The relation between the variability of polygenic morphological and monogenic biochemical traits as exemplified by Karakul sheep

A quantitative method for investigation of relationship between polygenic and monogenic traits has been proposed. It is based on examination of relationship between frequencies of distribution classes of an adaptive quantitative trait and frequencies of certain genetic character in the same classes. The method permits to locate a gene marker within a space of quantitative trait values. Using adaptively significant morpho-anatomic traits, it is possible to estimate indirectly adaptive values of gene markers under consideration, since, in accordance with the concept of adaptive norm, "average" phenotypes have maximal fitness, whereas deviative phenotypes transgress the bounds of the optimum. As a genetical character, genotype of certain biochemical locus, individual heterozygosity range or interlocus combinations of alleles could be used. The method has been applied to newborn Astrakhan lambs. Principal component analysis has been used to obtain complex characterization for six constitutional characters. Some regularities in location of homo- and heterozygous genotypes of the transferrin locus within a space of morphological characters' values have been revealed.     

Intermediate phenotypes in psychiatric disorders

The small effect size of most individual risk factors for psychiatric disorders likely reflects biological heterogeneity and diagnostic imprecision, which has encouraged genetic studies of intermediate biological phenotypes that are closer to the molecular effects of risk genes than are the clinical symptoms. Neuroimaging-based intermediate phenotypes have emerged as particularly promising because they map risk associated gene effects onto physiological processes in brain that are altered in patients and in their healthy relatives. Recent evidence using this approach has elucidated discrete, dissociable biological mechanisms of risk genes at the level of neural circuitries, and their related cognitive functions. This approach may greatly contribute to our understanding of the genetics and pathophysiology of psychiatric disorders.     

Genome-Wide Association Analysis of Adaptation Using Environmentally Predicted Traits

Current methods for studying the genetic basis of adaptation evaluate genetic associations with ecologically relevant traits or single environmental variables, under the implicit assumption that natural selection imposes correlations between phenotypes, environments and genotypes. In practice, observed trait and environmental data are manifestations of unknown selective forces and are only indirectly associated with adaptive genetic variation. In theory, improved estimation of these forces could enable more powerful detection of loci under selection. Here we present an approach in which we approximate adaptive variation by modeling phenotypes as a function of the environment and using the predicted trait in multivariate and univariate genome-wide association analysis (GWAS). Based on computer simulations and published flowering time data from the model plant Arabidopsis thaliana, we find that environmentally predicted traits lead to higher recovery of functional loci in multivariate GWAS and are more strongly correlated to allele frequencies at adaptive loci than individual environmental variables. Our results provide an example of the use of environmental data to obtain independent and meaningful information on adaptive genetic variation.     

What is an individual organism? A multilevel selection perspective

Most biologists implicitly define an individual organism as "one genome in one body." This definition is based on physiological and genetic criteria, but it is problematic for colonial organisms. We propose a definition based instead on the evolutionary criteria of alignment of fitness, export of fitness by germ-soma specialization, and adaptive functional organization. We consider how these concepts apply to various putative individual organisms. We conclude that complex multicellular organisms and colonies of eusocial insects satisfy these three criteria, but that, in most cases (with at least one notable exception), colonies of modular organisms and genetic chimeras do not. While species do not meet these criteria, they may meet the criteria for a broader concept--that of an evolutionary individual--and sexual reproduction may be a species-level exaptation for enhancing evolvability. We also review the costs and benefits of internal genetic heterogeneity within putative individuals, demonstrating that high relatedness is neither a necessary nor a sufficient condition for individuality, and that, in some cases, genetic variability may have adaptive benefits at the level of the whole.     

Genetic divergence among sympatric colour morphs of the Dalmatian wall lizard (<Emphasis Type="Italic">Podarcis melisellensis</Emphasis>)

If alternative phenotypes in polymorphic populations do not mate randomly, they can be used as model systems to study adaptive diversification and possibly the early stages of sympatric speciation. In this case, non random mating is expected to support genetic divergence among the different phenotypes. In the present study, we use population genetic analyses to test putatively neutral genetic divergence (of microsatellite loci) among three colour morphs of the lizard Podarcis melisellensis, which is associated with differences in male morphology, performance and behaviour. We found weak evidence of genetic divergence, indicating that gene flow is somewhat restricted among morphs and suggesting possible adaptive diversification.     

The immunological homunculus (immunculus) in normal state and pathology

The immunculus is considered as the system (general network) of constitutively expressed natural autoantibodies against different extracellular, membrane, cytoplasmic, and nuclear self-antigens (ubiquitous and organ-specific). It is specially noted that the repertoires of natural autoantibodies are surprisingly constant in healthy persons, independent of gender and age, and characterized by only minimal individual peculiarities (individual immune fingerprints). On the other hand, abnormal metabolic changes which precede the clinical manifestation of different diseases showed easily detected changes, rather quantitative than qualitative, in the systems of natural autoantibodies in patients' sera (immunculus distortions). This phenomena could supposedly be used for "mapping" the state of physiological norm in terms of the millions of natural autoantibody repertoires, and for elaboration of the methods for early (preclinical) detection of potentially pathogenic metabolic changes. Could the individual features of the general network of constitutively expressed natural autoantibodies reflect the functional state of the body and be used for "mapping" of normal and pathological functional state? Could the changes in production of some biologically active natural autoantibodies not only reflect the state of the body, but be used for partial compensation of functional deficiency of certain molecular systems? These and related questions are discussed in this article. The research project "immunculus" is proposed for international cooperative investigations.     

Regulatory Issues for Genetic Testing in Clinical Practice

Whereas deliver of health care is nationally based with great differences in ways of service provision and financing between countries, and thus not subject to international regulations, genetic testing has become more exposed to international regulations and conventions. This is due to an interest of protecting the individual for abuse by inappropriate use of genetic information, but also to the fact that a specimen from a person aimed for a medical (clinical genetic) test is considered as "tradable goods", and thus also subject to other non-medical associated regulations. There is a substantial transborder flow of samples for genetic testing thus requiring internationally accepted quality standards. Therefore, laboratories acting on an international market need to follow certain rules and regulations, also applicable to obtain high-quality standards nationally. Further, genetic testing for rare disorders is often provided by a limited number of non-commercial laboratories and associated with research programs for the individual disorders. International surveys have revealed that there is a general lack of high standards for quality assurance. This article is aimed to give an introduction and overview of regulations, conventions, and quality standards applicable for the laboratory who is seeking to improve there quality performance.     

Rapid divergence of animal personality and syndrome structure across an arid-aquatic habitat matrix

Intraspecific trait variation, including animal personalities and behavioural syndromes, affects how individual animals and populations interact with their environment. Within-species behavioural variation is widespread across animal taxa, which has substantial and unexplored implications for the ecological and evolutionary processes of animals. Accordingly, we sought to investigate individual behavioural characteristics in several populations of a desert-dwelling fish, the Australian desert goby (Chlamydogobius eremius). We reared first generation offspring in a common garden to compare non-ontogenic divergence in behavioural phenotypes between genetically interconnected populations from contrasting habitats (isolated groundwater springs versus hydrologically variable river waterholes). Despite the genetic connectedness of populations, fish had divergent bold-exploratory traits associated with their source habitat. This demonstrates divergence in risk-taking traits as a rapid phenotypic response to ecological pressures in arid aquatic habitats: neophilia may be suppressed by increased predation pressure and elevated by high intraspecific competition. Correlations between personality traits also differed between spring and river fish. River populations showed correlations between dispersal and novel environment behaviours, revealing an adaptive behavioural syndrome (related to dispersal and exploration) that was not found in spring populations. This illustrates the adaptive significance of heritable behavioural variation within and between populations, and their importance to animals persisting across contrasting habitats.     

New insights from the last decade of research in psychiatric genetics: discoveries,challenges and clinical implications

Psychiatric genetics has made substantial progress in the last decade, providing new insights into the genetic etiology of psychiatric disorders, and paving the way for precision psychiatry, in which individual genetic profiles may be used to personalize risk assessment and inform clinical decision-making. Long recognized to be heritable, recent evidence shows that psychiatric disorders are influenced by thousands of genetic variants acting together. Most of these variants are commonly occurring, meaning that every individual has a genetic risk to each psychiatric disorder, from low to high. A series of large-scale genetic studies have discovered an increasing number of common and rare genetic variants robustly associated with major psychiatric disorders. The most convincing biological interpretation of the genetic findings implicates altered synaptic function in autism spectrum disorder and schizophrenia. However, the mechanistic understanding is still incomplete. In line with their extensive clinical and epidemiological overlap, psychiatric disorders appear to exist on genetic continua and share a large degree of genetic risk with one another. This provides further support to the notion that current psychiatric diagnoses do not represent distinct pathogenic entities, which may inform ongoing attempts to reconceptualize psychiatric nosology. Psychiatric disorders also share genetic influences with a range of behavioral and somatic traits and diseases, including brain structures, cognitive function, immunological phenotypes and cardiovascular disease, suggesting shared genetic etiology of potential clinical importance. Current polygenic risk score tools, which predict individual genetic susceptibility to illness, do not yet provide clinically actionable information. However, their precision is likely to improve in the coming years, and they may eventually become part of clinical practice, stressing the need to educate clinicians and patients about their potential use and misuse. This review discusses key recent insights from psychiatric genetics and their possible clinical applications, and suggests future directions.     

Genetic dispersion analysis of the relationship of epilepsy to anomalies in brain bioelectrical activity

Estimation of genetic and environmental components of phenotypical dispersion of paroxysmal and nonparoxysmal EEG abnormalities in epilepsy (118 probands and 179 relatives) in two phenotypical model frames has been obtained. The alternative phenotypical model was shown to be more adequate than quasicontinual for EEG abnormalities, and the part of additive genetic component (GA) comprises 15.7% for paroxysmal abnormalities and 49.4% for nonparoxysmal type. In the component type "belonging to one generation" joint influence of genetic and environmental factors on the process of forming EEG abnormalities in ontogeny was observed. The GA value for "epilepsy manifestation" symptom equal to 72.9% in general selection of probands increases to 97.4% in the subgroup of patients with nonparoxysmal abnormalities and 67.4% in the subgroup of patients with paroxysmal EEG abnormalities. It has been suggested that paroxysmal EEG abnormalities reflect their own epileptic process, and as far as nonparoxysmal abnormalities are concerned, they present phenotypical manifestation of the genetic system of predisposition to epilepsy.     

Evolutionary engineering of Saccharomyces cerevisiae for improved industrially important properties

This article reviews evolutionary engineering of Saccharomyces cerevisiae. Following a brief introduction to the 'rational' metabolic engineering approach and its limitations such as extensive genetic and metabolic information requirement on the organism of interest, complexity of cellular physiological responses, and difficulties of cloning in industrial strains, evolutionary engineering is discussed as an alternative, inverse metabolic engineering strategy. Major evolutionary engineering applications with S. cerevisiae are then discussed in two general categories: (1) evolutionary engineering of substrate utilization and product formation and (2) evolutionary engineering of stress resistance. Recent developments in functional genomics methods allow rapid identification of the molecular basis of the desired phenotypes obtained by evolutionary engineering. To conclude, when used alone or in combination with rational metabolic engineering and/or computational methods to study and analyze processes of adaptive evolution, evolutionary engineering is a powerful strategy for improvement in industrially important, complex properties of S. cerevisiae.     

Brain trauma and autophagy: What flies and mice can teach us about conserved responses

Drosophila models have been successfully used to identify many genetic components that affect neurodegenerative disorders. Recently, there has been a growing interest in identifying innate and environmental factors that influence the individual outcomes following traumatic brain injury (TBI). This includes both severe TBI and more subtle, mild TBI (mTBI), which is common in people playing contact sports. Autophagy, as a clearance pathway, exerts protective effects in multiple neurological disease models. In a recent publication, we highlighted the development of a novel repetitive mTBI system using Drosophila, which recapitulates several phenotypes associated with trauma in mammalian models. In particular, flies subjected to mTBI exhibit an acute impairment of the macroautophagy/autophagy pathway that is restored 1 wk following traumatic injury exposure. These phenotypes closely resemble temporary autophagy defects observed in a mouse TBI model. Through these studies, we also identified methods to directly assess autophagic responses in the fly nervous system and laid the groundwork for future studies designed to identify genetic, epigenetic and environmental factors that have an impact on TBI outcomes.     

Vacuolar-type proton ATPase as regulator of membrane dynamics in multicellular organisms

Acidification inside membrane compartments is a common feature of all eukaryotic cells. The acidic milieu is involved in many physiological processes including secretion, protein processing, and others. However, its cellular relevance has not been well established beyond the results of in vitro studies involving cultured cell systems. In the last decade, human and mouse genetics have revealed that the acidification machinery is implicated in multiple pathophysiological disorders, and thus our understanding of physiological consequences of the defective acidification in multicellular organisms has improved. In invertebrates including Drosophila and nematodes, mutations of V-ATPase were found to lead the development of rather unexpected phenotypes. Studies have suggested that V-ATPase may be involved in membrane fusion and vesicle formation, important processes for membrane trafficking, and have further implied its involvement in cell–cell fusion. This rather novel idea arose from the phenotypes associated with genetic disorders involving V-ATPase genes in various genetic model systems. In this article, we focus and overview the non-classical, beyond proton-pumping function of the vacuolar-type ATPase in exo/endocytic systems.     

31° South: The physiology of adaptation to arid conditions in a passerine bird

Arid environments provide ideal ground for investigating the mechanisms of adaptive evolution. High temperatures and low water availability are relentless stressors for many endotherms, including birds; yet birds persist in deserts. While physiological adaptation probably involves metabolic phenotypes, the underlying mechanisms (plasticity, genetics) are largely uncharacterized. To explore this, we took an intraspecific approach that focused on a species that is resident over a mesic to arid gradient, the Karoo scrub‐robin (Cercotrichas coryphaeus). Specifically, we integrated environmental (climatic and primary productivity), physiological (metabolic rates: a measure of energy expenditure), genotypic (genetic variation underlying the machinery of energy production) and microbiome (involved in processing food from where energy is retrieved) data, to infer the mechanism of physiological adaptation. We that found the variation in energetic physiology phenotypes and gut microbiome composition are associated with environmental features as well as with variation in genes underlying energy metabolic pathways. Specifically, we identified a small list of candidate adaptive genes, some of them with known ties to relevant physiology phenotypes. Together our results suggest that selective pressures on energetic physiology mediated by genes related to energy homeostasis and possibly microbiota composition may facilitate adaptation to local conditions and provide an explanation to the high avian intraspecific divergence observed in harsh environments.     

Genome‐wide association and genome partitioning reveal novel genomic regions underlying variation in gastrointestinal nematode burden in a wild bird

Identifying the genetic architecture underlying complex phenotypes is a notoriously difficult problem that often impedes progress in understanding adaptive eco‐evolutionary processes in natural populations. Host–parasite interactions are fundamentally important drivers of evolutionary processes, but a lack of understanding of the genes involved in the host's response to chronic parasite insult makes it particularly difficult to understand the mechanisms of host life history trade‐offs and the adaptive dynamics involved. Here, we examine the genetic basis of gastrointestinal nematode (Trichostrongylus tenuis) burden in 695 red grouse (Lagopus lagopus scotica) individuals genotyped at 384 genome‐wide SNPs. We first use genome‐wide association to identify individual SNPs associated with nematode burden. We then partition genome‐wide heritability to identify chromosomes with greater heritability than expected from gene content, due to harbouring a multitude of additive SNPs with individually undetectable effects. We identified five SNPs on five chromosomes that accounted for differences of up to 556 worms per bird, but together explained at best 4.9% of the phenotypic variance. These SNPs were closely linked to genes representing a range of physiological processes including the immune system, protein degradation and energy metabolism. Genome partitioning indicated genome‐wide heritability of up to 29% and three chromosomes with excess heritability of up to 4.3% (total 8.9%). These results implicate SNPs and novel genomic regions underlying nematode burden in this system and suggest that this phenotype is somewhere between being based on few large‐effect genes (oligogenic) and based on a large number of genes with small individual but large combined effects (polygenic).     

The genetic architecture necessary for transgressive segregation is common in both natural and domesticated populations

Segregating hybrids often exhibit phenotypes that are extreme or novel relative to the parental lines. This phenomenon is referred to as transgressive segregation, and it provides a mechanism by which hybridization might contribute to adaptive evolution. Genetic studies indicate that transgressive segregation typically results from recombination between parental taxa that possess quantitative trait loci (QTLs) with antagonistic effects (i.e. QTLs with effects that are in the opposite direction to parental differences for those traits). To assess whether this genetic architecture is common, we tabulated the direction of allelic effects for 3252 QTLs from 749 traits and 96 studies. Most traits (63.6%) had at least one antagonistic QTL, indicating that the genetic substrate for transgressive segregation is common. Plants had significantly more antagonistic QTLs than animals, which agrees with previous reports that transgressive segregation is more common in plants than in animals. Likewise, antagonistic QTLs were more frequent in intra- than in interspecific crosses and in morphological than in physiological traits. These results indicate that transgressive segregation provides a general mechanism for the production of extreme phenotypes at both above and below the species level and testify to the possible creative part of hybridization in adaptive evolution and speciation.     

Molecular-genetic identification and certification of soybean (Glycine max L.) cultivars

An approach to certification of soybean genotypes has been developed. The procedure employs three methods of DNA analysis based on polymerase chain reaction (PCR): PCR with arbitrary primers (AP PCR), simple sequence repeat polymorphism (SSRP) analysis, and inter-simple sequence repeat (ISSR) analysis. The approach to certification proposed may be used in both genetic and breeding research and seed production. A "certificate" form that reflects the unique characteristics of each cultivar studied is proposed. The results of molecular genetic analysis of allele distribution in genotypes of soybean from different ecological geographic zones permit estimation of the adaptive significance of individual alleles.     

Levels of genetic variation in European silver fir (Abies alba)

The distribution of genetic variation at nine enzyme gene loci in the European range of silver fir is studied with the aim to characterize the genetic basis of this species' adaptive potentials. For this purpose, the basic notions of physiological and evolutionary adaptive potential are briefly discussed in connection with operating and latent genetic potentials of populations. A measure for the quantification of latent genetic potential is introduced together with a procedure that evaluates the detective power of the samples taken. The results obtained from application of this measure are in striking accordance with earlier suggestions based chiefly on ecophysiological traits, and which assume both low physiological and evolutionary adaptive potential in the central and northeastern European populations of silver fir. Moreover, careful consideration of the structural and functional characteristics of the enzymes used in the present study support the assumption that they are not selectively neutral, and in one case it can indeed be demonstrated that the two alleles at a locus are very likely to be under selection for temperature differences between central and southern European populations.