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PubMed1992

An optimizing principle of natural selection in evolutionary population genetics.

This paper brings together two themes in evolutionary population genetics theory. The first concerns Fisher's Fundamental Theorem of Natural Selection: a recent interpretation of this theorem claims that it is an exact result, relating to the so-called "partial" increase in mean fitness. The second theme concerns the desire to find an optimality principle in genetic evolution. Such a principle is found here: of all gene frequency changes which lead to the same partial increase in mean fitness as the natural selection gene frequency changes, the natural selection values minimize a generalized distance measure between parent and daughter generation gene frequency values.

Alleles↗
PubMed2001

Toward a new synthesis: population genetics and evolutionary developmental biology.

Despite the recent synthesis of developmental genetics and evolutionary biology, current theories of adaptation are still strictly phenomenological and do not yet consider the implications of how phenotypes are constructed from genotypes. Given the ubiquity of regulatory genetic pathways in developmental processes, we contend that study of the population genetics of these pathways should become a major research program. We discuss the role divergence in regulatory developmental genetic pathways may play in speciation, focusing on our theoretical and computational investigations. We also discuss the population genetics of molecular co-option, arguing that mutations of large effect are not needed for co-option. We offer a prospectus for future research, arguing for a new synthesis of the population genetics of development.

Adaptation, Biological↗
PubMed1997

Common patterns of genetic evolution in human solid tumors.

Human solid tumors develop multiple genetic evolutionary abnormalities as they evolve. Studies that have focused primarily on early colorectal cancer have suggested that genetic instability is a prominent feature of preinvasive disease. At least two separate mechanisms for the generation of genetic instability have been identified. The first, which involves widespread microsatellite instability in near-diploid cells, affects less than one-fifth of colon cancers. The second form of genetic instability is characterized by the development of p53 gene abnormalities that result in gross aneuploidy and multiple structural chromosomal changes. p53/aneuploidy affects most colon cancers, breast cancers, and many other solid tumors. This genetic evolutionary change commonly occurs at the interface between severe dysplasia and invasive disease. Specific post-aneuploid sequences of genetic changes that are relevant to tumor progression often involve the accumulation of multiple gain-of-function abnormalities in individual cells. The co-occurrence of Her-2/neu overexpression and EGF receptor overexpression in the same aneuploid cells defines an adeno/squamous genetic evolutionary sequence that is common to ductal breast cancers, non-small cell lung cancers, and other solid tumors. Later steps in this sequence include ras and c-myc overexpression. The neuroendocrine genetic evolutionary sequence is a separate branch of the p53/aneuploidy sequence with distinctive features that include loss of Rb and raf1 overexpression. Her-2/neu overexpression is not characteristic of this sequence; c-myc amplification/overexpression is common to both p53-associated sequences. The neuroendocrine sequence is found in small cell carcinoma of the lung and in minor proportions of other solid tumors, including breast cancer. Multiparameter cell-based methods are especially well suited for elucidation in human solid tumors of the genetic evolutionary sequences that could provide a rational scientific basis for determining prognosis and for optimizing therapy in individual cancer patients.

Aneuploidy↗
PubMed1996

Heterochrony and neotenic salamanders: possible clues for understanding the animal development and evolution.

A synthesis of developmental genetics with evolutionary genetics is now making possible to understand significant evolutionary changes in multicellular organisms. The key concept for unifying the two must be heterochrony. Heterochrony causes evolutionary modifications due to changes in timing and/or rate of development. The heterochrony is conventionally categorized into three patterns as neoteny (retardation in somatic development), progenesis (acceleration in gonadal development), and direct development (acceleration in somatic development, resulting in lack of larval or tadpole stages). A lot of species showing neoteny are known in urodeles, but not in anurans. Neotenic urodeles are also divided into three categories; permanent or obligate, "inducible" obligate and facultative neotenies. Hynobius retardatus, a specific population of which had been reported to show neoteny but is believed to be extinct at present, has become to be used for experimental analysis of heterochronic expression of several adult characters during its ontogeny. Gonadal maturation and a transition of globin subunits from larval to adult types have been shown to occur independently on the morphological metamorphosis in H. retardatus. Mechanisms underlying the heterochrony, including morphogenetic clock, heterochronic genes in Drosophila and C. elegans, temporal colinearity in Hox gene complex in mice, and atavistic transformation induced by altered expression of Hox genes are discussed in terms of current molecular biology.

Animals↗
PubMed2002

Psychopathology or adaptation? Genetic and evolutionary perspectives on individual differences and psychopathology.

A greater understanding of psychopathology will be found in the integration of genetic and evolutionary perspectives on adaptation and function. Evolutionary theory proposes that adaptive traits are reproduced more successfully than maladaptive ones. However, some traits, while contributing to fitness in the ancestral environment, may contribute to fitness no longer. This is known as mismatch theory. Evolutionarily informed research into various "pathologies" has yielded interesting results, some based on this theory. This paper serves to distinguish between genetic and evolutionary perspectives on psychopathology as well as to examine some recent research on the selective forces that may be implicated in psychopathy, anorexic behavior, and ADHD. We suggest that research into psychopathy in general would benefit from an evolutionary perspective and an examination of the assumptions behind past research.

Adaptation, Biological↗
PubMed1998

Behavioral genetics and evolutionary psychology: unified perspective on personality research.

Behavioral geneticists and evolutionary psychologists have generally pursued human behavioral analyses with little theoretical or methodological exchange. However, significant benefits might accrue from increased communication between these disciplines. The primary goals of this article are (1) to identify meaningful junctures between behavioral genetics and evolutionary psychology, (2) to describe behavioral genetic research designs and their applications to evolutionary analyses, and (3) to reassess current personality research in light of behavioral genetic and evolutionary concepts and techniques. The five-factor model of personality is conceptualized as subsuming variation in normative species-typical systems with adaptive functions in the human environment of evolutionary adaptation. Considered as universal evolved mechanisms, personality systems are often seen in dynamic conflict within individuals and as highly compartmentalized in their functioning between settings. However, genetically influenced individual differences in personality may also be understood within an evolutionary framework. Studies of the heritability of personality traits indicate broad-sense heritabilities in the 0.40-0.50 range with evidence of substantial nonadditive genetic variation and nonshared environmental influences. Evidence indicates that evolutionary theory (e.g., inclusive fitness theory) predicts patterns of social interaction (e.g., cooperation and bereavement) in relatives. Furthermore, variation in personality may constitute a range of viable strategies matching the opportunities available in the complex niche environment of human societies. Within this wide range of viable strategies, personality variation functions as a resource environment for individuals in the sense that personality variation is evaluated according to the interests of the evaluator (e.g., friendships, coalitions, or mate choice).

Biological Evolution↗
PubMed1996

On distinguishing unique combinations in biological sequences.

The problem of defining combinations of variants unique to a sequence is efficiently addressed as a set covering computation. The unique-combinations method is introduced, which identifies patterns in biological sequence data that distinguish a sequence from a group of other sequences. This method is further developed to describe features consistently present in one group of sequences but not in a second group. The approach is incorporated into a novel analytical tool, designed for use in studies of polymorphic sequence data, such as mitochondrial, human leukocyte antigen (HLA), or viral pathogen sequences. The unique combinations method is well suited to applications in medical genetics and evolutionary genetics. An example implementation of the unique-combinations method yields greatly improved risk assessment for insulin-dependent diabetes mellitus (IDDM) from amino acid patterns isolated in an analysis of HLA class II DQA1-DQB1 patient and control genotypes.

Algorithms↗
PubMed1989

Allelic and genotypic composition of ancestral Spanish and colonial Californian gene pools of Avena barbata: evolutionary implications.

Spanish explorers and colonists inadvertently started a massive experiment in evolutionary genetics when they accidentally introduced Avena barbata to California from Spain during the seventeenth and eighteenth centuries. Assays of the Spanish and Californian gene pools of this species for 15 loci show that the present day Spanish gene pool, particularly that of Southwestern Spain, is identical or virtually identical to that of California for five loci and closely similar for nine loci. Despite their similar allelic and single-locus genotypic compositions, the present-day Spanish and Californian gene pools are differently structured on a multilocus genetic basis. Evolutionary implications of these results are discussed.

Alleles↗
PubMed2006

Chemical genetic algorithms--evolutionary optimization of binary-to-real-value translation in genetic algorithms.

A chemical genetic algorithm (CGA) in which several types of molecules (information units) react with each other in a cell is proposed. Not only the information in DNA, but also smaller molecules responsible for the transcription and translation of DNA into amino acids, are adaptively changed during evolution, which optimizes the fundamental mapping from binary substrings in DNA ( genotype) to real values for a parameter set (phenotype). Through the struggle between cells containing a DNA unit and small molecular units, the codes (DNA) and the interpreter (the small molecular units) coevolve, and a specific output function, from which a cell's fitness is evaluated, is optimized. To demonstrate the effectiveness of the CGA, it is applied to a set of variable-separable and variable-inseparable problems, and it is shown that the CGA can robustly solve a wide range of optimization problems regardless of their fitness characteristics. To ascertain the optimization of the genotype-to-phenotype mapping by the CGA, we also conduct analytical experiments for some problems while observing the basin size of a global optimum solution in the binary genotype space. The results show that the CGA effectively augments the basin size, makes it easier for evolution to find a path to the global optimum solution, and enhances the GA's evolvability during evolution.

Algorithms↗
PubMed1997

On the use of neural network techniques to analyse sleep EEG data. First communication: application of evolutionary and genetic algorithms to reduce the feature space and to develop classification rules.

To automate sleep stage scoring, the system sleep analysis system to challenge innovative artificial networks (SASCIA) has been developed and implemented. The aims of our investigation were twofold: In addition to automatic sleep stage scoring the hypothesis was tested that the information of only 1 EEG channel (C4-A2) should be sufficient to automatically generate sleep profiles which are comparable with profiles made by sleep experts on the basis of at least 3-channel EEG (C4-A2), EOG and EMG, as EOG and EMG are seen as epiphenomena during sleep and the full information about the sleep stage should--according to our hypothesis--be available in the EEG. The main components of the SASCIA sleep analysis system are designed to meet the requirements of flexible adaptation to the interindividual differences of the sleep EEG. The core of the SASCIA sleep analysis system consists of neural networks. Supervised learning was implemented and the experts' scorings were included into the learning set and test set. The feature selections out of a large number (118) are performed by genetic algorithms and the topologies of the networks are optimized by evolutionary algorithms. Different mathematical procedures were used to evaluate and optimize the efficiency of the system. The profiles generated by SASCIA are in reasonable agreement with the sleep stages scored by experts according to RKR. The development of the system is communicated in three parts: the first communication deals with the application of the neural network techniques using evolutionary and genetic algorithms and with the selection of feature space. The second communication shows the training of these evolutionary optimized network techniques with multiple subjects and the application of context rules, while the third communication shows an improvement in the robustness by the simultaneous application of 9 different networks obtained from 9 subject types which were used in combination with context rules.

Algorithms↗
PubMed2002

Malformations of the craniofacial region: evolutionary, embryonic, genetic, and clinical perspectives.

Malformations of the craniofacial region are reviewed with respect to evolutionary, embryonic, genetic, and clinical perspectives under the following headings: How Old Is Our Head?, Head Organization Genes, Genetics of Craniofacial Anomalies, Craniofacial Derivatives, Anencephaly, Cephalocele, Holoprosencephaly, Craniosynostosis, Hypertelorism, Branchial Arch Anomalies, and Orofacial Clefting.

Abnormalities, Multiple↗
PubMedDate not supplied

Synthetic amphiploids in breeding--genetic and evolutionary studies in wheat.

Synthetic amphiploids play an important role in breeding programs of wheat and in the genetic and evolutionary studies of the wheat group. One of the most obvious uses of amphiploidy has been the development of hexaploid and octaploid Triticale. The utilization of synthetic amphiploids as a means of introducing commercially important features of related species into cultivated wheat is now well documented. The projects to produce hybrid wheat are based on the manipulation of cytoplasms and restorers by means of artificially obtained amphiploids. The amphiploidization of interspecific hybrids by treatment with colchicine results in homozygosity. Therefore, a direct use of synthetic amphiploids for genetic studies has been limited to some extent. More often they were used indirectly, viz. as the initial step in the production of single chromosome addition and substitution lines. Such lines were used for detailed and highly informative genetic analyses and also as sources of alien variation for wheat breeding. Crosses between some of the synthetic amphiploids resembling natural species and the cultivated wheats have been successfully used in the evolutionary studies of wheats.

Biological Evolution↗
PubMed2002

Arrangement and structural conservation of the mitochondrial control region of two species of Plecoptera: utility of tandem repeat-containing regions in studies of population genetics and evolutionary history.

Low levels of primary sequence similarity across insect taxa have led to the suggestion of conserved structural elements in the insect mitochondrial control region. Our aim was to determine whether previously described motifs and secondary structures exist in stoneflies (Plecoptera). Several motifs and structural elements previously described in Orthoptera and Diptera were found, including a conserved 'hairpin' structure that may play a role in the initiation of mtDNA replication. The repeat region had the highest percentage similarity, lowest A-T content and highest transition to transversion ratio, suggesting a unique evolutionary pattern for the repeats. Finally, we discuss the usefulness of the control region in population genetic and evolutionary studies.

Animals↗
PubMed1978

Genetic and evolutionary fitness.

The advantages and disadvantages of evolutionary fitness (probability that a single mutant line will not become extinct) and genetic fitness (mean fecundity) are compared. For deterministic processes the two are equivalent, but for stochastic branching processes they may be totally unrelated except that an absolute genetic fitness of unity or less implies an evolutionary fitness of zero. To know the variance as well as the mean family size does not in general uniquely determine the evolutionary fitness. Except where genetic fitness is close to unity, the impact of selection is shown to be rapid for the binomial, Poisson, negative binomial, and truncated negative binomial distributions. Evolutionary fitness, though somewhat cumbersome, has greater relevance to evolution, genetic counseling, and voluntary population control; but genetic fitness which is much easier to handle is the more appropriate measure where a large number of mutants is involved. Some empirical data on the transmission of various types of characters from parent to child are analyzed to allow comparison of genetic fitness, Crow's index, and a Malthusian parameter, with evolutionary fitness. There is a fair, but far from perfect, agreement among them. Multiple correlation of evolutionary fitness with mean and variance of family size taken jointly suggests a much more satisfactory approximation. It thus appears that, at the least, the population geneticist cannot afford to ignore the variance (which is not adequately represented in Crow's index). These relationships, based on two sets of data only may be accidental and should be invoked with caution. It seems more than likely that other aspects of the distribution of family size (eg, even higher moments) may contain relevant information in certain cases.

Biological Evolution↗
PubMedDate not supplied

Variable segment number in centipedes: population genetics meets evolutionary developmental biology.

The case studies of population genetics focus on intraspecific variation, but most cases--at least where the variation is polymorphic--deal with characters that are not directly linked to organismic structure or ontogeny. Conversely, the case studies of evolutionary developmental biology focus directly on structure/ontogeny, but usually involve only interspecific comparisons. To integrate these complementary approaches, it is desirable to have a model system that permits study of intraspecific variation in development, using a character whose genetic basis either is already known or can be elucidated. Segment number in geophilomorph centipedes is proposed as a possible model system of this kind. Segment number is variable in natural populations of geophilomorphs, while in the other centipede orders it is fixed, either completely (scutigeromorphs, lithobiomorphs), or at least within species (scolopendromorphs). Statistical analysis of data on the extent of variation in different geophilomorph species suggests that segment number may be of selective importance, rather than the variation being merely an inevitable consequence of the difficulty of achieving a high degree of repeatability when there is a large number of segments.

Animals↗
PubMed1998

Intracellular coexpression of epidermal growth factor receptor, Her-2/neu, and p21ras in human breast cancers: evidence for the existence of distinctive patterns of genetic evolution that are common to tumors from different patients.

Multiparameter flow cytometry studies were performed on cells from the primary tumors of 94 patients with breast cancer. Correlated cellular measurements of cell DNA content, Her-2/neu, epidermal growth factor receptor (EGFR), and p21ras levels were performed on each of 5,000 to 100,000 cells from each tumor. When criteria for positivity were matched with those in common use for immunohistochemical studies, 28 of 94 (30%) breast cancers were classified as positive for Her-2/neu overexpression. When similar criteria were applied to the EGFR measurements, 23 of 94 (24%) cases were classified as positive for EGFR overexpression. Similarly, 23 of 94 (24%) cases were classified as positive for p21ras overexpression. By conventional flow cytometric criteria for DNA ploidy, 24 cases were diploid, 28 were tetraploid, and 42 were aneuploid. When the measurements were treated as separate sets of data, the only statistically significant correlations noted were the high frequency of diploid tumors, which did not overexpress any of the three oncogenes studied (P < 0.05), and an association between Her-2/neu overexpression and aneuploidy (P < 0.03). When the data were treated as correlated intracellular measurements, 90 of the 94 tumors studied contained a population of cells in which the intracellular levels of Her-2/neu expression were directly correlated with the levels of EGFR expression in the same cells. The ratio of Her-2/neu molecules to EGFR molecules in the same cells exceeded 1 in the majority of tetraploid and aneuploid cases and was close to or less than 1 in the majority of diploid cases. In nearly all tumors, p21ras overexpression was observed only in cells that overexpressed Her-2/neu, EGFR, or both, and p21ras levels per cell were more closely correlated with levels of EGFR per cell in the same cells than with Her-2/neu levels per cell. The data are consistent with a model in which heterodimerization of Her-2/neu and EGFR in individual cells is achieved by one of several genetic evolutionary pathways, all of which commonly lead to p21ras overexpression. The two major genetic evolutionary pathways identified in this study are an aneuploid, Her-2/neu overexpression-driven pathway seen in 59 of 94 tumors, and a diploid, EGFR overexpression-driven pathway seen in 19 of 94 tumors. All tumors with Her-2/neu:EGFR ratios greater than 2 contained an infiltrating ductal carcinoma component, whereas all infiltrating pure lobular carcinomas had Her-2/ neu:EGFR ratios that were less than 2. All of the genetic evolutionary pathways identified in this study were represented among the 11 tumors from patients who experienced early tumor recurrences.

Analysis of Variance↗
PubMed2002

Evolutionary behavioral genetics in Drosophila.

Behavioral genes have a special evolutionary interest because they are potentially involved in speciation and in many forms of adaptation. Dozens of loci affecting different aspects of behavior have been already identified and cloned in Drosophila. Some of these genes determine variation in such ethologically complex phenotypes as the male "love song" that is produced during courtship and the locomotor "sleep-wake" activity cycles that are controlled by the circadian clock. Although the evolutionary analysis of most behavioral genes in Drosophila is relatively new, it has already given important insights into the forces shaping the molecular variation at these loci and their functional consequences.

Amino Acid Sequence↗
PubMed2025

Mitochondrial Impostors: Prevalence and Impacts of NUMTs on Genetic and Evolutionary Studies in Carnivora.

Nuclear mitochondrial pseudogenes are mitochondria-derived DNA sequences integrated into the nuclear genome, which can introduce errors in species identification, phylogenetic inference, and population genetics. Although nuclear mitochondrial pseudogene contamination has been reported in some Carnivora species, a systematic investigation into the prevalence and impacts of nuclear mitochondrial pseudogenes across an order is still lacking. In this study, 22,102 mitochondrial DNA sequences of 80 Carnivora species from 14 families and 54 genera were retrieved from the public National Center for Biotechnology Information database and further analyzed. Using alignment-based methods, 158 problematic sequences/sequence groups were identified and categorized into four types: nuclear mitochondrial pseudogenes, species misidentification or mislabeling, sequence errors, and anomalous sites. Among families, Felidae exhibited the highest rate of nuclear mitochondrial pseudogene contamination, particularly in species of the genus Panthera. In contrast, no nuclear mitochondrial pseudogene contamination was detected in members of Ursidae and Ailuridae. Phylogenetic analysis revealed multiple independent origins of nuclear mitochondrial pseudogene, with some tracing back to the common ancestor of Carnivora. To mitigate nuclear mitochondrial pseudogene-related errors, rigorous sequence verification strategies, such as sequence alignment and phylogenetic validation, should be implemented. In conclusion, our findings highlight the necessity of nuclear mitochondrial pseudogene awareness in genetic and evolutionary studies of Carnivora and other taxa.

Animals↗