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Environmental implications of gene flow from sugar beet to wild beet--current status and future research needs.

Gene flow via seed or pollen is a basic biological process in plant evolution. The ecological and genetic consequences of gene flow depend on the amount and direction of gene flow as well as on the fitness of hybrids. The assessment of potential risks of transgenic plants should take into account the fact that conventional crops can often cross with wild plants. The precautionary approach in risk management of genetically modified plants (GMPs) may make it necessary to monitor significant wild and weed populations that might be affected by transgene escape. Gene flow is hard to control in wind-pollinated plants like beet (Beta vulgaris). In addition, wild beet populations potentially can undergo evolutionary changes which might expand their geographical distribution. Unintended products of cultivated beets pollinated by wild beets are weed beets that bolt and flower during their first year of planting. Weed beets cause yield losses and can delay harvest. Wild beets are important plant genetic resources and the preservation of wild beet diversity in Europe has been considered in biosafety research. We present here the methodology and research approaches that can be used for monitoring the geographical distribution and diversity of Beta populations. It has recently been shown that a century of gene flow from Beta vulgaris ssp. vulgaris has not altered the genetic diversity of wild Beta vulgaris L. ssp. maritima (L.) Arcang. in the Italian sugar beet seed production area. Future research should focus on the potential evolution of transgenic wild beet populations in comparison to these baseline data. Two monitoring models are presented describing how endpoints can be measured: (1) "Pre-post" crop commercialization against today's baseline and (2) "Parallel" to crop commercialization against GMP free reference areas/ populations. Model 2 has the advantage of taking ongoing changes in genetic diversity and population dynamics into account. Model 1 is more applicable if gene flow is so strong that most areas/populations contain GMPs. Important traits that may change the ecology of populations are genes that confer tolerance to biotic and abiotic stress. An assessment of environmental effects can realistically only be based on endpoints and consequences of gene introgression, which may include economic values of biodiversity in littoral and other ecosystems containing wild beet. In general, there is still a great need to harmonize worldwide monitoring systems by the development of appropriate methods to evaluate the environmental impact of introgressed transgenes.

Beta vulgaris↗
PubMed2003

Mechanics of cuticular elastic energy storage in leg joints lacking extensor muscles in arachnids.

Certain leg joints in arachnids lack extensor muscles and have elastically deformable transarticular sclerites spanning their arthrodial membranes, an arrangement consistent with a model in which flexor muscles load transarticular sclerites during flexion and energy from elastic recoil is used for extension. This study quantifies the potential contribution of elastic recoil to extension torque at joints of the fourth leg of representative arachnids. Extension torques of isolated joints with and without transarticular sclerites were measured as the joint was rotated through angles and at angular velocities comparable with those used by walking animals. The procedure was repeated with the joint subjected to different internal fluid pressures in order to assess the potential role of hydraulically induced extension. The efficiency of elastic energy storage (resilience) in the absence of internal fluid pressure was 70-90% for joints with well-developed transarticular sclerites, and the magnitude of torque was similar to those produced by different joint extension mechanisms in other arthropods. Increased internal fluid pressure acted synergistically with transarticular sclerites in some joints but had little or no effect in others. Joints that lacked both extensor muscles and transarticular sclerites appeared to be specialized for hydraulic extension, and joints operated by antagonistic muscles lacked apparent specializations for either elastic or hydraulic extension. It is well known that elastic energy storage is a significant contributor to propulsion in running vertebrates and certain arthropods, where elastic elements are loaded as the center of mass falls during one phase of the locomotor cycle. However, transarticular sclerites are apparently loaded by contraction of flexor muscles when the leg is not in contact with the substratum. Hence the mechanism of a transarticular sclerite is more similar to the flight and jumping mechanisms of other arthropods than to running vertebrates. The evolutionary significance and potential mechanical advantages of the transarticular elastic mechanism are discussed.

Animals↗
PubMed2004

Nonneutral evolution of the transcribed pseudogene Makorin1-p1 in mice.

Pseudogenes are nonfunctional relics of formerly functional genes and are thought to evolve neutrally. In some pseudogenes, however, the molecular evolutionary patterns are atypical of neutrally evolving sequences, exhibiting sequence conservation, codon-usage bias, and other features associated with functional genes. Makorin1-p1 is a transcribed pseudogene first identified in the mouse Mus musculus. The transcript of Makorin1-p1 can regulate the stability of the transcript of its paralogous functional gene Makorin1. Specifically, the half-life of Makorin1 mRNA increases significantly in the presence of Makorin1-p1 transcript, and targeted deletion of Makorin1-p1 is lethal in mice. Here, we show that Makorin1-p1 originated after the separation of Mus and Rattus but before the divergence of M. musculus and M. pahari. The transcribed region of Makorin1-p1 exhibits rates of point and indel substitutions that are two to four times lower than those in the untranscribed region, suggesting that the transcribed region is under functional constraint and is not evolving neutrally. Although the transcript of Makorin1-p1 likely functions by its sequence similarity to Makorin1, we find no evidence of gene conversion between them, indicating that functional conservation alone is sufficient to maintain their coordinated evolution. A duplication-degeneration model is proposed to explain how Makorin1-p1 was co-opted into the regulatory system of Makorin1. There are over 10,000 pseudogenes in a typical mammalian genome, and it is plausible that many functional but untranslatable pseudogenes exist. Our results illustrate the potential of using evolutionary analysis to identify such pseudogenes from genome sequences.

Animals↗
PubMed2006

A general multivariate extension of Fisher's geometrical model and the distribution of mutation fitness effects across species.

The evolution of complex organisms is a puzzle for evolutionary theory because beneficial mutations should be less frequent in complex organisms, an effect termed "cost of complexity." However, little is known about how the distribution of mutation fitness effects (f(s)) varies across genomes. The main theoretical framework to address this issue is Fisher's geometric model and related phenotypic landscape models. However, it suffers from several restrictive assumptions. In this paper, we intend to show how several of these limitations may be overcome. We then propose a model of f(s) that extends Fisher's model to account for arbitrary mutational and selective interactions among n traits. We show that these interactions result in f(s) that would be predicted by a much smaller number of independent traits. We test our predictions by comparing empirical f(s) across species of various gene numbers as a surrogate to complexity. This survey reveals, as predicted, that mutations tend to be more deleterious, less variable, and less skewed in higher organisms. However, only limited difference in the shape of f(s) is observed from Escherichia coli to nematodes or fruit flies, a pattern consistent with a model of random phenotypic interactions across many traits. Overall, these results suggest that there may be a cost to phenotypic complexity although much weaker than previously suggested by earlier theoretical works. More generally, the model seems to qualitatively capture and possibly explain the variation of f(s) from lower to higher organisms, which opens a large array of potential applications in evolutionary genetics.

Animals↗
PubMed2001

Spatial population genetic structure in Trillium grandiflorum: the roles of dispersal, mating, history, and selection.

The roles of the various potential ecological and evolutionary causes of spatial population genetic structure (SPGS) cannot in general be inferred from the extant structure alone. However, a stage-specific analysis can provide clues as to the causes of SPGS. We conducted a stage-specific SPGS analysis of a mapped population of about 2000 Trillium grandiflorum (Liliaceae), a long-lived perennial herb. We compared SPGS for juvenile (J), nonreproductive (NR), and reproductive (R) stages. Fisher's exact test showed that genotypes had Hardy-Weinberg frequencies at all loci and stage classes. Allele frequencies did not differ between stages. Bootstrapped 99% confidence intervals (99%CI) indicate that F-statistic values are indistinguishable from zero, (except for a slightly negative FIT for the R stage). Spatial autocorrelation was used to calculate f the average kinship coefficient between individuals within distance intervals. Null hypothesis 99%CIs for f were constructed by repeatedly randomizing genotypic locations. Significant positive fine-scale genetic structure was detected in the R and NR stages, but not in the J stage. This structure was most pronounced in the R stage, and declined by about half in each remaining stage: near-neighbor f = 0.122, 0.065, 0.027, for R, NR, and J, respectively. For R and NR, the near-neighbor f lies outside the null hypothesis 99%CI, indicating kinship at approximately the level of half-sibs and first cousins, respectively. We also simulated the expected SPGS of juveniles post dispersal, based on measured R-stage SPGS, the mating system, and measured pollen and seed dispersal properties. This provides a null hypothesis expectation (as a 99%CI) for the J-stage correlogram, against which to test the likelihood that post-dispersal events have influenced J-stage SPGS. The actual J correlogram lies within the null hypothesis 99%CI for the shortest distance interval and nearly all other distance intervals indicating that the observed low recruitment, random mating and seed dispersal patterns are sufficient to account for the disappearance of SPSG between the R and the J stages. The observed increase in SPGS between J and R stages has two potential explanations: history and local selection. The observed low total allelic diversity is consistent with a past bottleneck: a possible historical explanation. Only a longitudinal stage-specific study of SPGS structure can distinguish between historical events and local selection as causes of increased structure with increasing life history stage.

Genetics, Population↗
PubMed1995

Concerted evolution of repetitive DNA sequences in eukaryotes.

A large fraction, sometimes the largest fraction, of a eukaryotic genome consists of repeated DNA sequences. Copy numbers range from several thousand to millions per diploid genome. All classes of repetitive DNA sequences examined to date exhibit apparently general, but little studied, patterns of "concerted evolution." Historically, concerted evolution has been defined as the nonindependent evolution of repetitive DNA sequences, resulting in a sequence similarity of repeating units that is greater within than among species. This intraspecific homogenization of repetitive sequence arrays is said to take place via the poorly understood mechanisms of "molecular drive." The evolutionary population dynamics of molecular drive remains largely unstudied in natural populations, and thus the potential significance of these evolutionary dynamics for population differentiation is unknown. This review attempts to demonstrate the potential importance of the mechanisms responsible for concerted evolution in the differentiation of populations. It contends that any natural grouping that is characterized by reproductive isolation and limited gene flow is capable of exhibiting concerted evolution of repetitive DNA arrays. Such effects are known to occur in protein and RNA-coding repetitive sequences, as well as in so-called "junk DNA," and thus have important implications for the differentiation and discrimination of natural populations.

Amphibians↗
PubMed2001

Sexual dimorphism in primate evolution.

Sexual dimorphism is a pervasive phenomenon among anthropoid primates. Comparative analyses over the past 30 years have greatly expanded our understanding of both variation in the expression of dimorphism among primates, and the underlying causes of sexual dimorphism. Dimorphism in body mass and canine tooth size is familiar, as is pelage and "sex skin" dimorphism. More recent analyses are documenting subtle differences in the pattern of skeletal dimorphism among primates. Comparative analyses have corroborated the sexual selection hypotheses, and have provided a more detailed understanding of the relationship between sexual selection, natural selection, and mating systems in primates. A clearer picture is emerging of the relative contribution of various selective and nonselective mechanisms in the evolution and expression of dimorphism. Most importantly, recent studies have shown that dimorphism is the product of changes in both male and female traits. Developmental studies demonstrate the variety of ontogenetic pathways that can lead to dimorphism, and provide additional insight into the selective mechanisms that influence dimorphism throughout the lifetime of an animal. Evidence from the fossil record suggests that dimorphism probably evolved in parallel twice, and the dimorphism in some extinct hominoids probably exceeded that of any living primate. Our advances in understanding the behavioral/ecological correlates of dimorphism in living primates have not improved our ability to reconstruct social systems in extinct species on the basis of dimorphism alone, beyond the inference of polygyny or intense male-male competition. However, our understanding of the behavioral/ecological correlates of growth and development, and of the expression of dimorphism as a function of separate changes in male and female traits, offers great potential for inferring evolutionary changes in behavior over time.

Animals↗
PubMed2005

Profiling serine protease substrate specificity with solution phase fluorogenic peptide microarrays.

A novel microarray-based proteolytic profiling assay enabled the rapid determination of protease substrate specificities with minimal sample and enzyme usage. A 722-member library of fluorogenic protease substrates of the general format Ac-Ala-X-X-(Arg/Lys)-coumarin was synthesized and microarrayed, along with fluorescent calibration standards, in glycerol nanodroplets on microscope slides. The arrays were then activated by deposition of an aerosolized enzyme solution, followed by incubation and fluorometric scanning. The specificities of human blood serine proteases (human thrombin, factor Xa, plasmin, and urokinase plasminogen activator) were examined. The arrays provided complete maps of protease specificity for all of the substrates tested and allowed for detection of cooperative interactions between substrate subsites. The arrays were further utilized to explore the conservation of thrombin specificity across species by comparing the proteolytic fingerprints of human, bovine, and salmon thrombin. These enzymes share nearly identical specificity profiles despite approximately 390 million years of divergent evolution. Fluorogenic substrate microarrays provide a rapid way to determine protease substrate specificity information that can be used for the design of selective inhibitors and substrates, the study of evolutionary divergence, and potentially, for diagnostic applications.

Amino Acid Motifs↗
PubMed1997

Stochastic Dispersal Processes in Plant Populations

A dispersal model for airborne pollen based on assumptions about wind directionality, gravity, and a wind threshold at which pollen is taken by the wind is developed, using a three dimensional diffusion approximation. The bivariate probability distribution of pollen receipt by flowers at the same height as the pollen source is derived. Gravity, vertical random movements, and vegetation density turn out to have similar effects on this distribution. Maximum likelihood methods for estimating the combined parameters from data with multiple point or continuous pollen sources, and one or more plant varieties, are developed. Using an example data set from the literature, it is shown that our model gives a better fit than more traditional descriptive dispersal models of the form e-ar b. We also show that estimates of important properties of the dispersal distribution, such as the variances, become considerably smaller using our model than for the more traditional models. Finally, we discuss potential extensions and evolutionary implications of these types of models. Copyright 1997 Academic Press

Journal Article↗
PubMed1998

Screening of conformationally constrained random polypeptide libraries displayed on a protein scaffold.

The selection of novel proteins or enzymes from random protein libraries has come to be a major objective in current biology, and these enzymes should prove useful in various biological and biomedical fields. New technologies such as in vitro selection of proteins in cell-free systems have high potential to realize evolutionary molecular engineering of proteins. This review highlights an application of insertional mutagenesis of proteins to evolutionary molecular engineering. Random sequence proteins are inserted into the surface of a host enzyme which serves as a scaffold to display random protein libraries. Constraints on random polypeptide conformations owing to the proximity of N- and C-termini on the scaffold would result in greater screening efficiency of libraries. The scaffold enzyme is also used as a probe for monitoring the hill climbing of random sequence proteins on a fitness landscape and navigating rapid protein folding in the sequence space.

Animals↗
PubMed2003

The evolution of enzyme specificity in Fasciola spp.

Fasciola spp., commonly known as liver fluke, are significant trematode parasites of livestock and humans. They secrete several cathepsin L-like cysteine proteases, some of which differ in enzymatic properties and timing of expression in the parasite's life cycle. A detailed sequence and evolutionary analysis is presented, based on 18 cathepsin L-like enzymes isolated from Fasciola spp. (including a novel clone identified in this study). The enzymes form a monophyletic group which has experienced several gene duplication events over the last approximately 135 million years, giving rise to the present-day enzymatic repertoire of the parasite. This timing of these duplications appears to correlate with important points in the evolution of the mammalian hosts. Furthermore, the dates suggest that Fasciola hepatica and Fasciola gigantica diverged around 19 million years ago. A novel analysis, based on the pattern of amino acid diversity, was used to identify sites in the enzyme that are predicted to be subject to positive adaptive evolution. Many of these sites occur within the active site cleft of the enzymes, and hence would be expected to lead to differences in substrate specificity. Using homology modeling, with reference to previously obtained biochemical data, we are able to predict S2 subsite specificity for these enzymes: specifically those that can accommodate bulky hydrophobic residues in the P2 position and those that cannot. A number of other positions subject to evolutionary pressure and potentially significant for enzyme function are also identified, including sites anticipated to diminish cystatin binding affinity.

Amino Acid Sequence↗
PubMed2004

Genetic and environmental variation in performance of a marine isopod: effects of eutrophication.

Environmental variation in food resources modifies performance of herbivores, in addition to genetic variation and maternal effects. In marine benthic habitats, eutrophication may modify herbivores' diets by changing host species composition or nutritional quality of algae for herbivores. We studied experimentally the effects of diet breadth and nutrient availability for the host algae on fitness components of the herbivorous isopod Idotea baltica. We fed the adult isopods with the brown algae Fucus vesiculosus and Pilayella littoralis and juveniles with the green alga Cladophora glomerata. By using half-sib families, we were able to separate the genetic, environmental and maternal effects on intermolt duration and size of the juveniles. The mothers confined to the diet consisting of both Fucus and Pilayella grew better and produced larger egg mass than those having consumed Fucus alone. Nutrient enhancement of algae did not influence the performance of the adult herbivores. However, the juveniles achieved twice the weight as well as shorter intermolt duration when consuming nutrient-treated C. glomerata. Mother's nutrition, either nutrient enrichment of her food algae or diet breadth, did not affect juvenile survival or growth as such, but we found evidence that the broader diet consumed by the mother mediated offspring performance by further accelerating growth rate of the offspring that fed on nutrient-treated alga. Intermolt duration was a highly heritable trait, but size showed very low heritability. Instead, maternal effects on size were substantial, suggesting that differences among mothers in their egg-provisioning ability strongly affect weight gain of their offspring. A high amount of additive genetic variance in intermolt duration implies potential for quick evolutionary responses in the growth schedule in the face of changes in the selective environment. We conclude that eutrophication, in addition to improving growth and reproduction of I. baltica by enhancing food quality and by providing opportunity for broader, more profitable diets, may act as a selective agent on life-history traits. Eutrophication of coastal waters is thus likely to reflect in herbivore density, population dynamics and eventually, grazing pressure of littoral macroalgae.

Analysis of Variance↗
PubMed2003

Mobile DNAs: the poacher turned gamekeeper.

The selfish DNA hypothesis imagines the genome as an ecological community, a collection of interacting DNA sequences with differing evolutionary origins and potentially different interests. We are now finding out more about the ways in which host sequences can enlist the help of formerly parasitic DNAs.

Adaptation, Biological↗
PubMed1997

The Hamilton-Zuk theory and initial test: an examination of some parasitological criticisms.

It has been supposed repeatedly that the Hamilton & Zuk paper of 1982 was parasitologically misconceived. These criticisms are shown to be inconsistent or mistaken. Various assumptions deemed unjustifiable by critics were either not made in the original paper, or have been made commonly, reasonably and pragmatically, by parasitologists themselves. The requirement by the theory for pathogenicity is examined, as is the need for the individuals to encounter the relevant parasites. The possible roles of parasite aggregation, parasites other than those directly involved, and costs of resistance, in making sosigonic selection less feasible are put into perspective. The rationale, interpretation and value of the preliminary comparative test with haematozoa are discussed. The advisability of incorporating host age, the location and timing of any sampling for parasites, and the actual ability of successful mates to resist disease is acknowledged. Attention is directed towards several specific observations. (1) It is a little recognised fact that Hamilton and Zuk assessed prevalence-showiness associations within surveys in restricted localities. (2) Many parasitological studies have not properly addressed the need to control for sampling effort when using prevalence data. (3) Contrary to some claims, the notion that haematozoa are sufficiently pathogenic is not unrealistic. (4) That non-resistant as well as resistant individuals might be free of patent or even latent infection at the time of mate choice was one of the possibilities mentioned originally. (5) In 1984, Eshel & Hamilton emphasised that environmental variation (whatever its source) has the potential to make mate selection for heritable characters based on perceptible variation less likely to evolve. (6) Hamilton & Zuk concluded that their findings "hint" that parasitism could be one agitator required for "good genes" sexual selection, a stance which is not immoderate. Lastly, the potential importance in evolutionary biology of parasite-mediated sexual selection as a form of co-evolution is considered briefly.

Host-Parasite Interactions↗
PubMed1997

HLA-G polymorphisms: neutral evolution or novel function?

HLA-G is a non-classical class Ib gene with many unusual features. Because of its unique expression pattern, which is primarily limited to fetal cells at the maternal fetal interface, this gene has gained the attention of many investigators. In this paper we review some of the novel features of HLA-G, with particular reference to polymorphic variants in the gene, and discuss the implications of these features for the potential function and evolutionary history of HLA-G.

Alleles↗
PubMed1997

Actin genes with unusual organization in the parasitic angiosperm Striga asiatica L. (Kuntze).

In order to better understand the regulation of cellular differentiation during haustorial development in parasitic angiosperms, we have begun to examine the structure and expression characteristics of genes encoding various components of the plant cytoskeleton in Striga asiatica L. (Kuntze). We describe here the cloning and characterization of three actin genes from Striga with significant similarity at the nucleotide level and encoding proteins having greater than 98% identity. However, the three genes (designated SAAc-1, SAAc-2 and SAAc-3) differ from each other in their organization and SAAc-3 contains an unusual exon-intron arrangement relative to genes encoding actins described in other higher plants. The significance of these observations concerning the evolutionary origins and potential roles of Striga actin genes is discussed.

Actins↗
PubMed1999

Evolution of Wolbachia pipientis transmission dynamics in insects.

Wolbachia pipientis is an intracellular bacterial parasite of arthropods that enhances its transmission by manipulating host reproduction, most commonly by inducing cytoplasmic incompatibility. The discovery of isolates with modified cytoplasmic incompatibility phenotypes and others with novel virulence properties is an indication of the potential breadth of evolutionary strategies employed by Wolbachia.

Animals↗
PubMed2003

Fungus-specific microsatellite primers of lichens: application for the assessment of genetic variation on different spatial scales in Lobaria pulmonaria.

We isolated 12 microsatellite loci for the epiphytic lichen-forming ascomycete Lobaria pulmonaria and studied their patterns of variation within and among populations from Canada and Switzerland. Even though several microsatellites exhibited high levels of variability at different spatial scales, we did not find any evidence for intrathalline variation. Most of the genetic variation was attributed to differences among individuals within populations. High genetic variation was also detected among L. pulmonaria samples taken from individual trees, suggesting that either multiple colonization events had occurred or that local recombination is frequent. The geographically structured distribution of alleles from several microsatellites indicated that L. pulmonaria from Canada and Switzerland represent two distinct evolutionary lineages. The potential to identify multiple alleles, and their transferability to closely related species, make microsatellites an ideal tool to study dispersal, population differentiation, and microevolution in lichens.

Alleles↗