Showing papers in "Genetica in 2002"

Transposable elements and the evolution of genome size in eukaryotes

Abstract: It is generally accepted that the wide variation in genome size observed among eukaryotic species is more closely correlated with the amount of repetitive DNA than with the number of coding genes. Major types of repetitive DNA include transposable elements, satellite DNAs, simple sequences and tandem repeats, but reliable estimates of the relative contributions of these various types to total genome size have been hard to obtain. With the advent of genome sequencing, such information is starting to become available, but no firm conclusions can yet be made from the limited data currently available. Here, the ways in which transposable elements contribute both directly and indirectly to genome size variation are explored. Limited evidence is provided to support the existence of an approximately linear relationship between total transposable element DNA and genome size. Copy numbers per family are low and globally constrained in small genomes, but vary widely in large genomes. Thus, the partial release of transposable element copy number constraints appears to be a major characteristic of large genomes.

Herbivorous insects: model systems for the comparative study of speciation ecology.

Abstract: Does ecological divergence drive species-level evolutionary diversification? How so and to what degree? These questions were central to the thinking of the evolutionary synthesis Only recently, however, has the ecology of speciation become an important focus of empirical study Here, we argue that ecologically specialized, phylogenetically diverse, and experimentally tractable herbivorous insect taxa offer great opportunities to study the myriad mechanisms by which ecology may cause reproductive isolation and promote speciation We call for the development and integrated experimental study of a taxonomic diversity of herbivore model systems and discuss the availability and recent evaluation of suitable taxa Most importantly, we describe a general comparative framework that can be used to rigorously test a variety of hypotheses about the relative contributions and the macroevolutionary generality of particular mechanisms Finally, we illustrate important issues for the experimental analysis of speciation ecology by demonstrating the consequences of specialized host associations for ecological divergence and premating isolation in Neochlamisus bebbianae leaf beetles

Mechanisms and rates of genome expansion and contraction in flowering plants

Abstract: Plant genomes are exceptional for their great variation in genome size, an outcome derived primarily from their frequent polyploid origins and from the amplification of retrotransposons. Although most studies of plant genome size variation have focused on developmental or physiological effects of nuclear DNA content that might influence plant fitness, more recent studies have begun to investigate possible mechanisms for plant genome expansion and contraction. Analyses of 'relatively neutral' genome components, like transposable elements, have been particularly fruitful, largely due to the enormous growth in genomic sequence information from many different plant species. Current data suggest that unequal recombination can slow the growth in genome size caused by retrotransposon amplification, but that illegitimate recombination and other deletion processes may be primarily responsible for the removal of non-essential DNA from small genome plants.

Genome size and developmental complexity.

Abstract: Haploid genome size (C-value) is correlated positively with cell size, and negatively with cell division rate, in a variety of taxa. Because these associations are causative, genome size has the potential to impact (and in turn, be influenced by) organism-level characters affected by variation in either of these cell-level parameters. One such organismal feature is development. Developmental rate, in particular, has been associated with genome size in numerous plant, vertebrate, and invertebrate groups. However, rate is only one side of the developmental coin; the other important component is complexity. When developmental complexity is held essentially constant, as among many plants, developmental rate is the visibly relevant parameter. In this case, genome size can impose thresholds on developmental lifestyle (and vice versa), as among annual versus perennial plants. When developmental rate is constrained (as during time-limited amphibian metamorphosis), complexity becomes the notable variable. An appreciation for this rate-complexity interaction has so far been lacking, but is essential for an understanding of the relationships between genome size and development. Moreover, such an expanded view may help to explain patterns of variation in taxa as diverse as insects and fish. In each case, a hierarchical approach is necessary which recognizes the complex interaction of evolutionary processes operating at several levels of biological organization.

DNA loss and evolution of genome size in Drosophila

Abstract: Mutation is often said to be random. Although it must be true that mutation is ignorant about the adaptive needs of the organism and thus is random relative to them as a rule, mutation is not truly random in other respects. Nucleotide substitutions, deletions, insertions, inversions, duplications and other types of mutation occur at different rates and are effected by different mechanisms. Moreover the rates of different mutations vary from organism to organism. Differences in mutational biases, along with natural selection, could impact gene and genome evolution in important ways. For instance, several recent studies have suggested that differences in insertion/deletion biases lead to profound differences in the rate of DNA loss in animals and that this difference per se can lead to significant changes in genome size. In particular, Drosophila melanogaster appears to have a very high rate of deletions and the correspondingly high rate of DNA loss and a very compact genome. To assess the validity of these studies we must first assess the validity of the measurements of indel biases themselves. Here I demonstrate the robustness of indel bias measurements in Drosophila, by comparing indel patterns in different types of nonfunctional sequences. The indel pattern and the high rate of DNA loss appears to be shared by all known nonfunctional sequences, both euchromatic and heterochromatic, transposable and non-transposable, repetitive and unique. Unfortunately all available nonfunctional sequences are untranscribed and thus effects of transcription on indel bias cannot be assessed. I also discuss in detail why it is unlikely that natural selection for or against DNA loss significantly affects current estimates of indel biases.

Feast and famine in plant genomes.

Abstract: Plant genomes vary over several orders of magnitude in size, even among closely related species, yet the origin, genesis and significance of this variation are not clear. Because DNA content varies over a sevenfold range among diploid species in the cotton genus (Gossypium) and its allies, this group offers opportunities for exploring patterns and mechanisms of genome size evolution. For example, the question has been raised whether plant genomes have a 'one-way ticket to genomic obesity', as a consequence of retroelement accumulation. Few empirical studies directly address this possibility, although it is consistent with recent insights gleaned from evolutionary genomic investigations. We used a phylogenetic approach to evaluate the directionality of genome size evolution among Gossypium species and their relatives in the cotton tribe (Gossypieae, Malvaceae). Our results suggest that both DNA content increase and decrease have occurred repeatedly during evolution. In contrast to a model of unidirectional genome size change, the frequency of inferred genome size contraction exceeded that of expansion. In conjunction with other evidence, this finding highlights the dynamic nature of plant genome size evolution, and suggests that poorly understood genomic contraction mechanisms operate on a more extensive scale that previously recognized. Moreover, the research sets the stage for fine-scale analysis of the evolutionary dynamics and directionality of change for the full spectrum of genomic constituents.

Recombination and the divergence of hybridizing species

Abstract: The interplay between hybridization and recombination can have a dramatic effect on the likelihood of speciation or persistence of incompletely isolated species. Many models have suggested recombination can oppose speciation, and several recent empirical investigations suggest that reductions in recombination between various components of reproductive isolation and/or adaptation can allow species to persist in the presence of gene flow. In this article, we discuss these ideas in relation to speciation models, phylogenetic analyses, and species concepts. In particular, we revisit genetic architectures and population mechanisms that create genetic correlations and facilitate divergence in the face of gene flow. Linkage among genes contributing to adaptation or reproductive isolation due to chromosomal rearrangements as well as pleiotropy or proximity of loci can greatly increase the odds of species divergence or persistence. Finally, we recommend recombination to be a focus of inquiry when studying the origins of biological diversity.

Sex determination in flies, fruitflies and butterflies.

Abstract: Sex determination mechanisms, differing in their modality, are widely represented in all the various animal taxa, even at the intraspecific level. Within the highly diversified Class Insecta, Drosophila has been used to unravel the mechanistic molecular and genetic interactions that are involved in sex determination. Indeed, the molecularly characterized genes of the Drosophila sex determination hierarchy X:A > Sxl > tra > dsx have been fruitful starting points in the cloning of homologous genes from other insect species. This cascade seems to control sex determination in all Drosophila species. However, no sex-specific regulatory Sxl homologues have been isolated from the Mediterranean fruitfly (medfly), Ceratitis capitata, the housefly, Musca domestica, Chrysomya rufifacies nor from the distantly related phorid fly Megaselia scalaris. Moreover, all these other species use primary signals different from the intricate X:A counting system of Drosophila. However, dsx homologues isolated from these and other dipteran species as well as from the silkmoth, Bombyx mori, share a conserved sex-specific regulation based on alternative splicing. An understanding of the sex determination mechanisms in insects that are of agricultural or public health importance may help in the development of improved methods for their control using the sterile insect technique.

Variation in female mate choice within guppy populations: population divergence, multiple ornaments and the maintenance of polymorphism.

Abstract: The evolutionary significance of variation in mate choice behaviour is currently a subject of some debate and considerable empirical study. Here, I review recent work on variation within and among guppy (Poecilia reticulata) populations in female mate choice and mating preferences. Empirical results demonstrate that there is substantial variation within and among populations in female responsiveness and choosiness, and much of this variation is genetic. Evidence for variation in preference functions also exists, but this appears to be more equivocal and the relative importance of genetic variation is less clear cut. In the second half of this review I discuss the potential significance of this variation to three important evolutionary issues: the presence of multiple male ornaments, the maintenance of polymorphism and divergence in mate recognition among populations. Studies of genetic variation in mate choice within populations indicate that females have complex, multivariate preferences that are able to evolve independently to some extent. These findings suggest that the presence of multiple male ornaments may be due to multiple female mating preferences. The extreme polymorphism in male guppy colour patterns demands explanation, yet no single satisfactory explanation has yet emerged. I review several old ideas and a few new ones in order to identify the most promising potential explanations for future empirical testing. Among these are negative frequency dependent selection, environmental heterogeneity coupled with gene flow, and genetic constraints. Last, I review the relative extent of within and among-population variation in mate choice and mating preferences in order to assess why guppies have not speciated despite a history of isolation and divergence. I argue that variation within guppy populations in mate choice and enhanced mating success of new immigrants to a pool are major impediments to population divergence of the magnitude that would be required for speciation to occur.

Genetic sexing strains in medfly, Ceratitis capitata, sterile insect technique programmes.

Abstract: The introduction of genetic sexing strains (GSS) into medfly, Ceratitis capitata(Wiedemann), sterile insect technique (SIT) programmes started in 1994 and it was accompanied by extensive evaluation of the strains both in field cages and in open field situations. Two male-linked translocation systems, one based on pupal colour, wp, and the other based on temperature sensitivity, tsl, have been used in medfly SIT programmes and they have quite different impacts on mass rearing strategy. In strains based on tsl, female zygotes are killed using high temperature and for wpstrains, female and male pupae are separated based on their colour. In all these systems the colony females are homozygous for the mutation requiring that the mutation is not too deleterious and the males are also semi-sterile due to the presence of a male-linked translocation. Managing strain stability during large-scale mass rearing has presented some problems that have been essentially solved by selecting particular translocations for GSS and by the introduction of a filter rearing system (FRS). The FRS operates by removing from the colony any recombinant individuals that threaten the integrity of the strain. The use of GSS opens up the possibility of using the SIT for suppression as opposed to eradication and different radiation strategies can be considered. Some of the many field trials of the strains that were carried out before the strains were introduced into operational programmes are reviewed and an overview is given of their current use.

Genetic Differentiation, Gene Flow and the Origin of Infestations of the Medfly, Ceratitis Capitata

Abstract: The genetic structure of natural populations of the economically important dipteran species Ceratitis capitatawas analysed using both biochemical and molecular markers. This revealed considerable genetic variation in populations from different geographic regions. The nature of this variation suggests that the evolutionary history of the species involved the spread of individuals from the ancestral African populations through Europe and, more recently, to Latin America, Hawaii and Australia. The observed variation can be explained by various evolutionary forces acting differentially in the different geographic areas, including genetic drift, bottleneck effects, selection and gene flow. The analysis of the intrinsic variability of the medfly's genome and the genetic relationships among populations of this pest is a prerequisite for any control programme.

Mass rearing of temperature sensitive genetic sexing strains in the Mediterranean fruit fly (Ceratitis capitata).

Abstract: Genetic sexing strains (GSS) based on the temperature sensitive lethal (tsl) mutation are being used to produce sterile male medflies for large scale sterile insect technique (SIT) programmes for this pest. The use of male-only strains increases the overall efficiency of the technique. Currently more than 1.4 billion sterile male-only pupae are produced per week in different facilities around the world. Due to the mutations used to construct these strains, that is, translocations and selectable markers, they require different and more careful mass rearing procedures than do bisexual strains (BSS). The basic rearing technology has been developed and can be used to produce only males on a predictable basis to a level of 99.9% accuracy. If specific rearing procedures are followed, then tsl-based GSS has a rearing efficiency that is equal to that of a BSS and it is already know that males produced by the tsl-based GSS are of equal quality to males produced by BSS. Based on current rearing technology the cost of production of male pupae is about the same for both types of strain. This is due to the large colony that is required for the tsl-based GSS. This paper discusses the considerations that need to be taken into account during mass rearing of GSS and identifies the most efficient production processes that are currently available.

Genome deterioration: loss of repeated sequences and accumulation of junk DNA

Abstract: A global survey of microbial genomes reveals a correlation between genome size, repeat content and lifestyle Free-living bacteria have large genomes with a high content of repeated sequences and self-propagating DNA, such as transposons and bacteriophages In contrast, obligate intracellular bacteria have small genomes with a low content of repeated sequences and no or few genetic parasites In extreme cases, such as in the 650 kb-genomes of aphid endosymbionts of the genus Buchnera all repeated sequences above 200 bp have been eliminated We speculate that the initial downsizing of the genomes of obligate symbionts and parasites occurred by homologous recombination at repeated genes, leading to the loss of large blocks of DNA as well as to the consumption of repeated sequences Further sequence elimination in these small genomes seems primarily to result from the accumulation of short deletions within genic sequences This process may lead to temporary increases in the genomic content of pseudogenes and ‘junk’ DNA We discuss causes and long-term consequences of extreme genome size reductions in obligate intracellular bacteria

Karyotypic diversity in polyploid gibel carp, Carassius auratus gibelio Bloch.

Abstract: Polyploid gibel carp, Carassius auratus gibelio, is an excellent model system for evolutionary genetics owing to its specific genetic background and reproductive modes. Comparative karyotype studies were performed in three cultured clones, one artificially manipulated group, and one mated group between two clones. Both the clones A and P had 156 chromosomes in their karyotypes, with 36 metacentric, 54 submetacentric, 36 subtelocentric, 24 acrocentric, and six small chromosomes. The karyotype of clone D contained 162 chromosomes, with 42 metacentric, 54 submetacentric, 36 subtelocentric, 24 acrocentric, and six small chromosomes. All the three clones had six small chromosomes in common. Group G, being originated from the clone D by artificial manipulation, showed supernumerary microchromosomes or chromosomal fragments, in addition to the normal chromosome complement that was identical to the clone D. The offspring from mating between clones D and A had 159 chromosomes. Comparing with the clone A, the DA offspring showed three extra metacentric chromosomes. In addition, variable RAPD fingerprint patterns and unusual SCAR marker inheritance were, respectively, detected among individuals of artificial group G and in the mated DA offspring. Both the chromosome and molecular findings suggest that genome reshuffling might have occurred by manipulation or mating of the clones.

Genome size and the accumulation of simple sequence repeats: implications of new data from genome sequencing projects.

Abstract: The relationship between the level of repetitiveness in genomic sequences and genome size has been re-investigated making use of the rapidly growing database of complete eubacterial and archaeal genome sequences combined with the fragmentary but now large amount of data from eukaryotic genomes. Relative simplicity factors (RSFs), which measure the repetitiveness of sequences, were calculated and significantly simple motifs (SSMs), which identify the kinds of sequences that are repeated, were identified. A previously reported correlation between genome size and repetitiveness was confirmed, but it was shown that the higher RSFs seen in eukaryotic genomes also reflect a generally higher level of repetitiveness independent of genome size differences. Differences in genome size are responsible for about 10% of the variance in RSF seen between species. The spectrum of SSMs seen within a genome differed markedly within the eubacteria but less so in eukaryotes and, particularly, in archaea. Species with SSM spectra that differ from the norm tend also to have high RSFs for their genome size and to be pathogens that make use of repetitive sequences to avoid host defence responses. Some of the variance in repetitiveness seen in other species may therefore also reflect the action of selection, although other forces such as variation in the effectiveness of mechanisms for regulating slippage errors of replication, may also be important.

Genetic and behavioral components of the cryptic species boundary between Laupala cerasina and L. kohalensis (Orthoptera: Gryllidae).

Abstract: Cryptic species are often hypothesized on the basis of differences in courtship signals. These signal differences suggest that mate recognition systems, which include both courtship signals and responses to those signals, have diverged between genetically isolated populations. Cryptic species are therefore thought to represent distinct genetic units, the boundaries of which are maintained by premating incompatibilities, specifically by receiver preferences for conspecific signals. Laupala cerasina and L. kohalensis are sympatric species of swordtail crickets endemic to the big island of Hawaii, that are distinguishable by differences in male courtship song. We first tested whether groupings hypothesized by acoustic similarity reflect genetic groupings, using AFLP data to estimate genetic relationships. Second, we tested whether genetic boundaries are maintained by female preferences for conspecific song characteristics. Phonotaxis trials were used to determine the extent of female preferences for conspecific male song. Results generally support both hypotheses, but suggest the presence of porous species boundaries.

Sexual isolation and speciation in bacteria.

Abstract: Like organisms from all other walks of life, bacteria are capable of sexual recombination. However, unlike most plants and animals, bacteria recombine only rarely, and when they do they are extremely promiscuous in their choice of sexual partners. There may be no absolute constraints on the evolutionary distances that can be traversed through recombination in the bacterial world, but interspecies recombination is reduced by a variety of factors, including ecological isolation, behavioral isolation, obstacles to DNA entry, restriction endonuclease activity, resistance to integration of divergent DNA sequences, reversal of recombination by mismatch repair, and functional incompatibility of recombined segments. Typically, individual bacterial species are genetically variable for most of these factors. Therefore, natural selection can modulate levels of sexual isolation, to increase the transfer of genes useful to the recipient while minimizing the transfer of harmful genes. Interspecies recombination is optimized when recombination involves short segments that are just long enough to transfer an adaptation, without co-transferring potentially harmful DNA flanking the adaptation. Natural selection has apparently acted to reduce sexual isolation between bacterial species. Evolution of sexual isolation is not a milestone toward speciation in bacteria, since bacterial recombination is too rare to oppose adaptive divergence between incipient species. Ironically, recombination between incipient bacterial species may actually foster the speciation process, by prohibiting one incipient species from out-competing the other to extinction. Interspecific recombination may also foster speciation by introducing novel gene loci from divergent species, allowing invasion of new niches.

Prospects for using genetic transformation for improved SIT and new biocontrol methods.

Abstract: The genetic manipulation of non-drosophilid insect species is possible by the creation of recombinant DNA constructs that can be integrated into host genomes by several transposon-based vector systems. This technology will allow the development and testing of a variety of systems that can improve existing biological control methods, and the development of new highly efficient methods. For programs such as sterile insect technique (SIT), transgenic strains may include fluorescent protein marker genes for detection of released insects, and conditional gene expression systems that will result in male sterility and female lethality for genetic sexing. Conditional expression systems include the yeast GAL4 system and the bacterial Tet-off and Tet-on systems that can, respectively, negatively or positively regulate expression of genes for lethality or sterility depending on a dietary source of tetracycline. Importantly, strains for male sterility must also incorporate an effective system for genetic sexing, since typically, surviving females would remain fertile. Models for the use of these expression systems and associated genetic material come from studies in Drosophila and, while many of these systems should be transferable to other insects, continued research will be necessary in insects of interest to clone genes, optimize germ-line transformation, and perform vector stability studies and risk assessment for their release as transgenic strains.

Male sterility thermal thresholds in Drosophila: D. simulans appears more cold-adapted than its sibling D. melanogaster.

Abstract: Numerous different criteria may be used for analysing species thermal adaptation. We compared male sterility thresholds in the two most investigated cosmopolitan siblings, D. melanogaster and D. simulans. A survey of various populations from Europe and North Africa evidenced consistent differences between the two species, and a detailed analysis was made on flies from Marrakech. Sharp sterility thresholds were observed in both species but at different temperatures: D. simulans appeared more tolerant to cold than its sibling (difference 1°C) but more sensitive to heat (difference 1.5°C). When transferred to an optimum temperature of 21°C, D. simulans males, sterilized by a low temperature, recovered more rapidly than males of D. melanogaster; the reverse was true on the high temperature side. The analysis of progeny number also revealed the better tolerance of D. simulans males to cold but a lesser tolerance to heat. From these observations, we might expect that D. simulans should be more successful in cold temperate countries than its sibling, while ecological observations point to the contrary. Our data clearly show the difficulty of comparing ecophysiological data to field observations, and also the need of extensive comparative life history studies in closely related species.

Repeated losses of TTAGG telomere repeats in evolution of beetles (Coleoptera).

Abstract: We studied the occurrence of (TTAGG) n telomere repeats in 12 species of beetles, representing main lineages of the Coleoptera phylogenetic tree, by Southern hybridization and fluorescence in situ hybridization (FISH). In contrast to other insect orders, beetles were heterogeneous with respect to the occurrence of TTAGG repeats. In addition, the presence or absence of (TTAGG) n motif was irrespective of phylogenetic relationships. In the suborder Polyphaga, six species displayed positive hybridization signals. These were Silpha obscura, Agrilus viridis, Ampedus sanguineus, Stegobium paniceum, Oryzaephilus surinamensis, and Leptinotarsa decemlineata. Whereas negative signals were obtained in three polyphagan species, Geotrupes stercorarius, Thanasimus formicarius, and Sitophilus granarius. In the suborder Adephaga, the TTAGG sequence was present in one species, Graphoderus cinereus, and absent in two species, Orectochilus villosus and Pterostichus oblongopunctatus. We concluded that the telomerase-dependent (TTAGG) n motif had been repeatedly lost in different phylogenetic branches of Coleoptera and probably replaced with another mechanism of telomere elongation. This had to happen at least 5–6 times. The results suggest a predisposition or a backup mechanism of telomere maintenance in the genome of beetles that enabled them to make frequent evolutionary changes in the telomere composition.

Jam packed genomes--a preliminary, comparative analysis of nucleomorphs.

Abstract: There are two ways eukaryotic cells can permanently acquire chloroplasts. They can take up a cyanobacterium and turn it into a chloroplast or they can engulf an alga that already has a chloroplast. The second method is far more common and there are at least seven major groups of protists that have obtained their chloroplasts, this way. In most cases little remains of the engulfed alga apart from its chloroplast, but in two groups, the cryptomonads and chlorarachniophytes, a small remnant nucleus of the engulfed alga is still present. These tiny nuclei, called nucleomorphs, are the smallest and most compact eukaryotic genomes known and recently the nucleomorph of the cryptomonad alga Guillardia theta, was completely sequenced (551 kilobases). The nucleomorph of the chlorarachniophyte Bigellowiella natans (380 kilobases), is also being sequenced and is about half complete. We discuss some of the similarities and differences that are emerging between these two nucleomorph genomes. Both genomes contain just three chromosomes that encode mainly housekeeping genes and a few proteins for chloroplast functions. The bulk of nucleomorph gene coding capacity, therefore, appears to be devoted to self perpetuation and creating gene and protein expression machineries to make a small number of essential chloroplast proteins. We discuss reasons why both nucleomorphs are extraordinarily compact and why their gene sequences are evolving rapidly.

Domesticated birds as a model for the genetics of speciation by sexual selection.

Abstract: In theory, even populations occupying identical environments can diverge in sexually selected traits, as a consequence of different mutational input. I evaluate the potential of this process by comparing the genetics of breeds of domesticated birds to what is known about the genetics of differences among species. Within domesticated species there is a strong correlation of time since domestication with the number of breeds. Descendants of the rock dove, Columba livia (the oldest domesticate) show differences in courtship, vocalizations, body shape, feather ornaments (crests and tails) and colors and color patterns. When nine other domesticated species are included there is a striking hierarchy, with more recent domesticates having a nested subset of these traits: the youngest domesticated species have breeds distinguished only by color. This suggests that selection of new, visible, mutations is driving the process of breed diversification, with mutations that appeal to the breeder happening the most frequently in color. In crosses among related species, color, feather ornaments and many vocalizations and displays show both intermediate dominance and pure dominance. Although the number of loci affecting each of these traits is typically unknown, limited evidence of the genetics of species’ differences suggests that some differences are due to the substitution of single genes of major effect. While neither the genetics of breeds nor the genetics of species provide a perfect model for the genetics of speciation, similarities between the two are sufficiently striking to infer that major, visible, mutations can provide the impetus underlying new directions of sexual selection.

Molecular phylogeny of genus Vigna subgenus Ceratotropis based on rDNA ITS and atpB-rbcL intergenic spacer of cpDNA sequences.

Abstract: The genetic diversity and phylogenetic relationships among species in the genus Vigna subgenus Ceratotropis were investigated using sequence data from the ribosomal DNA ITS and atpB-rbcL intergenic spacer of chloroplast DNA regions. While both sets of sequences were of similar lengths about 700 bp the rDNA-ITS was more informative than atpB-rbcL having 170% more polymorphic sites and five times as many parsimony-informative sites. The atpB-rbcL spacer may be appropriate for analysis of taxa above the species level in the genus Vigna. Results of analyzing rDNA-ITS revealed, with low level of statistical bias, separation of the subgenus into three groups that correspond to the three sections Aconitifoliae, Angulares, and Ceratotropis. The ancestral section is Aconitifoliae based on comparison with the outgroup species cowpea, Vigna unguiculata. The V. minima complex, V. minima, V. riukiuensis, and V. nakashimae, has a distinct evolutionary path within section Angulares. Other species in section Angulares are very closely related except V. trinervia. Vigna trinervia has an intermediate position between sections. Sequence data suggests one genome donor to V. reflexo-pilosa came from a lineage within section Angulares close to V. exilis, V. hirtella, and V. umbellata. Data presented supports the view that section Angulares is the most recently diversified section in the subgenus, as inferred by short terminal branch lengths among the species of this section.

Genetic relatedness among dioecious Ficus carica L. cultivars by random amplified polymorphic DNA analysis, and evaluation of agronomic and morphological characters.

Abstract: A collection of 64 fig (Ficus carica L.) accessions was characterized through the use of RAPD markers, and results were evaluated in conjunction with morphological and agronomical characters, in order to determine the genetic relatedness of genotypes with diverse geographic origin. The results indicate that fig cultivars have a rather narrow genetic base. Nevertheless, RAPD markers could detect enough polymorphism to differentiate even closely related genotypes (i.e., clones of the same cultivar) and a unique fingerprint for each of the genotypes studied was obtained. No wasteful duplications were found in the collection. Cluster analysis allowed the identification of groups in accordance with geographic origin, phenotypic data and pedigree. Taking into account the limited information concerning fig cultivar development, the results of this study, which provide information on the genetic relationships of genetically distinct material, dramatically increase the fundamental and practical value of the collection and represent an invaluable tool for fig germplasm management.

Expansion of genome coding regions by acquisition of new genes.

Abstract: As it is the case for non-coding regions, the coding regions of organisms can be expanded or shrunk during evolutionary processes. However, the dynamics of coding regions are expected to be more correlated with functional complexity and diversity than are the dynamics of non-coding regions. Hence, it is interesting to investigate the increase of diversity in coding regions – the origin and evolution of new genes – because this provides a new component to the genetic variation underlying the diversity of living organisms. Here, we examine what is known about the mechanisms responsible for the increase in gene number. Every mechanism affects genomes in a distinct way and to a different extent and it appears that certain organisms favor particular mechanisms. The detail of some interesting gene acquisitions reveals the extreme dynamism of genomes. Finally, we discuss what is known about the fate of new genes and conclude that many of the acquisitions are likely to have been driven by natural selection; they increase functional complexity, diversity, and/or adaptation of species. Despite this, the correlation between complexity of life and gene number is low and closely related species (with very similar life histories) can have very different number of genes. We call this phenomenon the G-value paradox.

Involvement of desat1 gene in the control of Drosophila melanogaster pheromone biosynthesis

Abstract: Cuticular pheromones in Drosophila melanogaster are unsaturated hydrocarbons with at least one double bond in position 7: 7-tricosene and 7-pentacosene in males and 7,11 -heptacosadiene and 7,11 -nonacosadiene in females. We have previously shown that a desaturase gene, desat1, located in chromosome region 87 C could be involved in this process: the Desat1 enzyme preferentially leads to the synthesis of palmitoleic acid, a precursor of omega7 fatty acids and 7-unsaturated hydrocarbons. Therefore, we have searched for P-elements in the 87 region and mapped them. One was found inserted into the first intron of the desat1 gene. Flies heterozygous for this insertion showed a large decrease in the level of 7-unsaturated hydrocarbons, comparable to that observed in flies heterozygous for a deficiency overlapping desat1. Less than 1 % of flies homozygous for this insertion were viable. They were characterized by dramatic pheromone decreases. After excision of the transposon, the pheromone phenotype was reversed in 69% of the lines and the other excision lines had more or less decreased amounts of 7-unsaturated hydrocarbons. All these results implicate desat1 in the synthesis of Drosophila pheromones.

The Evolution of Hybrid Infertility: Perpetual Coevolution between Gender-Specific and Sexually Antagonistic Genes

Abstract: A new hypothesis is proposed for the rapid evolution of postzygotic reproductive isolation via hybrid infertility. The hypothesis is motivated by two lines of experimental research from Drosophila melanogaster that demonstrate that sexually antagonistic fitness variation is abundant and that epistatic fitness variation on the Y chromosome is common. The hypothesis states that the expression of sexually antagonistic genes leads to a ‘gender-load’ in each sex. In response, gender-limited reproductive genes are selected to ameliorate, through pleiotropy, the expression of sexually antagonistic genes. Chronic coevolution between gender-limited genes and gender-unlimited sexually antagonistic genes causes rapid divergence of reproductive proteins among allopatric populations, ultimately leading to hybrid infertility.

Why so many noncoding nucleotides ? The eukaryote genome as an epigenetic machine

Abstract: It is recalled that dispensability of sequences and neutral substitution rate must not be construed to be markers of nonfunctionality. Different aspects of functionality relate to differently-sized nucleotide communities. At the time cells became nucleated, a boom of epigenetic processes led to uses of DNA that required many more nucleotides operating collectively than do functions definable in terms of classical genetics. Each order of magnitude of nucleotide plurality was colonized by functions germane to that order. The eukaryote genome became a great epigenetic machine. Sequences of different levels of nucleotide plurality are briefly discussed from the point of view of their functional relevance. By their activities as both transcribed genes and cis-acting repeats, SINEs and LINEs are the principal link between genetic and epigenetic processes. SINEs can act as local repeats to produce position effect variegation (PEV) in a nearby gene. PEV may thus represent a general method of overall transcriptional regulation at the level of cell collectivities. When tracking the scale dependence of nucleotide function, one finds the 100 kb order of nucleotide plurality to provide epigenetically the basis at once for PEV, imprinting, and cell determination, with sectorial repressibility a trait common to the three. In sectorial repressibility, introns may play a structural role favoring the stability of higher-order chromatin structures. At that level of nucleotide involvement, nonconserved nonhomologous nonprotein-coding sequences may often play the same structural roles. In addition, genomic distance per se – and, therefore, the mass of intervening nucleotides – can have functional effects. Distances between enhancers and promoters need to be probed in this respect. At the 1000 kb level of nucleotide function, attention is focused on the formation of centromeres. It is one of the levels of nucleotide plurality per function where specificity in the generation of DNA/protein complexes seems to depend more upon the structural fit among factors than upon the DNA sequence. This circumstance may explain in part the prevailing difficulty in recognizing the functional nature of sequences among non-protein-coding nucleotide arrays and the propensity among investigators to tag the majority of DNA sequences in higher organisms as functionally meaningless. Noncoding DNA often may not be ‘selected’ as an appropriate niche for a certain function, but be ‘elected’ in that capacity by a group of factors, as a preexisting sequence that is only now called upon to serve. Much of the non-protein-coding DNA may thus be only conditionally functional and in fact may never be elected to functions at a high level of nucleotide plurality. Eukaryotes are composites, at different levels of this plurality, of the functional and the nonfunctional, as well as of the conditionally functional and the outright functional. Thus, a sequence that is nonfunctional at one level of nucleotide plurality may participate in a functional sequence at a more inclusive level. In the end, every nucleotide is at least infinitesimally functional if, for metabolic and developmental reasons, the chromatin mass as such becomes a selectable entity. Given the scale dependence of nucleotide function, large amounts of ‘junk DNA’, contrary to common belief, must be assumed to contribute to the complexity of gene interaction systems and of organisms.

Improving Male Mating Competitiveness and Survival in the Field for Medfly, Ceratitis Capitata(Diptera: Tephritidae) SIT Programs

Abstract: The success of the sterile insect technique (SIT) depends critically upon mating between released sterilized males and wild females. In Hawaii, improvements in the efficiency of sterile males were attempted on two separate fronts – mating enhancement and survival improvement. In the former, two methods have been investigated – selective breeding and aromatherapy. In the latter, flies which survived in field cages for several days were selected and bred to produce progeny with enhanced survival ability compared to control flies. Regarding mating selection, standard laboratory-reared males that successfully mated with wild females in field cages were allowed to breed. F1 offspring were inbred, then the selection procedure was repeated for four additional cycles. In the aromatherapy procedure, laboratory-reared males were exposed to ginger root oil for several hours 1 day prior to testing in field cages. Compared to controls, the selected flies improved the mating competitiveness of male flies ca. 3-fold, irradiation reduced this increase to ca. 2.5-fold. Exposing the selected, hybrid strain raised the fitness of the lab males to ca. 9-fold that of wild males. In the ongoing survival selection study, we have obtained lines in which the selected males survived ca. 2-fold better than laboratory control males over several days in an outdoor field cage, with food and water provided. The goal is to combine the traits of higher survival and mating ability into a single strain for SIT release.

The evolution of sex determination systems in dipteran insects other than Drosophila.

Abstract: The multitude of sex determination mechanisms displayed in dipteran insects has usually been described in terms of variations on a single principle in which the primary signal of the primitive pathway consists of a single allelic difference at one locus. Evolution of sex determination mechanisms is thought to have occurred by the addition of genes below the top gene of the pathway. The elucidation of the complex sex determination pathway of Drosophila melanogaster, as well as recent evidence that the basal genes of the pathway seem to be conserved across metazoan genera both in structure and, to a lesser degree, in function, points towards the possibility that sex determination pathways may have evolved from the bottom-up. Further to this is the question of whether the dominant male-determining factor, M, which is found in a number of insect species, represents part of the ancient sex determination pathway or is a later addition to the pathway. This, together with the possibility that the M factors found in numerous dipteran insect species may have a common origin, is discussed. The similarities of the sex determination pathways under the control of M and the implications in relation to the construction of genetic sexing strains for biological control are also discussed.