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PubMed2003

Statistical decision theory and evolution.

Two recent articles by Geisler and Diehl use Bayesian statistical decision theory to model the co-evolution of predator and prey in a simple, game-like environment. The prey is characterized by its coloration. The predator is characterized by the chromatic sensitivity of its visual system and its willingness to attack. The authors demonstrate how the coloration of prey and the perceptual system of the predator co-evolve, converging to a Nash equilibrium for both species.

Journal Article↗

PubMed2003

Evaluation of the long-term corrosion behavior of dental amalgams: influence of palladium addition and particle morphology.

OBJECTIVES: The purpose of this investigation was to evaluate the long-term corrosion behavior of experimental amalgams as a function of particle morphology and palladium content. METHODS: Samples of four experimental high copper amalgams were prepared according to ADA specifications. Two of them had the same chemical composition but one had lathe cut particles (LCP) and the other had spherical particles (SP). The two others had spherical powders with an addition of 0.5 wt% of palladium (SP 0.5) and 1 wt% of palladium(SP 1) for the other. Corrosion resistance was evaluated by electrochemical techniques in Ringer's solution in a thermostated cell at 37 degrees C for samples aged 5, 8, 12, 16 months and 10 years. Potentiokinetic curves were drawn and the potential and the current density corresponding to the first anodic peak were registered. RESULTS: For all the amalgam samples the corrosion behavior improves over the 10-year period. SP samples exhibit a better behavior than LCP. Palladium addition improves corrosion behavior as compared to samples without palladium. No real difference is found regarding the amount of palladium between 0.5 and 1%. The potentials progress from a range between 0 and 20 mV/SCE to a range of 60-80 after 10 years. The stabilization of the potential begins after only 16 months. Except for the LCP, all the values converge to the same level of 80 mV/SCE. SIGNIFICANCE: The addition of no more than 0.5 wt% Palladium in a high copper amalgam powder improves the corrosion behavior of the amalgam up to a period of 10 years. The potential of the first anodic peak increases for each amalgam, probably in relation to the evolution of the structure of the material. Clinically, it is of interest to consider the good electrochemical behavior of older restorations when contemplating the repair or replacement of such fillings. At the same time, galvanic current can occur when a new amalgam restoration is placed in contact with an old one even if the same amalgam is used. In this situation, the new filling will be anodic and its degradation will be accelerated. The evaluation of the corrosion behavior of dental amalgams has to take into account the age of the samples.

Copper↗

PubMed1985

Nucleotide sequence encoding the biosynthetic dehydroquinase function of the penta-functional arom locus of Aspergillus nidulans.

The nucleotide sequence of a 1.9 Kb HindIII fragment of DNA derived from the arom locus of A.nidulans and encoding the biosynthetic dehydroquinase activity has been determined. The sequences encoding the biosynthetic and catabolic dehydroquinase enzymes of A.nidulans show no detectable homology, strongly suggesting convergent evolutionary pathways. The messenger RNA specified by the arom locus was detected as a 5.3 Kb RNA species.

Aspergillus nidulans↗

PubMed2026

Plant cis-regulatory grammar: Decoding the multidimensional code of transcriptional regulation for programmable crop engineering.

Cis-regulatory elements (CREs) orchestrate the spatiotemporal precision of gene expression that underlies plant development, adaptation, and domestication. Decoding the cis-regulatory grammar of plant genomes remains a central challenge in modern biology, with profound implications for programmable crop engineering. Here, recent conceptual and technological advances are synthesized to reshape our understanding of plant CREs. This review first argues that CRE function is not only an intrinsic property of DNA sequence alone but also emerges from a multidimensional context, including chromatin accessibility, histone modifications, three-dimensional genome topology, and cell type-specific regulatory landscapes. Furthermore, the convergence of single-cell epigenomics, high-throughput functional assays, and CRISPR-based dissection has begun to unravel this contextual grammar, revealing the computational principles governing transcriptional regulation. Critically, we propose that artificial intelligence (AI) platforms are catalyzing an ongoing transition from descriptive discovery to predictive engineering, wherein these platforms outperform natural evolution in designing synthetic CREs. Finally, a roadmap is outlined toward a plant regulatory grammar foundation model, which will enable truly predictive engineering of gene expression when fine-tuned for specific tasks. Collectively, the integration of single-cell resolution maps, precise genome editing, AI-driven design, and regulatory-compliant delivery systems promises to transform our ability to reprogram plant gene regulation for next-generation agriculture, bridging the gap between foundational regulatory biology and tangible crop improvement.

artificial intelligence↗

PubMed2004

Codon usage and bias in mitochondrial genomes of parasitic platyhelminthes.

Sequences of the complete protein-coding portions of the mitochondrial (mt) genome were analysed for 6 species of cestodes (including hydatid tapeworms and the pork tapeworm) and 5 species of trematodes (blood flukes and liver- and lung-flukes). A near-complete sequence was also available for an additional trematode (the blood fluke Schistosoma malayensis). All of these parasites belong to a large flatworm taxon named the Neodermata. Considerable variation was found in the base composition of the protein-coding genes among these neodermatans. This variation was reflected in statistically-significant differences in numbers of each inferred amino acid between many pairs of species. Both convergence and divergence in nucleotide, and hence amino acid, composition was noted among groups within the Neodermata. Considerable variation in skew (unequal representation of complementary bases on the same strand) was found among the species studied. A pattern is thus emerging of diversity in the mt genome in neodermatans that may cast light on evolution of mt genomes generally.

Amino Acid Sequence↗

PubMed2004

Morphological evolution in sea urchin development: hybrids provide insights into the pace of evolution.

Hybridisations between related species with divergent ontogenies can provide insights into the bases for evolutionary change in development. One example of such hybridisations involves sea urchin species that exhibit either standard larval (pluteal) stages or those that develop directly from embryo to adult without an intervening feeding larval stage. In such crosses, pluteal features were found to be restored in fertilisations of the eggs of some direct developing sea urchins (Heliocidaris erythrogramma) with the sperm of closely (Heliocidaris tuberculata) and distantly (Pseudoboletia maculata) related species with feeding larvae. Such results can be argued to support the punctuated equilibrium model-conservation in pluteal regulatory systems and a comparatively rapid switch to direct development in evolution.1,2 Generation of hybrids between distantly related direct developers may, however, indicate evolutionary convergence. The 'rescue' of pluteal features by paternal genomes may require maternal factors from H. erythrogramma because the larva of this species has pluteal features. In contrast, pluteal features were not restored in hybridisations with the eggs of Holopneustes purpurescens, which lacks pluteal features. How much of pluteal development can be lost before it cannot be rescued in such crosses? The answer awaits hybridisations among indirect and direct developing sea urchins differing in developmental phenotype, in parallel with investigations of the genetic programs involved.

Animals↗

PubMed2005

Environmental tolerance, heterogeneity, and the evolution of reversible plastic responses.

Phenotypic plasticity is a key factor for the success of organisms in heterogeneous environments. Although many forms of phenotypic plasticity can be induced and retracted repeatedly, few extant models have analyzed conditions for the evolution of reversible plasticity. We present a general model of reversible plasticity to examine how plastic shifts in the mode and breadth of environmental tolerance functions (that determine relative fitness) depend on time lags in response to environmental change, the pattern of individual exposure to inducing and noninducing environments, and the quality of available information about the environment. We couched the model in terms of prey-induced responses to variable predation regimes. With longer response lags relative to the rate of environmental change, the modes of tolerance functions in both the presence or absence of predators converge on a generalist strategy that lies intermediate between the optimal functions for the two environments in the absence of response lags. Incomplete information about the level of predation risk in inducing environments causes prey to have broader tolerance functions even at the cost of reduced maximal fitness. We give a detailed analysis of how these factors and interactions among them select for joint patterns of mode and breadth plasticity.

Adaptation, Biological↗

PubMed1998

Structure and evolution of parallel beta-helix proteins.

Three bacterial pectate lyases, a pectin lyase from Aspergillus niger, the structures of rhamnogalacturonase A from Aspergillus aculeatus, RGase A, and the P22-phage tailspike protein, TSP, display the right-handed parallel beta-helix architecture first seen in pectate lyase. The lyases have 7 complete coils while RGase A and TSP have 11 and 12, respectively. Each coil contains three beta-strands and three turn regions named PB1, T1, PB2, T2, PB3, and T3 in their order of occurrence. The lyases have homologous sequences but RGase A and TSP do not show obvious sequence homology either to the lyases or to each other. However, the structural similarities between all these molecules are so extensive that divergence from a common ancestor is much more probable than convergence to the same fold. The region PB2-T2-PB3 is the best conserved region in the lyases and shows the clearest structural similarity. Not only is the pleating and the direction of the hydrogen bonding in the sheets conserved, but so is the unusual alphaL-conformation turn between the two sheets. However, the overall shape, the position of long loops, a conserved alpha-helix that covers the amino-terminal end of the parallel beta-helix and stacks of residues in alphaR-conformation at the start of PB1 all suggest a common ancestor. The functional similarity, that the enzymes all bind alpha-galactose containing polymers at an equivalent site involving PB1 and its two flanking turn regions, further supports divergent evolution. We suggest that the stacking of the coils and the unusual near perpendicular junction of PB2 and PB3 make the parallel beta-helix fold especially likely to maintain similar main chain conformations during divergent evolution even after all vestige of similarity in primary structure has vanished.

Amino Acid Sequence↗

PubMed1995

The evolution of protamine P1 genes in dasyurid marsupials.

We report the complete DNA sequences of the protamine P1 gene and flanking regions for 13 species of the marsupial family Dasyuridae. The structure of the protamine locus is conserved in dasyurids and consists of two exons (of lengths 142-151 and 47 bp) separated by an intron (208-240 bp). A key feature of the dasyurid intron is a 38-40 bp duplication found in all species examined to date. This duplication apparently predates the radiation of modern dasyurid lineages and may be homologous to a similar feature in the marsupial mole (Notoryctes). Sequences from a species of Planigale demonstrate that this genus is unique among marsupials in possessing cysteine residues in its protamine P1 molecules. Cysteines may provide enhanced chemical stability for condensed sperm nuclei, a physiological feature that would converge on the common eutherian pattern. Phylogenetic analysis of the protamine genes yields a tree that is largely congruent with previous molecular systematic studies in two areas: (1) There are three main dasyurid lineages corresponding to the Sminthopsinae. Dasyurinae, and Phascogalinae; (2) Dasyurinae and Phascogalinae are sister groups. This study is the first estimate of dasyurid relationships based on a nuclear DNA sequence.

Amino Acid Sequence↗

PubMed2002

Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution.

To study the tempo and pattern of mitochondrial gene loss in plants, DNAs from 280 genera of flowering plants were surveyed for the presence or absence of 40 mitochondrial protein genes by Southern blot hybridization. All 14 ribosomal protein genes and both sdh genes have been lost from the mitochondrial genome many times (6 to 42) during angiosperm evolution, whereas only two losses were detected among the other 24 genes. The gene losses have a very patchy phylogenetic distribution, with periods of stasis followed by bursts of loss in certain lineages. Most of the oldest groups of angiosperms are still mired in a prolonged stasis in mitochondrial gene content, containing nearly the same set of genes as their algal ancestors more than a billion years ago. In sharp contrast, other plants have rapidly lost many or all of their 16 mitochondrial ribosomal protein and sdh genes, thereby converging on a reduced gene content more like that of an animal or fungus than a typical plant. In these and many lineages with more modest numbers of losses, the rate of ribosomal protein and sdh gene loss exceeds, sometimes greatly, the rate of mitochondrial synonymous substitutions. Most of these mitochondrial gene losses are probably the consequence of gene transfer to the nucleus; thus, rates of functional gene transfer also may vary dramatically in angiosperms.

Base Sequence↗

PubMed2004

Quantification of multicontrast vascular MR images with NLSnake, an active contour model: in vitro validation and in vivo evaluation.

Vessel-wall measurements from multicontrast MRI provide information on plaque structure and evolution. This requires the extraction of numerous contours. In this work a contour-extraction method is proposed that uses an active contour model (NLSnake) adapted for a wide range of MR vascular images. This new method employs length normalization for the purpose of deformation computation and offers the advantages of simplified parameter tuning, fast convergence, and minimal user interaction. The model can be initialized far from the boundaries of the region to be segmented, even by only one pixel. The accuracy and reproducibility of NLSnake endoluminal contours were assessed on vascular phantom MR angiography (MRA) and high-resolution in vitro MR images of rabbit aorta. An in vivo evaluation was performed on rabbit and clinical data for both internal and external vessel-wall contours. In phantoms with 95% stenoses, NLSnake measured 94.3% +/- 3.8%, and the accuracy was even better for milder stenoses. In the images of rabbit aorta, variability between NLSnake and experts was less than interobserver variability, while the maximum intravariability of NLSnake was equal to 1.25%. In conclusion, the NLSnake technique successfully quantified the vessel lumen in multicontrast MR images using constant parameters.

Animals↗

PubMed1994

Cytogenetic heterogeneity in a clear cell hidradenoma of the skin.

Short-term cultures from a clear cell hidradenoma, a benign skin tumor for which no chromosome data exist, were cytogenetically analyzed. A total of eight unrelated aberrant clones were identified. The karyotypic profiles of two separately processed parts of the sample--a tumor nodule and seemingly normal adjacent dermal tissue--were different. Characteristic for the tumor nodule was a single abnormal clonal population consisting of three subclones: 46,XY,der(2)inv(2)(p13q23)t(2;9)(p13;q22), der(9)t(2;9)(q23;q22),t(11;19)(q21;p13),t(12;19)(q24;p13)/46,idem, inv(1)(p32q44)/92,idemx2. The adjacent tissue contained, in addition to the clone found in the tumor nodule, a spectrum of unrelated clones, the largest of which also showed clonal evolution: 45-47,XY,t(3;6)(p25;p25),t(12;17)(q15;q12),-17,+r(17)x2 [cp]/45-47,idem,inv(5)(p15q22)/90-94,idemx2. The remaining six clones found in this part were small and had simpler numerical or structural aberrations. The multiclonal pattern observed in this hidradenoma seems to reflect both cytogenetic convergence and divergence during neoplastic progression. The presence of unrelated clones may be an indication that the tumor was of multicellular origin.

Acrospiroma↗

PubMed2002

Structure, function and DNA composition of Saccharomyces cerevisiae chromatin loops.

Recent localization of cohesin association regions along the yeast chromatin fibre suggests that compositional variability of DNA in yeast is related to the function and organization of the chromosomal loops. The bases of the loops, where the chromatin fibre is attached to the chromosomal axis, are AT-rich, bind cohesin, and are flanked by genes transcribed convergently. The hotspots of meiotic recombination are mainly found in the GC-rich parts of the loops, 'external' with respect to the chromosomal axis, frequently in the vicinity of the promoters of divergently transcribed genes. There are two possible reasons why the regions of the hotspots of recombination were enriched in GC content during evolution. One is a biased repair of recombination intermediates, and the second is a selective advantage due to an increased chromatin accessibility, which may have the carriers of GC-enriched alleles over the carriers of AT-rich alleles.

Base Composition↗

PubMed2001

Molecular biogeography of cave life: a study using mitochondrial DNA from bathysciine beetles.

This study focuses on phylogenetic relationships in two distinct species assemblages of cave-dwelling beetles with similar disjunct distributions in the Pyrenees and Sardinia. One assemblage contains six species in the genera Ovobathysciola (four species) and Patriziella (two species) on Sardinia and one species of Anillochlamys in the Pyrenees. Species within the two Sardinian genera co-occur in the same karst area. Although, they are believed to be each others closest relative, they have very different body types (globular body with short appendages in Ovobathysciola; elongated body with long appendages in Patriziella), which are believed to reflect different degrees of adaptation to cave life. The other assemblage of Bathysciine beetles includes three species in the genus Speonomus in the Pyrenees and one on Sardinia. All the species are rare and many are endangered. One issue of particular interest was whether Ovobathysciola and Patriziella are reciprocally monophyletic or whether each of the Patriziella species evolved independently from the co-occurring Ovobathysciola species, as the similar morphology of the Patriziella species might be due to convergence rather than common descent. Based on DNA sequences of the cytochrome oxidase I (COI) region of the mtDNA, neither scenario was supported. Rather, the two Patriziella species are sister taxa embedded within the Ovobathysciola radiation. In addition, the well-dated geological history of this region allowed us to calibrate absolute rates of COI evolution, the first such estimates for any insect. Finally this study suggests that the evolutionary acquisition of typical cave adaptations (e.g., elongated body and appendages) may occur at about the same rate as loss of traits (e.g., eyes and pigmentation) associated with cave life.

Animals↗

PubMed2003

Phylogeography and introgressive hybridization: chipmunks (genus Tamias) in the northern Rocky Mountains.

If phylogeographic studies are to be broadly used for assessing population-level processes relevant to speciation and systematics, the ability to identify and incorporate instances of hybridization into the analytical framework is essential. Here, we examine the evolutionary history of two chipmunk species, Tamias ruficaudus and Tamias amoenus, in the northern Rocky Mountains by integrating multivariate morphometrics of bacular (os penis) variation, phylogenetic estimation, and nested clade analysis with regional biogeography. Our results indicate multiple examples of mitochondrial DNA introgression layered within the evolutionary history of these nonsister species. Three of these events are most consistent with recent and/or ongoing asymmetric introgression of mitochondrial DNA across morphologically defined secondary contact zones. In addition, we find preliminary evidence where a fourth instance of nonconcordant characters may represent complete fixation of introgressed mitochondrial DNA via a more ancient hybridization event, although alternative explanations of convergence or incomplete sorting of ancestral polymorphisms cannot be dismissed with these data. The demonstration of hybridization among chipmunks with strongly differentiated bacular morphology contradicts long-standing assumptions that variation within this character is diagnostic of complete reproductive isolation within Tamias. Our results illustrate the utility of phylogeographic analyses for detecting instances of reticulate evolution and for incorporating this and other information in the inference of the evolutionary history of species.

Animals↗

PubMed2001

Genetic associations under mixed mating systems: the Bennett-Binet effect.

Using elementary algebraic geometry and computational commutative algebra, supported by the program Macaulay2, we studied and developed operators that define the zygotic and gametic evolution under a mixed-mating system with parameters s selfing rate, r recombination rate, and g relative fitness of inbreeders, for any possible combination of initial zygotic or gametic frequencies with two alleles at each of two loci. We found that (i) the allelic frequencies are preserved in every generation; (ii) the gametic frequencies converge to values that depend exclusively on the allelic frequencies; (iii) every zygotic population converges to a population in equilibrium with double heterozygotes equally frequent; (iv) the rate of convergence decreases to arbitrary small values with sufficiently small values of r or with sufficiently large values of s and (v) as g decreases, the maximal 'association between the two loci' occurs with higher values of selfing. We also found generalizations for the case of several alleles at each locus.

Alleles↗

PubMed2004

Occurrence of sulfated galactans in marine angiosperms: evolutionary implications.

We report for the first time that marine angiosperms (seagrasses) possess sulfated polysaccharides, which are absent in terrestrial and freshwater plants. The structure of the sulfated polysaccharide from the seagrass Ruppia maritima was determined. It is a sulfated D-galactan composed of the following regular tetrasaccharide repeating unit: [3-beta-D-Gal-2(OSO3)-1-->4-alpha-D-Gal-1-->4-alpha-D-Gal-1-->3-beta-D-Gal-4(OSO3)-1-->]. Sulfated galactans have been described previously in red algae and in marine invertebrates (ascidians and sea urchins). The sulfated galactan from the marine angiosperm has an intermediate structure when compared with the polysaccharides from these two other groups of organisms. Like marine invertebrate galactan, it expresses a regular repeating unit with a homogenous sulfation pattern. However, seagrass galactan contains the D-enantiomer of galactose instead of the L-isomer found in marine invertebrates. Like red algae, the marine angiosperm polysaccharide contains both alpha and beta units of D-galactose; however, these units are not distributed in an alternating order, as in algal galactan. Sulfated galactan is localized in the plant cell walls, mostly in rhizomes and roots, indicative of a relationship with the absorption of nutrients and of a possible structural function. The occurrence of sulfated galactans in marine organisms may be the result of physiological adaptations, which are not correlated with phylogenetic proximity. We suggest that convergent adaptation, due to environment pressure, may explain the occurrence of sulfated galactans in many marine organisms.

Alismatales↗

PubMed1989

The hippocampal complex of food-storing birds.

Three families of North American passerines--chickadees, nuthatches and jays--store food. Previous research has shown that memory for the spatial locations of caches is the principal mechanism of cache recovery. It has also been previously shown that the hippocampal complex (hippocampus and area parahippocampalis) plays an important role in memory for cache sites. The present study determined the volume of the hippocampal complex and the telencephalon in 3 food-storing families and in 10 non-food-storing families and subfamilies of passerines. The hippocampal complex is larger in food-storing birds than in non-food-storing birds. This difference is greater than expected from allometric relations among the hippocampal complex, telencephalon and body weight. Food-storing families are not more closely related to each other than they are to non-food-storing families and subfamilies, and the greater size of the hippocampal complex in food-storing birds is therefore the result of evolutionary convergence. Natural selection has led to a larger hippocampal complex in birds that rely on memory to recover spatially dispersed food caches.

Animals↗