Mutation and evolution of microsatellites in Drosophila melanogaster

Levels of nucleotide polymorphism in the Drosophila melanogaster genome are correlated with rates of recombination. This relationship may be due to hitchhiking of advantageous mutations (selective sweeps) or to continual removal of deleterious mutations from the genome (background selection). One test of the relative contributions of selective sweeps and background selection to the observed levels of variation in the genome of D. melanogaster is to compare levels of nucleotide variability (with a mutation rate on the order of 10(-9) per nucleotide per generation) with more rapidly evolving DNA loci such as microsatellites. This test depends critically on details of the mutational process of microsatellites. In this paper, we summarize our studies of microsatellite characteristics and mutation rates in D. melanogaster. We find that D. melanogaster microsatellites are short and have a mutation rate (6.5 x 10(-6) per locus per generation) several orders of magnitude lower than mammals studied to date. We further show that genetic variation at 18 dinucleotide repeat microsatellites in a population of D. melanogaster from Maryland is correlated with regional rates of recombination. These and other microsatellite data suggest that both background selection and selective sweeps may contribute to the correlation between DNA sequence variation and recombination in Drosophila.     

Different patterns of molecular evolution of influenza A viruses in avian and human population

Patterns of molecular evolution of the influenza virus proteins and genes are discussed. The subsets of all viral genes corresponding to statistically significant clusters on dendrogram were shown to fall into two distinct groups. The first group was characterized by the presence of an exact linear relationship between the year of the strain isolation and the evolutionary distance. The subsets of human influenza virus genes belong to this group. A method for eliminating the "frozen" strains from the subsets and for calculating the evolutionary rates without construction of phylogenetic trees has been elaborated. The substitution rates calculated according to this technique agreed with the data obtained previously. A linear relationship was not observed in the second group. This group was predominantly composed of avian influenza virus genes. The lack of linear correlation pointed to the cocirculation of a large amount of different influenza virus genomic segments in the avian population. An approach for an examination of the role of intragenic recombination in the development of the antigenic subtypes of hemagglutinin is suggested. Our results suggest that recombination did not play a considerable role in this process, and that all modern subtypes of this protein were probably formed before the introduction of the influenza viruses into the human population. These findings are consistent with the hypothesis that influenza viruses penetrated into human population from their pools in avian populations.     

Weak male-driven molecular evolution in rodents

In humans and rodents the male-to-female ratio of mutation rate (alpha m) has been suggested to be extremely large, so that the process of nucleotide substitution is almost completely male-driven. However, our sequence data from the last intron of the X chromosome-linked (Zfx) and Y chromosome-linked (Zfy) zinc finger protein genes suggest that alpha m is only approximately 2 in rodents with a 95% confidence interval from 1 to 3. Moreover, from published data on oogenesis and spermatogenesis we estimate the male-to-female ratio of the number of germ cell divisions per generation to be approximately 2 in rodents, confirming our estimate of alpha m and suggesting that errors in DNA replication are the primary source of mutation. As the estimated alpha m for rodents is only one-third of our previous estimate of approximately 6 for higher primates, there appear to be generation-time effects--i.e., alpha m decreases with decreasing generation time.     

The molecular evolution of development

Morphological differences between species, from simple single-character differences to large-scale variation in body plans, can be traced to changes in the timing and location of developmental events. This has led to a growing interest in understanding the genetic basis behind the evolution of developmental systems. Molecular evolutionary genetics provides one of several approaches to dissecting the evolution of developmental systems, by allowing us to reconstruct the history of developmental genetic pathways, infer the origin and diversification of developmental gene functions, and assess the relative contributions of various evolutionary forces in shaping regulatory gene evolution.     

Translational selection and molecular evolution

Fourteen commercial antibodies against human antioxidant enzymes were tested on whole cell lysates by Western analysis for specificity and species crossreactivity. All antibodies, except one, recognized pure protein antigen. All four catalase antibodies were of high quality, and they could also recognize the catalases from rat, mouse, dog, and hamster cells. Two CuZnSOD antibodies were very specific for CuZnSOD protein. They could also crossreact with CuZnSOD from rat, mouse, and hamster cells, but not from dog cells. All five MnSOD antibodies detected only very high levels of MnSOD. We believe that they could not properly be used in immunohistochemistry. Three GPX antibodies could not detect the specific GPX band from cell lysates. We believe that it is difficult to use these GPX antibodies in both Western blotting and immunohistochemistry.     

Models of molecular evolution and phylogeny

Phylogenetic reconstruction is a fast-growing field that is enriched by different statistical approaches and by findings and applications in a broad range of biological areas. Fundamental to these are the mathematical models used to describe the patterns of DNA base substitution and amino acid replacement. These may become some of the basic models for comparative genome research. We discuss these models, including the analysis of observed DNA base and amino acid mutation patterns, the concept of site heterogeneity, and the incorporation of structural biology data, all of which have become particularly important in recent years. We also describe the use of such models in phylogenetic reconstruction and statistical methods for the comparison of different models.     

Estimating the rate of evolution of the rate of molecular evolution

A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.     

Patterns of vertebrate neurogenesis and the paths of vertebrate evolution

Any substantial change in brain size requires a change in the number of neurons and their supporting elements in the brain, which in turn requires an alteration in either the rate, or the duration of neurogenesis. The schedule of neurogenesis is surprisingly stable in mammalian brains, and increases in the duration of neurogenesis have predictable outcomes: late-generated structures become disproportionately large. The olfactory bulb and associated limbic structures may deviate in some species from this general brain enlargement: in the rhesus monkey, reduction of limbic system size appears to be produced by an advance in the onset of terminal neurogenesis in limbic system structures. Not only neurogenesis but also many other features of neural maturation such as process extension and retraction, follow the same schedule with the same predictability. Although the underlying order of event onset remains the same for all of the mammals we have yet studied, changes in overall rate of neural maturation distinguish related subclasses, such as marsupial and placental mammals, and changes in duration of neurodevelopment distinguish species within subclasses. A substantial part of the regularity of event sequence in neurogenesis can be related directly to the two dimensions of the neuraxis in a recently proposed prosomeric segmentation of the forebrain [Rubenstein et al., Science, 266: 578, 1994]. Both the spatial and temporal organization of development have been highly conserved in mammalian brain evolution, showing strong constraint on the types of brain adaptations possible. The neural mechanisms for integrative behaviors may become localized to those locations that have enough plasticity in neuron number to support them.     

Automated analysis of multiplex microsatellites

The use of automated DNA fragment analysis with the Applied Biosystems 672 Genescanner system was evaluated in a routine diagnostic setting. The aim of the study was to compare automated fragment detection and analysis with conventional methods. For cystic fibrosis analysis the delta F508 mutation in exon 10 of the cystic fibrosis transmembrane regulator (CFTR) gene was multiplexed with two intragenic microsatellites. The analysis of the Prader-Willi/Angelman region of chromosome 15 used a panel of five microsatellites. For dystrophin, seven microsatellites covering the entire dystrophin gene were co-amplified. Automated analysis was faster and more accurate than analysis using radiolabelled products with sequencing gels, although some inconsistencies in the sizing of microsatellite alleles were seen.     

Remarkably high rate of molecular evolution of ruminant placental lactogens

Adenosine deaminase (ADA) is a deaminating enzyme consisting of isozymes ADA 1 and ADA 2. We measured the activities of total ADA, ADA 1 and ADA 2 in serum obtained from 42 patients with Parkinson's disease (PD). Patients were divided into 10 cases of stage I, 20 of II, 11 of III and 1 of IV according to the clinical stages described by Hoehn and Yahr. The total and ADA 2 activities were significantly higher in patients as compared with normal controls (p < 0.01, respectively). However, this study did not detect any tendency for elevated total ADA or its isozyme activities with advance in clinical stages described by Hoehn and Yahr. ADA and ADA 2 are thought to have important roles in the regulation of the immune function. On the other hand, recent reports have suggested that immunological abnormality may be responsible for the developing of PD. Our results also suggest that high serum ADA activity may be involved in the pathogenesis of PD through the alteration of the immune function.     

Alterations of microsatellites in neurofibromas of von Recklinghausen's disease

von Recklinghausen's disease, or type I neurofibromatosis, a common familial tumor syndrome, is characterized by the occurrence of multiple benign neoplasms of nerve sheath cells. The disease is caused by germ-line mutations of the NF1 gene, which encodes a member of the GTPase-activating superfamily of Ras regulatory proteins. We analyzed 5 dinucleotide repeat loci in DNAs from neurofibromas and matched normal skin from 16 NF1 patients. Eight cases (50%) manifested microsatellite alterations. Expansions or compressions of dinucleotide repeats were observed at one locus in four cases and at two loci in one case. Banding patterns compatible with the loss of a microsatellite allele were observed in four cases, including one that also presented microsatellite instability. The surprisingly high frequency of microsatellite alterations suggests that the NF1 gene or another gene(s) contributing to the pathogenesis of neurofibromas might be directly or indirectly implicated in the control of genomic integrity.     

Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline

Evolution of HIV-1 env sequences was studied in 15 seroconverting injection drug users selected for differences in the extent of CD4 T cell decline. The rates of increase of either sequence diversity at a given visit or divergence from the first seropositive visit were both higher in progressors than in nonprogressors. Viral evolution in individuals with rapid or moderate disease progression showed selection favoring nonsynonymous mutations, while nonprogressors with low viral loads selected against the nonsynonymous mutations that might have resulted in viruses with higher levels of replication. For 10 of the 15 subjects no single variant predominated over time. Evolution away from a dominant variant was followed frequently at a later time point by return to dominance of strains closely related to that variant. The observed evolutionary pattern is consistent with either selection against only the predominant virus or independent evolution occurring in different environments within the host. Differences in the level to which CD4 T cells fall in a given time period reflect not only quantitative differences in accumulation of mutations, but differences in the types of mutations that provide the best adaptation to the host environment.     

Diversity and molecular evolution of the RPS2 resistance gene in Arabidopsis thaliana

The RPS2 gene in Arabidopsis thaliana governs resistance to strains of the bacterial pathogen, Pseudomonas syringae pv. tomato, that express the avrRpt2 gene. The two loci are involved in a gene-for-gene interaction. Seventeen accessions of A. thaliana were sequenced to explore the diversity present in the coding region of the RPS2 locus. An unusually high level of nucleotide polymorphisms was found (1.26%), with nearly half of the observed polymorphisms resulting in amino acid changes in the RPS2 protein. Seven haplotypes (alleles) were identified and their evolutionary relationships deduced. Several of the alleles conferring resistance were found to be closely related, whereas susceptibility to disease was conferred by widely divergent alleles. The possibility of selection at the RPS2 locus is discussed.     

Accelerated evolution and molecular surface of venom phospholipase A2 enzymes

The objective of this study was to determine the in vitro shear bond strength (in megapascals) and location of bond failure with two light-cured glass ionomer resin systems. One system was a hybrid glass ionomer cement with resin (GC Orthodontics, Aslip, Ill), and the other system a glass-filled resin system (Reliance Orthodontic Products, Inc, Itasca, Ill). These systems, Fuji Ortho LC (GC Orthodontics) and Ultra Band Lok (Reliance), respectively, were compared to a light-cured composite resin. Maxillary premolar brackets (n = 200) were bonded to the facial surface of human premolar teeth. The two glass ionomer resin systems were each evaluated by two protocols, one according to the manufacturers' direction plus a variation of their respective technique. The five distinct groups (n = 40) were stored in 37 degreesC distilled water for 30 days and subjected to thermocycling before shear bond strength testing. The findings indicated that large variations existed between the bond strengths of the materials tested. The laboratory shear bond strength of the glass-filled resin glass ionomer cement (Reliance), whether tested in a dry or moist field, was similar to the composite control with all of the previous materials being significantly (P <.01) higher than both the hybrid glass ionomer cement groups (Fuji Ortho LC). However, the hybrid glass ionomer cement with enamel conditioner demonstrated a clinically acceptable mean megapascal value. The Adhesive Remnant Index values ranged from 0.53 to 1.62. The hybrid glass ionomer cement without enamel conditioning recorded the lowest mean adhesive remnant index score and the lowest mean megapascal score. Although both products are glass ionomer resin systems, their individual chemistries vary; this affects their clinical performance. Clinically, it may be suggested that glass ionomers used in a dry field may be beneficial for orthodontic bonding, and that glass ionomer resin systems used in a moist environment need an enamel conditioner.     

The lunatic fringe gene is a target of the molecular clock linked to somite segmentation in avian embryos

The most obvious segments of the vertebrate embryo are the trunk mesodermal somites which give rise to the segmented vertebral column and the skeletal muscles of the body. Mechanistic insights into vertebrate somitogenesis have recently been gained from observations of rhythmic expression of the avian hairy-related gene (c-hairy1) in chick presomitic mesoderm (PSM), suggesting the existence of a molecular clock linked to somite segmentation ([1]; reviewed in [2]). Here, we show that lunatic Fringe (IFng), a vertebrate homolog of the Drosophila Fringe gene, is also expressed rhythmically in PSM. The PSM expression of IFng was observed as coordinated pulses of mRNA resembling the expression of c-hairy1. We show that c-hairy1 and IFng expression in the PSM are coincident, indicating that both genes are responding to the same segmentation clock. The genes were found to differ in their regulation, however; in contrast to c-hairy1, IFng mRNA oscillations required continued protein synthesis, suggesting that IFng could be acting downstream of c-hairy1 in the clock mechanism. In Drosophila, Fringe has been shown to play a role in modulating Notch-Delta signalling [3,4], a pathway which in vertebrates has been implicated in defining somite boundaries [5-9]. These observations place the segmentation clock upstream of the Notch-Delta pathway during vertebrate somitogenesis.     

Evolution of Hawaiian drosophilidae. II. Patterns and rates of chromosome evolution in an antopocerus phylogeny

The phylogenetic relationships of seven species of the genus Antopocerus (Family Drosophilidae) have been determined by means of a study of the metaphase configurations and polytene chromosomes. Based on biogeographical, behavioral and cytogenetic information A. longiseta from Molokai is tentatively identified as the primitive species of the genus. The metaphase karyotypes of all Antopocerus species are either five pairs of rod chromosomes and a pair of dots (5R1D), or six rods (6R). Heterochromatin additions converted the dots to rods. Chromosome breakpoints for inversions also are clustered at heterochromatic loci. The chromosome segments between heterochromatic loci may represent sets of functionally related loci, evolving as a unit. The rate of chromosomal inversion substitution is estimated in the origin of the taxon (probably a subgenus of Drosophila rather than a separate genus). It averages no greater than one substitution per 1,000 years, or one per 5,000 generations. The average genetic death rate per generation of one individual per hundred is required to achieve this substitution rate. The rate of inversion substitution during radiation of this taxon may be only 4.4 X 10(-3) times as fast as that present in forming the taxon. Alternatively, radiation may have required only 250,000 years if rates of substitution are the same as in the origination of the taxon. Average rates of substitution reflect genetic accidents, selection pressures and rates of adaptation to new niches, as well as the rate of encountering new niches. Rate of adaptation probably is much greater in this instance than rate of encountering new niches. Rate of adaptation probably is much greater in this instance than rate of encountering new niches. Therefore, the average rate of evolution reflects more nearly biogeographic and ecological factors than genetic factors.