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PubMed1999

Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: a case for the genetic coherence of rhizobial lineages.

In prokaryotes, lateral gene transfer across chromosomal lineages may be mediated by plasmids, phages, transposable elements, and other accessory DNA elements. However, the importance of such transfer and the evolutionary forces that may restrict gene exchange remain largely unexplored in native settings. In this study, tests of phylogenetic congruence are employed to explore the range of horizontal transfer of symbiotic (sym) loci among distinct chromosomal lineages of native rhizobia, the nitrogen-fixing symbiont of legumes. Rhizobial strains isolated from nodules of several host plant genera were sequenced at three loci: symbiotic nodulation genes (nodB and nodC), the chromosomal housekeeping locus glutamine synthetase II (GSII), and a portion of the 16S rRNA gene. Molecular phylogenetic analysis shows that each locus generally subdivides strains into the same major groups, which correspond to the genera Rhizobium, Sinorhizobium, and Mesorhizobium. This broad phylogenetic congruence indicates a lack of lateral transfer across major chromosomal subdivisions, and it contrasts with previous studies of agricultural populations showing broad transfer of sym loci across divergent chromosomal lineages. A general correspondence of the three rhizobial genera with major legume groups suggests that host plant associations may be important in the differentiation of rhizobial nod and chromosomal loci and may restrict lateral transfer among strains. The second major result is a significant incongruence of nod and GSII phylogenies within rhizobial subdivisions, which strongly suggests horizontal transfer of nod genes among congenerics. This combined evidence for lateral gene transfer within, but not between, genetic subdivisions supports the view that rhizobial genera are "reproductively isolated" and diverge independently. Differences across rhizobial genera in the specificity of host associations imply that the evolutionary dynamics of the symbiosis vary considerably across lineages in native settings.

Base Sequence↗
PubMedDate not supplied

Genetic algorithm-assisted combinatorial search for a new green phosphor for use in tricolor white LEDs.

An evolutionary optimization process involving a genetic algorithm and combinatorial chemistry was employed for the development of green phosphors which are suitable for tricolor white-light-emitting diodes. To accomplish a high luminescent efficiency at 400 nm excitation, we screened a seven-cation oxide system including Tb, Gd, Ce, Mg, Si, Al, and B. The combination of a genetic algorithm and combinatorial chemistry enhanced the searching efficiency when applied for phosphor screening. As a result, the optimized composition was Tb(0.01)Gd(0.02)Ce(0.04)B(0.1)Si(0.83)O(delta), The luminance of this borosilicate glass was 67% that of ZnS:Cu,Al at 400-nm excitation.

Algorithms↗
PubMed2000

Genetics and biochemistry of secondary metabolites in plants: an evolutionary perspective.

The evolution of new genes to make novel secondary compounds in plants is an ongoing process and might account for most of the differences in gene function among plant genomes. Although there are many substrates and products in plant secondary metabolism, there are only a few types of reactions. Repeated evolution is a special form of convergent evolution in which new enzymes with the same function evolve independently in separate plant lineages from a shared pool of related enzymes with similar but not identical functions. This appears to be common in secondary metabolism and might confound the assignment of gene function based on sequence information alone.

Evolution, Molecular↗
PubMed2026

Transcriptional perturbation of LINE-1 elements reveals their cis-regulatory potential.

Long interspersed element-1 (LINE-1 or&#xa0;L1) retrotransposons constitute the largest transposable element family in mammalian genomes and contribute prominently to inter- and intra-individual genetic variation. Although most L1 elements are inactive, some evolutionary younger elements remain intact and genetically competent for transcription and occasionally retrotransposition. Despite being generally more abundant in gene-poor regions, intact or full-length L1s (FL-L1) are also enriched around specific classes of genes and on the eutherian X chromosome. How proximal FL-L1 may affect nearby gene expression remains unclear. Here, we examine this systematically using engineered mouse embryonic stem cells (ESCs) in which expression of one active L1 subfamily is perturbed. We find that FL-L1 activation leads to the misregulation of ~1024 genes, whereas FL-L1 repression affects ~81 genes. In most cases (68%), misexpressed genes contain an intronic FL-L1 or lie near a FL-L1 (<&#x2009;260&#x2009;kb). Gene ontology analysis shows that upon L1 activation, upregulated genes are enriched for neuronal function-related terms, suggesting that some L1 elements may have evolved to control neuronal gene networks. These results illustrate the cis-regulatory potential of FL-L1 elements and suggest a broader role for L1s than originally anticipated.

Animals↗
PubMed2005

Subterranean phylogeography of freshwater crayfishes shows extensive gene flow and surprisingly large population sizes.

Subterranean animals are currently viewed as highly imperiled, precariously avoiding extinction in an extreme environment of darkness. This assumption is based on a hypothesis that the reduction in visual systems and morphology common in cave faunas reflects a genetic inability to adapt and persist coupled with the perception of a habitat that is limited, disconnected, and fragile. Accordingly, 95% of cave fauna in the United States are presumed endangered due to surface environmental degradation and limited geographic distributions. Our study explores the subterranean phylogeography of stygobitic crayfishes in the southeastern United States, a global hotspot of groundwater biodiversity, using extensive geographic sampling and molecular data. Despite their endangered status, our results show that subterranean crayfish species have attained moderate to high levels of genetic diversity over their evolutionary histories with large population sizes and extensive gene flow among karst systems. We then compare the subterranean population histories to those of common surface stream-dwelling crayfishes. Our results show recent drastic declines in genetic variability in the surface crayfish and suggest that these species also warrant conservation attention.

Animals↗
PubMed2004

On the 28-gon symmetry inherent in the genetic code intertwined with aminoacyl-tRNA synthetases--the Lucas series.

Despite considerable efforts it has remained unclear what principle governs the selection of the 20 canonical amino acids in the genetic code. Based on a previous study of the 28-gonal and rotational symmetric arrangement of the 20 amino acids in the genetic code, new analyses of the organization of the genetic code system together with their intrinsic relation to the two classes of aminoacyl-tRNA synthetases are reported in this work. A close inspection revealed how the enzymes and the 20 gene-encoded amino acids are intertwined on the polyhedron model. Complementary and cooperative symmetries between class I and class II aminoacyl-tRNA synthetases displayed by a 28-gon organization are discussed, and we found that the two previously suggested evolutionary axes within the genetic code overlap the symmetry axes within the two classes of aminoacyl-tRNA synthetases. Moreover, it has been shown that the side-chain carbon-atom numbers (2, 1, 3, 4 and 7) in the overwhelming majority of the amino acids recognized by each of the two classes of aminoacyl-tRNA synthetases are determined by a mathematical relationship, the Lucas series. A stepwise co-evolutionary selection logic of the amino acids is manifested by the amino acid side-chain carbon-atom number balance at '17', when grouping the genetic code doublets in the 28-gon organization. The number '17' equals the sum of the initial five numbers in the Lucas series, which are 2, 1, 3, 4 and 7.

Amino Acids↗
PubMed2026

Polygenic and monogenic adaptation drive evolutionary rescue at different magnitudes of environmental change.

Understanding the genetic basis of rapid adaptation is key to predicting species' evolutionary responses to environmental change. However, it is still debatable whether many small-effect mutations or a few large-effect mutations underlie rapid adaptation, and how this knowledge can predict population survival or extinction. To address this question, we performed a series of ecologically grounded forward-in-time genetic simulations to study rapid adaptation and extinction with increasing magnitudes of environmental change. These simulations were seeded with genomic variation of the plant Arabidopsis thaliana to have a realistic genomic structure, with one (monogenic) to 1,000 (polygenic) variants with varying heritabilities contributing to an environmental adaptive trait. Our results revealed two distinct scenarios of rapid adaptation and population rescue. Under small-to-moderate environmental shifts, high polygenic traits increased evolutionary rescue probability. Under extreme environmental shifts, high polygenic traits lead predictably to extinction, yet monogenic traits sometimes produce one-off winning adaptive genotypes. We interpret our rapid evolutionary rescue findings in terms of the fundamental theorem of natural selection, where trait polygenicity shapes the distribution of genetic variance in fitness across replicates and, in turn, the probability of population survival, with polygenic architectures producing more stable and predictable fitness variance and monogenic architectures generating highly skewed and variable outcomes. These results highlight the insights genomics gives us into the (un)predictability of species' evolutionary responses to global change, with management implications for assisted adaptation and conservation.

Arabidopsis↗
PubMed2000

Plasticity, evolvability, and modularity in RNA.

RNA folding from sequences into secondary structures is a simple yet powerful, biophysically grounded model of a genotype-phenotype map in which concepts like plasticity, evolvability, epistasis, and modularity can not only be precisely defined and statistically measured but also reveal simultaneous and profoundly non-independent effects of natural selection. Molecular plasticity is viewed here as the capacity of an RNA sequence to assume a variety of energetically favorable shapes by equilibrating among them at constant temperature. Through simulations based on experimental designs, we study the dynamics of a population of RNA molecules that evolve toward a predefined target shape in a constant environment. Each shape in the plastic repertoire of a sequence contributes to the overall fitness of the sequence in proportion to the time the sequence spends in that shape. Plasticity is costly, since the more shapes a sequence can assume, the less time it spends in any one of them. Unsurprisingly, selection leads to a reduction of plasticity (environmental canalization). The most striking observation, however, is the simultaneous slow-down and eventual halting of the evolutionary process. The reduction of plasticity entails genetic canalization, that is, a dramatic loss of variability (and hence a loss of evolvability) to the point of lock-in. The causal bridge between environmental canalization and genetic canalization is provided by a correlation between the set of shapes in the plastic repertoire of a sequence and the set of dominant (minimum free energy) shapes in its genetic neighborhood. This statistical property of the RNA genotype-phenotype map, which we call plastogenetic congruence, traps populations in regions where most genetic variation is phenotypically neutral. We call this phenomenon neutral confinement. Analytical models of neutral confinement, made tractable by the assumption of perfect plastogenetic congruence, formally connect mutation rate, the topography of phenotype space, and evolvability. These models identify three mutational regimes: that corresponding to neutral confinement, an exploration threshold corresponding to a breakdown of neutral confinement with the simultaneous persistence of the dominant phenotype, and a classic error threshold corresponding to the loss of the dominant phenotype. In a final step, we analyze the structural properties of canalized phenotypes. The reduction of plasticity leads to extreme modularity, which we analyze from several perspectives: thermophysical (melting--the RNA version of a norm of reaction), kinetic (folding pathways--the RNA version of development), and genetic (transposability--the insensitivity to genetic context). The model thereby suggests a possible evolutionary origin of modularity as a side effect of environmental canalization.

Evolution, Molecular↗
PubMed2002

Statistics of selectively neutral genetic variation.

Random models of evolution are instrumental in extracting rates of microscopic evolutionary mechanisms from empirical observations on genetic variation in genome sequences. In this context it is necessary to know the statistical properties of empirical observables (such as the local homozygosity, for instance). Previous work relies on numerical results or assumes Gaussian approximations for the corresponding distributions. In this paper we give an analytical derivation of the statistical properties of the local homozygosity and other empirical observables assuming selective neutrality. We find that such distributions can be very non-Gaussian.

Alleles↗
PubMedDate not supplied

Genetic structure and admixture in urban populations of the Argentine North-West.

BACKGROUND: From the ethnic point of view, the Argentine North-West (ANW) constitutes one of the most noticeable areas in the country due to the cultural peculiarities that integrate it to the Andean world and the ethno-historical and demographic characteristics of how it became populated. AIM: The study analysed the genetic structure and diversity of the ANW urban populations, and the contribution of parental populations to its genetic pool. SUBJECTS AND METHODS: Previously reported data on allele frequencies of HLA-A and HLA-B loci of 1293 individuals from Jujuy, Salta, Tucumán, Santiago del Estero, Catamarca and La Rioja were used. Our estimates include: (a) genetic intra-population diversity; (b) genetic distances between populations; (c) linkage disequilibrium (LD); (d) admixture rates and genetic distances with respect to three parental populations (European, American Indian and African). RESULTS: Low intra-population genetic differentiation and low genetic distances between populations were found. Differential LD distribution varied according to province, with 60% variance due to intra-population differences. The Spanish contribution (50%) predominated in ANW, followed by the American Indian (40%) and African (10%) contributions, and a marked inter-population heterogeneity of genetic admixture rates was observed. The shortest genetic distance was found in the American Indian parental population, and the longest in the African parental population. CONCLUSION: Five hundred years after the Spanish conquest, urban populations at ANW that have probably been subject to the same evolutionary forces present low genetic diversity and a similar genetic structure. Genetic distances and admixture percentages observed agree with census and ethno-historical data on settlement in the region.

Argentina↗
PubMed1981

Photosynthesis of Grass Species Differing in Carbon Dioxide Fixation Pathways : VII. CHROMOSOME NUMBERS, METAPHASE I CHROMOSOME BEHAVIOR, AND MODE OF REPRODUCTION OF PHOTOSYNTHETICALLY DISTINCT PANICUM SPECIES.

Panicum species of the Laxa group were investigated in a series of published reports and were found to possess C(4), C(3), and intermediate photosynthetic characteristics. Taxonomic and other relationships among these plants, however, are not clear. It was the objective of this investigation to document chromosome number, metaphase I chromosome behavior, and mode of reproduction, including abnormalities in the embryo sac, for these species.Chromosome counts showed a basic number (x) of 10 and ploidy levels of diploid (2n = 2x = 20), tetraploid (2n = 4x = 40), and hexaploid (2n = 6x = 60) in this group of Panicum. One diploid and one tetraploid accession of the C(4) species, Panicum prionitis Griseb., were obtained. Of the intermediate species, Panicum milioides Nees ex Trin. was diploid, Panicum schenckii Hack. was hexaploid, and Panicum decipiens Nees, ex Trin. was found to possess two ploidy levels, one accession being diploid and the other accession being hexaploid. All the C(3) species, which included two accessions of Panicum laxum Sw., three accessions of Panicum hylaeicum Mez., and one accession of Panicum rivulare Trin., were tetraploid.Meiosis was regular with primarily bivalent pairing at metaphase I in all species except the tetraploid accession of P. prionitis which possessed from 4 to 10 tetravalents. Stainable pollen was high in all species, ranging from 70 to 99%. Embryo sac analyses showed a single sac in all plants except the tetraploid accession of P. prionitis, which was found to possess an additional sac at anthesis. An additional sac was also observed in some ovaries of the P. schenckii accession. Self-pollinated seed set was high in all accessions except the diploid accession of P. prionitis and one accession of P. laxum where no seed was set under bagged conditions.This information establishes, within the limits of this collection, a base for future studies on genetic, taxonomic, photosynthetic, and evolutionary relationships among these plants. Possession of the same basic chromosome number, regular meiotic pairing, a high degree of stainable pollen, and good seed set in most of the plants studied indicate possible success in making hybrids for a genetic study of photosynthetic pathways in Panicum.

Journal Article↗
PubMed2001

Genetic and structural organization of the aminophenol catabolic operon and its implication for evolutionary process.

The aminophenol (AP) catabolic operon in Pseudomonas putida HS12 mineralizing nitrobenzene was found to contain all the enzymes responsible for the conversion of AP to pyruvate and acetyl coenzyme A via extradiol meta cleavage of 2-aminophenol. The sequence and functional analyses of the corresponding genes of the operon revealed that the AP catabolic operon consists of one regulatory gene, nbzR, and the following nine structural genes, nbzJCaCbDGFEIH, which encode catabolic enzymes. The NbzR protein, which is divergently transcribed with respect to the structural genes, possesses a leucine zipper motif and a MarR homologous domain. It was also found that NbzR functions as a repressor for the AP catabolic operon through binding to the promoter region of the gene cluster in its dimeric form. A comparative study of the AP catabolic operon with other meta cleavage operons led us to suggest that the regulatory unit (nbzR) was derived from the MarR family and that the structural unit (nbzJCaCbDGFEIH) has evolved from the ancestral meta cleavage gene cluster. It is also proposed that these two functional units assembled through a modular type gene transfer and then have evolved divergently to acquire specialized substrate specificities (NbzCaCb and NbzD) and catalytic function (NbzE), resulting in the creation of the AP catabolic operon. The evolutionary process of the AP operon suggests how bacteria have efficiently acquired genetic diversity and expanded their metabolic capabilities by modular type gene transfer.

Amino Acid Sequence↗
PubMed2026

Genome-wide barriers to gene flow reveal the genetic basis of viviparity evolution in a lizard.

Viviparity (live-bearing) is a major evolutionary transition repeatedly linked with ecological and evolutionary diversification throughout vertebrates. Live-bearing reproduction entails a novel suite of phenotypes and life history traits, but the genetic processes by which such a reproductive innovation evolves are unknown. Remarkable among amniotes, the common lizard (Zootoca vivipara) has extant oviparous (egg-laying) and viviparous lineages and a to-date unresolved history of parity mode emergence. This species represents an ideal model to reconstruct the evolutionary and genetic mechanisms of how viviparity arises. By analyzing whole genomes of individuals from across the species' distribution, we robustly show that viviparity evolved once. However, gene flow from oviparous to viviparous populations is found to be long-term and extensive, causing pronounced gene tree discordance. We inferred signals of selection for viviparity in many independent regions across the genome, and these were recruited over considerable time. Genomic barriers to gene flow between oviparity and viviparity were found genome wide. These are enriched for regions under selection for parity mode and for genes known to be involved in pregnancy and parturition in squamates and mammals. Further implicating their functional role in viviparity, we show that genes in genomic regions under selection and resisting gene flow are more highly expressed in the uterus of viviparous lizards during pregnancy. Our study demonstrates that viviparity in an amniote evolved by selection in the face of gene flow and primarily by the genome-wide accumulation of functional regulatory variants. These results reveal how complex adaptive innovations can arise and be maintained.

Animals↗
PubMed2002

Genome organization and reorganization in evolution: formatting for computation and function.

This volume deals with the role of epigenetics in life and evolution. The most dynamic forms of functional genome formatting involve DNA interacting with cellular complexes that do not alter sequence information. Such important epigenetic phenomena are the main subjects of other articles in this volume. This article focuses on the long-lived form of genome formatting that lies within the DNA sequence itself. I argue for a computational view of genome function as the long-term information storage organelle of each cell. Structural formatting consists of organizing various signals and coding sequences into computationally ready systems facilitating genome expression and genome transmission. The basic features of genome organization can be understood by examining the E. coli lac operon as a paradigmatic genomic system. Multiple systems are connected through distributed signals and repetitive DNA to form higher-order genome system architectures. Molecular discoveries about mechanisms of DNA restructuring show that cells possess the natural genetic engineering functions necessary for evolutionary change by rearranging genomic components and reorganizing system architectures. The concepts of cellular computation and decision-making, genome system architecture, and natural genetic engineering combine to provide a new way of framing evolutionary theories and understanding genome sequence information.

Animals↗
PubMed2000

Genetic architecture of a wing size measure in Drosophila hibisci from two populations in eastern Australia.

Two models of evolutionary change invoke either additive genetic contributions to phenotypic traits (Fisher) or epistatic as well as additive effects (Wright). An earlier study of the flower-breeding Drosophila hibisci from two sites in eastern Australia reported additive and epistatic genetic effects as well as environmental effects on ovariole number. The present study of the same flies examines the genetic architecture of wing width, a trait that is correlated phenotypically with ovariole number and body size. A generation means analysis of flies reared at 25 degrees C indicated additive and epistatic genetic effects, but no consistent maternal effects, whereas for flies reared at three temperatures (18 degrees C, 21.5 degrees C, and 25 degrees C) linear and nonlinear environmental effects interacted with additive genetic effects. The genetic correlation matrix for ovariole number and wing width suggested negative genetic correlations between additive effects on one trait and epistatic effects on the other. Both traits provide evidence of genetic effects consistent with assumptions of Wright's shifting balance theory of evolution.

Animals↗
PubMed2005

Evolutionary history of the Drosophila bipectinata species complex.

Groups of recently diverged species offer invaluable glimpses into the history and genetic basis of speciation and phenotypic evolution. In this report, we combine phylogenetic and population-genetic approaches to reconstruct the evolutionary history of the Drosophila bipectinata species complex. This complex is a group of four closely related, largely sympatric species--D. bipectinata, D. parabipectinata, D. malerkotliana and D. pseudoananassae. Using the sequences of one mitochondrial and six nuclear loci, we show that D. bipectinata and D. parabipectinata are the two most closely related species, and that together with D. malerkotliana they form a monophyletic clade to which D. pseudoananassae is a relatively distant outgroup. Genetic divergence among D. bipectinata, D. parabipectinata and D. malerkotliana is extremely low, and we estimate that these species diverged only 283,000-385,000 years ago. We also find that mitochondrial DNA shows evidence of recent gene flow across species boundaries. Despite the low genetic divergence, species of the bipectinata complex show an unusually high degree of morphological differentiation. This contrast underscores the importance of understanding the genetic basis of functional differentiation among closely related species.

Alleles↗
PubMed1998

Evolution and ecology of spider coloration.

Genetic color variation provides a tangible link between the external phenotype of an organism and its underlying genetic determination and thus furnishes a tractable system with which to explore fundamental evolutionary phenomena. Here we examine the basis of color variation in spiders and its evolutionary and ecological implications. Reversible color changes, resulting from several mechanisms, are surprisingly widespread in the group and must be distinguished from true genetic variation for color to be used as an evolutionary tool. Genetic polymorphism occurs in a large number of families and is frequently sex limited: Sex linkage has not yet been demonstrated, nor have the forces promoting sex limitation been elucidated. It is argued that the production of color is metabolically costly and is principally maintained by the action of sight-hunting predators. Key avenues for future research are suggested.

Journal Article↗