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PubMed1997

The design of adaptive systems: optimal parameters for variation and selection in learning and development.

Some aspects of learning and development are based on evolutionary change within the organism. In trial and error learning, variant ideas or behaviors are generated and selective filters (learning rules) choose among the population of variants. Development may, in some cases, proceed by selection within a population of variant cellular lineages. This paper analyses abstract properties of selective systems to understand the evolutionary dynamics that occur within organisms. The Price Equation and Fisher's fundamental theorem of natural selection, two of the most powerful concepts in evolutionary genetics, are applied in a general way to internal selective systems in learning and development. This analysis emphasizes generative mechanisms and selective filters as genetically controlled phenotypes of individual organisms. Generative mechanisms create the variation on which selection acts. Selective filters determine the extent to which selection within the organism optimizes organismal performance. The methods of Price and Fisher provide a general way in which to partition evolutionary change into improvements caused by selection and the tendency of high performance variants to deteriorate because of competition or environmental change. This balance between selective improvement, at a rate equal to the variance in fitness, and a matching deterioration in performance, provides general insight into the common properties of adaptive systems in genetics, learning and development. These ideas are applied to a model of honey bee foraging. This example clarifies the relation between genes and phenotypes controlled by internal selective systems.

Adaptation, Physiological↗
PubMed2002

Molecular basis of adaptive convergence in experimental populations of RNA viruses.

Characterizing the molecular basis of adaptation is one of the most important goals in modern evolutionary genetics. Here, we report a full-genome sequence analysis of 21 independent populations of vesicular stomatitis ribovirus evolved on the same cell type but under different demographic regimes. Each demographic regime differed in the effective viral population size. Evolutionary convergences are widespread both at synonymous and nonsynonymous replacements as well as in an intergenic region. We also found evidence for epistasis among sites of the same and different loci. We explain convergences as the consequence of four factors: (1) environmental homogeneity that supposes an identical challenge for each population, (2) structural constraints within the genome, (3) epistatic interactions among sites that create the observed pattern of covariation, and (4) the phenomenon of clonal interference among competing genotypes carrying different beneficial mutations. Using these convergences, we have been able to estimate the fitness contribution of the identified mutations and epistatic groups. Keeping in mind statistical uncertainties, these estimates suggest that along with several beneficial mutations of major effect, many other mutations got fixed as part of a group of epistatic mutations.

Epistasis, Genetic↗
PubMed1989

The polymerase chain reaction.

The polymerase chain reaction (PCR) is a powerful new method for 'in vitro cloning'. It can selectively amplify a single molecule of template DNA several millionfold in a few hours and has made possible new approaches to problems in molecular genetics, evolutionary biology, and development.

Biological Evolution↗
PubMed2005

Isofemale lines in Drosophila: an empirical approach to quantitative trait analysis in natural populations.

Founding isofemale lines from wild collected females is a basic tool for investigating the genetic architecture of Drosophila natural populations. The method permits the analysis of quantitative traits under laboratory conditions, with a much broader scope than the mere evidence of a significant genetic heterogeneity among lines. Genetic variability is generally demonstrated by a significant coefficient of intraclass correlation, but several experimental precautions are needed and explained here. The relationship between classical (additive) heritability and intraclass correlation is not straightforward, presumably because the genetic bottlenecks due to the initiation of the lines unravel a significant, nonadditive genetic variance due to dominance and epistatic effects. It is thus suggested to consider intraclass correlation as a specific genetic parameter that enables comparisons between different traits, different populations or different environments. The use of isofemale lines is, however, not restricted to the calculation of an intraclass correlation. It can be used to estimate genetic correlations among traits or environments. The method is also convenient for the analysis of phenotypic plasticity in relation to an environmental gradient. A precise description of the response curves (the reaction norms) is possible, distinguishing trait parameters and plasticity parameters. A fairly general conclusion is that, for a given trait, mean value and plasticity are genetically independent. It is also possible to analyze traits, which, like sexual dimorphism, must be measured on different individuals, and even to demonstrate their genetic variability. In many cases, further empirical and theoretical analyses are possible and needed. It is argued that, in the future, isofemale lines will have an increasing significance among the various techniques appropriate to the analysis of quantitative evolutionary genetics in a diversity of species.

Animals↗
PubMed2000

Quantitative genetic variation of leaf size and shape in a mixed diploid and triploid population of Populus.

In the interspecific cross of Populus trichocarpa x P. deltoides, unexpected simultaneous occurrence of diploid hybrids and triploid hybrids (with two alleles from the female parent and one from the male parent at each locus) led us to examine the evolutionary genetic significance of this phenomenon. As expected, leaf size and shape of the triploid progeny are closer to the female P. trichocarpa than male P. deltoides parent. Although the pure triploid progeny population did not have higher genetic variance in leaf traits than the pure diploid population, the former appears to hide much non-additive genetic variance and display strong genetic control over the phenotypic plasticity of leaf traits. It is suggested that the cryptic non-additive variance, especially epistasis, can be released when a population is disturbed by changes in the environment. A mixed diploid and triploid progeny population combines phenotypic and genetic characteristics of both pure hybrids and is considered to be of adaptive significance for populars to survive and evolve in a fluctuating environment. The significant effect due to general and specific combining ability differences at the population level suggests that the population divergence of these two species is under additive and non-additive genetic control.

Diploidy↗
PubMed1996

The nature of quantitative genetic variation revisited: lessons from Drosophila bristles.

Most characters that distinguish one individual from another, like height or weight, vary continuously in populations. Continuous variation of these 'quantitative' traits is due to the simultaneous segregation of multiple quantitative trait loci (QTLs) as well as environmental influences. A major challenge in human medicine, animal and plant breeding and evolutionary genetics is to identify QTLs and determine their genetic properties. Studies of the classic quantitative traits, abdominal and sternopleural bristle numbers of Drosophila, have shown that: (1) many loci have small effects on bristle number, but a few have large effects and cause most of the genetic variation; (2) 'candidate' loci involved in bristle development often have large quantitative effects on bristle number; and (3) alleles at QTLs affecting bristle number have variable degrees of dominance, interact with each other, and affect other quantitative traits, including fitness. Lessons learned from this model system will be applicable to studies of the genetic basis of quantitative variation in other species.

Animals↗
PubMed2001

A molecular model for the evolution of endothermy in the theropod-bird lineage.

Ectothermy is a primitive state; therefore, a shared common ancestor of crocodiles, dinosaurs, and birds was at some point ectothermic. Birds, the extant descendants of the dinosaurs, are endothermic. Neither the metabolic transition within this lineage nor the place the dinosaurs held along the ectothermic-endothermic continuum is defined. This paper presents a conceptual model for the evolution of endothermy in the theropod-bird lineage. It is recognized that other animals (some fish, insects, etc.) are functionally endothermic. However, endothermy in other clades is beyond the scope of this paper, and we address the onset of endothermy in only the theropod/bird clade. The model begins with simple changes in a single gene of a common ancestor, and it includes a series of concomitant physiological and morphological changes, beginning perhaps as early as the first archosaurian common ancestor of dinosaurs and crocodiles. These changes continued to accumulate within the theropod-avian lineage, were maintained and refined through selective forces, and culminated in extant birds. Metabolic convergence or homoplasy is evident in the inherent differences between the endothermy of mammals and the endothermy of extant birds. The strength and usefulness of this model lie in the phylogenetic, genetic, evolutionary, and adaptive plausibility of each of the suggested developmental steps toward endothermy. The model, although conceptual in nature, relies on an extensive knowledge base developed by numerous workers in each of these areas. In addition, the model integrates known genetic, metabolic, and developmental aspects of extant taxa that phylogenetically bracket theropod dinosaurs for comparison with information derived from the fossil record of related extinct taxa.

Adaptation, Physiological↗
PubMed1994

Assortative mating in somatic traits and its consequences.

The problem of assortative mating embraces non-random mating of spouses. However, it is often discussed together with its consequences, which results from the fact that when we study similarities between spouses at various stages of their acquaintance and/or living together we must take into consideration not only the criteria of mating but also the consequences like, for instance, "resembling" (synchronous changes in husband and wife) and perhaps compensation of one's traits. This problem has not been sufficiently examined so far and further studies are necessary (Wolaánski 1970c, Nikityuk and Filipov 1975, Kasprzak and Wolański 1977, Thiessen and Gregg 1980, James 1989). The problem of assortative mating involves both the reasons principally genetic-evolutionary problems (Pearson 1896, Wolański and Siniarska 1983, 1984)--and the consequences as well, like, for instance homosis, that is transmitting to the offspring similar genes from defined loci, and heterosis, that is transmitting the different genes. Thus problem constitutes genetic foundations of auxology. Also an ecological problem is added, namely a synchronous resemble changes of spouses connected with similar living conditions and life style. Assortative mating seems to be a simple problem but in fact it is a scientific problem in which genetic, ecological and auxological approaches are combined. Below we will discuss assortative mating from these angles with reference to some anthropological traits. As a matter of fact, assortative mating is concerned with such a fundamental problem in the biomedical and social sciences as development the traits of the offspring (organism level) and of the whole future generations (population level). This is a problem of great importance by no means theoretical only. In our studies the main emphasis has been on spouses similarities in the morphological, physiological and psychomotor traits and also on some changes in the successive generations (which was connected with the lasting of marriage before the moment of investigations). The variations of traits of the populations were also taken into consideration as well as the effects of assortative mating of spouses on the development of their children. The above mentioned problems will constitute the contents of the present chapter. Studies on assortative mating have had a long tradition in Poland and most probably are one of the earliest in the world, apart from those conducted by Pearson (1896) in Great Britain and the Anonymous ones from 1903. This pertains mostly to B. Rosiński's (1923, 1925, 1926, 1929) investigations conducted in Poland in 1918 and on Polish immigrants to Brazil in 1931 and USA in 1929-30 (Stołyhwo 1931, Rosiński 1934).

Anthropometry↗
PubMed1995

Analytical solutions of the dinucleotide probability after and before random mutations.

The mutation process is a classical evolutionary genetic process mainly based on the (random) substitutions of one base (A = Adenine, C = Cytosine, G = Guanine, T = Thymine) for another. Two analytical solutions derived here allow us to analyse in genes the occurrence probabilities of motifs (e.g. dinucleotides) after substitutions (in the evolutionary sense: from the past to the present) and, unexpectedly, also before substitutions (after back substitutions, in the inverse evolutionary sense: from the present to the past). We generalize on the alphabet [A, C, G, T] of the analytical solutions and of the properties derived on the alphabet [R, Y] (R = purine = A or G, Y = pyrimidine = C or T). Application of the theory is based on the analytical solution giving the probabilities of the 16 dinucleotides AA, ..., TT in the protein (coding) genes of (nuclear) eukaryotes, viruses and prokaryotes and in (eukaryotic) introns after back substitutions (called primitive genes). After back substitutions, four of 16 dinucleotides--CG, TA, GT and AC--occur with low probabilities in each of these four primitive gene populations, except for CG in the primitive prokaryotic protein genes. In the primitive eukaryotic protein genes, the dinucleotide AT has also a significant low probability. We present the properties of the two analytical solutions, and the functions which may have these five dinucleotides in primitive genes are described in terms of biological signals.

Animals↗
PubMed2001

Limits on inferring genetic adaptation to high altitude in Himalayan and Andean populations.

Many physiological and anthropological studies have investigated the unique Andean and Himalayan populations that have resided for many hundreds of generations at high altitude (HA). A nonscientific survey of the extant literature reveals a relatively liberal tradition of inferring genetic (evolutionary) adaptation to HA in these groups, often based on limited evidence and/or based on study designs insufficient to fully address the issue. In order to provide some perspective, I review relevant methodological issues that should be considered before evolutionary inference is made. On the whole, this paper takes a conservative stance and cautions against evolutionary inference based on the serious limitations of currently applied research approaches.

Acclimatization↗
PubMed2000

Molecular evolution of vertebrate visual pigments.

Dramatic improvement of our understanding of the genetic basis of vision was brought by the molecular characterization of the bovine rhodopsin gene and the human rhodopsin and color opsin genes (Nathans and Hogness, 1983; Nathans et al., 1984, 1986a,b). The availability of cDNA clones from these studies has facilitated the isolation of retinal and nonretinal opsin genes and cDNA clones from a large variety of species. Today, the number of genomic and cDNA clones of opsin genes isolated from different vertebrate species exceeds 100 and is increasing rapidly. The opsin gene sequences reveal the importance of the origin and differentiation of various opsins and visual pigments. To understand the molecular genetic basis of spectral tuning of visual pigments, it is essential to establish correlations between a series of the sequences of visual pigments and their lambda(max) values. The potentially important amino acid changes identified in this way have to be tested whether they are in fact responsible for the lambda(max)-shifts using site-directed mutagenesis and cultured cells. A major goal of molecular evolutionary genetics is to understand the molecular mechanisms involved in functional adaptations of organisms to different environments, including the mechanisms of the regulation of the spectral absorption. Therefore, both molecular evolutionary analyses of visual pigments and vision science have an important common goal.

Animals↗
PubMed2003

Exponential mapping of quantitative trait loci governing allometric relationships in organisms.

Allometric scaling relationships or quarter-power rules, as a universal biological law, can be viewed as having some genetic component, and the particular genes (or quantitative trait loci, QTL) underlying these allometric relationships can be mapped using molecular markers. We develop a mathematical and statistical model for mapping allometric QTL on the basis of nonlinear power functions using Taylor's approximation theory. Simulation studies indicate that the QTL position and effect can be estimated using our model, but the estimation precision can be improved from the higher- over lower-order approximation when the sample size used and gene effects are small. The application of our approach in a real example from forest trees leads to successful detection of a QTL governing the allometric relationship between 3rd-year stem height and 3rd-year stem biomass. It is expected that our model will have broad implications for genetic, evolutionary, biomedical and breeding research.

Algorithms↗
PubMed1999

Toward an integrated genetic epidemiology of parasitic protozoa and other pathogens.

Due to the increase of human migrations, the appearance of emerging and reemerging endemies, growing antibiotic resistance, and climatic changes, infectious diseases most probably constitute the major challenge for medicine in the next century. The advent of molecular methods of pathogen characterization has considerably improved our knowledge of the epidemiology of these diseases. However, the use of concepts of evolutionary genetics for interpreting "molecular epidemiology" data remains limited, although the application of such methods would broaden considerably the scope of this field of research, and allow epidemiologic and taxonomic approaches to be ascertained on a much firmer basis. In turn, pathogens, hosts, and vectors provide fascinating models for basic research. The artificial character of the border between "basic" and "applied" research is especially apparent with regard to the "integrated genetic epidemiology of infectious diseases" concept. The goal of this chapter is to evaluate the respective impact, on the transmission and pathogenicity of infectious diseases, of the host's, the pathogen's, and the vector's (for vector-borne diseases) genetic diversity, and the interactions between these three parameters (coevolution phenomena).

Animals↗
PubMed2026

Genetic and environmental interactions outweigh mitonuclear coevolution for complex traits in Drosophila.

The interdependent relationship between mitochondrial and nuclear genomes is a powerful model for understanding how epistasis shapes the architecture and evolution of complex traits. Once considered a neutral marker, mitochondrial DNA variation is now recognized as critical to phenotypic evolution because of its epistatic interactions and history of coevolution with the nuclear genome. A central challenge in evolutionary genetics is to quantify the relative importance of stabilizing and directional selection shaping complex trait distributions within and among species. Both can act on interacting and/or co-evolving genes contributing to quantitative traits, but resolving their relative roles is complicated by the complex architecture of most traits. Here, we use a panel of 90 Drosophila mitonuclear genotypes to quantify the relative contributions of mitochondrial, nuclear, and environmental variation and their interactions to four metabolically demanding complex traits. We sample both within-species and between-species mitochondrial variation and observe stronger interaction effects attributable to within-species variation, consistent with stabilizing selection maintaining mitonuclear function. Additionally, culturing the flies on a mitochondrial Complex I inhibitor, rotenone, reveals significant genotype x environment (G×E and G×G×E) interaction effects, providing insight into how genetic variation can be maintained across changing environments. Our results have broader implications in medicine, where mitochondrial DNA donors with longer purifying selection histories may be safer for mitochondrial replacement therapies.

Journal Article↗
PubMed2000

Variation and selection at the CAULIFLOWER floral homeotic gene accompanying the evolution of domesticated Brassica oleracea.

The evolution of plant morphologies during domestication events provides clues to the origin of crop species and the evolutionary genetics of structural diversification. The CAULIFLOWER gene, a floral regulatory locus, has been implicated in the cauliflower phenotype in both Arabidopsis thaliana and Brassica oleracea. Molecular population genetic analysis indicates that alleles carrying a nonsense mutation in exon 5 of the B. oleracea CAULIFLOWER (BoCAL) gene are segregating in both wild and domesticated B. oleracea subspecies. Alleles carrying this nonsense mutation are nearly fixed in B. oleracea ssp. botrytis (domestic cauliflower) and B. oleracea ssp. italica (broccoli), both of which show evolutionary modifications of inflorescence structures. Tests for selection indicate that the pattern of variation at this locus is consistent with positive selection at BoCAL in these two subspecies. This nonsense polymorphism, however, is also present in both B. oleracea ssp. acephala (kale) and B. oleracea ssp. oleracea (wild cabbage). These results indicate that specific alleles of BoCAL were selected by early farmers during the domestication of modified inflorescence structures in B. oleracea.

Base Sequence↗
PubMed1997

T cell repertoire: genomic or somatic bias toward recognition of major histocompatibility complex molecules?

The prevailing concept about a major influence of thymic positive selection on shaping the T cell repertoire during ontogeny is confronted with an old idea emphasizing a dominant role for genetic (evolutionary) factors in molding the recognition potential of mature T cells. Our recent results are not readily interpreted without introducing a new version of the old concept, according to which complementarity to the major histocompatibility complex peptide-binding site is a major evolutionary selective pressure on T cell antigen receptor variable genes, with alloreactivity being a reflection of this fact.

Animals↗
PubMed2005

QTL-based evidence for the role of epistasis in evolution.

The extent to which epistasis contributes to adaptation and speciation has been a controversial topic in evolutionary genetics. One experimental approach to study epistasis is based on quantitative trait locus (QTL) mapping using molecular markers. Comparisons can be made among all possible pair-wise combinations of the markers, irrespective of whether an additive QTL is associated with a marker; several software packages have been developed that facilitate this. We review several examples of using this approach to identify epistatic QTLs for traits of evolutionary or ecological interest. While there is variability in the results, the number of epistatic QTL interactions is often greater than or equal to the number of additive QTLs. The magnitude of epistatic effects can be larger than the additive effects. Thus, epistatic interactions seem to be an important part of natural genetic variation. Future studies of epistatic QTLs could lead to descriptions of the genetic networks underlying variation for fitness-related traits.

Animals↗
PubMed1997

[Molecular paleogenetics of primates].

Genetic distances between the major members of the primate order obtained from data on blood serum antigens, amino-acid sequences of intracell proteins, electrophoretic gene markers, and nucleotide sequences of nuclear and mitochondrial DNA are analyzed. Conclusions regarding phylogeny and systematics of the primate order based on evidence of molecular evolutionary genetics are discussed.

Animals↗