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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↗

PubMed1992

Evolving views of viral evolution: towards an evolutionary biology of viruses.

Despite considerable interest in viral evolution, at least among virologists, viruses are rarely considered from the same evolutionary vantage point as other organisms. Early work of necessity emphasized phenotype and phenotypic variation (and therefore arguably was more oriented towards the broader biological and ecological perspectives). More recent work (essentially since the development of molecular evolution in the 1960's but beginning earlier) has concentrated on genotypic variation, with less clarity about the significance of such variations. Other aspects of evolutionary theory, especially considerations of natural selection and of evolutionary constraints, have not widely been applied to viruses, and an evolutionary framework for virology has long been lacking. This becomes apparent in considering 'emerging' viruses, which have often been treated on an ad hoc basis. It was often felt that, because previously unrecognized viruses are involved, mechanisms of viral emergence must mirror the unpredictability of mutations in the viral genome. However, most examples of viral emergence are independent of mutation, at least initially, and are often pre-existing viruses in changed circumstances ('viral traffic'). This conclusion also readily follows from ordinary Darwinian premises, which would require that, like other living species, 'new' organisms are descended only from existing species. In this respect, from a Darwinian perspective, viruses would appear to resemble other organisms.

Biological Evolution↗

PubMed1992

Behavioural endocrinology and reproduction: an evolutionary perspective.

It is a fact that those interested in immediate causation tend to be unaware of the great advances in evolutionary biology. Similarly, most scientists interested in ecological and evolutionary questions ignore advances in neurobiology and molecular biology. Quite simply, 'reductionists see little to be gained from holistic studies, and whole organism biologists do not recognize the value of molecular analysis' (Prosser 1986). This philosophical gap and lack of communication between molecular and physiological biologists with organismal and evolutionary biologists makes it difficult to be a generalist. Yet if we are to understand past, present, and perhaps even future behaviour, we must study how the different levels of biological organization are integrated. If done with foresight, it can lead to new discoveries not only in evolution and ecology, but also in physiology and even molecular biology. One of the first things we are impressed by is the great variety of animals, particularly their behaviours and their physiologies. With so many differences, are there any generalities? With the establishment of evolutionary theory, evidence that there is 'unity in diversity' has come with discoveries of common anatomical features, the cell cycle, conservation of intermediary metabolism, and the genetic code, to name but a few. While in vertebrates there appears to be a conservation of the neural circuits underlying sex behaviour, it is still too early to state the extent to which this concept can be extended to the hormonal mechanisms underlying behaviour. This chapter has documented how some widely-held assumptions are generalities only in a very restricted sense. I have tried to show how much of our conceptual understanding of the behavioural endocrinology stems from extensive studies on relatively few species. According to (Beach 1979), there are '... two cardinal rules that should govern not only the construction of animal models for human behaviour, but for all interspecific comparisons regardless of the behaviour and the species involved. The first rule is that meaningful comparisons are based not upon the formal characteristics of behaviour, but upon its causal mechanisms and functional outcomes.... The second rule is that the validity of interspecific generalization cannot exceed the reliability of intraspecific analysis. Significant comparison of a particular type of behaviour in two different species is impossible unless and until the behaviour has been adequately analyzed in each species by itself.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed2003

The morphogenesis of evolutionary developmental biology.

The early studies of evolutionary developmental biology (Evo-Devo) come from several sources. Tributaries flowing into Evo-Devo came from such disciplines as embryology, developmental genetics, evolutionary biology, ecology, paleontology, systematics, medical embryology and mathematical modeling. This essay will trace one of the major pathways, that from evolutionary embryology to Evo-Devo and it will show the interactions of this pathway with two other sources of Evo-Devo: ecological developmental biology and medical developmental biology. Together, these three fields are forming a more inclusive evolutionary developmental biology that is revitalizing and providing answers to old and important questions involving the formation of biodiversity on Earth. The phenotype of Evo-Devo is limited by internal constraints on what could be known given the methods and equipment of the time and it has been framed by external factors that include both academic and global politics.

Animals↗

PubMed2003

Evo-Devo: evolutionary developmental mechanisms.

Evolutionary developmental biology (Evo-Devo) as a discipline is concerned, among other things, with discovering and understanding the role of changes in developmental mechanisms in the evolutionary origin of aspects of the phenotype. In a very real sense, Evo-Devo opens the black box between genotype and phenotype, or more properly, phenotypes as multiple life history stages arise in many organisms from a single genotype. Changes in the timing or positioning of an aspect of development in a descendant relative to an ancestor (heterochrony and heterotopy) were two evolutionary developmental mechanisms identified by Ernst Haeckel in the 1870s. Many more have since been identified, in large part because of our enhanced understanding of development and because new mechanisms emerge as development proceeds: the transfer from maternal to zygotic genomic control; cell-to-cell interactions; cell differentiation and cell migration; embryonic inductions; functional interactions at the tissue and organ levels; growth. Within these emergent processes, gene networks and gene cascades (genetic modules) link the genotype with morphogenetic units (cellular modules, namely germ layers, embryonic fields or cellular condensations), while epigenetic processes such as embryonic inductions, tissue interactions and functional integration, link morphogenetic units to the phenotype. Evolutionary developmental mechanisms also include interactions between individuals of the same species, individuals of different species, and species and their biotic and/or abiotic environment. Such interactions link ecological communities. Importantly, there is little to distinguish the causality that underlies these interactions from that which underlies inductive interactions within embryos.

Animals↗

PubMed2005

Bitter and sweet/umami taste receptors with differently evolutionary pathways.

In this study,we investigated the evolutionary pathways of bitter, sweet and umami receptors using bioinformatic and phylogenetic analyses. Our results showed that the distantly evolutionary relationship between bitter and sweet/umami receptors. Our results also showed that bitter and sweet/umami receptors have differently evolutionary pathways,suggesting that the different evolutionary pathways may resulte in the differences of these three receptors in function.

Amino Acid Sequence↗

PubMed2005

Rapid evolutionary escape by large populations from local fitness peaks is likely in nature.

Fitness interactions between loci in the genome, or epistasis, can result in mutations that are individually deleterious but jointly beneficial. Such epistasis gives rise to multiple peaks on the genotypic fitness landscape. The problem of evolutionary escape from such local peaks has been a central problem of evolutionary genetics for at least 75 years. Much attention has focused on models of small populations, in which the sequential fixation of valley genotypes carrying individually deleterious mutations operates most quickly owing to genetic drift. However, valley genotypes can also be subject to mutation while transiently segregating, giving rise to copies of the high fitness escape genotype carrying the jointly beneficial mutations. In the absence of genetic recombination, these mutations may then fix simultaneously. The time for this process declines sharply with increasing population size, and it eventually comes to dominate evolutionary behavior. Here we develop an analytic expression for N(crit), the critical population size that defines the boundary between these regimes, which shows that both are likely to operate in nature. Frequent recombination may disrupt high-fitness escape genotypes produced in populations larger than N(crit) before they reach fixation, defining a third regime whose rate again slows with increasing population size. We develop a novel expression for this critical recombination rate, which shows that in large populations the simultaneous fixation of mutations that are beneficial only jointly is unlikely to be disrupted by genetic recombination if their map distance is on the order of the size of single genes. Thus, counterintuitively, mass selection alone offers a biologically realistic resolution to the problem of evolutionary escape from local fitness peaks in natural populations.

Biological Evolution↗

PubMed1991

An evolutionary view of viral regulatory genes.

It is my great honor to dedicate this article to Professor Ludwig C. Yen at the occasion of the Annual Meeting of the Chinese Society of Microbiology, commemorating his 101st Birthday. I have had the privilege of being one of the earliest students of Professor Yen, and as a staff member working for 16 years under him, I have been benefited enormously from his teachings. I am most grateful to Dr. Czausiung Yang and the executive board members of the Chinese Society of Microbiology for giving me this opportunity to present some of my research activities which would be relevant to Professor Yen's teachings. Introduction to the evolutionary view of host-parasite relationship was one of the many contributions Professor Yen made to enlighten students and colleagues as early as in 1940. As promulgated by Professor Yen, natural history of infectious diseases has witnessed the reality of Theobald Smith's premise, "pathogenicity of microorganisms is an accident in the evolutionary processes of host-parasite relationship, and the outcome of evolutionary forces is a modus vivendi (a feasible compromise) according to which the parasite and the host reach some sort of equilibrium which permits the survival of both"(1). These evolutionary concept has since become a common knowledge for modern students of infectious diseases. The natural history of recently discovered human retroviruses such as HTLVs (human T-lymphotropic viruses) and HIVs (human immunodeficiency viruses) has amply demonstrated the truth of the premise. I shall review some results of our research which would be of relevance to the evolution of viral quasispecies and variants, viral oncogenes, and the cellular as well as viral regulatory genes. I shall focus on the roles played by these genes in the delicate and complex balance of host-virus relationships, and on their association with cellular differentiation and oncogenesis.

Biological Evolution↗

PubMed2006

Protected polymorphism and evolutionary stability in pleiotropic models with trait-specific dominance.

When alleles have pleiotropic effects on a number of quantitative traits, the degree of dominance between a pair of alleles can be different for each trait. Such trait-specific dominance has been studied previously in models for the maintenance of genetic variation by antagonistic effects of an allele on two fitness components. By generalizing these models to an arbitrary number of fitness components or other phenotypic traits with different degrees of dominance, I show that genetic polymorphism is generally impossible without antagonistic fitness effects of different traits and without trait-specific dominance. I also investigate dominance and pleiotropy from a more long-term evolutionary perspective, allowing for the study of general ecological scenarios, and I discuss the effects of trait-specific dominance on evolutionary stability criteria. When selection is mainly directional and only trait-specific dominance and antagonism cause the emergence of polymorphism, then these polymorphisms can be overtaken by single mutants again, such that they are probably short-lived on an evolutionary time scale. Near evolutionarily singular points where directional selection is absent, trait-specific dominance and overdominance facilitate the emergence of polymorphism and cause evolutionary divergence in some cases. An important outcome of these models is that trait-specific dominance allows for the emergence of genetic polymorphisms without a selective disadvantage for heterozygotes. This removes the scope for the evolution of assortative mate choice and affects dominance modification. Sympatric speciation by disruptive ecological selection requires this heterozygote disadvantage in order to evolve, and therefore it becomes less plausible if the emergence of genetic polymorphism usually occurs via trait-specific dominance and antagonistic effects.

Biological Evolution↗

PubMed1976

Do evolutionary changes in cytochrome c structure reflect functional adaptations?

Following the demonstration that the rate of evolutionary change in the amino acid sequences of cytochromes c of eukaryotic species was not constant either for a single line of phylogenetic descent during different evolutionary intervals or for separate lines of descent, the concept that neutral mutations account for the vast majority of the evolutionary variations could no longer be accepted. Previous studies had shown that all eukaryotic cytochromes c tested appeared to be functionally indistinguishable in their reaction with mitochondrial respiratory chain components. However, an examination of the kinetics at low ionic strength led to the discovery of a high affinity reaction of cytochrome c with cytochrome c oxidase that revealed large differences in activity between the cytochromes of the horse, baker's yeast and the protist Euglena. Observed Km values for this reaction of 10(-7) to 10(-8) M appear to represent actual dissociation constants, as demonstrated by direct binding studies of cytochrome c with purified cytochrome c oxidase. The high affinity reaction is sensitive to ionic strength and inhibited by ADP and ATP in the range of physiological concentrations, ATP being three times as effective as ADP. The possibility is discussed that this effect of ATP on cytochrome c binding to its oxidase could provide the basis of a mechanism for mitochondrial respiratory control. The demonstration of differences between cytochrome c of various species in this kinetic system opens the way to a systematic study of the possible evolutionary adaptations of cytochromes c to their oxidases.

Amino Acid Sequence↗

PubMed1990

On the validity of von Baer's laws in evolutionary morphology.

The validity of von Baer's "laws" on the general and the specific in vertebrate morphogenesis (especially organogenesis) was varified. The author starts from the hypothesis that the rudiments of traits newly acquired during morphogenesis are not rigid, not immovable, during morphogenesis, but that the action of protracted stabilizing selection during the geological ages causes them to spread and pushes them back to the perfected and stabilized in adulthood, thereby shortening the recapitulation of ancestral traits, which may eventually disappear below the threshold of detectable morphogenesis. On the basis of this thesis of the dynamics of evolutionary morphogenesis (the author bases his considerations on his studies of the morphogenesis of the avian carpometacarpus and the nasal apparatus in Sauropsida), the author comes to the conclusion that these von Baer's rules presuppose rigidity and immovability of phylogenetic morphogenesis. In fact, the general and the specific in evolutionary morphogenesis (especially organogenesis) is continuously motion, the general changes to the specific and the specific to the general and both categories undergo incessant changes. Von Baer's rules are thus not generally valid, they cannot rank as laws and in many cases they do not apply to morphogenesis (especially organogenesis), particularly in the transitional phase of evolutionary morphogenesis, when the rudiments of progressive evolutionary deviations have reached the early phases of morphogenesis and recapitulation has disappeared - and the "general" has also disappeared.

Animals↗

PubMedDate not supplied

[Simulation of the macro-evolutionary process on computers].

The discussed model is designed for investigation of peculiarities and dynamics of the growth of evolutionary trees. The model is realized in FORTRAN, properties and principles of interaction of populations being the basis of this model. The results obtained reveal an extreme dependence of the pattern of evolutionary process from the parameters of competition, as well as the fact that evolutionary trees plotted with incomplete number of characters may be entirely different from real ones. It is concluded that many of the known evolutionary phenomena may be sufficiently described by a quantitative model based on the Darwinian principles.

Animals↗

PubMed1994

[Dynamics of evolutionary rates of proteins from small ribosomal subunits].

Phylogenetic analysis of small ribosomal subunit proteins was performed. Plausible taxon-specific acceleration of evolutionary rates ("leading") of base substitution of some ribosomal proteins and 16S rRNA sites in different phyletic lines were revealed. The limited number of synchronously changing proteins is discussed in terms of relay-race model of coevolution of ribosome. The analogy with dilemma of Haldane is drawn. Plausible differences in the evolutionary rates of regions with different secondary structure were revealed. Changes in correlation of evolutionary rates of regions with different secondary structure during leading were determined. It is anticipated that S14 with S19 ribosomal proteins and S7 with corresponding site on 16S rRNA change co-evolutionary.

Animals↗

PubMed1997

Global similarities in nucleotide base composition among disparate functional classes of single-stranded RNA imply adaptive evolutionary convergence.

The number of distinct functional classes of single-stranded RNAs (ssRNAs) and the number of sequences representing them are substantial and continue to increase. Organizing this data in an evolutionary context is essential, yet traditional comparative sequence analyses require that homologous sites can be identified. This prevents comparative analysis between sequences of different functional classes that share no site-to-site sequence similarity. Analysis within a single evolutionary lineage also limits evolutionary inference because shared ancestry confounds properties of molecular structure and function that are historically contingent with those that are imposed for biophysical reasons. Here, we apply a method of comparative analysis to ssRNAs that is not restricted to homologous sequences, and therefore enables comparison between distantly related or unrelated sequences, minimizing the effects of shared ancestry. This method is based on statistical similarities in nucleotide base composition among different functional classes of ssRNAs. In order to denote base composition unambiguously, we have calculated the fraction G+A and G+U content, in addition to the more commonly used fraction G+C content. These three parameters define RNA composition space, which we have visualized using interactive graphics software. We have examined the distribution of nucleotide composition from 15 distinct functional classes of ssRNAs from organisms spanning the universal phylogenetic tree and artificial ribozymes evolved in vitro. Surprisingly, these distributions are biased consistently in G+A and G+U content, both within and between functional classes, regardless of the more variable G+C content. Additionally, an analysis of the base composition of secondary structural elements indicates that paired and unpaired nucleotides, known to have different evolutionary rates, also have significantly different compositional biases. These universal compositional biases observed among ssRNAs sharing little or no sequence similarity suggest, contrary to current understanding, that base composition biases constitute a convergent adaptation among a wide variety of molecular functions.

Computer Graphics↗

PubMed2026

Genome-wide identification and evolutionary analysis of the ERF-VII gene family in the tea plant (Camellia sinensis) and functional characterization of CsRAP2.2 in response to cold stress.

The ERF-VII gene family, a critical branch of the AP2/ERF superfamily, is central to plant stress adaptation. However, its evolutionary history and function in tea plant (Camellia sinensis) remain unclear. Here, we performed integrated evolutionary, genomic, and functional analyses of ERF-VII genes across 14 plant lineages and 20 tea plant cultivars. The phylogenetic analysis revealed that ERF-VII proteins originated after vascular plant divergence, coinciding with the emergence of the N-terminal MCGGA/I motif linked to the oxygen-dependent N-degron pathway. Gymnosperms retained few conserved members, whereas angiosperms exhibited lineage-specific expansion-extensive in monocots via whole-genome duplication, moderate in eudicots with functional diversification. Pan-genome analysis across 20 tea plant cultivars further revealed varietal differences in ERF-VII gene distribution. Transcriptome profiling via the Tea Plant Information Archive identified CsRAP2.2 as a cold-inducible ERF-VII member with sustained expression under low-temperature stress. Functional assays demonstrated that silencing CsRAP2.2 reduced cold tolerance, while overexpression in tea leaves and heterologous expression in Arabidopsis thaliana enhanced cold tolerance by maintaining photosystem II efficiency, reducing membrane lipid peroxidation, and improving antioxidant capacity. Weighted gene co-expression network analysis positioned CsRAP2.2 as a regulatory hub integrating cold, hormone, and oxygen-sensing pathways. These results clarify the evolutionary trajectory of ERF-VII genes and establish CsRAP2.2 as a core cold-tolerance regulator in tea plant. These findings may inform future breeding of cold-resilient tea cultivars.

Camellia sinensis↗

PubMed2024

Comparative genomic analysis and functional investigations for MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria in ecology.

Microcystins (MCs) significantly threaten the ecosystem and public health. Biodegradation has emerged as a promising technology for removing MCs. Many MCs-degrading bacteria have been identified, including an indigenous bacterium Sphingopyxis sp. YF1 that could degrade MC-LR and Adda completely. Herein, we gained insight into the MCs biodegradation mechanisms and evolutionary dynamics of MCs-degrading bacteria, and revealed the toxic risks of the MCs degradation products. The biochemical characteristics and genetic repertoires of strain YF1 were explored. A comparative genomic analysis was performed on strain YF1 and six other MCs-degrading bacteria to investigate their functions. The degradation products were investigated, and the toxicity of the intermediates was analyzed through rigorous theoretical calculation. Strain YF1 might be a novel species that exhibited versatile substrate utilization capabilities. Many common genes and metabolic pathways were identified, shedding light on shared functions and catabolism in the MCs-degrading bacteria. The crucial genes involved in MCs catabolism mechanisms, including mlr and paa gene clusters, were identified successfully. These functional genes might experience horizontal gene transfer events, suggesting the evolutionary dynamics of these MCs-degrading bacteria in ecology. Moreover, the degradation products for MCs and Adda were summarized, and we found most of the intermediates exhibited lower toxicity to different organisms than the parent compound. These findings systematically revealed the MCs catabolism mechanisms and evolutionary dynamics of MCs-degrading bacteria. Consequently, this research contributed to the advancement of green biodegradation technology in aquatic ecology, which might protect human health from MCs.

Humans↗

PubMed2025

Evolutionary dynamics and genetic diversity of transposable elements revealed by resequencing data in maize population.

Zea mays (maize) is a globally significant crop with a complex genome enriched with transposable elements (TEs), which are crucial drivers of genomic diversity and plant evolution. In this study, we identified the TE insertion loci (TILs) from resequencing data of 103 maize accessions with the developed pipeline, and 64 293 non-redundant unique TILs were obtained in 82 maize accessions after filtering; approximately 80% (51 361) of loci showed insertion polymorphisms within the population. All TE superfamilies have low frequency in the maize population except for short interspersed nuclear elements, while some TE families have high fixed TE insertions, revealing distinct evolutionary dynamics among TE superfamilies and families. Genetic analysis using the transposon insertion polymorphism information from the maize population showed that the TE polymorphism loci can reflect their geographical origin and evolutionary relationships. Furthermore, TE insertions could also significantly impact gene expression, implying functional consequences for maize phenotypes and adaptation. These findings provide valuable insights into the evolutionary dynamics and genetic diversity of maize genomes, offering a valuable resource for molecular markers and association studies.

Zea mays↗

PubMed2026

Genetic and metabolite diversity of Sundaland Heptapleurum (Araliaceae) insight into evolutionary and specialized metabolite.

BACKGROUND: The genus Heptapleurum Gaertn (previously treated as Schefflera J.R.Forst. & G.Forst.) within the Araliaceae family is recognized for its significant medicinal value and complex taxonomy. However, an integrated understanding of its evolutionary and metabolite diversity remains unexplored, especially in the Sundaland region (i.e., Java and Sumatra). Here, we integrate genomics and metabolomics to unravel the evolutionary relationships and metabolite diversity of 10 Heptapleurum species from Sundaland. RESULTS: We assembled 10 new complete plastid genomes (plastomes) and 45S nuclear ribosomal DNA (nrDNA) sequences, identifying significant variation and potential key molecular markers. Metabolomics identified 152 metabolites, mainly phenolics and terpenoids. Metabolite profiles of H. rhynchocarpum and H. capituliferum were more correlated with phylogeny than with geography; these two species were separate from the main Heptapleurum clade. Four species, H. farinosum, H. longifolium, H. rigidum, and H. fastigiatum, have almost identical plastomes and 45S nrDNA structures, suggesting they may represent closely related species with different phenotypes, as evidenced by distinctive metabolite compositions. CONCLUSIONS: Crucially, there is an incongruence between the genetic and chemical phylogenies, underscoring that while chemotaxonomy reflects functional diversity, genetic data remains the definitive standard for evolutionary inference, with the potential for reclassifying H. rhynchocarpum and H. capituliferum. This study provides a foundation for future taxonomic revisions, conservation, and drug discovery of Heptapleurum.

Phylogeny↗