Good epidemiologic practice in retinitis pigmentosa: from phenotyping to biobanking

Inherited retinal dystrophies, such as retinitis pigmentosa (RP), include a group of relatively rare hereditary diseases caused by mutations in genes that code for proteins involved in the maintenance and function of the photoreceptor cells (cones and rods). The different forms of RP consist of progressive neurodegenerative disorders which are generally related to various and severe limitations of visual performances. In the course of typical RP (rod-cone dystrophy), the affected individuals first experience night-blindness and/or visual field constriction (secondary to rod dysfunctions), followed by variable alterations of the central vision (due to cone damages). On the other hand, during the atypical form of RP (cone-rod dystrophy), the cone's functionalities are prevalently disrupted in comparison with the rod's ones. The basic diagnosis of RP relies upon the documentation of unremitting loss in photoreceptor activity by electroretinogram and/or visual field testing. The prevalence of all RP typologies is variably reported in about one case for each 3000-5000 individuals, with a total of about two millions of affected persons worldwide. The inherited retinal dystrophies are sometimes the epiphenomenon of a complex framework (syndromic RP), but more often they represent an isolated disorder (about 85-90 % of cases). Although 200 causative RP mutations have been hitherto detected in more than 100 different genes, the molecular defect is identifiable in just about the 50% of the analyzed patients with RP. Not only the RP genotypes are very heterogeneous, but also the patients with the same mutation can be affected by different phenotypic manifestations. RP can be inherited as autosomal dominant, autosomal recessive or X-linked trait, and many sporadic forms are diagnosed in patients with no affected relatives. Dissecting the clinico-genetic complexity of RP has become an attainable objective by means of large-scale research projects, in which the collaboration between ophthalmologists, geneticists, and epidemiologists becomes a crucial aspect. In the present review, the main issues regarding clinical phenotyping and epidemiologic criticisms of RP are focused, especially highlighting the importance of both standardization of the diagnostic protocols and appropriateness of the disease's registration systems.     

Therapeutic challenges to retinitis pigmentosa: from neuroprotection to gene therapy

Syndromic retinitis pigmentosa (RP) is the result of several mutations expressed in rod photoreceptors, over 40 of which have so far been identified. Enormous efforts are being made to relate the advances in unraveling the patho-physiological mechanisms to therapeutic approaches in animal models, and eventually in clinical trials on humans. This review summarizes briefly the current clinical management of RP and focuses on the new exciting treatment possibilities. To date, there is no approved therapy able to stop the evolution of RP or restore vision. The current management includes an attempt at slowing down the degenerative process by vitamin supplementation, trying to treat ocular complications and to provide psychological support to blind patients. Novel therapeutic may be tailored dependant on the stage of the disease and can be divided in three groups. In the early stages, when there are surviving photoreceptors, the first approach would be to try to halt the degeneration by correction of the underlying biochemical abnormality in the visual cycle using gene therapy or pharmacological treatment. A second approach aims to cope with photoreceptor cell death using neurotrophic growth factors or anti-apoptotic factors, reducing the production of retino-toxic molecules, and limiting oxidative damage. In advanced stages, when there are few or no functional photoreceptors, strategies that may benefit include retinal transplantation, electronic retinal implants or a newly described optogenetic technique using a light-activated channel to genetically resensitize remnant cone-photoreceptor cells.     

Patterns of genotypic variation and phenotypic plasticity of light response in two tropical Piper (Piperaceae) species

Patterns of phenotypic plasticity and genotypic variation in light response of growth and photosynthesis were examined in two species of rain forest shrub that differ in ecological distribution within the forest. We further examined correlations among photosynthetic and growth traits. We hypothesized that the pioneer species, Piper sancti-felicis, would display greater phenotypic plasticity than the shade-tolerant species, Piper arieianum. We further proposed that, in both species, genotypic effects would be more apparent in growth-related traits than photosynthetic traits due to more concentrated selection pressure on gas-exchange traits. P. sancti-felicis did not demonstrate greater phenotypic plasticity of light response. Although many of the traits measured had significant genotype effects, neither species showed any significant effects of genotype on light response of photosynthesis, suggesting little genetic variation for this trait within populations. A principal components analysis clearly illustrated both species and light effects, with the treatments dividing neatly along the axis of the first principal component and the species separating along the second principal component axis. Results indicated general similarities between the species in their trait correlation structure and level of integration among traits, but characteristic differences were observed in the patterns of change between low and high light. Both species had more correlations than expected within groups of growth-related or photosynthetic traits; strong correlations of traits between these two groups were underrepresented. The similar pattern of genetic variation and phenotypic integration observed in these two congeners may be due more to their close phylogenetic relation than to their ecological distributions.     

Modular genetic architecture of floral morphology in Nicotiana: quantitative genetic and comparative phenotypic approaches to floral integration

Animal‐pollinated flowers are complex structures that may require a precise configuration of floral organs for proper function. As such, they represent an excellent system with which we can examine the role of phenotypic integration and modularity in morphological evolution. We use complementary quantitative genetic and comparative phenotypic approaches to examine correlations among floral characters in Nicotiana alata, N. forgetiana and their artificial fourth‐generation hybrids. Flowers of both species share basic patterns of genetic and phenotypic correlations characterized by at least two integrated character suites that are relatively independent of each other and are not disrupted by four generations of recombination in hybrids. We conclude that these integrated character suites represent phenotypic modules that are the product of a modular genetic architecture. Intrafloral modularity may have been critical for rapid specialization of these species to different pollinators.     

Genetic and phenotypic heterogeneity of multiple lentigines and precise diagnosis in four Chinese families with multiple lentigines

Lentigines are well-defined, small, brown macules resulting from the accumulation of melanin content in the basement membrane zone with an increase in the number of melanocytes. Hereditary multiple lentigines (ML) can be associated with multiple genes and are not commonly encountered in clinical practice. Patients can solely have skin involvement or present with multisystemic deformative phenotypes. This study aimed to describe four unrelated Chinese families presenting with ML as their first visit symptom. We performed whole-exome sequencing (WES) and Sanger sequencing on all patients and immediate family members for precise molecular diagnosis. Two novel variants c.1548 T > A (p.Ser516Arg) and c.1811C > A (p.Thr604Lys) in SASH1, and two recurrent variants c.1403C > T (p.Thr468Met) and c.1493G > T (p.Arg498Leu) in PTPN11, were identified in these four families. We also summarized the genes associated with ML and differential diagnosis of pigment abnormality. We suggested that the molecular diagnosis of ML should be emphasized because it can help in the clinical differential diagnosis and further genetic counseling and prognosis.     

Genetic and phenotypic correlations in a natural population of song sparrows

We estimated heritabilities, and genetic and phenotypic correlations between beak and body traits in the song sparrow ( Melospiza melodia ). We compared these estimates to values for the same traits in the Galápagos finches, Geospiza (Boag, 1983; Grant, 1983). Morphological variance is low in the song sparrow, and our results show that genetic and phenotypic correlations are considerably lower than correlations in the morphologically more variable Geospiza. Comparison using a larger sample of Galapagos populations confirms the existence of an association between variance and correlation for phenotypic values. We suggest two possible explanations for this association. First, most traits studied are functionally related, and the joint evolution of variance and correlation may have resulted from stabilizing selection about a line of optimal allometry between traits. Alternatively, introgression between populations and species could have caused correlation and variance to evolve jointly. Both selection and introgression were probably influential in producing the observed pattern, but it is not possible to estimate their relative importance with current data. Genetic and phenotypic correlations were correlated in the song sparrow, but heritabilities of traits varied greatly. As a result, the genetic variance-covariance matrix for traits is not simply a constant multiple of the phenotypic matrix. Evolutionary response to natural selection cannot, therefore, be predicted from the measurement of phenotypic characteristics alone.     

Fine-scale phenotypic change across a species transition zone in the genus neotoma: disentangling independent evolution from phylogenetic history

Zones of secondary contact between closely related species provide a rare opportunity to examine evidence of evolutionary processes that reinforce species boundaries and/or promote diversification. Here, we report on genetic and morphological variation in two sister species of woodrats, Neotoma fuscipes and N. macrotis, across a 30-km transition zone in the Sierra Nevada of California. We assessed whether these lineages readily hybridize, and whether their morphology suggests ecological interactions favoring phenotypic diversification. We combined measurements of body size and 11 craniodental traits from nine populations with genetic data to examine patterns of variation within and between species. We used phylogenetic autocorrelation methods to estimate the degree to which phenotypic variation in our dataset arose from independent evolution within populations versus phylogenetic history. Although no current sympatry or hybridization was evident, craniodental morphology diverged in both lineages near their distributional limits, whereas body size converged. The shift in craniodental morphology arose independently within populations whereas body size retained a strong phylogenetic signal, yet both patterns are consistent with expectations of phenotypic change based on different models of resource competition. Our findings demonstrate the importance of examining a suite of morphological traits across contact zones to provide a more complete picture of potential ecological interactions: competition may drive both diversification and convergence in different phenotypic traits.     

Evolution of phenotypic plasticity: Genetic differentiation and additive genetic variation for induced plant defence in wild arugula Eruca sativa

Phenotypic plasticity is the primary mechanism of organismal resilience to abiotic and biotic stress, and genetic differentiation in plasticity can evolve if stresses differ among populations. Inducible defence is a common form of adaptive phenotypic plasticity, and long‐standing theory predicts that its evolution is shaped by costs of the defensive traits, costs of plasticity and a trade‐off in allocation to constitutive versus induced traits. We used a common garden to study the evolution of defence in two native populations of wild arugula Eruca sativa (Brassicaceae) from contrasting desert and Mediterranean habitats that differ in attack by caterpillars and aphids. We report genetic differentiation and additive genetic variance for phenology, growth and three defensive traits (toxic glucosinolates, anti‐nutritive protease inhibitors and physical trichome barriers) as well their inducibility in response to the plant hormone jasmonic acid. The two populations were strongly differentiated for plasticity in nearly all traits. There was little evidence for costs of defence or plasticity, but constitutive and induced traits showed a consistent additive genetic trade‐off within each population for the three defensive traits. We conclude that these populations have evolutionarily diverged in inducible defence and retain ample potential for the future evolution of phenotypic plasticity in defence.     

Selection in a fluctuating environment leads to decreased genetic variation and facilitates the evolution of phenotypic plasticity

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.     

浙江扇脉杓兰野生居群的表型性状变异及其与地理-土壤养分因子的相关性

为揭示扇脉杓兰(Cypripedium japonicum Thunb.)表型性状的变异规律,以浙江临安6个野生居群(老殿、宝剑石、红蛇洞、清凉峰、大明山和里横塘)为研究对象,分析了叶片、萼片、子房及唇瓣等18个表型性状的变异幅度,并讨论了表型性状变异与地理-土壤养分因子间的相关性以及居群间和居群内的表型多样性.结果显示:6个居群18个表型性状(地径、下叶长、下叶宽、下叶长/宽比、上叶长、上叶宽、上叶长/宽比、中萼片长、中萼片宽、苞片长、苞片宽、子房长、花梗直径、花梗长、唇瓣长、唇瓣宽、植株展度和株高)测量值的F值为1.240 ～ 18.666,除花梗直径和株高外,其他16个性状均有极显著差异.各性状的变异系数为5.937％ ～ 26.349％,其中,唇瓣长的平均变异系数最小(6.119％)、苞片宽的平均变异系数最大(24.124％);居群间各性状的变异系数为8.139％～ 13.663％,平均变异系数为11.143％,其中,里横塘居群的平均变异系数最大、宝剑石居群的最小.各性状的多样性指数平均为1.977,其中地径的多样性指数最大(2.045)、苞片宽的最小(1.663).通过UPGMA聚类分析,可将6个居群划分为3组:清凉峰、大明山、老殿和宝剑石居群为1组;红蛇洞和里横塘居群分别各自成组,其中清凉峰和大明山居群的遗传距离最近.各表型性状间存在显著或极显著的相关关系;但仅地径与速效钾含量显著正相关(r=0.854),子房长、唇瓣长和宽与土壤全磷含量显著正相关(r值分别为0.916、0.854和0.914),植株展度与土壤pH显著正相关(r=0.810),其余性状与地理因子(包括经度、纬度和海拔)及土壤养分因子均无显著相关性.研究结果表明:扇脉杓兰野生居群表型性状存在丰富的变异和多样性,且与生境土壤中速效钾及全磷含量及土壤pH有关.     

Evolution of phenotypic plasticity: patterns of plasticity and the emergence of ecotypes

Phenotypic plasticity itself evolves, as does any other quantitative trait. A very different question is whether phenotypic plasticity causes evolution or is a major evolutionary mechanism. Existing models of the evolution of phenotypic plasticity cover many of the proposals in the literature about the role of phenotypic plasticity in evolution. I will extend existing models to cover adaptation to a novel environment, the appearance of ecotypes and possible covariation between phenotypic plasticity and mean trait value of ecotypes. Genetic assimilation does not sufficiently explain details of observed patterns. Phenotypic plasticity as a major mechanism for evolution--such as, invading new niches, speciation or macroevolution--has, at present, neither empirical nor model support.     

Hsp90 inhibition and the expression of phenotypic variability in the rainforest species Drosophila birchii

Recently a heat shock protein (Hsp90) has been implicated as controlling the expression of cryptic genetic variation through buffering developmental processes. The release of variability in canalized characters following Hsp90 inhibition has been established in model species including Drosophila melanogaster and Arabidopsis thaliana , but has not yet been examined in species with limited distributions. To test if Hsp90 has a role in releasing phenotypic variation in rainforest Drosophila species, developing larvae from a large (> 1000 individuals) outbred population of Drosophila birchii were treated with the Hsp90 inhibitors geldanamycin and radicicol, and morphological traits, desiccation resistance, and life-history traits were measured. The means of all traits were influenced by inhibition. Although only the phenotypic variances of two canalized bristle traits were affected consistently, variability for two of the continuously varying traits (fecundity and development time) were also affected, albeit inconsistently. There was also no effect of Hsp90 inhibition on the developmental stability of the morphological traits as measured by fluctuating asymmetry. Hsp90 inhibition did not increase phenotypic variability in desiccation resistance, a trait previously shown to represent an evolutionary limit in this species. These results question the extent to which Hsp90 buffers variation for both quantitative and discrete traits, and highlight the need for further empirical studies to determine the involvement of Hsp90 in canalization and developmental stability. Nevertheless the results demonstrated increased variability in canalized traits, consistent with observations in model systems. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 457–465.     

The genetics of phenotypic plasticity. IX. Genetic architecture, temperature, and sex differences in Drosophila melanogaster

Abstract.— We examined the genetic architecture of plasticity of thorax and wing length in response to temperature in Drosophila melanogaster . Reaction norms as a function of growth temperature were analyzed in 20 isofemale lines in a natural population collected from Grande Ferrade near Bordeaux (southern France) in two different years. We found evidence for a complex genetic architecture underlying the reaction norms and differences between males and females. Reaction norms were negative quadratics. Genetic correlations were moderately high between traits within environments. Among characteristic values, the magnitudes of genetic correlations varied among traits and sexes. We hypothesized that genetic correlations among environments would decrease as temperatures became more different. This expectation was upheld for only one trait, female thorax length. For males for both traits, the correlations were large for both very similar and very different temperatures. These correlations may constrain the evolution of the shape of the reaction norms. Whether the extent of independence implies specific regulatory genes or only a specific allelic regulation of trait genes can not be decided from our results.     

Idealization in evolutionary developmental investigation: a tension between phenotypic plasticity and normal stages

Idealization is a reasoning strategy that biologists use to describe, model and explain that purposefully departs from features known to be present in nature. Similar to other strategies of scientific reasoning, idealization combines distinctive strengths alongside of latent weaknesses. The study of ontogeny in model organisms is usually executed by establishing a set of normal stages for embryonic development, which enables researchers in different laboratory contexts to have standardized comparisons of experimental results. Normal stages are a form of idealization because they intentionally ignore known variation in development, including variation associated with phenotypic plasticity (e.g. via strict control of environmental variables). This is a tension between the phenomenon of plasticity and the practice of staging that has consequences for evolutionary developmental investigation because variation is conceptually removed as a part of rendering model organisms experimentally tractable. Two compensatory tactics for mitigating these consequences are discussed: employing a diversity of model organisms and adopting alternative periodizations.     

滇楸种质生长性状遗传变异及表型性状遗传多样性分析

为明确滇楸种质生长和表型性状的遗传变异程度及遗传多样性大小,提出合理的杂交育种策略。本研究对滇楸20个无性系进行了连年的生长性状测定,测量了其叶长、叶宽、皮孔长、皮孔宽、皮孔密度等表型性状。研究结果表明滇楸种质1、3、4和5 a树高及1~6 a胸径在无性系间差异均达显著水平。树高遗传变异系数和重复力随年份变化波动较大,胸径遗传变异系数和重复力年份间较为稳定,且重复力较高。表明滇楸种质胸径受遗传控制程度较大,且稳定性更高。滇楸种质叶长和叶宽遗传多样性指数较高,分别为2.016和2.012。皮孔性状遗传变异系数较高,皮孔长、皮孔面积和皮孔密度表型变异系数均超过20%,遗传变异系数均超过15%。说明滇楸种质表型变异较为丰富,具有较好的遗传改良基础。相关分析结果表明皮孔密度与生长呈负相关,皮孔大小与生长呈正相关。聚类分析将滇楸种质划分为4类,第Ⅰ类皮孔面积最大,密度最小;第Ⅱ类生长最慢,叶长最大;第Ⅲ类生长最快,叶形最宽;第Ⅳ类叶柄最长。     

Environmental effects on molecular and phenotypic variation in populations of Eruca sativa across a steep climatic gradient

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.