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PubMed2006

Two types of transmembrane homomeric interactions in the integrin receptor family are evolutionarily conserved.

Integrins are heterodimers, but recent in vitro and in vivo experiments suggest that they are also able to associate through their transmembrane domains to form homomeric interactions. Two fundamental questions are the biological relevance of these aggregates and their form of interaction in the membrane domain. Although in vitro experiments have shown the involvement of a GxxxG-like motif, several crosslinking in vivo data are consistent with an almost opposite form of interaction between the transmembrane alpha-helices. In the present work, we have explored these two questions using molecular dynamics simulations for all available integrin types. We have tested the hypothesis that homomeric interactions are evolutionary conserved, and essential for the cell, using conservative substitutions to filter out nonnative interactions. Our results show that two models, one involving a GxxxG-like motif (model I) and an almost opposite form of interaction (model II) are conserved across all alpha and beta integrin types, both in homodimers and homotrimers, with different specificities. No conserved interaction was found for homotetramers. Our results are completely independent from experimental data, both during molecular dynamics simulations and in the selection of the correct models. We rationalize previous seemingly conflicting findings regarding the nature of integrin interhelical homomeric interactions.

Amino Acid Motifs↗
PubMed2025

Amino Acid Substitutions in the Na+/K+-ATPase May Contribute to Salinity Tolerance in Insects.

Environmental salinity levels vary naturally across terrestrial ecosystems but can be heightened locally by coastal proximity and desertification as well as human activities such as road salt application and agriculture. Since salt is essential for many physiological processes in insects, rising environmental sodium concentrations may drive behavioral changes, where insects select environments and food sources with suitable sodium levels, or evolutionary changes in constitutive or plastic physiological mechanisms to process salt, potentially altering ecological dynamics and species interactions.Numerous hematophagous (blood feeding) insects such as the yellow-fever mosquito Aedes aeqypti are known to be able to breed in relatively saline environments. Among phytophagous (plant feeding) insects, grasshoppers can be important herbivores in arid and coastal salt-affected regions, whereas the monarch butterfly (Danaus plexippus) appears to perform relatively well on milkweed host plants growing in roadsides influenced by salt runoff. Several of these insects share a common trait: amino acid substitutions in the first extracellular loop of the Na+/K+-ATPase (NKA), a sodium pump crucial for maintaining ion balance. For the monarch these substitutions confer resistance to toxic cardenolides from milkweeds, but it is unclear whether NKA substitutions may influence salt tolerance.Here, we investigate whether the NKA substitutions found in these insects may contribute to salt tolerance using gene-edited Drosophila melanogaster mutant strains as models. We show that flies with substitution Q111L (found in Aedes mosquitoes) or a combination of Q111L and A119S (found in grasshoppers) exhibited greater salt tolerance, whereas flies carrying the combination of substitutions found in the monarch (Q111V, A119S, and N122H) did not.Our results suggest that the monarch may rely on alternate mechanisms for salt tolerance and that its NKA substitutions are important primarily for cardenolide resistance. However, substitution Q111L and the combination of Q111L and A119S may be relevant for salt tolerance in a variety of insects. Uncovering mechanisms of salt tolerance enhances our understanding of species distributions, ecological interactions, and evolutionary physiology in response to changing environmental salinity levels.

Journal Article↗
PubMed2004

Selection for gene clustering by tandem duplication.

In prokaryotic genomes, related genes are frequently clustered in operons and higher-order arrangements that reflect functional context. Organization emerges despite rearrangements that constantly shuffle gene and operon order. Evidence is presented that the tandem duplication of related genes acts as a driving evolutionary force in the origin and maintenance of clusters. Gene amplification can be viewed as a dynamic and reversible regulatory mechanism that facilitates adaptation to variable environments. Clustered genes confer selective benefits via their ability to be coamplified. During evolution, rearrangements that bring together related genes can be selected if they increase the fitness of the organism in which they reside. Similarly, the benefits of gene amplification can prevent the dispersal of existing clusters. Examples of frequent and spontaneous amplification of large genomic fragments are provided. The possibility is raised that tandem gene duplication works in concert with horizontal gene transfer as interrelated evolutionary forces for gene clustering.

Benzoates↗
PubMed2025

Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories.

Tumor evolution is driven by various mutational processes, ranging from single-nucleotide variants (SNVs) to large structural variants (SVs) to dynamic shifts in DNA methylation. Current short-read sequencing methods struggle to accurately capture the full spectrum of these genomic and epigenomic alterations due to inherent technical limitations. To overcome that, here we introduce an approach for long-read sequencing of single-cell derived subclones, and use it to profile 23 subclones of a mouse melanoma cell line, characterized with distinct growth phenotypes and treatment responses. We develop a computational framework for harmonization and joint analysis of different variant types in the evolutionary context. Uniquely, our framework enables detection of recurrent amplifications of putative driver genes, generated by independent SVs across different lineages, suggesting parallel evolution. In addition, our approach revealed gradual and lineage-specific methylation changes associated with aggressive clonal phenotypes. We also show our set of phylogeny-constrained variant calls along with openly released sequencing data can be a valuable resource for the development of new computational methods.

Journal Article↗
PubMed2000

Managing Environmental Stress: An Evaluation of Environmental Management of the Long Point Sandy Barrier, Lake Erie, Canada.

/ This paper assesses the extent to which key geomorphic components, processes, and stresses have been reflected in the management of a coastal sandy barrier environment. The management policies and practices of selected agencies responsible for Long Point, a World Biosphere Reserve along Lake Erie, Canada, were evaluated for consistency with these principles of environmental management for sandy barriers: maintaining natural stresses essential to sandy barrier development and maintenance;protecting sediment sources, transfers, and storage; recognizing spatial variability and cyclicity of natural stresses, such as barrier overwash events; and accepting and planning for long-term evolutionary changes in the sandy barrier environment. Generally, management policies and practices have not respected the dynamic and sensitive environment of Long Point because of limited mandates of the agencies involved, inconsistent policies, and failure to apply or enforce existing policies. This is particularly evident with local municipalities and less so for the Canadian Wildlife Service, the federal agency responsible for managing National Wildlife Areas at the point. In the developed areas of Long Point, landward sediment transfers and sediment storage in dunes have been impacted by cottage development, shore protection, and maintenance of roads and parking lots. Additionally, agencies responsible for managing Long Point have no jurisdiction over sediment sources as far as 95 km away. Evolutionary change of sandy barriers poses the greatest challenge to environmental managers.

Journal Article↗
PubMed1990

Retrovirus phylogeny and evolution.

The elucidation of complete genomic sequences from a wide variety of retroviruses and retrotransposons has allowed the construction of sequence-based phylogenies that reveal their evolutionary history. True retroviruses, whether exogenous or endogenous, tend to cluster into four major groups. Not only is there no distinction between exogenous and endogenous viruses, but their evolutionary limb lengths on the phylogenetic trees are comparable. This can be taken as evidence favoring a dynamic equilibrium balancing a constant invasion of germlines by infectious retroviruses on the one hand, with subsequent escape of endogenous viruses to alternative hosts on the other. Retroviruses share a common ancestry with a wide variety of retrotransposons and other reverse transcriptase-bearing entities. One of these retrotransposon groups, the Gypsy group, resembles the Moloney mouse group of retroviruses much more closely than it does other retroviruses. The simplest explanation is that the evolutionary rate of the retrotransposon is much slower than the retrovirus rate and that among the retroviruses the Moloney mouse group has been evolving more slowly than the other three groups, leaving the two short-limbed taxa more similar. The alternative explanation that these two groups actually shared a common ancestor more recently than has either with the other retrovirus groups is not supported by residue-by-residue character assessment.

Animals↗
PubMed2006

Genealogy of the nuclear beta-fibrinogen locus in a highly structured lizard species: comparison with mtDNA and evidence for intragenic recombination in the hybrid zone.

The study of nuclear genealogies in natural populations of nonmodel organisms is expected to provide novel insights into the evolutionary history of populations, especially when developed in the framework of well-established mtDNA phylogeographical scenarios. In the Iberian Peninsula, the endemic Schreiber's green lizard Lacerta schreiberi exhibits two highly divergent and allopatric mtDNA lineages that started to split during the late Pliocene. In this work, we performed a fine-scale analysis of the putative mtDNA contact zone together with a global analysis of the patterns of variation observed at the nuclear beta-fibrinogen intron 7 (beta-fibint7). Using a combination of DNA sequencing with single-strand conformational polymorphism (SSCP) analysis, we show that the observed genealogy at the beta-fibint7 locus reveals extensive admixture between two formerly isolated lizard populations while the two mtDNA lineages remain essentially allopatric. In addition, a private beta-fibint7 haplotype detected in the single population where both mtDNA lineages were found in sympatry is probably the result of intragenic recombination between the two more common and divergent beta-fibint7 haplotypes. Our results suggest that the progressive incorporation of nuclear genealogies in investigating the ancient demography and admixture dynamics of divergent genomes will be necessary to obtain a more comprehensive picture of the evolutionary history of organisms.

Animals↗
PubMed2000

The formal nature of emergent biological organization and its implications for understandings of closure.

This paper shows how recognition of biological form, of which the dynamics of closure is an integral part, is mandated by research on autopoietic systems, self-organization, evolutionary theory, and on topics in a variety of other areas, including infant and child development. It shows how a "matter pure and simple" (a mechanical concept of nature) is inimical to veridical understandings and explanations of emergent organization from the level of cells to the level of intact organisms--animate forms. By means of an analysis and discussion of writings by prominent researchers in diverse fields, a brief inquiry into neuron firing, and a consideration of intrinsic dynamics and primal animation, this paper shows that a principle of motion or animation informs biological nature. In other words, the fundamentally dynamic character of biological form at all levels exemplifies the kinetic character of living matter. The final section of this paper pinpoints implications for closure, emphasizing the need for an acknowledgement of the dynamics of closure and the need for theoretical and biological reformulations of living systems that incorporate that dynamics. It exemplifies the implication in each instance with reference to authors represented in this volume.

Biological Evolution↗
PubMed2006

Strong linkage disequilibrium near the selected Yr17 resistance gene in a wheat experimental population.

Dynamic management (DM) is a method of genetic resources conservation that aims at maintaining evolutionary process in subdivided populations cultivated in contrasted environments. Such populations are often submitted to strong natural selection as it was the case for experimental wheat populations maintained under DM. Understanding impacts of selection on genetic diversity around selected genes is necessary for the middle-term maintenance of genetic variability in DM populations. Evolution of diversity at six neutral markers located near the yellow rust resistance gene Yr17 has been studied for the parental lines and for generations 1, 5, 10 and 17 in one of the DM populations. Yr17 provided complete resistance to yellow rust in France until 1997 and thus was suspected to be under strong selection. The gene is located on a fragment introgressed in winter wheat from a wild species. The presence of the gene was estimated using a marker closely related to the gene. We showed that the Yr17 gene has been selected between generations 5 and 10. Generally, selection tends to reduce diversity around selected genes, generating linkage disequilibrium (LD) between a gene and adjacent markers. Here, the major effect of the Yr17 gene selection was a reduction of multilocus diversity and the maintenance of strong pre-existing LD in the zone surrounding the gene for a distance of 20 cM. As expected, the presence of the exogenous introgression was responsible for restrictions to recombination which contributed to the maintenance of strong correlations between loci. However, we found a noticeable number of recombinations around the gene indicating a progressive incorporation of the fragment into the wheat genome.

Alleles↗
PubMed2005

Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: functional and evolutionary implications.

The combined knowledge of the Arabidopsis genome and transcriptome now allows to get an integrated view of the dynamics and evolution of metabolic pathways in plants. We used publicly available sets of microarray data obtained in a wide range of different stress and developmental conditions to investigate the co-expression of genes encoding enzymes of secondary metabolism pathways, in particular indoles, phenylpropanoids, and flavonoids. We performed hierarchical clustering of gene expression profiles and found that major enzymes of each pathway display a clear and robust co-expression throughout all the conditions studied. Moreover, detailed analysis evidenced that some genes display co-regulation in particular physiological conditions only, certainly reflecting their modular recruitment into stress- or developmentally regulated biosynthetic pathways. The combination of these microarray data with sequence analysis allows to draw very precise hypotheses on the function of otherwise uncharacterized genes. To illustrate this approach, we focused our analysis on secondary metabolism glycosyltransferases (UGTs), a multigenic family involved in the conjugation of small molecules to sugars like glucose. We propose that UGT74B1 and UGT74C1 may be involved in aromatic and aliphatic glucosinolates synthesis, respectively. We also suggest that UGT75C1 may function as an anthocyanin-5-O-glucosyltransferase in planta. Therefore, this data-mining approach appears very powerful for the functional prediction of unknown genes, and could be transposed to virtually any other gene family. Finally, we suggest that analysis of expression pattern divergence of duplicated genes also provides some insight into the mechanisms of metabolic pathway evolution.

Arabidopsis↗
PubMed2004

The evolution of vocabulary.

Human language is unique among the communication systems of the natural world. The vocabulary of human language is unique in being both culturally transmitted and symbolic. In this paper I present an investigation into the factors involved in the evolution of such vocabulary systems. I investigate both the cultural evolution of vocabulary systems and the biological evolution of learning rules for vocabulary acquisition. Firstly, vocabularies are shown to evolve on a cultural time-scale so as to fit the expectations of learners-a population's vocabulary adapts to the biases of the learners in that population. A learning bias in favour of one-to-one mappings between meanings and words leads to the cultural evolution of communicatively optimal vocabulary systems, even in the absence of any explicit pressure for communication. Furthermore, the pressure to conform to the biases of learners is shown to outweigh natural selection acting on cultural transmission. Human language learners appear to bring a one-to-one bias to the acquisition of vocabulary systems. The functionality of human vocabulary may therefore be a consequence of the biases of human language learners. Secondly, the evolutionary stability of genetically transmitted vocabulary learning biases is investigated using both static and dynamic models. A one-to-one learning bias, which leads to the cultural evolution of optimal communication, is shown to be evolutionarily stable. However, the evolution de novo of this bias is complicated by the cumulative nature of the cultural evolution of vocabulary systems. This suggests that the biases of human language learners may not have evolved specifically and exclusively for the acquisition of communicatively functional vocabulary.

Cultural Evolution↗
PubMed2002

Life-long stability of neurons: a century of research on neurogenesis, neuronal death and neuron quantification in adult CNS.

In this chapter we provide an extensive review of 100 years of research on the stability of neurons in the mammalian brain, with special emphasis on humans. Although Cajal formulated the Neuronal Doctrine, he was wrong in his beliefs that adult neurogenesis did not occur and adult neurons are dying throughout life. These two beliefs became accepted "common knowledge" and have shaped much of neuroscience research and provided much of the basis for clinical treatment of age-related brain diseases. In this review, we consider adult neurogenesis from a historical and evolutionary perspective. It is concluded, that while adult neurogenesis is a factor in the dynamics of the dentate gyrus and olfactory bulb, it is probably not a major factor during the life-span in most brain areas. Likewise, the acceptance of neuronal death as an explanation for normal age-related senility is challenged with evidence collected over the last fifty years. Much of the problem in changing this common belief of dying neurons was the inadequacies of neuronal counting methods. In this review we discuss in detail implications of recent improvements in neuronal quantification. We conclude: First, age-related neuronal atrophy is the major factor in functional deterioration of existing neurons and could be slowed down, or even reversed by various pharmacological interventions. Second, in most cases neuronal degeneration during aging is a pathology that in principle may be avoided. Third, loss of myelin and of the white matter is more frequent and important than the limited neuronal death in normal aging.

Aging↗
PubMed1999

Landscape approaches to historical and contemporary gene flow in plants.

Growing interest in metapopulation dynamics and dispersal at a landscape level is promoting new approaches to the study of contemporary gene flow. These approaches have been fostered by the development of new genetic markers and statistical methods, as well as an awareness that contemporary gene flow cannot be reliably estimated by conventional methods based on genetic structure. Estimation of the spatial and temporal dynamics of pollen and seed movement with respect to extant landscape features can aid evolutionary and conservation biologists in predicting the demographic and genetic responses of species to naturally occurring or human-mediated population subdivision.

Journal Article↗
PubMed2001

Protein functional epitopes: hot spots, dynamics and combinatorial libraries.

Recent studies increasingly point to the importance of structural flexibility and plasticity in proteins, highlighting the evolutionary advantage. There are an increasing number of cases in which given, presumably specific, binding sites have been shown to bind a range of ligands with different compositions and shapes. These studies have also revealed that evolution tends to find convergent solutions for stable intermolecular associations, largely via conservation of polar residues as hot spots of binding energy. On the other hand, the ability to bind multiple ligands at a given site is largely derived from hinge-based motions. The consideration of these two factors in functional epitopes allows more realism and robustness in the description of protein binding surfaces and, as such, in applications to mutants, modeled structures and design. Efficient multiple structure comparison and hinge-bending structure comparison tools enable the construction of combinatorial binding epitope libraries.

Combinatorial Chemistry Techniques↗
PubMedDate not supplied

The scale independence of evolution.

In this paper, I argue that the ultimate causes of morphological, and hence developmental, evolution are scale independent. In other words, micro- and macroevolutionary patterns show fundamental similarities and therefore are most simply explained as being caused by the same kinds of evolutionary forces. I begin by examining the evolution of single lineages and argue that dynamics of adaptive evolution are the same for bacteria in test-tube evolution experiments and fossil lineages. Similarly, I argue that the essential features of adaptive radiations large and small can be attributed to conventional forces such as mutation and diversifying natural selection due to competition. I then address recent claims that the molecular features of metazoan development are the result of clade-level selection for evolvability, and suggest that these features can be more easily explained by conventional individual-level selection for the suppression of deleterious pleiotropic effects. Finally, I ask what must be known if we are to understand the ultimate causes of molecular and developmental diversity.

Biological Evolution↗
PubMed2002

Host range and local parasite adaptation.

Parasites may be expected to become locally adapted to their hosts. However, while many empirical studies have demonstrated local parasite adaptation, others have failed to demonstrate it, or have shown local parasite maladaptation. Researchers have suggested that gene flow can swamp local parasite-host dynamics and produce local adaptation only at certain geographical scales; others have argued that evolutionary lags can account for both null and maladaptive results. In this paper, we use item response theory (IRT) to test whether host range influences the likelihood of parasites locally adapting to their hosts. We collated 32 independent experiments testing for local adaptation, where parasites could be assigned as having either broad or narrow host ranges (BHR and NHR, respectively). Twenty-five tests based on BHR parasites had a significantly lower average effect size than seven NHR tests, indicating that studies based on BHR parasites are less likely to demonstrate local parasite adaptation. We argue that this may relate to evolutionary lags during diffuse coevolution of BHR parasites with their hosts, rather than differences in experimental approaches or other confounds between BHR and NHR studies.

Adaptation, Physiological↗
PubMed2003

Time-dependent random walks and the theory of complex adaptive systems.

Motivated by novel results in the theory of complex adaptive systems, we analyze the dynamics of random walks in which the jumping probabilities are time dependent. We determine the survival probability in the presence of an absorbing boundary. For an unbiased walk, the survival probability is maximized in the case of large temporal oscillations in the jumping probabilities. On the other hand, a random walker who is drifted towards the absorbing boundary performs best with a constant jumping probability. We use the results to reveal the underlying dynamics responsible for the phenomenon of self-segregation and clustering observed in the evolutionary minority game.

Adaptation, Biological↗
PubMed2007

Conservation, convergence, and divergence of light-responsive, circadian-regulated, and tissue-specific expression patterns during evolution of the Arabidopsis GATA gene family.

In vitro analyses of plant GATA transcription factors have implicated some proteins in light-mediated and circadian-regulated gene expression, and, more recently, the analysis of mutants has uncovered further diverse roles for plant GATA factors. To facilitate function discovery for the 29 GATA genes in Arabidopsis (Arabidopsis thaliana), we have experimentally verified gene structures and determined expression patterns of all family members across adult tissues and suspension cell cultures, as well as in response to light and signals from the circadian clock. These analyses have identified two genes that are strongly developmentally light regulated, expressed predominantly in photosynthetic tissue, and with transcript abundance peaking before dawn. In contrast, several GATA factor genes are light down-regulated. The products of these light-regulated genes are candidates for those proteins previously implicated in light-regulated transcription. Coexpression of these genes with well-characterized light-responsive transcripts across a large microarray data set supports these predictions. Other genes show additional tissue-specific expression patterns suggesting novel and unpredicted roles. Genome-wide analysis using coexpression scatter plots for paralogous gene pairs reveals unexpected differences in cocorrelated gene expression profiles. Clustering the Arabidopsis GATA factor gene family by similarity of expression patterns reveals that genes of recent descent do not uniformly show conserved current expression profiles, yet some genes showing more distant evolutionary origins have acquired common expression patterns. In addition to defining developmental and environmental dynamics of GATA transcript abundance, these analyses offer new insights into the evolution of gene expression profiles following gene duplication events.

Amino Acid Motifs↗