DNA turnover and the molecular clock

Summary Many detailed studies on the mechanisms by which different components of eukaryotic nuclear genomes have diverged reveal that the majority of sequences are seemingly not passively accumulating base substitutions in a clocklike manner solely determined by laws of diffusion at the population level. It appears that variation in the rates, units, biases, and gradients of several DNA turnover mechanisms are contributing to the course of DNA divergence. Turnover mechanisms have the potential to retard, maintain, or accelerate the rate of DNA differentiation between populations. Furthermore, examples are known of coding and noncoding DNA subject to the simultaneous operation of several turnover mechanisms leading to complex patterns of fine-scale restructuring and divergence, generally uninterpretable using selection and/or neutral drift arguments in isolation. Constancy in the rate of divergence, where observed over defined periods of time, could be a reflection of constancy in the rates and units of turnover. However, a consideration of the generally large disparity between rates of turnover and mutation reveals that DNA clocks, which would be independently driven by turnover in separate genomic components, would tend to be episodic. The utility of any given DNA sequence for measuring time and species relationships, like individual proteins, is proportional to the extent to which all contributing forces to the evolution of the sequence, internal and external, are understood.     

Behavioral estimates of male mating success tested by DNA fingerprinting in a polygynous mammal

We used DNA fingerprinting to determine paternity of 80 calvesborn into the individually monitored population of red deer(Cervus elaphus) on the Isle of Rum, Scotland. Using the paternityinformation, we investigated the assumptions and predictionsof behavioral estimates of male mating success, on which previousstudies in this population have relied. Over an 11- day intervalin the rut centered on a female's estimated date of conception,the probability that a male fathers a calf is closely relatedto the number of days he holds the female in his harem, increasingfrom 0.12 for 1 day to 1.0 for 6 days or more. We compared threemethods for estimating the reproductive success of individualmales from field observations of harem membership with truesuccess revealed by DNA fingerprinting. All three methods accuratelyidentified the relative success of individual males but werepoor predictors of absolute success: the behavioral methodsunderestimate the true success of successful males and overestimatethe success of many males who, in fact, fail to father any calves.In consequence, variance in male mating success is greater thanprevious behavioral estimates for this population suggested.Both harem membership data and observations of mating and otherestrous behavior can be used to identify males most likely tofather a specific calf.     

Evolving the improbable

The debate about the evolutionary roles of natural selection and molecular drive cannot be resolved by assigning probabilities with hind-sight to unique events in the evolution of complex adaptations. Hoyle dismisses natural selection by calculating, erroneously, the improbability of assembling by chance a string of amino acids in the order in which they occur in a given protein. Dawkins dismisses molecular drive on the same false grounds of the improbability of making the right decision, by chance, at each step in a long series of steps in the evolution of a given trait. Calculation of the probability, at any given step, of a successful match between fortuitous genetic variation and fortuitous environmental heterogeneity requires detailed knowledge of all parameters at that step. Such information is an essential requirement for quantifying the roles of natural selection and molecular drive in the evolution of one actual series of steps out of many potential series.     

Genetic relationships between subspecies of the tsetse fly Glossina morsitans inferred from variation in mitochondrial DNA sequences

A 750 base pair segment of DNA from the tsetse fly Glossina morsitans morsitans was isolated by means of molecular cloning. It was shown by DNA hybridization to have substantial sequence homology with a defined region of the mitochondrial genomes of several Drosophila species. When used as a probe against DNA prepared from single tsetse flies, the cloned sequence revealed local restriction site variation between members of the G. morsitans subspecies complex. This feature was used to demonstrate maternal inheritance of the sequence in progeny of hybrid crosses and to assemble comparative restriction maps for a 3-kilobase segment of each mitochondrial genome. The data obtained from these exercises point to a higher genetic identity between G. m. morsitans and G. m. centralis than between either form and G. m. submorsitans.     

The effect of labiate herbs and white clover onPlutella xylostella oviposition

Small-scale greenhouse intercrop experiments were carried out, with Brussels sprouts (Brassica oleracea gemmifera L.) as crop plants and the herbs sage (Salvia officinalis L.) and thyme (Thymus vulgaris L.) as intercrops. Significant reductions in diamond-back moth (Plutella xylostella (L.)) oviposition were observed on intercropped brassicas.Green polyethylene models were shown to simulate the effect of the herbs. Contrast was shown to have no effect on oviposition by the diamond-back moth.An intercrop of white clover (Trifolium repens L.) vs. an intercrop of thyme, resulted in significantly lower egg-loads on brassicas associated with clover. An olfactory effect is postulated to account for this difference.

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Effets de la présence de Labiées et de treèfle blanc sur la ponte dePlutella xylotella

Résumé Le chou de Bruxelles (Brassica oleracea gemmifera L.), comme plante cultivée, et la sauge (Salvia officinalis L.) et le thym (Thymus vulgaris L.), ont été utilisés en serre pour des expériences à petite échelle sur les associations culturales. Une diminution significative de la ponte de la teigne du chou (Plutella xylostella L.) a été observée sur ces choux de Bruxelles.Des leurres en polystyrène vert ont été placés pour simuler l'effet des mauvaises herbes. Ils n'ont eu aucun effet sur la ponte de la teigne.L'association avec le trèfle blanc (Trifolium repens L.), comparée à celle avec le thym, a entrainé une ponte, sur choux de Bruxelles associés au trèfle significativement plus faible. On peut envisager que cette différence est due à une influence olfactive.

     

Genome Sequence of the Fleming Strain of Micrococcus luteus,a Simple Free-Living Actinobacterium

Micrococcus luteus (NCTC2665, “Fleming strain”) has one of the smallest genomes of free-living actinobacteria sequenced to date, comprising a single circular chromosome of 2,501,097 bp (G+C content, 73%) predicted to encode 2,403 proteins. The genome shows extensive synteny with that of the closely related organism, Kocuria rhizophila, from which it was taxonomically separated relatively recently. Despite its small size, the genome harbors 73 insertion sequence (IS) elements, almost all of which are closely related to elements found in other actinobacteria. An IS element is inserted into the rrs gene of one of only two rrn operons found in M. luteus. The genome encodes only four sigma factors and 14 response regulators, a finding indicative of adaptation to a rather strict ecological niche (mammalian skin). The high sensitivity of M. luteus to β-lactam antibiotics may result from the presence of a reduced set of penicillin-binding proteins and the absence of a wblC gene, which plays an important role in the antibiotic resistance in other actinobacteria. Consistent with the restricted range of compounds it can use as a sole source of carbon for energy and growth, M. luteus has a minimal complement of genes concerned with carbohydrate transport and metabolism and its inability to utilize glucose as a sole carbon source may be due to the apparent absence of a gene encoding glucokinase. Uniquely among characterized bacteria, M. luteus appears to be able to metabolize glycogen only via trehalose and to make trehalose only via glycogen. It has very few genes associated with secondary metabolism. In contrast to most other actinobacteria, M. luteus encodes only one resuscitation-promoting factor (Rpf) required for emergence from dormancy, and its complement of other dormancy-related proteins is also much reduced. M. luteus is capable of long-chain alkene biosynthesis, which is of interest for advanced biofuel production; a three-gene cluster essential for this metabolism has been identified in the genome.Micrococcus luteus, the type species of the genus Micrococcus (family Micrococcaceae, order Actinomycetales) (117), is an obligate aerobe. Three biovars have been distinguished (138). Its simple, coccoid morphology delayed the recognition of its relationship to actinomycetes, which are typically morphologically more complex. In the currently accepted phylogenetic tree of the actinobacteria, Micrococcus clusters with Arthrobacter and Renibacterium. Some other coccoid actinobacteria originally also called Micrococcus, but reclassified into four new genera (Kocuria, Nesterenkonia, Kytococcus, and Dermacoccus), are more distant relatives (121). The genus Micrococcus now includes only five species: M. luteus, M. lylae, M. antarcticus, M. endophyticus, and M. flavus (20, 69, 70, 121).We report here the genome sequence of Micrococcus luteus NCTC2665 (DSM 20030^T), a strain of historical interest, since Fleming used it to demonstrate bacteriolytic activity (due to lysozyme) in a variety of body tissues and secretions (29, 30), leading to its designation as Micrococcus lysodeikticus until its taxonomic status was clarified in 1972 (59). M. luteus has been used in a number of scientific contexts. The ease with which its cell wall could be removed made it a favored source of bacterial cell membranes and protoplasts for investigations in bioenergetics (28, 34, 89, 93). Because of the exceptionally high GC content of its DNA, M. luteus was used to investigate the relationship between codon usage and tRNA representation in bacterial genomes (51, 52, 61). Although it does not form endospores, M. luteus can enter a profoundly dormant state, which could explain why it may routinely be isolated from amber (39). Dormancy has been convincingly demonstrated under laboratory conditions (53-55, 83), and a secreted protein (Rpf) with muralytic activity is involved in the process of resuscitation (81, 82, 84, 85, 87, 125, 133).Micrococci are also of biotechnological interest. In addition to the extensive exploitation of these and related organisms by the pharmaceutical industry for testing and assaying compounds for antibacterial activity, micrococci can synthesize long-chain alkenes (1, 2, 127). They are also potentially useful for ore dressing and bioremediation applications, since they are able to concentrate heavy metals from low-grade ores (26, 66, 67, 116).Given its intrinsic historical and biological importance, and its biotechnological potential, it is perhaps surprising that the genome sequence of M. luteus was not determined previously (130). We consider here the strikingly small genome sequence in these contexts and also in relation to the morphological simplicity of M. luteus compared to many of its actinobacterial relatives, which include important pathogens as well as developmentally complex, antibiotic-producing bacteria with some of the largest bacterial genomes.