrick, Philip W
Adaptive genetic variation has been thought to originate primarily from either new mutation or standing variation. Another potential source of adaptive variation is adaptive variants from other (donor) species that are introgressed into the (recipient) species, termed adaptive introgression. Here, the various attributes of these three potential sources of adaptive variation are compared. For example, the rate of adaptive change is generally thought to be faster from standing variation, slower from mutation and potentially intermediate from adaptive introgression. Additionally, the higher initial frequency of adaptive variation from standing variation and lower initial frequency from mutation might result in a higher probability of fixation of the adaptive variants for standing variation. Adaptive variation from introgression might have higher initial frequency than new adaptive mutations but lower than that from standing variation, again making the impact of adaptive introgression variation potentially intermediate. Adaptive introgressive variants might have multiple changes within a gene and affect multiple loci, an advantage also potentially found for adaptive standing variation but not for new adaptive mutants. The processes that might produce a common variant in two taxa, convergence, trans-species polymorphism from incomplete lineage sorting or from balancing selection and adaptive introgression, are also compared. Finally, potential examples of adaptive introgression in animals, including balancing selection for multiple alleles for major histocompatibility complex (MHC), S and csd genes, pesticide resistance in mice, black colour in wolves and white colour in coyotes, Neanderthal or Denisovan ancestry in humans, mimicry genes in Heliconius butterflies, beak traits in Darwin's finches, yellow skin in chickens and non-native ancestry in an endangered native salamander, are examined.
Lianou, Alexandra; Nychas, George-John E; Koutsoumanis, Konstantinos P
The objective of this study was the assessment of the stationary-phase, low-pH-inducible acid tolerance response (ATR) of different Salmonella enterica strains. For this purpose, 30 strains of the pathogen were grown in tryptone soy broth in the absence (non-adapted cultures) and presence (1% w/v; acid-adapted cultures) of glucose, and then subjected to 4-h acid challenge trials at pH 3.0. Surviving populations of each strain were determined at 1-h intervals, and the Weibull model was fitted to the derived microbiological data. Extensive variability in the acid stress responses of the tested S. enterica strains was observed, with the total population reductions (log CFU/ml) attained in 4 h of acid challenge ranging from 0.9 to 5.5 and from 0.6 to 7.0 for the non-adapted and acid-adapted cultures, respectively. As demonstrated by the model scale parameter δ and shape parameter p, the effect of acid adaptation on the inactivation curves was strain-specific. Although acid adaptation resulted in enhanced acid survival for the majority of the tested strains, there were strains exhibiting similar or decreased acid resistance compared to their non-adapted counterparts. Moreover, acid adaptation appeared to decrease the strain variability of δ whereas increasing the strain variability of p: the coefficient of variation of δ among the tested strains was 97.2 and 54.9% for the non-adapted and acid-adapted cultures, respectively, while the corresponding values for p were 12.7 and 48.1%. The data of the present study, which is the first one to systematically evaluate the adaptive ATR of multiple S. enterica strains, clearly demonstrate that this phenotype (attempted to be induced by growing the pathogen in the presence of glucose) is strain-dependent.
Wright, John Timothy; Puranik, Chaitanya P; Farrington, Frank
Focal dermal hypoplasia (FDH) or Goltz Syndrome (OMIM# 305600) is an X-linked dominant ectodermal dysplasia caused by mutations in the PORCN gene. This gene encodes an endoplasmic reticulum transmembrane protein that is involved in processing the embryonically critical WNT signaling proteins. Individuals diagnosed with FDH were recruited to participate in the study through the National Foundation for Ectodermal Dysplasia. Individuals were evaluated to characterize the FDH phenotype. Each participant completed a brief dental survey and oral evaluation using artificial light. To identify the oral soft and hard tissue findings 19 individuals (16 female and 3 male) participated with a median age of 10 years (range 2-56 years). Soft and hard tissue defects were present in 68% (13) and 94% (18) of the patients, respectively. Dental anomalies were highly prevalent with 68% (13) demonstrating vertical enamel grooving, 52% (10) having peg shaped tooth deformities, and 78% (15) having enamel hypoplasia with or without discoloration. Cleft lip and cleft palate presented in 15% (3) of the participants. Other findings included 57% (11) having intra-oral lipoma or papilloma with no site predilection. Dental malocclusions were common with 63% (12) having some degree of malocclusion with 15% (3) of participants having class III malocclusion with an anterior dental cross bite. Participants frequently reported speech problems or difficulty with chewing (73%; N = 14). This study shows there is marked variation in the oral phenotype of individuals with FDH and underscores the important role of WNT signaling in oro-facial development.
Helbig, Ingo; Swinkels, Marielle E M; Aten, Emmelien; Caliebe, Almuth; van 't Slot, Ruben; Boor, Rainer; von Spiczak, Sarah; Muhle, Hiltrud; Jähn, Johanna A; van Binsbergen, Ellen; van Nieuwenhuizen, Onno; Jansen, Floor E; Braun, Kees P J; de Haan, Gerrit-Jan; Tommerup, Niels; Stephani, Ulrich; Hjalgrim, Helle; Poot, Martin; Lindhout, Dick; Brilstra, Eva H; Møller, Rikke S; Koeleman, Bobby PC
A genetic contribution to a broad range of epilepsies has been postulated, and particularly copy number variations (CNVs) have emerged as significant genetic risk factors. However, the role of CNVs in patients with epilepsies with complex phenotypes is not known. Therefore, we investigated the role of CNVs in patients with unclassified epilepsies and complex phenotypes. A total of 222 patients from three European countries, including patients with structural lesions on magnetic resonance imaging (MRI), dysmorphic features, and multiple congenital anomalies, were clinically evaluated and screened for CNVs. MRI findings including acquired or developmental lesions and patient characteristics were subdivided and analyzed in subgroups. MRI data were available for 88.3% of patients, of whom 41.6% had abnormal MRI findings. Eighty-eight rare CNVs were discovered in 71 out of 222 patients (31.9%). Segregation of all identified variants could be assessed in 42 patients, 11 of which were de novo. The frequency of all structural variants and de novo variants was not statistically different between patients with or without MRI abnormalities or MRI subcategories. Patients with dysmorphic features were more likely to carry a rare CNV. Genome-wide screening methods for rare CNVs may provide clues for the genetic etiology in patients with a broader range of epilepsies than previously anticipated, including in patients with various brain anomalies detectable by MRI. Performing genome-wide screens for rare CNVs can be a valuable contribution to the routine diagnostic workup in patients with a broad range of childhood epilepsies. PMID:24281369
Stock, Jay T
The "negrito hypothesis" suggests that populations of small-bodied foragers in South and Southeast Asia who share common phenotypic characteristics may also share a common, ancient origin. The key defining characteristics of the "negrito" phenotype, small body size, dark skin, and tightly curled hair, have been interpreted as linking these populations to sub-Saharan Africans. The underlying assumption of this interpretation is that the observed phenotypic similarities likely reflect shared ancestry rather than phenotypic convergence. Current genetic evidence is inconclusive, as it both demonstrates that negrito populations have genetic affinities with neighboring populations but also rare and ancient variation that suggests considerable isolation. This study investigates the skeletal phenotype of Andaman Islanders and Aeta foragers from the Philippines in the context of the phenotypic variation among other hunter-gatherers globally, to test whether they show a common, unique physique apart from small body size. Particular emphasis is placed on the comparison of negrito phenotypes to African, Asian, and Australian hunter-gatherer diversity to investigate phenotypic similarities to other populations globally. The results demonstrate that despite sharing small adult stature, the Andaman Islanders and Aeta show variation in body dimensions. In particular, the Andaman Islanders share a pattern of narrow bi-iliac breadth and short upper limbs with the Khoisan (Later Stone Age Southern Africans), whereas the Aeta and Efé show broader bi-iliac breadths relative to lower limb lengths. Although general similarities in size and proportions remain between the Andamanese and Aeta, differences in humero-femoral indices and arm length between these groups and the Efé demonstrate that there is not a generic "pygmy" phenotype. Our interpretations of negrito origins and adaptation must account for this phenotypic variation.
Baillie, Shauna M.; Muir, Andrew M.; Hansen, Michael J.; Krueger, Charles C.; Bentzen, Paul
BackgroundAdaptive radiation involving a colonizing phenotype that rapidly evolves into at least one other ecological variant, or ecotype, has been observed in a variety of freshwater fishes in post-glacial environments. However, few studies consider how phenotypic traits vary with regard to neutral genetic partitioning along ecological gradients. Here, we present the first detailed investigation of lake trout Salvelinus namaycushthat considers variation as a cline rather than discriminatory among ecotypes. Genetic and phenotypic traits organized along common ecological gradients of water depth and geographic distance provide important insights into diversification processes in a lake with high levels of human disturbance from over-fishing.ResultsFour putative lake trout ecotypes could not be distinguished using population genetic methods, despite morphological differences. Neutral genetic partitioning in lake trout was stronger along a gradient of water depth, than by locality or ecotype. Contemporary genetic migration patterns were consistent with isolation-by-depth. Historical gene flow patterns indicated colonization from shallow to deep water. Comparison of phenotypic (Pst) and neutral genetic variation (Fst) revealed that morphological traits related to swimming performance (e.g., buoyancy, pelvic fin length) departed more strongly from neutral expectations along a depth gradient than craniofacial feeding traits. Elevated phenotypic variance with increasing water depth in pelvic fin length indicated possible ongoing character release and diversification. Finally, differences in early growth rate and asymptotic fish length across depth strata may be associated with limiting factors attributable to cold deep-water environments.ConclusionWe provide evidence of reductions in gene flow and divergent natural selection associated with water depth in Lake Superior. Such information is relevant for documenting intraspecific biodiversity in the largest freshwater lake
Albertin, Warren; Marullo, Philippe; Bely, Marina; Aigle, Michel; Bourgais, Aurélie; Langella, Olivier; Balliau, Thierry; Chevret, Didier; Valot, Benoît; da Silva, Telma; Dillmann, Christine; de Vienne, Dominique; Sicard, Delphine
Enzymes can be post-translationally modified, leading to isoforms with different properties. The phenotypic consequences of the quantitative variability of isoforms have never been studied. We used quantitative proteomics to dissect the relationships between the abundances of the enzymes and isoforms of alcoholic fermentation, metabolic traits, and growth-related traits in Saccharomyces cerevisiae. Although the enzymatic pool allocated to the fermentation proteome was constant over the culture media and the strains considered, there was variation in abundance of individual enzymes and sometimes much more of their isoforms, which suggests the existence of selective constraints on total protein abundance and trade-offs between isoforms. Variations in abundance of some isoforms were significantly associated to metabolic traits and growth-related traits. In particular, cell size and maximum population size were highly correlated to the degree of N-terminal acetylation of the alcohol dehydrogenase. The fermentation proteome was found to be shaped by human selection, through the differential targeting of a few isoforms for each food-processing origin of strains. These results highlight the importance of post-translational modifications in the diversity of metabolic and life-history traits. PMID:23271801
Fowler, William; Lim, Sim Lin; Enright, Neal; He, Tianhua
Declining rainfall is projected to have negative impacts on the demographic performance of plant species. Little is known about the adaptive capacity of species to respond to drying climates, and whether adaptation can keep pace with climate change. In fire-prone ecosystems, episodic recruitment of perennial plant species in the first year post-fire imposes a specific selection environment, offering a unique opportunity to quantify the scope for adaptive response to climate change. We examined the growth of seedlings of four fire-killed species under control and drought conditions for seeds from populations established in years following fire receiving average-to-above-average winter rainfall, or well-below-average winter rainfall. We show that offspring of plants that had established under drought had more efficient water uptake, and/or stored more water per unit biomass, or developed denser leaves, and all maintained higher survival in simulated drought than did offspring of plants established in average annual rainfall years. Adaptive phenotypic responses were not consistent across all traits and species, while plants that had established under severe drought or established in years with average-to-above-average rainfall had an overall different physiological response when growing either with or without water constraints. Seedlings descended from plants established under severe drought also had elevated gene expression in key pathways relating to stress response. Our results demonstrate the capacity for rapid adaptation to climate change through phenotypic variation and regulation of gene expression. However, effective and rapid adaptation to climate change may vary among species depending on their capacity to maintain robust populations under multiple stresses. PMID:28018654
Sánchez-Romero, María Antonia; Casadesús, Josep
Antibiotic-resistant isolates of Salmonella enterica were selected on plates containing lethal concentrations of rifampicin, kanamycin, and nalidixic acid. The stability of the resistance phenotype was scored after nonselective growth. Rifampicin-resistant (Rifr) isolates were stable, suggesting that they had arisen by mutation. Mutations in the rpoB gene were detected indeed in Rifr mutants. In contrast, a fraction of kanamycin-resistant (Kmr) and nalidixic acid-resistant (Nalr) isolates showed reduced resistance after nonselective growth, suggesting that mechanisms other than mutation had contributed to bacterial survival upon lethal selection. Single-cell analysis revealed heterogeneity in expression of the porin gene ompC, and subpopulation separation provided evidence that reduced ompC expression confers adaptive resistance to kanamycin. In the case of Nalr isolates, mutations in the gyrA gene were present in most nalidixic acid-resistant isolates. However, the efflux pump inhibitor Phe-Arg-β-naphtylamide (PAβN) reduced the level of resistance in Nalr mutants, indicating that active efflux contributes to the overall level of nalidixic acid resistance. Heterogeneous efflux pump activity was detected in single cells and colonies, and a correlation between high efflux and increased resistance to nalidixic acid was found. These observations suggest that fluctuations in the expression and the activity of critical functions of the bacterial cell, alone or combined with mutations, can contribute to adaptive resistance to antibiotics. PMID:24351930
Sánchez-Romero, María Antonia; Casadesús, Josep
Antibiotic-resistant isolates of Salmonella enterica were selected on plates containing lethal concentrations of rifampicin, kanamycin, and nalidixic acid. The stability of the resistance phenotype was scored after nonselective growth. Rifampicin-resistant (Rif(r)) isolates were stable, suggesting that they had arisen by mutation. Mutations in the rpoB gene were detected indeed in Rif(r) mutants. In contrast, a fraction of kanamycin-resistant (Km(r)) and nalidixic acid-resistant (Nal(r)) isolates showed reduced resistance after nonselective growth, suggesting that mechanisms other than mutation had contributed to bacterial survival upon lethal selection. Single-cell analysis revealed heterogeneity in expression of the porin gene ompC, and subpopulation separation provided evidence that reduced ompC expression confers adaptive resistance to kanamycin. In the case of Nal(r) isolates, mutations in the gyrA gene were present in most nalidixic acid-resistant isolates. However, the efflux pump inhibitor Phe-Arg-β-naphtylamide (PAβN) reduced the level of resistance in Nal(r) mutants, indicating that active efflux contributes to the overall level of nalidixic acid resistance. Heterogeneous efflux pump activity was detected in single cells and colonies, and a correlation between high efflux and increased resistance to nalidixic acid was found. These observations suggest that fluctuations in the expression and the activity of critical functions of the bacterial cell, alone or combined with mutations, can contribute to adaptive resistance to antibiotics.
Lang, Zhaobo; Xie, Shaojun; Zhu, Jian-Kang
Intraspecific phenotypic diversity is controlled by natural genetic and epigenetic variation. Kawakatsu et al. recently sequenced the DNA methylomes of a global collection of over 1000 Arabidopsis accessions, and have thereby provided a comprehensive resource for studying natural genetic and epigenetic variation as well as the association of such variation with phenotypic diversity.
Background Phenotypic evolution and its role in the diversification of organisms is a central topic in evolutionary biology. A neglected factor during the modern evolutionary synthesis, adaptive phenotypic plasticity, more recently attracted the attention of many evolutionary biologists and is now recognized as an important ingredient in both population persistence and diversification. The traits and directions in which an ancestral source population displays phenotypic plasticity might partly determine the trajectories in morphospace, which are accessible for an adaptive radiation, starting from the colonization of a novel environment. In the case of repeated colonizations of similar environments from the same source population this "flexible stem" hypothesis predicts similar phenotypes to arise in repeated subsequent radiations. The Midas Cichlid (Amphilophus spp.) in Nicaragua has radiated in parallel in several crater-lakes seeded by populations originating from the Nicaraguan Great Lakes. Here, we tested phenotypic plasticity in the pharyngeal jaw of Midas Cichlids. The pharyngeal jaw apparatus of cichlids, a second set of jaws functionally decoupled from the oral ones, is known to mediate ecological specialization and often differs strongly between sister-species. Results We performed a common garden experiment raising three groups of Midas cichlids on food differing in hardness and calcium content. Analyzing the lower pharyngeal jaw-bones we find significant differences between diet groups qualitatively resembling the differences found between specialized species. Observed differences in pharyngeal jaw expression between groups were attributable to the diet's mechanical resistance, whereas surplus calcium in the diet was not found to be of importance. Conclusions The pharyngeal jaw apparatus of Midas Cichlids can be expressed plastically if stimulated mechanically during feeding. Since this trait is commonly differentiated - among other traits - between
Garmendia, Junkal; Martí-Lliteras, Pau; Moleres, Javier; Puig, Carmen; Bengoechea, José A
The human respiratory tract contains a highly adapted microbiota including commensal and opportunistic pathogens. Noncapsulated or nontypable Haemophilus influenzae (NTHi) is a human-restricted member of the normal airway microbiota in healthy carriers and an opportunistic pathogen in immunocompromised individuals. The duality of NTHi as a colonizer and as a symptomatic infectious agent is closely related to its adaptation to the host, which in turn greatly relies on the genetic plasticity of the bacterium and is facilitated by its condition as a natural competent. The variable genotype of NTHi accounts for its heterogeneous gene expression and variable phenotype, leading to differential host-pathogen interplay among isolates. Here we review our current knowledge of NTHi diversity in terms of genotype, gene expression, antigenic variation, and the phenotypes associated with colonization and pathogenesis. The potential benefits of NTHi diversity studies discussed herein include the unraveling of pathogenicity clues, the generation of tools to predict virulence from genomic data, and the exploitation of a unique natural system for the continuous monitoring of long-term bacterial evolution in human airways exposed to noxious agents. Finally, we highlight the challenge of monitoring both the pathogen and the host in longitudinal studies, and of applying comparative genomics to clarify the meaning of the vast NTHi genetic diversity and its translation to virulence phenotypes.
Silva, K B; Bruzi, A T; Zuffo, A M; Zambiazzi, E V; Soares, I O; de Rezende, P M; Fronza, V; Vilela, G D L; Botelho, F B S; Teixeira, C M; de O Coelho, M A
The aim of this study was to verify the adaptability and stability of soybean cultivars with regards to yield and oil content. Data of soybean yield and oil content were used from experiments set up in six environments in the 2011/12 and 2012/13 crop seasons in the municipalities of Patos de Minas, Uberaba, Lavras, and São Gotardo, Minas Gerais, Brazil, testing 36 commercial soybean cultivars of both conventional and transgenic varieties. The Wricke method and GGE biplot analysis were used to evaluate adaptability and stability of these cultivars. Large variations were observed in grain yield in relation to the different environments studied, showing that these materials are adaptable. The cultivars exhibited significant differences in oil content. The cultivars BRSGO204 (Goiânia) and BRSMG (Garantia) exhibited the greatest average grain yield in the different environments studied, and the cultivar BRSMG 760 SRR had the greatest oil content among the cultivars evaluated. Ecovalence was adopted to identify the most stable cultivars, and the estimates were nearly uniform both for grain yield and oil content, showing a variation of 0.07 and 0.01%, respectively. The GGE biplot was efficient at identifying cultivars with high adaptability and phenotype stability.
Realini, María Florencia; Poggio, Lidia; Cámara-Hernández, Julián; González, Graciela Esther
Genome size variation accompanies the diversification and evolution of many plant species. Relationships between DNA amount and phenotypic and cytological characteristics form the basis of most hypotheses that ascribe a biological role to genome size. The goal of the present research was to investigate the intra-specific variation in the DNA content in maize populations from Northeastern Argentina and further explore the relationship between genome size and the phenotypic traits seed weight and length of the vegetative cycle. Moreover, cytological parameters such as the percentage of heterochromatin as well as the number, position and sequence composition of knobs were analysed and their relationships with 2C DNA values were explored. The populations analysed presented significant differences in 2C DNA amount, from 4.62 to 6.29 pg, representing 36.15 % of the inter-populational variation. Moreover, intra-populational genome size variation was found, varying from 1.08 to 1.63-fold. The variation in the percentage of knob heterochromatin as well as in the number, chromosome position and sequence composition of the knobs was detected among and within the populations. Although a positive relationship between genome size and the percentage of heterochromatin was observed, a significant correlation was not found. This confirms that other non-coding repetitive DNA sequences are contributing to the genome size variation. A positive relationship between DNA amount and the seed weight has been reported in a large number of species, this relationship was not found in the populations studied here. The length of the vegetative cycle showed a positive correlation with the percentage of heterochromatin. This result allowed attributing an adaptive effect to heterochromatin since the length of this cycle would be optimized via selection for an appropriate percentage of heterochromatin. PMID:26644343
Tobler, M; Carson, E W
Hybridization can generate novel phenotypes, and in combination with divergent selection along environmental gradients, can play a driving role in phenotypic diversification. This study examined the influence of introgressive hybridization and environmental variation on the phenotypic diversity of two pupfish species (Cyprinodon atrorus and Cyprinodon bifasciatus) endemic to the Cuatro Ciénegas basin, Mexico. These species occupy opposite environmental extremes and are comprised of multiple, intraspecifically isolated populations. However, interspecific hybridization occurs to various degrees within connecting, intermediate environments. Using geometric morphometric analysis, extensive variation of body shape was observed between and within species, and phenotypic variation was strongly correlated with environmental conditions. Furthermore, some introgressed populations exhibited unique phenotypes not found in either of the parents, and overall morphospace occupation was significantly higher in introgressed populations when compared to the parentals. Overall, we find environmental variation and transgressive segregation both appear to have been important in shaping phenotypic variation in this system.
Ito-Harashima, Sayoko; Hartzog, Phillip E; Sinha, Himanshu; McCusker, John H
Extensive phenotypic diversity or variation exists in clonal populations of microorganisms and is thought to play a role in adaptation to novel environments. This phenotypic variation or instability, which occurs by multiple mechanisms, may be a form of cellular differentiation and a stochastic means for modulating gene expression. This work dissects a case of phenotypic variation in a clinically derived Saccharomyces cerevisiae strain involving a cox15 ochre mutation, which acts as a reporter. The ochre mutation reverts to sense at a low frequency while tRNA-Tyr ochre suppressors (SUP-o) arise at a very high frequency to produce this phenotypic variation. The SUP-o mutations are highly pleiotropic. In addition, although all SUP-o mutations within the eight-member tRNA-Tyr gene family suppress the ochre mutation reporter, there are considerable phenotypic differences among the different SUP-o mutants. Finally, and of particular interest, there is a strong position effect on mutation frequency within the eight-member tRNA-Tyr gene family, with one locus, SUP6, mutating at a much higher than average frequency and two other loci, SUP2 and SUP8, mutating at much lower than average frequencies. Mechanisms for the position effect on mutation frequency are evaluated. PMID:12196388
Coon, Andrew; Carson, Robert; Debes, Paul V.
The study of population differentiation in the context of ecological speciation is commonly assessed using populations with obvious discreteness. Fewer studies have examined diversifying populations with occasional adaptive variation and minor reproductive isolation, so factors impeding or facilitating the progress of early stage differentiation are less understood. We detected non-random genetic structuring in lake trout (Salvelinus namaycush) inhabiting a large, pristine, postglacial lake (Mistassini Lake, Canada), with up to five discernible genetic clusters having distinctions in body shape, size, colouration and head shape. However, genetic differentiation was low (FST = 0.017) and genetic clustering was largely incongruent between several population- and individual-based clustering approaches. Genotype- and phenotype-environment associations with spatial habitat, depth and fish community structure (competitors and prey) were either inconsistent or weak. Striking morphological variation was often more continuous within than among defined genetic clusters. Low genetic differentiation was a consequence of relatively high contemporary gene flow despite large effective population sizes, not migration-drift disequilibrium. Our results suggest a highly plastic propensity for occupying multiple habitat niches in lake trout and a low cost of morphological plasticity, which may constrain the speed and extent of adaptive divergence. We discuss how factors relating to niche conservatism in this species may also influence how plasticity affects adaptive divergence, even where ample ecological opportunity apparently exists. PMID:27680019
Lind, M I; Johansson, F
Phenotypic plasticity can be important for local adaptation, because it enables individuals to survive in a novel environment until genetic changes have been accumulated by genetic accommodation. By analysing the relationship between development rate and growth rate, it can be determined whether plasticity in life-history traits is caused by changed physiology or behaviour. We extended this to examine whether plasticity had been aiding local adaptation, by investigating whether the plastic response had been fixed in locally adapted populations. Tadpoles from island populations of Rana temporaria, locally adapted to different pool-drying regimes, were monitored in a common garden. Individual differences in development rate were caused by different foraging efficiency. However, developmental plasticity was physiologically mediated by trading off growth against development rate. Surprisingly, plasticity has not aided local adaptation to time-stressed environments, because local adaptation was not caused by genetic assimilation but on selection on the standing genetic variation in development time.
Kowalski, Andrzej; Pa Yga, Jan; Górnicka-Michalska, Ewa; Bernacki, Zenon; Adamski, Marek
Our goal was to characterize a phenotypic variation of the pheasant erythrocyte linker histone subtype H1.c. By using two-dimensional polyacrylamide gel electrophoresis three histone H1.c phenotypes were identified. The differently migrating allelic variants H1.c1 and H1.c2 formed either two homozygous phenotypes, c1 and c2, or a single heterozygous phenotype, c1c2. In the pheasant population screened, birds with phenotype c2 were the most common (frequency 0.761) while individuals with phenotype c1 were rare (frequency 0.043).
Yan, Dong; Willett, Thomas L; Gu, Xiao-Mei; Martinez-Mier, E Angeles; Sardone, Laura; McShane, Lauren; Grynpas, Marc; Everett, Eric T
Excessive systemic exposure to fluoride (F) can lead to disturbances in bone homeostasis and dental enamel development. We have previously shown strain-specific responses to F in the development of dental fluorosis (DF) and in bone formation/mineralization. The current study was undertaken to further investigate F responsive variations in bone metabolism and to determine possible relationships with DF susceptibility. Seven-week-old male mice from FVB/NJ, C57BL/6J, C3H/HeJ, A/J, 129S1/SvImJ, AKR/J, DBA/2J, and BALB/cByJ inbred strains were exposed to NaF (0 or 50 ppm as F(-)) in drinking water for 60 days. Sera were collected for F, Ca, Mg, PO(4), iPTH, sRANKL, and ALP levels. Bone marrow cells were subjected to ex vivo cell culture for osteoclast potential and CFU colony assays (CFU-fibroblast, CFU-osteoblast, CFU-erythrocyte/granulocyte/macrophage/megakaryocyte, CFU-granulocyte/macrophage, CFU-macrophage, and CFU-granulocyte). Femurs and vertebrae were subjected to micro-CT analyses, biomechanical testing, and F, Mg, and Ca content assays. DF was evaluated using quantitative fluorescence and clinical criteria. Strain-specific responses to F were observed for DF, serum studies, ex vivo cell culture studies, and bone quality. Among the strains, there were no patterns or significant correlations between DF severity and the actions of F on bone homeostasis (serum studies, ex vivo assays, or bone quality parameters). The genetic background continues to play a role in the actions of F on tooth enamel development and bone homeostasis. F exposure led to variable phenotypic responses between strains involving dental enamel development and bone metabolism.
Yan, Dong; Willett, Thomas L.; Gu, Xiao-Mei; Martinez-Mier, E. Angeles; Sardone, Laura; McShane, Lauren; Grynpas, Marc; Everett, Eric T.
Excessive systemic exposure to fluoride (F) can lead to disturbances in bone homeostasis and dental enamel development. We have previously shown strain-specific responses to F in the development of dental fluorosis (DF) and in bone formation/mineralization. The current study was undertaken to further investigate F responsive variations in bone metabolism and to determine possible relationships with DF susceptibility. Seven-week-old male mice from FVB/NJ, C57BL/6J, C3H/HeJ, A/J, 129S1/SvImJ, AKR/J, DBA/2J, and BALB/cByJ inbred strains were exposed to NaF (0 or 50 ppm as F–) in drinking water for 60 days. Sera were collected for F, Ca, Mg, PO4, iPTH, sRANKL, and ALP levels. Bone marrow cells were subjected to ex vivo cell culture for osteoclast potential and CFU colony assays (CFU-fibroblast, CFU-osteoblast, CFU-erythrocyte/granulocyte/macrophage/megakaryocyte, CFU-granulocyte/macrophage, CFU-macrophage, and CFU-granulocyte). Femurs and vertebrae were subjected to micro-CT analyses, biomechanical testing, and F, Mg, and Ca content assays. DF was evaluated using quantitative fluorescence and clinical criteria. Strain-specific responses to F were observed for DF, serum studies, ex vivo cell culture studies, and bone quality. Among the strains, there were no patterns or significant correlations between DF severity and the actions of F on bone homeostasis (serum studies, ex vivo assays, or bone quality parameters). The genetic background continues to play a role in the actions of F on tooth enamel development and bone homeostasis. F exposure led to variable phenotypic responses between strains involving dental enamel development and bone metabolism. PMID:21555858
Song, Xianwei; Cao, Xiaofeng
Transposable elements (TEs) have long been regarded as 'selfish DNA', and are generally silenced by epigenetic mechanisms. However, work in the past decade has identified positive roles for TEs in generating genomic novelty and diversity in plants. In particular, recent studies suggested that TE-induced epigenetic alterations and modification of gene expression contribute to phenotypic variation and adaptation to geography or stress. These findings have led many to regard TEs, not as junk DNA, but as sources of control elements and genomic diversity. As a staple food crop and model system for genomic research on monocot plants, rice (Oryza sativa) has a modest-sized genome that harbors massive numbers of DNA transposons (class II transposable elements) scattered across the genome, which may make TE regulation of genes more prevalent. In this review, we summarize recent progress in research on the functions of rice TEs in modulating gene expression and creating new genes. We also examine the contributions of TEs to phenotypic diversity and adaptation to environmental conditions.
Chipps, S.R.; Dunbar, J.A.; Wahl, David H.
Bluegill sunfish (Lepomis macrochirus) are known to diversify into two forms specialized for foraging on either limnetic or littoral prey. Because juvenile bluegills seek vegetative cover in the presence of largemouth bass (Micropterus salmoides) predators, natural selection should favor the littoral body design at size ranges most vulnerable to predation. Yet within bluegill populations, both limnetic and littoral forms occur where vegetation and predators are present. While adaptive for foraging in different environments, does habitat-linked phenotypic variation also influence predator evasiveness for juvenile bluegills? We evaluate this question by quantifying susceptibility to predation for two groups of morphologically distinct bluegills; a limnetic form characteristic of bluegills inhabiting open water areas (limnetic bluegill) and a littoral form characteristic of bluegills inhabiting dense vegetation (littoral bluegill). In a series of predation trials, we found that bluegill behaviors differed in open water habitat but not in simulated vegetation. In open water habitat, limnetic bluegills formed more dense shoaling aggregations, maintained a larger distance from the predator, and required longer amounts of time to capture than littoral bluegill. When provided with simulated vegetation, largemouth bass spent longer amounts of time pursuing littoral bluegill and captured significantly fewer littoral bluegills than limnetic fish. Hence, morphological and behavioral variation in bluegills was linked to differential susceptibility to predation in open water and vegetated environments. Combined with previous studies, these findings show that morphological and behavioral adaptations enhance both foraging performance and predator evasiveness in different lake habitats.
Ruiz-Montoya, Lorena; Núñez-Farfán, Juan
Host race formation in phytophagous insects can be an early stage of adaptive speciation. However, the evolution of phenotypic plasticity in host use is another possible outcome. Using a reciprocal transplant experiment we tested the hypothesis of local adaptation in the aphid Brevicoryne brassicae. Aphid genotypes derived from two sympatric host plants, Brassica oleracea and B. campestris, were assessed in order to measure the extent of phenotypic plasticity in morphological and life history traits in relation to the host plants. We obtained an index of phenotypic plasticity for each genotype. Morphological variation of aphids was summarized by principal components analysis. Significant effects of recipient host on morphological variation and life history traits (establishment, age at first reproduction, number of nymphs, and intrinsic growth rate) were detected. We did not detected genotype × host plant interaction; in general the genotypes developed better on B. campestris, independent of the host plant species from which they were collected. Therefore, there was no evidence to suggest local adaptation. Regarding plasticity, significant differences among genotypes in the index of plasticity were detected. Furthermore, significant selection on PC1 (general aphid body size) on B. campestris, and on PC1 and PC2 (body length relative to body size) on B. oleracea was detected. The elevation of the reaction norm of PC1 and the slope of the reaction norm for PC2 (i.e., plasticity) were under directional selection. Thus, host plant species constitute distinct selective environments for B. brassicae. Aphid genotypes expressed different phenotypes in response to the host plant with low or nil fitness costs. Phenotypic plasticity and gene flow limits natural selection for host specialization promoting the maintenance of genetic variation in host exploitation.
Ruiz-Montoya, Lorena; Núñez-Farfán, Juan
Host race formation in phytophagous insects can be an early stage of adaptive speciation. However, the evolution of phenotypic plasticity in host use is another possible outcome. Using a reciprocal transplant experiment we tested the hypothesis of local adaptation in the aphid Brevicoryne brassicae. Aphid genotypes derived from two sympatric host plants, Brassica oleracea and B. campestris, were assessed in order to measure the extent of phenotypic plasticity in morphological and life history traits in relation to the host plants. We obtained an index of phenotypic plasticity for each genotype. Morphological variation of aphids was summarized by principal components analysis. Significant effects of recipient host on morphological variation and life history traits (establishment, age at first reproduction, number of nymphs, and intrinsic growth rate) were detected. We did not detected genotype × host plant interaction; in general the genotypes developed better on B. campestris, independent of the host plant species from which they were collected. Therefore, there was no evidence to suggest local adaptation. Regarding plasticity, significant differences among genotypes in the index of plasticity were detected. Furthermore, significant selection on PC1 (general aphid body size) on B. campestris, and on PC1 and PC2 (body length relative to body size) on B. oleracea was detected. The elevation of the reaction norm of PC1 and the slope of the reaction norm for PC2 (i.e., plasticity) were under directional selection. Thus, host plant species constitute distinct selective environments for B. brassicae. Aphid genotypes expressed different phenotypes in response to the host plant with low or nil fitness costs. Phenotypic plasticity and gene flow limits natural selection for host specialization promoting the maintenance of genetic variation in host exploitation. PMID:24265743
Schneider, Ralf F; Meyer, Axel
There is increasing evidence that phenotypic plasticity can promote population divergence by facilitating phenotypic diversification and, eventually, genetic divergence. When a 'plastic' population colonizes a new habitat, it has the possibility to occupy multiple niches by expressing several distinct phenotypes. These initially reflect the population's plastic range but may later become genetically fixed by selection via the process of 'genetic assimilation' (GA). Through this process multiple specialized sister lineages can arise that share a common plastic ancestor - the 'flexible stem'. Here, we review possible molecular mechanisms through which natural selection could fix an initially plastic trait during GA. These mechanisms could also explain how GA may contribute to cryptic genetic variation that can subsequently be coopted into other phenotypes or traits, but also lead to nonadaptive responses. We outline the predicted patterns of genetic and transcriptional divergence accompanying flexible stem radiations. The analysis of such patterns of (retained) adaptive and nonadaptive plastic responses within and across radiating lineages can inform on the state of ongoing GA. We conclude that, depending on the stability of the environment, the molecular architecture underlying plastic traits can facilitate diversification, followed by fixation and consolidation of an adaptive phenotype and degeneration of nonadaptive ones. Additionally, the process of GA may increase the cryptic genetic variation of populations, which on one hand may serve as substrate for evolution, but on another may be responsible for nonadaptive responses that consolidate local allopatry and thus reproductive isolation.
Phifer-Rixey, M; Heckman, M; Trussell, G C; Schmidt, P S
Clines can signal spatially varying selection and therefore have long been used to investigate the role of environmental heterogeneity in maintaining genetic variation. However, clinal patterns alone are not sufficient to reject neutrality or to establish the mechanism of selection. Indirect, inferential methods can be used to address neutrality and mechanism, but fully understanding the adaptive significance of clinal variation ultimately requires a direct approach. Ecological model systems such as the rocky intertidal provide a useful context for direct experimentation and can serve as a complement to studies in more traditional genetic model systems. In this study, we use indirect and direct approaches to investigate the role of environmental heterogeneity in the maintenance of shell colour polymorphism in the flat periwinkle snail, Littorina obtusata. We document replicated clines in shell colour morph frequencies over thermal gradients at two spatial scales, contrasting with patterns at previously reported microsatellite loci. In addition, experimental results demonstrate that that shell colour has predictable effects on shell temperature and that these differences in temperature, in turn, coincide with patterns of survivorship under episodic thermal stress. Direct manipulation of shell colour revealed that shell colour, and not a correlated character, was the target of selection. Our study provides evidence that spatially varying selection via thermal regime contributes to the maintenance of shell colour phenotype variation in L. obtusata in the sampled areas of the Gulf of Maine.
Humans are physiologically and morphologically diverse. Such diversities have been shaped by demographic history and adaptation to local environments, including regional climate, landscape, food source, culture, and pathogens since their expansion within and out of Africa between 50,000 and 100,000 ...
Kitazawa, Miho S.; Fujimoto, Koichi
Background and Aims Phenotypic variation in floral morphologies contributes to speciation by testing various morphologies that might have higher adaptivity, leading eventually to phylogenetic diversity. Species diversity has been recognized, however, by modal morphologies where the variation is averaged out, so little is known about the relationship between the variation and the diversity. Methods We analysed quantitatively the intraspecific variation of the organ numbers within flowers of Ranunculaceae, a family which branched near the monocot–eudicot separation, and the numbers of flowers within the capitula of Asteraceae, one of the most diverse families of eudicots. We used four elementary statistical quantities: mean, standard deviation (s.d.), degree of symmetry (skewness) and steepness (kurtosis). Key Results While these four quantities vary among populations, we found a common relationship between s.d. and the mean number of petals and sepals in Ranunculaceae and number of flowers per capitulum in Asteraceae. The s.d. is equal to the square root of the difference between the mean and specific number, showing robustness: for example, 3 in Ficaria sepals, 5 in Ranunculus petals and Anemone tepals, and 13 in Farfugium ray florets. This square-root relationship was not applicable to Eranthis petals which show little correlation between the s.d. and mean, and the stamens and carpels of Ranunculaceae whose s.d. is proportional to the mean. The specific values found in the square-root relationship provide a novel way to find the species-representative phenotype among varied morphologies. Conclusions The representative phenotype is, in most cases, unique to the species or genus level, despite intraspecific differences of average phenotype among populations. The type of variation shown by the statistical quantities indicates not only the robustness of the morphologies but also how flowering plants changed during evolution among representative phenotypes that
Nonaka, Etsuko; Svanbäck, Richard; Thibert-Plante, Xavier; Englund, Göran; Brännström, Åke
Phenotypic plasticity is the ability of one genotype to produce different phenotypes depending on environmental conditions. Several conceptual models emphasize the role of plasticity in promoting reproductive isolation and, ultimately, speciation in populations that forage on two or more resources. These models predict that plasticity plays a critical role in the early stages of speciation, prior to genetic divergence, by facilitating fast phenotypic divergence. The ability to plastically express alternative phenotypes may, however, interfere with the early phase of the formation of reproductive barriers, especially in the absence of geographic barriers. Here, we quantitatively investigate mechanisms under which plasticity can influence progress toward adaptive genetic diversification and ecological speciation. We use a stochastic, individual-based model of a predator-prey system incorporating sexual reproduction and mate choice in the predator. Our results show that evolving plasticity promotes the evolution of reproductive isolation under diversifying environments when individuals are able to correctly select a more profitable habitat with respect to their phenotypes (i.e., adaptive habitat choice) and to assortatively mate with relatively similar phenotypes. On the other hand, plasticity facilitates the evolution of plastic generalists when individuals have a limited capacity for adaptive habitat choice. We conclude that plasticity can accelerate the evolution of a reproductive barrier toward adaptive diversification and ecological speciation through enhanced phenotypic differentiation between diverging phenotypes.
Loesch, Danuta Z.; Huggins, Richard M.; Hagerman, Randi J.
Data on the relationships between cognitive and physical phenotypes, and a deficit of fragile X mental retardation 1 (FMR1) gene-specific protein product, FMRP, are presented and discussed in context with earlier findings. The previously unpublished results obtained, using standard procedures of regression and correlations, showed highly…
Lamarque, Laurent J.; Porté, Annabel J.; Eymeric, Camille; Lasnier, Jean-Baptiste; Lortie, Christopher J.; Delzon, Sylvain
Phenotypic plasticity is a key mechanism associated with the spread of exotic plants and previous studies have found that invasive species are generally more plastic than co-occurring species. Comparatively, the evolution of phenotypic plasticity in plant invasion has received less attention, and in particular, the genetic basis of plasticity is largely unexamined. Native from North America, Acer negundo L. is aggressively impacting the riparian forests of southern and eastern Europe thanks to higher plasticity relative to co-occurring native species. We therefore tested here whether invasive populations have evolved increased plasticity since introduction. The performance of 1152 seedlings from 8 native and 8 invasive populations was compared in response to nutrient availability. Irrespective of nutrients, invasive populations had higher growth and greater allocation to above-ground biomass relative to their native conspecifics. More importantly, invasive genotypes did not show increased plasticity in any of the 20 traits examined. This result suggests that the high magnitude of plasticity to nutrient variation of invasive seedlings might be pre-adapted in the native range. Invasiveness of A. negundo could be explained by higher mean values of traits due to genetic differentiation rather than by evolution of increased plasticity. PMID:24040212
Divergent natural selection, adaptive divergence and gene flow may interact in a number of ways. Recent studies have focused on the balance between selection and gene flow in natural populations, and empirical work has shown that gene flow can constrain adaptive divergence, and that divergent selection can constrain gene flow. A caveat is that phenotypic diversification may be under the direct influence of environmental factors (i.e. it may be due to phenotypic plasticity), in addition to partial genetic influence. In this case, phenotypic divergence may occur between populations despite high gene flow that imposes a constraint on genetic divergence. Plasticity may dampen the effects of natural selection by allowing individuals to rapidly adapt phenotypically to new conditions, thus slowing adaptive genetic divergence. On the other hand, plasticity may promote future adaptive divergence by allowing populations to persist in novel environments. Plasticity may promote gene flow between selective regimes by allowing dispersers to adapt to alternate conditions, or high gene flow may result in the selection for increased plasticity. Here I expand frameworks for understanding relationships among selection, adaptation and gene flow to include the effects of phenotypic plasticity in natural populations, and highlight its importance in evolutionary diversification.
Erickson, Keesha E; Otoupal, Peter B; Chatterjee, Anushree
The root cause of the antibiotic resistance crisis is the ability of bacteria to evolve resistance to a multitude of antibiotics and other environmental toxins. The regulation of adaptation is difficult to pinpoint due to extensive phenotypic heterogeneity arising during evolution. Here, we investigate the mechanisms underlying general bacterial adaptation by evolving wild-type Escherichia coli populations to dissimilar chemical toxins. We demonstrate the presence of extensive inter- and intrapopulation phenotypic heterogeneity across adapted populations in multiple traits, including minimum inhibitory concentration, growth rate, and lag time. To search for a common response across the heterogeneous adapted populations, we measured gene expression in three stress-response networks: the mar regulon, the general stress response, and the SOS response. While few genes were differentially expressed, clustering revealed that interpopulation gene expression variability in adapted populations was distinct from that of unadapted populations. Notably, we observed both increases and decreases in gene expression variability upon adaptation. Sequencing select genes revealed that the observed gene expression trends are not necessarily attributable to genetic changes. To further explore the connection between gene expression variability and adaptation, we propagated single-gene knockout and CRISPR (clustered regularly interspaced short palindromic repeats) interference strains and quantified impact on adaptation to antibiotics. We identified significant correlations that suggest genes with low expression variability have greater impact on adaptation. This study provides evidence that gene expression variability can be used as an indicator of bacterial adaptive resistance, even in the face of the pervasive phenotypic heterogeneity underlying adaptation.
Krismer, Jasmin; Tamminen, Manu; Fontana, Simone; Zenobi, Renato; Narwani, Anita
Phenotypic variation is vital for microbial populations to survive environmental perturbations. Both genetic and non-genetic factors contribute to an organism's phenotypic variation and therefore its fitness. To investigate the correlation between genetic diversity and phenotypic variation, we applied our recently developed mass spectrometry method that allows for the simultaneous measurement of more than 25 different lipids and pigments with high throughput in the unicellular microalga Chlamydomonas reinhardtii. We monitored the impact of nitrogen limitation on a genetically diverse wild-type strain CC-1690 and two isoclonal isolates from CC-1690 named ANC3 and ANC5. Measuring molecular composition of thousands of single cells at different time points of the experiment allowed us to capture a dynamic picture of the phenotypic composition and adaptation of the populations over time. Although the genetically diverse population maintained phenotypic variation over the whole time course of the experiment, the isoclonal cultures showed higher synchronicity in their phenotypic response. Furthermore, the genetically diverse population showed equal or greater phenotypic variation over the whole time range in multidimensional trait space compared with isoclonal populations. However, along individual trait axes non-genetic variance was higher in isoclonal populations.The ISME Journal advance online publication, 9 December 2016; doi:10.1038/ismej.2016.167.
Background The extent of phenotypic differentiation in response to local environmental conditions is a key component of species adaptation and persistence. Understanding the structuring of phenotypic diversity in response to local environmental pressures can provide important insights into species evolutionary dynamics and responses to environmental change. This work examines the influence of steep environmental gradients on intraspecific phenotypic variation and tests two hypotheses about how the tropical soft grass mouse, Akodon mollis (Cricetidae, Rodentia), contends with the disparate environmental conditions encompassed by its broad distribution. Specifically, we test if the species expresses a geographically unstructured, or generalist, phenotype throughout its range or if it shows geographically localized morphological differentiation across disparate environments. Results Using geometric morphometric and ecomorphological analyses of skull shape variation we found that despite distinct environmental conditions, geographically structured morphological variation is limited, with the notable exception of a distinct morphological disjunction at the high-elevation forest-grassland transition in the southern portion of A. mollis distribution. Based on genetic analyses, geographic isolation alone does not explain this localized phenotype, given that similar levels of genetic differentiation were also observed among individuals inhabiting other ecosystems that are nonetheless not distinct morphologically. Conclusions Instead of phenotypic specialization across environments in these tropical mountains, there was limited differentiation of skull shape and size across the broad range of A. mollis, with the exception of individuals from the puna, the highest-elevation ecosystem. The high morphological variance among individuals, together with a weak association with local environmental conditions, not only highlights the flexibility of A. mollis’ skull, but also
Gupta, N; Oppenheim, IM; Kauvar, EF; Tayebi, N; Sidransky, E
Gaucher disease (GD), the most common lysosomal storage disease, results from a deficiency of the lysosomal enzyme glucocerebrosidase. GD has been classified into 3 types, of which type 2 (the acute neuronopathic form) is most severe, presenting pre- or perinatally, or in the first few months of life. Traditionally, type 2 GD was considered to have the most uniform clinical phenotype when compared to other GD subtypes. However, case studies over time have demonstrated that type 2 GD, like types 1 and 3, manifests with a spectrum of phenotypes. This review includes case reports that illustrate the broad range of clinical presentations encountered in type 2 GD, as well as a discussion of associated manifestations, pathological findings, diagnostic techniques, and a review of current therapies. While type 2 GD is generally associated with severe mutations in the glucocerebrosidase gene, there is also significant genotypic heterogeneity observed. PMID:20880730
Evans, J; Thomas, S; Dillon, D; Gavel, D; Phillion, D; Macintosh, B
High-contrast adaptive optics systems, such as those needed to image extrasolar planets, are known to require excellent wavefront control and diffraction suppression. At the Laboratory for Adaptive Optics on the Extreme Adaptive Optics testbed, we have already demonstrated wavefront control of better than 1 nm rms within controllable spatial frequencies. Corresponding contrast measurements, however, are limited by amplitude variations, including those introduced by the micro-electrical-mechanical-systems (MEMS) deformable mirror. Results from experimental measurements and wave optic simulations of amplitude variations on the ExAO testbed are presented. We find systematic intensity variations of about 2% rms, and intensity variations with the MEMS to be 6%. Some errors are introduced by phase and amplitude mixing because the MEMS is not conjugate to the pupil, but independent measurements of MEMS reflectivity suggest that some error is introduced by small non-uniformities in the reflectivity.
Belete, Merzu Kebede; Balázsi, Gábor
Stochastic switching between alternative phenotypic states is a common cellular survival strategy during unforeseen environmental fluctuations. Cells can switch between different subpopulations that proliferate at different rates in different environments. Optimal population growth is typically assumed to occur when phenotypic switching rates match environmental switching rates. However, it is not well understood how this optimum behaves as a function of the growth rates of phenotypically different cells. In this study, we use mathematical and computational models to test how the actual parameters associated with optimal population growth differ from those assumed to be optimal. We find that the predicted optimum is practically always valid if the environmental durations are long. However, the regime of validity narrows as environmental durations shorten, especially if subpopulation growth rate differences differ from each other (are asymmetric) in two environments. Furthermore, we study the fate of mutants with switching rates previously predicted to be optimal. We find that mutants which match their phenotypic switching rates with the environmental ones can only sweep the population if the assumed optimum is valid, but not otherwise.
Belete, Merzu Kebede; Balázsi, Gábor
Stochastic switching between alternative phenotypic states is a common cellular survival strategy during unforeseen environmental fluctuations. Cells can switch between different subpopulations that proliferate at different rates in different environments. Optimal population growth is typically assumed to occur when phenotypic switching rates match environmental switching rates. However, it is not well understood how this optimum behaves as a function of the growth rates of phenotypically different cells. In this study, we use mathematical and computational models to test how the actual parameters associated with optimal population growth differ from those assumed to be optimal. We find that the predicted optimum is practically always valid if the environmental durations are long. However, the regime of validity narrows as environmental durations shorten, especially if subpopulation growth rate differences differ from each other (are asymmetric) in two environments. Furthermore, we study the fate of mutants with switching rates previously predicted to be optimal. We find that mutants which match their phenotypic switching rates with the environmental ones can only sweep the population if the assumed optimum is valid, but not otherwise.
Spangenburg, E. E.; Williams, J. H.; Roy, R. R.; Talmadge, R. J.; Spangenberg, E. E. (Principal Investigator)
Calcineurin (CaN) has been implicated as a signaling molecule that can transduce physiological stimuli (e.g., contractile activity) into molecular signals that initiate slow-fiber phenotypic gene expression and muscle growth. To determine the influence of muscle phenotype and atrophy on CaN levels in muscle, the levels of soluble CaN in rat muscles of varying phenotype, as assessed by myosin heavy chain (MHC)-isoform proportions, were determined by Western blotting. CaN levels were significantly greater in the plantaris muscle containing predominantly fast (IIx and IIb) MHC isoforms, compared with the soleus (predominantly type I MHC) or vastus intermedius (VI, contains all 4 adult MHC isoforms). Three months after a complete spinal cord transection (ST), the CaN levels in the VI muscle were significantly reduced, despite a significant increase in fast MHC isoforms. Surprisingly, the levels of CaN in the VI were highly correlated with muscle mass but not MHC isoform proportions in ST and control rats. These data demonstrate that CaN levels in skeletal muscle are highly correlated to muscle mass and that the normal relationship with phenotype is lost after ST.
Francuski, Lj; Matić, I; Ludoški, J; Milankov, V
Eristalis tenax L. (Diptera: Syrphidae) is commonly known as the drone fly (adult) or rat-tailed maggot (immature). Both adults and immature stages are identified as potential mechanical vectors of mycobacterial pathogens, and early-stage maggots cause accidental myiasis. We compared four samples from Mount Fruška Gora, Serbia, with the aim of obtaining insights into the temporal variations and sexual dimorphism in the species. This integrative approach was based on allozyme loci, morphometric wing parameters (shape and size) and abdominal colour patterns. Consistent sexual dimorphism was observed, indicating that male specimens had lighter abdomens and smaller and narrower wings than females. The distribution of genetic diversity at polymorphic loci indicated genetic divergence among collection dates. Landmark-based geometric morphometrics revealed, contrary to the lack of divergence in wing size, significant wing shape variation throughout the year. In addition, temporal changes in the frequencies of the abdominal patterns observed are likely to relate to the biology of the species and ecological factors in the locality. Hence, the present study expands our knowledge of the genetic diversity and phenotypic plasticity of E. tenax. The quantification of such variability represents a step towards the evaluation of the adaptive potential of this species of medical and epidemiological importance.
Gibert, Jean P; Brassil, Chad E
Natural populations often show variation in traits that can affect the strength of interspecific interactions. Interaction strengths in turn influence the fate of pairwise interacting populations and the stability of food webs. Understanding the mechanisms relating individual phenotypic variation to interaction strengths is thus central to assess how trait variation affects population and community dynamics. We incorporated nonheritable variation in attack rates and handling times into a classical consumer–resource model to investigate how variation may alter interaction strengths, population dynamics, species persistence, and invasiveness. We found that individual variation influences species persistence through its effect on interaction strengths. In many scenarios, interaction strengths decrease with variation, which in turn affects species coexistence and stability. Because environmental change alters the direction and strength of selection acting upon phenotypic traits, our results have implications for species coexistence in a context of habitat fragmentation, climate change, and the arrival of exotic species to native ecosystems. PMID:25478159
Khorkavtsiv, Ia D; Ripets'kyĭ, R T; Baïk, O L
On agar-Knop medium containing 0.5 microM HgCl2 about one third of microregenerants of the clone from the individual gametophyte cell of the moss Pottia intermedia survived and gave rise to protonemal mats. The high survival percentage testifies to epigenetic nature of adaptation. The latter proved to be correlated to the increase of leaf cell number and of peroxidase activity as well as to intensification of activity zone of peroxidase isoform with MM in limits of 66 kD and to appearance of two isoforms of the enzyme on electrophoregrams. The increase of peroxidase activity, though considerably weaker expressed, has been stated at 0.2 microM HgCl2 when practically all regenerants survived and on the mercury-free medium epigenetically adapted regenerants differed from physiologically adapted ones only in intensification of activity zone of peroxidase isoform with 66 kD. This gives reason to regard the adaptation of the regenerants to 0.5 microM HgCl2 as intensified epigenocopy of modification and indicates the generality of mechanisms of both types of adaptation.
Männik, Katrin; Mägi, Reedik; Macé, Aurélien; Cole, Ben; Guyatt, Anna; Shihab, Hashem A.; Maillard, Anne M.; Alavere, Helene; Kolk, Anneli; Reigo, Anu; Mihailov, Evelin; Leitsalu, Liis; Ferreira, Anne-Maud; Nõukas, Margit; Teumer, Alexander; Salvi, Erika; Cusi, Daniele; McGue, Matt; Iacono, William G.; Gaunt, Tom R.; Beckmann, Jacques S.; Jacquemont, Sébastien; Kutalik, Zoltán; Pankratz, Nathan; Timpson, Nicholas; Metspalu, Andres; Reymond, Alexandre
Importance The association of rare copy number variants (CNVs) with complex disorders is almost exclusively evaluated using clinically ascertained cohorts. As a result, the contribution of these genetic variants to cognitive phenotypes in the general population remains unclear. Objectives - To investigate the clinical features of genomic disorders in adult carriers without clinical pre-selection. - To assess the genome-wide burden of rare CNVs on carriers’ educational attainment and intellectual disability prevalence in the general population. Design, Setting, and Participants The population biobank of Estonia (EGCUT) contains 52,000 participants, or 5% of the Estonian adults, enrolled in 2002-2010. General practitioners examined participants and filled out a questionnaire of health- and lifestyle-related questions, as well as reported diagnoses. As EGCUT is representative of the country's population, we investigated a random sample of 7877 individuals for CNV analysis and genotype-phenotype associations with education and disease traits. Main Outcomes and Measures Phenotypes of genomic disorders in the general population, prevalence of autosomal CNVs, and association of the latter variants with decreased educational attainment and increased prevalence of intellectual disability. Results We identified 56 carriers of genomic disorders. Their phenotypes are reminiscent of those described for carriers of identical rearrangements ascertained in clinical cohorts. We also generated a genome-wide map of rare (frequency ≤0.05%) autosomal CNVs and identified 10.5% of the screened general population (n=831) as carriers of CNVs ≥250kb. Carriers of deletions ≥250kb or duplications ≥1Mb show, compared to the Estonian population, a greater prevalence of intellectual disability (P=0.0015, OR=3.16, (95%CI: 1.51-5.98); P=0.0083, OR=3.67, (95%CI: 1.29-8.54), respectively), reduced mean education attainment (a proxy for intelligence; P=1.06e-04; P=5.024e-05, respectively
A number of examples are presented indicating the types of variation that may be expected in the responses of the human population to deleterious agents of an endogeneous or exogenous nature. If one assumes that the variations in repair in the normal population are reflected in large variations in carcinogenic risk per unit of exposure, then the dose-response curves at low doses cannot be extrapolated from high doeses without knowing the distribution of sensitivities among humans. The probability of determining this range by ecpidemiological studies on a random population by small. On the other hand, the probability of determining the range by careful genetic and molecular studies appears high enough so that such experiments now are being carried out. They cannot be carried out on real populations, using chronic exposures. Hence, the ability to estimate dose-response relations in the low dose region on human populations can only be by making theoretical constructs that, in turn, are dependent on fundamental research. 12 refs., 2 tabs.
Rudman, Seth M; Rodriguez-Cabal, Mariano A; Stier, Adrian; Sato, Takuya; Heavyside, Julian; El-Sabaawi, Rana W; Crutsinger, Gregory M
Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an ecosystem impacts its ecology. Using two species that co-occur and demonstrate adaptation to their natal environments, black cottonwood (Populus trichocarpa) and three-spined stickleback (Gasterosteus aculeatus), we investigated the effects of intraspecific phenotypic variation on both top-down and bottom-up forces using a large-scale aquatic mesocosm experiment. Black cottonwood genotypes exhibit genetic variation in their productivity and consequently their leaf litter subsidies to the aquatic system, which mediates the strength of top-down effects from stickleback on prey abundances. Abundances of four common invertebrate prey species and available phosphorous, the most critically limiting nutrient in freshwater systems, are dictated by the interaction between genetic variation in cottonwood productivity and stickleback morphology. These interactive effects fit with ecological theory on the relationship between productivity and top-down control and are comparable in strength to the effects of predator addition. Our results illustrate that intraspecific variation, which can evolve rapidly, is an under-appreciated driver of community structure and ecosystem function, demonstrating that a multi-trophic perspective is essential to understanding the role of evolution in structuring ecological patterns.
Philippe, Anne-Sophie; Jeanson, Raphael; Pasquaretta, Cristian; Rebaudo, Francois; Sueur, Cedric; Mery, Frederic
Aggregation behaviour is the tendency for animals to group together, which may have important consequences on individual fitness. We used a combination of experimental and simulation approaches to study how genetic variation and social environment interact to influence aggregation dynamics in Drosophila. To do this, we used two different natural lines of Drosophila that arise from a polymorphism in the foraging gene (rovers and sitters). We placed groups of flies in a heated arena. Flies could freely move towards one of two small, cooler refuge areas. In groups of the same strain, sitters had a greater tendency to aggregate. The observed behavioural variation was based on only two parameters: the probability of entering a refuge and the likelihood of choosing a refuge based on the number of individuals present. We then directly addressed how different strains interact by mixing rovers and sitters within a group. Aggregation behaviour of each line was strongly affected by the presence of the other strain, without changing the decision rules used by each. Individuals obeying local rules shaped complex group dynamics via a constant feedback loop between the individual and the group. This study could help to identify the circumstances under which particular group compositions may improve individual fitness through underlying aggregation mechanisms under specific environmental conditions. PMID:27009219
Rengefors, Karin; Logares, Ramiro; Laybourn-Parry, Johanna; Gast, Rebecca J
Here we investigated whether there is evidence of local adaptation in strains of an ancestrally marine dinoflagellate to the lacustrine environment they now inhabit (optimal genotypes) and/or if they have evolved phenotypic plasticity (a range of phenotypes). Eleven strains of Polarella glacialis were isolated and cultured from three different environments: the polar seas, a hyposaline and a hypersaline Antarctic lake. Local adaptation was tested by comparing growth rates of lacustrine and marine strains at their own and reciprocal site conditions. To determine phenotypic plasticity, we measured the reaction norm for salinity. We found evidence of both, limited local adaptation and higher phenotypic plasticity in lacustrine strains when compared with marine ancestors. At extreme high salinities, local lake strains outperformed other strains, and at extreme low salinities, strains from the hyposaline lake outperformed all other strains. The data suggest that lake populations may have evolved higher phenotypic plasticity in the lake habitats compared with the sea, presumably due to the high temporal variability in salinity in the lacustrine systems. Moreover, the interval of salinity tolerance differed between strains from the hyposaline and hypersaline lakes, indicating local adaptation promoted by different salinity.
Nicotra, Adrienne B; Segal, Deborah L; Hoyle, Gemma L; Schrey, Aaron W; Verhoeven, Koen J F; Richards, Christina L
Environmentally induced phenotypic plasticity may be a critical component of response to changing environments. We examined local differentiation and adaptive phenotypic plasticity in response to elevated temperature in half-sib lines collected across an elevation gradient for the alpine herb, Wahlenbergia ceracea. Using Amplified Fragment Length Polymorphism (AFLP), we found low but significant genetic differentiation between low- and high-elevation seedlings, and seedlings originating from low elevations grew faster and showed stronger temperature responses (more plasticity) than those from medium and high elevations. Furthermore, plasticity was more often adaptive for plants of low-elevation origin and maladaptive for plants of high elevation. With methylation sensitive-AFLP (MS-AFLP), we revealed an increase in epigenetic variation in response to temperature in low-elevation seedlings. Although we did not find significant direct correlations between MS-AFLP loci and phenotypes, our results demonstrate that adaptive plasticity in temperature response to warming varies over fine spatial scales and suggest the involvement of epigenetic mechanisms in this response. PMID:25691987
Gaitán-Espitia, Juan Diego; Villanueva, Paola A; Lopez, Jorge; Torres, Rodrigo; Navarro, Jorge M; Bacigalupe, Leonardo D
Phenotypic plasticity is expected to play a major adaptive role in the response of species to ocean acidification (OA), by providing broader tolerances to changes in pCO2 conditions. However, tolerances and sensitivities to future OA may differ among populations within a species because of their particular environmental context and genetic backgrounds. Here, using the climatic variability hypothesis (CVH), we explored this conceptual framework in populations of the sea urchin Loxechinus albus across natural fluctuating pCO2/pH environments. Although elevated pCO2 affected the morphology, physiology, development and survival of sea urchin larvae, the magnitude of these effects differed among populations. These differences were consistent with the predictions of the CVH showing greater tolerance to OA in populations experiencing greater local variation in seawater pCO2/pH. Considering geographical differences in plasticity, tolerances and sensitivities to increased pCO2 will provide more accurate predictions for species responses to future OA.
Snell-Rood, E C; Swanson, E M; Young, R L
Understanding why organisms vary in developmental plasticity has implications for predicting population responses to changing environments and the maintenance of intraspecific variation. The epiphenotype hypothesis posits that the timing of development can constrain plasticity—the earlier alternate phenotypes begin to develop, the greater the difference that can result amongst the final traits. This research extends this idea by considering how life history timing shapes the opportunity for the environment to influence trait development. We test the prediction that the earlier an individual begins to actively interact with and explore their environment, the greater the opportunity for plasticity and thus variation in foraging traits. This research focuses on life history variation across four groups of birds using museum specimens and measurements from the literature. We reasoned that greater phenotypic plasticity, through either environmental effects or genotype-by-environment interactions in development, would be manifest in larger trait ranges (bills and tarsi) within species. Among shorebirds and ducks, we found that species with relatively shorter incubation times tended to show greater phenotypic variation. Across warblers and sparrows, we found little support linking timing of flight and trait variation. Overall, our results also suggest a pattern between body size and trait variation, consistent with constraints on egg size that might result in larger species having more environmental influences on development. Taken together, our results provide some support for the hypothesis that variation in life histories affects how the environment shapes development, through either the expression of plasticity or the release of cryptic genetic variation. PMID:26039409
Westberg, Erik; Ohali, Shachar; Shevelevich, Anatoly; Fine, Pinchas; Barazani, Oz
In Israel Eruca sativa has a geographically narrow distribution across a steep climatic gradient that ranges from mesic Mediterranean to hot desert environments. These conditions offer an opportunity to study the influence of the environment on intraspecific genetic variation. For this, we combined an analysis of neutral genetic markers with a phenotypic evaluation in common-garden experiments, and environmental characterization of populations that included climatic and edaphic parameters, as well as geographic distribution. A Bayesian clustering of individuals from nine representative populations based on amplified fragment length polymorphism (AFLP) divided the populations into a southern and a northern geographic cluster, with one admixed population at the geographic border between them. Linear mixed models, with cluster added as a grouping factor, revealed no clear effects of environment or geography on genetic distances, but this may be due to a strong association of geography and environment with genetic clusters. However, environmental factors accounted for part of the phenotypic variation observed in the common-garden experiments. In addition, candidate loci for selection were identified by association with environmental parameters and by two outlier methods. One locus, identified by all three methods, also showed an association with trichome density and herbivore damage, in net-house and field experiments, respectively. Accordingly, we propose that because trichomes are directly linked to defense against both herbivores and excess radiation, they could potentially be related to adaptive variation in these populations. These results demonstrate the value of combining environmental and phenotypic data with a detailed genetic survey when studying adaptation in plant populations. This article describes the use of several types of data to estimate the influence of the environment on intraspecific genetic variation in populations originating from a steep
Westberg, Erik; Ohali, Shachar; Shevelevich, Anatoly; Fine, Pinchas; Barazani, Oz
Abstract In Israel Eruca sativa has a geographically narrow distribution across a steep climatic gradient that ranges from mesic Mediterranean to hot desert environments. These conditions offer an opportunity to study the influence of the environment on intraspecific genetic variation. For this, we combined an analysis of neutral genetic markers with a phenotypic evaluation in common-garden experiments, and environmental characterization of populations that included climatic and edaphic parameters, as well as geographic distribution. A Bayesian clustering of individuals from nine representative populations based on amplified fragment length polymorphism (AFLP) divided the populations into a southern and a northern geographic cluster, with one admixed population at the geographic border between them. Linear mixed models, with cluster added as a grouping factor, revealed no clear effects of environment or geography on genetic distances, but this may be due to a strong association of geography and environment with genetic clusters. However, environmental factors accounted for part of the phenotypic variation observed in the common-garden experiments. In addition, candidate loci for selection were identified by association with environmental parameters and by two outlier methods. One locus, identified by all three methods, also showed an association with trichome density and herbivore damage, in net-house and field experiments, respectively. Accordingly, we propose that because trichomes are directly linked to defense against both herbivores and excess radiation, they could potentially be related to adaptive variation in these populations. These results demonstrate the value of combining environmental and phenotypic data with a detailed genetic survey when studying adaptation in plant populations. This article describes the use of several types of data to estimate the influence of the environment on intraspecific genetic variation in populations originating from a
Gerstein, Aleeza C.; Berman, Judith
Variation is the spice of life or, in the case of evolution, variation is the necessary material on which selection can act to enable adaptation. Karyotypic variation in ploidy (the number of homologous chromosome sets) and aneuploidy (imbalance in the number of chromosomes) are fundamentally different than other types of genomic variants. Karyotypic variation emerges through different molecular mechanisms than other mutational events, and unlike mutations that alter the genome at the base pair level, rapid reversion to the wild type chromosome number is often possible. Although karyotypic variation has long been noted and discussed by biologists, interest in the importance of karyotypic variants in evolutionary processes has spiked in recent years, and much remains to be discovered about how karyotypic variants are produced and subsequently selected. PMID:26321163
Mesko, Norbert; Bereczkei, Tamas
Although facial features that are considered beautiful have been investigated across cultures using the framework of sexual selection theory, the effects of head hair on esthetic evaluations have rarely been examined from an evolutionary perspective. In the present study the effects of six hair-styles (short, medium-length, long, disheveled, knot [hair bun], unkempt) on female facial attractiveness were examined in four dimensions (femininity, youth, health, sexiness) relative to faces without visible head hair ("basic face"). Three evolutionary hypotheses were tested (covering hypothesis, healthy mate theory, and good genes model); only the good genes model was supported by our data. According to this theory, individuals who can afford the high costs of long hair are those who have good phenotypic and genetic quality. In accordance with this hypothesis, we found that only long and medium-length hair had a significant positive effect on ratings of women's attractiveness; the other hairstyles did not influence the evaluation of their physical beauty. Furthermore, these two hairstyles caused a much larger change in the dimension of health than in the rest of the dimensions. Finally, male raters considered the longer-haired female subjects' health status better, especially if the subjects were less attractive women. The possible relationships between facial attractiveness and hair are discussed, and alternative explanations are presented.
Wang, M D; Dzama, K; Rees, D J G; Muchadeyi, F C
Africa is host to diverse and locally adapted cattle breeds that are expected to survive the harsh and extreme tropical environments associated with diseases and parasite infections, heat stress and episodes of feed and water scarcity. Genomic copy number variations (CNVs) are considered to be primary role players in cattle breed formation and adaptation where isolation and genetic drift together with subsequent mutations have created an enormous diversity of local populations. CNVs are modifications in DNA structure comprising deletions, duplications and insertions that are >1 kb in size. Despite attracting much attention, the frequency and pattern of bovine CNV events, especially in African cattle breeds, are for the most part largely unknown. Characterization of genetic variation in the indigenous cattle of Africa will be a vital step toward dissecting the molecular mechanisms underlying phenotypic variation and local adaptation. This review therefore aims to describe the current knowledge regarding bovine CNVs and the implications and potentials they encompass for dissecting genetic adaptation and the genotypic skeleton of tropical African cattle populations.
Fu, Shi-Jian; Cao, Zhen-Dong; Yan, Guan-Jie; Fu, Cheng; Pang, Xu
The Wujiang River, a tributary of the Three Gorges Reservoir, has many dams along its length. These dams alter the river's natural habitat and produce various flow regimes and degrees of predator stress. To test whether the swimming performance and external body shape of pale chub (Zacco platypus) have changed as a result of alterations in the flow regime and predator conditions, we measured the steady (U(crit)) and unsteady (fast-start) swimming performances and morphological characteristics of fish collected from different sites along the Wujiang River. We also calculated the maximum respiratory capacity and cost of transport (COT). We demonstrated significant differences in swimming performance and morphological traits among the sampling sites. Steady swimming performance was positively correlated with water velocity and negatively correlated with the abundance of predators, whereas unsteady swimming performance was negatively correlated with water velocity. The body shape was significantly correlated with both swimming performance and ecological parameters. These findings suggested that selection pressure on swimming performance results in a higher U(crit) and a more streamlined body shape in fast-flow and (or) in habitats with low predator stress and subsequently results in a lower COT. These characteristics were accompanied by a poorer fast-start performance than that of the fish from the slow-flow and (or) high-predator habitats. The divergence in U(crit) may also be due in part to variation in respiratory capacity.
Gralka, Matti; Stiewe, Fabian; Farrell, Fred; Möbius, Wolfram; Waclaw, Bartlomiej; Hallatschek, Oskar
The coupling of ecology and evolution during range expansions enables mutations to establish at expanding range margins and reach high frequencies. This phenomenon, called allele surfing, is thought to have caused revolutions in the gene pool of many species, most evidently in microbial communities. It has remained unclear, however, under which conditions allele surfing promotes or hinders adaptation. Here, using microbial experiments and simulations, we show that, starting with standing adaptive variation, range expansions generate a larger increase in mean fitness than spatially uniform population expansions. The adaptation gain results from 'soft' selective sweeps emerging from surfing beneficial mutations. The rate of these surfing events is shown to sensitively depend on the strength of genetic drift, which varies among strains and environmental conditions. More generally, allele surfing promotes the rate of adaptation per biomass produced, which could help developing biofilms and other resource-limited populations to cope with environmental challenges.
Gautam, Pramod; Chaurasia, Amit; Bhattacharya, Aniket; Grover, Ritika; Mukerji, Mitali; Natarajan, Vivek T
Several studies have demonstrated the role of climatic factors in shaping skin phenotypes, particularly pigmentation. Keratinization is another well-designed feature of human skin, which is involved in modulating transepidermal water loss (TEWL). Although this physiological process is closely linked to climate, presently it is not clear whether genetic diversity is observed in keratinization and whether this process also responds to the environmental pressure. To address this, we adopted a multipronged approach, which involved analysis of 1) copy number variations in diverse Indian and HapMap populations from varied geographical regions; 2) genetic association with geoclimatic parameters in 61 populations of dbCLINE database in a set of 549 genes from four processes namely keratinization, pigmentation, epidermal differentiation, and housekeeping functions; 3) sequence divergence in 4,316 orthologous promoters and corresponding exonic regions of human and chimpanzee with macaque as outgroup, and 4) protein sequence divergence (Ka/Ks) across nine vertebrate classes, which differ in their extent of TEWL. Our analyses demonstrate that keratinization and epidermal differentiation genes are under accelerated evolution in the human lineage, relative to pigmentation and housekeeping genes. We show that this entire pathway may have been driven by environmental selection pressure through concordant functional polymorphisms across several genes involved in skin keratinization. Remarkably, this underappreciated function of skin may be a crucial determinant of adaptation to diverse environmental pressures across world populations.
Zapata, Juan C.; Salvato, Maria S.
Arenavirus particles are enveloped and contain two single-strand RNA genomic segments with ambisense coding. Genetic plasticity of the arenaviruses comes from transcription errors, segment reassortment, and permissive genomic packaging, and results in their remarkable ability, as a group, to infect a wide variety of hosts. In this review, we discuss some in vitro studies of virus genetic and phenotypic variation after exposure to selective pressures such as high viral dose, mutagens and antivirals. Additionally, we discuss the variation in vivo of selected isolates of Old World arenaviruses, particularly after infection of different animal species. We also discuss the recent emergence of new arenaviruses in the context of our observations of sequence variations that appear to be host-specific. PMID:23344562
Zapata, Juan C; Salvato, Maria S
Arenavirus particles are enveloped and contain two single-strand RNA genomic segments with ambisense coding. Genetic plasticity of the arenaviruses comes from transcription errors, segment reassortment, and permissive genomic packaging, and results in their remarkable ability, as a group, to infect a wide variety of hosts. In this review, we discuss some in vitro studies of virus genetic and phenotypic variation after exposure to selective pressures such as high viral dose, mutagens and antivirals. Additionally, we discuss the variation in vivo of selected isolates of Old World arenaviruses, particularly after infection of different animal species. We also discuss the recent emergence of new arenaviruses in the context of our observations of sequence variations that appear to be host-specific.
Smrcka, Alan V.; Szarek, Stan R.
Protein synthesis and protein degradation rates were measured in three desert annual species at four different experimental temperatures. The taxa chosen for this study were the C3 winter annuals, Bowlesia incana Ruiz & Pavon and Plantago insularis Eastw., and a C4 summer annual, Atriplex elegans (Moq.) D. Dietr. Peak rates of protein synthesis correlated well with the preferred habitat temperatures of B. incana and A. elegans; optima occurred at 25 and 35°C, respectively. Plants of P. insularis showed an optimum protein synthesis rate at 35°C; however, this optimum rate was considerably lower than for the other two species. Higher activation energies for protein synthesis tended to parallel adaptation to higher temperature habitats. Responses of protein degradation to temperature in A. elegans and B. incana were consistent with their natural thermal regimes, when evaluated for the transition from 25 to 35°C. Again, protein degradation in P. insularis shows an intermediate response to temperature during the 25 to 35°C transition. PMID:16664583
Ralph, Peter L.; Coop, Graham
The extent to which populations experiencing shared selective pressures adapt through a shared genetic response is relevant to many questions in evolutionary biology. In a number of well studied traits and species, it appears that convergent evolution within species is common. In this paper, we explore how standing, genetic variation contributes to convergent genetic responses in a geographically spread population, extending our previous work on the topic. Geographically limited dispersal slows the spread of each selected allele, hence allowing other alleles – newly arisen mutants or present as standing variation – to spread before any one comes to dominate the population. When such alleles meet, their progress is substantially slowed – if the alleles are selectively equivalent, they mix slowly, dividing the species range into a random tessellation, which can be well understood by analogy to a Poisson process model of crystallization. In this framework, we derive the geographic scale over which a typical allele is expected to dominate, the time it takes the species to adapt as a whole, and the proportion of adaptive alleles that arise from standing variation. Finally, we explore how negative pleiotropic effects of alleles before an environment change can bias the subset of alleles that contribute to the species’ adaptive response. We apply the results to the many geographically localized G6PD deficiency alleles thought to confer resistance to malaria, where the large mutational target size makes it a likely candidate for adaptation from standing variation, despite the selective cost of G6PD deficiency alleles in the absence of malaria. We find the numbers and geographic spread of these alleles matches our predictions reasonably well, consistent with the view that they arose from a combination of standing variation and new mutations since the advent of malaria. Our results suggest that much of adaptation may be geographically local even when selection
Alderete, J F
Trichomonas vaginalis isolate NYH286 was fractionated with immunoglobulin G of sera from patients with trichomoniasis. Subpopulations of trichomonads with phenotypes of either patient serum-immunoglobulin G reactive (PS+) or nonreactive (PS-) were obtained. Flow cytofluorometry of PS+ and PS- subpopulations with a monoclonal antibody called C20A3 which reacts with a high-molecular-weight immunogen of T. vaginalis gave corresponding fluorescent (positive) and nonfluorescent (negative) phenotypes. No relationship was seen between PS+ and PS- phenotypes and binding of soybean agglutinin, wheat germ agglutinin, and concanavalin A, showing that PS- organisms still possessed carbohydrate moieties on their surfaces based on lectin binding. Phenotypic variation among the PS+ and PS- trichomonads was observed during in vitro growth. A positive-to-negative phenotype shift was also recorded for parasites obtained from lesions of mice subcutaneously infected with PS+ trichomonads. The involvement of surface proteins in the differential PS+ and PS- reactions was supported by soluble antigen and whole cell radioimmunoprecipitation assays. Finally, enhanced parasitism and killing of HeLa cells in monolayer cultures were observed for PS- subpopulations as compared with PS+ counterparts. The data support the idea that phenotypic variation for T. vaginalis may be coordinated for a repertoire of trichomonad immunogens and that such membrane dynamics influence expression of virulence determinants for these sexually transmitted disease agents. Images PMID:3497876
Volis, Sergei; Ormanbekova, Danara; Yermekbayev, Kanat
Species can adapt to new environmental conditions either through individual phenotypic plasticity, intraspecific genetic differentiation in adaptive traits, or both. Wild emmer wheat, Triticum dicoccoides, an annual grass with major distribution in Eastern Mediterranean region, is predicted to experience in the near future, as a result of global climate change, conditions more arid than in any part of the current species distribution. To understand the role of the above two means of adaptation, and the effect of population range position, we analyzed reaction norms, extent of plasticity, and phenotypic selection across two experimental environments of high and low water availability in two core and two peripheral populations of this species. We studied 12 quantitative traits, but focused primarily on the onset of reproduction and maternal investment, which are traits that are closely related to fitness and presumably involved in local adaptation in the studied species. We hypothesized that the population showing superior performance under novel environmental conditions will either be genetically differentiated in quantitative traits or exhibit higher phenotypic plasticity than the less successful populations. We found the core population K to be the most plastic in all three trait categories (phenology, reproductive traits, and fitness) and most successful among populations studied, in both experimental environments; at the same time, the core K population was clearly genetically differentiated from the two edge populations. Our results suggest that (1) two means of successful adaptation to new environmental conditions, phenotypic plasticity and adaptive genetic differentiation, are not mutually exclusive ways of achieving high adaptive ability; and (2) colonists from some core populations can be more successful in establishing beyond the current species range than colonists from the range extreme periphery with conditions seemingly closest to those in the new
Upadhyaya, H D; Kashiwagi, J; Varshney, R K; Gaur, P M; Saxena, K B; Krishnamurthy, L; Gowda, C L L; Pundir, R P S; Chaturvedi, S K; Basu, P S; Singh, I P
The chickpea and pigeonpea are protein-rich grain legumes used for human consumption in many countries. Grain yield of these crops is low to moderate in the semi-arid tropics with large variation due to high GxE interaction. In the Indian subcontinent chickpea is grown in the post-rainy winter season on receding soil moisture, and in other countries during the cool and dry post winter or spring seasons. The pigeonpea is sown during rainy season which flowers and matures in post-rainy season. The rainy months are hot and humid with diurnal temperature varying between 25 and 35°C (maximum) and 20 and 25°C (minimum) with an erratic rainfall. The available soil water during post-rainy season is about 200-250 mm which is bare minimum to meet the normal evapotranspiration. Thus occurrence of drought is frequent and at varying degrees. To enhance productivity of these crops cultivars tolerant to drought need to be developed. ICRISAT conserves a large number of accessions of chickpea (>20,000) and pigeonpea (>15,000). However only a small proportion (<1%) has been used in crop improvement programs mainly due to non-availability of reliable information on traits of economic importance. To overcome this, core and mini core collections (10% of core, 1% of entire collection) have been developed. Using the mini core approach, trait-specific donor lines were identified for agronomic, quality, and stress related traits in both crops. Composite collections were developed both in chickpea (3000 accessions) and pigeonpea (1000 accessions), genotyped using SSR markers and genotype based reference sets of 300 accessions selected for each crop. Screening methods for different drought-tolerant traits such as early maturity (drought escape), large and deep root system, high water-use efficiency, smaller leaflets, reduced canopy temperature, carbon isotope discrimination, high leaf chlorophyll content (drought avoidance), and breeding strategies for improving drought tolerance have
Aspinwall, Michael J; Loik, Michael E; Resco de Dios, Victor; Tjoelker, Mark G; Payton, Paxton R; Tissue, David T
Climate change threatens the ability of agriculture and forestry to meet growing global demands for food, fibre and wood products. Information gathered from genotype-by-environment interactions (G × E), which demonstrate intraspecific variation in phenotypic plasticity (the ability of a genotype to alter its phenotype in response to environmental change), may prove important for bolstering agricultural and forest productivity under climate change. Nonetheless, very few studies have explicitly quantified genotype plasticity-productivity relationships in agriculture or forestry. Here, we conceptualize the importance of intraspecific variation in agricultural and forest species plasticity, and discuss the physiological and genetic factors contributing to intraspecific variation in phenotypic plasticity. Our discussion highlights the need for an integrated understanding of the mechanisms of G × E, more extensive assessments of genotypic responses to climate change under field conditions, and explicit testing of genotype plasticity-productivity relationships. Ultimately, further investigation of intraspecific variation in phenotypic plasticity in agriculture and forestry may prove important for identifying genotypes capable of increasing or sustaining productivity under more extreme climatic conditions.
The proportion of phenotypic variation accounted for (Rp2) is an important characteristic of a DNA test. Therefore, several estimators of this quantity were evaluated by simulation of 500 replicates of a population of 1000 progeny of 100 sires (3 levels of narrow sense heritability and 4 levels of ...
Handelsman, Corey A; Broder, E Dale; Dalton, Christopher M; Ruell, Emily W; Myrick, Christopher A; Reznick, David N; Ghalambor, Cameron K
Novel environments often impose directional selection for a new phenotypic optimum. Novel environments, however, can also change the distribution of phenotypes exposed to selection by inducing phenotypic plasticity. Plasticity can produce phenotypes that either align with or oppose the direction of selection. When plasticity and selection are parallel, plasticity is considered adaptive because it provides a better pairing between the phenotype and the environment. If the plastic response is incomplete and falls short of producing the optimum phenotype, synergistic selection can lead to genetic divergence and bring the phenotype closer to the optimum. In contrast, non-adaptive plasticity should increase the strength of selection, because phenotypes will be further from the local optimum, requiring antagonistic selection to overcome the phenotype-environment mismatch and facilitate adaptive divergence. We test these ideas by documenting predator-induced plasticity for resting metabolic rate and growth rate in populations of the Trinidadian guppy (Poecilia reticulata) adapted to high and low predation. We find reduced metabolic rates and growth rates when cues from a predator are present during development, a pattern suggestive of adaptive and non-adaptive plasticity, respectively. When we compared populations recently transplanted from a high-predation environment into four streams lacking predators, we found evidence for rapid adaptive evolution both in metabolism and growth rate. We discuss the implications for predicting how traits will respond to selection, depending on the type of plasticity they exhibit.
Jones, I M; Thomas, C B; Xi, T; Mohrenweiser, H W; Nelson, D O
Elucidating the relationship between polymorphic sequences and risk of common disease is a challenge. For example, although it is clear that variation in DNA repair genes is associated with familial cancer, aging and neurological disease, progress toward identifying polymorphisms associated with elevated risk of sporadic disease has been slow. This is partly due to the complexity of the genetic variation, the existence of large numbers of mostly low frequency variants and the contribution of many genes to variation in susceptibility. There has been limited development of methods to find associations between genotypes having many polymorphisms and pathway function or health outcome. We have explored several statistical methods for identifying polymorphisms associated with variation in DNA repair phenotypes. The model system used was 80 cell lines that had been resequenced to identify variation; 191 single nucleotide substitution polymorphisms (SNPs) are included, of which 172 are in 31 base excision repair pathway genes, 19 in 5 anti-oxidation genes, and DNA repair phenotypes based on single strand breaks measured by the alkaline Comet assay. Univariate analyses were of limited value in identifying SNPs associated with phenotype variation. Of the multivariable model selection methods tested: the easiest that provided reduced error of prediction of phenotype was simple counting of the variant alleles predicted to encode proteins with reduced activity, which led to a genotype including 52 SNPs; the best and most parsimonious model was achieved using a two-step analysis without regard to potential functional relevance: first SNPs were ranked by importance determined by Random Forests Regression (RFR), followed by cross-validation in a second round of RFR modeling that included ever more SNPs in declining order of importance. With this approach 6 SNPs were found to minimize prediction error. The results should encourage research into utilization of multivariate
Gaupp, Rosmarie; Lei, Shulei; Reed, Joseph M; Peisker, Henrik; Boyle-Vavra, Susan; Bayer, Arnold S; Bischoff, Markus; Herrmann, Mathias; Daum, Robert S; Powers, Robert; Somerville, Greg A
Staphylococcus aureus is a major cause of nosocomial and community-acquired infections. The success of S. aureus as a pathogen is due in part to its many virulence determinants and resistance to antimicrobials. In particular, methicillin-resistant S. aureus has emerged as a major cause of infections and led to increased use of the antibiotics vancomycin and daptomycin, which has increased the isolation of vancomycin-intermediate S. aureus and daptomycin-nonsusceptible S. aureus strains. The most common mechanism by which S. aureus acquires intermediate resistance to antibiotics is by adapting its physiology and metabolism to permit growth in the presence of these antibiotics, a process known as adaptive resistance. To better understand the physiological and metabolic changes associated with adaptive resistance, six daptomycin-susceptible and -nonsusceptible isogenic strain pairs were examined for changes in growth, competitive fitness, and metabolic alterations. Interestingly, daptomycin nonsusceptibility coincides with a slightly delayed transition to the postexponential growth phase and alterations in metabolism. Specifically, daptomycin-nonsusceptible strains have decreased tricarboxylic acid cycle activity, which correlates with increased synthesis of pyrimidines and purines and increased carbon flow to pathways associated with wall teichoic acid and peptidoglycan biosynthesis. Importantly, these data provided an opportunity to alter the daptomycin nonsusceptibility phenotype by manipulating bacterial metabolism, a first step in developing compounds that target metabolic pathways that can be used in combination with daptomycin to reduce treatment failures.
Gaupp, Rosmarie; Lei, Shulei; Reed, Joseph M.; Peisker, Henrik; Boyle-Vavra, Susan; Bayer, Arnold S.; Bischoff, Markus; Herrmann, Mathias; Daum, Robert S.
Staphylococcus aureus is a major cause of nosocomial and community-acquired infections. The success of S. aureus as a pathogen is due in part to its many virulence determinants and resistance to antimicrobials. In particular, methicillin-resistant S. aureus has emerged as a major cause of infections and led to increased use of the antibiotics vancomycin and daptomycin, which has increased the isolation of vancomycin-intermediate S. aureus and daptomycin-nonsusceptible S. aureus strains. The most common mechanism by which S. aureus acquires intermediate resistance to antibiotics is by adapting its physiology and metabolism to permit growth in the presence of these antibiotics, a process known as adaptive resistance. To better understand the physiological and metabolic changes associated with adaptive resistance, six daptomycin-susceptible and -nonsusceptible isogenic strain pairs were examined for changes in growth, competitive fitness, and metabolic alterations. Interestingly, daptomycin nonsusceptibility coincides with a slightly delayed transition to the postexponential growth phase and alterations in metabolism. Specifically, daptomycin-nonsusceptible strains have decreased tricarboxylic acid cycle activity, which correlates with increased synthesis of pyrimidines and purines and increased carbon flow to pathways associated with wall teichoic acid and peptidoglycan biosynthesis. Importantly, these data provided an opportunity to alter the daptomycin nonsusceptibility phenotype by manipulating bacterial metabolism, a first step in developing compounds that target metabolic pathways that can be used in combination with daptomycin to reduce treatment failures. PMID:25963986
Simões, Patrício M V; Ott, Swidbert R; Niven, Jeremy E
The ability to learn and store information should be adapted to the environment in which animals operate to confer a selective advantage. Yet the relationship between learning, memory, and the environment is poorly understood, and further complicated by phenotypic plasticity caused by the very environment in which learning and memory need to operate. Many insect species show polyphenism, an extreme form of phenotypic plasticity, allowing them to occupy distinct environments by producing two or more alternative phenotypes. Yet how the learning and memories capabilities of these alternative phenotypes are adapted to their specific environments remains unknown for most polyphenic insect species. The desert locust can exist as one of two extreme phenotypes or phases, solitarious and gregarious. Recent studies of associative food-odor learning in this locust have shown that aversive but not appetitive learning differs between phases. Furthermore, switching from the solitarious to the gregarious phase (gregarization) prevents locusts acquiring new learned aversions, enabling them to convert an aversive memory formed in the solitarious phase to an appetitive one in the gregarious phase. This conversion provides a neuroecological mechanism that matches key changes in the behavioral environments of the two phases. These findings emphasize the importance of understanding the neural mechanisms that generate ecologically relevant behaviors and the interactions between different forms of behavioral plasticity.
Schneider, Ralf F; Li, Yuanhao; Meyer, Axel; Gunter, Helen M
Phenotypic plasticity is the ability of organisms with a given genotype to develop different phenotypes according to environmental stimuli, resulting in individuals that are better adapted to local conditions. In spite of their ecological importance, the developmental regulatory networks underlying plastic phenotypes often remain uncharacterized. We examined the regulatory basis of diet-induced plasticity in the lower pharyngeal jaw (LPJ) of the cichlid fish Astatoreochromis alluaudi, a model species in the study of adaptive plasticity. Through raising juvenile A. alluaudi on either a hard or soft diet (hard-shelled or pulverized snails) for between 1 and 8 months, we gained insight into the temporal regulation of 19 previously identified candidate genes during the early stages of plasticity development. Plasticity in LPJ morphology was first detected between 3 and 5 months of diet treatment. The candidate genes, belonging to various functional categories, displayed dynamic expression patterns that consistently preceded the onset of morphological divergence and putatively contribute to the initiation of the plastic phenotypes. Within functional categories, we observed striking co-expression, and transcription factor binding site analysis was used to examine the prospective basis of their coregulation. We propose a regulatory network of LPJ plasticity in cichlids, presenting evidence for regulatory crosstalk between bone and muscle tissues, which putatively facilitates the development of this highly integrated trait. Through incorporating a developmental time-course into a phenotypic plasticity study, we have identified an interconnected, environmentally responsive regulatory network that shapes the development of plasticity in a key innovation of East African cichlids.
Sampson, B J; Rinehart, T A; Kirker, G T; Stringer, S J; Werle, C T
We investigated fitness in natural populations of a managed solitary bee Osmia ribifloris Cockerell (Hymenoptera: Megachilidae) from sites separated from 400 to 2,700 km. Parental wild bees originated in central Texas (TX), central-northern Utah (UT), and central California (CA). They were then intercrossed and raised inside a mesh enclosure in southern Mississippi (MS). Females from all possible mated pairs of O. ribifloris produced F1 broods with 30-40% female cocoons and outcrossed progeny were 30% heavier. Mitochondrial (COI) genomes of the four populations revealed three distinct clades, a TX-CA clade, a UT clade, and an MS clade, the latter (MS) representing captive progeny of CA and UT bees. Although classified as separate subspecies, TX and CA populations from 30° N to 38° N latitude shared 98% similarity in COI genomes and the greatest brood biomass per nest straw (600- to 700-mg brood). Thus, TX and CA bees show greater adaptation for southern U.S. sites. In contrast, UT-sourced bees were more distantly related to TX and CA bees and also produced ∼50% fewer brood. These results, taken together, confirm that adult O. ribifloris from all trap-nest sites are genetically compatible, but some phenotypic variation exists that could affect this species performance as a commercial blueberry pollinator. Males, their sperm, or perhaps a substance in their sperm helped stabilize our captive bee population by promoting legitimate nesting over nest usurpation. Otherwise, without insemination, 50% fewer females nested (they nested 14 d late) and 20% usurped nests, killing 33-67% of brood in affected nests.
Ruiz-Montoya, L; Zúñiga, G; Cisneros, R; Salinas-Moreno, Y; Peña-Martínez, R; Machkour-M'Rabet, S
The study of phenotypic and genetic variation of obligate parthenogenetic organisms contributes to an understanding of evolution in the absence of genetic variation produced by sexual reproduction. Eriosoma lanigerum Hausmann undergoes obligate parthenogenesis in Mexico City, Mexico, due to the unavailability of the host plants required for sexual reproduction. We analysed the phenotypic and genetic variation of E. lanigerum in relation to the dry and wet season and plant phenology. Aphids were collected on two occasions per season on a secondary host plant, Pyracantha koidzumii, at five different sites in the southern area of Mexico City, Mexico. Thirteen morphological characteristics were measured from 147 to 276 individuals per site and per season. A multivariate analysis of variance was performed to test the effect of the season, site and their interaction on morphological traits. Morphological variation was summarised using a principal component analysis. Genetic variation was described using six enzymatic loci, four of which were polymorphic. Our study showed that the site and season has a significant effect on morphological trait variation. The largest aphids were recorded during cold temperatures with low relative humidity and when the plant was at the end of the fruiting period. The mean genetic diversity was low (mean H e = .161), and populations were genetically structured by season and site. Morphological and genetic variations appear to be associated with environmental factors that directly affect aphid development and/or indirectly by host plant phenology.
Lemke, Isgard Holle; Kolb, Annette; Diekmann, Martin Reemt
Phenotypic plasticity is the ability of organisms to express different phenotypes under different environmental conditions. It may buffer individuals both against short-term environmental fluctuations and long-term effects of global change. A plastic behaviour in response to changes in the environment may be especially important in species with low migration rates and colonization capacities, such as in many forest plants in present-day fragmented landscapes. We compared the phenotypic trait variation (used as a proxy for the amount of phenotypic plasticity) of five forest herbs (Brachypodium sylvaticum, Circaea lutetiana, Impatiens noli-tangere, Sanicula europaea and Stachys sylvatica) between two regions in Germany that differ in their overall environmental conditions (Bremen in the northwest, Freiburg in the southwest; 5 species × 2 regions × 8-15 populations × 25-50 individuals). In addition, we measured light intensity and important soil parameters (soil pH, moisture, K, P and N) in all populations. We found consistent differences in trait variability between the two regions in several species. In Brachypodium and Stachys both vegetative and reproductive traits were more variable in Freiburg. Similarly, reproductive traits of Impatiens and Sanicula appeared to be more variable in Freiburg, while in both species at least one of the vegetative traits was more variable in Bremen. Mean local environmental conditions also affected trait variation; in most of the species both vegetative and reproductive traits were more variable in sites with higher nutrient contents and higher light availability. Across all traits and both regions, seed or fruit production was most variable. In summary, at least some of the studied forest herbs appear to respond strongly to large-scale environmental differences, showing a higher trait variability in the more southern region. Given the assumption that phenotypic trait variation is positively associated with phenotypic plasticity
Pohl, Mary Ann; Zhang, William; Shah, Sunny; Sanabria-Valentín, Edgardo L.; Perez-Perez, Guillermo I.; Blaser, Martin J.
Background Helicobacter pylori is a persistent colonizer of the human gastric mucosa, which can lead to the development peptic ulcer disease and gastric adenocarcinomas. However, H. pylori can asymptomatically colonize a host for years. One factor that has been hypothesized to contribute to such persistence is the production of Lewis (Le) antigens in the lipopolysaccharide layer of the bacterial outer membrane as a form of molecular mimicry, since humans also express these antigens on their gastric mucosa. Humans and H. pylori both are polymorphic for Le expression, which is driven in H. pylori by variation at the Le synthesis loci. In this report we sought to characterize Le genotypic and phenotypic variation in geographically diverse H. pylori isolates. Materials and Methods From patients undergoing endoscopy in 29 countries, we determined Le phenotypes of 78 H. pylori strains, and performed genotyping of the galT and β-(1,3)galT loci in 113 H. pylori strains. Results Le antigen phenotyping revealed a significant (p <0.0001) association between type 1 (Lea and Leb) expression and strains of East-Asian origin. Genotyping revealed a significant correlation between strain origin and the size of the promoter region upstream of the Le synthesis gene, galT (p <0.0001). Conclusion These results indicate that the heterogeneity of human Le phenotypes are reflected in their H. pylori colonizing strains, and suggest new loci that can be studied to assess variation of Le expression. PMID:22059399
Carey, John C; Allanson, Judith E; Hennekam, Raoul C M; Biesecker, Leslie G
In 2005, the authors of this article formed an international working group to develop standardized definitions and terms to describe the physical variations used in human phenotypic analyses. This project, which came to be known as the Elements of Morphology, resulted in six articles proposing consensus definitions for almost 400 phenotypic variations of the head and face; periorbital region; ear, nose, and philtrum; mouth and lips; and hands and feet. Every variation was accompanied by a representative figure depicting the feature. The articles were published in the January 2009 issue of the American Journal of Medical Genetics Part A and are available for free access on both the Journal's Web page and a National Institutes of Health-based site. The publication of the Elements' definitions has spawned an ongoing dialogue about the proposed terms to describe the phenotype. The working group considered the six articles as only the first step in the process, and four more articles on proposed terminology for the trunk, genital region, skin, and remainder of the limb terms are in preparation. The secondary outcome of the Elements project is the provision of a working methodology for the establishment of standardized terminology and definitions for phenotype analysis in general.
Benard, Michael F; Middlemis Maher, Jessica
Phenotype is often correlated with resource use, which suggests that as phenotypic variation in a population increases, intraspecific competition will decrease. However, few studies have experimentally tested the prediction that increased intraspecific phenotypic variation leads to reduced competitive effects (e.g., on growth rate, survival or reproductive rate). We investigated this prediction with two experiments on wood frogs (Rana sylvatica). In the first experiment, we found that a frog's size was positively correlated with the size of its preferred prey, indicating that the feeding niche of the frogs changed with size. In the second experiment, we used an experimental design in which we held the initial mass of "focal" frogs constant, but varied the initial mass of their competitors. We found a significant quadratic effect of the average mass of competitors: focal frog growth was lowest when raised with similar-sized competitors, and highest when raised with competitors that were larger or smaller. Our results demonstrate that growth rates increase (i.e., competitive intensity decreases) when individuals are less similar to other members of the population and exhibit less overlap in resource use. Thus, changes in the amount of phenotypic variation in a population may ultimately affect population-level processes, such as population growth rate and extinction risk.
Fischer, Ken S.; Fukai, Shu; Kumar, Arvind; Leung, Hei; Jongdee, Boonrat
This paper is a section of the book “Drought phenotyping in crops: from theory to practice” (Monneveux Philippe and Ribaut Jean-Marcel eds, published by CGIAR Generation Challenge Programme. Texcoco, Mexico). The section describes recent experience in drought phenotyping in rice which is one of the most drought-susceptible crops. The section contains genetic and genomic resources for drought adaptation and methods for selection of drought-resistant varieties in rice. In appendix, there is experience from Thailand on integration of direct selection for grain yield and physiological traits to confer drought resistance. PMID:22934036
Guan, Guobo; Dai, Yu; Nobile, Clarissa J.; Liang, Weihong; Cao, Chengjun; Zhang, Qiuyu; Zhong, Jin; Huang, Guanghua
Non-genetic phenotypic variations play a critical role in the adaption to environmental changes in microbial organisms. Candida albicans, a major human fungal pathogen, can switch between several morphological phenotypes. This ability is critical for its commensal lifestyle and for its ability to cause infections. Here, we report the discovery of a novel morphological form in C. albicans, referred to as the “gray” phenotype, which forms a tristable phenotypic switching system with the previously reported white and opaque phenotypes. White, gray, and opaque cell types differ in a number of aspects including cellular and colony appearances, mating competency, secreted aspartyl proteinase (Sap) activities, and virulence. Of the three cell types, gray cells exhibit the highest Sap activity and the highest ability to cause cutaneous infections. The three phenotypes form a tristable phenotypic switching system, which is independent of the regulation of the mating type locus (MTL). Gray cells mate over 1,000 times more efficiently than do white cells, but less efficiently than do opaque cells. We further demonstrate that the master regulator of white-opaque switching, Wor1, is essential for opaque cell formation, but is not required for white-gray transitions. The Efg1 regulator is required for maintenance of the white phenotype, but is not required for gray-opaque transitions. Interestingly, the wor1/wor1 efg1/efg1 double mutant is locked in the gray phenotype, suggesting that Wor1 and Efg1 could function coordinately and play a central role in the regulation of gray cell formation. Global transcriptional analysis indicates that white, gray, and opaque cells exhibit distinct gene expression profiles, which partly explain their differences in causing infections, adaptation ability to diverse host niches, metabolic profiles, and stress responses. Therefore, the white-gray-opaque tristable phenotypic switching system in C. albicans may play a significant role in a wide
Drobniak, Szymon M; Dyrcz, Andrzej; Sudyka, Joanna; Cichoń, Mariusz
The evolution of brood parasitism has long attracted considerable attention among behavioural ecologists, especially in the common cuckoo system. Common cuckoos (Cuculus canorus) are obligatory brood parasites, laying eggs in nests of passerines and specializing on specific host species. Specialized races of cuckoos are genetically distinct. Often in a given area, cuckoos encounter multiple hosts showing substantial variation in egg morphology. Exploiting different hosts should lead to egg-phenotype specialization in cuckoos to match egg phenotypes of the hosts. Here we test this assumption using a wild population of two sympatrically occurring host species: the great reed warbler (Acrocephalus arundinaceus) and reed warbler (A. scirpaceus). Using colour spectrophotometry, egg shell dynamometry and egg size measurements, we studied egg morphologies of cuckoos parasitizing these two hosts. In spite of observing clear differences between host egg phenotypes, we found no clear differences in cuckoo egg morphologies. Interestingly, although chromatically cuckoo eggs were more similar to reed warbler eggs, after taking into account achromatic differences, cuckoo eggs seemed to be equally similar to both host species. We hypothesize that such pattern may represent an initial stage of an averaging strategy of cuckoos, that--instead of specializing for specific hosts or exploiting only one host--adapt to multiple hosts.
Lauter, Nick; Doebley, John
How new discrete states of morphological traits evolve is poorly understood. One possibility is that single-gene changes underlie the evolution of new discrete character states and that evolution is dependent on the occurrence of new single-gene mutations. Another possibility is that multiple-gene changes are required to elevate an individual or population above a threshold required to produce the new character state. A prediction of the latter model is that genetic variation for the traits should exist in natural populations in the absence of phenotypic variation. To test this idea, we studied traits that are phenotypically invariant within teosinte and for which teosinte is discretely different from its near relative, maize. By employing a QTL mapping strategy to analyze the progeny of a testcross between an F(1) of two teosintes and a maize inbred line, we identified cryptic genetic variation in teosinte for traits that are invariant in teosinte. We argue that such cryptic genetic variation can contribute to the evolution of novelty when reconfigured to exceed the threshold necessary for phenotypic expression or by acting to modify or stabilize the effects of major mutations.
Gallagher, Jennifer E.G.; Zheng, Wei; Rong, Xiaoqing; Miranda, Noraliz; Lin, Zhixiang; Dunn, Barbara; Zhao, Hongyu; Snyder, Michael P.
Genetic basis of phenotypic differences in individuals is an important area in biology and personalized medicine. Analysis of divergent Saccharomyces cerevisiae strains grown under different conditions revealed extensive variation in response to both drugs (e.g., 4-nitroquinoline 1-oxide [4NQO]) and different carbon sources. Differences in 4NQO resistance were due to amino acid variation in the transcription factor Yrr1. Yrr1YJM789 conferred 4NQO resistance but caused slower growth on glycerol, and vice versa with Yrr1S96, indicating that alleles of Yrr1 confer distinct phenotypes. The binding targets of Yrr1 alleles from diverse yeast strains varied considerably among different strains grown under the same conditions as well as for the same strain under different conditions, indicating that distinct molecular programs are conferred by the different Yrr1 alleles. Our results demonstrate that genetic variations in one important control gene (YRR1), lead to distinct regulatory programs and phenotypes in individuals. We term these polymorphic control genes “master variators.” PMID:24532717
Eichstaedt, Christina A.; Antão, Tiago; Pagani, Luca; Cardona, Alexia; Kivisild, Toomas; Mormina, Maru
During their migrations out of Africa, humans successfully colonised and adapted to a wide range of habitats, including extreme high altitude environments, where reduced atmospheric oxygen (hypoxia) imposes a number of physiological challenges. This study evaluates genetic and phenotypic variation in the Colla population living in the Argentinean Andes above 3500 m and compares it to the nearby lowland Wichí group in an attempt to pinpoint evolutionary mechanisms underlying adaptation to high altitude hypoxia. We genotyped 730,525 SNPs in 25 individuals from each population. In genome-wide scans of extended haplotype homozygosity Collas showed the strongest signal around VEGFB, which plays an essential role in the ischemic heart, and ELTD1, another gene crucial for heart development and prevention of cardiac hypertrophy. Moreover, pathway enrichment analysis showed an overrepresentation of pathways associated with cardiac morphology. Taken together, these findings suggest that Colla highlanders may have evolved a toolkit of adaptative mechanisms resulting in cardiac reinforcement, most likely to counteract the adverse effects of the permanently increased haematocrit and associated shear forces that characterise the Andean response to hypoxia. Regulation of cerebral vascular flow also appears to be part of the adaptive response in Collas. These findings are not only relevant to understand the evolution of hypoxia protection in high altitude populations but may also suggest new avenues for medical research into conditions where hypoxia constitutes a detrimental factor. PMID:24686296
Hallsson, L R; Björklund, M
Changes in the environment are expected to induce changes in the quantitative genetic variation, which influences the ability of a population to adapt to environmental change. Furthermore, environmental changes are not constant in time, but fluctuate. Here, we investigate the effect of rapid, continuous and/or fluctuating temperature changes in the seed beetle Callosobruchus maculatus, using an evolution experiment followed by a split-brood experiment. In line with expectations, individuals responded in a plastic way and had an overall higher potential to respond to selection after a rapid change in the environment. After selection in an environment with increasing temperature, plasticity remained unchanged (or decreased) and environmental variation decreased, especially when fluctuations were added; these results were unexpected. As expected, the genetic variation decreased after fluctuating selection. Our results suggest that fluctuations in the environment have major impact on the response of a population to environmental change; in a highly variable environment with low predictability, a plastic response might not be beneficial and the response is genetically and environmentally canalized resulting in a low potential to respond to selection and low environmental sensitivity. Interestingly, we found greater variation for phenotypic plasticity after selection, suggesting that the potential for plasticity to evolve is facilitated after exposure to environmental fluctuations. Our study highlights that environmental fluctuations should be considered when investigating the response of a population to environmental change.
Barroso, L M A; Teodoro, P E; Nascimento, M; Torres, F E; Dos Santos, A; Corrêa, A M; Sagrilo, E; Corrêa, C C G; Silva, F A; Ceccon, G
This study aimed to verify that a Bayesian approach could be used for the selection of upright cowpea genotypes with high adaptability and phenotypic stability, and the study also evaluated the efficiency of using informative and minimally informative a priori distributions. Six trials were conducted in randomized blocks, and the grain yield of 17 upright cowpea genotypes was assessed. To represent the minimally informative a priori distributions, a probability distribution with high variance was used, and a meta-analysis concept was adopted to represent the informative a priori distributions. Bayes factors were used to conduct comparisons between the a priori distributions. The Bayesian approach was effective for selection of upright cowpea genotypes with high adaptability and phenotypic stability using the Eberhart and Russell method. Bayes factors indicated that the use of informative a priori distributions provided more accurate results than minimally informative a priori distributions.
Yi, Xiao; Dean, Antony M
We report the evolution of a phenotypically plastic behavior that circumvents the hardwired trade-off that exists when resources are partitioned between growth and motility in Escherichia coli. We propagated cultures in a cyclical environment, alternating between growth up to carrying capacity and selection for chemotaxis. Initial adaptations boosted overall swimming speed at the expense of growth. The effect of the trade-off was subsequently eased through a change in behavior; while individual cells reduced motility during exponential growth, the faction of the population that was motile increased as the carrying capacity was approached. This plastic behavior was produced by a single amino acid replacement in FliA, a regulatory protein central to the chemotaxis network. Our results illustrate how phenotypic plasticity potentiates evolvability by opening up new regions of the adaptive landscape.
Rokyta, Darin R.; Margres, Mark J.; Calvin, Kate
Protein expression is a major link in the genotype–phenotype relationship, and processes affecting protein abundances, such as rates of transcription and translation, could contribute to phenotypic evolution if they generate heritable variation. Recent work has suggested that mRNA abundances do not accurately predict final protein abundances, which would imply that post-transcriptional regulatory processes contribute significantly to phenotypes. Post-transcriptional processes also appear to buffer changes in transcriptional patterns as species diverge, suggesting that the transcriptional changes have little or no effect on the phenotypes undergoing study. We tested for concordance between mRNA and protein expression levels in snake venoms by means of mRNA-seq and quantitative mass spectrometry for 11 snakes representing 10 species, six genera, and three families. In contrast to most previous work, we found high correlations between venom gland transcriptomes and venom proteomes for 10 of our 11 comparisons. We tested for protein-level buffering of transcriptional changes during species divergence by comparing the difference between transcript abundance and protein abundance for three pairs of species and one intraspecific pair. We found no evidence for buffering during divergence of our three species pairs but did find evidence for protein-level buffering for our single intraspecific comparison, suggesting that buffering, if present, was a transient phenomenon in venom divergence. Our results demonstrated that post-transcriptional mechanisms did not contribute significantly to phenotypic evolution in venoms and suggest a more prominent and direct role for cis-regulatory evolution in phenotypic variation, particularly for snake venoms. PMID:26358130
Rokyta, Darin R; Margres, Mark J; Calvin, Kate
Protein expression is a major link in the genotype-phenotype relationship, and processes affecting protein abundances, such as rates of transcription and translation, could contribute to phenotypic evolution if they generate heritable variation. Recent work has suggested that mRNA abundances do not accurately predict final protein abundances, which would imply that post-transcriptional regulatory processes contribute significantly to phenotypes. Post-transcriptional processes also appear to buffer changes in transcriptional patterns as species diverge, suggesting that the transcriptional changes have little or no effect on the phenotypes undergoing study. We tested for concordance between mRNA and protein expression levels in snake venoms by means of mRNA-seq and quantitative mass spectrometry for 11 snakes representing 10 species, six genera, and three families. In contrast to most previous work, we found high correlations between venom gland transcriptomes and venom proteomes for 10 of our 11 comparisons. We tested for protein-level buffering of transcriptional changes during species divergence by comparing the difference between transcript abundance and protein abundance for three pairs of species and one intraspecific pair. We found no evidence for buffering during divergence of our three species pairs but did find evidence for protein-level buffering for our single intraspecific comparison, suggesting that buffering, if present, was a transient phenomenon in venom divergence. Our results demonstrated that post-transcriptional mechanisms did not contribute significantly to phenotypic evolution in venoms and suggest a more prominent and direct role for cis-regulatory evolution in phenotypic variation, particularly for snake venoms.
Valladares, Fernando; Matesanz, Silvia; Guilhaumon, François; Araújo, Miguel B; Balaguer, Luis; Benito-Garzón, Marta; Cornwell, Will; Gianoli, Ernesto; van Kleunen, Mark; Naya, Daniel E; Nicotra, Adrienne B; Poorter, Hendrik; Zavala, Miguel A
Species are the unit of analysis in many global change and conservation biology studies; however, species are not uniform entities but are composed of different, sometimes locally adapted, populations differing in plasticity. We examined how intraspecific variation in thermal niches and phenotypic plasticity will affect species distributions in a warming climate. We first developed a conceptual model linking plasticity and niche breadth, providing five alternative intraspecific scenarios that are consistent with existing literature. Secondly, we used ecological niche-modeling techniques to quantify the impact of each intraspecific scenario on the distribution of a virtual species across a geographically realistic setting. Finally, we performed an analogous modeling exercise using real data on the climatic niches of different tree provenances. We show that when population differentiation is accounted for and dispersal is restricted, forecasts of species range shifts under climate change are even more pessimistic than those using the conventional assumption of homogeneously high plasticity across a species' range. Suitable population-level data are not available for most species so identifying general patterns of population differentiation could fill this gap. However, the literature review revealed contrasting patterns among species, urging greater levels of integration among empirical, modeling and theoretical research on intraspecific phenotypic variation.
Hanson, China A.; Marston, Marcia F.; Martiny, Jennifer B. H.
Despite the important role of phages in marine systems, little is understood about how their diversity is distributed in space. Biogeographic patterns of marine phages may be difficult to detect due to their vast genetic diversity, which may not be accurately represented by conserved marker genes. To investigate the spatial biogeographic structure of marine phages, we isolated over 400 cyanophages on Synechococcus host strain WH7803 at three coastal locations in the United States (Rhode Island, Washington, and southern California). Approximately 90% of the cyanophage isolates were myoviruses, while the other 10% were podoviruses. The diversity of isolates was further characterized in two ways: (i) taxonomically, using conserved marker genes and (ii) phenotypically, by testing isolates for their ability to infect a suite of hosts, or their “host range.” Because host range is a highly variable trait even among closely related isolates, we hypothesized that host range phenotypes of cyanophage isolates would vary more strongly among locations than would taxonomic composition. Instead, we found evidence for strong biogeographic variation both in taxonomic composition and host range phenotypes, with little taxonomic overlap among the three coastal regions. For both taxonomic composition and host range phenotypes, cyanophage communities from California and Rhode Island were the most dissimilar, while Washington communities exhibited similarity to each of the other two locations. These results suggest that selection imposed by spatial variation in host dynamics influence the biogeographic distribution of cyanophages. PMID:27446023
Dobler, R; Reinhardt, K
Sperm-competition success (SCS) is seen as centrally important for evolutionary change: superior fathers sire superior sons and thereby inherit the traits that make them superior. Additional hypotheses, that phenotypic plasticity in SCS and sperm ageing explain variation in paternity, are less considered. Even though various alleles have individually been shown to be correlated with variation in SCS, few studies have addressed the heritability, or evolvability, of overall SCS. Those studies that have addressed found low or no heritability and have not examined evolvability. They have further not excluded phenotypic plasticity, and temporal effects on SCS, despite their known dramatic effects on sperm function. In Drosophila melanogaster, we found that both standard components of sperm competition, sperm defence and sperm offence, showed nonsignificant heritability across several offspring cohorts. Instead, our analysis revealed, for the first time, the existence of phenotypic plasticity in SCS across an extreme environment (5% CO2 ), and an influence of sperm ageing. Evolvability of SCS was substantial for sperm defence but weak for sperm offence. Our results suggest that the paradigm of explaining evolution by sperm competition is more complex and will benefit from further experimental work on the heritability or evolvability of SCS, measuring phenotypic plasticity, and separating the effects of sperm competition and sperm ageing.
Roesti, Marius; Gavrilets, Sergey; Hendry, Andrew P.; Salzburger, Walter; Berner, Daniel
Parallel adaptation is common and may often occur from shared genetic variation, but the genomic consequences of this process remain poorly understood. We first use individual-based simulations to demonstrate that comparisons among populations adapted in parallel from shared variation reveal a characteristic genomic signature around a selected locus: a low divergence valley centered at the locus and flanked by twin peaks of high divergence. This signature is initiated by the hitchhiking of haplotype tracts differing among derived populations in the broader neighborhood of the selected locus (driving the high divergence twin peaks) and shared haplotype tracts in the tight neighborhood of the locus (driving the low divergence valley). This initial hitchhiking signature is reinforced over time because the selected locus acts as a barrier to gene flow from the source to the derived populations, thus promoting divergence by drift in its close neighborhood. We next empirically confirm the peak-valley-peak signature by combining targeted and RAD sequence data at three candidate adaptation genes in multiple marine (source) and freshwater (derived) populations of threespine stickleback. Finally, we use a genome-wide screen for the peak-valley-peak signature to discover additional genome regions involved in parallel marine-freshwater divergence. Our findings offer a new explanation for heterogeneous genomic divergence and thus challenge the standard view that peaks in population divergence harbor divergently selected loci, and that low-divergence regions result from balancing selection or localized introgression. We anticipate that genome scans for peak-valley-peak divergence signatures will promote the discovery of adaptation genes in other organisms. PMID:24635356
Dash, Debasis; Mukerji, Mitali
Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation. PMID:25398783
The first goal of this paper was to overview modern approaches to local adaptation, with a focus on the use of population genomics data to detect signals of natural selection in fishes. Several mechanisms are discussed that may enhance the maintenance of genetic variation and evolutionary potential, which have been overlooked and should be considered in future theoretical development and predictive models: the prevalence of soft sweeps, polygenic basis of adaptation, balancing selection and transient polymorphisms, parallel evolution, as well as epigenetic variation. Research on fish population genomics has provided ample evidence for local adaptation at the genome level. Pervasive adaptive evolution, however, seems to almost never involve the fixation of beneficial alleles. Instead, adaptation apparently proceeds most commonly by soft sweeps entailing shifts in frequencies of alleles being shared between differentially adapted populations. One obvious factor contributing to the maintenance of standing genetic variation in the face of selective pressures is that adaptive phenotypic traits are most often highly polygenic, and consequently the response to selection should derive mostly from allelic co-variances among causative loci rather than pronounced allele frequency changes. Balancing selection in its various forms may also play an important role in maintaining adaptive genetic variation and the evolutionary potential of species to cope with environmental change. A large body of literature on fishes also shows that repeated evolution of adaptive phenotypes is a ubiquitous evolutionary phenomenon that seems to occur most often via different genetic solutions, further adding to the potential options of species to cope with a changing environment. Moreover, a paradox is emerging from recent fish studies whereby populations of highly reduced effective population sizes and impoverished genetic diversity can apparently retain their adaptive potential in some
Le Bars, Hervé; Bonnaure-Mallet, Martine; Barloy-Hubler, Frédérique; Jolivet-Gougeon, Anne; Bousarghin, Latifa
The metabolic adaptation of strong mutator strains was studied to better understand the link between the strong mutator phenotype and virulence. Analysis of the growth curves of isogenic strains of Salmonella, which were previously grown in M63 glucose media, revealed that the exponential phase of growth was reached earlier in an M63 acetate medium with strong mutator strains (mutated in mutS or in mutL) than with normomutator strains (P<0.05). Complemented strains confirmed the direct role of the strong mutator phenotype in this faster metabolic adaptation to the assimilation of acetate. In a mixed cell population, proliferation of strong mutators over normomutators was observed when the carbon source was switched from glucose to acetate. These results add to the sparse body of knowledge about strong mutators and highlight the selective advantage conferred by the strong mutator phenotype to adapt to a switch of carbon source in the environment. This work may provide clinically useful information given that there is a high prevalence of strong mutators among pathogenic strains of Salmonella and that acetate is the principal short chain fatty acid of the human terminal ileum and colon where Salmonella infection is localized.
Kovach, Ryan P; Joyce, John E; Echave, Jesse D; Lindberg, Mark S; Tallmon, David A
Climate-induced phenological shifts can influence population, evolutionary, and ecological dynamics, but our understanding of these phenomena is hampered by a lack of long-term demographic data. We use a multi-decade census of 5 salmonid species representing 14 life histories in a warming Alaskan stream to address the following key questions about climate change and phenology: How consistent are temporal patterns and drivers of phenology for similar species and alternative life histories? Are shifts in phenology associated with changes in phenotypic variation? How do phenological changes influence the availability of resource subsidies? For most salmonid species, life stages, and life histories, freshwater temperature influences migration timing--migration events are occurring earlier in time (mean = 1.7 days earlier per decade over the 3-5 decades), and the number of days over which migration events occur is decreasing (mean = 1.5 days per decade). Temporal trends in migration timing were not correlated with changes in intra-annual phenotypic variation, suggesting that these components of the phenotypic distribution have responded to environmental change independently. Despite commonalities across species and life histories, there was important biocomplexity in the form of disparate shifts in migration timing and variation in the environmental factors influencing migration timing for alternative life history strategies in the same population. Overall, adult populations have been stable during these phenotypic and environmental changes (λ ≈ 1.0), but the temporal availability of salmon as a resource in freshwater has decreased by nearly 30 days since 1971 due to changes in the median date of migration timing and decreases in intra-annual variation in migration timing. These novel observations advance our understanding of phenological change in response to climate warming, and indicate that climate change has influenced the ecology of salmon populations
Kovach, Ryan P.; Joyce, John E.; Echave, Jesse D.; Lindberg, Mark S.; Tallmon, David A.
Climate-induced phenological shifts can influence population, evolutionary, and ecological dynamics, but our understanding of these phenomena is hampered by a lack of long-term demographic data. We use a multi-decade census of 5 salmonid species representing 14 life histories in a warming Alaskan stream to address the following key questions about climate change and phenology: How consistent are temporal patterns and drivers of phenology for similar species and alternative life histories? Are shifts in phenology associated with changes in phenotypic variation? How do phenological changes influence the availability of resource subsidies? For most salmonid species, life stages, and life histories, freshwater temperature influences migration timing – migration events are occurring earlier in time (mean = 1.7 days earlier per decade over the 3–5 decades), and the number of days over which migration events occur is decreasing (mean = 1.5 days per decade). Temporal trends in migration timing were not correlated with changes in intra-annual phenotypic variation, suggesting that these components of the phenotypic distribution have responded to environmental change independently. Despite commonalities across species and life histories, there was important biocomplexity in the form of disparate shifts in migration timing and variation in the environmental factors influencing migration timing for alternative life history strategies in the same population. Overall, adult populations have been stable during these phenotypic and environmental changes (λ ≈1.0), but the temporal availability of salmon as a resource in freshwater has decreased by nearly 30 days since 1971 due to changes in the median date of migration timing and decreases in intra-annual variation in migration timing. These novel observations advance our understanding of phenological change in response to climate warming, and indicate that climate change has influenced the ecology of salmon
Pascoal, Sonia; Carvalho, Gary; Creer, Simon; Rock, Jenny; Kawaii, Kei; Mendo, Sonia; Hughes, Roger
Assessment of plastic and heritable components of phenotypic variation is crucial for understanding the evolution of adaptive character traits in heterogeneous environments. We assessed the above in relation to adaptive shell morphology of the rocky intertidal snail Nucella lapillus by reciprocal transplantation of snails between two shores differing in wave action and rearing snails of the same provenance in a common garden. Results were compared with those reported for similar experiments conducted elsewhere. Microsatellite variation indicated limited gene flow between the populations. Intrinsic growth rate was greater in exposed-site than sheltered-site snails, but the reverse was true of absolute growth rate, suggesting heritable compensation for reduced foraging opportunity at the exposed site. Shell morphology of reciprocal transplants partially converged through plasticity toward that of native snails. Shell morphology of F2s in the common garden partially retained characteristics of the P-generation, suggesting genetic control. A maternal effect was revealed by greater resemblance of F1s than F2s to the P-generation. The observed synergistic effects of plastic, maternal and genetic control of shell-shape may be expected to maximise fitness when environmental characteristics become unpredictable through dispersal. PMID:22299035
Moon, Clara; Baldridge, Megan T; Wallace, Meghan A; Burnham, Carey-Ann D; Virgin, Herbert W; Stappenbeck, Thaddeus S
The proliferation of genetically modified mouse models has exposed phenotypic variation between investigators and institutions that has been challenging to control. In many cases, the microbiota is the presumed cause of the variation. Current solutions to account for phenotypic variability include littermate and maternal controls or defined microbial consortia in gnotobiotic mice. In conventionally raised mice, the microbiome is transmitted from the dam. Here we show that microbially driven dichotomous faecal immunoglobulin-A (IgA) levels in wild-type mice within the same facility mimic the effects of chromosomal mutations. We observe in multiple facilities that vertically transmissible bacteria in IgA-low mice dominantly lower faecal IgA levels in IgA-high mice after co-housing or faecal transplantation. In response to injury, IgA-low mice show increased damage that is transferable by faecal transplantation and driven by faecal IgA differences. We find that bacteria from IgA-low mice degrade the secretory component of secretory IgA as well as IgA itself. These data indicate that phenotypic comparisons between mice must take into account the non-chromosomal hereditary variation between different breeders. We propose faecal IgA as one marker of microbial variability and conclude that co-housing and/or faecal transplantation enables analysis of progeny from different dams.
Bourguet, D; Lenormand, T; Guillemaud, T; Marcel, V; Fournier, D; Raymond, M
Newly arisen adaptive alleles such as insecticide resistance genes represent a good opportunity to investigate the theories put forth to explain the molecular basis of dominance and its possible evolution. Dominance levels of insecticide resistance conferred by insensitive alleles of the acetylcholinesterase gene were analyzed in five resistant strains of the mosquito Culex pipiens. Dominance levels were found to differ between strains, varying from partial recessivity to complete dominance. This variation was not explained by differences in catalytic properties of the enzyme, since four of the five resistant strains had identical inhibition properties for the insensitive acetylcholinesterase. Among these four laboratory strains and in individuals collected from natural populations, we found a correlation between increased acetylcholinesterase activities and higher dominance levels. We propose a molecular explanation for how variation in acetylcholinesterase activity may result in variation of dominance level. We also conjecture that the four resistant strains did not differ in their amino acid sequence in the catalytically active regions of acetylcholinesterase, but that the expression of the gene was regulated by either neighboring or distant sites, thereby modifying the dominance level. Under this interpretation, dominance levels may evolve in this system, since heritable variation in acetylcholinesterase activity was found.
Mathur, Vinayak; Schmidt, Paul S
Identifying mechanisms of adaptation to variable environments is essential in developing a comprehensive understanding of evolutionary dynamics in natural populations. Phenotypic plasticity allows for phenotypic change in response to changes in the environment, and as such may play a major role in adaptation to environmental heterogeneity. Here, the plasticity of stress response in Drosophila melanogaster originating from two distinct geographic regions and ecological habitats was examined. Adults were given a short-term, 5-day exposure to combinations of temperature and photoperiod to elicit a plastic response for three fundamental aspects of stress tolerance that vary adaptively with geography. This was replicated both in the laboratory and in outdoor enclosures in the field. In the laboratory, geographic origin was the primary determinant of the stress response. Temperature and the interaction between temperature and photoperiod also significantly affected stress resistance. In the outdoor enclosures, plasticity was distinct among traits and between geographic regions. These results demonstrate that short-term exposure of adults to ecologically relevant environmental cues results in predictable effects on multiple aspects of fitness. These patterns of plasticity vary among traits and are highly distinct between the two examined geographic regions, consistent with patterns of local adaptation to climate and associated environmental parameters.
Klein, Benjamin; Destephens, Anthony; Dumeny, Leanne; Hu, Qiongyao; He, Yong; O'Malley, Kerri; Jiang, Zhihua; Tran-Son-Tay, Roger; Berceli, Scott
Pathologic vascular adaptation following local injury is the primary driver for accelerated intimal hyperplasia and an occlusive phenotype. Smooth muscle cell (SMC) proliferation within the wall, and migration into the developing intima, is a major component of this remodeling response. The primary objective in the current study was to investigate the effect of the local biomechanical forces on early vein graft adaptation, specifically focusing on the spatial and temporal response of SMC proliferation and conversion from a contractile to synthetic architecture. Taking advantage of the differential adaptation that occurs during exposure to divergent flow environments, vein grafts were implanted in rabbits to create two distinct flow environments and harvested at times ranging from 2 h to 28 days. Using an algorithm for the virtual reconstruction of unfixed, histologic specimens, immunohistochemical tracking of DNA synthesis, and high-throughput transcriptional analysis, the spatial and temporal changes in graft morphology, cell proliferation, and SMC phenotype were catalogued. Notable findings include a burst of cell proliferation at 7 days post-implantation, which was significantly augmented by exposure to a reduced flow environment. Compared to the adjacent media, proliferation rates were 3-fold greater in the intima, and a specific spatial distribution of these proliferating cells was identified, with a major peak in the sub-endothelial region and a second peak centering on the internal elastic lamina. Genomic markers of a contractile SMC phenotype were reduced as early as 2 h post-implantation and reached a nadir at 7 days. Network analysis of upstream regulatory pathways identified GATA6 and KLF5 as important transcription factors that regulate this shift in SMC phenotype.
Tong, Xiaoling; Bear, Ashley; Liew, Seng Fatt; Bhardwaj, Shivam; Wasik, Bethany R.; Dinwiddie, April; Bastianelli, Carole; Cheong, Wei Fun; Wenk, Markus R.; Cao, Hui
Bodies are often made of repeated units, or serial homologs, that develop using the same core gene regulatory network. Local inputs and modifications to this network allow serial homologs to evolve different morphologies, but currently we do not understand which modifications allow these repeated traits to evolve different levels of phenotypic plasticity. Here we describe variation in phenotypic plasticity across serial homologous eyespots of the butterfly Bicyclus anynana, hypothesized to be under selection for similar or different functions in the wet and dry seasonal forms. Specifically, we document the presence of eyespot size and scale brightness plasticity in hindwing eyespots hypothesized to vary in function across seasons, and reduced size plasticity and absence of brightness plasticity in forewing eyespots hypothesized to have the same function across seasons. By exploring the molecular and physiological causes of this variation in plasticity across fore and hindwing serial homologs we discover that: 1) temperature experienced during the wandering stages of larval development alters titers of an ecdysteroid hormone, 20-hydroxyecdysone (20E), in the hemolymph of wet and dry seasonal forms at that stage; 2) the 20E receptor (EcR) is differentially expressed in the forewing and hindwing eyespot centers of both seasonal forms during this critical developmental stage; and 3) manipulations of EcR signaling disproportionately affected hindwing eyespots relative to forewing eyespots. We propose that differential EcR expression across forewing and hindwing eyespots at a critical stage of development explains the variation in levels of phenotypic plasticity across these serial homologues. This finding provides a novel signaling pathway, 20E, and a novel molecular candidate, EcR, for the regulation of levels of phenotypic plasticity across body parts or serial homologs. PMID:26405828
Monteiro, Antónia; Tong, Xiaoling; Bear, Ashley; Liew, Seng Fatt; Bhardwaj, Shivam; Wasik, Bethany R; Dinwiddie, April; Bastianelli, Carole; Cheong, Wei Fun; Wenk, Markus R; Cao, Hui; Prudic, Kathleen L
Bodies are often made of repeated units, or serial homologs, that develop using the same core gene regulatory network. Local inputs and modifications to this network allow serial homologs to evolve different morphologies, but currently we do not understand which modifications allow these repeated traits to evolve different levels of phenotypic plasticity. Here we describe variation in phenotypic plasticity across serial homologous eyespots of the butterfly Bicyclus anynana, hypothesized to be under selection for similar or different functions in the wet and dry seasonal forms. Specifically, we document the presence of eyespot size and scale brightness plasticity in hindwing eyespots hypothesized to vary in function across seasons, and reduced size plasticity and absence of brightness plasticity in forewing eyespots hypothesized to have the same function across seasons. By exploring the molecular and physiological causes of this variation in plasticity across fore and hindwing serial homologs we discover that: 1) temperature experienced during the wandering stages of larval development alters titers of an ecdysteroid hormone, 20-hydroxyecdysone (20E), in the hemolymph of wet and dry seasonal forms at that stage; 2) the 20E receptor (EcR) is differentially expressed in the forewing and hindwing eyespot centers of both seasonal forms during this critical developmental stage; and 3) manipulations of EcR signaling disproportionately affected hindwing eyespots relative to forewing eyespots. We propose that differential EcR expression across forewing and hindwing eyespots at a critical stage of development explains the variation in levels of phenotypic plasticity across these serial homologues. This finding provides a novel signaling pathway, 20E, and a novel molecular candidate, EcR, for the regulation of levels of phenotypic plasticity across body parts or serial homologs.
Pan, Qingchun; Li, Lin; Yang, Xiaohong; Tong, Hao; Xu, Shutu; Li, Zhigang; Li, Weiya; Muehlbauer, Gary J; Li, Jiansheng; Yan, Jianbing
Meiotic recombination is a major driver of genetic diversity, species evolution, and agricultural improvement. Thus, an understanding of the genetic recombination landscape across the maize (Zea mays) genome will provide insight and tools for further study of maize evolution and improvement. Here, we used c. 50 000 single nucleotide polymorphisms to precisely map recombination events in 12 artificial maize segregating populations. We observed substantial variation in the recombination frequency and distribution along the ten maize chromosomes among the 12 populations and identified 143 recombination hot regions. Recombination breakpoints were partitioned into intragenic and intergenic events. Interestingly, an increase in the number of genes containing recombination events was accompanied by a decrease in the number of recombination events per gene. This kept the overall number of intragenic recombination events nearly invariable in a given population, suggesting that the recombination variation observed among populations was largely attributed to intergenic recombination. However, significant associations between intragenic recombination events and variation in gene expression and agronomic traits were observed, suggesting potential roles for intragenic recombination in plant phenotypic diversity. Our results provide a comprehensive view of the maize recombination landscape, and show an association between recombination, gene expression and phenotypic variation, which may enhance crop genetic improvement.
Merilä, Juha; Hendry, Andrew P
Many studies have recorded phenotypic changes in natural populations and attributed them to climate change. However, controversy and uncertainty has arisen around three levels of inference in such studies. First, it has proven difficult to conclusively distinguish whether phenotypic changes are genetically based or the result of phenotypic plasticity. Second, whether or not the change is adaptive is usually assumed rather than tested. Third, inferences that climate change is the specific causal agent have rarely involved the testing – and exclusion – of other potential drivers. We here review the various ways in which the above inferences have been attempted, and evaluate the strength of support that each approach can provide. This methodological assessment sets the stage for 11 accompanying review articles that attempt comprehensive syntheses of what is currently known – and not known – about responses to climate change in a variety of taxa and in theory. Summarizing and relying on the results of these reviews, we arrive at the conclusion that evidence for genetic adaptation to climate change has been found in some systems, but is still relatively scarce. Most importantly, it is clear that more studies are needed – and these must employ better inferential methods – before general conclusions can be drawn. Overall, we hope that the present paper and special issue provide inspiration for future research and guidelines on best practices for its execution. PMID:24454544
Peirson, B R Erick
Plant ecologist Anthony David Bradshaw's account of the evolution of adaptive phenotypic plasticity remains central to contemporary research aimed at understanding how organisms persist in heterogeneous environments. Bradshaw suggested that changes in particular traits in response to specific environmental factors could be under direct genetic control, and that natural selection could therefore act directly to shape those responses: plasticity was not "noise" obscuring a genetic signal, but could be specific and refined just as any other adaptive phenotypic trait. In this paper, I document the contexts and development of Bradshaw's investigation of phenotypic plasticity in plants, including a series of unreported experiments in the late 1950s and early 1960s. Contrary to the mythology that later emerged around Bradshaw's ideas, Bradshaw was engaged in a serious and sustained empirical research program concerning plasticity in the 1950s and 1960s that went far beyond a single review paper. Moreover, that work was not isolated, but was surrounded by an already rich theoretical discourse and a substantial body of empirical research concerning the evolution of developmental plasticity and stability. Bradshaw recast the problem of how to understand (and control) plasticity and stability within an epistemic framework focused on genetic differences and natural selection.
Vaysse, Amaury; Ratnakumar, Abhirami; Derrien, Thomas; Axelsson, Erik; Rosengren Pielberg, Gerli; Sigurdsson, Snaevar; Fall, Tove; Seppälä, Eija H; Hansen, Mark S T; Lawley, Cindy T; Karlsson, Elinor K; Bannasch, Danika; Vilà, Carles; Lohi, Hannes; Galibert, Francis; Fredholm, Merete; Häggström, Jens; Hedhammar, Ake; André, Catherine; Lindblad-Toh, Kerstin; Hitte, Christophe; Webster, Matthew T
The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse breeds using a newly developed high-density genotyping array consisting of >170,000 evenly spaced SNPs. We first identify 44 genomic regions exhibiting extreme differentiation across multiple breeds. Genetic variation in these regions correlates with variation in several phenotypic traits that vary between breeds, and we identify novel associations with both morphological and behavioral traits. We next scan the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for developmental genes. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits. This study provides a catalogue of genomic regions showing extreme reduction in genetic variation or population differentiation in dogs, including many linked to phenotypic variation. The many blocks of reduced haplotype diversity observed across the genome in dog breeds are the result of both selection and genetic drift, but extended blocks of homozygosity on a megabase scale appear to be best explained by selection. Further elucidation of the variants under selection will help to uncover the genetic basis of complex traits and disease.
There is abundant evidence that the probability of successful establishment in novel environments increases with number of individuals in founder groups and with number of repeated introductions. Theory posits that the genotypic and phenotypic variation among individuals should also be important, but few studies have examined whether founder diversity influences establishment independent of propagule pressure, nor whether the effect is model or context dependent. I summarize the results of 18 experimental studies and report on a metaanalysis that provides strong evidence that higher levels of genotypic and phenotypic diversity in founder groups increase establishment success in plants and animals. The effect of diversity is stronger in experiments carried out under natural conditions in the wild than under seminatural or standardized laboratory conditions. The realization that genetic and phenotypic variation is key to successful establishment may improve the outcome of reintroduction and translocation programs used to vitalize or restore declining and extinct populations. Founder diversity may also improve the ability of invasive species to establish and subsequently spread in environments outside of their native community, and enhance the ability of pathogens and parasites to colonize and invade the environment constituted by their hosts. It is argued that exchange of ideas, methodological approaches, and insights of the role of diversity for establishment in different contexts may further our knowledge, vitalize future research, and improve management plans in different disciplines. PMID:24367109
Lo Cascio Sætre, Camilla; Coleiro, Charles; Austad, Martin; Gauci, Mark; Sætre, Glenn-Peter; Voje, Kjetil Lysne; Eroukhmanoff, Fabrice
Real-time observation of adaptive evolution in the wild is rare and limited to cases of marked, often anthropogenic, environmental change. Here we present the case of a small population of reed warblers (Acrocephalus scirpaceus) over a period of 19 years (1996-2014) after colonizing a restored wetland habitat in Malta. Our data show a population decrease in body mass, following a trajectory consistent with a population ascending an adaptive peak, a so-called Ornstein-Uhlenbeck process. We corroborate these findings with genetic and ecological data, revealing that individual survival is correlated with body mass, and more than half of the variation in mean population fitness is explained by variation in body mass. Despite a small effective population size, an adaptive response has taken place within a decade. A founder event from a large, genetically variable source population to the southern range margin of the reed warbler distribution likely facilitated this process.
Lo Cascio Sætre, Camilla; Coleiro, Charles; Austad, Martin; Gauci, Mark; Sætre, Glenn-Peter; Voje, Kjetil Lysne; Eroukhmanoff, Fabrice
Real-time observation of adaptive evolution in the wild is rare and limited to cases of marked, often anthropogenic, environmental change. Here we present the case of a small population of reed warblers (Acrocephalus scirpaceus) over a period of 19 years (1996–2014) after colonizing a restored wetland habitat in Malta. Our data show a population decrease in body mass, following a trajectory consistent with a population ascending an adaptive peak, a so-called Ornstein–Uhlenbeck process. We corroborate these findings with genetic and ecological data, revealing that individual survival is correlated with body mass, and more than half of the variation in mean population fitness is explained by variation in body mass. Despite a small effective population size, an adaptive response has taken place within a decade. A founder event from a large, genetically variable source population to the southern range margin of the reed warbler distribution likely facilitated this process. PMID:28106055
Versteegh, M A; Helm, B; Kleynhans, E J; Gwinner, E; Tieleman, B I
Animals cope with seasonal variation in environmental factors by adjustments of physiology and life history. When seasonal variation is partly predictable, such adjustments can be based on a genetic component or be phenotypically flexible. Animals have to allocate limited resources over different demands, including immune function. Accordingly, immune traits could change seasonally, and such changes could have a genetic component that differs between environments. We tested this hypothesis in genotypically distinct groups of a widespread songbird, the stonechat (Saxicola torquata). We compared variation in immunity during 1 year in long-distance migrants, short-distance migrants, tropical residents and hybrids in a common garden environment. Additionally, we investigated phenotypically flexible responses to temperature by applying different temperature regimes to one group. We assessed constitutive immunity by measuring hemagglutination, hemolysis, haptoglobin and bactericidal ability against Escherichia coli and Staphylococcus aureus. Genotypic groups differed in patterns of variation of all measured immune indices except haptoglobin. Hybrids differed from, but were rarely intermediate to, parental subspecies. Temperature treatment only influenced patterns of hemolysis and bactericidal ability against E. coli. We conclude that seasonal variation in constitutive immunity has a genetic component, that heredity does not follow simple Mendelian rules, and that some immune measures are relatively rigid while others are more flexible. Furthermore, our results support the idea that seasonal variability in constitutive immunity is associated with variability in environment and annual-cycle demands. This study stresses the importance of considering seasonal variation in immune function in relation to the ecology and life history of the organism of interest.
Liang, Xiaoyu; Wang, Zhenchuan; Sha, Qiuying; Zhang, Shuanglin
Currently, the analyses of most genome-wide association studies (GWAS) have been performed on a single phenotype. There is increasing evidence showing that pleiotropy is a widespread phenomenon in complex diseases. Therefore, using only one single phenotype may lose statistical power to identify the underlying genetic mechanism. There is an increasing need to develop and apply powerful statistical tests to detect association between multiple phenotypes and a genetic variant. In this paper, we develop an Adaptive Fisher’s Combination (AFC) method for joint analysis of multiple phenotypes in association studies. The AFC method combines p-values obtained in standard univariate GWAS by using the optimal number of p-values which is determined by the data. We perform extensive simulations to evaluate the performance of the AFC method and compare the power of our method with the powers of TATES, Tippett’s method, Fisher’s combination test, MANOVA, MultiPhen, and SUMSCORE. Our simulation studies show that the proposed method has correct type I error rates and is either the most powerful test or comparable with the most powerful test. Finally, we illustrate our proposed methodology by analyzing whole-genome genotyping data from a lung function study. PMID:27694844
Phenotypic plasticity represents one of the most important ways that organisms adaptively respond to environmental variation. Alternate phenotypes produced through phenotypic plasiticity generally arise through conditional gene expression, which is predicted to result in relaxed selective constrain...
Dutra Filho, J A; Junior, T C; Simões Neto, D E
In the present study, we assessed the agro-industrial performance of 22 sugarcane genotypes adaptable to edaphoclimatic conditions in production microregions in the State of Pernambuco, Brazil, and we recommended the commercial cultivation of select genotypes. The variables analyzed were as follows: sucrose percentage in cane juice, tonnage of saccharose per hectare (TPH), sugarcane tonnage per hectare (TCH), fiber, solid soluble contents, total recoverable sugar tonnage (ATR), and total recoverable sugar tonnage per hectare (ATR t/ha). A randomized block design with 4 repeats was used. Combined variance of the experiments, genetic parameter estimates, and environment stratification were analyzed. Phenotypic adaptability and stability were analyzed using the Annicchiarico and Wricke methods and analysis of variance. Genetic gain was estimated using the classic index and sum of ranks. Genotype selection was efficient for TPH, TCH, and ATR t/ha. Genotypes presented a great potential for improvement and a similar response pattern in Litoral Norte and Mata Sul microregions for TPH and TCH and Litoral Norte and Litoral Sul microregions for ATR t/ha. Genotypes SP78-4764, RB813804, and SP79-101 showed better productivity and phenotypic adaptability and stability, according to the Wricke and Annicchiarico methods. These genotypes can be recommended for cultivation in the sugarcane belt in the State of Pernambuco.
Scott, N.J.; Reynolds, R.P.
A collection of 98 breeding Mexican Ducks (Anas platyrhynchos diazi) was made in Mexico from six areas between the United States border with Chihuahua and Lake Chapala, Jalisco, in order to study geographic variation. Plumage indices showed a relatively smooth clinal change from north to south; northern populations were most influenced by the Northern Mallard (A. platyrhynchos) phenotype. Measurements of total, wing, and culmen lengths and bill width were usually significantly larger in males at any one site, but showed no regular geographic trends. Hybridization between platyrhynchos and diazi phenotypes may or may not be increasing in the middle Rio Grande and Rio Conchos valleys; available data are insufficient to decide. A spring 1978 aerial census yielded an estimate of 55,500 diazi -like birds in Mexico. Populations of diazi appear to be as large as the available habitat allows; management should be directed towards increasing and stabilizing the nesting habitat; and the stability of the zone of intergradation should be investigated.
Carneiro, Ana; Airey, David; Thompson, Brent; Zhu, C; Rinchik, Eugene M; Lu, Lu; Chesler, Elissa J; Erikson, Keith; Blakely, Randy
The human serotonin (5-hydroxytryptamine, 5-HT) transporter (hSERT, SLC6A4) figures prominently in the etiology or treatment of many prevalent neurobehavioral disorders including anxiety, alcoholism, depression, autism and obsessive-compulsive disorder (OCD). Here we utilize naturally occurring polymorphisms in recombinant inbred (RI) lines to identify novel phenotypes associated with altered SERT function. The widely used mouse strain C57BL/6J, harbors a SERT haplotype defined by two nonsynonymous coding variants (Gly39 and Lys152 (GK)). At these positions, many other mouse lines, including DBA/2J, encode Glu39 and Arg152 (ER haplotype), assignments found also in hSERT. Synaptosomal 5-HT transport studies revealed reduced uptake associated with the GK variant. Heterologous expression studies confirmed a reduced SERT turnover rate for the GK variant. Experimental and in silico approaches using RI lines (C57Bl/6J X DBA/2J=BXD) identifies multiple anatomical, biochemical and behavioral phenotypes specifically impacted by GK/ER variation. Among our findings are multiple traits associated with anxiety and alcohol consumption, as well as of the control of dopamine (DA) signaling. Further bioinformatic analysis of BXD phenotypes, combined with biochemical evaluation of SERT knockout mice, nominates SERT-dependent 5-HT signaling as a major determinant of midbrain iron homeostasis that, in turn, dictates ironregulated DA phenotypes. Our studies provide a novel example of the power of coordinated in vitro, in vivo and in silico approaches using murine RI lines to elucidate and quantify the system-level impact of gene variation.
Hong, Kuk-Ki; Nielsen, Jens
In a previous study, system level analysis of adaptively evolved yeast mutants showing improved galactose utilization revealed relevant mutations. The governing mutations were suggested to be in the Ras/PKA signaling pathway and ergosterol metabolism. Here, site-directed mutants having one of the mutations RAS2(Lys77), RAS2(Tyr112), and ERG5(Pro370) were constructed and evaluated. The mutants were also combined with overexpression of PGM2, earlier proved as a beneficial target for galactose utilization. The constructed strains were analyzed for their gross phenotype, transcriptome and targeted metabolites, and the results were compared to those obtained from reference strains and the evolved strains. The RAS2(Lys77) mutation resulted in the highest specific galactose uptake rate among all of the strains with an increased maximum specific growth rate on galactose. The RAS2(Tyr112) mutation also improved the specific galactose uptake rate and also resulted in many transcriptional changes, including ergosterol metabolism. The ERG5(Pro370) mutation only showed a small improvement, but when it was combined with PGM2 overexpression, the phenotype was almost the same as that of the evolved mutants. Combination of the RAS2 mutations with PGM2 overexpression also led to a complete recovery of the adaptive phenotype in galactose utilization. Recovery of the gross phenotype by the reconstructed mutants was achieved with much fewer changes in the genome and transcriptome than for the evolved mutants. Our study demonstrates how the identification of specific mutations by systems biology can direct new metabolic engineering strategies for improving galactose utilization by yeast.
Although morphological transitions (such as hyphae and pseudohyphae formation) are a common feature among fungi, the encapsulated pathogenic yeast Cryptococcus neoformans is found during infection as blastoconidia. However, this fungus exhibits striking variations in cellular structure and size, which have important consequences during infection. This review will summarize the main aspects related with phenotypic and morphological variations in C. neoformans, which can be divided in three classes. Two of them are related to changes in the capsule, while the third one involves changes in the whole cell. The three morphological and phenotypic variations in C. neoformans can be classified as: (1) changes in capsule structure, (2) changes in capsule size, and (3) changes in the total size of the cell, which can be achieved by the formation of cryptococcal giant/titan cells or microforms. These changes have profound consequences on the interaction with the host, involving survival, phagocytosis escape and immune evasion and dissemination. This article will summarize the main features of these changes, and highlight their importance during the interaction with the host and how they contribute to the development of the disease.
Although morphological transitions (such as hyphae and pseudohyphae formation) are a common feature among fungi, the encapsulated pathogenic yeast Cryptococcus neoformans is found during infection as blastoconidia. However, this fungus exhibits striking variations in cellular structure and size, which have important consequences during infection. This review will summarize the main aspects related with phenotypic and morphological variations in C. neoformans, which can be divided in three classes. Two of them are related to changes in the capsule, while the third one involves changes in the whole cell. The three morphological and phenotypic variations in C. neoformans can be classified as: (1) changes in capsule structure, (2) changes in capsule size, and (3) changes in the total size of the cell, which can be achieved by the formation of cryptococcal giant/titan cells or microforms. These changes have profound consequences on the interaction with the host, involving survival, phagocytosis escape and immune evasion and dissemination. This article will summarize the main features of these changes, and highlight their importance during the interaction with the host and how they contribute to the development of the disease. PMID:21922016
Thorpe, Roger S; Barlow, Axel; Malhotra, Anita; Surget-Groba, Yann
Global warming will impact species in a number of ways, and it is important to know the extent to which natural populations can adapt to anthropogenic climate change by natural selection. Parallel microevolution within separate species can demonstrate natural selection, but several studies of homoplasy have not yet revealed examples of widespread parallel evolution in a generic radiation. Taking into account primary phylogeographic divisions, we investigate numerous quantitative traits (size, shape, scalation, colour pattern and hue) in anole radiations from the mountainous Lesser Antillean islands. Adaptation to climatic differences can lead to very pronounced differences between spatially close populations with all studied traits showing some evidence of parallel evolution. Traits from shape, scalation, pattern and hue (particularly the latter) show widespread evolutionary parallels within these species in response to altitudinal climate variation greater than extreme anthropogenic climate change predicted for 2080. This gives strong evidence of the ability to adapt to climate variation by natural selection throughout this radiation. As anoles can evolve very rapidly, it suggests anthropogenic climate change is likely to be less of a conservation threat than other factors, such as habitat loss and invasive species, in this, Lesser Antillean, biodiversity hot spot.
Metcalfe, N B; Van Leeuwen, T E; Killen, S S
There is increasing interest in documenting and explaining the existence of marked intraspecific variation in metabolic rate in animals, with fishes providing some of the best-studied examples. After accounting for variation due to other factors, there can typically be a two to three-fold variation among individual fishes for both standard and maximum metabolic rate (SMR and MMR). This variation is reasonably consistent over time (provided that conditions remain stable), and its underlying causes may be influenced by both genes and developmental conditions. In this paper, current knowledge of the extent and causes of individual variation in SMR, MMR and aerobic scope (AS), collectively its metabolic phenotype, is reviewed and potential links among metabolism, behaviour and performance are described. Intraspecific variation in metabolism has been found to be related to other traits: fishes with a relatively high SMR tend to be more dominant and grow faster in high food environments, but may lose their advantage and are more prone to risk-taking when conditions deteriorate. In contrast to the wide body of research examining links between SMR and behavioural traits, very little work has been directed towards understanding the ecological consequences of individual variation in MMR and AS. Although AS can differ among populations of the same species in response to performance demands, virtually nothing is known about the effects of AS on individual behaviours such as those associated with foraging or predator avoidance. Further, while factors such as food availability, temperature, hypoxia and the fish's social environment are known to alter resting and MMRs in fishes, there is a paucity of studies examining how these effects vary among individuals, and how this variation relates to behaviour. Given the observed links between metabolism and measures of performance, understanding the metabolic responses of individuals to changing environments will be a key area for
Yao, Chen; Chen, Brian H.; Joehanes, Roby; Otlu, Burcak; Zhang, Xiaoling; Liu, Chunyu; Huan, Tianxiao; Tastan, Oznur; Cupples, L. Adrienne; Meigs, James B.; Fox, Caroline S.; Freedman, Jane E.; Courchesne, Paul; O’Donnell, Christopher J.; Munson, Peter J.; Keles, Sunduz; Levy, Daniel
Background Cardiovascular disease (CVD) reflects a highly coordinated complex of traits. Although genome-wide association studies have reported numerous single nucleotide polymorphisms (SNPs) to be associated with CVD, the role of most of these variants in disease processes remains unknown. Methods and Results We built a CVD network using 1512 SNPs associated with 21 CVD traits in genome-wide association studies (at P≤5×10−8) and cross-linked different traits by virtue of their shared SNP associations. We then explored whole blood gene expression in relation to these SNPs in 5257 participants in the Framingham Heart Study. At a false discovery rate <0.05, we identified 370 cis-expression quantitative trait loci (eQTLs; SNPs associated with altered expression of nearby genes) and 44 trans-eQTLs (SNPs associated with altered expression of remote genes). The eQTL network revealed 13 CVD-related modules. Searching for association of eQTL genes with CVD risk factors (lipids, blood pressure, fasting blood glucose, and body mass index) in the same individuals, we found examples in which the expression of eQTL genes was significantly associated with these CVD phenotypes. In addition, mediation tests suggested that a subset of SNPs previously associated with CVD phenotypes in genome-wide association studies may exert their function by altering expression of eQTL genes (eg, LDLR and PCSK7), which in turn may promote interindividual variation in phenotypes. Conclusions Using a network approach to analyze CVD traits, we identified complex networks of SNP-phenotype and SNP-transcript connections. Integrating the CVD network with phenotypic data, we identified biological pathways that may provide insights into potential drug targets for treatment or prevention of CVD. PMID:25533967
Perussia, Bice; Chen, Yingying; Loza, Matthew J
We have defined the existence of developmental relationships among human peripheral NK cells with distinct phenotypic and functional characteristics. These findings closely parallel the changes that occur in vivo during NK cell development, and in vitro in experimental culture systems supporting NK cell generation from hematopoietic progenitors. These new insights provide a simplified framework to understand NK cell immunobiology and the cellular bases for their roles in innate immunity, initiation and maintenance of immune responses via regulation of adaptive and accessory cell functions, and immune pathologies.
Li, Peijin; Tao, Zhen; Dean, Caroline
The extent to which natural polymorphisms in noncoding sequences have functional consequences is still unknown. A large proportion of the natural variation in flowering in Arabidopsis thaliana accessions is due to noncoding cis polymorphisms that define distinct haplotypes of FLOWERING LOCUS C (FLC). Here, we show that a single natural intronic polymorphism in one haplotype affects FLC expression and thus flowering by specifically changing splicing of the FLC antisense transcript COOLAIR. Altered antisense splicing increases FLC expression via a cotranscriptional mechanism involving capping of the FLC nascent transcript. Single noncoding polymorphisms can therefore be a major contributor to phenotypic evolution through modulation of noncoding transcripts.
Li, Dongming; Zhang, Lijuan; Wang, Ting; Liu, Huan; Yang, Jinhua; Chen, Guifen
To improve the adaptive optics (AO) image's quality, we study the AO image restoration algorithm based on wavefront reconstruction technology and adaptive total variation (TV) method in this paper. Firstly, the wavefront reconstruction using Zernike polynomial is used for initial estimated for the point spread function (PSF). Then, we develop our proposed iterative solutions for AO images restoration, addressing the joint deconvolution issue. The image restoration experiments are performed to verify the image restoration effect of our proposed algorithm. The experimental results show that, compared with the RL-IBD algorithm and Wiener-IBD algorithm, we can see that GMG measures (for real AO image) from our algorithm are increased by 36.92%, and 27.44% respectively, and the computation time are decreased by 7.2%, and 3.4% respectively, and its estimation accuracy is significantly improved.
Martí-Raga, Maria; Peltier, Emilien; Mas, Albert; Beltran, Gemma; Marullo, Philippe
Hybridization is known to improve complex traits due to heterosis and phenotypic robustness. However, these phenomena have been rarely explained at the molecular level. Here, the genetic determinism of Saccharomyces cerevisiae fermentation performance was investigated using a QTL mapping approach on an F1-progeny population. Three main QTL were detected, with positive alleles coming from both parental strains. The heterosis effect found in the hybrid was partially explained by three loci showing pseudooverdominance and dominance effects. The molecular dissection of those QTL revealed that the adaptation to second fermentation is related to pH, lipid, or osmotic regulation. Our results suggest that the stressful conditions of second fermentation have driven the selection of rare genetic variants adapted to maintain yeast cell homeostasis and, in particular, to low pH conditions.
Martí-Raga, Maria; Peltier, Emilien; Mas, Albert; Beltran, Gemma; Marullo, Philippe
Hybridization is known to improve complex traits due to heterosis and phenotypic robustness. However, these phenomena have been rarely explained at the molecular level. Here, the genetic determinism of Saccharomyces cerevisiae fermentation performance was investigated using a QTL mapping approach on an F1-progeny population. Three main QTL were detected, with positive alleles coming from both parental strains. The heterosis effect found in the hybrid was partially explained by three loci showing pseudooverdominance and dominance effects. The molecular dissection of those QTL revealed that the adaptation to second fermentation is related to pH, lipid, or osmotic regulation. Our results suggest that the stressful conditions of second fermentation have driven the selection of rare genetic variants adapted to maintain yeast cell homeostasis and, in particular, to low pH conditions. PMID:27903630
Hoekstra, Hopi E; Drumm, Kristen E; Nachman, Michael W
Patterns of geographic variation in phenotype or genotype may provide evidence for natural selection. Here, we compare phenotypic variation in color, allele frequencies of a pigmentation gene (the melanocortin-1 receptor, Mc1r), and patterns of neutral mitochondrial DNA (mtDNA) variation in rock pocket mice (Chaetodipus intermedius) across a habitat gradient in southern Arizona. Pocket mice inhabiting volcanic lava have dark coats with unbanded, uniformly melanic hairs, whereas mice from nearby light-colored granitic rocks have light coats with banded hairs. This color polymorphism is a presumed adaptation to avoid predation. Previous work has demonstrated that two Mc1r alleles, D and d, differ by four amino acids, and are responsible for the color polymorphism: DD and Dd genotypes are melanic whereas dd genotypes are light colored. To determine the frequency of the two Mc1r allelic classes across the dark-colored lava and neighboring light-colored granite, we sequenced the Mc1r gene in 175 individuals from a 35-km transect in the Pinacate lava region. We also sequenced two neutral mtDNA genes, COIII and ND3, in the same individuals. We found a strong correlation between Mc1r allele frequency and habitat color and no correlation between mtDNA markers and habitat color. Using estimates of migration from mtDNA haplotypes between dark- and light-colored sampling sites and Mc1r allele frequencies at each site, we estimated selection coefficients against mismatched Mc1r alleles, assuming a simple model of migration-selection balance. Habitat-dependent selection appears strong but asymmetric: selection is stronger against light mice on dark rock than against melanic mice on light rock. Together these results suggest that natural selection acts to match pocket mouse coat color to substrate color, despite high levels of gene flow between light and melanic populations.
Background There is a growing concern that global climate change will affect the potential for pathogen transmission by insect species that are vectors of human diseases. One of these species is the former European malaria vector, Anopheles atroparvus. Levels of population differentiation of An. atroparvus from southern Europe were characterized as a first attempt to elucidate patterns of population structure of this former malaria vector. Results are discussed in light of a hypothetical situation of re-establishment of malaria transmission. Methods Genetic and phenotypic variation was analysed in nine mosquito samples collected from five European countries, using eight microsatellite loci and geometric morphometrics on 21 wing landmarks. Results Levels of genetic diversity were comparable to those reported for tropical malaria vectors. Low levels of genetic (0.004
Rainey, P B
The effect of phenotypic variation on attachment of Pseudomonas tolaasii and P. putida to Agaricus bisporus mycelium was investigated. Quantitative studies demonstrated the ability of each isolate to attach rapidly and firmly to A. bisporus mycelium and significant differences in attachment of wild-type and phenotypic variant strains were observed. This was most pronounced in P. tolaasii, where the percentage attachment of the wild-type form was always greater than that of the phenotypic variant. The medium upon which the bacteria were cultured, prior to conducting an attachment assay, had a significant effect on their ability to attach. Attachment of the wild-type form of P. putida was enhanced when the assay was performed in the presence of CaCl2, suggesting the involvement of electrostatic forces. No correlation was observed between bacterial hydrophobicity and ability to attach to A. bisporus mycelium. Scanning electron microscopy confirmed the results obtained from the quantitative studies and provided further evidence for marked differences in the ability of the pseudomonads to attach to mycelium. Fibrillar structures and amorphous material were frequently associated with attached cells and appeared to anchor bacteria to each other and to the hyphal surface. A time-course study of attachment using transmission electron microscopy revealed the presence of uneven fibrillar material on the surface of cells. This material stained positive for polysaccharide and may be involved in ensuring rapid, firm attachment of the cells.
Ibeagha-Awemu, Eveline M; Zhao, Xin
Improvement in animal productivity has been achieved over the years through careful breeding and selection programs. Today, variations in the genome are gaining increasing importance in livestock improvement strategies. Genomic information alone, however, explains only a part of the phenotypic variance in traits. It is likely that a portion of the unaccounted variance is embedded in the epigenome. The epigenome encompasses epigenetic marks such as DNA methylation, histone tail modifications, chromatin remodeling, and other molecules that can transmit epigenetic information such as non-coding RNA species. Epigenetic factors respond to external or internal environmental cues such as nutrition, pathogens, and climate, and have the ability to change gene expression leading to emergence of specific phenotypes. Accumulating evidence shows that epigenetic marks influence gene expression and phenotypic outcome in livestock species. This review examines available evidence of the influence of epigenetic marks on livestock (cattle, sheep, goat, and pig) traits and discusses the potential for consideration of epigenetic markers in livestock improvement programs. However, epigenetic research activities on farm animal species are currently limited partly due to lack of recognition, funding and a global network of researchers. Therefore, considerable less attention has been given to epigenetic research in livestock species in comparison to extensive work in humans and model organisms. Elucidating therefore the epigenetic determinants of animal diseases and complex traits may represent one of the principal challenges to use epigenetic markers for further improvement of animal productivity.
Ibeagha-Awemu, Eveline M.; Zhao, Xin
Improvement in animal productivity has been achieved over the years through careful breeding and selection programs. Today, variations in the genome are gaining increasing importance in livestock improvement strategies. Genomic information alone, however, explains only a part of the phenotypic variance in traits. It is likely that a portion of the unaccounted variance is embedded in the epigenome. The epigenome encompasses epigenetic marks such as DNA methylation, histone tail modifications, chromatin remodeling, and other molecules that can transmit epigenetic information such as non-coding RNA species. Epigenetic factors respond to external or internal environmental cues such as nutrition, pathogens, and climate, and have the ability to change gene expression leading to emergence of specific phenotypes. Accumulating evidence shows that epigenetic marks influence gene expression and phenotypic outcome in livestock species. This review examines available evidence of the influence of epigenetic marks on livestock (cattle, sheep, goat, and pig) traits and discusses the potential for consideration of epigenetic markers in livestock improvement programs. However, epigenetic research activities on farm animal species are currently limited partly due to lack of recognition, funding and a global network of researchers. Therefore, considerable less attention has been given to epigenetic research in livestock species in comparison to extensive work in humans and model organisms. Elucidating therefore the epigenetic determinants of animal diseases and complex traits may represent one of the principal challenges to use epigenetic markers for further improvement of animal productivity. PMID:26442116
Blandón-Díaz, J U; Widmark, A-K; Hannukkala, A; Andersson, B; Högberg, N; Yuen, J E
Late blight caused by Phytophthora infestans (Mont.) de Bary is a constraint to both potato and tomato crops in Nicaragua. The hypothesis that the Nicaraguan population of P. infestans is genotypically and phenotypically diverse and potentially subdivided based on host association was tested. A collection of isolates was analyzed using genotypic markers (microsatellites and mitochondrial DNA haplotype) and phenotypic markers (mating type, virulence, and fungicide sensitivity). The genotypic analysis revealed no polymorphism in 121 of 132 isolates of P. infestans tested. Only the Ia haplotype and the A2 mating type were detected. Most of the tested isolates were resistant to metalaxyl. The virulence testing showed variation among isolates of P. infestans. No evidence was found of population differentiation among potato and tomato isolates of P. infestans based on the genotypic and phenotypic analysis. We conclude that the Nicaraguan population of P. infestans consists of a single clonal lineage (NI-1) which belongs to the A2 mating type and the Ia mitochondrial DNA haplotype. Moreover, based on the markers used, this population of P. infestans does not resemble the population in countries from which potato seed is imported to Nicaragua or the population in neighboring countries. The data presented here indicate that the NI-1 clonal lineage is the primary pathogen on both potato and tomato, and its success on both host species is unique in a South American context.
Gould, B; Geber, M
Population genetic theory predicts that the availability of appropriate standing genetic variation should facilitate rapid evolution when species are introduced to new environments. However, few tests of rapid evolution have been paired with empirical surveys for the presence of previously identified adaptive genetic variants in natural populations. In this study, we examined local adaptation to soil Al toxicity in the introduced range of sweet vernal grass (Anthoxanthum odoratum), and we genotyped populations for the presence of Al tolerance alleles previously identified at the long-term ecological Park Grass Experiment (PGE, Harpenden, UK) in the species native range. We found that markers associated with Al tolerance at the PGE were present at appreciable frequency in introduced populations. Despite this, there was no strong evidence of local adaptation to soil Al toxicity among populations. Populations demonstrated significantly different intrinsic root growth rates in the absence of Al. This suggests that selection on correlated root growth traits may constrain the ability of populations to evolve significantly different root growth responses to Al. Our results demonstrate that genotype-phenotype associations may differ substantially between the native and introduced parts of a species range and that adaptive alleles from a native species range may not necessarily promote phenotypic differentiation in the introduced range.
Mattenberger, Florian; Sabater-Muñoz, Beatriz; Toft, Christina; Fares, Mario A.
Gene and genome duplication are the major sources of biological innovations in plants and animals. Functional and transcriptional divergence between the copies after gene duplication has been considered the main driver of innovations . However, here we show that increased phenotypic plasticity after duplication plays a more major role than thought before in the origin of adaptations. We perform an exhaustive analysis of the transcriptional alterations of duplicated genes in the unicellular eukaryote Saccharomyces cerevisiae when challenged with five different environmental stresses. Analysis of the transcriptomes of yeast shows that gene duplication increases the transcriptional response to environmental changes, with duplicated genes exhibiting signatures of adaptive transcriptional patterns in response to stress. The mechanism of duplication matters, with whole-genome duplicates being more transcriptionally altered than small-scale duplicates. The predominant transcriptional pattern follows the classic theory of evolution by gene duplication; with one gene copy remaining unaltered under stress, while its sister copy presents large transcriptional plasticity and a prominent role in adaptation. Moreover, we find additional transcriptional profiles that are suggestive of neo- and subfunctionalization of duplicate gene copies. These patterns are strongly correlated with the functional dependencies and sequence divergence profiles of gene copies. We show that, unlike singletons, duplicates respond more specifically to stress, supporting the role of natural selection in the transcriptional plasticity of duplicates. Our results reveal the underlying transcriptional complexity of duplicated genes and its role in the origin of adaptations. PMID:27799339
Mattenberger, Florian; Sabater-Muñoz, Beatriz; Toft, Christina; Fares, Mario A
Gene and genome duplication are the major sources of biological innovations in plants and animals. Functional and transcriptional divergence between the copies after gene duplication has been considered the main driver of innovations . However, here we show that increased phenotypic plasticity after duplication plays a more major role than thought before in the origin of adaptations. We perform an exhaustive analysis of the transcriptional alterations of duplicated genes in the unicellular eukaryote Saccharomyces cerevisiae when challenged with five different environmental stresses. Analysis of the transcriptomes of yeast shows that gene duplication increases the transcriptional response to environmental changes, with duplicated genes exhibiting signatures of adaptive transcriptional patterns in response to stress. The mechanism of duplication matters, with whole-genome duplicates being more transcriptionally altered than small-scale duplicates. The predominant transcriptional pattern follows the classic theory of evolution by gene duplication; with one gene copy remaining unaltered under stress, while its sister copy presents large transcriptional plasticity and a prominent role in adaptation. Moreover, we find additional transcriptional profiles that are suggestive of neo- and subfunctionalization of duplicate gene copies. These patterns are strongly correlated with the functional dependencies and sequence divergence profiles of gene copies. We show that, unlike singletons, duplicates respond more specifically to stress, supporting the role of natural selection in the transcriptional plasticity of duplicates. Our results reveal the underlying transcriptional complexity of duplicated genes and its role in the origin of adaptations.
Kim, Junghi; Bai, Yun; Pan, Wei
We study the problem of testing for single marker-multiple phenotype associations based on genome-wide association study (GWAS) summary statistics without access to individual-level genotype and phenotype data. For most published GWASs, because obtaining summary data is substantially easier than accessing individual-level phenotype and genotype data, while often multiple correlated traits have been collected, the problem studied here has become increasingly important. We propose a powerful adaptive test and compare its performance with some existing tests. We illustrate its applications to analyses of a meta-analyzed GWAS dataset with three blood lipid traits and another with sex-stratified anthropometric traits, and further demonstrate its potential power gain over some existing methods through realistic simulation studies. We start from the situation with only one set of (possibly meta-analyzed) genome-wide summary statistics, then extend the method to meta-analysis of multiple sets of genome-wide summary statistics, each from one GWAS. We expect the proposed test to be useful in practice as more powerful than or complementary to existing methods.
Yokoyama, Shozo; Tada, Takashi; Zhang, Huan; Britt, Lyle
Vertebrate ancestors appeared in a uniform, shallow water environment, but modern species flourish in highly variable niches. A striking array of phenotypes exhibited by contemporary animals is assumed to have evolved by accumulating a series of selectively advantageous mutations. However, the experimental test of such adaptive events at the molecular level is remarkably difficult. One testable phenotype, dim-light vision, is mediated by rhodopsins. Here, we engineered 11 ancestral rhodopsins and show that those in early ancestors absorbed light maximally (λmax) at 500 nm, from which contemporary rhodopsins with variable λmaxs of 480–525 nm evolved on at least 18 separate occasions. These highly environment-specific adaptations seem to have occurred largely by amino acid replacements at 12 sites, and most of those at the remaining 191 (≈94%) sites have undergone neutral evolution. The comparison between these results and those inferred by commonly-used parsimony and Bayesian methods demonstrates that statistical tests of positive selection can be misleading without experimental support and that the molecular basis of spectral tuning in rhodopsins should be elucidated by mutagenesis analyses using ancestral pigments. PMID:18768804
Barton, Michael D.; Petronio, Michael; Giarrizzo, Juan G.; Bowling, Bethany V.
Microbial adaptation to environmental conditions is a complex process, including acquisition of positive traits through horizontal gene transfer or the modification of existing genes through duplication and/or mutation. In this study, we examined the adaptation of a Pseudomonas fluorescens isolate (R124) from the nutrient-limited mineral environment of a silica cave in comparison with P. fluorescens isolates from surface soil and the rhizosphere. Examination of metal homeostasis gene pathways demonstrated a high degree of conservation, suggesting that such systems remain functionally similar across chemical environments. The examination of genomic islands unique to our strain revealed the presence of genes involved in carbohydrate metabolism, aromatic carbon metabolism, and carbon turnover, confirmed through phenotypic assays, suggesting the acquisition of potentially novel mechanisms for energy metabolism in this strain. We also identified a twitching motility phenotype active at low-nutrient concentrations that may allow alternative exploratory mechanisms for this organism in a geochemical environment. Two sets of candidate twitching motility genes are present within the genome, one on the chromosome and one on a plasmid; however, a plasmid knockout identified the functional gene as being present on the chromosome. This work highlights the plasticity of the Pseudomonas genome, allowing the acquisition of novel nutrient-scavenging pathways across diverse geochemical environments while maintaining a core of functional stress response genes. PMID:23995634
Salinas, Francisco; de Boer, Carl G; Abarca, Valentina; García, Verónica; Cuevas, Mara; Araos, Sebastian; Larrondo, Luis F; Martínez, Claudio; Cubillos, Francisco A
Linkage mapping studies in model organisms have typically focused their efforts in polymorphisms within coding regions, ignoring those within regulatory regions that may contribute to gene expression variation. In this context, differences in transcript abundance are frequently proposed as a source of phenotypic diversity between individuals, however, until now, little molecular evidence has been provided. Here, we examined Allele Specific Expression (ASE) in six F1 hybrids from Saccharomyces cerevisiae derived from crosses between representative strains of the four main lineages described in yeast. ASE varied between crosses with levels ranging between 28% and 60%. Part of the variation in expression levels could be explained by differences in transcription factors binding to polymorphic cis-regulations and to differences in trans-activation depending on the allelic form of the TF. Analysis on highly expressed alleles on each background suggested ASN1 as a candidate transcript underlying nitrogen consumption differences between two strains. Further promoter allele swap analysis under fermentation conditions confirmed that coding and non-coding regions explained aspartic and glutamic acid consumption differences, likely due to a polymorphism affecting Uga3 binding. Together, we provide a new catalogue of variants to bridge the gap between genotype and phenotype.
Sellers, R S; Clifford, C B; Treuting, P M; Brayton, C
Inbred laboratory mouse strains are highly divergent in their immune response patterns as a result of genetic mutations and polymorphisms. The generation of genetically engineered mice (GEM) has, in the past, used embryonic stem (ES) cells for gene targeting from various 129 substrains followed by backcrossing into more fecund mouse strains. Although common inbred mice are considered "immune competent," many have variations in their immune system-some of which have been described-that may affect the phenotype. Recognition of these immune variations among commonly used inbred mouse strains is essential for the accurate interpretation of expected phenotypes or those that may arise unexpectedly. In GEM developed to study specific components of the immune system, accurate evaluation of immune responses must take into consideration not only the gene of interest but also how the background strain and microbial milieu contribute to the manifestation of findings in these mice. This article discusses points to consider regarding immunological differences between the common inbred laboratory mouse strains, particularly in their use as background strains in GEM.
Salinas, Francisco; de Boer, Carl G.; Abarca, Valentina; García, Verónica; Cuevas, Mara; Araos, Sebastian; Larrondo, Luis F.; Martínez, Claudio; Cubillos, Francisco A.
Linkage mapping studies in model organisms have typically focused their efforts in polymorphisms within coding regions, ignoring those within regulatory regions that may contribute to gene expression variation. In this context, differences in transcript abundance are frequently proposed as a source of phenotypic diversity between individuals, however, until now, little molecular evidence has been provided. Here, we examined Allele Specific Expression (ASE) in six F1 hybrids from Saccharomyces cerevisiae derived from crosses between representative strains of the four main lineages described in yeast. ASE varied between crosses with levels ranging between 28% and 60%. Part of the variation in expression levels could be explained by differences in transcription factors binding to polymorphic cis-regulations and to differences in trans-activation depending on the allelic form of the TF. Analysis on highly expressed alleles on each background suggested ASN1 as a candidate transcript underlying nitrogen consumption differences between two strains. Further promoter allele swap analysis under fermentation conditions confirmed that coding and non-coding regions explained aspartic and glutamic acid consumption differences, likely due to a polymorphism affecting Uga3 binding. Together, we provide a new catalogue of variants to bridge the gap between genotype and phenotype. PMID:26898953
Mezquida, Eduardo T; Benkman, Craig W
Understanding the causes of variation in biotic interaction strength and phenotypic selection remains one of the outstanding goals of evolutionary ecology. Here we examine the variation in strength of interactions between two seed predators, common crossbills (Loxia curvirostra) and European red squirrels (Sciurus vulgaris), and mountain pine (Pinus uncinata) at and below tree limit in the Pyrenees, and how this translates into phenotypic selection. Seed predation by crossbills increased whereas seed predation by squirrels decreased with increasing elevation and as the canopy became more open. Overall, seed predation by crossbills averaged about twice that by squirrels, and the intensity of selection exerted by crossbills averaged between 2.6 and 7.5 times greater than by squirrels. The higher levels of seed predation by crossbills than squirrels were related to the relatively open nature of most of the forests, and the higher intensity of selection exerted by crossbills resulted from their higher levels of seed predation. However, most of the differences in selection intensity between crossbills and squirrels were the result of habitat features having a greater effect on the foraging behavior of squirrels than of crossbills, causing selection to be much lower for squirrels than for crossbills.
Zhang, Ke; Zhang, Li-Jie; Fang, Ya-Hong; Jin, Xin-Na; Qi, Lei; Wu, Xue-Chang; Zheng, Dao-Qiong
Genomic structural variation (GSV) is a ubiquitous phenomenon observed in the genomes of Saccharomyces cerevisiae strains with different genetic backgrounds; however, the physiological and phenotypic effects of GSV are not well understood. Here, we first revealed the genetic characteristics of a widely used industrial S. cerevisiae strain, ZTW1, by whole genome sequencing. ZTW1 was identified as an aneuploidy strain and a large-scale GSV was observed in the ZTW1 genome compared with the genome of a diploid strain YJS329. These GSV events led to copy number variations (CNVs) in many chromosomal segments as well as one whole chromosome in the ZTW1 genome. Changes in the DNA dosage of certain functional genes directly affected their expression levels and the resultant ZTW1 phenotypes. Moreover, CNVs of large chromosomal regions triggered an aneuploidy stress in ZTW1. This stress decreased the proliferation ability and tolerance of ZTW1 to various stresses, while aneuploidy response stress may also provide some benefits to the fermentation performance of the yeast, including increased fermentation rates and decreased byproduct generation. This work reveals genomic characters of the bioethanol S. cerevisiae strain ZTW1 and suggests that GSV is an important kind of mutation that changes the traits of industrial S. cerevisiae strains.
Moore, Wendy; Robertson, James A
Ant-nest beetles (Paussus) are the quintessential Trojan horses of the insect world. They hack the complex communication system of ants, allowing them to blend into the ant society and be treated as royalty, all the while preying upon the ants and the ants' brood and duping the ants into rearing their young. Here we present results of the first molecular-based phylogeny of ant-nest beetles, which reveals that this symbiosis has produced one of the most stunning examples of rapid adaptive radiation documented to date. The most recent ancestor of a Paussus clade endemic to Madagascar is only 2.6 million years old. This species gave rise to a remarkably phenotypically diverse clade of 86 extant species with a net diversification interval of 0.38-0.81 million years, a rate of radiation faster than classic textbook examples of large, recent, rapid radiations such as Anolis lizards on Caribbean islands, cichlids of the East African Great Lakes, finches on the Galápagos Islands, and Drosophila and tetragnathid spiders on the Hawaiian Islands. In order for Paussus to adapt to a new host ant species, the beetle's ability to perceive, deceive, and communicate with the new host must evolve quickly and in synchrony in both the larval and adult life stages, resulting in unusually strong selective pressure levied by their host ants. Data on host associations suggest that the history of host shifts may help explain both the striking phenotypic diversity within the Malagasy radiation and the evolution of phenotypically similar yet distantly related species in Madagascar and Africa.
Xu, Liang; Huber, Heidrun; During, Heinjo J; Dong, Ming; Anten, Niels P R
Shoot elongation is one of the main plastic responses of plants to burial, a ubiquitous stress factor in dry ecosystems. Yet, intraspecific variation in this response to burial and the extent to which this variation is functionally coordinated with variation in other trait responses are largely unknown. We subjected seedlings of the shrub Caragana intermedia from 18 maternal parents (i.e. different half-sib families) to repeated partial burial to investigate how burial affects shoot growth, stem mechanical traits and associated plasticity. Burial increased both stem elongation and diameter growth of plants, but decreased biomass production. Half-sib families had different rates of shoot elongation, and differed in their response to burial with respect to biomechanical stem properties. Across half-sib families, the magnitude of these responses in mechanical traits was positively correlated with the magnitude of the stem elongation response. These results indicate that plasticity in different stem traits in response to sand burial and intraspecific variation therein are functionally coordinated with respect to mechanical stability. The results emphasize the importance of considering functionally coordinated traits when analyzing phenotypic plasticity in plants.
Liu, Hanmei; Wang, Xuewen; Wei, Bin; Wang, Yongbin; Liu, Yinghong; Zhang, Junjie; Hu, Yufeng; Yu, Guowu; Li, Jian; Xu, Zhanbin; Huang, Yubi
In southwest China, some maize landraces have long been isolated geographically, and have phenotypes that differ from those of widely grown cultivars. These landraces may harbor rich genetic variation responsible for those phenotypes. Four-row Wax is one such landrace, with four rows of kernels on the cob. We resequenced the genome of Four-row Wax, obtaining 50.46 Gb sequence at 21.87× coverage, then identified and characterized 3,252,194 SNPs, 213,181 short InDels (1-5 bp) and 39,631 structural variations (greater than 5 bp). Of those, 312,511 (9.6%) SNPs were novel compared to the most detailed haplotype map (HapMap) SNP database of maize. Characterization of variations in reported kernel row number (KRN) related genes and KRN QTL regions revealed potential causal mutations in fea2, td1, kn1, and te1. Genome-wide comparisons revealed abundant genetic variations in Four-row Wax, which may be associated with environmental adaptation. The sequence and SNP variations described here enrich genetic resources of maize, and provide guidance into study of seed numbers for crop yield improvement.
Anderson, Jill T.; Inouye, David W.; McKinney, Amy M.; Colautti, Robert I.; Mitchell-Olds, Tom
Anthropogenic climate change has already altered the timing of major life-history transitions, such as the initiation of reproduction. Both phenotypic plasticity and adaptive evolution can underlie rapid phenological shifts in response to climate change, but their relative contributions are poorly understood. Here, we combine a continuous 38 year field survey with quantitative genetic field experiments to assess adaptation in the context of climate change. We focused on Boechera stricta (Brassicaeae), a mustard native to the US Rocky Mountains. Flowering phenology advanced significantly from 1973 to 2011, and was strongly associated with warmer temperatures and earlier snowmelt dates. Strong directional selection favoured earlier flowering in contemporary environments (2010–2011). Climate change could drive this directional selection, and promote even earlier flowering as temperatures continue to increase. Our quantitative genetic analyses predict a response to selection of 0.2 to 0.5 days acceleration in flowering per generation, which could account for more than 20 per cent of the phenological change observed in the long-term dataset. However, the strength of directional selection and the predicted evolutionary response are likely much greater now than even 30 years ago because of rapidly changing climatic conditions. We predict that adaptation will likely be necessary for long-term in situ persistence in the context of climate change. PMID:22787021
Oliveira, V M; Hamawaki, O T; Nogueira, A O; Sousa, L B; Santos, F M; Hamawaki, R L
Advances in genetic enhancement techniques have led to an increase in soybean production. Thus, soybean is currently one the most economically important cultured species worldwide. The objectives of the present study were to study the interaction of soybean genotypes per environment in terms of grain productivity and to evaluate their phenotypic adaptability and stability, with the final aim of selecting lineages with high productivity, wide adaptability, and high stability. Seven soybean genotypes, consisting of five lineages developed by the soybean genetic enhancement program of the Universidade Federal de Uberlândia (Brazil) and two controls, were evaluated during several annual cycles in seven different environments. A randomized complete block design (RCBD) with three replicates was adopted in each site. This study followed the methodology proposed by Eberhart and Russel and Lin and Binns, with modifications by Carneiro, and the AMMI (additive main effects and multiplicative interaction model) analysis. The average productivity of soybean cultivars in the trials was 2739.26 kg/ha. The L01V13 genotype and the UFUS Guarani cultivar had wide adaptation according to the methodology proposed by Eberhart and Russel and Lin and Binns, with modifications by Carneiro. When analyzed with the AMMI model, the UFUS Guarani cultivar showed high stability. In general, the methodologies studied are complementary and, when used together, increase the reliability of the classification, providing support for the use of specific soybean cultivars in different environments.
Corrêa, A M; Teodoro, P E; Gonçalves, M C; Barroso, L M A; Nascimento, M; Santos, A; Torres, F E
This study used Bayesian inference to investigate the genotype x environment interaction in common bean grown in Mato Grosso do Sul State, and it also evaluated the efficiency of using informative and minimally informative a priori distributions. Six trials were conducted in randomized blocks, and the grain yield of 13 common bean genotypes was assessed. To represent the minimally informative a priori distributions, a probability distribution with high variance was used, and a meta-analysis concept was adopted to represent the informative a priori distributions. Bayes factors were used to conduct comparisons between the a priori distributions. The Bayesian inference was effective for the selection of upright common bean genotypes with high adaptability and phenotypic stability using the Eberhart and Russell method. Bayes factors indicated that the use of informative a priori distributions provided more accurate results than minimally informative a priori distributions. According to Bayesian inference, the EMGOPA-201, BAMBUÍ, CNF 4999, CNF 4129 A 54, and CNFv 8025 genotypes had specific adaptability to favorable environments, while the IAPAR 14 and IAC CARIOCA ETE genotypes had specific adaptability to unfavorable environments.
Anderson, Jill T; Inouye, David W; McKinney, Amy M; Colautti, Robert I; Mitchell-Olds, Tom
Anthropogenic climate change has already altered the timing of major life-history transitions, such as the initiation of reproduction. Both phenotypic plasticity and adaptive evolution can underlie rapid phenological shifts in response to climate change, but their relative contributions are poorly understood. Here, we combine a continuous 38 year field survey with quantitative genetic field experiments to assess adaptation in the context of climate change. We focused on Boechera stricta (Brassicaeae), a mustard native to the US Rocky Mountains. Flowering phenology advanced significantly from 1973 to 2011, and was strongly associated with warmer temperatures and earlier snowmelt dates. Strong directional selection favoured earlier flowering in contemporary environments (2010-2011). Climate change could drive this directional selection, and promote even earlier flowering as temperatures continue to increase. Our quantitative genetic analyses predict a response to selection of 0.2 to 0.5 days acceleration in flowering per generation, which could account for more than 20 per cent of the phenological change observed in the long-term dataset. However, the strength of directional selection and the predicted evolutionary response are likely much greater now than even 30 years ago because of rapidly changing climatic conditions. We predict that adaptation will likely be necessary for long-term in situ persistence in the context of climate change.
Ching, Carly; Gozzi, Kevin; Heinemann, Björn; Chai, Yunrong; Godoy, Veronica G
In the nosocomial opportunistic pathogen Acinetobacter baumannii, RecA-dependent mutagenesis, which causes antibiotic resistance acquisition, is linked to the DNA damage response (DDR). Notably, unlike the Escherichia coli paradigm, recA and DDR gene expression in A. baumannii are bimodal. Namely, there is phenotypic variation upon DNA damage, which may provide a bet-hedging strategy for survival. Thus, understanding recA gene regulation is key to elucidate the yet unknown DDR regulation in A. baumannii Here, we identify a structured 5' Untranslated Region (5' UTR) in the recA transcript which serves as a cis-regulatory element. We show that a predicted stem-loop structure in this 5' UTR affects mRNA half-life and underlies bimodal gene expression and thus phenotypic variation in response to ciprofloxacin treatment. We furthermore show that the stem-loop structure of the recA 5' UTR influences intracellular RecA protein levels and, in vivo, impairing the formation of the stem-loop structure of the recA 5' UTR lowers cell survival to UV treatment and decreases rifampicin resistance acquisition from DNA damage-induced mutagenesis. We hypothesize that the 5' UTR allows for stable recA transcripts during stress, including antibiotic treatment, enabling cells to maintain suitable RecA levels for survival. This innovative strategy to regulate the DDR in A. baumannii may contribute to its success as a pathogen.ImportanceAcinetobacter baumannii is an opportunistic pathogen quickly gaining antibiotic resistances. Mutagenesis and antibiotic resistance acquisition are linked to the DNA damage response (DDR). However, how the DDR is regulated in A. baumannii remains unknown, since unlike most bacteria, A. baumannii does not follow the regulation of the Escherichia coli paradigm. Here, we have started to uncover the mechanisms regulating the novel A. baumannii DDR. We have found that a cis-acting 5' UTR regulates recA transcript stability, RecA protein levels, and DNA damage
Glew, M. D.; Browning, Glenn F.; Markham, Philip F.; Walker, Ian D.
Chickens were infected with a pathogenic strain of Mycoplasma gallisepticum, and the expression of pMGA, the major surface protein, was inferred by examination of colonies from ex vivo cells. Within 2 days postinfection, 40% of cells had ceased the expression of the original pMGA surface protein (pMGA1.1), and by day 6, the majority of recovered cells were in this category. The switch in pMGA phenotype which had occurred in vivo was reversible, since most colonies produced from ex vivo progenitors exhibited frequent pMGA1.1+ sectors. After prolonged in vivo habitation, increasing proportions of recovered cells gave rise to variant pMGA colonies which had switched from the expression of pMGA1.1 to another gene, pMGA1.2, concomitant with the acquisition of a (GAA)12 motif 5′ to its promoter. Collectively, the results suggest that changes in M. gallisepticum pMGA gene expression in vivo are normal, common, and possibly obligate events for successful colonization of the host. Surprisingly, the initial cessation of pMGA1.1 expression occurred in the absence of detectable pMGA antibodies and seemed to precede the adaptive immune response. PMID:10992515
Audí, Laura; Mullis, Primus E.; Moreno, Francisca; González Casado, Isabel; López-Siguero, Juan Pedro; Corripio, Raquel; Bermúdez de la Vega, José Antonio; Blanco, José Antonio; Flück, Christa E.
MAMLD1 is thought to cause disordered sex development in 46,XY patients. But its role is controversial because some MAMLD1 variants are also detected in normal individuals, several MAMLD1 mutations have wild-type activity in functional tests, and the male Mamld1-knockout mouse has normal genitalia and reproduction. Our aim was to search for MAMLD1 variations in 108 46,XY patients with disordered sex development, and to test them functionally. We detected MAMDL1 variations and compared SNP frequencies in controls and patients. We tested MAMLD1 transcriptional activity on promoters involved in sex development and assessed the effect of MAMLD1 on androgen production. MAMLD1 expression in normal steroid-producing tissues and mutant MAMLD1 protein expression were also assessed. Nine MAMLD1 mutations (7 novel) were characterized. In vitro, most MAMLD1 variants acted similarly to wild type. Only the L210X mutation showed loss of function in all tests. We detected no effect of wild-type or MAMLD1 variants on CYP17A1 enzyme activity in our cell experiments, and Western blots revealed no significant differences for MAMLD1 protein expression. MAMLD1 was expressed in human adult testes and adrenals. In conclusion, our data support the notion that MAMLD1 sequence variations may not suffice to explain the phenotype in carriers and that MAMLD1 may also have a role in adult life. PMID:26580071
Mulder, Han A; Gienapp, Philip; Visser, Marcel E
Variation in traits is essential for natural selection to operate and genetic and environmental effects can contribute to this phenotypic variation. From domesticated populations, we know that families can differ in their level of within-family variance, which leads to the intriguing situation that within-family variance can be heritable. For offspring traits, such as birth weight, this implies that within-family variance in traits can vary among families and can thus be shaped by natural selection. Empirical evidence for this in wild populations is however lacking. We investigated whether within-family variance in fledging weight is heritable in a wild great tit (Parus major) population and whether these differences are associated with fitness. We found significant evidence for genetic variance in within-family variance. The genetic coefficient of variation (GCV) was 0.18 and 0.25, when considering fledging weight a parental or offspring trait, respectively. We found a significant quadratic relationship between within-family variance and fitness: families with low or high within-family variance had lower fitness than families with intermediate within-family variance. Our results show that within-family variance can respond to selection and provides evidence for stabilizing selection on within-family variance.
Miyatake, Takahisa; Katayama, Kohji; Takeda, Yukari; Nakashima, Akiko; Sugita, Atsushi; Mizumoto, Makoto
The adaptation of death-feigning (thanatosis), a subject that has been overlooked in evolutionary biology, was inferred in a model prey-and-predator system. We studied phenotypic variation among individuals, fitness differences, and the inheritance of death-feigning behaviour in the red flour beetle, Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae). Two-way artificial selections for the duration of death-feigning, over 10 generations, showed a clear direct response in the trait and a correlated response in the frequency of death-feigning, thus indicating variation and inheritance of death-feigning behaviour. A comparison of the two selected strains with divergent frequencies of death-feigning showed a significant difference in the fitness for survival when a model predator, a female Adanson jumper spider, Hasarius adansoni Audouin (Araneomophae: Salticidae), was presented to the beetles. The frequency of predation was lower among beetles from strains selected for long-duration than among those for short-duration death-feigning. The results indicate the possibility of the evolution of death-feigning under natural selection.
Fisher, Lorraine H. C.; Han, Jiwan; Corke, Fiona M. K.; Akinyemi, Aderemi; Didion, Thomas; Nielsen, Klaus K.; Doonan, John H.; Mur, Luis A. J.; Bosch, Maurice
Drought is an important environmental stress limiting the productivity of major crops worldwide. Understanding drought tolerance and possible mechanisms for improving drought resistance is therefore a prerequisite to develop drought-tolerant crops that produce significant yields with reduced amounts of water. Brachypodium distachyon (Brachypodium) is a key model species for cereals, forage grasses, and energy grasses. In this study, initial screening of a Brachypodium germplasm collection consisting of 138 different ecotypes exposed to progressive drought, highlighted the natural variation in morphology, biomass accumulation, and responses to drought stress. A core set of ten ecotypes, classified as being either tolerant, susceptible or intermediate, in response to drought stress, were exposed to mild or severe (respectively, 15 and 0% soil water content) drought stress and phenomic parameters linked to growth and color changes were assessed. When exposed to severe drought stress, phenotypic data and metabolite profiling combined with multivariate analysis revealed a remarkable consistency in separating the selected ecotypes into their different pre-defined drought tolerance groups. Increases in several metabolites, including for the phytohormones jasmonic acid and salicylic acid, and TCA-cycle intermediates, were positively correlated with biomass yield and with reduced yellow pixel counts; suggestive of delayed senescence, both key target traits for crop improvement to drought stress. While metabolite analysis also separated ecotypes into the distinct tolerance groupings after exposure to mild drought stress, similar analysis of the phenotypic data failed to do so, confirming the value of metabolomics to investigate early responses to drought stress. The results highlight the potential of combining the analyses of phenotypic and metabolic responses to identify key mechanisms and markers associated with drought tolerance in both the Brachypodium model plant as
Sadeh, Naomi; Wolf, Erika J.; Logue, Mark W.; Hayes, Jasmeet P.; Stone, Annjanette; Griffin, L. Michelle; Schichman, Steven A.; Miller, Mark W.
Background "DNA methylation of the SKA2 gene has recently been implicated as a biomarker of suicide risk and posttraumatic stress disorder (PTSD). To examine the specificity and reliability of these findings, we examined associations between SKA2 DNA methylation, broad dimensions of psychiatric symptoms, and suicide phenotypes in adults with high levels of trauma exposure. Methods A total of 466 White, non-Hispanic veterans and their intimate partners (65% male) underwent clinical assessment and had blood drawn for genotyping and methylation analysis. DNA methylation of the CpG locus cg13989295 and genotype at the methylation-associated single-nucleotide polymorphism (SNP) rs7208505 were examined in relation to current and lifetime PTSD, internalizing and externalizing psychopathology, and suicide phenotypes (ideation, plans, and attempts). Results DNA methylation at the previously implicated SKA2 CpG locus (cg13989295) was associated with current and lifetime symptoms of internalizing (but not externalizing) disorders. SKA2 methylation levels also predicted higher rates of current suicidal thoughts and behaviors, even after including well-established psychiatric risk factors for suicide in the model. Associations between PTSD and SKA2 were not significant, and genetic variation at the methylation-associated SNP (rs7208505) was not related to any of the phenotypes examined. Conclusions SKA2 methylation may index a general propensity to experience stress-related psychopathology, including internalizing disorders and suicidal thoughts and behaviors. This study demonstrates that SKA2 methylation levels explain unique variance in suicide risk not captured by clinical symptom interviews, providing further evidence of its potential utility as a biomarker of suicide risk and stress-related psychopathology. PMID:27038412
Eskin-Schwartz, Marina; Basel-Vanagaite, Lina; David, Michael; Lagovsky, Irina; Ben-Amitai, Dan; Smirin-Yosef, Pola; Atzmony, Lihi; Hodak, Emmilia
Psoriasis is a multifactorial chronic inflammatory disease. Monogenic psoriasis has been described recently, including dominantly inherited plaque and generalized pustular types, related to activating mutations in the CARD14 gene. We describe here a family with CARD14-related psoriasis, exhibiting an extreme variability of clinical presentation (from mild plaque-type to generalized pustular psoriasis) and early disease onset. The affected family members harboured the c.349G>A [p.Gly117Ser] mutation in CARD14, which has not previously been linked to pustular psoriatic phenotype. Furthermore, most severely affected individuals carried 3 additional CARD14 coding region polymorphisms (rs2066964, rs34367357 and rs11652075), suggesting their possible effect on disease expression. Early-onset psoriasis co-segregated with the HLA-C*0602, indicating that HLA-C*0602 could potentially modulate the time of disease onset. In summary, this paper describes a family with CARD14-related psoriasis and discusses the possible influence of the specific haplotypes on intra-familial variation in the clinical phenotype of the disease.
García-Rodríguez, Yolanda Magdalena; Torres-Gurrola, Guadalupe; Meléndez-González, Claudio; Espinosa-García, Francisco J
The Hass avocado tree Persea americana cv. Hass was derived from a single hybrid tree of P. americana var. drymifolia and P. americana var. guatemalensis, and it is propagated clonally by grafting. This cultivar is the most widely planted in the world but its profile of secondary metabolites has been studied rarely despite of its importance in plant protection. We illustrate the variability of the volatilome of mature leaves by describing the average chemical composition and the phenotypic variability found in 70 trees. Contrary to the uniformity expected in the Hass cultivar, high variability coefficients were found for most of the 36 detected foliar volatile compounds; furthermore we found six chemotypes grouping the foliar phenotypes of the sampled trees using hierarchical cluster analysis. About 48% of trees were grouped in one chemotype; five chemotypes grouped the remaining trees. The compounds that determined these chemotypes were: estragole, α-farnesene, β-caryophyllene, germacrene D, α-cubebene and eugenol. This striking variation in a cultivar propagated clonally is discussed in terms of somatic mutation.
Rodríguez, Juan G.; Hernández, Adriana C.; Helguera-Repetto, Cecilia; Aguilar Ayala, Diana; Guadarrama-Medina, Rosalina; Anzóla, Juan M.; Bustos, Jose R.; Zambrano, María M.; González-y-Merchand, Jorge
ABSTRACT Strong evidence supports the idea that fatty acids rather than carbohydrates are the main energy source of Mycobacterium tuberculosis during infection and latency. Despite that important role, a complete scenario of the bacterium’s metabolism when lipids are the main energy source is still lacking. Here we report the development of an in vitro model to analyze adaptation of M. tuberculosis during assimilation of long-chain fatty acids as sole carbon sources. The global lipid transcriptome revealed a shift toward the glyoxylate cycle, the overexpression of main regulators whiB3, dosR, and Rv0081, and the increased expression of several genes related to reductive stress. Our evidence showed that lipid storage seems to be the selected mechanism used by M. tuberculosis to ameliorate the assumed damage of reductive stress and that concomitantly the bacilli acquired a slowed-growth and drug-tolerant phenotype, all characteristics previously associated with the dormant stage. Additionally, intergenic regions were also detected, including the unexpected upregulation of tRNAs that suggest a new role for these molecules in the acquisition of a drug-tolerant phenotype by dormant bacilli. Finally, a set of lipid signature genes for the adaptation process was also identified. This in vitro model represents a suitable condition to illustrate the participation of reductive stress in drugs’ activity against dormant bacilli, an aspect scarcely investigated to date. This approach provides a new perspective to the understanding of latent infection and suggests the participation of previously undetected molecules. PMID:24846381
Vedder, Oscar; Bouwhuis, Sandra; Sheldon, Ben C
Predictions about the fate of species or populations under climate change scenarios typically neglect adaptive evolution and phenotypic plasticity, the two major mechanisms by which organisms can adapt to changing local conditions. As a consequence, we have little understanding of the scope for organisms to track changing environments by in situ adaptation. Here, we use a detailed individual-specific long-term population study of great tits (Parus major) breeding in Wytham Woods, Oxford, UK to parameterise a mechanistic model and thus directly estimate the rate of environmental change to which in situ adaptation is possible. Using the effect of changes in early spring temperature on temporal synchrony between birds and a critical food resource, we focus in particular on the contribution of phenotypic plasticity to population persistence. Despite using conservative estimates for evolutionary and reproductive potential, our results suggest little risk of population extinction under projected local temperature change; however, this conclusion relies heavily on the extent to which phenotypic plasticity tracks the changing environment. Extrapolating the model to a broad range of life histories in birds suggests that the importance of phenotypic plasticity for adjustment to projected rates of temperature change increases with slower life histories, owing to lower evolutionary potential. Understanding the determinants and constraints on phenotypic plasticity in natural populations is thus crucial for characterising the risks that rapidly changing environments pose for the persistence of such populations.
Vedder, Oscar; Bouwhuis, Sandra; Sheldon, Ben C.
Predictions about the fate of species or populations under climate change scenarios typically neglect adaptive evolution and phenotypic plasticity, the two major mechanisms by which organisms can adapt to changing local conditions. As a consequence, we have little understanding of the scope for organisms to track changing environments by in situ adaptation. Here, we use a detailed individual-specific long-term population study of great tits (Parus major) breeding in Wytham Woods, Oxford, UK to parameterise a mechanistic model and thus directly estimate the rate of environmental change to which in situ adaptation is possible. Using the effect of changes in early spring temperature on temporal synchrony between birds and a critical food resource, we focus in particular on the contribution of phenotypic plasticity to population persistence. Despite using conservative estimates for evolutionary and reproductive potential, our results suggest little risk of population extinction under projected local temperature change; however, this conclusion relies heavily on the extent to which phenotypic plasticity tracks the changing environment. Extrapolating the model to a broad range of life histories in birds suggests that the importance of phenotypic plasticity for adjustment to projected rates of temperature change increases with slower life histories, owing to lower evolutionary potential. Understanding the determinants and constraints on phenotypic plasticity in natural populations is thus crucial for characterising the risks that rapidly changing environments pose for the persistence of such populations. PMID:23874152
Goldstein, J.; Braverman, M.; Salafia, C.; Buckley, P.
The antigenic phenotype of human villous stromal macrophages (M phi s) from first and third trimester placentas was analyzed using a large number of monoclonal antibodies (MAbs) to monocyte (Mo)/M phi-associated cell membrane determinants. The purpose of this study was to investigate M phi phenotypic heterogeneity to create a database for the correlation of M phi phenotype with specific immunologic functions. The results showed that villous stromal mononuclear cells express many cell surface antigens found on Mo and M phi s and that they are morphologically diverse, ranging in appearance from classic Hofbauer cells to spindle-shaped cells with long cytoplasmic processes. Villous stromal M phi s were the numerically dominant cell type in this structure and exhibited some major phenotypic differences from M phi s in other tissues. Comparison of first- and third-trimester placentas revealed variation in antigen expression with increasing gestational age, in particular of class II major histocompatibility complex (MHC) determinants: HLA-DR and HLA-DP antigen density was low on first-trimester villous M phi s and much higher on third-trimester M phi s while HLA-DQ was undetectable in the first trimester but present on cells in third trimester placentas. The CD1 (T6) antigen, found on Langerhans (LH) cells and cortical thymocytes, was detected on villous M phi s by two thirds of the MAbs directed against different epitopes on this determinant. Furthermore, comparison with similar studies of lymphoid tissues showed that villous M phi s and dendritic cells share the expression of a number of other cell surface antigens. Finally, it was shown that M phi s in first- and third-trimester villi exhibit strong reactivity with MAbs (Leu 3a,b) to the CD4 antigen that serves as the receptor for the human immunodeficiency virus (HIV), suggesting that these cells may be a portal of entry or reservoir for this virus in the fetuses of pregnant, HIV+ women. Images Figure 1 Figure 1 PMID
Turapov, Obolbek; O'Connor, Benjamin D.; Sarybaeva, Asel A.; Williams, Caroline; Patel, Hemu; Kadyrov, Abdullaat S.; Sarybaev, Akpay S.; Woltmann, Gerrit; Barer, Michael R.
Tuberculous sputum contains multiple Mycobacterium tuberculosis populations with different requirements for isolation in vitro. These include cells that form colonies on solid media (plateable M. tuberculosis), cells requiring standard liquid medium for growth (nonplateable M. tuberculosis), and cells requiring supplementation of liquid medium with culture supernatant (SN) for growth (SN-dependent M. tuberculosis). Here, we describe protocols for the cryopreservation and direct assessment of antimicrobial tolerance of these M. tuberculosis populations within sputum. Our results show that first-line drugs achieved only modest bactericidal effects on all three populations over 7 days (1 to 2.5 log10 reductions), and SN-dependent M. tuberculosis was more tolerant to streptomycin and isoniazid than the plateable and nonplateable M. tuberculosis strains. Susceptibility of plateable M. tuberculosis to bactericidal drugs was significantly increased after passage in vitro; thus, tolerance observed in the sputum samples from the population groups was likely associated with mycobacterial adaptation to the host environment at some time prior to expectoration. Our findings support the use of a simple ex vivo system for testing drug efficacies against mycobacteria that have phenotypically adapted during tuberculosis infection. PMID:26883695
Porlier, Melody; Charmantier, Anne; Bourgault, Patrice; Perret, Philippe; Blondel, Jacques; Garant, Dany
1. Phenotypic plasticity, the response of individual phenotypes to their environment, can allow organisms to cope with spatio-temporal variation in environmental conditions. Recent studies have shown that variation exists among individuals in their capacity to adjust their traits to environmental changes and that this individual plasticity can be under strong selection. Yet, little is known on the extent and ultimate causes of variation between populations and individuals in plasticity patterns. 2. In passerines, timing of breeding is a key life-history trait strongly related to fitness and is known to vary with the environment, but few studies have investigated the within-species variation in individual plasticity. 3. Here, we studied between- and within-population variation in breeding time, phenotypic plasticity and selection patterns for this trait in four Mediterranean populations of blue tits (Cyanistes caeruleus) breeding in habitats varying in structure and quality. 4. Although there was no significant warming over the course of the study, we found evidence for earlier onset of breeding in warmer years in all populations, with reduced plasticity in the less predictable environment. In two of four populations, there was significant inter-individual variation in plasticity for laying date. Interestingly, selection for earlier laying date was significant only in populations where there was no inter-individual differences in plasticity. 5. Our results show that generalization of plasticity patterns among populations of the same species might be challenging even at a small spatial scale and that the amount of within-individual variation in phenotypic plasticity may be linked to selective pressures acting on these phenotypic traits.
Ebel, Gregory D; Carricaburu, Justin; Young, David; Bernard, Kristen A; Kramer, Laura D
West Nile virus (WNV) strains circulating during the first five years of WNV transmission in New York were collected, partial nucleotide sequences were determined, and in vitro and in vivo phenotypic analyses of selected strains were undertaken to determine whether observed increases in the intensity of enzootic and epidemic transmission in New York State during 2002 and 2003 were associated with viral genetic changes. Functionally diverse regions of the WNV genome were also compared to determine whether some regions may be more or less variable than others. The complete envelope coding regions of 67 strains and fragments of the nonstructural protein 5 (NS5) and 3' noncoding regions of 39 strains collected during 2002 and 2003 were examined. West Nile virus in New York remains relatively genetically homogeneous. Viral genetic diversity was greater in 2002 and 2003 at both the nucleotide and amino acid levels than in previous years due to the emergence of a new WNV genotype in 2002. This genotype persisted and became dominant in 2003. Envelope and NS5 coding regions were approximately two-fold more likely than the 3' untranslated region to contain nucleotide substitutions, and the envelope region was approximately three-fold more likely to contain amino acid substitutions than the NS5 region. Variation was noted in in vivo mosquito transmission assays, but not in in vitro growth studies. Strains belonging to the epizootiologically dominant clade were transmitted after approximately two fewer days of extrinsic incubation, providing a possible mechanism for the dominance of this clade. The observed increase in the intensity of WNV transmission beginning in 2002 was associated with an increase in viral genetic diversity that was the result of the emergence of an additional phylogenetic clade. This genotype seems to possess an advantage over previously recognized WNV strains in mosquito transmission phenotype.
Lemons, Christopher J.; King, Seth A.; Davidson, Kimberly A.; Puranik, Cynthia S.; Fulmer, Deborah; Mrachko, Alicia A.; Partanen, Jane; Al Otaiba, Stephanie; Fidler, Deborah J.
Many children with Down syndrome demonstrate deficits in phonological awareness, a prerequisite to learning to read in an alphabetic language. The purpose of this study was to determine whether adapting a commercially available phonological awareness program to better align with characteristics associated with the behavioral phenotype of Down…
Wu, Tong; Shi, Yaoyao; Liu, Youwen; He, Chongjun
An adaptive total variation method based on the combination of speckle statistics and total variation restoration is proposed and developed for reducing speckle noise in optical coherence tomography (OCT) images. The statistical distribution of the speckle noise in OCT image is investigated and measured. With the measured parameters such as the mean value and variance of the speckle noise, the OCT image is restored by the adaptive total variation restoration method. The adaptive total variation restoration algorithm was applied to the OCT images of a volunteer's hand skin, which showed effective speckle noise reduction and image quality improvement. For image quality comparison, the commonly used median filtering method was also applied to the same images to reduce the speckle noise. The measured results demonstrate the superior performance of the adaptive total variation restoration method in terms of image signal-to-noise ratio, equivalent number of looks, contrast-to-noise ratio, and mean square error.
BERGLAND, ALAN O.; TOBLER, RAY; GONZÁLEZ, JOSEFA; SCHMIDT, PAUL; PETROV, DMITRI
Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by both historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome-wide among populations of Drosophila melanogaster sampled in North America and Australia. We contrast patterns of clinal variation in these continents with patterns of differentiation among ancestral European and African populations. Using established and novel methods we derive here, we show that recently derived North America and Australia populations were likely founded by both European and African lineages and that this hybridization event likely contributed to genome-wide patterns of parallel clinal variation between continents. The pervasive effects of admixture mean that differentiation at only several hundred loci can be attributed to the operation of spatially varying selection using an FST outlier approach. Our results provide novel insight into the well-studied system of clinal differentiation in D. melanogaster and provide a context for future studies seeking to identify loci contributing to local adaptation in a wide variety of organisms, including other invasive species as well as temperate endemics. PMID:26547394
Li, Yan; Wu, Dong-Dong; Boyko, Adam R; Wang, Guo-Dong; Wu, Shi-Fang; Irwin, David M; Zhang, Ya-Ping
With the assistance of their human companions, dogs have dispersed into new environments during the expansion of human civilization. Tibetan Mastiff (TM), a native of the Tibetan Plateau, was derived from the domesticated Chinese native dog and, like Tibetans, has adapted to the extreme environment of high altitude. Here, we genotyped genome-wide single-nucleotide polymorphisms (SNPs) from 32 TMs and compared them with SNPs from 20 Chinese native dogs and 14 gray wolves (Canis lupus). We identified 16 genes with signals of positive selection in the TM, with 12 of these candidate genes associated with functions that have roles in adaptation to high-altitude adaptation, such as EPAS1, SIRT7, PLXNA4, and MAFG that have roles in responses to hypoxia. This study provides important information on the genetic diversity of the TM and potential mechanisms for adaptation to hypoxia.
Appels, R; Barrero, R; Bellgard, M
Advances in our understanding of genome structure provide consistent evidence for the existence of a core genome representing species classically defined by phenotype, as well as conditionally dispensable components of the genome that shows extensive variation between individuals of a given species. Generally, conservation of phenotypic features between species reflects conserved features of the genome; however, this is evidently not necessarily always the case as demonstrated by the analysis of the tunicate chordate Oikopleura dioica. In both plants and animals, the methylation activity of DNA and histones continues to present new variables for modifying (eventually) the phenotype of an organism and provides for structural variation that builds on the point mutations, rearrangements, indels, and amplification of retrotransposable elements traditionally considered. The translation of the advances in the structure/function analysis of the genome to industry is facilitated through the capture of research outputs in "toolboxes" that remain accessible in the public domain.
Dermo disease impacts nearly every region where oysters are cultured in the Eastern U.S. and is a significant concern to industry stakeholders. Efforts to breed for Dermo resistance in the Eastern Oyster have had modest success, yet the range of existing phenotypic variation with respect to Dermo r...
Dermo disease impacts nearly every region where oysters are cultured in the Eastern U.S. and is a significant concern to industry stakeholders. Efforts to breed for Dermo resistance in the Eastern Oyster have had modest success, yet the range of existing phenotypic variation with respect to Dermo ...
Ground-level ozone reduces yield in crops such as soybean (Glycine max (L.) Merr.). Phenotypic variation has been observed for this trait in multiple species; however, breeding for ozone tolerance has been limited. A recombinant inbred population was developed from soybean genotypes differing in tol...
Tsujii, Yuki; Onoda, Yusuke; Izuno, Ayako; Isagi, Yuji; Kitayama, Kanehiro
Metrosideros polymorpha, a dominant tree species in the Hawaiian Islands, shows an extreme phenotypic polymorphism both across gradients of climatic/edaphic conditions and within populations, making it a potentially useful model species for evolutionary study. In order to understand how the phenotypic diversity is maintained within populations as well as across populations, we examined the diversities of several leaf and stem functional traits across five elevations and two soil substrates on the volcanic mountain of Mauna Loa, on the island of Hawaii. Leaf dry mass per area (LMA), a key leaf functional trait, was particularly focused on and analyzed in relation to its underlying components-namely, tissue LMA and trichome LMA (LMA = tissue LMA + trichome LMA). Across populations, tissue LMA increased linearly with elevation while trichome LMA showed unimodal patterns with elevation, which were better correlated with temperature and rainfall, respectively. Substantial phenotypic variations were also found within populations. Interestingly, the variations of tissue LMA were often negatively correlated to trichome LMA within populations, which contrasts with the cross-populations pattern, where a strong positive correlation between tissue LMA and trichome LMA was found. This suggests that phenotypic variations within populations were substantially influenced by local ecological processes. Soil depth (an indicator of local water availability) and tree size (an indicator of colonized timing) modestly explained the within-population variations, implying other local environmental factors and/or random processes are also important in local phenotypic diversity. This study provides an insight about how phenotypic diversity of plant species is maintained from local to landscape levels.
Semlitsch, R.D.; Gibbons, J.W.
Phenotypic variation in metamorphosis and paedomorphosis in the salamander Ambystoma talpoideum was examined to determine its environmental or genetic basis. Eight artificial ponds were maintained, four at each of two environmental treatments: constant water level, to simulate fish-free permanent breeding ponds, and gradual drying out, to simulate temporary breeding ponds. Two populations of salamanders were used, derived from two breeding ponds having different frequencies of paedomorphosis. The water level in the drying treatment was lowered during the last 10 wk of the experimental period with no apparent differences in water chemistry parameters between treatments and only a slight change in water temperature during the last 2 wk. The effects of water level were potentially confounded by those of water temperature, density of larvae, and amount food. Population differences in the frequency of metamorphosis and paedomorphosis could potentially represent genetic differences resulting from the different selective regimes that individuals encounter in breeding ponds varying in drying frequency. 35 references, 3 figures, 4 tables.
McFadden, S A
Proper bodily response to environmental toxicants presumably requires proper function of the xenobiotic (foreign chemical) detoxification pathways. Links between phenotypic variations in xenobiotic metabolism and adverse environmental response have long been sought. Metabolism of the drug S-carboxymethyl-L-cysteine (SCMC) is polymorphous in the population, having a bimodal distribution of metabolites, 2.5% of the general population are thought to be nonmetabolizers. The researchers developing this data feel this implies a polymorphism in sulfoxidation of the amino acid cysteine to sulfate. While this interpretation is somewhat controversial, these metabolic differences reflected may have significant effects. Additionally, a significant number of individuals with environmental intolerance or chronic disease have impaired sulfation of phenolic xenobiotics. This impairment is demonstrated with the probe drug acetaminophen and is presumably due to starvation of the sulfotransferases for sulfate substrate. Reduced metabolism of SCMC has been found with increased frequency in individuals with several degenerative neurological and immunological conditions and drug intolerances, including Alzheimer's disease, Parkinson's disease, motor neuron disease, rheumatoid arthritis, and delayed food sensitivity. Impaired sulfation has been found in many of these conditions, and preliminary data suggests that it may be important in multiple chemical sensitivities and diet responsive autism. In addition, impaired sulfation may be relevant to intolerance of phenol, tyramine, and phenylic food constituents, and it may be a factor in the success of the Feingold diet. These studies indicate the need for the development of genetic and functional tests of xenobiotic metabolism as tools for further research in epidemiology and risk assessment.
Fang, Hao; Toyofuku, Masanori; Kiyokawa, Tatsunori; Ichihashi, Akihiro; Tateda, Kazuhiro; Nomura, Nobuhiko
Bacteria participate in social behaviors by communicating with each other and forming surface-associated biofilms. In Pseudomonas aeruginosa, such social behaviors are affected greatly by the environment. Although P. aeruginosa survive under anaerobic conditions, previous studies indicate that quorum sensing is attenuated under such conditions, and that this leads to decreased activity of extracellular virulence factors as compared to aerobic conditions. Hence it has come into question whether P. aeruginosa are virulent under anaerobic conditions. Here, we compared various phenotypes between PAO1 and clinical isolates under anaerobic conditions. Our data revealed that when grown anaerobically, growth and cell morphology greatly differed among the strains. One of the clinical isolates produced comparable amounts of quorum-sensing signaling molecules and extracellular virulence factors under aerobic and anaerobic conditions, while the other strains showed low production under anaerobic conditions. Biofilm formation also exhibited strain-dependent variations, suggesting that there are several mechanisms that lead to biofilm formation under anaerobic conditions. Taken together, these results indicate that the impact of anaerobiosis on the social interactions of P. aeruginosa is strain dependent, and suggest that multiple regulatory mechanisms are involved in the regulation of quorum sensing and biofilm formation under anaerobic conditions.
Benkman, Craig W; Smith, Julie W; Maier, Monika; Hansen, Leif; Talluto, Matt V
Phenotypic selection that is sustained over time underlies both anagenesis and cladogenesis, but the conditions that lead to such selection and what causes variation in selection are not well known. We measured the selection exerted by three species of predispersal seed predators of lodgepole pine (Pinus contorta latifolia) in the South Hills, Idaho, and found that net selection on different cone and seed traits exerted by red crossbills (Loxia curvirostra) and cone borer moths (Eucosma recissoriana) over 10 years of seed crops was similar to that measured in another mountain range. We also found that the strength of selection increased as seed predation increased, which provides a mechanism for the correlation between the escalation of seed defenses and the density of seed predators. Red crossbills consume the most seeds and selection they exert accounts for much of the selection experienced by lodgepole pine, providing additional support for a coevolutionary arms race between crossbills and lodgepole pine in the South Hills. The third seed predator, hairy woodpeckers (Picoides villosus), consumed less than one-sixth as many seeds as crossbills. Across the northern Rocky Mountains, woodpecker abundance and therefore selective impact appears limited by the elevated seed defenses of lodgepole pine.
Park, Go Eun; Kim, Ki Woo; Lee, Don Koo; Hyun, Jung Oh
Leaf stomatal characteristics of Siberian elm (Ulmus pumila) were investigated by electron microscopy and white light scanning interferometry. On the basis of average annual precipitations, two types of tree specimens were collected from Korea, China, and Mongolia: (1) trees under normal environmental conditions and (2) trees under arid conditions. Field emission scanning electron microscopy revealed oval-shaped stomata on the lower surface, and they were ca. 20 μm in width. In-lens secondary electron imaging showed differences in electron density and stomatal pore depth between the two types. According to the line profile analysis by white light scanning interferometry, stomata under arid conditions appeared to have higher levels of the stomatal pore depth than ones under normal conditions. Focused ion beam-field emission electron microscopy supported the increased stomatal pore depth with the increasing drought stress gradient. These results suggest that complementary microscopy can be employed to unravel the adaptive phenotypic plasticity of Siberian elm in response to drought stress.
Burbrink, Frank T; Chen, Xin; Myers, Edward A; Brandley, Matthew C; Pyron, R Alexander
Adaptive radiation (AR) theory predicts that groups sharing the same source of ecological opportunity (EO) will experience deterministic species diversification and morphological evolution. Thus, deterministic ecological and morphological evolution should be correlated with deterministic patterns in the tempo and mode of speciation for groups in similar habitats and time periods. We test this hypothesis using well-sampled phylogenies of four squamate groups that colonized the New World (NW) in the Late Oligocene. We use both standard and coalescent models to assess species diversification, as well as likelihood models to examine morphological evolution. All squamate groups show similar early pulses of speciation, as well as diversity-dependent ecological limits on clade size at a continental scale. In contrast, processes of morphological evolution are not easily predictable and do not show similar pulses of early and rapid change. Patterns of morphological and species diversification thus appear uncoupled across these groups. This indicates that the processes that drive diversification and disparification are not mechanistically linked, even among similar groups of taxa experiencing the same sources of EO. It also suggests that processes of phenotypic diversification cannot be predicted solely from the existence of an AR or knowledge of the process of diversification.
Kwon, Deok Ho; Kang, Taek-Jun; Kim, Young Ho; Lee, Si Hyeock
Rapid resistance detection is necessary for the adaptive management of acaricide-resistant populations of Tetranychus urticae. Detection of phenotypic and genotypic resistance was conducted by employing residual contact vial bioassay (RCV) and quantitative sequencing (QS) methods, respectively. RCV was useful for detecting the acaricide resistance levels of T. urticae, particularly for on-site resistance detection; however, it was only applicable for rapid-acting acaricides (12 out of 19 tested acaricides). QS was effective for determining the frequencies of resistance alleles on a population basis, which corresponded to 12 nonsynonymous point mutations associated with target-site resistance to five types of acaricides [organophosphates (monocrotophos, pirimiphos-methyl, dimethoate and chlorpyrifos), pyrethroids (fenpropathrin and bifenthrin), abamectin, bifenazate and etoxazole]. Most field-collected mites exhibited high levels of multiple resistance, as determined by RCV and QS data, suggesting the seriousness of their current acaricide resistance status in rose cultivation areas in Korea. The correlation analyses revealed moderate to high levels of positive relationships between the resistance allele frequencies and the actual resistance levels in only five of the acaricides evaluated, which limits the general application of allele frequency as a direct indicator for estimating actual resistance levels. Nevertheless, the resistance allele frequency data alone allowed for the evaluation of the genetic resistance potential and background of test mite populations. The combined use of RCV and QS provides basic information on resistance levels, which is essential for choosing appropriate acaricides for the management of resistant T. urticae. PMID:26545209
Boehmer, A L; Brinkmann, A O; Nijman, R M; Verleun-Mooijman, M C; de Ruiter, P; Niermeijer, M F; Drop, S L
Mutations in the androgen receptor (AR) gene result in a wide range of phenotypes of the androgen insensitivity syndrome (AIS). Inter- and intrafamilial differences in the phenotypic expression of identical AR mutations are known, suggesting modifying factors in establishing the phenotype. Two 46,XY siblings with partial AIS sharing the same AR gene mutation, R846H, but showing very different phenotypes are studied. Their parents are first cousins. One sibling with grade 5 AIS was raised as a girl; the other sibling with grade 3 AIS was raised as a boy. In both siblings serum levels of hormones were measured; a sex hormone-binding globulin (SHBG) suppression test was completed; and mutation analysis of the AR gene, Scatchard, and SDS-PAGE analysis of the AR protein was performed. Furthermore, 5alpha-reductase 2 expression and activity in genital skin fibroblasts were investigated, and the 5alpha-reductase 2 gene was sequenced. The decrease in SHBG serum levels in a SHBG suppression test did not suggest differences in androgen sensitivity as the cause of the phenotypic variation. Also, androgen binding characteristics of the AR, AR expression levels, and the phosphorylation pattern of the AR on hormone binding were identical in both siblings. However, 5alpha-reductase 2 activity was normal in genital skin fibroblasts from the phenotypic male patient but undetectable in genital skin fibroblasts from the phenotypic female patient. The lack of 5alpha-reductase 2 activity was due to absent or reduced expression of 5alpha-reductase 2 in genital skin fibroblasts from the phenotypic female patient. Exon and flanking intron sequences of the 5alpha-reductase 2 gene showed no mutations in either sibling. Additional intragenic polymorphic marker analysis gave no evidence for different inherited alleles for the 5alpha-reductase 2 gene in the two siblings. Therefore, the absent or reduced expression of 5alpha-reductase 2 is likely to be additional to the AIS. Distinct phenotypic
Machado-Schiaffino, Gonzalo; Henning, Frederico; Meyer, Axel
The spectacular species richness of cichlids and their diversity in morphology, coloration, and behavior have made them an ideal model for the study of speciation and adaptive evolution. Hypertrophic lips evolved repeatedly and independently in African and Neotropical cichlid radiations. Cichlids with hypertrophic lips forage predominantly in rocky crevices and it has been hypothesized that mechanical stress caused by friction could result in larger lips through phenotypic plasticity. To test the influence of the environment on the size and development of lips, we conducted a series of breeding and feeding experiments on Midas cichlids. Full-sibs of Amphilophus labiatus (thick-lipped) and Amphilophus citrinellus (thin-lipped) each were split into a control group which was fed food from the water column and a treatment group whose food was fixed to substrates. We found strong evidence for phenotypic plasticity on lip area in the thick-lipped species, but not in the thin-lipped species. Intermediate phenotypic values were observed in hybrids from thick- and thin-lipped species reared under "control" conditions. Thus, both a genetic, but also a phenotypic plastic component is involved in the development of hypertrophic lips in Neotropical cichlids. Moreover, species-specific adaptive phenotypic plasticity was found, suggesting that plasticity is selected for in recent thick-lipped species.
Ogura, Takehiko; Busch, Wolfgang
Tremendous natural variation of growth and development exists within species. Uncovering the molecular mechanisms that tune growth and development promises to shed light on a broad set of biological issues including genotype to phenotype relations, regulatory mechanisms of biological processes and evolutionary questions. Recent progress in sequencing and data processing capabilities has enabled Genome Wide Association Studies (GWASs) to identify DNA sequence polymorphisms that underlie the variation of biological traits. In the last years, GWASs have proven powerful in revealing the complex genetic bases of many phenotypes in various plant species. Here we highlight successful recent GWASs that uncovered mechanistic and sequence bases of trait variation related to plant growth and development and discuss important considerations for conducting successful GWASs.
Soerensen, Mette; Nygaard, Marianne; Debrabant, Birgit; Mengel-From, Jonas; Dato, Serena; Thinggaard, Mikael; Christensen, Kaare; Christiansen, Lene
In this study we explored the association between aging-related phenotypes previously reported to predict survival in old age and variation in 77 genes from the DNA repair pathway, 32 genes from the growth hormone 1/ insulin-like growth factor 1/insulin (GH/IGF-1/INS) signalling pathway and 16 additional genes repeatedly considered as candidates for human longevity: APOE, APOA4, APOC3, ACE, CETP, HFE, IL6, IL6R, MTHFR, TGFB1, SIRTs 1, 3, 6; and HSPAs 1A, 1L, 14. Altogether, 1,049 single nucleotide polymorphisms (SNPs) were genotyped in 1,088 oldest-old (age 92-93 years) Danes and analysed with phenotype data on physical functioning (hand grip strength), cognitive functioning (mini mental state examination and a cognitive composite score), activity of daily living and self-rated health. Five SNPs showed association to one of the phenotypes; however, none of these SNPs were associated with a change in the relevant phenotype over time (7 years of follow-up) and none of the SNPs could be confirmed in a replication sample of 1,281 oldest-old Danes (age 94-100). Hence, our study does not support association between common variation in the investigated longevity candidate genes and aging-related phenotypes consistently shown to predict survival. It is possible that larger sample sizes are needed to robustly reveal associations with small effect sizes.
Anazi, Shamsa; Alshamekh, Shomoukh; Alkuraya, Fowzan S.
The use of autozygosity as a mapping tool in the search for autosomal recessive disease genes is well established. We hypothesized that autozygosity not only unmasks the recessiveness of disease causing variants, but can also reveal natural knockouts of genes with less obvious phenotypic consequences. To test this hypothesis, we exome sequenced 77 well phenotyped individuals born to first cousin parents in search of genes that are biallelically inactivated. Using a very conservative estimate, we show that each of these individuals carries biallelic inactivation of 22.8 genes on average. For many of the 169 genes that appear to be biallelically inactivated, available data support involvement in modulating metabolism, immunity, perception, external appearance and other phenotypic aspects, and appear therefore to contribute to human phenotypic variation. Other genes with biallelic inactivation may contribute in yet unknown mechanisms or may be on their way to conversion into pseudogenes due to true recent dispensability. We conclude that sequencing the autozygome is an efficient way to map the contribution of genes to human phenotypic variation that goes beyond the classical definition of disease. PMID:24367280
Knebel, Birgit; Lehr, Stefan; Janssen, Onno E; Hahn, Susanne; Jacob, Sylvia; Nitzgen, Ulrike; Müller-Wieland, Dirk; Kotzka, Jorg
Polygenic diseases with a broad phenotypic spectrum, such as polycystic ovary syndrome (PCOS), present a particular challenge in terms of identifying the underlying genetic mechanisms, nevertheless genetic variants have impact on the individual phenotype. We aimed to determine if next to genetic variations like SNPs further mechanisms might play a role in the pathogenesis of PCOS. We examined the effect of copy-number variations (CNVs) on metabolic phenotypes in PCOS. The intragenic rs1244979, rs2815752 in NEGR1 gene, and rs780094 in GCKR gene were genotyped and CNVs were determined by droplet digital polymerase chain reaction (ddPCR) in PCOS patients (n = 153) and controls without metabolic syndrome (n = 142). The study indicated that SNPs are not associated with the pathogenesis of PCOS but affect metabolic phenotypes. The CNVs investigated show a lower variability in PCOS than in CON. Furthermore, we provided direct evidence that the copy number, but not the genotype of the CNV in the genomic regions of rs780094(GCKR) is associated with low level of high-density lipoprotein cholesterol in PCOS. This study supports the hypothesis that not only genetic variants, but also CNVs in metabolically relevant genes, have an effect on metabolic phenotypes in our group of PCOS patients.
Batista, V S P; Fernandes, F A; Cordeiro-Estrela, P; Sarquis, O; Lima, M M
Triatoma brasiliensis (Hemiptera: Reduviidae) is an important vector of Chagas' disease in both sylvatic and peridomestic ecotopes. Discriminating between these populations of Triatominae has been proposed as a means of investigating re-infestation rates of human dwellings. Geometric morphometrics have been widely applied in the study of Triatominae polymorphisms at species and population levels. This study characterizes morphometric differences between sylvatic and peridomestic populations, as well as between sexes in T. brasiliensis specimens from Jaguaruana, Ceará, in northeastern Brazil. No differences in either the shape or size of the cephalic capsule were apparent between sexes or ecotopes. However, the wings showed differentiation in shape and size. Sexual dimorphism was detected, with females presenting significantly higher values and conformations. Size differentiation was also evident, with sylvatic specimens being generally larger than peridomestic examples. These results indicate that differences in the wings of T. brasiliensis may be related to the existence of phenotypic plasticity, and variations in size and shape may be associated with different ecotopes, possibly as a result of conditions in each micro-habitat, such as temperature, relative humidity, food supply and density.
Hung, H-Y; Browne, C; Guill, K; Coles, N; Eller, M; Garcia, A; Lepak, N; Melia-Hancock, S; Oropeza-Rosas, M; Salvo, S; Upadyayula, N; Buckler, E S; Flint-Garcia, S; McMullen, M D; Rocheford, T R; Holland, J B
Appropriate selection of parents for the development of mapping populations is pivotal to maximizing the power of quantitative trait loci detection. Trait genotypic variation within a family is indicative of the family's informativeness for genetic studies. Accurate prediction of the most useful parental combinations within a species would help guide quantitative genetics studies. We tested the reliability of genotypic and phenotypic distance estimators between pairs of maize inbred lines to predict genotypic variation for quantitative traits within families derived from biparental crosses. We developed 25 families composed of ~200 random recombinant inbred lines each from crosses between a common reference parent inbred, B73, and 25 diverse maize inbreds. Parents and families were evaluated for 19 quantitative traits across up to 11 environments. Genetic distances (GDs) among parents were estimated with 44 simple sequence repeat and 2303 single-nucleotide polymorphism markers. GDs among parents had no predictive value for progeny variation, which is most likely due to the choice of neutral markers. In contrast, we observed for about half of the traits measured a positive correlation between phenotypic parental distances and within-family genetic variance estimates. Consequently, the choice of promising segregating populations can be based on selecting phenotypically diverse parents. These results are congruent with models of genetic architecture that posit numerous genes affecting quantitative traits, each segregating for allelic series, with dispersal of allelic effects across diverse genetic material. This architecture, common to many quantitative traits in maize, limits the predictive value of parental genotypic or phenotypic values on progeny variance.
Dong, Ning; Prentice, Iain Colin; Evans, Bradley J.; Caddy-Retalic, Stefan; Lowe, Andrew J.; Wright, Ian J.
, as predicted from local growing conditions. This finding is consistent with a
plant-centred approach to modelling, emphasizing the adaptive regulation of traits. Models that account for biodiversity will also need to partition community-level trait variation into components due to phenotypic plasticity and/or genotypic differentiation within species vs. progressive species replacement, along environmental gradients. Our analysis suggests that variation in Narea is about evenly split between these two modes.
Dutra Filho, J A; Junior, T C; Simões Neto, D E
We assessed the agroindustrial performance of 25 sugarcane genotypes adapted to the edaphoclimatic conditions of the State of Pernambuco, Brazil, within the microregions Mata Norte, Mata Sul, Região Central, Litoral Norte, and Litoral Sul. The variables analyzed were POL tonnage per hectare, sugarcane tonnage per hectare, fiber and total recoverable sugar tonnage per hectare, using a randomized block design with four repetitions. Combined variance of experiments, genetic parameter estimates, decomposition of the genotype-environment interaction, and environment stratification were analyzed. Phenotype adaptability and stability were also analyzed. The various genotypes presented great potential for improvement and a similar response pattern to the microregions Centro and Mata Sul of the state of Pernambuco. Genotypes RB863129, RB867515, RB92579, RB953180, SP81-3250, RB75126, and RB942520 were better in productivity and phenotype adaptability and stability compared to genotypes RB892700, RB943365, SP79-1011, Q138, RB943538, SP78-4764, RB953281, RB943066, RB928064, RB93509, RB72454, RB952675, RB952991, RB943161, RB942898, RB872552, RB952900, and RB942849. These genotypes are recommended as cultivation options in the sugarcane belt in the state of Pernambuco, since they stand out in terms of phenotype adaptability and stability as evaluated using the method by Annicchiarico, Lin and Bins, and the method by Eberhart and Russel.
Harrison, T. G.; Saunders, N. A.; Haththotuwa, A.; Hallas, G.; Birtles, R. J.; Taylor, A. G.
One hundred and seventy-nine isolates of Legionella pneumophila serogroup 1, obtained from a site associated with an outbreak of Legionnaires' disease, were examined by monoclonal antibody subgrouping, restriction fragment length polymorphism typing, restriction endonuclease analysis and plasmid content. Nine distinct phenotypes were detected but at the genotypic level all strains were closely related. The data presented indicate that phenotypic variation of a single parent strain can occur within an environmental site. The implications of these findings are discussed in relation to the investigation of outbreaks of Legionnaires' disease. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:1969803
Gould, Billie; McCouch, Susan; Geber, Monica
Studies of the wild grass Anthoxanthum odoratum at the long-term Park Grass Experiment (PGE, Harpenden, UK) document a well-known example of rapid plant evolution in response to environmental change. Repeated fertilizer applications have acidified the soil in some experimental plots over the past 150+ years, and Anthoxanthum subpopulations have quickly become locally adapted. Early reciprocal transplants showed subpopulation differentiation specifically in response to soil aluminium (Al) toxicity across the experiment, even at small (30 m) spatial scales. Almost 40 years after its original measurement, we reassessed the degree of local adaptation to soil Al at the PGE using updated phenotyping methods and identified genes with variation linked to the tolerance trait. Root growth assays show that plants are locally adapted to soil Al at both the seedling and adult growth stages, but to a smaller extent than previously inferred. Among a large suite of candidate loci that were previously shown to have Al-sensitive expression differences between sensitive and tolerant plants, three loci contained SNPs that are associated with both Al tolerance and soil acidity: an Al-sensitive malate transporter (ALMT), a tonoplast intrinsic protein (TIP) and the putative homolog of the rice cell-wall modification gene STAR1. Natural genetic variation at these loci is likely to have contributed to the recent rapid evolution at PGE. Continued study of Al tolerance variants in Anthoxanthum will allow us to test hypotheses about the nature and source of genetic variation that enables some species to adapt to soil acidification and other types of rapid environmental change.
Gautam, Pramod; Jha, Pankaj; Kumar, Dhirendra; Tyagi, Shivani; Varma, Binuja; Dash, Debasis; Mukhopadhyay, Arijit; Mukerji, Mitali
Copy number variations (CNVs) have provided a dynamic aspect to the apparently static human genome. We have analyzed CNVs larger than 100 kb in 477 healthy individuals from 26 diverse Indian populations of different linguistic, ethnic and geographic backgrounds. These CNVRs were identified using the Affymetrix 50K Xba 240 Array. We observed 1,425 and 1,337 CNVRs in the deletion and amplification sets, respectively, after pooling data from all the populations. More than 50% of the genes encompassed entirely in CNVs had both deletions and amplifications. There was wide variability across populations not only with respect to CNV extent (ranging from 0.04-1.14% of genome under deletion and 0.11-0.86% under amplification) but also in terms of functional enrichments of processes like keratinization, serine proteases and their inhibitors, cadherins, homeobox, olfactory receptors etc. These did not correlate with linguistic, ethnic, geographic backgrounds and size of populations. Certain processes were near exclusive to deletion (serine proteases, keratinization, olfactory receptors, GPCRs) or duplication (homeobox, serine protease inhibitors, embryonic limb morphogenesis) datasets. Populations having same enriched processes were observed to contain genes from different genomic loci. Comparison of polymorphic CNVRs (5% or more) with those cataloged in Database of Genomic Variants revealed that 78% (2473) of the genes in CNVRs in Indian populations are novel. Validation of CNVs using Sequenom MassARRAY revealed extensive heterogeneity in CNV boundaries. Exploration of CNV profiles in such diverse populations would provide a widely valuable resource for understanding diversity in phenotypes and disease.
Stuart-Fox, Devi; Godinho, Raquel; Goüy de Bellocq, Joëlle; Irwin, Nancy R.; Brito, José Carlos; Moussalli, Adnan; Široký, Pavel; Hugall, Andrew F.; Baird, Stuart J. E.
Background Molecular genetic studies are revealing an increasing number of cryptic lineages or species, which are highly genetically divergent but apparently cannot be distinguished morphologically. This observation gives rise to three important questions: 1) have these cryptic lineages diverged in phenotypic traits that may not be obvious to humans; 2) when cryptic lineages come into secondary contact, what are the evolutionary consequences: stable co-existence, replacement, admixture or differentiation and 3) what processes influence the evolutionary dynamics of these secondary contact zones? Methodology/Principal Findings To address these questions, we first tested whether males of the Iberian lizard Lacerta schreiberi from two highly genetically divergent, yet morphologically cryptic lineages on either side of an east-west secondary contact could be differentiated based on detailed analysis of morphology, coloration and parasite load. Next, we tested whether these differences could be driven by pre-copulatory intra-sexual selection (male-male competition). Compared to eastern males, western males had fewer parasites, were in better body condition and were more intensely coloured. Although subtle environmental variation across the hybrid zone could explain the differences in parasite load and body condition, these were uncorrelated with colour expression, suggesting that the differences in coloration reflect heritable divergence. The lineages did not differ in their aggressive behaviour or competitive ability. However, body size, which predicted male aggressiveness, was positively correlated with the colour traits that differed between genetic backgrounds. Conclusions/Significance Our study confirms that these cryptic lineages differ in several aspects that are likely to influence fitness. Although there were no clear differences in male competitive ability, our results suggest a potential indirect role for intra-sexual selection. Specifically, if lizards use
Oubida, Regis W.; Gantulga, Dashzeveg; Zhang, Man; Zhou, Lecong; Bawa, Rajesh; Holliday, Jason A.
Local adaptation to climate in temperate forest trees involves the integration of multiple physiological, morphological, and phenological traits. Latitudinal clines are frequently observed for these traits, but environmental constraints also track longitude and altitude. We combined extensive phenotyping of 12 candidate adaptive traits, multivariate regression trees, quantitative genetics, and a genome-wide panel of SNP markers to better understand the interplay among geography, climate, and adaptation to abiotic factors in Populus trichocarpa. Heritabilities were low to moderate (0.13–0.32) and population differentiation for many traits exceeded the 99th percentile of the genome-wide distribution of FST, suggesting local adaptation. When climate variables were taken as predictors and the 12 traits as response variables in a multivariate regression tree analysis, evapotranspiration (Eref) explained the most variation, with subsequent splits related to mean temperature of the warmest month, frost-free period (FFP), and mean annual precipitation (MAP). These grouping matched relatively well the splits using geographic variables as predictors: the northernmost groups (short FFP and low Eref) had the lowest growth, and lowest cold injury index; the southern British Columbia group (low Eref and intermediate temperatures) had average growth and cold injury index; the group from the coast of California and Oregon (high Eref and FFP) had the highest growth performance and the highest cold injury index; and the southernmost, high-altitude group (with high Eref and low FFP) performed poorly, had high cold injury index, and lower water use efficiency. Taken together, these results suggest variation in both temperature and water availability across the range shape multivariate adaptive traits in poplar. PMID:25870603
Oubida, Regis W; Gantulga, Dashzeveg; Zhang, Man; Zhou, Lecong; Bawa, Rajesh; Holliday, Jason A
Local adaptation to climate in temperate forest trees involves the integration of multiple physiological, morphological, and phenological traits. Latitudinal clines are frequently observed for these traits, but environmental constraints also track longitude and altitude. We combined extensive phenotyping of 12 candidate adaptive traits, multivariate regression trees, quantitative genetics, and a genome-wide panel of SNP markers to better understand the interplay among geography, climate, and adaptation to abiotic factors in Populus trichocarpa. Heritabilities were low to moderate (0.13-0.32) and population differentiation for many traits exceeded the 99th percentile of the genome-wide distribution of FST, suggesting local adaptation. When climate variables were taken as predictors and the 12 traits as response variables in a multivariate regression tree analysis, evapotranspiration (Eref) explained the most variation, with subsequent splits related to mean temperature of the warmest month, frost-free period (FFP), and mean annual precipitation (MAP). These grouping matched relatively well the splits using geographic variables as predictors: the northernmost groups (short FFP and low Eref) had the lowest growth, and lowest cold injury index; the southern British Columbia group (low Eref and intermediate temperatures) had average growth and cold injury index; the group from the coast of California and Oregon (high Eref and FFP) had the highest growth performance and the highest cold injury index; and the southernmost, high-altitude group (with high Eref and low FFP) performed poorly, had high cold injury index, and lower water use efficiency. Taken together, these results suggest variation in both temperature and water availability across the range shape multivariate adaptive traits in poplar.
Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in "Brassica rapa" Fast Plants
Batzli, Janet M.; Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dosa, Katalin; Pfammatter, Jesse
Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory…
Winandy, L; Denoël, M
Secondary sexual traits may evolve under the antagonistic context of sexual and natural selection. In some polymorphic species, these traits are only expressed during the breeding period and are differently expressed in alternative phenotypes. However, it is unknown whether such phenotypes exhibit phenotypic plasticity of seasonal ornamentations in response to environmental pressures such as in the presence of fish (predation risk). This is an important question to understand the evolution of polyphenisms. We used facultative paedomorphosis in newts as a model system because it involves the coexistence of paedomorphs that retain gills in the adult stage with metamorphs that have undergone metamorphosis, but also because newts exhibit seasonal sexual traits. Our aim was therefore to determine the influence of fish on the development of seasonal ornamentation in the two phenotypes of the palmate newt (Lissotriton helveticus). During the entire newt breeding period, we assessed the importance of phenotype and fish presence with an information-theoretic approach. Our results showed that paedomorphs presented much less developed ornamentation than metamorphs and those ornamentations varied over time. Fish inhibited the development of sexual traits but differently between phenotypes: in contrast to metamorphs, paedomorphs lack the phenotypic plasticity of sexual traits to environmental risk. This study points out that internal and external parameters act in complex ways in the expression of seasonal sexual ornamentations and that similar environmental pressure can induce a contrasted evolution in alternative phenotypes.
Commercial and experimental genetic resources were established and investigated for a range of reproductive and disease susceptibility phenotypes. The phenotyping efforts were accompanied with RNA and whole genome sequencing and novel assemblies of the swine genome. The efforts were complemented wit...
Damaghi, Mehdi; Gillies, Robert
The inter- and intra-tumoral metabolic phenotypes of tumors are heterogeneous, and this is related to microenvironments that select for increased glycolysis. Increased glycolysis leads to decreased pH, and these local microenvironment effects lead to further selection. Hence, heterogeneity of phenotypes is an indirect consequence of altering microenvironments during carcinogenesis. In early stages of growth, tumors are stratified, with the most aggressive cells developing within the acidic interior of the tumor. However, these cells eventually find themselves at the tumor edge, where they invade into the normal tissue via acid-mediated invasion. We believe acid adaptation during the evolution of cancer cells in their niche is a Rubicon that, once crossed, allows cells to invade into and outcompete normal stromal tissue. In this study, we illustrate some acid-induced phenotypic changes due to acidosis resulting in more aggressiveness and invasiveness of cancer cells.
Chrast, Jacqueline; Gu, Wenli; Gheldof, Nele; Pradervand, Sylvain; Schütz, Frédéric; Young, Juan I.; Lupski, James R.; Reymond, Alexandre; Walz, Katherina
A large fraction of genome variation between individuals is comprised of submicroscopic copy number variation of genomic DNA segments. We assessed the relative contribution of structural changes and gene dosage alterations on phenotypic outcomes with mouse models of Smith-Magenis and Potocki-Lupski syndromes. We phenotyped mice with 1n (Deletion/+), 2n (+/+), 3n (Duplication/+), and balanced 2n compound heterozygous (Deletion/Duplication) copies of the same region. Parallel to the observations made in humans, such variation in gene copy number was sufficient to generate phenotypic consequences: in a number of cases diametrically opposing phenotypes were associated with gain versus loss of gene content. Surprisingly, some neurobehavioral traits were not rescued by restoration of the normal gene copy number. Transcriptome profiling showed that a highly significant propensity of transcriptional changes map to the engineered interval in the five assessed tissues. A statistically significant overrepresentation of the genes mapping to the entire length of the engineered chromosome was also found in the top-ranked differentially expressed genes in the mice containing rearranged chromosomes, regardless of the nature of the rearrangement, an observation robust across different cell lineages of the central nervous system. Our data indicate that a structural change at a given position of the human genome may affect not only locus and adjacent gene expression but also “genome regulation.” Furthermore, structural change can cause the same perturbation in particular pathways regardless of gene dosage. Thus, the presence of a genomic structural change, as well as gene dosage imbalance, contributes to the ultimate phenotype. PMID:21124890
Ricard, Guénola; Molina, Jessica; Chrast, Jacqueline; Gu, Wenli; Gheldof, Nele; Pradervand, Sylvain; Schütz, Frédéric; Young, Juan I; Lupski, James R; Reymond, Alexandre; Walz, Katherina
A large fraction of genome variation between individuals is comprised of submicroscopic copy number variation of genomic DNA segments. We assessed the relative contribution of structural changes and gene dosage alterations on phenotypic outcomes with mouse models of Smith-Magenis and Potocki-Lupski syndromes. We phenotyped mice with 1n (Deletion/+), 2n (+/+), 3n (Duplication/+), and balanced 2n compound heterozygous (Deletion/Duplication) copies of the same region. Parallel to the observations made in humans, such variation in gene copy number was sufficient to generate phenotypic consequences: in a number of cases diametrically opposing phenotypes were associated with gain versus loss of gene content. Surprisingly, some neurobehavioral traits were not rescued by restoration of the normal gene copy number. Transcriptome profiling showed that a highly significant propensity of transcriptional changes map to the engineered interval in the five assessed tissues. A statistically significant overrepresentation of the genes mapping to the entire length of the engineered chromosome was also found in the top-ranked differentially expressed genes in the mice containing rearranged chromosomes, regardless of the nature of the rearrangement, an observation robust across different cell lineages of the central nervous system. Our data indicate that a structural change at a given position of the human genome may affect not only locus and adjacent gene expression but also "genome regulation." Furthermore, structural change can cause the same perturbation in particular pathways regardless of gene dosage. Thus, the presence of a genomic structural change, as well as gene dosage imbalance, contributes to the ultimate phenotype.
Ward, David; Shrestha, Madan K.; Golan-Goldhirsh, Avi
Background and Aims The ecological, evolutionary and genetic bases of population differentiation in a variable environment are often related to the selection pressures that plants experience. We compared differences in several growth- and defence-related traits in two isolated populations of Acacia raddiana trees from sites at either end of an extreme environmental gradient in the Negev desert. Methods We used random amplified polymorphic DNA (RAPD) to determine the molecular differences between populations. We grew plants under two levels of water, three levels of nutrients and three levels of herbivory to test for phenotypic plasticity and adaptive phenotypic plasticity. Key Results The RAPD analyses showed that these populations are highly genetically differentiated. Phenotypic plasticity in various morphological traits in A. raddiana was related to patterns of population genetic differentiation between the two study sites. Although we did not test for maternal effects in these long-lived trees, significant genotype × environment (G × E) interactions in some of these traits indicated that such plasticity may be adaptive. Conclusions The main selection pressure in this desert environment, perhaps unsurprisingly, is water. Increased water availability resulted in greater growth in the southern population, which normally receives far less rain than the northern population. Even under the conditions that we defined as low water and/or nutrients, the performance of the seedlings from the southern population was significantly better, perhaps reflecting selection for these traits. Consistent with previous studies of this genus, there was no evidence of trade-offs between physical and chemical defences and plant growth parameters in this study. Rather, there appeared to be positive correlations between plant size and defence parameters. The great variation in several traits in both populations may result in a diverse potential for responding to selection pressures in
Forsman, Z H; Knapp, I S S; Tisthammer, K; Eaton, D A R; Belcaid, M; Toonen, R J
Major gaps remain in our understanding of the ecology, evolution, biodiversity, biogeography, extinction risk, and adaptive potential of reef building corals. One of the central challenges remains that there are few informative genetic markers for studying boundaries between species, and variation within species. Reduced representation sequencing approaches, such as RADseq (Restriction site Associated DNA sequencing) have great potential for resolving such relationships. However, it is necessary to identify loci in order to make inferences for endosymbiotic organisms such as corals. Here, we examined twenty-one coral holobiont ezRAD libraries from Hawai'i, focusing on P. lobata and P. compressa, two species with contrasting morphology and habitat preference that previous studies have not resolved. We used a combination of de novo assembly and reference mapping approaches to identify and compare loci: we used reference mapping to extract and compare nearly complete mitochondrial genomes, ribosomal arrays, and histone genes. We used de novo clustering and phylogenomic methods to compare the complete holobiont data set with coral and symbiont subsets that map to transcriptomic data. In addition, we used reference assemblies to examine genetic structure from SNPs (Single Nucleotide Polymorphisms). All approaches resolved outgroup taxa but failed to resolve P. lobata and P. compressa as distinct, with mito-nuclear discordance and shared mitochondrial haplotypes within the species complex. The holobiont and 'coral transcriptomic' datasets were highly concordant, revealing stronger genetic structure between sites than between coral morphospecies. These results suggest that either branching morphology is a polymorphic trait, or that these species frequently hybridize. This study provides examples of several approaches to acquire, identify, and compare loci across metagenomic samples such as the coral holobiont while providing insights into the nature of coral variability.
Lindgren, B; Laurila, A
In ectothermic organisms, declining season length and lower temperature towards higher latitudes often select for latitudinal variation in growth and development. However, the energetic mechanisms underlying this adaptive variation are largely unknown. We investigated growth, food intake and growth efficiency of Rana temporaria tadpoles from eight populations along a 1500 km latitudinal gradient across Sweden. To gain an insight into the mechanisms of adaptation at organ level, we also examined variation in tadpole gut length. The tadpoles were raised at two temperatures (16 and 20 degrees C) in a laboratory common garden experiment. We found increased growth rate towards higher latitudes, regardless of temperature treatment. This increase in growth was not because of a higher food intake rate, but populations from higher latitudes had higher growth efficiency, i.e. they were more efficient at converting ingested food into body mass. Low temperature reduced growth efficiency most strongly in southern populations. Relative gut length increased with latitude, and tadpoles at low temperature tended to have longer guts. However, variation in gut length was not the sole adaptive explanation for increased growth efficiency as latitude and body length still explained significant amounts of variation in growth efficiency. Hence, additional energetic adaptations are probably involved in growth efficiency variation along the latitudinal gradient.
Harrison, Ashley J; Gamsiz, Ece D; Berkowitz, Isaac C; Nagpal, Shailender; Jerskey, Beth A
Oxytocin regulates social behavior in animal models. Research supports an association between genetic variation in the oxytocin receptor gene (OXTR) and autism spectrum disorders (ASD). In this study, we examine the association between the OXTR gene and a specific social phenotype within ASD. This genotype-phenotype investigation may provide insight into how OXTR conveys risk for social impairment. The current study investigated 10 SNPS in the OXTR gene that have been previously shown to be associated with ASD. We examine the association of these SNPs with both a social phenotype and a repetitive behavior phenotype comprised of behaviors commonly impaired in ASD in the Simons simplex collection (SSC). Using a large sample to examine the association between OXTR and ASD (n = range: 485-1002), we find evidence to support a relation between two OXTR SNPs and the examined social phenotype among children diagnosed with ASD. Greater impairment on the social responsiveness scale standardized total score and on several subdomains was observed among individuals with one or more copies of the minor frequency allele in both rs7632287 and rs237884. Linkage disequilibrium (LD) mapping suggests that these two SNPs are in LD within and overlapping the 3' untranslated region (3'-UTR) of the OXTR gene. These two SNPs were also associated with greater impairment on the repetitive behavior scale. Results of this study indicate that social impairment and repetitive behaviors in ASD are associated with genomic variation in the 3'UTR of the OXTR gene. These variants may be linked to an allele that alters stability of the mRNA message although further work is necessary to test this hypothesis.
Lemons, Christopher J; King, Seth A; Davidson, Kimberly A; Puranik, Cynthia S; Fulmer, Deborah; Mrachko, Alicia A; Partanen, Jane; Al Otaiba, Stephanie; Fidler, Deborah J
Many children with Down syndrome demonstrate deficits in phonological awareness, a prerequisite to learning to read in an alphabetic language. The purpose of this study was to determine whether adapting a commercially available phonological awareness program to better align with characteristics associated with the behavioral phenotype of Down syndrome would increase children's learning of phonological awareness, letter sounds, and words. Five children with Down syndrome, ages 6 to 8 years, participated in a multiple baseline across participants single case design experiment in which response to an adapted phonological awareness intervention was compared with response to the nonadapted program. Results indicate a functional relation between the adapted program and phonological awareness. Suggestions for future research and implications for practice are provided.
Hung, H-Y; Browne, C; Guill, K; Coles, N; Eller, M; Garcia, A; Lepak, N; Melia-Hancock, S; Oropeza-Rosas, M; Salvo, S; Upadyayula, N; Buckler, E S; Flint-Garcia, S; McMullen, M D; Rocheford, T R; Holland, J B
Appropriate selection of parents for the development of mapping populations is pivotal to maximizing the power of quantitative trait loci detection. Trait genotypic variation within a family is indicative of the family's informativeness for genetic studies. Accurate prediction of the most useful parental combinations within a species would help guide quantitative genetics studies. We tested the reliability of genotypic and phenotypic distance estimators between pairs of maize inbred lines to predict genotypic variation for quantitative traits within families derived from biparental crosses. We developed 25 families composed of ∼200 random recombinant inbred lines each from crosses between a common reference parent inbred, B73, and 25 diverse maize inbreds. Parents and families were evaluated for 19 quantitative traits across up to 11 environments. Genetic distances (GDs) among parents were estimated with 44 simple sequence repeat and 2303 single-nucleotide polymorphism markers. GDs among parents had no predictive value for progeny variation, which is most likely due to the choice of neutral markers. In contrast, we observed for about half of the traits measured a positive correlation between phenotypic parental distances and within-family genetic variance estimates. Consequently, the choice of promising segregating populations can be based on selecting phenotypically diverse parents. These results are congruent with models of genetic architecture that posit numerous genes affecting quantitative traits, each segregating for allelic series, with dispersal of allelic effects across diverse genetic material. This architecture, common to many quantitative traits in maize, limits the predictive value of parental genotypic or phenotypic values on progeny variance. PMID:22027895
Stillwell, R. Craig; Blanckenhorn, Wolf U.; Teder, Tiit; Davidowitz, Goggy; Fox, Charles W.
Males and females of nearly all animals differ in their body size, a phenomenon called sexual size dimorphism (SSD). The degree and direction of SSD vary considerably among taxa, including among populations within species. A considerable amount of this variation is due to sex differences in body size plasticity. We examine how variation in these sex differences is generated by exploring sex differences in plasticity in growth rate and development time and the physiological regulation of these differences (e.g., sex differences in regulation by the endocrine system). We explore adaptive hypotheses proposed to explain sex differences in plasticity, including those that predict that plasticity will be lowest for traits under strong selection (adaptive canalization) or greatest for traits under strong directional selection (condition dependence), but few studies have tested these hypotheses. Studies that combine proximate and ultimate mechanisms offer great promise for understanding variation in SSD and sex differences in body size plasticity in insects. PMID:19728836
Letcher, B.H.; Coombs, J.A.; Nislow, K.H.
Phenotypic variation in body size can result from within-cohort variation in birth dates, among-individual growth variation and size-selective processes. We explore the relative effects of these processes on the maintenance of wide observed body size variation in stream-dwelling brook trout (Salvelinus fontinalis). Based on the analyses of multiple recaptures of individual fish, it appears that size distributions are largely determined by the maintenance of early size variation. We found no evidence for size-dependent compensatory growth (which would reduce size variation) and found no indication that size-dependent survival substantially influenced body size distributions. Depensatory growth (faster growth by larger individuals) reinforced early size variation, but was relatively strong only during the first sampling interval (age-0, fall). Maternal decisions on the timing and location of spawning could have a major influence on early, and as our results suggest, later (>age-0) size distributions. If this is the case, our estimates of heritability of body size (body length=0.25) will be dominated by processes that generate and maintain early size differences. As a result, evolutionary responses to environmental change that are mediated by body size may be largely expressed via changes in the timing and location of reproduction. Published 2011. This article is a US Government work and is in the public domain in the USA.
Granell, Raquel; Henderson, A John; Timpson, Nicholas; Evans, David M; St Pourcain, Beate; Kemp, John P; Ring, Susan M; Ho, Karen; Montgomery, Stephen B; Dermitzakis, Emmanouil T.; Sterne, Jonathan A
Background Genome-wide association studies have identified associations of genetic variants at 17q21 near ORMDL3 with childhood asthma. Objectives To find out whether associations in this region are specific to particular asthma phenotypes and specific to ORMDL3. Methods We examined associations between 244 independent single nucleotide polymorphisms (SNPs) plus 13 previously identified asthma-related SNPs in the region between 34 and 36 Mb on chromosome 17 and early wheezing phenotypes, doctor-diagnosed asthma and atopy at 7½ years, bronchial hyper-responsiveness and lung function at 8½ years in 7,045 children from the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort study. With this, cis expression quantitative trait loci (eQTL) signals for the same SNPs were assessed in 875 samples across genes in the same region. Results The strongest evidence for phenotypic association was seen for persistent wheezing (rs8076131 near ORMDL3, relative risk ratio (RRR) 1.60 (95% CI 1.40, 1.84), p=1.4×10−11, rs2305480 near GSDML 1.60; 1.39-1.83, p=1.5×10−11 and rs9303277 near IKZF3 1.57; 1.37-1.79, p=4.4×10−11). Similar, but less precisely estimated effects were seen for intermediate-onset wheeze, but there was little evidence of associations with other wheezing phenotypes. There was some evidence of associations with bronchial hyper responsiveness. SNPs across the whole region show strong evidence of association with differential levels of expression at GSDML, IKZF3 and MED24, as well as ORMDL3. Conclusions Associations of SNPs in the 17q21 locus are specific to asthma and to specific wheezing phenotypes, and are not explained by associations with intermediate phenotypes, such as atopy or lung function. PMID:23154084
Polly, P David; Polyakov, Andrei V; Ilyashenko, Vadim B; Onischenko, Sergei S; White, Thomas A; Shchipanov, Nikolay A; Bulatova, Nina S; Pavlova, Svetlana V; Borodin, Pavel M; Searle, Jeremy B
Sorex araneus, the Common shrew, is a species with more than 70 karyotypic races, many of which form parapatric hybrid zones, making it a model for studying chromosomal speciation. Hybrids between races have reduced fitness, but microsatellite markers have demonstrated considerable gene flow between them, calling into question whether the chromosomal barriers actually do contribute to genetic divergence. We studied phenotypic clines across two hybrid zones with especially complex heterozygotes. Hybrids between the Novosibirsk and Tomsk races produce chains of nine and three chromosomes at meiosis, and hybrids between the Moscow and Seliger races produce chains of eleven. Our goal was to determine whether phenotypes show evidence of reduced gene flow at hybrid zones. We used maximum likelihood to fit tanh cline models to geometric shape data and found that phenotypic clines in skulls and mandibles across these zones had similar centers and widths as chromosomal clines. The amount of phenotypic differentiation across the zones is greater than expected if it were dissipating due to unrestricted gene flow given the amount of time since contact, but it is less than expected to have accumulated from drift during allopatric separation in glacial refugia. Only if heritability is very low, Ne very high, and the time spent in allopatry very short, will the differences we observe be large enough to match the expectation of drift. Our results therefore suggest that phenotypic differentiation has been lost through gene flow since post-glacial secondary contact, but not as quickly as would be expected if there was free gene flow across the hybrid zones. The chromosomal tension zones are confirmed to be partial barriers that prevent differentiated races from becoming phenotypically homogenous.
Weischenfeldt, Joachim; Symmons, Orsolya; Spitz, François; Korbel, Jan O
Genomic structural variants have long been implicated in phenotypic diversity and human disease, but dissecting the mechanisms by which they exert their functional impact has proven elusive. Recently however, developments in high-throughput DNA sequencing and chromosomal engineering technology have facilitated the analysis of structural variants in human populations and model systems in unprecedented detail. In this Review, we describe how structural variants can affect molecular and cellular processes, leading to complex organismal phenotypes, including human disease. We further present advances in delineating disease-causing elements that are affected by structural variants, and we discuss future directions for research on the functional consequences of structural variants.
Hermisson, Joachim; Pennings, Pleuni S
A population can adapt to a rapid environmental change or habitat expansion in two ways. It may adapt either through new beneficial mutations that subsequently sweep through the population or by using alleles from the standing genetic variation. We use diffusion theory to calculate the probabilities for selective adaptations and find a large increase in the fixation probability for weak substitutions, if alleles originate from the standing genetic variation. We then determine the parameter regions where each scenario-standing variation vs. new mutations-is more likely. Adaptations from the standing genetic variation are favored if either the selective advantage is weak or the selection coefficient and the mutation rate are both high. Finally, we analyze the probability of "soft sweeps," where multiple copies of the selected allele contribute to a substitution, and discuss the consequences for the footprint of selection on linked neutral variation. We find that soft sweeps with weaker selective footprints are likely under both scenarios if the mutation rate and/or the selection coefficient is high.
Maize is highly genetically and phenotypically diverse. Tropical maize and teosinte are important genetic resources that harbor unique alleles not found in temperate maize hybrids. To access these resources, breeders must be able to extract favorable unique alleles from tropical maize and teosinte f...
Chaves, Jaime A; Cooper, Elizabeth A; Hendry, Andrew P; Podos, Jeffrey; De León, Luis F; Raeymaekers, Joost A M; MacMillan, W Owen; Uy, J Albert C
Adaptive radiation unfolds as selection acts on the genetic variation underlying functional traits. The nature of this variation can be revealed by studying the tips of an ongoing adaptive radiation. We studied genomic variation at the tips of the Darwin's finch radiation; specifically focusing on polymorphism within, and variation among, three sympatric species of the genus Geospiza. Using restriction site-associated DNA (RAD-seq), we characterized 32 569 single-nucleotide polymorphisms (SNPs), from which 11 outlier SNPs for beak and body size were uncovered by a genomewide association study (GWAS). Principal component analysis revealed that these 11 SNPs formed four statistically linked groups. Stepwise regression then revealed that the first PC score, which included 6 of the 11 top SNPs, explained over 80% of the variation in beak size, suggesting that selection on these traits influences multiple correlated loci. The two SNPs most strongly associated with beak size were near genes associated with beak morphology across deeper branches of the radiation: delta-like 1 homologue (DLK1) and high-mobility group AT-hook 2 (HMGA2). Our results suggest that (i) key adaptive traits are associated with a small fraction of the genome (11 of 32 569 SNPs), (ii) SNPs linked to the candidate genes are dispersed throughout the genome (on several chromosomes), and (iii) micro- and macro-evolutionary variation (roots and tips of the radiation) involve some shared and some unique genomic regions.
Krtinić, B; Ludoški, J; Milankov, V
Culex (Culex) pipiens s.l. (Diptera: Culicidae) comprises two distinct biotypes, pipiens ('rural') and molestus ('urban'), both of which are thought to have differing capacities due to different host preferences. To better understand West Nile encephalitis epidemiology and improve risk assessment, local distinction between these forms is essential. This study assesses phenotypic variation at larval and adult stages of 'urban' and 'rural' biotypes of the species by complementary use of meristic, univariate and multivariate traits analyzed by traditional and geometric morphometrics. Third- and fourth-instar larvae from a broad area of the city of Novi Sad (Serbia) were collected and reared in the laboratory. After adult eclosion, the sex of each larva was recorded based on the sex of the corresponding adult. Examination of the association between variations of larval traits revealed contrasting variations regarding pecten spines vs. siphonal size and siphonal shape in the 'rural' biotype. Siphons of larvae collected in marshes and forest ecosystems outside urban areas were found to be the largest, but possessed the smallest number of pecten spines. In addition, statistically significant female-biased sexual dimorphism was observed in siphonal size, wing size and wing shape. Finally, we propose that an integrative approach is essential in delimitation of Cx. pipiens s.l. biotypes, since their differentiation was not possible based solely on larval and adult traits. Our findings shed light on the phenotypic plasticity important for population persistence in the changing environment of these medically important taxa.
This research targets the case of Kalman filtering as applied to linear time-invariant systems having unknown process noise covariance and measurement noise covariance matrices and addresses the problem represented by the incomplete a priori knowledge of these two filter initialization parameters. The goal of this research is to determine in realtime both the process covariance matrix and the noise covariance matrix in the context of adaptive Kalman filtering. The resultant filter, called evolutionary adaptive Kalman filter, is able to adapt to sudden noise variations and constitutes a hybrid solution for adaptive Kalman filtering based on metaheuristic algorithms. MATLAB/Simulink simulation using several processes and covariance matrices plus comparison with other filters was selected as validation method. The Cramer-Rae Lower Bound (CRLB) was used as performance criterion. The thesis begins with a description of the problem under consideration (the design of a Kalman filter that is able to adapt to sudden noise variations) followed by a typical application (INS-GPS integrated navigation system) and by a statistical analysis of publications related to adaptive Kalman filtering. Next, the thesis presents the current architectures of the adaptive Kalman filtering: the innovation adaptive estimator (IAE) and the multiple model adaptive estimator (MMAE). It briefly presents their formulation, their behavior, and the limit of their performances. The thesis continues with the architectural synthesis of the evolutionary adaptive Kalman filter. The steps involved in the solution of the problem under consideration is also presented: an analysis of Kalman filtering and sub-optimal filtering methods, a comparison of current adaptive Kalman and sub-optimal filtering methods, the emergence of evolutionary adaptive Kalman filter as an enrichment of sub-optimal filtering with the help of biological-inspired computational intelligence methods, and the step-by-step architectural
Wang, Huange; Paulo, Joao; Kruijer, Willem; Boer, Martin; Jansen, Hans; Tikunov, Yury; Usadel, Björn; van Heusden, Sjaak; Bovy, Arnaud; van Eeuwijk, Fred
Modeling genotype-phenotype relationships is a central objective in plant genetics and breeding. Commonly, variations in phenotypic traits are modeled directly in relation to variations at the DNA level, regardless of intermediate levels of biological variation. Here we present an integrative method for the simultaneous modeling of a set of multilevel phenotypic responses to variations at the DNA level. More specifically, for ripe tomato fruits, we use Gaussian graphical models and causal inference techniques to learn the dependencies of 24 sensory traits on 29 metabolites and the dependencies of those sensory and metabolic traits on 21 QTLs. The inferred dependency network which, though not essentially representing biological pathways, suggests how the effects of allele substitutions propagate through multilevel phenotypes. Such simultaneous study of the underlying genetic architecture and multifactorial interactions is expected to enhance the prediction and manipulation of complex traits.
Kitajima, João Paulo; Tahira, Ana Carolina; Feio-dos-Santos, Ana Cecília; Fock, Rodrigo Ambrósio; Lisboa, Bianca Cristina Garcia; Simões, Sérgio Nery; Krepischi, Ana C. V.; Rosenberg, Carla; Lourenço, Naila Cristina; Passos-Bueno, Maria Rita; Brentani, Helena
It has been proposed that copy number variations (CNVs) are associated with increased risk of autism spectrum disorder (ASD) and, in conjunction with other genetic changes, contribute to the heterogeneity of ASD phenotypes. Array comparative genomic hybridization (aCGH) and exome sequencing, together with systems genetics and network analyses, are being used as tools for the study of complex disorders of unknown etiology, especially those characterized by significant genetic and phenotypic heterogeneity. Therefore, to characterize the complex genotype-phenotype relationship, we performed aCGH and sequenced the exomes of two affected siblings with ASD symptoms, dysmorphic features, and intellectual disability, searching for de novo CNVs, as well as for de novo and rare inherited point variations—single nucleotide variants (SNVs) or small insertions and deletions (indels)—with probable functional impacts. With aCGH, we identified, in both siblings, a duplication in the 4p16.3 region and a deletion at 8p23.3, inherited by a paternal balanced translocation, t(4, 8) (p16; p23). Exome variant analysis found a total of 316 variants, of which 102 were shared by both siblings, 128 were in the male sibling exome data, and 86 were in the female exome data. Our integrative network analysis showed that the siblings’ shared translocation could explain their similar syndromic phenotype, including overgrowth, macrocephaly, and intellectual disability. However, exome data aggregate genes to those already connected from their translocation, which are important to the robustness of the network and contribute to the understanding of the broader spectrum of psychiatric symptoms. This study shows the importance of using an integrative approach to explore genotype-phenotype variability. PMID:28118382
Ramírez-Valiente, Jose Alberto; Sánchez-Gómez, David; Aranda, Ismael; Valladares, Fernando
Plants distributed across a wide range of environmental conditions are submitted to differential selective pressures. Long-term selection can lead to the development of adaptations to the local environment, generating ecotypic differentiation. Additionally, plant species can cope with this environmental variability by phenotypic plasticity. In this study, we examine the importance of both processes in coping with environmental heterogeneity in the Mediterranean sclerophyllous cork oak Quercus suber. For this purpose, we measured growth and key functional traits at the leaf level in 9-year-old plants across 2 years of contrasting precipitation (2005 and 2006) in a common garden. Plants were grown from acorns originated from 13 populations spanning a wide range of climates along the distribution range of the species. The traits measured were: leaf size (LS), specific leaf area (SLA), carbon isotope discrimination (Delta(13)C) and leaf nitrogen content per unit mass (N(mass)). Inter-population differences in LS, SLA and Delta(13)C were found. These differences were associated with rainfall and temperature at the sites of origin, suggesting local adaptation in response to diverging climates. Additionally, SLA and LS exhibited positive responses to the increase in annual rainfall. Year effect explained 28% of the total phenotypic variance in LS and 2.7% in SLA. There was a significant genotype x environment interaction for shoot growth and a phenotypic correlation between the difference in shoot growth among years and the annual mean temperature at origin. This suggests that populations originating from warm sites can benefit more from wet conditions than populations from cool sites. Finally, we investigated the relationships between functional traits and aboveground growth by several regression models. Our results showed that plants with lower SLA presented larger aboveground growth in a dry year and plants with larger leaf sizes displayed larger growth rates in both
Hannon, Eilis; Lunnon, Katie; Schalkwyk, Leonard; Mill, Jonathan
Given the tissue-specific nature of epigenetic processes, the assessment of disease-relevant tissue is an important consideration for epigenome-wide association studies (EWAS). Little is known about whether easily accessible tissues, such as whole blood, can be used to address questions about interindividual epigenomic variation in inaccessible tissues, such as the brain. We quantified DNA methylation in matched DNA samples isolated from whole blood and 4 brain regions (prefrontal cortex, entorhinal cortex, superior temporal gyrus, and cerebellum) from 122 individuals. We explored co-variation between tissues and the extent to which methylomic variation in blood is predictive of interindividual variation identified in the brain. For the majority of DNA methylation sites, interindividual variation in whole blood is not a strong predictor of interindividual variation in the brain, although the relationship with cortical regions is stronger than with the cerebellum. Variation at a subset of probes is strongly correlated across tissues, even in instances when the actual level of DNA methylation is significantly different between them. A substantial proportion of this co-variation, however, is likely to result from genetic influences. Our data suggest that for the majority of the genome, a blood-based EWAS for disorders where brain is presumed to be the primary tissue of interest will give limited information relating to underlying pathological processes. These results do not, however, discount the utility of using a blood-based EWAS to identify biomarkers of disease phenotypes manifest in the brain. We have generated a searchable database for the interpretation of data from blood-based EWAS analyses ( http://epigenetics.essex.ac.uk/bloodbrain/).
Hess, Jon E; Campbell, Nathan R; Close, David A; Docker, Margaret F; Narum, Shawn R
Unlike most anadromous fishes that have evolved strict homing behaviour, Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within-region population genetic heterogeneity coupled with the morphological and behavioural diversity described for the species suggest that adaptive genetic variation underlying fitness traits may be responsible. We employed restriction site-associated DNA sequencing to genotype 4439 quality filtered single nucleotide polymorphism (SNP) loci for 518 individuals collected across a broad geographical area including British Columbia, Washington, Oregon and California. A subset of putatively neutral markers (N = 4068) identified a significant amount of variation among three broad populations: northern British Columbia, Columbia River/southern coast and 'dwarf' adults (F(CT) = 0.02, P ≪ 0.001). Additionally, 162 SNPs were identified as adaptive through outlier tests, and inclusion of these markers revealed a signal of adaptive variation related to geography and life history. The majority of the 162 adaptive SNPs were not independent and formed four groups of linked loci. Analyses with matsam software found that 42 of these outlier SNPs were significantly associated with geography, run timing and dwarf life history, and 27 of these 42 SNPs aligned with known genes or highly conserved genomic regions using the genome browser available for sea lamprey. This study provides both neutral and adaptive context for observed genetic divergence among collections and thus reconciles previous findings of population genetic heterogeneity within a species that displays extensive gene flow.
Delzon, Sylvain; Vitasse, Yann; Alberto, Florian; Bresson, Caroline; Kremer, Antoine
Under current climate change, research on inherent adaptive capacities of organisms is crucial to assess future evolutionary changes of natural populations. Genetic diversity and phenotypic plasticity constitute adaptative capacities that could allow populations to respond to new environmental conditions. The aim of the present study was (i) to determine whether there are genetic variations among populations from altitudinal gradients using a lowland common garden experiment and (ii) to assess the magnitude of phenotypic plasticity using a reciprocal transplant experiment (5 elevations from 100 to 1600 m asl.) for leaf phenology (flushing and senescence) and growth of two fagaceae species (Fagus sylvatica and Quercus petraea). We found significant differences in phenology among provenances for most species, and evidenced that these among-population differences in phenology were related to annual temperature of the provenance sites for both species. It's noteworthy that, along the same climatic gradient, the species exhibited opposite genetic clines: beech populations from high elevation flushed earlier than those of low elevation, whereas we observed an opposite trend for oak. Finally, we highlighted that both phenology timing and growth rate were highly consistent year to year. The results demonstrated that in spite of the proximity of the populations in their natural area, altitude led to genetic differentiations in their phenology and growth. Moreover, a high phenological plasticity was found for both species. We evidenced that reaction norms of flushing timing to temperature followed linear clinal trends for both species with an average shift of 5.7 days per degree increase. Timing of leaf senescence exhibited hyperbolic trends for beech and no or slight trends for oak. Furthermore, within species, there was no difference in magnitude of phenological plasticity among populations neither for flushing, nor for senescence. Consequently, for both species, the
Lynch, H T; Smyrk, T C; Lanspa, S J; Lynch, P M; Watson, P; Strayhorn, P C; Bronson, E K; Lynch, J F; Priluck, I A; Appelman, H D
Clinical, pathologic, and genetic studies on two colorectal cancer-prone families have disclosed right-sided colonic flat adenomas and colorectal cancer. Adenomatous polyp counts exceeded those found in hereditary nonpolyposis colorectal cancer (HNPCC) but were fewer than in familial adenomatous polyposis (FAP). Colon cancer occurred at a later age than in HNPCC or FAP and showed right-sided predominance. The older age of patients with colonic cancer, the right-sided predominance of colon cancer, and the paucity of rectal adenomas make FAP unlikely. Vertical transmission of polyps and colon cancer fit the pattern of autosomal dominant inheritance. A characteristic feature of this phenotype is the predominance of flat adenomas. Molecular genetic studies, with careful description of phenotype, should help clarify classification.
Azimi-Garakani, C; Beardmore, J A
The distribution of tongue-rolling phenotypes in a sample (n = 477) of undergraduate students of the University College of Swansea (U.K.) was studied. The birthplaces of these students were also recorded. England was divided into six areas, and Wales was left as an area on its own. The data suggest that those students who come from north-east are more non-rollers, which may be due to mixture with Scandinavians.
Capela, Carlos; Dossou, Ange Dodji; Silva-Gomes, Rita; Sopoh, Ghislain Emmanuel; Makoutode, Michel; Menino, João Filipe; Fraga, Alexandra Gabriel; Cunha, Cristina; Carvalho, Agostinho; Rodrigues, Fernando; Pedrosa, Jorge
Introduction Buruli ulcer (BU) is a severe necrotizing human skin disease caused by Mycobacterium ulcerans. Clinically, presentation is a sum of these diverse pathogenic hits subjected to critical immune-regulatory mechanisms. Among them, autophagy has been demonstrated as a cellular process of critical importance. Since microtubules and dynein are affected by mycolactone, the critical pathogenic exotoxin produced by M. ulcerans, cytoskeleton-related changes might potentially impair the autophagic process and impact the risk and progression of infection. Objective Genetic variants in the autophagy-related genes NOD2, PARK2 and ATG16L1 has been associated with susceptibility to mycobacterial diseases. Here, we investigated their association with BU risk, its severe phenotypes and its progression to an ulcerative form. Methods Genetic variants were genotyped using KASPar chemistry in 208 BU patients (70.2% with an ulcerative form and 28% in severe WHO category 3 phenotype) and 300 healthy endemic controls. Results The rs1333955 SNP in PARK2 was significantly associated with increased susceptibility to BU [odds ratio (OR), 1.43; P = 0.05]. In addition, both the rs9302752 and rs2066842 SNPs in NOD2 gee significantly increased the predisposition of patients to develop category 3 (OR, 2.23; P = 0.02; and OR 12.7; P = 0.03, respectively, whereas the rs2241880 SNP in ATG16L1 was found to significantly protect patients from presenting the ulcer phenotype (OR, 0.35; P = 0.02). Conclusion Our findings indicate that specific genetic variants in autophagy-related genes influence susceptibility to the development of BU and its progression to severe phenotypes. PMID:27128681
Lee, S-K; Lee, Z H; Lee, S-J; Ahn, B-D; Kim, Y-J; Lee, S-H; Kim, J-W
Tricho-dento-osseous syndrome (TDO) is an autosomal-dominant disease characterized by curly hair at birth, enamel hypoplasia, taurodontism, and a thick cortical bone. A common DLX3 gene mutation (c.571_574delGGGG) has been identified in multiple families with variable clinical phenotypes. Recently, another DLX3 gene mutation (c.561_562delCT) was reported to cause amelogenesis imperfecta with taurodontism (AIHHT). We identified a Korean family with overlapping phenotypes of TDO and AIHHT. We performed mutational analysis to discover its genetic etiology. The identified mutation was c.561_562delCT mutation in the DLX3 gene. The enamel was hypomature and hypoplastic. The characteristic taurodontic features were not identified. Increased bone density or thickness could not be revealed by cephalometric, hand-wrist, and panoramic radiographs. Affected individuals reported that their nails were brittle, and they had curly hair at birth. This study clearly showed that the c.561_562delCT mutation had not only enamel defects, but also other clinical phenotypes resembling those of TDO syndrome.
Zhang, Jingyi; Li, Yonggui; Zhu, Yonggang; Li, Binwu
Estimation and prediction of noise power are very important for communication anti-jamming and efficient allocation of spectrum resources in adaptive wireless communication and cognitive radio. In order to estimate and predict the time-varying noise power caused by natural factors and jamming in the high frequency channel, Variational Bayesian algorithm and adaptive ARMA time series are proposed. Through establishing the time-varying noise power model, which controlled by the noise variance rate, the noise power can be estimated with Variational Bayesian algorithm, and the results show that the estimation error is related to observation interval. What's more, through the analysis of the correlation characteristics of the estimation power, noise power can be predicted based on adaptive ARMA time series, and the results show that it will be available to predict the noise power in next 5 intervals with the proportional error less than 0.2.
Yuan, Qiangqiang; Zhang, Liangpei; Shen, Huanfeng
Total variation is used as a popular and effective image prior model in the regularization-based image processing fields. However, as the total variation model favors a piecewise constant solution, the processing result under high noise intensity in the flat regions of the image is often poor, and some pseudoedges are produced. In this paper, we develop a regional spatially adaptive total variation model. Initially, the spatial information is extracted based on each pixel, and then two filtering processes are added to suppress the effect of pseudoedges. In addition, the spatial information weight is constructed and classified with k-means clustering, and the regularization strength in each region is controlled by the clustering center value. The experimental results, on both simulated and real datasets, show that the proposed approach can effectively reduce the pseudoedges of the total variation regularization in the flat regions, and maintain the partial smoothness of the high-resolution image. More importantly, compared with the traditional pixel-based spatial information adaptive approach, the proposed region-based spatial information adaptive total variation model can better avoid the effect of noise on the spatial information extraction, and maintains robustness with changes in the noise intensity in the super-resolution process.
Bikard, David; Marraffini, Luciano A
Bacteria are constantly challenged by bacteriophages (viruses that infect bacteria), the most abundant microorganism on earth. Bacteria have evolved a variety of immunity mechanisms to resist bacteriophage infection. In response, bacteriophages can evolve counter-resistance mechanisms and launch a 'virus versus host' evolutionary arms race. In this context, rapid evolution is fundamental for the survival of the bacterial cell. Programmed genetic variation mechanisms at loci involved in immunity against bacteriophages generate diversity at a much faster rate than random point mutation and enable bacteria to quickly adapt and repel infection. Diversity-generating retroelements (DGRs) and phase variation mechanisms enhance the generic (innate) immune response against bacteriophages. On the other hand, the integration of small bacteriophage sequences in CRISPR loci provide bacteria with a virus-specific and sequence-specific adaptive immune response. Therefore, although using different molecular mechanisms, both prokaryotes and higher organisms rely on programmed genetic variation to increase genetic diversity and fight rapidly evolving infectious agents.
Dressler, Anastasia; Perelli, Valentina; Bozza, Margherita; Bargagna, Stefania
The autistic phenotype in Down syndrome (DS) is marked by a characteristic pattern of stereotypies, anxiety and social withdrawal. Our aim was to study adaptive behaviour in DS with and without autistic comorbidity using the Vineland Adaptive Behaviour Scales (VABS), the Childhood Autism Rating Scales (CARS) and the DSM IV-TR criteria. We assessed 24 individuals and established three groups: Down syndrome (DS), DS and autistic disorder (DS-AD), and autistic disorder (AD). The DS and DS-AD groups showed statistically significantly similar strengths on the VABS (in receptive and domestic skills). The DS and DS-AD subjects also showed similar strengths on the CARS (in imitation and relating), differing significantly from the AD group. The profile of adaptive functioning and symptoms in DS-AD seemed to be more similar to that found in DS than to the profile emerging in AD. We suggest that the comorbidity of austistic symptoms in DS hampered the acquisition of adaptive skills more than did the presence of DS alone.
Pascacio-Villafán, Carlos; Williams, Trevor; Birke, Andrea; Aluja, Martín
Our understanding of how food modulates animal phenotypes and mediate trade-offs between life-history traits has benefited greatly from the study of combinations of nutritional and non-nutritional food components, such as plant secondary metabolites. We used a fruit fly pest, Anastrepha ludens, to examine phenotypic variation across larval, pupal and adult stages as a function of larval food with varying nutrient balance and content of chlorogenic acid, a secondary metabolite. Larval insects that fed on carbohydrate-biased diets relative to protein exhibited longer larval and pupal developmental periods, were often heavier as pupae and resisted desiccation and starvation for longer periods in the adult stage than insects fed on highly protein-biased diets. Except for a potential conflict between pupal development time and adult desiccation and starvation resistance, we did not detect physiological trade-offs mediated by the nutritional balance in larval food. Chlorogenic acid affected A. ludens development in a concentration and nutrient-dependent manner. Nutrients and host plant secondary metabolites in the larval diet induced changes in A. ludens phenotype and could influence fruit fly ecological interactions. We provide a unique experimental and modelling approach useful in generating predictive models of life history traits in a variety of organisms. PMID:27406923
Pascacio-Villafán, Carlos; Williams, Trevor; Birke, Andrea; Aluja, Martín
Our understanding of how food modulates animal phenotypes and mediate trade-offs between life-history traits has benefited greatly from the study of combinations of nutritional and non-nutritional food components, such as plant secondary metabolites. We used a fruit fly pest, Anastrepha ludens, to examine phenotypic variation across larval, pupal and adult stages as a function of larval food with varying nutrient balance and content of chlorogenic acid, a secondary metabolite. Larval insects that fed on carbohydrate-biased diets relative to protein exhibited longer larval and pupal developmental periods, were often heavier as pupae and resisted desiccation and starvation for longer periods in the adult stage than insects fed on highly protein-biased diets. Except for a potential conflict between pupal development time and adult desiccation and starvation resistance, we did not detect physiological trade-offs mediated by the nutritional balance in larval food. Chlorogenic acid affected A. ludens development in a concentration and nutrient-dependent manner. Nutrients and host plant secondary metabolites in the larval diet induced changes in A. ludens phenotype and could influence fruit fly ecological interactions. We provide a unique experimental and modelling approach useful in generating predictive models of life history traits in a variety of organisms.
Renaud, Sabrina; Auffray, Jean-Christophe; Michaux, Jacques
Within a group of organisms, some morphologies are more readily generated than others due to internal developmental constraints. Such constraints can channel evolutionary changes into directions corresponding to the greatest intraspecific variation. Long-term evolutionary outputs, however, depend on the stability of these intraspecific patterns of variation over time and from the interplay between internal constraints and selective regimes. To address these questions, the relationship between the structure of phenotypic variance covariance matrices and direction of morphological evolution was investigated using teeth of fossil rodents. One lineage considered here leads to Stephanomys, a highly specialized genus characterized by a dental pattern supposedly favoring grass eating. Stephanomys evolved in the context of directional selection related to the climatic trend of global cooling causing an increasing proportion of grasslands in southwestern Europe. The initial divergence (up to approximately 6.5 mya) was channeled along the direction of greatest intraspecific variation, whereas after 6.5 mya, morphological evolution departed from the direction favored by internal constraints. This departure from the "lines of least resistance" was likely the consequence of an environmental degradation causing a selective gradient strong enough to overwhelm the constraints to phenotypic evolution. However, in a context of stabilizing selection, these constraints actually channel evolution, as exemplified by the lineage of Apodemus. This lineage retained a primitive diet and dental pattern over the last 10 myr. Limited morphological changes occurred nevertheless in accordance with the main patterns of intraspecific variation. The importance of these lines of least resistance directing long-term morphological evolution may explain parallel evolution of some dental patterns in murine evolution.
Filannino, Pasquale; Di Cagno, Raffaella; Crecchio, Carmine; De Virgilio, Caterina; De Angelis, Maria; Gobbetti, Marco
Lactobacillus plantarum has been isolated from a large variety of ecological niches, thus highlighting its remarkable environmental adaptability as a generalist. Plant fermentation conditions markedly affect the functional features of L. plantarum strains. We investigated the plant niche-specific traits of L. plantarum through whole-transcriptome and phenotypic microarray profiles. Carrot (CJ) and pineapple (PJ) juices were chosen as model systems, and MRS broth was used as a control. A set of 3,122 genes was expressed, and 21 to 31% of genes were differentially expressed depending on the plant niche and cell physiological state. L. plantarum C2 seemed to specifically respond to plant media conditions. When L. plantarum was cultured in CJ, useful pathways were activated, which were aimed to sense the environment, save energy and adopt alternative routes for NAD+ regeneration. In PJ the acidic environment caused a transcriptional switching, which was network-linked to an acid tolerance response involving carbohydrate flow, amino acid and protein metabolism, pH homeostasis and membrane fluidity. The most prominent phenotypic dissimilarities observed in cells grown in CJ and PJ were related to carbon and nitrogen metabolism, respectively. Summarising, a snapshot of a carrot and pineapple sensing and adaptive regulation model for L. plantarum C2 was proposed. PMID:27273017
Joyner, Dominique; Fortney, Julian; Chakraborty, Romy; Hazen, Terry
The Biolog OmniLog? Phenotype MicroArray (PM) plate technology was successfully adapted to generate a select phenotypic profile of the strict anaerobe Geobacter metallireducens (G.m.). The profile generated for G.m. provides insight into the chemical sensitivity of the organism as well as some of its metabolic capabilities when grown with a basal medium containing acetate and Fe(III). The PM technology was developed for aerobic organisms. The reduction of a tetrazolium dye by the test organism represents metabolic activity on the array which is detected and measured by the OmniLog(R) system. We have previously adapted the technology for the anaerobic sulfate reducing bacterium Desulfovibrio vulgaris. In this work, we have taken the technology a step further by adapting it for the iron reducing obligate anaerobe Geobacter metallireducens. In an osmotic stress microarray it was determined that the organism has higher sensitivity to impermeable solutes 3-6percent KCl and 2-5percent NaNO3 that result in osmotic stress by osmosis to the cell than to permeable non-ionic solutes represented by 5-20percent ethylene glycol and 2-3percent urea. The osmotic stress microarray also includes an array of osmoprotectants and precursor molecules that were screened to identify substrates that would provide osmotic protection to NaCl stress. None of the substrates tested conferred resistance to elevated concentrations of salt. Verification studies in which G.m. was grown in defined medium amended with 100mM NaCl (MIC) and the common osmoprotectants betaine, glycine and proline supported the PM findings. Further verification was done by analysis of transcriptomic profiles of G.m. grown under 100mM NaCl stress that revealed up-regulation of genes related to degradation rather than accumulation of the above-mentioned osmoprotectants. The phenotypic profile, supported by additional analysis indicates that the accumulation of these osmoprotectants as a response to salt stress does not
Ganie, Mohd Ashraf; Marwaha, Raman Kumar; Dhingra, Atul; Nisar, Sobia; Mani, Kaliavani; Masoodi, Shariq; Chakraborty, Semanti; Rashid, Aafia
Polycystic ovary syndrome (PCOS) is a heterogeneous disorder that demonstrates ethnic and regional differences. To assess the phenotypic variability among Indian PCOS women, we evaluated clinical, biochemical and hormonal parameters of these women being followed in two tertiary care institutions located in Delhi and Srinagar. A total of 299 (210 PCOS diagnosed by Rotterdam 2003 criteria and 89 healthy) women underwent estimation of T4, TSH, LH, FSH, total testosterone, prolactin, cortisol, 17OHP, and lipid profile, in addition to post OGTT, C-peptide, insulin, and glucose measurements. Among women with PCOS, mean age, age of menarche, height, systolic, diastolic blood pressure, and serum LH were comparable. PCOS women from Delhi had significantly higher BMI (26.99 ± 5.38 versus 24.77 ± 4.32 kg/m(2); P = 0.01), glucose intolerance (36 versus 10%), insulin resistance as measured by HOMA-IR (4.20 ± 3.39 versus 3.01 ± 2.6; P = 0.006) and QUICKI (0.140 ± 0.013 versus 0.147 ± 0.015; P = 0.03) while PCOS from Srinagar had higher FG score (12.12 ± 3.91 versus 10.32 ± 2.22; P = 0.01) and serum total testosterone levels (0.65 ± 0.69 versus 0.86 ± 0.41 ng/ml; P = 0.01. Two clear phenotypes, i.e. obese hyperinsulinaemic dysglycemic women from Delhi and lean hyperandrogenic women from Srinagar are emerging. This is the first report on North Indian women with PCOS showing phenotypic differences in clinical, biochemical and hormonal parameters despite being in the same region.
tubercu- losis granulomas in guinea pig, rabbit, and nonhuman primate PLOS Computational Biology | www.ploscompbiol.org 1 September 2012 | Volume 8...Phenotypic metabolic changes of M. tuberculosis H37Rv under hypoxia The persistence of M. tuberculosis in human granulomas is partly due to its...Carrillo J, Allen SS, et al. (2008) Tuberculous granulomas are hypoxic in guinea pigs, rabbits, and nonhuman primates. Infect Immun 76: 2333–2340. 23
Anacker, Brian L; Rank, Nathan E; Hüberli, Daniel; Garbelotto, Matteo; Gordon, Sarah; Harnik, Tami; Whitkus, Richard; Meentemeyer, Ross
Sudden oak death is an emerging forest disease caused by the invasive pathogen Phytophthora ramorum. Genetic and environmental factors affecting susceptibility to P. ramorum in the key inoculum-producing host tree Umbellularia californica (bay laurel) were examined across a heterogeneous landscape in California, USA. Laboratory susceptibility trials were conducted on detached leaves and assessed field disease levels for 97 host trees from 12 225-m(2) plots. Genotype and phenotype characteristics were assessed for each tree. Effects of plot-level environmental conditions (understory microclimate, amount of solar radiation and topographic moisture potential) on disease expression were also evaluated. Susceptibility varied significantly among U. californica trees, with a fivefold difference in leaf lesion size. Lesion size was positively related to leaf area, but not to other phenotypic traits or to field disease level. Genetic diversity was structured at three spatial scales, but primarily among individuals within plots. Lesion size was significantly related to amplified fragment length polymorphism (AFLP) markers, but local environment explained most variation in field disease level. Thus, substantial genetic variation in susceptibility to P. ramorum occurs in its principal foliar host U. californica, but local environment mediates expression of susceptibility in nature.
Miyadera, Keiko; Acland, Gregory M; Aguirre, Gustavo D
Considerable clinical and molecular variations have been known in retinal blinding diseases in man and also in dogs. Different forms of retinal diseases occur in specific breed(s) caused by mutations segregating within each isolated breeding population. While molecular studies to find genes and mutations underlying retinal diseases in dogs have benefited largely from the phenotypic and genetic uniformity within a breed, within- and across-breed variations have often played a key role in elucidating the molecular basis. The increasing knowledge of phenotypic, allelic, and genetic heterogeneities in canine retinal degeneration has shown that the overall picture is rather more complicated than initially thought. Over the past 20 years, various approaches have been developed and tested to search for genes and mutations underlying genetic traits in dogs, depending on the availability of genetic tools and sample resources. Candidate gene, linkage analysis, and genome-wide association studies have so far identified 24 mutations in 18 genes underlying retinal diseases in at least 58 dog breeds. Many of these genes have been associated with retinal diseases in humans, thus providing opportunities to study the role in pathogenesis and in normal vision. Application in therapeutic interventions such as gene therapy has proven successful initially in a naturally occurring dog model followed by trials in human patients. Other genes whose human homologs have not been associated with retinal diseases are potential candidates to explain equivalent human diseases and contribute to the understanding of their function in vision.
Acland, Gregory M.
Considerable clinical and molecular variations have been known in retinal blinding diseases in man and also in dogs. Different forms of retinal diseases occur in specific breed(s) caused by mutations segregating within each isolated breeding population. While molecular studies to find genes and mutations underlying retinal diseases in dogs have benefited largely from the phenotypic and genetic uniformity within a breed, within- and across-breed variations have often played a key role in elucidating the molecular basis. The increasing knowledge of phenotypic, allelic, and genetic heterogeneities in canine retinal degeneration has shown that the overall picture is rather more complicated than initially thought. Over the past 20 years, various approaches have been developed and tested to search for genes and mutations underlying genetic traits in dogs, depending on the availability of genetic tools and sample resources. Candidate gene, linkage analysis, and genome-wide association studies have so far identified 24 mutations in 18 genes underlying retinal diseases in at least 58 dog breeds. Many of these genes have been associated with retinal diseases in humans, thus providing opportunities to study the role in pathogenesis and in normal vision. Application in therapeutic interventions such as gene therapy has proven successful initially in a naturally occurring dog model followed by trials in human patients. Other genes whose human homologs have not been associated with retinal diseases are potential candidates to explain equivalent human diseases and contribute to the understanding of their function in vision. PMID:22065099
Jing, Hai-Chun; Kornyukhin, Dmitry; Kanyuka, Kostya; Orford, Simon; Zlatska, Anastasiya; Mitrofanova, Olga P; Koebner, Robert; Hammond-Kosack, Kim
Einkorn wheat Triticum monococcum (2n=2x=14, A(m)A(m)) is one of the earliest domesticated crops. However, it was abandoned for cultivation before the Bronze Age and has infrequently been used in wheat breeding. Little is known about the genetic variation in adaptively important biological traits in T. monococcum. A collection of 30 accessions of diverse geographic origins were characterized for phenotypic variation in various agro-morphological traits including grain storage proteins and endosperm texture, nucleotide-binding site (NBS) domain profiles of resistance (R) genes and resistance gene analogues (RGAs), and germination under salt and drought stresses. Forty-six SSR (single sequence repeat) markers from bread wheat (T. aestivum, 2n=6x=42, AABBDD) A genome were used to establish trait-marker associations using linear mixed models. Multiple significant associations were identified, some of which were on chromosomal regions containing previously known genetic loci. It is concluded that T. monococcum possesses large genetic diversity in multiple traits. The findings also indicate that the efficiency of association mapping is much higher in T. monococcum than in other plant species. The use of T. monococcum as a reference species for wheat functional genomics is discussed.
Grabowski, Paul P; Morris, Geoffrey P; Casler, Michael D; Borevitz, Justin O
Geographic patterns of genetic variation are shaped by multiple evolutionary processes, including genetic drift, migration and natural selection. Switchgrass (Panicum virgatum L.) has strong genetic and adaptive differentiation despite life history characteristics that promote high levels of gene flow and can homogenize intraspecific differences, such as wind-pollination and self-incompatibility. To better understand how historical and contemporary factors shape variation in switchgrass, we use genotyping-by-sequencing to characterize switchgrass from across its range at 98 042 SNPs. Population structuring reflects biogeographic and ploidy differences within and between switchgrass ecotypes and indicates that biogeographic history, ploidy incompatibilities and differential adaptation each have important roles in shaping ecotypic differentiation in switchgrass. At one extreme, we determine that two Panicum taxa are not separate species but are actually conspecific, ecologically divergent types of switchgrass adapted to the extreme conditions of coastal sand dune habitats. Conversely, we identify natural hybrids among lowland and upland ecotypes and visualize their genome-wide patterns of admixture. Furthermore, we determine that genetic differentiation between primarily tetraploid and octoploid lineages is not caused solely by ploidy differences. Rather, genetic diversity in primarily octoploid lineages is consistent with a history of admixture. This suggests that polyploidy in switchgrass is promoted by admixture of diverged lineages, which may be important for maintaining genetic differentiation between switchgrass ecotypes where they are sympatric. These results provide new insights into the mechanisms shaping variation in widespread species and provide a foundation for dissecting the genetic basis of adaptation in switchgrass. PMID:24962137
Joyce, Susan A; Clarke, David J
Photorhabdus is a genus of entomopathogenic Gram-negative bacteria that belong to the family Enterobactericeae. Remarkably, at the same time as being pathogenic to insect larvae, Photorhabdus also have a mutualistic relationship with entomophagous nematodes of the family Heterorhabditiae. Photorhabdus can be isolated in two phenotypically distinct forms, termed the primary and secondary variant. Both variants grow equally well and are equally virulent when injected into insect larvae. However, only the primary variant can colonize the intestinal tract of the IJ stage of the nematode and support nematode growth and development. The primary variant expresses several phenotypes that are absent from the secondary variant, including the production of extracellular enzymes, pigments, antibiotics and light. In this study, we use Photorhabdus temperata strain K122 to show that these primary-specific products are symbiosis factors, i.e. factors that are required for nematode growth and development. We also show that, in P. temperata K122, the production of these symbiosis factors is repressed in the secondary variant by the protein encoded by a gene with homology to hexA from Erwinia. Moreover, the derepression of the symbiosis factors in the secondary variant results in a significant attenuation of virulence to larvae of the greater wax moth, Galleria mellonella. This suggests that, during a normal infection, pathogenicity and symbiosis must be temporally separated and that HexA is involved in the regulation of this pathogen-symbiont transition.
Pease, James B.; Haak, David C.; Hahn, Matthew W.; Moyle, Leonie C.
Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a “PhyloGWAS” approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations. PMID:26871574
Lovell, John T; Grogan, Kelsi; Sharbel, Timothy F; McKay, John K
Determining the relative contribution of population genetic processes to the distribution of natural variation is a major goal of evolutionary biology. Here, we take advantage of variation in mating system to test the hypothesis that local adaptation is constrained by asexual reproduction. We explored patterns of variation in ecological traits and genome-wide molecular markers in Boechera spatifolia (Brassicaceae), a species that contains both apomictic (asexual) and sexual individuals. Using a combination of quantitative genetics, neutral genetic (SSR) and genome-wide single nucleotide polymorphism, we assessed the hypothesis that asexual lineages should have reduced signatures of adaptation relative to sexual conspecifics. All three measures (traits, SSRs, SNPs) demonstrated that apomicts are genetically distinct from sexuals, regardless of population location. Additionally, phylogenetic clustering revealed that the apomictic group shared a single common ancestor. Across the landscape, sexual genome-wide SNP variation was strongly associated with latitude (r(2) > 0.9), indicating that sexual populations have differentiated across an environmental gradient. Furthermore, flowering time and growth rate, as assessed in a common garden, strongly covary with the elevation and latitude of the source population. Despite a wide geographic distribution that largely overlaps with sexual populations, there was little evidence for differentiation in molecular markers or quantitative characters among apomictic populations. Combined, these data indicated that, in contrast to asexual populations, sexual populations show evidence of local adaptation.
Xu, Qin; Zhu, Caiyun; Fan, Yangyang; Song, Zhihong; Xing, Shilai; Liu, Wei; Yan, Juan; Sang, Tao
Expression variation plays an important role in plant adaptation, but little is known about the factors impacting the expression variation when population adapts to changing environment. We used RNA-seq data from 80 individuals in 14 Miscanthus lutarioriparius populations, which were transplanted into a harsh environment from native habitat, to investigate the expression level, expression diversity and genetic diversity for genes expressed in both environments. The expression level of genes with lower expression level or without SNP tended to be more changeable in new environment, which suggested highly expressed genes experienced stronger purifying selection than those at lower level. Low proportion of genes with population effect confirmed the weak population structure and frequent gene flow in these populations. Meanwhile, the number of genes with environment effect was the most frequent compared with that with population effect. Our results showed that environment and genetic diversity were the main factors determining gene expression variation in population. This study could facilitate understanding the mechanisms of global gene expression variation when plant population adapts to changing environment. PMID:27150248
Lasky, Jesse R; Des Marais, David L; Lowry, David B; Povolotskaya, Inna; McKay, John K; Richards, James H; Keitt, Timothy H; Juenger, Thomas E
Gene expression varies widely in natural populations, yet the proximate and ultimate causes of this variation are poorly known. Understanding how variation in gene expression affects abiotic stress tolerance, fitness, and adaptation is central to the field of evolutionary genetics. We tested the hypothesis that genes with natural genetic variation in their expression responses to abiotic stress are likely to be involved in local adaptation to climate in Arabidopsis thaliana. Specifically, we compared genes with consistent expression responses to environmental stress (expression stress responsive, "eSR") to genes with genetically variable responses to abiotic stress (expression genotype-by-environment interaction, "eGEI"). We found that on average genes that exhibited eGEI in response to drought or cold had greater polymorphism in promoter regions and stronger associations with climate than those of eSR genes or genomic controls. We also found that transcription factor binding sites known to respond to environmental stressors, especially abscisic acid responsive elements, showed significantly higher polymorphism in drought eGEI genes in comparison to eSR genes. By contrast, eSR genes tended to exhibit relatively greater pairwise haplotype sharing, lower promoter diversity, and fewer nonsynonymous polymorphisms, suggesting purifying selection or selective sweeps. Our results indicate that cis-regulatory evolution and genetic variation in stress responsive gene expression may be important mechanisms of local adaptation to climatic selective gradients.
Quibod, Ian Lorenzo; Perez-Quintero, Alvaro; Booher, Nicholas J.; Dossa, Gerbert S.; Grande, Genelou; Szurek, Boris; Vera Cruz, Casiana; Bogdanove, Adam J.; Oliva, Ricardo
Understanding the processes that shaped contemporary pathogen populations in agricultural landscapes is quite important to define appropriate management strategies and to support crop improvement efforts. Here, we took advantage of an historical record to examine the adaptation pathway of the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo) in a semi-isolated environment represented in the Philippine archipelago. By comparing genomes of key Xoo groups we showed that modern populations derived from three Asian lineages. We also showed that diversification of virulence factors occurred within each lineage, most likely driven by host adaptation, and it was essential to shape contemporary pathogen races. This finding is particularly important because it expands our understanding of pathogen adaptation to modern agriculture. PMID:27667260
Hughes, A Randall; Hanley, Torrance C; Byers, James E; Grabowski, Jonathan H; Malek, Jennafer C; Piehler, Michael F; Kimbro, David L
Functional trait variation within and across populations can strongly influence population, community, and ecosystem processes, but the relative contributions of genetic vs. environmental factors to this variation are often not clear, potentially complicating conservation and restoration efforts. For example, local adaptation, a particular type of genetic by environmental (G*E) interaction in which the fitness of a population in its own habitat is greater than in other habitats, is often invoked in management practices, even in the absence of supporting evidence. Despite increasing attention to the potential for G*E interactions, few studies have tested multiple populations and environments simultaneously, limiting our understanding of the spatial consistency in patterns of adaptive genetic variation. In addition, few studies explicitly differentiate adaptation in response to predation from other biological and environmental factors. We conducted a reciprocal transplant experiment of first-generation eastern oyster (Crassostrea virginica) juveniles from six populations across three field sites spanning 1000 km in the southeastern Atlantic Bight in both the presence and absence of predation to test for G*E variation in this economically valuable and ecologically important species. We documented significant G*E variation in survival and growth, yet there was no evidence for local adaptation. Condition varied across oyster cohorts: Offspring of northern populations had better condition than offspring from the center of our region. Oyster populations in the southeastern Atlantic Bight differ in juvenile survival, growth, and condition, yet offspring from local broodstock do not have higher survival or growth than those from farther away. In the absence of population-specific performance information, oyster restoration and aquaculture may benefit from incorporating multiple populations into their practices.
K, Shamnamole; Jalali, Saakshi; Scaria, Vinod; Bhardwaj, Anshu
Human mitochondrial DNA (mtDNA) encodes a set of 37 genes which are essential structural and functional components of the electron transport chain. Variations in these genes have been implicated in a broad spectrum of diseases and are extensively reported in literature and various databases. In this study, we describe MitoLSDB, an integrated platform to catalogue disease association studies on mtDNA (http://mitolsdb.igib.res.in). The main goal of MitoLSDB is to provide a central platform for direct submissions of novel variants that can be curated by the Mitochondrial Research Community. MitoLSDB provides access to standardized and annotated data from literature and databases encompassing information from 5231 individuals, 675 populations and 27 phenotypes. This platform is developed using the Leiden Open (source) Variation Database (LOVD) software. MitoLSDB houses information on all 37 genes in each population amounting to 132397 variants, 5147 unique variants. For each variant its genomic location as per the Revised Cambridge Reference Sequence, codon and amino acid change for variations in protein-coding regions, frequency, disease/phenotype, population, reference and remarks are also listed. MitoLSDB curators have also reported errors documented in literature which includes 94 phantom mutations, 10 NUMTs, six documentation errors and one artefactual recombination. MitoLSDB is the largest repository of mtDNA variants systematically standardized and presented using the LOVD platform. We believe that this is a good starting resource to curate mtDNA variants and will facilitate direct submissions enhancing data coverage, annotation in context of pathogenesis and quality control by ensuring non-redundancy in reporting novel disease associated variants. PMID:23585830
Yin, Li; Sun, Mingzeng; Ilic, Zoran; Leffert, Hyam L; Sell, Stewart
Liver progenitor cells (LPCs) cloned from adult rat livers following allyl alcohol injury express hematopoietic stem cell and early hepatic lineage markers when cultured on feeder layers; under these conditions, neither mature hepatocyte nor bile duct, Ito, stellate, Kupffer cell, or macrophage markers are detected. These phenotypes have remained stable without aneuploidy or morphological transformation after more than 100 population doublings. When cultured without feeder layers, the early lineage markers disappear, and mature hepatocyte markers are expressed; mature hepatocytic differentiation and cell size are also augmented by polypeptide and steroidal growth factors. In contrast to hepatocytic potential, duct-like structures and biliary epithelial markers are expressed on Matrigel. Because they were derived without carcinogens or mutagens, these bipotential LPC lines provide novel tools for models of cellular plasticity and hepatocarcinogenesis, as well as lines for use in cellular transplantation, gene therapy, and bioreactor construction.
Hu, Yinan; Albertson, R. Craig
Adaptive variation in the craniofacial skeleton is a key component of resource specialization and habitat divergence in vertebrates, but the proximate genetic mechanisms that underlie complex patterns of craniofacial variation are largely unknown. Here we demonstrate that the Hedgehog (Hh) signaling pathway mediates widespread variation across a complex functional system that affects the kinematics of lower jaw depression—the opercular four-bar linkage apparatus—among Lake Malawi cichlids. By using a combined quantitative trait locus mapping and population genetics approach, we show that allelic variation in the Hh receptor, ptch1, affects the development of distinct bony elements in the head that represent two of three movable links in this functional system. The evolutionarily derived allele is found in species that feed from the water column, and is associated with shifts in anatomy that translate to a four-bar system capable of faster jaw rotation. Alternatively, the ancestral allele is found in species that feed on attached algae, and is associated with the development of a four-bar system that predicts slower jaw movement. Experimental manipulation of the Hh pathway during cichlid development recapitulates functionally salient natural variation in craniofacial geometry. In all, these results significantly extend our understanding of the mechanisms that fine-tune the craniofacial skeletal complex during adaptation to new foraging niches. PMID:24912175
Hu, Yinan; Albertson, R Craig
Adaptive variation in the craniofacial skeleton is a key component of resource specialization and habitat divergence in vertebrates, but the proximate genetic mechanisms that underlie complex patterns of craniofacial variation are largely unknown. Here we demonstrate that the Hedgehog (Hh) signaling pathway mediates widespread variation across a complex functional system that affects the kinematics of lower jaw depression--the opercular four-bar linkage apparatus--among Lake Malawi cichlids. By using a combined quantitative trait locus mapping and population genetics approach, we show that allelic variation in the Hh receptor, ptch1, affects the development of distinct bony elements in the head that represent two of three movable links in this functional system. The evolutionarily derived allele is found in species that feed from the water column, and is associated with shifts in anatomy that translate to a four-bar system capable of faster jaw rotation. Alternatively, the ancestral allele is found in species that feed on attached algae, and is associated with the development of a four-bar system that predicts slower jaw movement. Experimental manipulation of the Hh pathway during cichlid development recapitulates functionally salient natural variation in craniofacial geometry. In all, these results significantly extend our understanding of the mechanisms that fine-tune the craniofacial skeletal complex during adaptation to new foraging niches.
Meng, T.-T.; Wang, H.; Harrison, S. P.; Prentice, I. C.; Ni, J.; Wang, G.
Dynamic global vegetation models (DGVMs) typically rely on plant functional types (PFTs), which are assigned distinct environmental tolerances and replace one another progressively along environmental gradients. Fixed values of traits are assigned to each PFT; modelled trait variation along gradients is thus driven by PFT replacement. But empirical studies have revealed "universal" scaling relationships (quantitative trait variations with climate that are similar within and between species, PFTs and communities); and continuous, adaptive trait variation has been proposed to replace PFTs as the basis for next-generation DGVMs. Here we analyse quantitative leaf-trait variation on long temperature and moisture gradients in China with a view to understanding the relative importance of PFT replacement vs. continuous adaptive variation within PFTs. Leaf area (LA), specific leaf area (SLA), leaf dry matter content (LDMC) and nitrogen content of dry matter were measured on all species at 80 sites ranging from temperate to tropical climates and from dense forests to deserts. Chlorophyll fluorescence traits and carbon, phosphorus and potassium contents were measured at 47 sites. Generalized linear models were used to relate log-transformed trait values to growing-season temperature and moisture indices, with or without PFT identity as a predictor, and to test for differences in trait responses among PFTs. Continuous trait variation was found to be ubiquitous. Responses to moisture availability were generally similar within and between PFTs, but biophysical traits (LA, SLA and LDMC) of forbs and grasses responded differently from woody plants. SLA and LDMC responses to temperature were dominated by the prevalence of evergreen PFTs with thick, dense leaves at the warm end of the gradient. Nutrient (N, P and K) responses to climate gradients were generally similar within all PFTs. Area-based nutrients generally declined with moisture; Narea and Karea declined with temperature
Fan, Shaohua; Meyer, Axel
African cichlid fishes are an ideal system for studying explosive rates of speciation and the origin of diversity in adaptive radiation. Within the last few million years, more than 2000 species have evolved in the Great Lakes of East Africa, the largest adaptive radiation in vertebrates. These young species show spectacular diversity in their coloration, morphology and behavior. However, little is known about the genomic basis of this astonishing diversity. Recently, five African cichlid genomes were sequenced, including that of the Nile Tilapia (Oreochromis niloticus), a basal and only relatively moderately diversified lineage, and the genomes of four representative endemic species of the adaptive radiations, Neolamprologus brichardi, Astatotilapia burtoni, Metriaclima zebra, and Pundamila nyererei. Using the Tilapia genome as a reference genome, we generated a high-resolution genomic variation map, consisting of single nucleotide polymorphisms (SNPs), short insertions and deletions (indels), inversions and deletions. In total, around 18.8, 17.7, 17.0, and 17.0 million SNPs, 2.3, 2.2, 1.4, and 1.9 million indels, 262, 306, 162, and 154 inversions, and 3509, 2705, 2710, and 2634 deletions were inferred to have evolved in N. brichardi, A. burtoni, P. nyererei, and M. zebra, respectively. Many of these variations affected the annotated gene regions in the genome. Different patterns of genetic variation were detected during the adaptive radiation of African cichlid fishes. For SNPs, the highest rate of evolution was detected in the common ancestor of N. brichardi, A. burtoni, P. nyererei, and M. zebra. However, for the evolution of inversions and deletions, we found that the rates at the terminal taxa are substantially higher than the rates at the ancestral lineages. The high-resolution map provides an ideal opportunity to understand the genomic bases of the adaptive radiation of African cichlid fishes. PMID:24917883
Background In island archipelagos, where islands have experienced repeated periods of fragmentation and connection through cyclic changes in sea level, complex among-island distributions might reflect historical distributional changes or local evolution. We test the relative importance of these mechanisms in an endemic radiation of Rhagada land snails in the Dampier Archipelago, a continental archipelago off the coast of Western Australia, where ten morphospecies have complex, overlapping distributions. Results We obtained partial mtDNA sequence (COI) for 1015 snails collected from 213 locations across 30 Islands, and used Bayesian phylogenetic analysis and Analysis of Molecular Variance (AMOVA) to determine whether geography or the morphological taxonomy best explains the pattern of molecular evolution. Rather than forming distinct monophyletic groups, as would be expected if they had single, independent origins, all of the widely distributed morphospecies were polyphyletic, distributed among several well-supported clades, each of which included several morphospecies. Each mitochondrial clade had a clear, cohesive geographic distribution, together forming a series of parapatric replacements separated by narrow contact zones. AMOVA revealed further incongruence between mtDNA diversity and morphological variation within clades, as the taxonomic hypothesis always explained a low or non-significant proportion of the molecular variation. In contrast, the pattern of mtDNA evolution closely reflected contemporary and historical marine barriers. Conclusions Despite opportunities for distributional changes during periods when the islands were connected, there is no evidence that dispersal has contributed to the geographic variation of shell form at the broad scale. Based on an estimate of dispersal made previously for Rhagada, we conclude that the periods of connection have been too short in duration to allow for extensive overland dispersal or deep mitochondrial
Ryan, Annette C; Dodd, Ian C; Rothwell, Shane A; Jones, Ros; Tardieu, Francois; Draye, Xavier; Davies, William J
There is increasing interest in rapidly identifying genotypes with improved water use efficiency, exemplified by the development of whole plant phenotyping platforms that automatically measure plant growth and water use. Transpirational responses to atmospheric vapour pressure deficit (VPD) and whole plant water use efficiency (WUE, defined as the accumulation of above ground biomass per unit of water used) were measured in 100 maize (Zea mays L.) genotypes. Using a glasshouse based phenotyping platform with naturally varying VPD (1.5-3.8kPa), a 2-fold variation in WUE was identified in well-watered plants. Regression analysis of transpiration versus VPD under these conditions, and subsequent whole plant gas exchange at imposed VPDs (0.8-3.4kPa) showed identical responses in specific genotypes. Genotype response of transpiration versus VPD fell into two categories: 1) a linear increase in transpiration rate with VPD with low (high WUE) or high (low WUE) transpiration rate at all VPDs, 2) a non-linear response with a pronounced change point at low VPD (high WUE) or high VPD (low WUE). In the latter group, high WUE genotypes required a significantly lower VPD before transpiration was restricted, and had a significantly lower rate of transpiration in response to VPD after this point, when compared to low WUE genotypes. Change point values were significantly positively correlated with stomatal sensitivity to VPD. A change point in stomatal response to VPD may explain why some genotypes show contradictory WUE rankings according to whether they are measured under glasshouse or field conditions. Furthermore, this novel use of a high throughput phenotyping platform successfully reproduced the gas exchange responses of individuals measured in whole plant chambers, accelerating the identification of plants with high WUE.
Ciota, Alexander T; Payne, Anne F; Kramer, Laura D
West Nile virus (WNV; Flaviviridae, Flavivirus) is the most geographically widespread arthropod-borne virus (arbovirus) in the world and is found in multiple ecologically distinct settings. Despite the likelihood of frequent exposure to novel hosts, studies evaluating the capacity and correlates of host range expansions or shifts of WNV and other arboviruses are generally lacking. We utilized experimental evolution of WNV in an Amblyomma americanum tick cell line to model an invertebrate host shift and evaluate the adaptive potential of WNV outside of its primary transmission cycle. Our results demonstrate that highly significant gains in replicative ability in ixodid tick cells are attainable for WNV but are also associated with widespread genetic change and significant phenotypic costs in vitro. Decreased fitness in primary hosts could represent a barrier to frequent exploitation of hard ticks by WNV in nature.
Ciota, Alexander T.; Payne, Anne F.; Kramer, Laura D.
West Nile virus (WNV; Flaviviridae, Flavivirus) is the most geographically widespread arthropod-borne virus (arbovirus) in the world and is found in multiple ecologically distinct settings. Despite the likelihood of frequent exposure to novel hosts, studies evaluating the capacity and correlates of host range expansions or shifts of WNV and other arboviruses are generally lacking. We utilized experimental evolution of WNV in an Amblyomma americanum tick cell line to model an invertebrate host shift and evaluate the adaptive potential of WNV outside of its primary transmission cycle. Our results demonstrate that highly significant gains in replicative ability in ixodid tick cells are attainable for WNV but are also associated with widespread genetic change and significant phenotypic costs in vitro. Decreased fitness in primary hosts could represent a barrier to frequent exploitation of hard ticks by WNV in nature. PMID:25863877
Rodriguez, Monica; Rau, Domenico; Angioi, Simonetta A.; Bellucci, Elisa; Bitocchi, Elena; Nanni, Laura; Knüpffer, Helmut; Negri, Valeria; Papa, Roberto; Attene, Giovanna
Relatively few studies have extensively analysed the genetic diversity of the runner bean through molecular markers. Here, we used six chloroplast microsatellites (cpSSRs) to investigate the cytoplasmic diversity of 331 European domesticated accessions of the scarlet runner bean (Phaseolus coccineus L.), including the botanical varieties albiflorus, bicolor and coccineus, and a sample of 49 domesticated and wild accessions from Mesoamerica. We further explored the pattern of diversity of the European landraces using 12 phenotypic traits on 262 individuals. For 158 European accessions, we studied the relationships between cpSSR polymorphisms and phenotypic traits. Additionally, to gain insights into the role of gene flow and migration, for a subset of 115 accessions, we compared and contrasted the results obtained by cpSSRs and phenotypic traits with those obtained in a previous study with 12 nuclear microsatellites (nuSSRs). Our results suggest that both demographic and selective factors have roles in the shaping of the population genetic structure of the European runner bean. In particular, we infer the existence of a moderate-to-strong cytoplasmic bottleneck that followed the expansion of the crop into Europe, and we deduce multiple domestication events for this species. We also observe an adaptive population differentiation in the phenology across a latitudinal gradient, which suggests that selection led to the diversification of the runner bean in Europe. The botanical varieties albiflorus, bicolor and coccineus, which are based solely on flower colour, cannot be distinguished based on these cpSSRs and nuSSRs, nor according to the 12 quantitative traits. PMID:23451209
Davidson, Amy Michelle; Jennions, Michael; Nicotra, Adrienne B
Do invasive plant species have greater phenotypic plasticity than non-invasive species? And, if so, how does this affect their fitness relative to native, non-invasive species? What role might this play in plant invasions? To answer these long-standing questions, we conducted a meta-analysis using data from 75 invasive/non-invasive species pairs. Our analysis shows that invasive species demonstrate significantly higher phenotypic plasticity than non-invasive species. To examine the adaptive benefit of this plasticity, we plotted fitness proxies against measures of plasticity in several growth, morphological and physiological traits to test whether greater plasticity is associated with an improvement in estimated fitness. Invasive species were nearly always more plastic in their response to greater resource availability than non-invasives but this plasticity was only sometimes associated with a fitness benefit. Intriguingly, non-invasive species maintained greater fitness homoeostasis when comparing growth between low and average resource availability. Our finding that invasive species are more plastic in a variety of traits but that non-invasive species respond just as well, if not better, when resources are limiting, has interesting implications for predicting responses to global change.
MANEL, STÉPHANIE; GUGERLI, FELIX; THUILLER, WILFRIED; ALVAREZ, NADIR; LEGENDRE, PIERRE; HOLDEREGGER, ROLF; GIELLY, LUDOVIC; TABERLET, PIERRE
Identifying adaptive genetic variation is a challenging task, in particular in non-model species for which genomic information is still limited or absent. Here, we studied distribution patterns of amplified fragment length polymorphisms (AFLPs) in response to environmental variation, in 13 alpine plant species consistently sampled across the entire European Alps. Multiple linear regressions were performed between AFLP allele frequencies per site as dependent variables and two categories of independent variables, namely Moran’s eigenvector map MEM variables (to account for spatial and unaccounted environmental variation, and historical demographic processes) and environmental variables. These associations allowed the identification of 153 loci of ecological relevance. Univariate regressions between allele frequency and each environmental factor further showed that loci of ecological relevance were mainly correlated with MEM variables. We found that precipitation and temperature were the best environmental predictors, whereas topographic factors were rarely involved in environmental associations. Climatic factors, subject to rapid variation as a result of the current global warming, are known to strongly influence the fate of alpine plants. Our study shows, for the first time for a large number of species, that the same environmental variables are drivers of plant adaptation at the scale of a whole biome, here the European Alps. PMID:22680783
Appelbaum, Tatyana; Becker, Doreen; Santana, Evelyn
Purpose Canine X-linked progressive retinal atrophy 1 (XLPRA1) caused by a mutation in retinitis pigmentosa (RP) GTPase regulator (RPGR) exon ORF15 showed significant variability in disease onset in a colony of dogs that all inherited the same mutant X chromosome. Defective protein trafficking has been detected in XLPRA1 before any discernible degeneration of the photoreceptors. We hypothesized that the severity of the photoreceptor degeneration in affected dogs may be associated with defects in genes involved in ciliary trafficking. To this end, we examined six genes as potential disease modifiers. We also examined the expression levels of 24 genes involved in ciliary trafficking (seven), visual pathway (five), neuronal maintenance genes (six), and cellular stress response (six) to evaluate their possible involvement in early stages of the disease. Methods Samples from a pedigree derived from a single XLPRA1-affected male dog outcrossed to unrelated healthy mix-bred or purebred females were used for immunohistochemistry (IHC), western blot, mutational and haplotype analysis, and gene expression (GE). Cell-specific markers were used to examine retinal remodeling in the disease. Single nucleotide polymorphisms (SNPs) spanning the entire RPGR interacting and protein trafficking genes (RAB8A, RPGRIP1L, CEP290, CC2D2A, DFNB31, and RAB11B) were genotyped in the pedigree. Quantitative real-time PCR (qRT-PCR) was used to examine the expression of a total of 24 genes, including the six genes listed. Results Examination of cryosections from XLPRA1-affected animals of similar age (3–4 years) with different disease severity phenotype revealed mislocalization of opsins and upregulation of the Müller cell gliosis marker GFAP. Four to ten haplotypes per gene were identified in RAB8A, RPGRIP1L, CEP290, CC2D2A, DFNB31, and RAB11B for further assessment as potential genetic modifiers of XLPRA1. No correlation was found between the haplotypes and disease severity. During
Alonso-Blanco, Carlos; Aarts, Mark G.M.; Bentsink, Leonie; Keurentjes, Joost J.B.; Reymond, Matthieu; Vreugdenhil, Dick; Koornneef, Maarten
Nearly 100 genes and functional polymorphisms underlying natural variation in plant development and physiology have been identified. In crop plants, these include genes involved in domestication traits, such as those related to plant architecture, fruit and seed structure and morphology, as well as yield and quality traits improved by subsequent crop breeding. In wild plants, comparable traits have been dissected mainly in Arabidopsis thaliana. In this review, we discuss the major contributions of the analysis of natural variation to our understanding of plant development and physiology, focusing in particular on the timing of germination and flowering, plant growth and morphology, primary metabolism, and mineral accumulation. Overall, functional polymorphisms appear in all types of genes and gene regions, and they may have multiple mutational causes. However, understanding this diversity in relation to adaptation and environmental variation is a challenge for which tools are now available. PMID:19574434
Jodice, C.; Malaspina, P.; Persichetti, F.; Novelletto, A.; Terrenato, L. ); Spadaro, M.; Morocutti, C. ); Giunti, P. Institute of Neurology, London ); Harding, A.E. ); Frontali, M. )
Trinucleotide repeat expansion has been found in 64 subjects from 19 families: 57 patients with SCA1 and 7 subjects predicted, by haplotype analysis, to carry the mutation. Comparison with a large set of normal chromosomes shows two distinct distributions, with a much wider variation among expanded chromosomes. The sex of transmitting parent plays a major role in the size distribution of expanded alleles, those with >54 repeats being transmitted by affected fathers exclusively. The data suggest that alleles with >54 repeats have a reduced chance of survival; these appear to be replaced in each generation by further expansion of alleles in the low- to medium-expanded repeat range, preferentially in male transmission. Detailed clinical follow-up of a subset of patients demonstrates significant relationships between increasing repeat number on expanded chromosomes and earlier age at onset, faster progression of the disease, and earlier age at death.
Husby, Arild; Kawakami, Takeshi; Rönnegård, Lars; Smeds, Linnéa; Ellegren, Hans; Qvarnström, Anna
Understanding the genetic basis of traits involved in adaptation is a major challenge in evolutionary biology but remains poorly understood. Here, we use genome-wide association mapping using a custom 50 k single nucleotide polymorphism (SNP) array in a natural population of collared flycatchers to examine the genetic basis of clutch size, an important life-history trait in many animal species. We found evidence for an association on chromosome 18 where one SNP significant at the genome-wide level explained 3.9% of the phenotypic variance. We also detected two suggestive quantitative trait loci (QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were generally weak and not significant, although there was some indication of a sex-by-genotype interaction for lifetime reproductive success at the suggestive QTL on chromosome 26. This implies that sexual antagonism may play a role in maintaining genetic variation at this QTL. Our findings provide candidate regions for a classic avian life-history trait that will be useful for future studies examining the molecular and cellular function of, as well as evolutionary mechanisms operating at, these loci.
Background Consuming moderate amounts of lean red meat as part of a balanced diet valuably contributes to intakes of essential nutrients. In this study, we merged phenotypic and genotypic information to characterize the variation in lipid profile and sensory parameters and to represent the diversity among 15 cattle populations. Correlations between fat content, organoleptic characteristics and lipid profiles were also investigated. Methods A sample of 436 largely unrelated purebred bulls belonging to 15 breeds and reared under comparable management conditions was analyzed. Phenotypic data -including fatness score, fat percentage, individual fatty acids (FA) profiles and sensory panel tests- and genotypic information from 11 polymorphisms was used. Results The correlation coefficients between muscle total lipid measurements and absolute vs. relative amounts of polyunsaturated FA (PUFA) were in opposite directions. Increasing carcass fat leads to an increasing amount of FAs in triglycerides, but at the same time the relative amount of PUFAs is decreasing, which is in concordance with the negative correlation obtained here between the percentage of PUFA and fat measurements, as well as the weaker correlation between total phospholipids and total lipid muscle content compared with neutral lipids. Concerning organoleptic characteristics, a negative correlation between flavour scores and the percentage of total PUFA, particularly to n-6 fraction, was found. The correlation between juiciness and texture is higher than with flavour scores. The distribution of SNPs plotted by principal components analysis (PCA) mainly reflects their known trait associations, although influenced by their specific breed allele frequencies. Conclusions The results presented here help to understand the phenotypic and genotypic background underlying variations in FA composition and sensory parameters between breeds. The wide range of traits and breeds studied, along with the genotypic
Sousa, Leijiane F; Portes-Junior, José A; Nicolau, Carolina A; Bernardoni, Juliana L; Nishiyama-Jr, Milton Y; Amazonas, Diana R; Freitas-de-Sousa, Luciana A; Mourão, Rosa Hv; Chalkidis, Hipócrates M; Valente, Richard H; Moura-da-Silva, Ana M
Venom variability is commonly reported for venomous snakes including Bothrops atrox. Here, we compared the composition of venoms from B. atrox snakes collected at Amazonian conserved habitats (terra-firme upland forest and várzea) and human modified areas (pasture and degraded areas). Venom samples were submitted to shotgun proteomic analysis as a whole or compared after fractionation by reversed-phase chromatography. Whole venom proteomes revealed a similar composition among the venoms with predominance of SVMPs, CTLs, and SVSPs and intermediate amounts of PLA2s and LAAOs. However, when distribution of particular isoforms was analyzed by either method, the venom from várzea snakes showed a decrease in hemorrhagic SVMPs and an increase in SVSPs, and procoagulant SVMPs and PLA2s. These differences were validated by experimental approaches including both enzymatic and in vivo assays, and indicated restrictions in respect to antivenom efficacy to variable components. Thus, proteomic analysis at the isoform level combined to in silico prediction of functional properties may indicate venom biological activity. These results also suggest that the prevalence of functionally distinct isoforms contributes to the variability of the venoms and could reflect the adaptation of B. atrox to distinct prey communities in different Amazon habitats.
Weiss, Julia; Mühlemann, Joëlle K.; Ruiz-Hernández, Victoria; Dudareva, Natalia; Egea-Cortines, Marcos
The genus Antirrhinum comprises about 28 species with a center of origin in the Iberian Peninsula. They show an important diversity of growing niches. We have performed a comprehensive analysis of scent profiles in eight wild species, Antirrhinum linkianum, A. tortuosum, A. cirrigherum, A. latifolium, A. meonanthum, A. braun-blanquetii, A. barrelieri, and A. graniticum. We used also two laboratory inbred lines A. majus, 165E and Sippe50. We identified 63 volatile organic compounds (VOCs) belonging to phenylpropanoids, benzenoids, mono- and sesquiterpenes, nitrogen-containing compounds, and aliphatic alcohols previously described in plants. Twenty-four VOCs were produced at levels higher than 2% of total VOC emission, while other VOCs were emitted in trace amounts. The absolute scent emission varied during flower maturation and species. The lowest emitting was A. meonanthum while A. tortuosum had the largest emissions. Species were clustered according to their scent profiles and the resulting dendrogram matched the current species phylogeny. However, two accessions, A. majus Sippe 50 and A. braun-blanquetii, showed development-specific changes in their VOC composition, suggesting a precise control and fine tuning of scent profiles. Cluster analysis of the different scent components failed to identify a specific synthesis pathway, indicating a key role of scent profiles as blends. There is considerable degree of chemodiversity in scent profiles in Antirrhinum. The specific developmental stage plays an important role in scent quantitative emissions. The relative robustness of the bouquets could be an adaptation to local pollinators. PMID:28066463
Background Salmonella enterica serovar Enteritidis (S. Enteritidis) has caused major epidemics of gastrointestinal infection in many different countries. In this study we investigate genome divergence and pathogenic potential in S. Enteritidis isolated before, during and after an epidemic in Uruguay. Results 266 S. Enteritidis isolates were genotyped using RAPD-PCR and a selection were subjected to PFGE analysis. From these, 29 isolates spanning different periods, genetic profiles and sources of isolation were assayed for their ability to infect human epithelial cells and subjected to comparative genomic hybridization using a Salmonella pan-array and the sequenced strain S. Enteritidis PT4 P125109 as reference. Six other isolates from distant countries were included as external comparators. Two hundred and thirty three chromosomal genes as well as the virulence plasmid were found as variable among S. Enteritidis isolates. Ten out of the 16 chromosomal regions that varied between different isolates correspond to phage-like regions. The 2 oldest pre-epidemic isolates lack phage SE20 and harbour other phage encoded genes that are absent in the sequenced strain. Besides variation in prophage, we found variation in genes involved in metabolism and bacterial fitness. Five epidemic strains lack the complete Salmonella virulence plasmid. Significantly, strains with indistinguishable genetic patterns still showed major differences in their ability to infect epithelial cells, indicating that the approach used was insufficient to detect the genetic basis of this differential behaviour. Conclusion The recent epidemic of S. Enteritidis infection in Uruguay has been driven by the introduction of closely related strains of phage type 4 lineage. Our results confirm previous reports demonstrating a high degree of genetic homogeneity among S. Enteritidis isolates. However, 10 of the regions of variability described here are for the first time reported as being variable in S
Beattie, M.L.; Kim, J.-W.; Gong, S.-G.; Murdoch-Kinch, C.A.; Simmer, J.P.; Hu, J.C.-C.
Dentinogenesis imperfecta (DGI) and dentin dysplasia (DD) are allelic disorders that primarily affect the formation of tooth dentin. Both conditions are autosomal-dominant and can be caused by mutations in the dentin sialophospho-protein gene (DSPP, 4q21.3). We recruited 23 members of a four-generation kindred, including ten persons with dentin defects, and tested the hypothesis that these defects are linked to DSPP. The primary dentition showed amber discoloration, pulp obliteration, and severe attrition. The secondary dentition showed either pulp obliteration with bulbous crowns and gray discoloration or thistle-tube pulp configurations, normal crowns, and mild gray discoloration. Haplotype analyses showed no recombination between three 4q21-q24 markers and the disease locus. Mutational analyses identified no coding or intron junction sequence variations associated with affection status in DMP1, MEPE, or the DSP portion of DSPP. The defects in the permanent dentition were typically mild and consistent with a diagnosis of DD-II, but some dental features associated with DGI-II were also present. We conclude that DD-II and DGI-II are milder and more severe forms, respectively, of the same disease. PMID:16567553
Rucker, James J.H.; Tansey, Katherine E.; Rivera, Margarita; Pinto, Dalila; Cohen-Woods, Sarah; Uher, Rudolf; Aitchison, Katherine J.; Craddock, Nick; Owen, Michael J.; Jones, Lisa; Jones, Ian; Korszun, Ania; Barnes, Michael R.; Preisig, Martin; Mors, Ole; Maier, Wolfgang; Rice, John; Rietschel, Marcella; Holsboer, Florian; Farmer, Anne E.; Craig, Ian W.; Scherer, Stephen W.; McGuffin, Peter; Breen, Gerome
Background Defining the molecular genomic basis of the likelihood of developing depressive disorder is a considerable challenge. We previously associated rare, exonic deletion copy number variants (CNV) with recurrent depressive disorder (RDD). Sex chromosome abnormalities also have been observed to co-occur with RDD. Methods In this reanalysis of our RDD dataset (N = 3106 cases; 459 screened control samples and 2699 population control samples), we further investigated the role of larger CNVs and chromosomal abnormalities in RDD and performed association analyses with clinical data derived from this dataset. Results We found an enrichment of Turner’s syndrome among cases of depression compared with the frequency observed in a large population sample (N = 34,910) of live-born infants collected in Denmark (two-sided p = .023, odds ratio = 7.76 [95% confidence interval = 1.79–33.6]), a case of diploid/triploid mosaicism, and several cases of uniparental isodisomy. In contrast to our previous analysis, large deletion CNVs were no more frequent in cases than control samples, although deletion CNVs in cases contained more genes than control samples (two-sided p = .0002). Conclusions After statistical correction for multiple comparisons, our data do not support a substantial role for CNVs in RDD, although (as has been observed in similar samples) occasional cases may harbor large variants with etiological significance. Genetic pleiotropy and sample heterogeneity suggest that very large sample sizes are required to study conclusively the role of genetic variation in mood disorders. PMID:25861698
Tully, Thomas; Potapov, Mikhail
We describe and compare the external morphology of eleven clonal strains and one sexual lineage of the globally distributed Folsomia candida, known as “standard” test Collembola. Of the 18 morphological characters studied, we measured 14 to have significant between-strains genetic variations, 9 of these had high heritabilities (>78%). The quantified morphological polymorphism was used to analyse the within-species relationships between strains by using both a parsimony analysis and a distance tree. These two detailed morphological phylogenies have revealed that the parthenogenetic strains grouped themselves into two major clades. However the exact position of the sexual strain remains unclear and further analysis is needed to confirm its exact relationship with the parthenogenetic ones. The two morphologically based clades were found to be the same as the ones previously described using molecular analysis. This shows that despite large within-strain variations, morphological characters can be used to differentiate some strains that have diverged within a single morphospecies. We discuss the potential evolutionary interpretations and consequences of these different levels of phenotypic variability. PMID:26355293
Araneda, Cristián; Larraín, María Angélica; Hecht, Benjamin; Narum, Shawn
Chilean mussel populations have been thought to be panmictic with limited genetic structure. Genotyping-by-sequencing approaches have enabled investigation of genomewide variation that may better distinguish populations that have evolved in different environments. We investigated neutral and adaptive genetic variation in Mytilus from six locations in southern Chile with 1240 SNPs obtained with RAD-seq. Differentiation among locations with 891 neutral SNPs was low (FST = 0.005). Higher differentiation was obtained with a panel of 58 putative outlier SNPs (FST = 0.114) indicating the potential for local adaptation. This panel identified clusters of genetically related individuals and demonstrated that much of the differentiation (~92%) could be attributed to the three major regions and environments: extreme conditions in Patagonia, inner bay influenced by aquaculture (Reloncaví), and outer bay (Chiloé Island). Patagonia samples were most distinct, but additional analysis carried out excluding this collection also revealed adaptive divergence between inner and outer bay samples. The four locations within Reloncaví area were most similar with all panels of markers, likely due to similar environments, high gene flow by aquaculture practices, and low geographical distance. Our results and the SNP markers developed will be a powerful tool supporting management and programs of this harvested species.
Page, Tony; Southwell, Ian; Russell, Mike; Tate, Hanington; Tungon, Joseph; Sam, Chanel; Dickinson, Geoff; Robson, Ken; Leakey, Roger R B
Phenotypic variation in heartwood and essential-oil characters of Santalum austrocaledonicum was assessed across eleven populations on seven islands of Vanuatu. Trees differed significantly in their percentage heartwood cross-sectional area and this varied independently of stem diameter. The concentrations of the four major essential-oil constituents (alpha-santalol, beta-santalol, (Z)-beta-curcumen-12-ol, and cis-nuciferol) of alcohol-extracted heartwood exhibited at least tenfold and continuous tree-to-tree variation. Commercially important components alpha- and beta-santalol found in individual trees ranged from 0.8-47% and 0-24.1%, respectively, across all populations, and significant (P<0.05) differences for each were found between individual populations. The Erromango population was unique in that the mean concentrations of its monocyclic ((Z)-beta-curcumen-12-ol and cis-nuciferol) sesquiterpenes exceeded those of its bi- and tricyclic (alpha- and beta-santalol) sesquiterpenes. Heartwood colour varied between trees and spanned 65 colour categories, but no identifiable relationships were found between heartwood colour and alpha- and beta-santalol, although a weak relationship was evident between colour saturation and total oil concentration. These results indicate that the heartwood colour is not a reliable predictive trait for oil quality. The results of this study highlight the knowledge gaps in fundamental understanding of heartwood biology in Santalum genus. The intraspecific variation in heartwood cross-sectional area, oil concentration, and oil quality traits is of considerable importance to the domestication of sandalwood and present opportunities for the development of highly superior S. austrocaledonicum cultivars that conform to the industry's International Standards used for S. album.
Barreiro, Esther; Sznajder, Jacob I
Quadriceps muscle dysfunction occurs in one-third of patients with chronic obstructive pulmonary disease (COPD) in very early stages of their condition, even prior to the development of airway obstruction. Among several factors, deconditioning and muscle mass loss are the most relevant contributing factors leading to this dysfunction. Moreover, epigenetics, defined as the process whereby gene expression is regulated by heritable mechanisms that do not affect DNA sequence, could be involved in the susceptibility to muscle dysfunction, pathogenesis, and progression. Herein, we review the role of epigenetic mechanisms in muscle development and adaptation to environmental factors such as immobilization and exercise, and their implications in the pathophysiology and susceptibility to muscle dysfunction in COPD. The epigenetic modifications identified so far include DNA methylation, histone acetylation and methylation, and non-coding RNAs such as microRNAs (miRNAs). In the present review, we describe the specific contribution of epigenetic mechanisms to the regulation of embryonic myogenesis, muscle structure and metabolism, immobilization, and exercise, and in muscles of COPD patients. Events related to muscle development and regeneration and the response to exercise and immobilization are tightly regulated by epigenetic mechanisms. These environmental factors play a key role in the outcome of muscle mass and function as well as in the susceptibility to muscle dysfunction in COPD. Future research remains to be done to shed light on the specific target pathways of miRNA function and other epigenetic mechanisms in the susceptibility, pathogenesis, and progression of COPD muscle dysfunction.
Mursinoff, Sini; Tack, Ayco J M
Theory suggests that below-ground spatial heterogeneity may mediate host-parasite evolutionary dynamics and patterns of local adaptation, but this has rarely been tested in natural systems. Here, we test experimentally for the impact of spatial variation in the abiotic and biotic soil environment on the evolutionary outcome of the interaction between the host plant Plantago lanceolata and its specialist foliar pathogen Podosphaera plantaginis. Plants showed no adaptation to the local soil environment in the absence of natural enemies. However, quantitative, but not qualitative, plant resistance against local pathogens was higher when plants were grown in their local field soil than when they were grown in nonlocal field soil. This pattern was robust when extending the spatial scale beyond a single region, but disappeared with soil sterilization, indicating that soil biota mediated plant adaptation. We conclude that below-ground biotic heterogeneity mediates above-ground patterns of plant adaptation, resulting in increased plant resistance when plants are grown in their local soil environment. From an applied perspective, our findings emphasize the importance of using locally selected seeds in restoration ecology and low-input agriculture.
Winham, Stacey J.; Preuss, Ulrich W.; Geske, Jennifer R.; Zill, Peter; Heit, John A.; Bakalkin, Georgy; Biernacka, Joanna M.; Karpyak, Victor M.
We previously demonstrated that prodynorphin (PDYN) haplotypes and single nucleotide polymorphism (SNP) rs2281285 are associated with alcohol dependence and the propensity to drink in negative emotional states, and recent studies suggest that PDYN gene effects on substance dependence risk may be sex-related. We examined sex-dependent associations of PDYN variation with alcohol dependence and related phenotypes, including negative craving, time until relapse after treatment and the length of sobriety episodes before seeking treatment, in discovery and validation cohorts of European ancestry. We found a significant haplotype-by-sex interaction (p = 0.03), suggesting association with alcohol dependence in males (p = 1E-4) but not females. The rs2281285 G allele increased risk for alcohol dependence in males in the discovery cohort (OR = 1.49, p = 0.002), with a similar trend in the validation cohort (OR = 1.35, p = 0.086). However, rs2281285 showed a trend towards association with increased negative craving in females in both the discovery (beta = 10.16, p = 0.045) and validation samples (OR = 7.11, p = 0.066). In the discovery cohort, rs2281285 was associated with time until relapse after treatment in females (HR = 1.72, p = 0.037); in the validation cohort, it was associated with increased length of sobriety episodes before treatment in males (beta = 13.49, p = 0.001). Our findings suggest that sex-dependent effects of PDYN variants in alcohol dependence are phenotype-specific. PMID:26502829
Ciborowski, Kate; Jordan, William C; Garcia de Leaniz, Carlos; Consuegra, Sofia
The role of marginal populations for the long-term maintenance of species’ genetic diversity and evolutionary potential is particularly timely in view of the range shifts caused by climate change. The Centre-Periphery hypothesis predicts that marginal populations should bear reduced genetic diversity and have low evolutionary potential. We analysed temporal stability at neutral microsatellite and adaptive MHC genetic variation over five decades in four marginal Atlantic salmon populations located at the southern limit of the species’ distribution with a complicated demographic history, which includes stocking with foreign and native salmon for at least 2 decades. We found a temporal increase in neutral genetic variation, as well as temporal instability in population structuring, highlighting the importance of temporal analyses in studies that examine the genetic diversity of peripheral populations at the margins of the species’ range, particularly in face of climate change. PMID:28186200
Edge, Christopher B; Rollinson, Njal; Brooks, Ronald J; Congdon, Justin D; Iverson, John B; Janzen, Fredric J; Litzgus, Jacqueline D
Life histories evolve in response to constraints on the time available for growth and development. Nesting date and its plasticity in response to spring temperature may therefore be important components of fitness in oviparous ectotherms near their northern range limit, as reproducing early provides more time for embryos to complete development before winter. We used data collected over several decades to compare air temperature and nest date plasticity in populations of painted turtles and snapping turtles from a relatively warm environment (southeastern Michigan) near the southern extent of the last glacial maximum to a relatively cool environment (central Ontario) near the northern extent of post-glacial recolonization. For painted turtles, population-level differences in reaction norm elevation for two phenological traits were consistent with adaptation to time constraints, but no differences in reaction norm slopes were observed. For snapping turtle populations, the difference in reaction norm elevation for a single phenological trait was in the opposite direction of what was expected under adaptation to time constraints, and no difference in reaction norm slope was observed. Finally, among-individual variation in individual plasticity for nesting date was detected only in the northern population of snapping turtles, suggesting that reaction norms are less canalized in this northern population. Overall, we observed evidence of phenological adaptation, and possibly maladaptation, to time constraints in long-lived reptiles. Where present, (mal)adaptation occurred by virtue of differences in reaction norm elevation, not reaction norm slope. Glacial history, generation time, and genetic constraint may all play an important role in the evolution of phenological timing and its plasticity in long-lived reptiles.
Haubek, Dorte; Gjørup, Hans; Jensen, Lillian G; Juncker, Inger; Nyegaard, Mette; Børglum, Anders D; Poulsen, Sven; Hertz, Jens M
BACKGROUND. Autosomal dominant hypocalcified amelogenesis imperfecta (ADHCAI) is a disease with severe dental manifestations. OBJECTIVES. The aims were by means of a genome-wide linkage scan to search for the gene underlying the ADHCAI phenotype in a Danish five-generation family and to study the phenotypic variation of the enamel in affected family members. RESULTS. Significant linkage was found to a locus at chromosome 8q24.3 comprising the gene FAM83H identified to be responsible for ADHCAI in other families. Subsequent sequencing of FAM83H in affected family members revealed a novel nonsense mutation, p.Y302X. Limited phenotypic variation was found among affected family members with loss of translucency and discoloration of the enamel. Extensive posteruptive loss of enamel was found in all teeth of affected subjects. The tip of the cusps on the premolars and molars and a zone along the gingival margin seemed resistant to posteruptive loss of enamel. We have screened FAM83H in another five unrelated Danish patients with a phenotype of ADHCAI similar to that in the five-generation family, and identified a de novo FAM83H nonsense mutation, p.Q452X in one of these patients. CONCLUSION. We have identified a FAM83H mutation in two of six unrelated families with ADHCAI and found limited phenotypic variation of the enamel in these patients.
Meyer, Christopher G.; Villoutreix, Romain; Platt, Alexander; Morton, Timothy C.; Roux, Fabrice; Bergelson, Joy
The “mustard oil bomb” is a major defense mechanism in the Brassicaceae, which includes crops such as canola and the model plant Arabidopsis thaliana. These plants produce and store blends of amino acid-derived secondary metabolites called glucosinolates. Upon tissue rupture by natural enemies, the myrosinase enzyme hydrolyses glucosinolates, releasing defense molecules. Brassicaceae display extensive variation in the mixture of glucosinolates that they produce. To investigate the genetics underlying natural variation in glucosinolate profiles, we conducted a large genome-wide association study of 22 methionine-derived glucosinolates using A. thaliana accessions from across Europe. We found that 36% of among accession variation in overall glucosinolate profile was explained by genetic differentiation at only three known loci from the glucosinolate pathway. Glucosinolate-related SNPs were up to 490-fold enriched in the extreme tail of the genome-wide FST scan, indicating strong selection on loci controlling this pathway. Glucosinolate profiles displayed a striking longitudinal gradient with alkenyl and hydroxyalkenyl glucosinolates enriched in the West. We detected a significant contribution of glucosinolate loci toward general herbivore resistance and lifetime fitness in common garden experiments conducted in France, where accessions are enriched in hydroxyalkenyls. In addition to demonstrating the adaptive value of glucosinolate profile variation, we also detected long-distance linkage disequilibrium at two underlying loci, GS-OH and GS-ELONG. Locally cooccurring alleles at these loci display epistatic effects on herbivore resistance and fitness in ecologically realistic conditions. Together, our results suggest that natural selection has favored a locally adaptive configuration of physically unlinked loci in Western Europe. PMID:25775585
Wright, Dominic; Boije, Henrik; Meadows, Jennifer R. S.; Bed'hom, Bertrand; Gourichon, David; Vieaud, Agathe; Tixier-Boichard, Michèle; Rubin, Carl-Johan; Imsland, Freyja; Hallböök, Finn; Andersson, Leif
Pea-comb is a dominant mutation in chickens that drastically reduces the size of the comb and wattles. It is an adaptive trait in cold climates as it reduces heat loss and makes the chicken less susceptible to frost lesions. Here we report that Pea-comb is caused by a massive amplification of a duplicated sequence located near evolutionary conserved non-coding sequences in intron 1 of the gene encoding the SOX5 transcription factor. This must be the causative mutation since all other polymorphisms associated with the Pea-comb allele were excluded by genetic analysis. SOX5 controls cell fate and differentiation and is essential for skeletal development, chondrocyte differentiation, and extracellular matrix production. Immunostaining in early embryos demonstrated that Pea-comb is associated with ectopic expression of SOX5 in mesenchymal cells located just beneath the surface ectoderm where the comb and wattles will subsequently develop. The results imply that the duplication expansion interferes with the regulation of SOX5 expression during the differentiation of cells crucial for the development of comb and wattles. The study provides novel insight into the nature of mutations that contribute to phenotypic evolution and is the first description of a spontaneous and fully viable mutation in this developmentally important gene. PMID:19521496
Barp, E A; Soares, G L G; Gosmann, G; Machado, A M; Vecchi, C; Moreira, G R P
Leaf morphology may vary considerably even within a branch of Passiflora suberosa plants. Leaves are of a typical green type in shaded areas, but in open fields turn into violet, and apparently have greater thickness and trichome density. The proximate causes and the adaptive meaning, if any, for the existence of the violet morph are still unknown. By cultivating P. suberosa clones under two light regimes (total and partial exposure to sunlight), we consecutively induced (first year) and then reversed (second year) the appearance of the violet morph. We evaluated the corresponding changes in morpho-anatomic and chemical leaf characteristics. Plants that were grown under partial sunlight had a greater size and did not alter their green color, but those grown under total sunlight changed into violet, were smaller in size and their leaves were tougher, thicker, and had a greater number of trichomes. The violet morph had increased anthocyanins and phenolic derivatives. It also showed cellular hypertrophy, a greater number of cell layers in the mesophyll, and a lignified pericycle. Since these morphs are interchangeable by changing light conditions, we inferred that they are not determined by genotypic diversity, but are mainly a result of a physiological response to light stress, and thus part of P. suberosa phenotypic plasticity.
Flukes, Emma B; Wright, Jeffrey T; Johnson, Craig R
Southeastern Australian waters are warming at nearly four times the global average rate (~0.7°C · century(-1) ) driven by strengthening incursions of the warm oligotrophic East Australian Current. The growth rate hypothesis (GRH) predicts that nutrient depletion will impact more severely on seaweeds at high latitudes with compressed growth seasons. This study investigates the effects of temperature and nutrients on the ecophysiology of the habitat-forming seaweed Phyllospora comosa in a laboratory experiment using temperature (12°C, 17°C, 22°C) and nutrient (0.5, 1.0, 3.0 μM NO3 (-) ) scenarios representative of observed variation among geographic regions. Changes in growth, photosynthetic characteristics (via chlorophyll fluorescence), pigment content, tissue chemistry (δ(13) C, % C, % N, C:N) and nucleic acid characteristics (absolute RNA and DNA, RNA:DNA ratios) were determined in seaweeds derived from cool, high-latitude and warm, low-latitude portions of the species' range. Performance of P. comosa was unaffected by nitrate availability but was strongly temperature-dependent, with photosynthetic efficiency, growth, and survival significantly impaired at 22°C. While some physiological processes (photosynthesis, nucleic acid, and accessory pigment synthesis) responded rapidly to temperature, others (C/N dynamics, carbon concentrating processes) were largely invariant and biogeographic variation in these characteristics may only occur through genetic adaptation. No link was detected between nutrient availability, RNA synthesis and growth, and the GRH was not supported in this species. While P. comosa at high latitudes may be less susceptible to oligotrophy than predicted by the GRH, warming water temperatures will have deleterious effects on this species across its range unless rapid adaptation is possible.
Voelckel, Marie-Antoinette; Girardot, Lydie; Giusiano, Bernard; Levy, Nicolas; Philip, Nicole
Microdeletion at the 22q11 locus is characterised by a high clinical variability. Congenital heart defects (CHD) are the most life-threatening manifestations of the syndrome and affect approximately 50% of patients carrying the deleted chromosome 22. The causes of this phenotype variability remain unknown although several hypotheses have been raised. It has been suggested that allelic variations at the haploid locus could modify the phenotypic expression. Regarding this hypothesis, TBX1 was thought to be a major candidate to the cardiac phenotype or its severity in patients carrying the 22q11 microdeletion. A mutational screening was performed in this gene, in a series of 39 deleted patients, with and without CHD. The results indicate that mutations in TBX1 are not likely to be involved in the cardiac phenotype observed in del22q11 patients.
Lazić, Marko M; Carretero, Miguel A; Crnobrnja-Isailović, Jelka; Kaliontzopoulou, Antigoni
When populations experience suboptimal conditions, the mechanisms involved in the regulation of phenotypic variation can be challenged, resulting in increased phenotypic variance. This kind of disturbance can be diagnosed by using morphometric tools to study morphological patterns at different hierarchical levels and evaluate canalization, developmental stability, integration, modularity, and allometry. We assess the effect of urbanization on phenotypic variation in the common wall lizard (Podarcis muralis) by using geometric morphometrics to assess disturbance to head shape development. The head shapes of urban lizards were more variable and less symmetric, suggesting that urban living is more likely to disturb development. Head shape variation was congruent within and across individuals, which indicated that canalization and developmental stability are two related phenomena in these organisms. Furthermore, urban lizards exhibited smaller mean head sizes, divergent size-shape allometries, and increased deviation from within-group allometric lines. This suggests that mechanisms regulating head shape allometry may also be disrupted. The integrated evaluation of several measures of developmental instability at different hierarchical levels, which provided in this case congruent results, can be a powerful methodological guide for future studies, as it enhances the detection of environmental disturbances on phenotypic variation and aids biological interpretation of the results.
Jaiswal, Virendra; Ghoshal, Ujjala; Mittal, Balraj; Dhole, Tapan N; Ghoshal, Uday C
Genotypes of Entamoeba histolytica (E. histolytica) may contribute clinical phenotypes of amoebiasis such as amoebic liver abscess (ALA), dysentery and asymptomatic cyst passers state. Hence, we evaluated allelic variation due to short tandem repeats (STRs) in tRNA gene of E. histolytica and clinical phenotypes of amoebiasis. Asymptomatic cyst passers (n=24), patients with dysentery (n=56) and ALA (n=107) were included. Extracted DNA from stool (dysentery, asymptomatic cyst passers) and liver aspirate was amplified using 6 E. histolytica specific tRNA-linked STRs (D-A, A-L, N-K2, R-R, S-Q, and S(TGA)-D) primers. PCR products were subjected to sequencing. Association between allelic variation and clinical phenotypes was analyzed. A total of 9 allelic variations were found in D-A, 8 in A-L, 4 in N-K2, 5 in R-R, 10 in S(TAG)-D and 7 in S-Q loci. A significant association was found between allelic variants and clinical phenotypes of amoebiasis. This study reveals that allelic variation due to short tandem repeats (STRs) in tRNA gene of E. histolytica is associated different clinical outcome of amoebiasis.
Amarillo-Suárez, Angela R; Fox, Charles W
For insects that develop inside discrete hosts, both host size and host quality constrain offspring growth, influencing the evolution of body size and life history traits. Using a two-generation common garden experiment, we quantified the contribution of maternal and rearing hosts to differences in growth and life history traits between populations of the seed-feeding beetle Stator limbatus that use a large-seeded host, Acacia greggii, and a small-seeded host, Pseudosamanea guachapele. Populations differed genetically for all traits when beetles were raised in a common garden. Contrary to expectations from the local adaptation hypothesis, beetles from all populations were larger, developed faster and had higher survivorship when reared on seeds of A. greggii (the larger host), irrespective of their native host. We observed two host plant-mediated maternal effects: offspring matured sooner, regardless of their rearing host, when their mothers were reared on P. guachapele (this was not caused by an effect of rearing host on egg size), and females laid larger eggs on P. guachapele. This is the first study to document plasticity by S. limbatus in response to P. guachapele, suggesting that plasticity is an ancestral trait in S. limbatus that likely plays an important role in diet expansion. Although differences between populations in growth and life history traits are likely adaptations to their host plants, host-associated maternal effects, partly mediated by maternal egg size plasticity, influence growth and life history traits and likely play an important role in the evolution of the breadth of S. limbatus' diet. More generally, phenotypic plasticity mediates the fitness consequences of using novel hosts, likely facilitating colonization of new hosts, but also buffering herbivores from selection post-colonization. Plasticity in response to novel versus normal hosts varied among our study populations such that disentangling the historical role of plasticity in
George, Jan-Peter; Grabner, Michael; Karanitsch-Ackerl, Sandra; Mayer, Konrad; Weißenbacher, Lambert; Schueler, Silvio
Assessing intra-specific variation in drought stress response is required to mitigate the consequences of climate change on forest ecosystems. Previous studies suggest that European larch (Larix decidua Mill.), an important European conifer in mountainous and alpine forests, is highly vulnerable to drought. In light of this, we estimated the genetic variation in drought sensitivity and its degree of genetic determination in a 50-year-old common garden experiment in the drought-prone northeastern Austria. Tree ring data from larch provenances originating from across the species' natural range were used to estimate the drought reaction in four consecutive drought events (1977, 1981, 1990-1994, and 2003) with extremely low standardized precipitation- and evapotranspiration-index values that affected growth in all provenances. We found significant differences among provenances across the four drought periods for the trees' capacity to withstand drought (resistance) and for their capacity to reach pre-drought growth levels after drought (resilience). Provenances from the species' northern distribution limit in the Polish lowlands were found to be more drought resistant and showed higher stability across all drought periods than provenances from mountainous habitats at the southern fringe. The degree of genetic determination, as estimated by the repeatability, ranged up to 0.39, but significantly differed among provenances, indicating varying degrees of natural selection at the provenance origin. Generally, the relationship between the provenances' source climate and drought behavior was weak, suggesting that the contrasting patterns of drought response are a result of both genetic divergence out of different refugial lineages and local adaptation to summer or winter drought conditions. Our analysis suggests that European larch posseses high genetic variation among and within provenances that can be used for assisted migration and breeding programs.
Tsui, Po-Hsiang; Wan, Yung-Liang; Huang, Chih-Chung; Wang, Ming-Chen
The Nakagami parameter is associated with the Nakagami distribution estimated from ultrasonic backscattered signals and closely reflects the scatterer concentrations in tissues. There is an interest in exploring the possibility of enhancing the ability of the Nakagami parameter to characterize tissues. In this paper, we explore the effect of adaptive thresholdfiltering based on the noise-assisted empirical mode decomposition of the ultrasonic backscattered signals on the Nakagami parameter as a function of scatterer concentration for improving the Nakagami parameter performance. We carried out phantom experiments using 5 MHz focused and nonfocused transducers. Before filtering, the dynamic ranges of the Nakagami parameter, estimated using focused and nonfocused transducers between the scatterer concentrations of 2 and 32 scatterers/mm3, were 0.44 and 0.1, respectively. After filtering, the dynamic ranges of the Nakagami parameter, using the focused and nonfocused transducers, were 0.71 and 0.79, respectively. The experimental results showed that the adaptive threshold filter makes the Nakagami parameter measured by a focused transducer more sensitive to the variation in the scatterer concentration. The proposed method also endows the Nakagami parameter measured by a nonfocused transducer with the ability to differentiate various scatterer concentrations. However, the Nakagami parameters estimated by focused and nonfocused transducers after adaptive threshold filtering have different physical meanings: the former represents the statistics of signals backscattered from unresolvable scatterers while the latter is associated with stronger resolvable scatterers or local inhomogeneity due to scatterer aggregation.
Tine, Mbaye; Kuhl, Heiner; Gagnaire, Pierre-Alexandre; Louro, Bruno; Desmarais, Erick; Martins, Rute S.T.; Hecht, Jochen; Knaust, Florian; Belkhir, Khalid; Klages, Sven; Dieterich, Roland; Stueber, Kurt; Piferrer, Francesc; Guinand, Bruno; Bierne, Nicolas; Volckaert, Filip A. M.; Bargelloni, Luca; Power, Deborah M.; Bonhomme, François; Canario, Adelino V. M.; Reinhardt, Richard
The European sea bass (Dicentrarchus labrax) is a temperate-zone euryhaline teleost of prime importance for aquaculture and fisheries. This species is subdivided into two naturally hybridizing lineages, one inhabiting the north-eastern Atlantic Ocean and the other the Mediterranean and Black seas. Here we provide a high-quality chromosome-scale assembly of its genome that shows a high degree of synteny with the more highly derived teleosts. We find expansions of gene families specifically associated with ion and water regulation, highlighting adaptation to variation in salinity. We further generate a genome-wide variation map through RAD-sequencing of Atlantic and Mediterranean populations. We show that variation in local recombination rates strongly influences the genomic landscape of diversity within and differentiation between lineages. Comparing predictions of alternative demographic models to the joint allele-frequency spectrum indicates that genomic islands of differentiation between sea bass lineages were generated by varying rates of introgression across the genome following a period of geographical isolation. PMID:25534655
Tine, Mbaye; Kuhl, Heiner; Gagnaire, Pierre-Alexandre; Louro, Bruno; Desmarais, Erick; Martins, Rute S T; Hecht, Jochen; Knaust, Florian; Belkhir, Khalid; Klages, Sven; Dieterich, Roland; Stueber, Kurt; Piferrer, Francesc; Guinand, Bruno; Bierne, Nicolas; Volckaert, Filip A M; Bargelloni, Luca; Power, Deborah M; Bonhomme, François; Canario, Adelino V M; Reinhardt, Richard
The European sea bass (Dicentrarchus labrax) is a temperate-zone euryhaline teleost of prime importance for aquaculture and fisheries. This species is subdivided into two naturally hybridizing lineages, one inhabiting the north-eastern Atlantic Ocean and the other the Mediterranean and Black seas. Here we provide a high-quality chromosome-scale assembly of its genome that shows a high degree of synteny with the more highly derived teleosts. We find expansions of gene families specifically associated with ion and water regulation, highlighting adaptation to variation in salinity. We further generate a genome-wide variation map through RAD-sequencing of Atlantic and Mediterranean populations. We show that variation in local recombination rates strongly influences the genomic landscape of diversity within and differentiation between lineages. Comparing predictions of alternative demographic models to the joint allele-frequency spectrum indicates that genomic islands of differentiation between sea bass lineages were generated by varying rates of introgression across the genome following a period of geographical isolation.
Beyond Punnett squares: Student word association and explanations of phenotypic variation through an integrative quantitative genetics unit investigating anthocyanin inheritance and expression in Brassica rapa Fast plants.
Batzli, Janet M; Smith, Amber R; Williams, Paul H; McGee, Seth A; Dósa, Katalin; Pfammatter, Jesse
Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory course focused on the inheritance and expression of a quantitative trait in varying environments. We utilized Brassica rapa Fast Plants as a model organism to study variation in the phenotype anthocyanin pigment intensity. As an initial curriculum assessment, we used free word association to examine students' cognitive structures before and after the unit and explanations in students' final research posters with particular focus on variation (Pv = Gv + Ev). Comparison of pre- and postunit word frequency revealed a shift in words and a pattern of co-occurring concepts indicative of change in cognitive structure, with particular focus on "variation" as a proposed threshold concept and primary goal for students' explanations. Given review of 53 posters, we found ∼50% of students capable of intermediate to high-level explanations combining both Gv and Ev influence on expression of anthocyanin intensity (Pv). While far from "plug and play," this conceptually rich, inquiry-based unit holds promise for effective integration of quantitative and Mendelian genetics.
Altitudinal clines in body size can result from the effects of natural and sexual selection on growth rates and developing times in seasonal environments. Short growing and reproductive seasons constrain the body size that adults can attain and their reproductive success. Little is known about the effects of altitudinal climatic variation on the diversification of Neotropical insects. In central Mexico, in addition to altitude, highly heterogeneous topography generates diverse climates that can occur even at the same latitude. Altitudinal variation and heterogeneous topography open an opportunity to test the relative impact of climatic variation on body size adaptations. In this study, we investigated the relationship between altitudinal climatic variation and body size, and the divergence rates of sexual size dimorphism (SSD) in Neotropical grasshoppers of the genus Sphenarium using a phylogenetic comparative approach. In order to distinguish the relative impact of natural and sexual selection on the diversification of the group, we also tracked the altitudinal distribution of the species and trends of both body size and SSD on the phylogeny of Sphenarium. The correlative evidence suggests no relationship between altitude and body size. However, larger species were associated with places having a warmer winter season in which the temporal window for development and reproduction can be longer. Nonetheless, the largest species were also associated with highly seasonal environments. Moreover, large body size and high levels of SSD have evolved independently several times throughout the history of the group and male body size has experienced a greater evolutionary divergence than females. These lines of evidence suggest that natural selection, associated with seasonality and sexual selection, on maturation time and body size could have enhanced the diversification of this insect group. PMID:26684616
Sanabria-Urbán, Salomón; Song, Hojun; Oyama, Ken; González-Rodríguez, Antonio; Serrano-Meneses, Martin A; Cueva Del Castillo, Raúl
Altitudinal clines in body size can result from the effects of natural and sexual selection on growth rates and developing times in seasonal environments. Short growing and reproductive seasons constrain the body size that adults can attain and their reproductive success. Little is known about the effects of altitudinal climatic variation on the diversification of Neotropical insects. In central Mexico, in addition to altitude, highly heterogeneous topography generates diverse climates that can occur even at the same latitude. Altitudinal variation and heterogeneous topography open an opportunity to test the relative impact of climatic variation on body size adaptations. In this study, we investigated the relationship between altitudinal climatic variation and body size, and the divergence rates of sexual size dimorphism (SSD) in Neotropical grasshoppers of the genus Sphenarium using a phylogenetic comparative approach. In order to distinguish the relative impact of natural and sexual selection on the diversification of the group, we also tracked the altitudinal distribution of the species and trends of both body size and SSD on the phylogeny of Sphenarium. The correlative evidence suggests no relationship between altitude and body size. However, larger species were associated with places having a warmer winter season in which the temporal window for development and reproduction can be longer. Nonetheless, the largest species were also associated with highly seasonal environments. Moreover, large body size and high levels of SSD have evolved independently several times throughout the history of the group and male body size has experienced a greater evolutionary divergence than females. These lines of evidence suggest that natural selection, associated with seasonality and sexual selection, on maturation time and body size could have enhanced the diversification of this insect group.
Kellermeier, Fabian; Chardon, Fabien; Amtmann, Anna
Root architecture is a highly plastic and environmentally responsive trait that enables plants to counteract nutrient scarcities with different foraging strategies. In potassium (K) deficiency (low K), seedlings of the Arabidopsis (Arabidopsis thaliana) reference accession Columbia (Col-0) show a strong reduction of lateral root elongation. To date, it is not clear whether this is a direct consequence of the lack of K as an osmoticum or a triggered response to maintain the growth of other organs under limiting conditions. In this study, we made use of natural variation within Arabidopsis to look for novel root architectural responses to low K. A comprehensive set of 14 differentially responding root parameters were quantified in K-starved and K-replete plants. We identified a phenotypic gradient that links two extreme strategies of morphological adaptation to low K arising from a major tradeoff between main root (MR) and lateral root elongation. Accessions adopting strategy I (e.g. Col-0) maintained MR growth but compromised lateral root elongation, whereas strategy II genotypes (e.g. Catania-1) arrested MR elongation in favor of lateral branching. K resupply and histochemical staining resolved the temporal and spatial patterns of these responses. Quantitative trait locus analysis of K-dependent root architectures within a Col-0 × Catania-1 recombinant inbred line population identified several loci each of which determined a particular subset of root architectural parameters. Our results indicate the existence of genomic hubs in the coordinated control of root growth in stress conditions and provide resources to facilitate the identification of the underlying genes. PMID:23329148
Hand, Brian K; Muhlfeld, Clint C.; Wade, Alisa A.; Kovach, Ryan; Whited, Diane C.; Narum, Shawn R.; Matala, Andrew P; Ackerman, Michael W.; Garner, B. A.; Kimball, John S; Stanford, Jack A.; Luikart, Gordon
Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.
Hand, Brian K; Muhlfeld, Clint C; Wade, Alisa A; Kovach, Ryan P; Whited, Diane C; Narum, Shawn R; Matala, Andrew P; Ackerman, Michael W; Garner, Brittany A; Kimball, John S; Stanford, Jack A; Luikart, Gordon
Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST ) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.
Svetec, Nicolas; Cridland, Julie M.; Zhao, Li; Begun, David J.
Despite decades of work, our understanding of the distribution of fitness effects of segregating genetic variants in natural populations remains largely incomplete. One form of selection that can maintain genetic variation is spatially varying selection, such as that leading to latitudinal clines. While the introduction of population genomic approaches to understanding spatially varying selection has generated much excitement, little successful effort has been devoted to moving beyond genome scans for selection to experimental analysis of the relevant biology and the development of experimentally motivated hypotheses regarding the agents of selection; it remains an interesting question as to whether the vast majority of population genomic work will lead to satisfying biological insights. Here, motivated by population genomic results, we investigate how spatially varying selection in the genetic model system, Drosophila melanogaster, has led to genetic differences between populations in several components of the DNA damage response. UVB incidence, which is negatively correlated with latitude, is an important agent of DNA damage. We show that sensitivity of early embryos to UVB exposure is strongly correlated with latitude such that low latitude populations show much lower sensitivity to UVB. We then show that lines with lower embryo UVB sensitivity also exhibit increased capacity for repair of damaged sperm DNA by the oocyte. A comparison of the early embryo transcriptome in high and low latitude embryos provides evidence that one mechanism of adaptive DNA repair differences between populations is the greater abundance of DNA repair transcripts in the eggs of low latitude females. Finally, we use population genomic comparisons of high and low latitude samples to reveal evidence that multiple components of the DNA damage response and both coding and non-coding variation likely contribute to adaptive differences in DNA repair between populations. PMID:26950216
Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in Brassica rapa Fast Plants
Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dósa, Katalin; Pfammatter, Jesse
Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question “What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev),” we developed a 4-wk unit for an inquiry-based laboratory course focused on the inheritance and expression of a quantitative trait in varying environments. We utilized Brassica rapa Fast Plants as a model organism to study variation in the phenotype anthocyanin pigment intensity. As an initial curriculum assessment, we used free word association to examine students’ cognitive structures before and after the unit and explanations in students’ final research posters with particular focus on variation (Pv = Gv + Ev). Comparison of pre- and postunit word frequency revealed a shift in words and a pattern of co-occurring concepts indicative of change in cognitive structure, with particular focus on “variation” as a proposed threshold concept and primary goal for students’ explanations. Given review of 53 posters, we found ∼50% of students capable of intermediate to high-level explanations combining both Gv and Ev influence on expression of anthocyanin intensity (Pv). While far from “plug and play,” this conceptually rich, inquiry-based unit holds promise for effective integration of quantitative and Mendelian genetics. PMID:25185225
Heinberg, Adina; Siu, Edwin; Stern, Chaya; Lawrence, Elizabeth A; Ferdig, Michael T; Deitsch, Kirk W; Kirkman, Laura A
Summary Resistance to antimalarials targeting the folate pathway is widespread. GTP-cyclohydrolase (gch1), the first enzyme in this pathway, exhibits extensive copy number variation (CNV) in parasite isolates from areas with a history of longstanding antifolate use. Increased CN of gch1 is associated with a greater number of point mutations in enzymes targeted by the antifolates, pyrimethamine and sulfadoxine. While these observations suggest that increases in gch1 CN are an adaptation to drug pressure, changes in CN have not been experimentally demonstrated to directly alter drug susceptibility. To determine if changes in gch1 expression alone modify pyrimethamine sensitivity, we manipulated gch1 CN in several parasite lines to test the effect on drug sensitivity. We report that increases in gch1 CN alter pyrimethamine resistance in most parasites lines. However we find evidence of a detrimental effect of very high levels of gch1 overexpression in parasite lines with high endogenous levels of gch1 expression, revealing the importance of maintaining balance in the folate pathway and implicating changes in gch1 expression in preserving proper metabolic flux. This work expands our understanding of parasite adaptation to drug pressure and provides a possible mechanism for how specific mutations become fixed within parasite populations. PMID:23347134
Bajaj, Chandrajit L; Xu, Guoliang; Zhang, Qin
We present a variational approach to smooth molecular (proteins, nucleic acids) surface constructions, starting from atomic coordinates, as available from the protein and nucleic-acid data banks. Molecular dynamics (MD) simulations traditionally used in understanding protein and nucleic-acid folding processes, are based on molecular force fields, and require smooth models of these molecular surfaces. To accelerate MD simulations, a popular methodology is to employ coarse grained molecular models, which represent clusters of atoms with similar physical properties by psuedo- atoms, resulting in coarser resolution molecular surfaces. We consider generation of these mixed-resolution or adaptive molecular surfaces. Our approach starts from deriving a general form second order geometric partial differential equation in the level-set formulation, by minimizing a first order energy functional which additionally includes a regularization term to minimize the occurrence of chemically infeasible molecular surface pockets or tunnel-like artifacts. To achieve even higher computational efficiency, a fast cubic B-spline C(2) interpolation algorithm is also utilized. A narrow band, tri-cubic B-spline level-set method is then used to provide C(2) smooth and resolution adaptive molecular surfaces.
Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong
Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gene, SD1. Based on a performance evaluation of the HRPF and GWAS results, we demonstrate that high-throughput phenotyping has the potential to replace traditional phenotyping techniques and can provide valuable gene identification information. The combination of the multifunctional phenotyping tools HRPF and GWAS provides deep insights into the genetic architecture of important traits. PMID:25295980
Blackman, Chris J; Aspinwall, Michael J; Tissue, David T; Rymer, Paul D
The ability of plants to maintain an intact water transport system in leaves under drought conditions is intimately linked to survival and can been be seen as adaptive in shaping species climatic limits. Large differences in leaf hydraulic vulnerability to drought are known among species from contrasting climates, yet whether this trait varies among populations within a single species and, furthermore, whether it is altered by changes in growth conditions, remain unclear. We examined intraspecific variation in both leaf water transport capacity (Kleaf) and leaf hydraulic vulnerability to drought (P50leaf) among eight populations of Corymbia calophylla (R. Br.) K.D. Hill & L.A.S. Johnson (Myrtaceae) from both cool and warm climatic regions grown reciprocally under two temperature treatments representing the cool and warm edge of the species distribution. Kleaf did not vary between cool and warm-climate populations, nor was it affected by variable growth temperature. In contrast, population origin and growth temperature independently altered P50leaf. Using data pooled across growth temperatures, cool-climate populations showed significantly higher leaf hydraulic vulnerability (P50leaf = -3.55 ± 0.18 MPa) than warm-climate populations (P50leaf = -3.78 ± 0.08 MPa). Across populations, P50leaf decreased as population home-climate temperature increased, but was unrelated to rainfall and aridity. For populations from both cool and warm climatic regions, P50leaf was lower under the warmer growth conditions. These results provide evidence of trait plasticity in leaf hydraulic vulnerability to drought in response to variable growth temperature. Furthermore, they suggest that climate, and in particular temperature, may be a strong selective force in shaping intraspecific variation in leaf hydraulic vulnerability to drought.
Gong, Changfei; Zeng, Dong; Bian, Zhaoying; Huang, Jing; Zhang, Xinyu; Zhang, Hua; Lu, Lijun; Feng, Qianjin; Liang, Zhengrong; Ma, Jianhua
Dynamic myocardial perfusion computed tomography (MPCT) is a promising technique for diagnosis and risk stratification of coronary artery disease by assessing the myocardial perfusion hemodynamic maps (MPHM). Meanwhile, the repeated scanning of the same region results in a relatively large radiation dose to patients potentially. In this work, we present a robust MPCT deconvolution algorithm with adaptive-weighted tensor total variation regularization to estimate residue function accurately under the low-dose context, which is termed `MPD-AwTTV'. More specifically, the AwTTV regularization takes into account the anisotropic edge property of the MPCT images compared with the conventional total variation (TV) regularization, which can mitigate the drawbacks of TV regularization. Subsequently, an effective iterative algorithm was adopted to minimize the associative objective function. Experimental results on a modified XCAT phantom demonstrated that the present MPD-AwTTV algorithm outperforms and is superior to other existing deconvolution algorithms in terms of noise-induced artifacts suppression, edge details preservation and accurate MPHM estimation.
An optimal adaptive data assimilation algorithm is derived using the maximum likelihood method based on a conditional Gaussian probability density function for the first-guess and direct observations of the state variables but including local estimates of the observation and first-guess error statistics. An interpolation of the first-guess field to the observation coordinates is not required under the assumption of locally homogeneous statistics for the random atmosphere. However, the definition of observation error requires a definition of model 'truth' which is defined as a spatial average of the continuous random atmospheric variables. Then the total observation error consists of two independent components: an instrument error and an observation sampling error defined by the spatial average of the observation and the statistics of the local turbulence. Estimates of the observation sampling error statistics are determined from an ensemble of background or first-guess fields or from the analysis of the raw data from instrumented aircraft, Doppler lidars, or radar profilers. The spatial variations of the sampling error are referenced to the local turbulence conditions at each analysis coordinate and therefore each observation can have a different observation error for each nearby analysis coordinate. The extension of the adaptive assimilation concept to include the spatial variations in observation error for statistical interpolation, 3D-Var, 4D-Var, extended Kalman filtering, and ensemble Kalman filtering is also presented for the traditional meaning of observation error, i.e. each observation is assigned a single error. The conditional analysis error is derived for a single observation at the analysis coordinate and multiple observations around the analysis point. Example calculations of the conditional analysis error are presented for a few simple set of observation and measurement geometries to demonstrate the impact of the spatially variable observation errors
Bobadilla Landey, Roberto; Cenci, Alberto; Georget, Frédéric; Bertrand, Benoît; Camayo, Gloria; Dechamp, Eveline; Herrera, Juan Carlos; Santoni, Sylvain; Lashermes, Philippe; Simpson, June; Etienne, Hervé
Embryogenic suspensions that involve extensive cell division are risky in respect to genome and epigenome instability. Elevated frequencies of somaclonal variation in embryogenic suspension-derived plants were reported in many species, including coffee. This problem could be overcome by using culture conditions that allow moderate cell proliferation. In view of true-to-type large-scale propagation of C. arabica hybrids, suspension protocols based on low 2,4-D concentrations and short proliferation periods were developed. As mechanisms leading to somaclonal variation are often complex, the phenotypic, genetic and epigenetic changes were jointly assessed so as to accurately evaluate the conformity of suspension-derived plants. The effects of embryogenic suspensions and secondary embryogenesis, used as proliferation systems, on the genetic conformity of somatic embryogenesis-derived plants (emblings) were assessed in two hybrids. When applied over a 6 month period, both systems ensured very low somaclonal variation rates, as observed through massive phenotypic observations in field plots (0.74% from 200 000 plant). Molecular AFLP and MSAP analyses performed on 145 three year-old emblings showed that polymorphism between mother plants and emblings was extremely low, i.e. ranges of 0–0.003% and 0.07–0.18% respectively, with no significant difference between the proliferation systems for the two hybrids. No embling was found to cumulate more than three methylation polymorphisms. No relation was established between the variant phenotype (27 variants studied) and a particular MSAP pattern. Chromosome counting showed that 7 of the 11 variant emblings analyzed were characterized by the loss of 1–3 chromosomes. This work showed that both embryogenic suspensions and secondary embryogenesis are reliable for true-to-type propagation of elite material. Molecular analyses revealed that genetic and epigenetic alterations are particularly limited during coffee somatic
Garduño-Paz, M V; Demetriou, M; Adams, C E
Landmark-based geometric morphometric analysis was used to detect differences in scale shape between ecologically distinct phenotypes of Arctic charr Salvelinus alpinus coexisting in the same lake. Relative warp analysis and standard multivariate analyses of the partial warps, obtained after a Procrustes superimposition, showed that scale landmarks were efficient in discriminating among two closely related alternative phenotypes within each of the two lakes. In Loch Tay, S. alpinus exhibited a bimodal body size-frequency distribution among sexually mature fish, whereas in Loch Awe, S. alpinus are unimodal in body size but segregated into two distinct spawning phenotypes. In both lakes, alternative phenotypes showed significant differences in foraging ecology, habitat use and life history. It is probable that differences in scale shape reflect differences in ecology of these forms.
Sampedro, Luis; Llusia, Joan; Peñuelas, Josep; Zas, Rafael
Oleoresin produced and stored in pine tree leaves provides direct resistance to herbivores, while leaf volatile terpenes (LVT) in the resin are also powerful airborne infochemicals. Resin concentration and profile show considerable spatial and temporal phenotypic variation within and among pine populations. LVT biochemistry is known to be under genetic control, and although LVT should be plastic to diverse abiotic and biotic environmental factors such as nutrient availability and herbivore attack, little is known about their relative contributions and interactive effects. The aim of this paper was to clarify whether reduced phosphorus availability could increase the LVT concentration and affect the expression of herbivore-derived induced defences, and how plasticity would contribute to the phenotypic variation of LVT. The constitutive and methyl-jasmonate (MeJa) induced LVT concentration and profile were analysed in 17 half-sib Pinus pinaster families growing under two levels of P-availability (complete and P-limited fertilization). Individual terpene concentrations showed large additive genetic variation, which was more pronounced in the control than in MeJa-induced pines. MeJa application did not affect the LVT concentration, but significantly modified the LVT profile by depleting the α-pinene content and reducing the sesquiterpene fraction. Low P-availability strongly reduced plant growth and foliar nutrient concentrations, but did not affect LVT concentration and profile, and did not interact with MeJa-induction. Results indicate a strong homeostasis of LVT concentration to P-availability, and minor changes in the LVT profile due to MeJa-induction. Genetic variation appears to be the main source of phenotypic variation affecting the LVT concentration in this pine species. PMID:20952630
Sampedro, Luis; Moreira, Xoaquín; Llusia, Joan; Peñuelas, Josep; Zas, Rafael
Oleoresin produced and stored in pine tree leaves provides direct resistance to herbivores, while leaf volatile terpenes (LVT) in the resin are also powerful airborne infochemicals. Resin concentration and profile show considerable spatial and temporal phenotypic variation within and among pine populations. LVT biochemistry is known to be under genetic control, and although LVT should be plastic to diverse abiotic and biotic environmental factors such as nutrient availability and herbivore attack, little is known about their relative contributions and interactive effects. The aim of this paper was to clarify whether reduced phosphorus availability could increase the LVT concentration and affect the expression of herbivore-derived induced defences, and how plasticity would contribute to the phenotypic variation of LVT. The constitutive and methyl-jasmonate (MeJa) induced LVT concentration and profile were analysed in 17 half-sib Pinus pinaster families growing under two levels of P-availability (complete and P-limited fertilization). Individual terpene concentrations showed large additive genetic variation, which was more pronounced in the control than in MeJa-induced pines. MeJa application did not affect the LVT concentration, but significantly modified the LVT profile by depleting the α-pinene content and reducing the sesquiterpene fraction. Low P-availability strongly reduced plant growth and foliar nutrient concentrations, but did not affect LVT concentration and profile, and did not interact with MeJa-induction. Results indicate a strong homeostasis of LVT concentration to P-availability, and minor changes in the LVT profile due to MeJa-induction. Genetic variation appears to be the main source of phenotypic variation affecting the LVT concentration in this pine species.
Shi, Qi; Sun, Nanbo; Sun, Tao; Wang, Jing; Tan, Shan
The exposure of normal tissues to high radiation during cone-beam CT (CBCT) imaging increases the risk of cancer and genetic defects. Statistical iterative algorithms with the total variation (TV) penalty have been widely used for low dose CBCT reconstruction, with state-of-the-art performance in suppressing noise and preserving edges. However, TV is a first-order penalty and sometimes leads to the so-called staircase effect, particularly over regions with smooth intensity transition in the reconstruction images. A second-order penalty known as the Hessian penalty was recently used to replace TV to suppress the staircase effect in CBCT reconstruction at the cost of slightly blurring object edges. In this study, we proposed a new penalty, the TV-H, which combines TV and Hessian penalties for CBCT reconstruction in a structure-adaptive way. The TV-H penalty automatically differentiates the edges, gradual transition and uniform local regions within an image using the voxel gradient, and adaptively weights TV and Hessian according to the local image structures in the reconstruction process. Our proposed penalty retains the benefits of TV, including noise suppression and edge preservation. It also maintains the structures in regions with gradual intensity transition more successfully. A majorization-minimization (MM) approach was designed to optimize the objective energy function constructed with the TV-H penalty. The MM approach employed a quadratic upper bound of the original objective function, and the original optimization problem was changed to a series of quadratic optimization problems, which could be efficiently solved using the Gauss-Seidel update strategy. We tested the reconstruction algorithm on two simulated digital phantoms and two physical phantoms. Our experiments indicated that the TV-H penalty visually and quantitatively outperformed both TV and Hessian penalties.
Shi, Qi; Sun, Nanbo; Sun, Tao; Wang, Jing; Tan, Shan
The exposure of normal tissues to high radiation during cone-beam CT (CBCT) imaging increases the risk of cancer and genetic defects. Statistical iterative algorithms with the total variation (TV) penalty have been widely used for low dose CBCT reconstruction, with state-of-the-art performance in suppressing noise and preserving edges. However, TV is a first-order penalty and sometimes leads to the so-called staircase effect, particularly over regions with smooth intensity transition in the reconstruction images. A second-order penalty known as the Hessian penalty was recently used to replace TV to suppress the staircase effect in CBCT reconstruction at the cost of slightly blurring object edges. In this study, we proposed a new penalty, the TV-H, which combines TV and Hessian penalties for CBCT reconstruction in a structure-adaptive way. The TV-H penalty automatically differentiates the edges, gradual transition and uniform local regions within an image using the voxel gradient, and adaptively weights TV and Hessian according to the local image structures in the reconstruction process. Our proposed penalty retains the benefits of TV, including noise suppression and edge preservation. It also maintains the structures in regions with gradual intensity transition more successfully. A majorization-minimization (MM) approach was designed to optimize the objective energy function constructed with the TV-H penalty. The MM approach employed a quadratic upper bound of the original objective function, and the original optimization problem was changed to a series of quadratic optimization problems, which could be efficiently solved using the Gauss-Seidel update strategy. We tested the reconstruction algorithm on two simulated digital phantoms and two physical phantoms. Our experiments indicated that the TV-H penalty visually and quantitatively outperformed both TV and Hessian penalties. PMID:27699100
Geerse, Daphne J; Coolen, Bert H; Roerdink, Melvyn
The ability to adapt walking to environmental circumstances is an important aspect of walking, yet difficult to assess. The Interactive Walkway was developed to assess walking adaptability by augmenting a multi-Kinect-v2 10-m walkway with gait-dependent visual context (stepping targets, obstacles) using real-time processed markerless full-body kinematics. In this study we determined Interactive Walkway's usability for walking-adaptability assessments in terms of between-systems agreement and sensitivity to task and subject variations. Under varying task constraints, 21 healthy subjects performed obstacle-avoidance, sudden-stops-and-starts and goal-directed-stepping tasks. Various continuous walking-adaptability outcome measures were concurrently determined with the Interactive Walkway and a gold-standard motion-registration system: available response time, obstacle-avoidance and sudden-stop margins, step length, stepping accuracy and walking speed. The same holds for dichotomous classifications of success and failure for obstacle-avoidance and sudden-stops tasks and performed short-stride versus long-stride obstacle-avoidance strategies. Continuous walking-adaptability outcome measures generally agreed well between systems (high intraclass correlation coefficients for absolute agreement, low biases and narrow limits of agreement) and were highly sensitive to task and subject variations. Success and failure ratings varied with available response times and obstacle types and agreed between systems for 85-96% of the trials while obstacle-avoidance strategies were always classified correctly. We conclude that Interactive Walkway walking-adaptability outcome measures are reliable and sensitive to task and subject variations, even in high-functioning subjects. We therefore deem Interactive Walkway walking-adaptability assessments usable for obtaining an objective and more task-specific examination of one's ability to walk, which may be feasible for both high
Krausz, Csilla; Giachini, Claudia; Xue, Yali; O’Brya, Moira K.; Gromoll, Joerg; Rajpert-de Meyts, Ewa; Oliva, Rafael; Aknin-Seifer, Isabelle; Erdei, Edit; Jorgensen, Niels; Simoni, Manuela; Ballescà, José Luis; Levy, Rachel; Balercia, Giancarlo; Piomboni, Paola; Nieschlag, Eberhard; Forti, Gianni; McLachlan, Rob; Tyler-Smith, Chris
Background Previous studies have compared sperm phenotypes between men with partial  deletions within the AZFc region of the Y chromosome with non-carriers, with variable results. Here, we have investigated a separate question, the basis of the variation in sperm phenotype within gr/gr deletion carriers, which ranges from normozoospermia to azoospermia. Differences in the genes removed by independent gr/gr deletions, the occurrence of subsequent duplications or the presence of linked modifying variants elsewhere on the chromosome have been suggested as possible causal factors. We set out to test these possibilities in a large sample of gr/gr deletion carriers with known phenotypes spanning the complete range. Results We assembled a collection of 169 men diagnosed with gr/gr deletions from six centres in Europe and one in Australia, and characterized the DAZ and CDY1 copies retained, the presence or absence of duplications and the Y-chromosomal haplogroup. Although our study had good power to detect factors that accounted for ≥5.5% of the variation in sperm concentration, no such factor was detected. A negative effect of gr/gr deletions followed by b2/b4 duplication was observed within the normospermic group, which remains to be further explored in a larger study population. Finally, we observed significant geographical differences in the frequency of different subtypes of gr/gr deletions which may have relevance for the interpretation of case control studies dealing with admixed populations. Conclusions We conclude that the phenotypic variation of gr/gr carriers in men of European origin is largely independent of the Y-chromosomal background. PMID:18782837
Wang, Yanqiang; Luo, Chenglong; Liu, Ranran; Qu, Hao; Shu, Dingming; Wen, Jie; Crooijmans, Richard P. M. A.; Zhao, Yiqiang; Hu, Xiaoxiang; Li, Ning
Muffs and beard (Mb) is a phenotype in chickens where groups of elongated feathers gather from both sides of the face (muffs) and below the beak (beard). It is an autosomal, incomplete dominant phenotype encoded by the Muffs and beard (Mb) locus. Here we use genome-wide association (GWA) analysis, linkage analysis, Identity-by-Descent (IBD) mapping, array-CGH, genome re-sequencing and expression analysis to show that the Mb allele causing the Mb phenotype is a derived allele where a complex structural variation (SV) on GGA27 leads to an altered expression of the gene HOXB8. This Mb allele was shown to be completely associated with the Mb phenotype in nine other independent Mb chicken breeds. The Mb allele differs from the wild-type mb allele by three duplications, one in tandem and two that are translocated to that of the tandem repeat around 1.70 Mb on GGA27. The duplications contain total seven annotated genes and their expression was tested during distinct stages of Mb morphogenesis. A continuous high ectopic expression of HOXB8 was found in the facial skin of Mb chickens, strongly suggesting that HOXB8 directs this regional feather-development. In conclusion, our results provide an interesting example of how genomic structural rearrangements alter the regulation of genes leading to novel phenotypes. Further, it again illustrates the value of utilizing derived phenotypes in domestic animals to dissect the genetic basis of developmental traits, herein providing novel insights into the likely role of HOXB8 in feather development and differentiation. PMID:27253709
Liu, Ryan Wen; Shi, Lin; Huang, Wenhua; Xu, Jing; Yu, Simon Chun Ho; Wang, Defeng
Magnetic resonance imaging (MRI) is an outstanding medical imaging modality but the quality often suffers from noise pollution during image acquisition and transmission. The purpose of this study is to enhance image quality using feature-preserving denoising method. In current literature, most existing MRI denoising methods did not simultaneously take the global image prior and local image features into account. The denoising method proposed in this paper is implemented based on an assumption of spatially varying Rician noise map. A two-step wavelet-domain estimation method is developed to extract the noise map. Following a Bayesian modeling approach, a generalized total variation-based MRI denoising model is proposed based on global hyper-Laplacian prior and Rician noise assumption. The proposed model has the properties of backward diffusion in local normal directions and forward diffusion in local tangent directions. To further improve the denoising performance, a local variance estimator-based method is introduced to calculate the spatially adaptive regularization parameters related to local image features and spatially varying noise map. The main benefit of the proposed method is that it takes full advantage of the global MR image prior and local image features. Numerous experiments have been conducted on both synthetic and real MR data sets to compare our proposed model with some state-of-the-art denoising methods. The experimental results have demonstrated the superior performance of our proposed model in terms of quantitative and qualitative image quality evaluations.
Lestari, Dessi Puji; Furui, Sadaoki
Recognition errors of proper nouns and foreign words significantly decrease the performance of ASR-based speech applications such as voice dialing systems, speech summarization, spoken document retrieval, and spoken query-based information retrieval (IR). The reason is that proper nouns and words that come from other languages are usually the most important key words. The loss of such words due to misrecognition in turn leads to a loss of significant information from the speech source. This paper focuses on how to improve the performance of Indonesian ASR by alleviating the problem of pronunciation variation of proper nouns and foreign words (English words in particular). To improve the proper noun recognition accuracy, proper-noun specific acoustic models are created by supervised adaptation using maximum likelihood linear regression (MLLR). To improve English word recognition, the pronunciation of English words contained in the lexicon is fixed by using rule-based English-to-Indonesian phoneme mapping. The effectiveness of the proposed method was confirmed through spoken query based Indonesian IR. We used Inference Network-based (IN-based) IR and compared its results with those of the classical Vector Space Model (VSM) IR, both using a tf-idf weighting schema. Experimental results show that IN-based IR outperforms VSM IR.
Gong, Changmei; Shao, Xiaopeng; Wu, Tengfei
Multiple scattering of light in highly disordered medium can break the diffraction limit of conventional optical system combined with image reconstruction method. Once the transmission matrix of the imaging system is obtained, the target image can be reconstructed from its speckle pattern by image reconstruction algorithm. Nevertheless, the restored image attained by common image reconstruction algorithms such as Tikhonov regularization has a relatively low signal-tonoise ratio (SNR) due to the experimental noise and reconstruction noise, greatly reducing the quality of the result image. In this paper, the speckle pattern of the test image is simulated by the combination of light propagation theories and statistical optics theories. Subsequently, an adaptive total variation (ATV) algorithm—the TV minimization by augmented Lagrangian and alternating direction algorithms (TVAL3), which is based on augmented Lagrangian and alternating direction algorithm, is utilized to reconstruct the target image. Numerical simulation experimental results show that, the TVAL3 algorithm can effectively suppress the noise of the restored image and preserve more image details, thus greatly boosts the SNR of the restored image. It also indicates that, compared with the image directly formed by `clean' system, the reconstructed results can overcoming the diffraction limit of the `clean' system, therefore being conductive to the observation of cells and protein molecules in biological tissues and other structures in micro/nano scale.
Trotter, M.V.; Weissman, D.B.; Peterson, G.I.; Peck, K.M.; Masel, J.
The existence of complex (multiple-step) genetic adaptations that are ‘irreducible’ (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here we demonstrate, using a simple model, that evolution can cross wide valleys to produce ‘irreducibly complex’ adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics imply an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations. PMID:25178652
Whitehead, Andrew; Galvez, Fernando; Zhang, Shujun; Williams, Larissa M; Oleksiak, Marjorie F
Evolutionary solutions to the physiological challenges of life in highly variable habitats can span the continuum from evolution of a cosmopolitan plastic phenotype to the evolution of locally adapted phenotypes. Killifish (Fundulus sp.) have evolved both highly plastic and locally adapted phenotypes within different selective contexts, providing a comparative system in which to explore the genomic underpinnings of physiological plasticity and adaptive variation. Importantly, extensive variation exists among populations and species for tolerance to a variety of stressors, and we exploit this variation in comparative studies to yield insights into the genomic basis of evolved phenotypic variation. Notably, species of Fundulus occupy the continuum of osmotic habitats from freshwater to marine and populations within Fundulus heteroclitus span far greater variation in pollution tolerance than across all species of fish. Here, we explore how transcriptome regulation underpins extreme physiological plasticity on osmotic shock and how genomic and transcriptomic variation is associated with locally evolved pollution tolerance. We show that F. heteroclitus quickly acclimate to extreme osmotic shock by mounting a dramatic rapid transcriptomic response including an early crisis control phase followed by a tissue remodeling phase involving many regulatory pathways. We also show that convergent evolution of locally adapted pollution tolerance involves complex patterns of gene expression and genome sequence variation, which is confounded with body-weight dependence for some genes. Similarly, exploiting the natural phenotypic variation associated with other established and emerging model organisms is likely to greatly accelerate the pace of discovery of the genomic basis of phenotypic variation.
Noormohammadi, Amir H
The interactions between avian mycoplasmas and their host cells are far more complex than might be anticipated from their apparent structural and functional simplicity. Phenotypic diversity in the form of reversible phase variation, antigenic variation or size variation is an adaptive mechanism that enables avian mycoplasmas to survive in a hostile and highly evolved host. Despite significant similarities between major membrane antigens of Mycoplasma gallisepticum and Mycoplasma synoviae, the molecular mechanisms that mediate phenotypic variation in these two pathogens are completely different. Throughout the years, these mechanisms have evolved side by side with their host immune system and provided mycoplasmas the capacity to colonize, invade and persist in an intricate host. In this article, recent advances in the understanding of the molecular mechanisms of phenotypic variation are reviewed, and implications of such variation in pathogenesis of the disease and development of vaccines and diagnostic assays are outlined.
Zhao, Yang; Ren, Ji-Long; Wang, Ming-Yang; Zhang, Sheng-Ting; Liu, Yu; Li, Min; Cao, Yi-Bin; Zu, Hu-Yue; Chen, Xiao-Cheng; Wu, Chung-I; Nevo, Eviatar; Chen, Xue-Qun; Du, Ji-Zeng
Mutational changes in p53 correlate well with tumorigenesis. Remarkably, however, relatively little is known about the role that p53 variations may play in environmental adaptation. Here we report that codon asparagine-104 (104N) and glutamic acid-104 (104E), respectively, of the p53 gene in the wild zokor (Myospalax baileyi) and root vole (Microtus oeconomus) are adaptively variable, meeting the environmental stresses of the Tibetan plateau. They differ from serine-104 (104S) seen in other rodents, including the lowland subterranean zokor Myospalax cansus, and from serine 106 (106S) in humans. Based on site-directed mutational analysis in human cell lines, the codon 104N variation in M. baileyi is responsible for the adaptive balance of the transactivation of apoptotic genes under hypoxia, cold, and acidic stresses. The 104E p53 variant in Microtus oeconomus suppresses apoptotic gene transactivation and cell apoptosis. Neither 104N nor 104E affects the cell-cycle genes. We propose that these variations in p53 codon 104 are an outcome of environmental adaptation and evolutionary selection that enhance cellular strategies for surviving the environmental stresses of hypoxia and cold (in M. baileyi and M. oeconomus) and hypercapnia (in M. baileyi) in the stressful environments of the Qinghai-Tibet plateau. PMID:24297887
Fox, Jeremy W; Harder, Lawrence D
Local adaptation occurs when different environments are dominated by different specialist genotypes, each of which is relatively fit in its local conditions and relatively unfit under other conditions. Analogously, ecological species sorting occurs when different environments are dominated by different competing species, each of which is relatively fit in its local conditions. The simplest theory predicts that spatial, but not temporal, environmental variation selects for local adaptation (or generates species sorting), but this prediction is difficult to test. Although organisms can be reciprocally transplanted among sites, doing so among times seems implausible. Here, we describe a reciprocal transplant experiment testing for local adaptation or species sorting of lake bacteria in response to both temporal and spatial variation in water chemistry. The experiment used a -80°C freezer as a "time machine." Bacterial isolates and water samples were frozen for later use, allowing transplantation of older isolates "forward in time" and newer isolates "backward in time." Surprisingly, local maladaptation predominated over local adaptation in both space and time. Such local maladaptation may indicate that adaptation, or the analogous species sorting process, fails to keep pace with temporal fluctuations in water chemistry. This hypothesis could be tested with more finely resolved temporal data.
Peng, Jialin; Dong, Fangfang; Chen, Yunmei; Kong, Dexing
Purpose: Liver segmentation from computed tomography images is a challenging task owing to pixel intensity overlapping, ambiguous edges, and complex backgrounds. The authors address this problem with a novel active surface scheme, which minimizes an energy functional combining both edge- and region-based information. Methods: In this semiautomatic method, the evolving surface is principally attracted to strong edges but is facilitated by the region-based information where edge information is missing. As avoiding oversegmentation is the primary challenge, the authors take into account multiple features and appearance context information. Discriminative cues, such as multilayer consecutiveness and local organ deformation are also implicitly incorporated. Case-specific intensity and appearance constraints are included to cope with the typically large appearance variations over multiple images. Spatially adaptive balancing weights are employed to handle the nonuniformity of image features. Results: Comparisons and validations on difficult cases showed that the authors’ model can effectively discriminate the liver from adhering background tissues. Boundaries weak in gradient or with no local evidence (e.g., small edge gaps or parts with similar intensity to the background) were delineated without additional user constraint. With an average surface distance of 0.9 mm and an average volume overlap of 93.9% on the MICCAI data set, the authors’ model outperformed most state-of-the-art methods. Validations on eight volumes with different initial conditions had segmentation score variances mostly less than unity. Conclusions: The proposed model can efficiently delineate ambiguous liver edges from complex tissue backgrounds with reproducibility. Quantitative validations and comparative results demonstrate the accuracy and efficacy of the model.
Consistent data across animal populations are required to inform genomic science aimed at finding important adaptive genetic variations. The ADAPTMap Digital Phenotype Collection Method is a new procedure to provide consistent phenotypic data by digital enumeration of categorical and continuous valu...
Arroyo, Beatriz; Mougeot, François; Bretagnolle, Vincent
Whether human disturbance can lead to directional selection and phenotypic change in behaviour in species with limited behavioural plasticity is poorly understood in wild animal populations. Using a 19-year study on Montagu's harrier, we report a long-term increase in boldness towards humans during nest visits. The probability of females fleeing or being passive during nest visits decreased, while defence intensity steadily increased over the study period. These behavioural responses towards humans were significantly repeatable. The phenotypic composition of the breeding population changed throughout the study period (4-5 harrier generations), with a gradual disappearance of shy individuals, leading to a greater proportion of bolder ones and a more behaviourally homogeneous population. We further show that nest visit frequency increased nest failure probability and reduced productivity of shy females, but not of bold ones. Long-term research or conservation programmes needing nest visits can therefore lead to subtle but relevant population compositional changes that require further attention.
van Loon, Janine E.; Sanders, Yvonne V.; de Wee, Eva M.; Kruip, Marieke J. H. A.; de Maat, Moniek P. M.; Leebeek, Frank W. G.
Background In type 1 von Willebrand Disease (VWD) patients, von Willebrand Factor (VWF) levels and bleeding symptoms are highly variable. Recently, the association between genetic variations in STXBP5 and STX2 with VWF levels has been discovered in the general population. We assessed the relationship between genetic variations in STXBP5 and STX2, VWF levels, and bleeding phenotype in type 1 VWD patients. Methods In 158 patients diagnosed with type 1 VWD according to the current ISTH guidelines, we genotyped three tagging-SNPs in STXBP5 and STX2 and analyzed their relationship with VWF:Ag levels and the severity of the bleeding phenotype, as assessed by the Tosetto bleeding score. Results In STX2, rs7978987 was significantly associated with VWF:Ag levels (bèta-coefficient (β) = −0.04 IU/mL per allele, [95%CI −0.07;−0.001], p = 0.04) and VWF:CB activity (β = −0.12 IU/mL per allele, [95%CI −0.17;−0.06], p<0.0001). For rs1039084 in STXBP5 a similar trend with VWF:Ag levels was observed: (β = −0.03 IU/mL per allele [95% CI −0.06;0.003], p = 0.07). In women, homozygous carriers of the minor alleles of both SNPs in STXBP5 had a significantly higher bleeding score than homozygous carriers of the major alleles. (Rs1039084 p = 0.01 and rs9399599 p = 0.02). Conclusions Genetic variation in STX2 is associated with VWF:Ag levels in patients diagnosed with type 1 VWD. In addition, genetic variation in STXBP5 is associated with bleeding phenotype in female VWD patients. Our findings may partly explain the variable VWF levels and bleeding phenotype in type 1 VWD patients. PMID:22792389
Tschaplinski, Timothy J; Tuskan, Gerald A; Sewell, Mitchell; Gebre, G; Todd Jr, Donald E; Pendley, Carrie D
Elucidation of the mechanisms of dehydration tolerance in popular (Populus sp.) trees will permit development of biochemical and molecular indicators to indentify dehydration-tolerant genotypes during genetic selection. The objectives of the study were to characterize the degree of phenotypic variation in osmotic potential (a determinant of dehydration tolerance), determine the relationship between osmotic potential at full turgor and relative growth rate, and identify quantitative trait loci (QTL) for osmotic potential in an advanced-generation, interpsecific popular pedigree established in contrasting environments.
Scott, Graham R; Elogio, Todd S; Lui, Mikaela A; Storz, Jay F; Cheviron, Zachary A
At high-altitude, small mammals are faced with the energetic challenge of sustaining thermogenesis and aerobic exercise in spite of the reduced O2 availability. Under conditions of hypoxic cold stress, metabolic demands of shivering thermogenesis and locomotion may require enhancements in the oxidative capacity and O2 diffusion capacity of skeletal muscle to compensate for the diminished tissue O2 supply. We used common-garden experiments involving highland and lowland deer mice (Peromyscus maniculatus) to investigate the transcriptional underpinnings of genetically based population differences and plasticity in muscle phenotype. We tested highland and lowland mice that were sampled in their native environments as well as lab-raised F1 progeny of wild-caught mice. Experiments revealed that highland natives had consistently greater oxidative fiber density and capillarity in the gastrocnemius muscle. RNA sequencing analyses revealed population differences in transcript abundance for 68 genes that clustered into two discrete transcriptional modules, and a large suite of transcripts (589 genes) with plastic expression patterns that clustered into five modules. The expression of two transcriptional modules was correlated with the oxidative phenotype and capillarity of the muscle, and these phenotype-associated modules were enriched for genes involved in energy metabolism, muscle plasticity, vascular development, and cell stress response. Although most of the individual transcripts that were differentially expressed between populations were negatively correlated with muscle phenotype, several genes involved in energy metabolism (e.g., Ckmt1, Ehhadh, Acaa1a) and angiogenesis (Notch4) were more highly expressed in highlanders, and the regulators of mitochondrial biogenesis, PGC-1α (Ppargc1a) and mitochondrial transcription factor A (Tfam), were positively correlated with muscle oxidative phenotype. These results suggest that evolved population differences in the oxidative
The choice of populations for quantitative genetics experiments impacts inferences about genetic architecture and prospective selection gains. Plant breeding and quantitative genetics studies are often conducted in one or a few among many possible biparental families. Trait genotypic variation withi...
Incarnato, Danny; Ward, Ben J.; van Oosterhout, Cock; Bradbury, Ian; Hanson, Mark; Bentzen, Paul
The relative importance of genetic versus epigenetic changes in adaptive evolution is a hotly debated topic, with studies showing that some species appear to be able to adapt rapidly without significant genetic change. Epigenetic mechanisms may be particularly important for the evolutionary potential of species with long maturation times and low reproductive potential (‘K-strategists’), particularly when faced with rapidly changing environmental conditions. Here we study the transcriptome of two populations of the winter skate (Leucoraja ocellata), a typical ‘K-strategist’, in Atlantic Canada; an endemic population in the southern Gulf of St Lawrence and a large population on the Scotian Shelf. The endemic population has been able to adapt to a 10°C higher water temperature over short evolutionary time (7000 years), dramatically reducing its body size (by 45%) significantly below the minimum maturation size of Scotian Shelf and other populations of winter skate, as well as exhibiting other adaptations in life history and physiology. We demonstrate that the adaptive response to selection has an epigenetic basis, cataloguing 3653 changes in gene expression that may have enabled this species to rapidly respond to the novel environment. We argue that the epigenetic augmentation of species evolutionary potential (its regulation though gene expression) can enable K-strategists to survive and adapt to different environments, and this mechanism may be particularly important for the persistence of sharks, skates and rays in the light of future climate change. PMID:27853546
Roulin, Anne C; Mariadassou, Mahendra; Hall, Matthew D; Walser, Jean-Claude; Haag, Christoph; Ebert, Dieter
Local adaptation is a key process for the maintenance of genetic diversity and population diversification. A better understanding of the mechanisms that allow (or prevent) local adaptation constitutes a key in apprehending how and at what spatial scale it occurs. The production of resting stages is found in many taxa and reflects an adaptation to outlast adverse environmental conditions. Daphnia magna (Crustacea) can alternate between asexual and sexual reproduction, the latter being linked to dormancy, as resting stages can only be produced sexually. In this species, on a continental scale, resting-stage production is locally adapted--that is, it is induced when the photoperiod indicates the imminence of habitat deterioration. Here, we aimed to explore whether selection is strong enough to maintain local adaptation at a scale of a few kilometers. We assessed life-history traits of 64 D. magna clones originating from 11 populations of a metapopulation with permanent and intermittent pool habitats. We found large within- and between-population variation for all dormancy-related traits, but no evidence for the hypothesized higher resting-stage production in animals from intermittent habitats. We discuss how gene flow, founder events, or other forms of selection might interfere with the process of local adaptation.
Deng, Luzhen; Mi, Deling; He, Peng; Feng, Peng; Yu, Pengwei; Chen, Mianyi; Li, Zhichao; Wang, Jian; Wei, Biao
For lack of directivity in Total Variation (TV) which only uses x-coordinate and y-coordinate gradient transform as its sparse representation approach during the iteration process, this paper brought in Adaptive-weighted Diagonal Total Variation (AwDTV) that uses the diagonal direction gradient to constraint reconstructed image and adds associated weights which are expressed as an exponential function and can be adaptively adjusted by the local image-intensity diagonal gradient for the purpose of preserving the edge details, then using the steepest descent method to solve the optimization problem. Finally, we did two sets of numerical simulation and the results show that the proposed algorithm can reconstruct high-quality CT images from few-views projection, which has lower Root Mean Square Error (RMSE) and higher Universal Quality Index (UQI) than Algebraic Reconstruction Technique (ART) and TV-based reconstruction method.
Buesching, Christina Dagmar; Heistermann, Michael; Macdonald, David W
Elevated testosterone levels can lower condition and increase parasites. We analysed testosterone in 84 blood samples of wild European badgers Meles meles collected at regular intervals (winter = mating season; spring = end of mating season; summer = minor mating peak; autumn = reproductive quiescence), and related variation to body condition, subcaudal gland secretion, parasite burden, and bite wounding. All males showed elevated levels in winter and low levels in autumn. In neither season did testosterone correlate with fitness-related parameters. However, two different endocrinological phenotypes existed in spring and summer. Whilst some males lowered their testosterone to levels comparable to autumnal quiescence (Type 1), others maintained elevated levels comparable to those during winter (Type 2). In spring and summer high levels were correlated with lower body condition and increased parasite burden, and Type 2 males tended to suffer higher mortality rates than Type 1. No animals older than 6 years adopted phenotype 2, indicating that males either switch phenotypes with age or that Type 2 results in lower life expectancy, evidencing the costs of male reproduction in badgers.
Franchini, Paolo; Colangelo, Paolo; Meyer, Axel; Fruciano, Carmelo
The Western European house mouse, Mus musculus domesticus, is well-known for the high frequency of Robertsonian fusions that have rapidly produced more than 50 karyotipic races, making it an ideal model for studying the mechanisms of chromosomal speciation. The mouse mandible is one of the traits studied most intensively to investigate the effect of Robertsonian fusions on phenotypic variation within and between populations. This complex bone structure has also been widely used to study the level of integration between different morphogenetic units. Here, with the aim of testing the effect of different karyotypic assets on the morphology of the mouse mandible and on its level of modularity, we performed morphometric analyses of mice from a contact area between two highly metacentric races in Central Italy. We found no difference in size, while the mandible shape was found to be different between the two Robertsonian races, even after accounting for the genetic relationships among individuals and geographic proximity. Our results support the existence of two modules that indicate a certain degree of evolutionary independence, but no difference in the strength of modularity between chromosomal races. Moreover, the ascending ramus showed more pronounced interpopulation/race phenotypic differences than the alveolar region, an effect that could be associated to their different polygenic architecture. This study suggests that chromosomal rearrangements play a role in the house mouse phenotypic divergence, and that the two modules of the mouse mandible are differentially affected by environmental factors and genetic makeup.
Dastgheyb, Sana S; Otto, Michael
Host niches can differ strongly regarding, for example, oxygen tension, pH or nutrient availability. Staphylococcus aureus and other staphylococci are common colonizers of human epithelia as well as important human pathogens. The phenotypes that they show in different host environments, and the corresponding bacterial transcriptomes and proteomes, are currently under intense investigation. In this review, we examine the available literature describing staphylococcal phenotypes, such as expression of virulence factors, gross morphologic characteristics and growth patterns, in various physiological environments. Going forward, these studies will help researchers and clinicians to form an enhanced and more detailed picture of the interactions existing between the host and staphylococci as some of its most frequent colonizers and invaders. PMID:26584249
García-Navas, V; Ferrer, E S; Sanz, J J; Ortego, J
Dispersal and local patterns of adaptation play a major role on the ecological and evolutionary trajectory of natural populations. In this study, we employ a combination of genetic (25 microsatellite markers) and field-based information (seven study years) to analyse the impact of immigration and local patterns of adaptation in two nearby (<7 km) blue tit (Cyanistes caeruleus) populations. We used genetic assignment analyses to identify immigrant individuals and found that dispersal rate is female-biased (72%). Data on lifetime reproductive success indicated that immigrant females produced fewer local recruits than their philopatric counterparts whereas immigrant males recruited more offspring than those that remained in their natal location. In spite of the considerably higher immigration rates of females, our results indicate that, in absolute terms, their demographic and genetic impact in the receiving populations is lower than that in immigrant males. Immigrants often brought novel alleles into the studied populations and a high proportion of them were transmitted to their recruits, indicating that the genetic impact of immigrants is not ephemeral. Although only a few kilometres apart, the two study populations were genetically differentiated and showed strong divergence in different phenotypic and life-history traits. An almost absent inter-population dispersal, together with the fact that both populations receive immigrants from different source populations, is probably the main cause of the observed pattern of genetic differentiation. However, phenotypic differentiation (PST) for all the studied traits greatly exceeded neutral genetic differentiation (FST), indicating that divergent natural selection is the prevailing factor determining the evolutionary trajectory of these populations. Our study highlights the importance of integrating individual- and population-based approaches to obtain a comprehensive view about the role of dispersal and natural selection
Noels, Kimberly A; Clément, Richard
This study examined whether the acculturation of ethnic identity is first evident in more public situations with greater opportunity for intercultural interaction and eventually penetrates more intimate situations. It also investigated whether situational variations in identity are associated with cross-cultural adaptation. First-generation (G1), second-generation (G2) and mixed-parentage second-generation (G2.5) young adult Canadians (n = 137, n = 169, and n = 91, respectively) completed a questionnaire assessing their heritage and Canadian identities across four situational domains (family, friends, university and community), global heritage identity and cross-cultural adaptation. Consistent with the acculturation penetration hypothesis, the results showed Canadian identity was stronger than heritage identity in public domains, but the converse was true in the family domain; moreover, the difference between the identities in the family domain was attenuated in later generations. Situational variability indicated better adaptation for the G1 cohort, but poorer adaptation for the G2.5 cohort. For the G2 cohort, facets of global identity moderated the relation, such that those with a weaker global identity experienced greater difficulties and hassles with greater identity variability but those with a stronger identity did not. These results are interpreted in light of potential interpersonal issues implied by situational variation for each generation cohort.
Messamah, Branwen; Kellermann, Vanessa; Malte, Hans; Loeschcke, Volker; Overgaard, Johannes
Metabolic cold adaptation (MCA) is a controversial hypothesis suggesting that cold adapted species display an elevated metabolic rate (MR) compared to their warm climate relatives. Here we test for the presence of MCA in 65 species of drosophilid flies reared under common garden conditions. MR was measured at both 10 and 20°C for both sexes and data were analyzed in relation to the natural thermal environment of these species. We found considerable interspecific variation in MR ranging from 1.34 to 8.99µWmg(-1) at 10°C. As predicted by Bergmann's rule body mass of fly species correlated negatively with annual mean temperature (AMT), such that larger species were found in colder environments. Because larger flies have a higher total MR we found MR to vary with AMT, however, after inclusion of mass as a co-variate we found no significant effect of AMT. Furthermore, we did not find that thermal sensitivity of MR (Q10) varied with AMT. Based on this broad collection of species we therefore conclude that there is no adaptive pattern of metabolic cold adaptation within drosophilid species ranging from sub-arctic to tropical environments.
Early maize adaptation to different agricultural environments was an important process associated with the creation of a stable food supply that allowed the evolution of human civilization in the Americas. To explore the mechanisms of maize adaptation, genomic, transcriptomic and phenomic data were ...
Bainard, Jillian D; Bainard, Luke D; Henry, Thomas A; Fazekas, Aron J; Newmaster, Steven G
Genome size (C-value) and endopolyploidy (endoreduplication index, EI) are known to correlate with various morphological and ecological traits, in addition to phylogenetic placement. A phylogenetically controlled multivariate analysis was used to explore the relationships between DNA content and phenotype in angiosperms. Seeds from 41 angiosperm species (17 families) were grown in a common glasshouse experiment. Genome size (2C-value and 1Cx-value) and EI (in four tissues: leaf, stem, root, petal) were determined using flow cytometry. The phylogenetic signal was calculated for each measure of DNA content, and phylogenetic canonical correlation analysis (PCCA) explored how the variation in genome size and EI was correlated with 18 morphological and ecological traits. Phylogenetic signal (λ) was strongest for EI in all tissues, and λ was stronger for the 2C-value than the 1Cx-value. PCCA revealed that EI was correlated with pollen length, stem height, seed mass, dispersal mechanism, arbuscular mycorrhizal association, life history and flowering time, and EI and genome size were both correlated with stem height and life history. PCCA provided an effective way to explore multiple factors of DNA content variation and phenotypic traits in a phylogenetic context. Traits that were correlated significantly with DNA content were linked to plant competitive ability.
Hamilton City Board of Education (Ontario).
Suggestions for studying the topic of variation of individuals and objects (balls) to help develop elementary school students' measurement, comparison, classification, evaluation, and data collection and recording skills are made. General suggestions of variables that can be investigated are made for the study of human variation. Twelve specific…
Scott, Ian M; Ward, Jane L; Miller, Sonia J; Beale, Michael H
In chilling conditions (5°C), salicylic acid (SA)-deficient mutants (sid2, eds5 and NahG) of Arabidopsis thaliana produced more biomass than wild type (Col-0), whereas the SA overproducer cpr1 was extremely stunted. The hypothesis that these phenotypes were reflected in metabolism was explored using 600 MHz (1) H nuclear magnetic resonance (NMR) analysis of unfractionated polar shoot extracts. Biomass-related metabolic phenotypes were identified as multivariate data models of these NMR 'fingerprints'. These included principal components that correlated with biomass. Also, partial least squares-regression models were found to predict the relative size of plants in previously unseen experiments in different light intensities, or relative size of one genotype from the others. The dominant signal in these models was fumarate, which was high in SA-deficient mutants, intermediate in Col-0 and low in cpr1 at 5°C. Among signals negatively correlated with biomass, malate was prominent. Abundance of transcripts of the FUM2 cytosolic fumarase (At5g50950) showed strong positive correlation with fumarate levels and with biomass, whereas no significant differences were found for the FUM1 mitochondrial fumarase (At2g47510). It was confirmed that the morphological effects of SA under chilling find expression in the metabolome, with a role of fumarate highlighted.
Mathew, Sarah; Perreault, Charles
The behavioural variation among human societies is vast and unmatched in the animal world. It is unclear whether this variation is due to variation in the ecological environment or to differences in cultural traditions. Underlying this debate is a more fundamental question: is the richness of humans' behavioural repertoire due to non-cultural mechanisms, such as causal reasoning, inventiveness, reaction norms, trial-and-error learning and evoked culture, or is it due to the population-level dynamics of cultural transmission? Here, we measure the relative contribution of environment and cultural history in explaining the behavioural variation of 172 Native American tribes at the time of European contact. We find that the effect of cultural history is typically larger than that of environment. Behaviours also persist over millennia within cultural lineages. This indicates that human behaviour is not predominantly determined by single-generation adaptive responses, contra theories that emphasize non-cultural mechanisms as determinants of human behaviour. Rather, the main mode of human adaptation is social learning mechanisms that operate over multiple generations.
Mathew, Sarah; Perreault, Charles
The behavioural variation among human societies is vast and unmatched in the animal world. It is unclear whether this variation is due to variation in the ecological environment or to differences in cultural traditions. Underlying this debate is a more fundamental question: is the richness of humans’ behavioural repertoire due to non-cultural mechanisms, such as causal reasoning, inventiveness, reaction norms, trial-and-error learning and evoked culture, or is it due to the population-level dynamics of cultural transmission? Here, we measure the relative contribution of environment and cultural history in explaining the behavioural variation of 172 Native American tribes at the time of European contact. We find that the effect of cultural history is typically larger than that of environment. Behaviours also persist over millennia within cultural lineages. This indicates that human behaviour is not predominantly determined by single-generation adaptive responses, contra theories that emphasize non-cultural mechanisms as determinants of human behaviour. Rather, the main mode of human adaptation is social learning mechanisms that operate over multiple generations. PMID:26085589
Broom, Donald M
The term adaptation is used in biology in three different ways. It may refer to changes which occur at the cell and organ level, or at the individual level, or at the level of gene action and evolutionary processes. Adaptation by cells, especially nerve cells helps in: communication within the body, the distinguishing of stimuli, the avoidance of overload and the conservation of energy. The time course and complexity of these mechanisms varies. Adaptive characters of organisms, including adaptive behaviours, increase fitness so this adaptation is evolutionary. The major part of this paper concerns adaptation by individuals and its relationships to welfare. In complex animals, feed forward control is widely used. Individuals predict problems and adapt by acting before the environmental effect is substantial. Much of adaptation involves brain control and animals have a set of needs, located in the brain and acting largely via motivational mechanisms, to regulate life. Needs may be for resources but are also for actions and stimuli which are part of the mechanism which has evolved to obtain the resources. Hence pigs do not just need food but need to be able to carry out actions like rooting in earth or manipulating materials which are part of foraging behaviour. The welfare of an individual is its state as regards its attempts to cope with its environment. This state includes various adaptive mechanisms including feelings and those which cope with disease. The part of welfare which is concerned with coping with pathology is health. Disease, which implies some significant effect of pathology, always results in poor welfare. Welfare varies over a range from very good, when adaptation is effective and there are feelings of pleasure or contentment, to very poor. A key point concerning the concept of individual adaptation in relation to welfare is that welfare may be good or poor while adaptation is occurring. Some adaptation is very easy and energetically cheap and
Talluto, Matthew V.; Benkman, Craig W.
Recent work has demonstrated that evolutionary processes shape ecological dynamics on relatively short timescales (eco-evolutionary dynamics), but demonstrating these effects at large spatial scales in natural landscapes has proven difficult. We used empirical studies and modeling to investigate how selective pressures from fire and predispersal seed predation affect the evolution of serotiny, an ecologically important trait. Serotiny is a highly heritable key reproductive trait in Rocky Mountain lodgepole pine (Pinus contorta subsp. latifolia), a conifer that dominates millions of hectares in western North America. In these forests, the frequency of serotiny determines postfire seedling density with corresponding community- and ecosystem-level effects. We found that serotinous individuals have a selective advantage at high fire frequencies and low predation pressure; however, very high seed predation shifted the selective advantage to nonserotinous individuals even at high fire frequencies. Simulation modeling suggests that spatial variation in the frequency of serotiny results from heterogeneity in these two selective agents. These results, combined with previous findings showing a negative association between the density of seed predators and the frequency of serotiny at both landscape and continental scales, demonstrate that contemporary patterns in serotiny reflect an evolutionary response to conflicting selection pressures from fire and seed predation. Thus, we show that variation in the frequency of a heritable polygenic trait depends on spatial variation in two dominant selective agents, and, importantly, the effects of the local trait variation propagate with profound consequences to the structure and function of communities and ecosystems across a large landscape. PMID:24979772
Talluto, Matthew V; Benkman, Craig W
Recent work has demonstrated that evolutionary processes shape ecological dynamics on relatively short timescales (eco-evolutionary dynamics), but demonstrating these effects at large spatial scales in natural landscapes has proven difficult. We used empirical studies and modeling to investigate how selective pressures from fire and predispersal seed predation affect the evolution of serotiny, an ecologically important trait. Serotiny is a highly heritable key reproductive trait in Rocky Mountain lodgepole pine (Pinus contorta subsp. latifolia), a conifer that dominates millions of hectares in western North America. In these forests, the frequency of serotiny determines postfire seedling density with corresponding community- and ecosystem-level effects. We found that serotinous individuals have a selective advantage at high fire frequencies and low predation pressure; however, very high seed predation shifted the selective advantage to nonserotinous individuals even at high fire frequencies. Simulation modeling suggests that spatial variation in the frequency of serotiny results from heterogeneity in these two selective agents. These results, combined with previous findings showing a negative association between the density of seed predators and the frequency of serotiny at both landscape and continental scales, demonstrate that contemporary patterns in serotiny reflect an evolutionary response to conflicting selection pressures from fire and seed predation. Thus, we show that variation in the frequency of a heritable polygenic trait depends on spatial variation in two dominant selective agents, and, importantly, the effects of the local trait variation propagate with profound consequences to the structure and function of communities and ecosystems across a large landscape.
Victorio, Carla Bianca Luena; Xu, Yishi; Ng, Qimei; Chow, Vincent T K; Chua, Kaw Bing
Since its identification in 1969, Enterovirus 71 (EV71) has been causing periodic outbreaks of infection in children worldwide and most prominently in the Asia-Pacific Region. Understanding the pathogenesis of Enterovirus 71 (EV71) is hampered by the virus's inability to infect small animals and replicate in their derived in vitro cultured cells. This manuscript describes the phenotypic and genotypic characteristics of two selected EV71 strains (EV71:TLLm and EV71:TLLmv), which have been adapted to replicate in mouse-derived NIH/3T3 cells, in contrast to the original parental virus which is only able to replicate in primate cell lines. The EV71:TLLm strain exhibited productive infection in all primate and rodent cell lines tested, while EV71:TLLmv exhibited greater preference for mouse cell lines. EV71:TLLmv displayed higher degree of adaptation and temperature adaptability in NIH/3T3 cells than in Vero cells, suggesting much higher fitness in NIH/3T3 cells. In comparison with the parental EV71:BS strain, the adapted strains accumulated multiple adaptive mutations in the genome resulting in amino acid substitutions, most notably in the capsid-encoding region (P1) and viral RNA-dependent RNA polymerase (3D). Two mutations, E167D and L169F, were mapped to the VP1 canyon that binds the SCARB2 receptor on host cells. Another two mutations, S135T and K140I, were located in the VP2 neutralization epitope spanning amino acids 136-150. This is the first report of human EV71 with the ability to productively infect rodent cell lines in vitro.
Muir, A P; Biek, R; Thomas, R; Mable, B K
Both environmental and genetic influences can result in phenotypic variation. Quantifying the relative contributions of local adaptation and phenotypic plasticity to phenotypes is key to understanding the effect of environmental variation on populations. Identifying the selective pressures that drive divergence is an important, but often lacking, next step. High gene flow between high- and low-altitude common frog (Rana temporaria) breeding sites has previously been demonstrated in Scotland. The aim of this study was to assess whether local adaptation occurs in the face of high gene flow and to identify potential environmental selection pressures that drive adaptation. Phenotypic variation in larval traits was quantified in R. temporaria from paired high- and low-altitude sites using three common temperature treatments. Local adaptation was assessed using QST–FST analyses, and quantitative phenotypic divergence was related to environmental parameters using Mantel tests. Although evidence of local adaptation was found for all traits measured, only variation in larval period and growth rate was consistent with adaptation to altitude. Moreover, this was only evident in the three mountains with the highest high-altitude sites. This variation was correlated with mean summer and winter temperatures, suggesting that temperature parameters are potentially strong selective pressures maintaining local adaptation, despite high gene flow. PMID:24330274
Marsden, Clare D; Woodroffe, Rosie; Mills, Michael G L; McNutt, J Weldon; Creel, Scott; Groom, Rosemary; Emmanuel, Masenga; Cleaveland, Sarah; Kat, Pieter; Rasmussen, Gregory S A; Ginsberg, Joshua; Lines, Robin; André, Jean-Marc; Begg, Colleen; Wayne, Robert K; Mable, Barbara K
Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the major histocompatibility complex (MHC), are increasingly being incorporated into genetic studies. In this study, we combined neutral (microsatellite, mtDNA) and adaptive (MHC class II DLA-DRB1 locus) markers to elucidate the factors influencing patterns of genetic variation in the African wild dog (Lycaon pictus); an endangered canid that has suffered extensive declines in distribution and abundance. Our genetic analyses found all extant wild dog populations to be relatively small (N(e) < 30). Furthermore, through coalescent modelling, we detected a genetic signature of a recent and substantial demographic decline, which correlates with human expansion, but contrasts with findings in some other African mammals. We found strong structuring of wild dog popu