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PubMed1996

Natural selection and random genetic drift as causes of evolution on islands.

The evolutionary processes responsible for adaptation and speciation on islands differ in several ways from those on the mainland. Most attention has been given to the random genetic drift that arises when a population is founded from just a few colonizing genomes. Theoretical obstacles to "founder effect speciation' are discussed, together with recent proposals for avoiding them. It is argued that although certain kinds of epistasis can facilitate the evolution of strong reproductive isolation, this favours divergence by selection as much as by random drift.

Alleles↗

PubMed1987

A plasma-membrane associated ATPase from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius.

Thermoacidophilic archaebacteria have gained much interest because of their phylogenetic distance to eubacteria and eukaryotes and also because of their unique living conditions. Investigation of the energy-converting system therefore offers a key for understanding the evolutionary position and environmental adaptation of these unusual bacteria. A plasma-membrane-associated adenosine triphosphatase with specific activities of 0.3-0.6 mumol min-1 (mg protein)-1 has been detected in the thermoacidophilic archaebacterium Sulfolobus acidocaldarius (DSM 639). The enzyme exhibits two optima at pH 5.5 and 8.0, sulfite activation leads to only one optimum at pH 6.25. In the presence of the divalent cations Mg2+ or Mn2+ it hydrolyzes ATP with highest reactivity and also other purine and pyrimidine nucleotides, but not ADP and pyrophosphate. A specific stimulation by monovalent cations is not observed. The ATPase activity is not inhibited by N,N'-dicyclohexylcarbodiimide, azide or vanadate, but it is by the vascular ATPase inhibitor nitrate with an [I]50 of 8 mM. Linear Arrhenius plots up to 75 degrees C reflect pronounced adaptation to the hot environment of the archaebacterium. The solubilized ATPase as localized by activity staining in non-denaturating gels and further analyzed by sodium dodecyl sulfate electrophoresis is composed of two major polypeptides of 65 and 51 kDa reminiscent of the alpha and beta subunits of eubacterial and eukaryotic F0F1-ATPases. The ATPase is suggested as a probable candidate for a reversibly acting ATP synthase responsible for oxidative phosphorylation found in Sulfolobus acidocaldarius.

Adenosine Triphosphatases↗

PubMed2005

Virulent variants emerging in mice infected with the apathogenic prototype strain of the parvovirus minute virus of mice exhibit a capsid with low avidity for a primary receptor.

The mechanisms involved in the emergence of virulent mammalian viruses were investigated in the adult immunodeficient SCID mouse infected by the attenuated prototype strain of the parvovirus Minute Virus of Mice (MVMp). Cloned MVMp intravenously inoculated in mice consistently evolved during weeks of subclinical infection to variants showing altered plaque phenotypes. All the isolated large-plaque variants spread systemically from the oronasal cavity and replicated in major organs (brain, kidney, liver), in sharp contrast to the absolute inability of the MVMp and small-plaque variants to productively invade SCID organs by this natural route of infection. The virulent variants retained the MVMp capacity to infect mouse fibroblasts, consistent with the lack of genetic changes across the 220-to-335 amino acid sequence of VP2, a capsid domain containing main determinants of MVM tropism. However, the capsid of the virulent variants shared a lower affinity than the wild type for a primary receptor used in the cytotoxic infection. The capsid gene of a virulent variant engineered in the MVMp background endowed the recombinant virus with a large-plaque phenotype, lower affinity for the receptor, and productive invasiveness by the oronasal route in SCID mice, eventually leading to 100% mortality. In the analysis of virulence in mice, both MVMp and the recombinant virus similarly gained the bloodstream 1 to 2 days postoronasal inoculation and remained infectious when adsorbed to blood cells in vitro. However, the wild-type MVMp was cleared from circulation a few days afterwards, in contrast to the viremia of the recombinant virus, which was sustained for life. Significantly, attachment to an abundant receptor of primary mouse kidney epithelial cells by both viruses could be quantitatively competed by wild-type MVMp capsids, indicating that virulence is not due to an extended receptor usage in target tissues. We conclude that the selection of capsid-receptor interactions of low affinity, which favors systemic infection, is a major evolutionary process in the adaptation of parvoviruses to new hosts and in the cause of disease.

Animals↗

PubMed1997

Mechanisms of plant virus evolution.

Plant viruses utilize several mechanisms to generate the large amount of genetic diversity found both within and between species. Plant RNA viruses and pararetroviruses probably have highly error prone replication mechanisms, that result in numerous mutations and a quasispecies nature. The plant DNA viruses also exhibit diversity, but the source of this is less clear. Plant viruses frequently use recombination and reassortment as driving forces in evolution, and, occasionally, other mechanisms such as gene duplication and overprinting. The amount of variation found in different species of plant viruses is remarkably different, even though there is no evidence that the mutation rate varies. The origin of plant viruses is uncertain, but several possible theories are proposed. The relationships between some plant and animal viruses suggests a common origin, possibly an insect virus. The propensity for rapid adaptation makes tracing the evolutionary history of viruses difficult, and long term control of virus disease nearly impossible, but it provides an excellent model system for studying general mechanisms of molecular evolution.

Journal Article↗

PubMedDate not supplied

Otoneuroscience and space vestibulo-neuroscience in the new century.

From a clinically oriented point of view, efforts of otoneuroscience should be directed toward an improvement of the management of dizzy and vertiginous patients. At present, the main obstacles in this field are: (1) the lack of specific therapies for many of the clinical diagnoses. This reduces the necessity of clinical vestibular diagnosis to a pragmatic exclusion of the few diseases with therapeutic consequences; (2) the lack of feedback to confirm or disprove clinical diagnoses; (3) poor knowledge of the pathophysiology of many of the otoneurological diseases; experiments in animal models may be helpful in this respect; (4) most progress in medicine originates from the results of numerous, poorly controlled 'unscientific' trial and error experiments obtained during treatment of patients; training clinicians in more scientific, critical thinking would help to increase the profits that can be realized from this important source of information; and (5) to date, information obtained during zero-gravity experiments in space have not yet led to important consequences in treatment of patients under 1-g conditions, but are important for a possible evolutionary step of mammals adapting to a new environment.

Adaptation, Physiological↗

PubMed2025

Reference genome bias in light of species-specific chromosomal reorganization and translocations.

BACKGROUND: Whole-genome sequencing efforts, have during the past decade, unveiled the central role of genomic rearrangements-such as chromosomal inversions-in evolutionary processes, including local adaptation in a wide range of taxa. However, employment of reference genomes from distantly or even closely related species for mapping and the subsequent variant calling can lead to errors and/or biases in the datasets generated for downstream analyses. RESULTS: Here, we capitalize on the recently generated chromosome-anchored genome assemblies for Arctic cod (Arctogadus glacialis), polar cod (Boreogadus saida), and Atlantic cod (Gadus morhua) to evaluate the extent and consequences of reference bias on population sequencing datasets (approx. 15-20 × coverage) for both Arctic cod and polar cod. Our findings demonstrate that the choice of reference genome impacts the mapping statistics, including mapping depth and mapping quality, as well as core population genetic estimates, such as heterozygosity levels, nucleotide diversity (π), and cross-species genetic divergence (DXY). Furthermore, using a more distantly related reference genome can lead to inaccurate detection and characterization of chromosomal inversions, i.e., in terms of size (length) and location (position), due to inter-chromosomal reorganizations between species. Additionally, we observe that some of the verified species-specific inversions are split across multiple genomic regions when mapped against a heterospecific reference. CONCLUSIONS: Inaccurate identification of chromosomal rearrangements as well as biased population genetic measures could potentially lead to erroneous interpretation of species-specific genomic diversity, impede the resolution of local adaptation, and thus, impact predictions of their genomic potential to respond to climatic and other environmental perturbations.

Animals↗

PubMed2005

Entropic stabilization of proteins and its proteomic consequences.

Evolutionary traces of thermophilic adaptation are manifest, on the whole-genome level, in compositional biases toward certain types of amino acids. However, it is sometimes difficult to discern their causes without a clear understanding of underlying physical mechanisms of thermal stabilization of proteins. For example, it is well-known that hyperthermophiles feature a greater proportion of charged residues, but, surprisingly, the excess of positively charged residues is almost entirely due to lysines but not arginines in the majority of hyperthermophilic genomes. All-atom simulations show that lysines have a much greater number of accessible rotamers than arginines of similar degree of burial in folded states of proteins. This finding suggests that lysines would preferentially entropically stabilize the native state. Indeed, we show in computational experiments that arginine-to-lysine amino acid substitutions result in noticeable stabilization of proteins. We then hypothesize that if evolution uses this physical mechanism as a complement to electrostatic stabilization in its strategies of thermophilic adaptation, then hyperthermostable organisms would have much greater content of lysines in their proteomes than comparably sized and similarly charged arginines. Consistent with that, high-throughput comparative analysis of complete proteomes shows extremely strong bias toward arginine-to-lysine replacement in hyperthermophilic organisms and overall much greater content of lysines than arginines in hyperthermophiles. This finding cannot be explained by genomic GC compositional biases or by the universal trend of amino acid gain and loss in protein evolution. We discovered here a novel entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state and demonstrated its immediate proteomic implications. Our study provides an example of how analysis of a fundamental physical mechanism of thermostability helps to resolve a puzzle in comparative genomics as to why amino acid compositions of hyperthermophilic proteomes are significantly biased toward lysines but not similarly charged arginines.

Aminopeptidases↗

PubMed2005

Locomotor compensation creates a mismatch between laboratory and field estimates of escape speed in lizards: a cautionary tale for performance-to-fitness studies.

A key assumption in evolutionary studies of locomotor adaptation is that standard laboratory measures of performance accurately reflect what animals do under natural circumstances. One widely examined measure of performance is maximum sprint speed, which is believed to be important for eluding predators, capturing prey, and defending territories. Previous studies linking maximum sprint speed to fitness have focused on laboratory measurements, and we suggest that such analyses may be appropriate for some species and intraspecific classes, but not others. We provide evidence for a general inverse relationship between maximum laboratory sprint speed and the percentage of maximum capacity that animals use when escaping from a threat in the field (the model of locomotor compensation). Further, absolute values of field escape speed and maximum laboratory speed are not significantly related when comparing across a diverse group of Anolis and lacertid lizards. We show that this pattern of locomotor compensation holds both within (i.e., among intraspecific classes) and among lizard species (with some exceptions). We propose a simple method of plotting field escape speed (y-axis) versus maximum laboratory speed (x-axis) among species and/or intraspecific classes that allows researchers to determine whether their study organisms are good candidates for relating laboratory performance to fitness. We suggest that species that reside directly on, or near the "best fitness line" (field escape speed = maximum laboratory speed) are most likely to bear fruit for such studies.

Analysis of Variance↗

PubMed1979

[Psychiatric perspectives of ethological anthropology].

Ethological anthropology is characterized as a biologically-based discipline aimed at the study of overt behaviour. Two of its main features are presented and discussed: its historical character and its protective nature. The first is a direct result of its being based upon evolutionary principles, emphasizing the adaptive character of behaviour and tracing back its origins and causation to phylogenetic adaptation and ontogenetic modification. The protective aspect is contrasted with other approaches--reflective theories--which adding a predominant role in the causation of behaviour to environmental influences. Within ethological theory the distinction is made between peristolabile and peristostable behaviours on the basis of their liability to environmental modification during individual development. For psychiatric research, ethological concepts are relevant both from a methodological and a theoretical standpoint. Their usefulness in comparative, transcultural and psychophysiologic studies is pointed out, as well as their applicability to research on human non-verbal communication and implicit behaviour. The contention is advanced that they provide an integrative framework of reference which combined with other approaches may permit the development of a comprehensive theory of human behaviour.

Anthropology, Cultural↗

PubMed1984

Laughter.

Knowledge of laughter, other than of its clinical manifestations, is tenuous. A unique, ubiquitous human phenomenon, laughter has largely been neglected by medical investigators and relegated to philosophers and naturalists, particularly Darwin. Clinical manifestations are well described, but the many physiological changes accompanying laughter are not. Neurological pathways remain speculative, and those described are based on pathological evidence. Laughter, as a behavior, has many causes, including humor, incongruity, relief, and a sense of well-being. Laughter may have developed for its cathartic effects and adaptive value. As an evolutionary device, laughter may have served to thwart aggression, spread information, and preserve social unity. Laughter's potential for a variety of clinical uses awaits future investigation.

Adolescent↗

PubMed2004

Evolutionary expressed sequence tag analysis of Drosophila female reproductive tracts identifies genes subjected to positive selection.

Genes whose products are involved in reproduction include some of the fastest-evolving genes found within the genomes of several organisms. Drosophila has long been used to study the function and evolutionary dynamics of genes thought to be involved in sperm competition and sexual conflict, two processes that have been hypothesized to drive the adaptive evolution of reproductive molecules. Several seminal fluid proteins (Acps) made in the Drosophila male reproductive tract show evidence of rapid adaptive evolution. To identify candidate genes in the female reproductive tract that may be involved in female-male interactions and that may thus have been subjected to adaptive evolution, we used an evolutionary bioinformatics approach to analyze sequences from a cDNA library that we have generated from Drosophila female reproductive tracts. We further demonstrate that several of these genes have been subjected to positive selection. Their expression in female reproductive tracts, presence of signal sequences/transmembrane domains, and rapid adaptive evolution indicate that they are prime candidates to encode female reproductive molecules that interact with rapidly evolving male Acps.

Animals↗

PubMed2025

The evolutionary trajectories and gene regulatory roles of nuclear-integrated plastid DNA: clues for enhancing environmental adaptation in Caryophyllales.

Environmental stimuli can induce the transfer of chloroplast DNA to the nuclear genome, resulting in nuclear-integrated plastid DNAs (NUPTs). However, their role in plant adaptability remains unclear. Species within the Caryophyllales order, known for their adaptation to extreme environments, provide an ideal model for studying the evolutionary dynamics and functions of NUPTs. In this study, we analyzed NUPTs in 24 Caryophyllales species to investigate their evolution and regulatory roles in gene expression, particularly in response to environmental stimuli. We found significant interspecies variation in NUPT abundance, ranging from 566 insertions in Amaranthus cruentus to 3585 in Beta vulgaris, with sizes spanning from 100 bp to over 100 kb. Approximately 62% of NUPTs were inserted within the last 20 million years, while some species exhibit insertion peaks dating back 49 million years. NUPT presence/absence polymorphisms in six related species suggest that NUPT insertions and deletions are dynamic processes influenced by phylogeny. NUPTs predominantly integrate into intergenic regions but also insert into genes and promoters, with certain regions acting as hotspots. Notably, NUPTs introduce numerous environmental-responsive cis-acting elements in promoter regions. Genes with NUPT insertions in their promoters are significantly enriched for functions related to environmental response. Further luciferase assays in Spinacia oleracea demonstrated that NUPT insertions can regulate the expression of genes related to environmental responses, indicating their potential role in adaptive evolution. Overall, our study provides insights into NUPT evolution and their influence on gene function and plant adaptability to environmental stimuli.

Plastids↗

PubMed2000

Embodiment of evolutionary computation in general agents.

Holland's Adaptation in Natural and Artificial Systems largely dealt with how systems, comprised of many self-interested entities, can and should adapt as a whole. This seminal book led to the last 25 years of work in genetic algorithms (GAs) and related forms of evolutionary computation (EC). In recent years, the expansion of the Internet, other telecommunications technologies, and other large scale networks have led to a world where large numbers of semi-autonomous software entities (i.e., agents) will be interacting in an open, universal system. This development cast the importance of Holland's legacy in a new light. This paper argues that Holland's fundamental arguments, and the years of developments that have followed, have a direct impact on systems of general network agents, regardless of whether they explicitly exploit EC. However, it also argues that the techniques and theories of EC cannot be directly transferred to the world of general agents (rather than EC-specific) without examination of effects that are embodied in general software agents. This paper introduces a framework for EC interchanges between general-purpose software agents. Preliminary results are shown that illustrate the EC effects of asynchronous actions of agents within this framework. Building on this framework, coevolutionary agents that interact in a simulated producer/consumer economy are introduced. Using these preliminary results as illustrations, areas for future investigation of embodied EC software agents are discussed.

Algorithms↗

PubMed2002

Radiation hormesis: challenging LNT theory via ecological and evolutionary considerations.

Ecological and evolutionary considerations suggest that radiation hormesis is made up of two underlying components. The first (a) is background radiation hormesis based upon the background exposure to which all organisms are subjected throughout evolutionary time. The second and much larger component (b) is stress-derived radiation hormesis arising as a protective mechanism derived from metabolic adaptation to environmental stresses throughout evolutionary time especially from climate-based extremes. Since (b) > > (a), hormesis for ionizing radiation becomes an evolutionary expectation at exposures substantially exceeding background. This biological model renders linear no-threshold theory invalid. Accumulating evidence from experimental organisms ranging from protozoa to rodents, and from demographic studies on humans, is consistent with this interpretation. Although hormesis is not universally accepted, the model presented can be subjected to hypothesis-based empirical investigations in a range of organisms. At this stage, however, two consequences follow from this evolutionary model: (1) hormesis does not connote a value judgement usually expressed as a benefit; and (2) there is an emerging and increasingly convincing case for reviewing and relaxing some recommended radiation protection exposure levels in the low range.

Adaptation, Physiological↗

PubMed2005

Adaptive evolution of eye degeneration in the Mexican blind cavefish.

The evolutionary mechanisms responsible for eye degeneration in cave-adapted animals have not been resolved. Opposing hypotheses invoking neural mutation or natural selection, each with certain genetic and developmental expectations, have been advanced to explain eye regression, although little or no experimental evidence has been presented to support or reject either theory. Here we review recent developmental and molecular studies in the teleost Astyanax mexicanus, a single species consisting of a sighted surface-dwelling form (surface fish) and many blind cave-dwelling forms (cavefish), which shed new light on this problem. The manner of eye development and degeneration, the ability to experimentally restore eyes, gene expression patterns, and comparisons between different cavefish populations all provide important clues for understanding the evolutionary forces responsible for eye degeneration. A key discovery is that Hedgehog midline signaling is expanded and inhibits eye formation by inducing lens apoptosis in cavefish embryos. Accordingly, eyes could have been lost by default as a consequence of natural selection for constructive traits, such as feeding structures, which are positively regulated by Hh signaling. We conclude from these studies that eye degeneration in cavefish may be caused by adaptive evolution and pleiotropy.

Adaptation, Physiological↗

PubMed2005

The evolution of mutation rate in finite asexual populations.

In this article, we model analytically the evolution of mutation rate in asexual organisms. Three selective forces are present. First, everything else being equal, individuals with higher mutation rate have a larger fitness, thanks to the energy and time saved by not replicating DNA accurately. Second, as a flip side, the genome of these individuals is replicated with errors that may negatively affect fitness. Third, and conversely, replication errors have a potential benefit if beneficial mutations are to be generated. Our model describes the fate of modifiers of mutation rate under the three forces and allows us to predict the long-term evolutionary trajectory of mutation rate. We obtain three major results. First, in asexuals, the needs for both adaptation and genome preservation are not evolutionary forces that can stabilize mutation rate at an intermediate optimum. When adaptation has a significant role, it primarily destabilizes mutation rate and yields the emergence of strong-effect mutators. Second, in contrast to what is usually believed, the appearance of modifiers with large mutation rate is more likely when the fitness cost of each deleterious mutation is weak, because the cost of replication errors is then paid after a delay. Third, in small populations, and even if adaptations are needed, mutation rate is always blocked at the minimum attainable level, because the rate of adaptation is too slow to play a significant role. Only populations whose size is above a critical mass see their mutation rate affected by the need for adaptation.

Adaptation, Physiological↗

PubMed2025

Genomic analysis of xerophyte Salweenia species provides insights into the alpine dry-warm valleys divergence and survival history.

Salweenia species are evergreen shrubs capable of preventing desertification and maintaining the health of alpine dry-warm ecosystems in the Hengduan Mountains. However, both the narrowly distributed S. bouffordiana and its more widespread close relative S. wardii are endemic and endangered. Furthermore, their small population sizes render each of these species at risk of extinction. To infer how past climate changes have shaped the evolutionary history of these species, we developed a chromosome-level S. bouffordiana genome (788 Mb) and compared the two species' evolutionary histories, genetic loads and the genomic adaptions to local environmental conditions using whole-genome resequencing data. Our findings reveal a sharp population decline from the Pliocene to the Quaternary. However, populations of S. bouffordiana then started to recover before declining further, while S. wardii populations continued to decline until recently. Abundant homozygous-derived variants accumulated in the two species, particularly in S. bouffordiana, while the species with the most heterozygous variants was S. wardii. Accumulated extensive inbreeding effects but possessed few LOF mutations and few highly deleterious variants in the S. bouffordiana that have experienced the most severe demographic bottlenecks, most likely because of purging effects. This accelerating decline cascade will likely be detrimental to the consequences for the species' future viability and adaptive potential. Overall, this study improves our understanding of the evolutionary history of Salweenia shrubs tolerant to extreme environments and offers a genetic resource for future breeding and conservation efforts.

Genome, Plant↗

PubMed2001

The hormetic zone: an ecological and evolutionary perspective based upon habitat characteristics and fitness selection.

Fitness varies nonlinearly with environmental variables such as temperature, water availability, and nutrition, with maximum fitness at intermediate levels between more stressful extremes. For environmental agents that are highly toxic at exposures that substantially exceed background levels, fitness is maximized at concentrations near zero--a phenomenon often referred to as hormesis. Two main components are suggested: (1) background hormesis, which derives from the direct adaptation of organisms to their habitats; and (2) stress-derived hormonesis, which derives from metabolic reserves that are maintained as an adaptation to environmental stresses through evolutionary time. These reserves provide protection from lesser correlated stresses. This article discusses illustrative examples, including ethanol and ionizing radiation, aimed at placing hormesis into an ecological and evolutionary context. A unifying approach comes from fitness-stress continua that underlie responses to abiotic variables, whereby selection for maximum metabolic efficiency and hence fitness in adaptation to habitats in nature underlies hormetic zones. Within this reductionist model, more specific metabolic mechanisms to explain hormesis are beginning to emerge, depending upon the agent and the taxon in question. Some limited research possibilities based upon this evolutionary perspective are indicated.

Adaptation, Physiological↗