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PubMed1998

Hierarchical and cybernetic nature of biologic systems and their relevance to homeostatic adaptation to low-level exposures to oxidative stress-inducing agents.

During evolution in an aerobic environment, multicellular organisms survived by adaptive responses to both the endogenous oxidative metabolism in the cells of the organism and the chemicals and low-level radiation to which they had been exposed. The defense repertoire exists at all levels of the biological hierarchy--from the molecular and biochemical level to the cellular and tissue level to the organ and organ system level. Cells contain preventive antioxidants to suppress oxidative damage to membranes. Cells also contain proteins and DNA; built-in redundancies for damaged molecules and organelles; tightly coupled redox systems; pools of reductants; antioxidants; DNA repair mechanisms and sensitive sensor molecules such as nuclear factor kappa beta; and signal transduction mechanisms affecting both transcription and post-translational modification of proteins needed to cope with oxidative stress. The biologic consequences of the low-level radiation that exceeds the background level of oxidative damage could be necrosis or apoptosis, cell proliferation, or cell differentiation. These effects are triggered by oxidative stress-induced signal transduction mechanisms--an epigenetic, not genotoxic, process. If the end points of cell proliferation, differentiation, or cell death are not seen at frequencies above background levels in an organism, it is unlikely that low-level radiation would play a role in the multistep processes of chronic diseases such as cancer. The mechanism linked to homeostatic regulation of proliferation and adaptive functions in a multicellular organism could provide protection of any one cell receiving deposited energy by the radiation tract through the sharing of reductants and by triggering apoptosis of target stem cells. Examples of the role of gap junctional intercellular communication in the adaptive response of cells and the bystander effect illustrate how the interaction of cells can modulate the effect of radiation on the single cell.

Adaptation, Physiological↗
PubMed2001

Thermal hysteresis proteins.

Extreme environments present a wealth of biochemical adaptations. Thermal hysteresis proteins (THPs) have been found in vertebrates, invertebrates, plants, bacteria and fungi and are able to depress the freezing point of water (in the presence of ice crystals) in a non-colligative manner by binding to the surface of nascent ice crystals. The THPs comprise a disparate group of proteins with a variety of tertiary structures and often no common sequence similarities or structural motifs. Different THPs bind to different faces of the ice crystal, and no single mechanism has been proposed to account for THP ice binding affinity and specificity. Experimentally THPs have been used in the cryopreservation of tissues and cells and to induce cold tolerance in freeze susceptible organisms. THPs represent a remarkable example of parallel and convergent evolution with different proteins being adapted for an anti-freeze role.

Adaptation, Biological↗
PubMed2001

Adaptation of autocatalytic fluctuations to diffusive noise.

Evolution of a system of diffusing and proliferating mortal reactants is analyzed in the presence of randomly moving catalysts. While the continuum description of the problem predicts reactant extinction as the average growth rate becomes negative, growth rate fluctuations induced by the discrete nature of the agents are shown to allow for an active phase, where reactants proliferate as their spatial configuration adapts to the fluctuations of the catalyst density. The model is explored by employing field theoretical techniques, numerical simulations, and strong coupling analysis. For d< or =2, the system is shown to exhibits an active phase at any growth rate, while for d>2 a kinetic phase transition is predicted. The applicability of this model as a prototype for a host of phenomena that exhibit self-organization is discussed.

Journal Article↗
PubMed2005

Variable domains and a VpreB-like molecule are present in a jawless vertebrate.

Immunoglobulins (Igs) and T cell antigen receptors (TCRs) that undergo somatic diversification have not been identified in the two extant orders of jawless vertebrates, which occupy essential positions in terms of understanding the evolution of the emergence of adaptive immunity. Using a single motif-dependent PCR-based approach coupled with a vector that allows selection of cDNAs encoding secretion signal sequences, four different genes encoding Ig V-type domains were identified in the sea lamprey (Petromyzon marinus). One of the predicted proteins encoded by these genes shares structural characteristics with mammalian VpreB molecules, including the absence of a recognizable transmembrane region, a relatively high proportion of charged amino acids in its C-terminal tail and distinctive features of its secretion signal peptide. This is the first indication of a molecule related to the B cell receptor (BCR) complex in a species that diverged prior to the jawed vertebrates in which RAG-mediated adaptive immunity is first encountered.

Amino Acid Sequence↗
PubMed2005

Missense meanderings in sequence space: a biophysical view of protein evolution.

Proteins are finicky molecules; they are barely stable and are prone to aggregate, but they must function in a crowded environment that is full of degradative enzymes bent on their destruction. It is no surprise that many common diseases are due to missense mutations that affect protein stability and aggregation. Here we review the literature on biophysics as it relates to molecular evolution, focusing on how protein stability and aggregation affect organismal fitness. We then advance a biophysical model of protein evolution that helps us to understand phenomena that range from the dynamics of molecular adaptation to the clock-like rate of protein evolution.

Adaptation, Biological↗
PubMed2000

What determines the rate of sequence evolution?

High rates of amino-acid sequence evolution have sometimes been considered to be diagnostic for genes undergoing adaptive change. However, two recent studies have shown that rapid evolution of amino-acid sequence can also be congruent with neutrality.

Adaptation, Physiological↗
PubMed2025

Subgenomic divergence and functional innovation following whole-genome duplication in Maleae species of Rosaceae.

Whole-genome duplication (WGD) drives plant evolution by inducing karyotype rearrangements and gene loss through subgenome fractionation. In this study, we investigate post-WGD evolutionary dynamics in Rosaceae, focusing on Maleae species, which uniquely experienced an additional WGD. Using phylogenetic and synteny analyses, we reveal that chromosomal breakpoints act as hotspots for localized fractionation, contributing to blurred homoeologous origins and influencing gene retention patterns. Here, we reconstruct karyotype evolution across Rosaceae subfamilies, highlighting chromosome reductions and lineage-specific rearrangements in Dryadoideae, Rosoideae, and Amygdaloideae. We also identify a bias for retaining transcription factors and hormone-related genes from older WGDs in subsequent polyploidy events. Transcriptome analysis classifies WGD-derived genes in Maleae species, such as apple and loquat, into three expression groups, with hormone-enriched genes playing roles in lignification and fruit-related innovations. These findings demonstrate the interplay between chromosomal breakpoints, biased retention, and functional divergence, revealing their contributions to genomic and phenotypic evolution in Maleae and their adaptive success within Rosaceae.

Genome, Plant↗
PubMed1983

Climate and the evolution of brachycephalization.

Significant associations of cranial shape for 82 ethnic groups and seven climate variables are described. Variation among current populations is partially attributed to cold adaptation throughout the Pleistocene. Application of data files tabulated by the authors is described for a number of problems. Temporal distribution of 115 specimens indicates a geometric trend (CI = 76.7-1.96 log time X 10(3) ). Cranial indices are summarized within alternative taxonomic models and between climatic ecotypes. Evidence supports the hypothesis of cold adaptation among "Classic" Neandertals. Limitations of the thermodynamic model are discussed. It is probable that a decrease of the cranial index occurs from the Middle to Upper Paleolithic. During the Holocene, the index increases under all climatic conditions.

Adaptation, Biological↗
PubMed2004

Human birthweight evolution across contrasting environments.

We explore from both theoretical and empirical perspectives the hypothesis that a significant part of the worldwide variability in human birthweight results from adaptive responses to local selective pressures. We first developed an agent-based model to simulate the process of evolutionary selection on life history strategy, and then we performed a comparative analysis across 89 countries worldwide. The model illustrates that optimal birthweight depends on which fitness-reducing risk locally predominates (somatic diseases, parasitic diseases or adverse environmental conditions). When fitness variations between individuals mainly result from somatic diseases (e.g. industrialized countries), or conversely from infectious and parasitic diseases (e.g. developing countries), selection is expected to favour individuals producing larger children. Conversely, when environmental risks increase in relative importance, selective pressures for producing children with high birthweight are reduced. The comparative analysis supports these theoretical expectations, in particular the finding that birthweight is higher than predicted in highly parasitized countries.

Adaptation, Physiological↗
PubMed2025

Adaptation in a keystone grazer under novel predation pressure.

Understanding how species adapt to environmental change is necessary to protect biodiversity and ecosystem services. Growing evidence suggests species can adapt rapidly to novel selection pressures like predation from invasive species, but the repeatability and predictability of selection remain poorly understood in wild populations. We tested how a keystone aquatic herbivore, Daphnia pulicaria, evolved in response to predation pressure by the introduced zooplanktivore Bythotrephes longimanus. Using high-resolution 210Pb-dated sediment cores from 12 lakes in Ontario (Canada), which primarily differed in invasion status by Bythotrephes, we compared Daphnia population genetic structure over time using whole-genome sequencing of individual resting embryos. We found strong genetic differentiation between populations approximately 70 years before versus 30 years after reported Bythotrephes invasion, with no difference over this period in uninvaded lakes. Compared with uninvaded lakes, we identified, on average, 64 times more loci were putatively under selection in the invaded lakes. Differentiated loci were mainly associated with known reproductive and stress responses, and mean body size consistently increased by 14.1% over time in invaded lakes. These results suggest Daphnia populations were repeatedly acquiring heritable genetic adaptations to escape gape-limited predation. More generally, our results suggest some aspects of environmental change predictably shape genome evolution.

Animals↗
PubMed2001

Evolutionary assembly of the milkweed fauna: cytochrome oxidase I and the age of Tetraopes beetles.

The insects that feed on the related plant families Apocynaceae and Asclepiadaceae (here collectively termed "milkweeds") comprise a "component community" of highly specialized, distinctive lineages of species that frequently sequester toxic cardiac glycosides from their host plants for defense against predators and are thus often aposematic, advertising their consequent unpalatability. Such sets of specialized lineages provide opportunities for comparative studies of the rate of adaptation, diversification, and habitat-related effects on molecular evolution. The cerambycid genus Tetraopes is the most diverse of the new world milkweed herbivores and the species are generally host specific, being restricted to single, different species of Asclepias, more often so than most other milkweed insects. Previous work revealed correspondence between the phylogeny of these beetles and that of their hosts. The present study provides analyses of near-complete DNA sequences for Tetraopes and relatives that are used to establish a molecular clock and temporal framework for Tetraopes evolution with their milkweed hosts.

Adaptation, Physiological↗
PubMed1999

The genomics of adaptation in yeast.

A recent study has combined methods of experimental evolution and DNA microarray technology to examine evolved changes in gene expression in yeast, providing intriguing insights into the genetics of adaptation and functional genomics, and pointing to future uses of microarray technology in evolutionary genetics.

Adaptation, Physiological↗
PubMed2004

Beyond Arabidopsis. Translational biology meets evolutionary developmental biology.

Developmental processes shape plant morphologies, which constitute important adaptive traits selected for during evolution. Identifying the genes that act in developmental pathways and determining how they are modified during evolution is the focus of the field of evolutionary developmental biology, or evo-devo. Knowledge of genetic pathways in the plant model Arabidopsis serves as the starting point for investigating how the toolkit of developmental pathways has been used and reused to form different plant body plans. One productive approach is to identify genes in other species that are orthologous to genes known to control developmental pathways in Arabidopsis and then determine what changes have occurred in the protein coding sequence or in the gene's expression to produce an altered morphology. A second approach relies on natural variation among wild populations or crop plants. Natural variation can be exploited to identify quantitative trait loci that underlie important developmental traits and, thus, define those genes that are responsible for adaptive changes. The possibility of applying comparative genomics approaches to Arabidopsis and related species promises profound new insights into the interplay of evolution and development.

Arabidopsis↗
PubMed1992

Acid secretion, 1932-92: advances, adaptations, and paradoxes.

This paper reviews the evolution of our understanding of various aspects of gastric acid secretion over the past 60 years. Embryologic aspects and neonatal acid secretion are considered, and the relationship between parietal cell mass and acid secretion and the changing concepts of parietal cell activation are discussed. The effect of aging on acid secretion and the relevance of acid secretion in health and disease are reviewed, and current views on adaptation to therapeutic inhibition of acid secretion presented. The aetiologic link between acid secretion and ulcer disease is re-examined, and the role of pepsin, growth factors, and Helicobacter pylori briefly considered.

Adaptation, Physiological↗
PubMed2026

Nuclear DNA of plastid origin (NUPTs), neglected driver of genome variation and evolutionary innovation.

Plant nuclear genomes contain a variable, though typically minor, fraction of DNA sequences of plastid origin known as NUPTs. Unlike the massive transfer of DNA and genes from the proto-organelle genome to the nucleus that occurred during the endosymbiotic event that gave rise to plastids, the formation of NUPTs is an ongoing process that does not imply concomitant DNA loss. Although NUPTs are generally considered to be potentially deleterious insertions that are continuously generated and rapidly eliminated at near-constant turnover rates, accumulating evidence reveals alternative evolutionary trajectories. In this review, we discuss recent findings that highlight the episodic formation of NUPTs, their subsequent proliferation, and their eventual long-term fixation within the nuclear genome. We also explore their non-random spatial association with specific genomic elements. NUPTs show preferential overlap with specific superfamilies of transposable elements, which may facilitate their proliferation and dispersal throughout the nuclear genome. Regarding protein-coding genes, the contribution of NUPTs varies among species. In contrast, NUPTs are found to be consistently enriched among certain classes of non-coding RNA genes, notably rRNA, tRNA, and specific regulatory RNA families, suggesting that they are involved in the evolution of gene regulation and translational machinery. Overall, these findings underscore the unexpected complexity of the mechanisms underlying NUPT formation and support the idea that they are a significant source of genome variation and evolutionary innovation. Further research is necessary to fully elucidate the mechanisms underlying NUPT formation, as well as to determine their potential adaptive significance in plant genome evolution.

Plastids↗
PubMed2005

Adaptation and incipient sympatric speciation of Bacillus simplex under microclimatic contrast at "Evolution Canyons" I and II, Israel.

The microevolutionary dynamics of prokaryotes in natural habitats, such as soil, is poorly understood in contrast to our increasing knowledge on their immense diversity. We performed microevolutionary analyses on 945 soil isolates of Bacillus simplex from "Evolution Canyons" I (Carmel, Israel) and II (Galilee, Israel). These canyons represent similar ecological replicates, separated by 40 km, with highly contrasting interslope abiotic and biotic conditions in each (within a distance of only 100-400 m). Strains representing genetic groups were identical in their 16S sequences, suggesting high genetic similarity and monophyletic origin. Parallel and nested phylogenetic structures correlated with ecological contrasts rather than geographical distance. Additionally, slope-specific populations differed substantially in their diversity. The levels of DNA repair (determined by UV sensitivity) and spontaneous mutation rate (resistance to rifampicin) relate to ecological stress and phylogeny. Altogether, the results suggest adaptive radiation at a microscale. We discuss the observed adaptive population structures in the context of incipient sympatric speciation in soil bacteria. We conclude that, despite different biology, prokaryotes, like sexually reproducing eukaryotes, may consist of true species and parallel ecological speciation in eukaryotes.

Adaptation, Physiological↗