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PubMed2005

Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication.

Human subtelomeres are polymorphic patchworks of interchromosomal segmental duplications at the ends of chromosomes. Here we provide evidence that these patchworks arose recently through repeated translocations between chromosome ends. We assess the relative contribution of the principal mechanisms of ectopic DNA repair to the formation of subtelomeric duplications and find that non-homologous end-joining predominates. Once subtelomeric duplications arise, they are prone to homology-based sequence transfers as shown by the incongruent phylogenetic relationships of neighbouring sections. Interchromosomal recombination of subtelomeres is a potent force for recent change. Cytogenetic and sequence analyses reveal that pieces of the subtelomeric patchwork have changed location and copy number with unprecedented frequency during primate evolution. Half of the known subtelomeric sequence has formed recently, through human-specific sequence transfers and duplications. Subtelomeric dynamics result in a gene duplication rate significantly higher than the genome average and could have both advantageous and pathological consequences in human biology. More generally, our analyses suggest an evolutionary cycle between segmental polymorphisms and genome rearrangements.

Animals↗
PubMed2003

Early hominin speciation at the Plio/Pleistocene transition.

Over the last half-decade or so, there has been an explosion in the recognition of hominin genera and species. We now have the late Miocene genera Orrorin and Sahelanthropus, the mid Pliocene genus Kenyanthropus, three new Pliocene species of Australopithecus (A. anamensis, A. garhi and A. bahrelghazali) and a sub species of Ardipithecus (Ar. r. kadabba) to contend with. Excepting also the more traditional species allocated to Paranthropus, Australopithecus and early Homo we are approaching around 15 species over 5 million years (excluding hominin evolution over the last one million years). Can such a large number of hominin species be justified? An examination of extant hominid (Gorilla gorilla, Pan troglodytes, and Pan paniscus) anatomical variability indicates that the range of fossil hominin variability supports the recognition of this large number of fossil species. It is also shown that not all hominins are directly related to the emergence of early Homo and as such have become extinct. Indeed the traditional australopithecine species 'A'. anamensis, 'A'. afarensis and 'A'. garhi are considered here to belong to a distinct genus Praeanthropus. They are also argued not be hominins, but rather an as yet undefined hominid group from which the more derived hominins evolved. The first hominin is represented by A. africanus or a hominin very much like it. The Paranthropus clade is defined by a derived heterochronic condition of peramorphosis, associated with sequential progenesis (contraction of successive growth stages) in brain and dental development, but a mixture of peramorphic and paedomorphic features in its craniofacial anatomy. Conversely, Kenyanthropus and Homo both share a pattern of peramorphosis, associated with sequential hypermorphosis (prolongation of successive growth stages) in brain development, and paedomorphosis processes in cranial, facial and dental development. This suggests, that these two clades share an important synapomorphy not recognised in the parsimony analyses, suggesting that they may form a sister group relationship to the exclusion of Paranthropus. This highlights the need to re-interpret phylogenetic results in terms of function and development. The rapid speciation and extinction as argued here is in keeping with other fossil groups in Africa at the Plio/Pleistocene transition. This emphasises that we must approach the pre-australopithecines and hominins as part of the endemic African fauna, and not in isolation to the evolutionary and climatic processes that were operating all around them.

Africa↗
PubMed2000

Competition and the Effect of Spatial Resource Heterogeneity on Evolutionary Diversification.

A model is presented to explore how the form of selection arising from competition for resources is affected by spatial resource heterogeneity. The model consists of a single species occupying two patches connected by migration, where the two patches can differ in the type of resources that they contain. The main goal is to determine the conditions under which competition for resources results in disruptive selection (i.e., selection favoring a polymorphism) since it is this form of selection that will give rise to the evolutionary diversification of resource exploitation strategies. In particular, comparing the conditions giving rise to disruptive selection when the two patches are identical to the conditions when they contain different resources reveals the effect of spatial resource heterogeneity. Results show that when the patches are identical, the conditions giving rise to disruptive selection are identical to those that give rise to character displacement in previous models. When the patches are different, the conditions giving rise to disruptive selection can be either more or less stringent depending upon demographic parameters such as the intrinsic rate of increase and the migration rate. Surprisingly, spatial resource heterogeneity can actually make forms of evolutionary diversification such as character displacement less likely. It is also found that results are dependent on how the resource exploitation strategies and the spatial resource heterogeneity affect the population dynamics. One robust conclusion however, is that spatial resource heterogeneity always has a disruptive effect when the migration rate between patches is low.

Journal Article↗
PubMed2000

Competition and the Effect of Spatial Resource Heterogeneity on Evolutionary Diversification.

A model is presented to explore how the form of selection arising from competition for resources is affected by spatial resource heterogeneity. The model consists of a single species occupying two patches connected by migration, where the two patches can differ in the type of resources that they contain. The main goal is to determine the conditions under which competition for resources results in disruptive selection (i.e., selection favoring a polymorphism) since it is this form of selection that will give rise to the evolutionary diversification of resource exploitation strategies. In particular, comparing the conditions giving rise to disruptive selection when the two patches are identical to the conditions when they contain different resources reveals the effect of spatial resource heterogeneity. Results show that when the patches are identical, the conditions giving rise to disruptive selection are identical to those that give rise to character displacement in previous models. When the patches are different, the conditions giving rise to disruptive selection can be either more or less stringent depending upon demographic parameters such as the intrinsic rate of increase and the migration rate. Surprisingly, spatial resource heterogeneity can actually make forms of evolutionary diversification such as character displacement less likely. It is also found that results are dependent on how the resource exploitation strategies and the spatial resource heterogeneity affect the population dynamics. One robust conclusion however, is that spatial resource heterogeneity always has a disruptive effect when the migration rate between patches is low.

Lotka‐Volterra↗
PubMed1990

The ecology and evolution of inducible defenses.

Inducible defenses are responses activated through a previous encounter with a consumer or competitor that confer some degree of resistance to subsequent attacks. While the importance of inducible resistance has long been known in host-parasite interactions, it is only recently that its importance has emerged in other natural systems. Although the structural defenses produced by invertebrates to their competitors and predators are by no means the same as an immune response triggered by parasites, these responses all share the properties of (1) specificity, (2) amplification and (3) memory. This review discusses the following ecological consequences and evolutionary causes of inducible defenses: (1) Inducible defenses render historical factors important in biological interactions and can affect the probability of individual survival and growth, as well as affect population dynamics of consumers in some circumstances. (2) Although the benefits of inducible defenses are often balanced by fitness costs, including reduced growth, reproductive output and survivorship, the role of costs and benefits in the evolution of inducible defenses is by no means clear. A more integrated approach would involve a multivariate analysis of the role of natural selection on the inducible characters of interest, their norms of reaction and correlated fitness characters. (3) The disproportionate representation of inducible, morphological defenses among clonal organisms may be due to both a higher rate of origination and enhanced selection to maintain these defenses in clonal taxa. (4) Inducible defenses should be most common when reliable cues are available, attacks by biological agents are unpredictable, and the fitness gains of defenses are balanced by the costs. An integrated approach to studying inducible defenses would thus combine mechanistic estimates of costs, population-level estimates of defense effectiveness, and genetic estimates of correlations between fitness and inducible characters. This will allow us to estimate rates of evolution in these phenotypically plastic threshold characters.

Animals↗
PubMed2003

Evolutionary characteristics of HIV type 1 variants resistant to protease inhibitors in the absence of drug-selective pressure.

To understand the evolutionary characteristics of HIV-1 variants resistant to protease inhibitors (PI), the replicating plasma virus was analyzed in three patients shifted to PI-sparing regimen after virological failure. The dynamic features of carryover mutations associated with PI resistance in the absence of selective pressure on the protease gene indicate that viral variants resistant to reverse transcriptase inhibitors and bearing mutations of the protease sequence can maintain efficient replication capacity in vivo.

Drug Resistance, Viral↗
PubMed2006

Evolution of the Rho family of ras-like GTPases in eukaryotes.

GTPases of the Rho family are molecular switches that play important roles in converting and amplifying external signals into cellular effects. Originally demonstrated to control the dynamics of the F-actin cytoskeleton, Rho GTPases have been implicated in many basic cellular processes that influence cell proliferation, differentiation, motility, adhesion, survival, or secretion. To elucidate the evolutionary history of the Rho family, we have analyzed over 20 species covering major eukaryotic clades from unicellular organisms to mammals, including platypus and opossum, and have reconstructed the ontogeny and the chronology of emergence of the different subfamilies. Our data establish that the 20 mammalian Rho members are structured into 8 subfamilies, among which Rac is the founder of the whole family. Rho, Cdc42, RhoUV, and RhoBTB subfamilies appeared before Coelomates and RhoJQ, Cdc42 isoforms, RhoDF, and Rnd emerged in chordates. In vertebrates, gene duplications and retrotranspositions increased the size of each chordate Rho subfamily, whereas RhoH, the last subfamily, arose probably by horizontal gene transfer. Rac1b, a Rac1 isoform generated by alternative splicing, emerged in amniotes, and RhoD, only in therians. Analysis of Rho mRNA expression patterns in mouse tissues shows that recent subfamilies have tissue-specific and low-level expression that supports their implication only in narrow time windows or in differentiated metabolic functions. These findings give a comprehensive view of the evolutionary canvas of the Rho family and provide guides for future structure and evolution studies of other components of Rho signaling pathways, in particular regulators of the RhoGEF family.

Amino Acid Sequence↗
PubMed2004

Scale development in fish: a review, with description of sonic hedgehog (shh) expression in the zebrafish (Danio rerio).

In the first part of this paper we review current knowledge regarding fish scales, focusing on elasmoid scales, the only type found in two model species, the zebrafish and the medaka. After reviewing the structure of scales and their evolutionary origin, we describe the formation of the squamation pattern. The regularity of this process suggests a pre-patterning of the skin before scale initiation. We then summarise the dynamics of scale development on the basis of morphological observations. In the absence of molecular data, these observations support the existence of genetic cascades involved in the control of scale development. In the second part of this paper, we illustrate the potential that scale development offers as a model to study organogenesis mediated by epithelial-mesenchymal interactions. Using the zebrafish (Danio rerio), we have combined alizarin red staining, light and transmission electron microscopy and in situ hybridisation using an anti-sense RNA probe for the sonic hedgehog (shh) gene. Scales develop late in ontogeny (30 days post-fertilisation) and close to the epidermal cover. Only cells of the basal epidermal layer express shh. Transcripts are first detected after the scale papillae have formed. Thus, shh is not involved in the mechanisms controlling squamation patterning and scale initiation. As the scales enlarge, shh expression is progressively restricted to a subset of basal epidermal cells located in the region that overlies their posterior field. This pattern of expression suggests that shh may be involved in the control of scale morphogenesis and differentiation in relationship with the formation of the epidermal fold in the posterior region.

Animals↗
PubMed1988

Immunoregulation in murine malaria. Susceptibility of inbred mice to infection with Plasmodium yoelii depends on the dynamic interplay of host and parasite genes.

Inbred and H-2 congenic mouse strains were tested for their ability to resist infections with the non-lethal 17X or with the lethal YM isolates of Plasmodium yoelii. DBA/2 and B10.D2 mice, which best resisted infections with non-lethal P. yoelii, were exquisitely susceptible to infection with lethal isolates of this malaria species. In contrast, B6 and B10 mice, which were susceptible to infection with non-lethal P. yoelii, were resistant to infection with the lethal isolates. This reversal of host response phenotype was influenced by H-2 genes, as evidenced by the divergent responses of the H-2 congenic strains B10 and B10.D2. However, a survey of mouse strains sharing common H-2 genes, but expressing different genetic backgrounds, demonstrated that genes outside the H-2 complex also influence the outcome of P. yoelii infections. By enumerating the numbers of P. yoelii-specific antibody-secreting cells in the spleens of infected mice, it was demonstrated that B6 mice, although susceptible to infection with non-lethal P. yoelii, nonetheless made a far stronger anti-parasite response after infection than did resistant DBA/2 mice. Using FACS analysis it was shown that infected B6 mice also produced large amounts of antibodies which bound to the surface of uninfected RBC. Thus, in B6 mice infected with non-lethal P. yoelii, a strong parasite-induced immune response was associated with susceptibility rather than resistance to infection. When T cell-deficient nude mice and their normal littermates were infected with the different isolates of P. yoelii, the nude mice had lower levels of parasitemia and higher RBC counts during the early stages of these infections, and lived longer than did normal littermates after infection with the lethal isolate. These data and the data from studies of B6 and DBA/2 mice support the idea that a strong immune response may be associated with susceptibility rather than resistance to P. yoelii, at least during the early stages of the infection. The finding that a single strain of mouse may present as resistant to infection with one P. yoelii isolate yet be exquisitely susceptible to infection with another suggests that the outcome of these murine malaria infections is dependent on a dynamic interplay between host and parasite genes. Thus, when genetic variability exists in both the host and the parasite populations, as would occur in nature, there may be little directed evolutionary change toward one phenotype or another.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2004

Evolutionary optimization with data collocation for reverse engineering of biological networks.

MOTIVATION: Modern experimental biology is moving away from analyses of single elements to whole-organism measurements. Such measured time-course data contain a wealth of information about the structure and dynamic of the pathway or network. The dynamic modeling of the whole systems is formulated as a reverse problem that requires a well-suited mathematical model and a very efficient computational method to identify the model structure and parameters. Numerical integration for differential equations and finding global parameter values are still two major challenges in this field of the parameter estimation of nonlinear dynamic biological systems. RESULTS: We compare three techniques of parameter estimation for nonlinear dynamic biological systems. In the proposed scheme, the modified collocation method is applied to convert the differential equations to the system of algebraic equations. The observed time-course data are then substituted into the algebraic system equations to decouple system interactions in order to obtain the approximate model profiles. Hybrid differential evolution (HDE) with population size of five is able to find a global solution. The method is not only suited for parameter estimation but also can be applied for structure identification. The solution obtained by HDE is then used as the starting point for a local search method to yield the refined estimates.

Algorithms↗
PubMed1998

[Structural, dynamic and interaction studies of proteins: the example of immunology].

The three-dimensional structure of a protein or of one of its functional domains cannot be predicted simply from the amino-acid sequence. It has to be determined either in the crystal, generally by X-ray diffraction, or in solution by high resolution NMR, or it can be modelled by comparison with a highly homologous protein. It cannot be represented simply by an average set of atomic coordinates. The dynamics of the molecule is part of its definition. The relative role of the structure and of the local and segmental mobility will be illustrated for recognition processes, mainly in immunological reactions. A unique conformational domain, member of the immunoglobulin superfamily, recognises differently its partners for an antigen-antibody reaction or for a cell adhesion process involving immunological determinants such as CD2 or CD4. Similar structural domains can be observed for completely different amino acid sequences, with the same type of dynamical properties, e.g. in neocarzinostatin. Restrained mobility of CDR loops and water molecules participation at the interface can explain the rapid binding of the ligands in AG/AB reactions, but cellular adhesion involves more hydrophobic and rigid interactions. This difference can be related to evolutionary aspects. Recognition mechanisms in cellular immunology, e.g. that of an intracellular foreign viral protein by a T lymphocyte cell, involve rather different biochemical processes in the so-called "peptidic self" model including proteolysis and cell surface presentation of the resulting peptides by MHC Class I proteins. These complexes are then recognised by the T cell receptors. The binding site of the TCR alpha and beta chains are structurally related to the antigen binding site of immunoglobulins. The peptide is anchored at both C- and N-terminals and should possess a restrained mobility. Recognition is thus a similar structural and dynamical process as in AG/AB reactions but is more secure due to the larger number of epitopes for a single protein.

Antigen-Antibody Reactions↗
PubMed2025

Conserved HSFA1-dependent chromatin dynamics drive heat stress responses in plants.

Eukaryotic organisms remodel chromatin landscapes to regulate gene expression in response to environmental stress. In plants, heat stress (HS) induces widespread chromatin changes, yet the role of heat shock transcription factors (HSFs) in chromatin remodeling and their evolutionary conservation remains unclear. Using Marchantia polymorpha Mphsf mutants and Arabidopsis thaliana Athsfa1s mutants, we identify HSFA1 as a key regulator of HS-induced cis-regulatory element (CRE) accessibility, a mechanism conserved across land plants, mice, and humans. Gene regulatory network modeling reveals parallel transcription factor subnetworks, with MpWRKY10 and MpABI5B acting as indirect and negative HS regulators. We further showed that ABA modulates gene expression in an HSFA1-dependent manner without inducing chromatin remodeling. Finally, we develop a machine learning framework integrating chromatin accessibility and CRE information to predict gene expression across species, revealing stress-responsive regulatory logic at the transcriptional level. These findings provide insights into how TFs coordinate chromatin architecture to drive stress adaptation.

Heat-Shock Response↗
PubMed2004

The evolution dynamics of model proteins.

Explicit simulations of protein evolution, where protein chains are described at a molecular, although simplified, level provide important information to understand the similarities found to exist between known proteins. The results of such simulations suggest that a number of evolutionary-related quantities, such as the distribution of sequence similarity for structurally similar proteins, are controlled by evolutionary kinetics and do not reflect an equilibrium state. An important result for phylogeny is that a subset of the residues of each protein evolve on a much larger time scale than the other residues.

Journal Article↗
PubMedDate not supplied

From wheels to wings with evolutionary spiking circuits.

We give an overview of the EPFL indoor flying project, whose goal is to evolve neural controllers for autonomous, adaptive, indoor micro-flyers. Indoor flight is still a challenge because it requires miniaturization, energy efficiency, and control of nonlinear flight dynamics. This ongoing project consists of developing a flying, vision-based micro-robot, a bio-inspired controller composed of adaptive spiking neurons directly mapped into digital microcontrollers, and a method to evolve such a neural controller without human intervention. This article describes the motivation and methodology used to reach our goal as well as the results of a number of preliminary experiments on vision-based wheeled and flying robots.

Action Potentials↗
PubMed2006

Cancer progression by non-clonal chromosome aberrations.

The establishment of the correct conceptual framework is vital to any scientific discipline including cancer research. Influenced by hematologic cancer studies, the current cancer concept focuses on the stepwise patterns of progression as defined by specific recurrent genetic aberrations. This concept has faced a tough challenge as the majority of cancer cases follow non-linear patterns and display stochastic progression. In light of the recent discovery that genomic instability is directly linked to stochastic non-clonal chromosome aberrations (NCCAs), and that cancer progression can be characterized as a dynamic relationship between NCCAs and recurrent clonal chromosome aberrations (CCAs), we propose that the dynamics of NCCAs is a key element for karyotypic evolution in solid tumors. To support this viewpoint, we briefly discuss various basic elements responsible for cancer initiation and progression within an evolutionary context. We argue that even though stochastic changes can be detected at various levels of genetic organization, such as at the gene level and epigenetic level, it is primarily detected at the chromosomal or genome level. Thus, NCCA-mediated genomic variation plays a dominant role in cancer progression. To further illustrate the involvement of NCCA/CCA cycles in the pattern of cancer evolution, four cancer evolutionary models have been proposed based on the comparative analysis of karyotype patterns of various types of cancer.

Animals↗
PubMed1998

Ecological mechanisms of evolution by natural selection: causal processes generating density-and-frequency dependent fitness.

The current theory of natural selection explains that adaptive evolution occurs because genotypes with greater survival or reproductive tendencies, due to their particular biological properties, tend to increase in frequency over the lesser ones in a common environment; therefore, the former will eventually replace the latter. In nature, such a selection process most often occurs in a local population which is nested in a community involving local ecological dynamics which are not clearly articulated in the explanatory scheme of the theory. This paper seeks to explicate such an ecological process giving rise to the evolution of a local population with a particular focus on dynamic effects of an increase in the number of invasive, new types on the fate of old ones. Arguments using the ecological-mechanistic model, representing negative interactions among alternative types of organisms, suggest major ecological mechanisms by which the new replace the old; a selective increase in the number of one type leads to a decrease in the equilibrial abundance of a limiting resource, an increase in the density of conspecifics, and/or an increase in the density of predators, which would in turn lower the per capita reproductive rate, or raise the morality rate of another and make it extinct. Thus, replacement due to selection is associated with such dynamic shifts in equilibria occurring in a local community. The analysis of three (a resource, a prey and a predator) and four species (those plus a top predator) models suggests that evolutionary processes cannot be predicted without reference to the web structure of the community, that some fitness components causing a selective increase in a particular type can have, in some cases, nothing to do with factors causing selective decreases in alternatives, and that evolution of some traits can occur without resource competition.

Animals↗
PubMed1976

Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA.

The problem of choosing an alignment of two or more nucleotide sequences is particularly difficult for nucleic acids, such as 5S ribosomal RNA, which do not code for protein and for which secondary structure is unknown. Given a set of 'costs' for the various types of replacement mutations and for base insertion or deletion, we present a dynamic programming algorithm which finds the optimal (least costly) alignment for a set of N sequences simultaneously, where each sequence is associated with one of the N tips of a given evolutionary tree. Concurrently, protosequences are constructed corresponding to the ancestral nodes of the tree. A version of this algorithm, modified to be computationally feasible, is implemented to align the sequences of 5S RNA from nine organisms. Complete sets of alignments and protosequence reconstructions are done for a large number of different configurations of mutation costs. Examination of the family of curbes of total replacements inferred versus the ratio of transitions/transversions inferred, each curve corresponding to a given number of insertions-deletions inferred, provides a method for estimating relative costs and relative frequencies for these different types of mutations.

Base Sequence↗
PubMed2006

Selective stabilization and synaptic specificity: a new cell-biological model.

How are appropriate connections between neurons sorted from the overwhelming surplus of potential, yet inappropriate, connections? Despite the apparently improbable nature of the process, brains wire themselves with a high degree of reproducibility that has been conserved across evolutionary history. Here, we outline a viable cell-biological model for generating synaptic specificity that features selection of nascent synapses based on adhesion and recognition. This process uses the highly dynamic and stochastic nature of intracellular trafficking to generate reproducible patterns of synaptic connectivity.

Animals↗