High genomic deleterious mutation rates in hominids

It has been suggested that humans may suffer a high genomic deleterious mutation rate. Here we test this hypothesis by applying a variant of a molecular approach to estimate the deleterious mutation rate in hominids from the level of selective constraint in DNA sequences. Under conservative assumptions, we estimate that an average of 4.2 amino-acid-altering mutations per diploid per generation have occurred in the human lineage since humans separated from chimpanzees. Of these mutations, we estimate that at least 38% have been eliminated by natural selection, indicating that there have been more than 1.6 new deleterious mutations per diploid genome per generation. Thus, the deleterious mutation rate specific to protein-coding sequences alone is close to the upper limit tolerable by a species such as humans that has a low reproductive rate, indicating that the effects of deleterious mutations may have combined synergistically. Furthermore, the level of selective constraint in hominid protein-coding sequences is atypically low. A large number of slightly deleterious mutations may therefore have become fixed in hominid lineages.     

Characterization of deleterious mutations in outcrossing populations

Deng and Lynch recently proposed estimating the rate and effects of deleterious genomic mutations from changes in the mean and genetic variance of fitness upon selfing/outcrossing in outcrossing/highly selfing populations. The utility of our original estimation approach is limited in outcrossing populations, since selfing may not always be feasible. Here we extend the approach to any form of inbreeding in outcrossing populations. By simulations, the statistical properties of the estimation under a common form of inbreeding (sib mating) are investigated under a range of biologically plausible situations. The efficiencies of different degrees of inbreeding and two different experimental designs of estimation are also investigated. We found that estimation using the total genetic variation in the inbred generation is generally more efficient than employing the genetic variation among the mean of inbred families, and that higher degree of inbreeding employed in experiments yields higher power for estimation. The simulation results of the magnitude and direction of estimation bias under variable or epistatic mutation effects may provide a basis for accurate inferences of deleterious mutations. Simulations accounting for environmental variance of fitness suggest that, under full-sib mating, our extension can achieve reasonably well an estimation with sample sizes of only approximately 2000-3000.     

EMS-induced polygenic mutation rates for nine quantitative characters in Drosophila melanogaster

Polygenic mutations were induced by treating Drosophila melanogaster adult males with 2.5 mM EMS. The treated second chromosomes, along with untreated controls, were then made homozygous, and five life history, two behavioral, and two morphological traits were measured. EMS mutagenesis led to reduced performance for life history traits. Changes in means and increments in genetic variance were relatively much higher for life history than for morphological traits, implying large differences in mutational target size. Maximum likelihood was used to estimate mutation rates and parameters of distributions of mutation effects, but parameters were strongly confounded with one another. Several traits showed evidence of leptokurtic distributions of effects and mean effects smaller than a few percent of trait means. Distributions of effects for all traits were strongly asymmetrical, and most mutations were deleterious. Correlations between life history mutation effects were positive. Mutation parameters for one generation of spontaneous mutation were predicted by scaling parameter estimates from the EMS experiment, extrapolated to the whole genome. Predicted mutational coefficients of variation were in good agreement with published estimates. Predicted changes in means were up to 0.14% or 0.6% for life history traits, depending on the model of scaling assumed.     

The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster

In a recent study, we reported that the combined average mutation rate of 10 di-, 6 tri-, and 8 tetranucleotide repeats in Drosophila melanogaster was 6.3 x 10(-6) mutations per locus per generation, a rate substantially below that of microsatellite repeat units in mammals studied to date (range = 10(-2)-10(-5) per locus per generation). To obtain a more precise estimate of mutation rate for dinucleotide repeat motifs alone, we assayed 39 new dinucleotide repeat microsatellite loci in the mutation accumulation lines from our earlier study. Our estimate of mutation rate for a total of 49 dinucleotide repeats is 9.3 x 10(-6) per locus per generation, only slightly higher than the estimate from our earlier study. We also estimated the relative difference in microsatellite mutation rate among di-, tri-, and tetranucleotide repeats in the genome of D. melanogaster using a method based on population variation, and we found that tri- and tetranucleotide repeats mutate at rates 6.4 and 8.4 times slower than that of dinucleotide repeats, respectively. The slower mutation rates of tri- and tetranucleotide repeats appear to be associated with a relatively short repeat unit length of these repeat motifs in the genome of D. melanogaster. A positive correlation between repeat unit length and allelic variation suggests that mutation rate increases as the repeat unit lengths of microsatellites increase.     

High mutation rate of a long microsatellite allele in Drosophila melanogaster provides evidence for allele-specific mutation rates

Within recent years, microsatellite have become one of the most powerful genetic markers in biology. For several mammalian species, microsatellite mutation rates have been estimated on the order of 10(-3)-10(-5). A recent study, however, demonstrated mutation rates in Drosophila melanogaster of at least one order of magnitude lower than those in mammals. To further test this result, we examined mutation rates of different microsatellite loci using a larger sample size. We screened 24 microsatellite loci in 119 D. melanogaster lines maintained for approximately 250 generations and detected 9 microsatellite mutations. The average mutation rate of 6.3 x 10(-6) is identical to the mutation rate from a previous study. Most interestingly, all nine mutations occurred at the same allele of one locus (DROYANETSB). This hypermutable allele has 28 dinucleotide repeats and is among the longest microsatellite reported in D. melanogaster. The allele-specific mutation rate of 3.0 x 10(-4) per generation is within the range of mammalian mutation rates. Future microsatellite analyses will have to account for the dramatic differences in allele-specific mutation rates.     

The effect of overdominance on characterizing deleterious mutations in large natural populations

Alternatives to the mutation-accumulation approach have been developed to characterize deleterious genomic mutations. However, they all depend on the assumption that the standing genetic variation in natural populations is solely due to mutation-selection (M-S) balance and therefore that overdominance does not contribute to heterosis. Despite tremendous efforts, the extent to which this assumption is valid is unknown. With different degrees of violation of the M-S balance assumption in large equilibrium populations, we investigated the statistical properties and the robustness of these alternative methods in the presence of overdominance. We found that for dominant mutations, estimates for U (genomic mutation rate) will be biased upward and those for h (mean dominance coefficient) and s (mean selection coefficient), biased downward when additional overdominant mutations are present. However, the degree of bias is generally moderate and depends largely on the magnitude of the contribution of overdominant mutations to heterosis or genetic variation. This renders the estimates of U and s not always biased under variable mutation effects that, when working alone, cause U and s to be underestimated. The contributions to heterosis and genetic variation from overdominant mutations are monotonic but not linearly proportional to each other. Our results not only provide a basis for the correct inference of deleterious mutation parameters from natural populations, but also alleviate the biggest concern in applying the new approaches, thus paving the way for reliably estimating properties of deleterious mutations.     

Fear-potentiated startle in two strains of inbred mice.

The fear-potentiated startle paradigm has been used with great success to examine conditioned fear in both rats and humans. The purpose of this study was to examine fear-potentiated startle in inbred mice. One-month-old C57BL/6J (C57) and DBA/2J (DBA) mice were given tone?+?foot shock training trials. The amplitude of the acoustic startle reflex was measured in the presence and absence of the tone both before and after training. Both strains showed fear-potentiated startle after training as evidenced by larger startle amplitudes in the presence of the tone than in its absence. However, the magnitude of fear-potentiated startle was greater in DBA mice than in C57 mice. These results not only demonstrate fear-potentiated startle in mice for the first time but also suggest that fear-potentiated startle can be influenced by characteristics of the mouse strain. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Inversion polymorphism in natural populations of Drosophila bipectinata

Inversion polymorphism was studied in seven natural populations of Drosophila bipectinata, five from northern and two from southern India. Chromosomal analysis of these populations revealed the presence of three paracentric inversions which are widespread in populations of D. bipectinata. Quantitative data indicated that the frequency of inversions and the level of inversion heterozygosity were very low in populations of D. bipectinata. There is no evidence for genetic differentiation between populations as a result of inversion polymorphism. These findings provide evidence for rigid chromosomal polymorphism in D. bipectinata. Significant non-random associations between inversions indicated epistatic interaction between inversions in natural populations of D. bipectinata.     

Daily variations in pineal melatonin concentrations in inbred and outbred mice

Magnetic resonance imaging (MRI), single photon emission computed tomography (SPECT) and magnetic resonance spectroscopy (MRS) were successively recorded in a 3-year-old girl with the acute hemiplegia syndrome. She was admitted to our hospital with complaints of fever, loss of consciousness and right side dominant clonic convulsions evolving into status epilepticus, and then recovered with sequelae of aphasia and right hemiparesis. Electroencephalography showed a generalized slow rhythm at the onset, and very low activities on the left hemisphere in the follow-up records. Brain CT and MRI revealed edema of the left hemisphere initially, followed by left side dominant brain atrophy. No cerebral vascular lesion was detected by magnetic resonance angiography. N-Isopropyl-[123I]-iodoamphetamine SPECT showed marked hypoperfusion of the left hemisphere accompanied by crossed cerebellar diaschisis. MRS at the initial stage detected decreased N-acetyl-aspartic acid and increased lactic acid signals in the bilateral hemisphere, which subsequently normalized only on the right side. These findings suggested brain damage and neural cell death in the left cerebral hemisphere, caused by acute encephalopathy. SPECT and MRS are useful new techniques to study the pathophysiology of the acute hemiplegia syndrome.     

Genotype dependence of monoamine oxidase in inbred strains of mice

MAO activity was found to be influenced by the genotype or strain of mouse up to 20 days of age. The strain differences observed may derive from different rates of brain development. A number of neurological mutations comprizing three pathological classes had no effect on MAO.     

Genetic determinants of sensitivity to ethanol in inbred mice.

Mice from 15 inbred strains (n?=?27–40 per strain) differed in sensitivity to ethanol-induced effects on open-field activity, hypothermia, rotarod ataxia, and anesthesia. Sensitivities to the different behavioral responses were generally uncorrelated. This suggests that the genetic determinants of behavioral sensitivity to one domain of ethanol effects are unrelated to those determining other responses. On the other hand, some variables were genetically related. For example, those strains sensitive to the loss of righting reflex induced by higher doses of ethanol showed reduced activity in the open field at lower doses and were more sensitive to ethanol-induced decreases in rearing. More generally, the pattern of results suggests that genetically influenced sensitivity to ethanol is not a monolithic phenomenon. Rather, it is specific to the particular response variable studied. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Primary aggressive motivation in three inbred strains of mice.

30 male mice from 3 inbred strains (BALB/cJ, RF/J, and SJL/J), isolated since 35 days of age, were run at 135 days in a T maze, and acquired a position response when the opportunity to attack a nonaggressive S was used as a reinforcer. Results are interpreted as evidence for primary intraspecific aggressive motivation. Strain differences were significant. Significant warm-up effects were also obtained, including persistent increases in number of correct T-maze choices from 1st to later trials given each day. An identically composed group of 30 food-deprived Ss were run in the maze for food reward. Eating was uniformly a highly effective reinforcer. However, in the 2 best-performing strains the effectiveness of aggression reinforcement following warm-up approached that of reinforcement by eating. (26 ref.) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Use of isolated inbred human populations for identification of disease genes

The genetic mapping of disease loci involves the use of patient phenotype and genotype data in the search for genetic markers that segregate, or are associated with, a trait or disorder. Genetically isolated populations offer many advantages for such studies. The high degree of inbreeding and/or founder effects in some small population isolates result in an increased incidence of recessive disorders. Monogenic disorders are less likely to show non-allelic heterogeneity in isolated populations than in more diverse populations. The use of isolated populations also reduces the complexity of polygenic disorders by reducing the number of loci probably involved in the disorder. Finally, a variety of strategies can be used with particular efficacy for the mapping of disease genes in isolated populations.     

Genetic determinants of sensitivity to diazepam in inbred mice.

Mice from 15 standard inbred strains were tested for sensitivity to several effects of acute diazepam (DZ). Strains differed in sensitivity to DZ-induced: low-dose stimulation and high-dose depression of locomotor activity, hypothermia, and ataxia assessed on a rotarod. Correlations among strain means indicated that sensitivity to a particular effect of DZ generalized well across doses. Sensitivities to some of the different behavioral responses also were significantly correlated. For example, strains sensitive to DZ-induced increases in activity were significantly less sensitive to the drug's hypothermic effects. These results suggest that there are multiple genetic determinants of behavioral sensitivity to DZ effects. That is, genetically influenced sensitivity to DZ is not monolithic but is somewhat specific to the particular response variable studied, a result that also characterizes genetic control of responses to other drugs. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Acoustic startle and prepulse inhibition in 40 inbred strains of mice.

A high-throughput phenotype screening protocol was used to measure the acoustic startle response (ASR) and prepulse inhibition (PPI) in mice. ASRs were evoked by noise bursts; prepulses for PPI were 70 dB sound pressure level tones of 4, 12, and 20 kHz. Forty inbred strains of mice were tested (in most cases using 10 males and 10 females of each strain). The data on both the ASR and PPI had high internal and test-retest reliability and showed large differences among inbred strains, indicative of strong genetic influences. Previously obtained measures of hearing sensitivity in the same inbred strains were not significantly correlated with ASR or PPI measures. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Measurements of the behavioral effects of albino mutation in mice (Mus musculus): Comparisons of coisogenic inbred and hybrid lines.

The effects of the albino gene on mouse behavior were examined, particularly its possible interactions with nonallelic genes (epistasis). More generally, the possible effects of genetic background (inbreeding depression or hybrid vigor) on the effects of the mutation were also considered. Tasks requiring either predominantly motor or predominantly cognitive capacity were studied for coisogenic albino and pigmented mice from either an inbred strain (C57BL/6 c/c vs C57BL/6 +/c) or an F? heterozygous generation (F? c/c vs F? +/c) from a BALB/c?×?C57BL/6 +/c cross. Results show a clear albino gene effect in the 2 lines and provide further evidence that the gene is the effective factor. There was no significant interaction between the mutation and the genotypic group (C57BL/6 or F?), which indicates that the effects of the mutation act approximately in an additive fashion between loci in these groups. (13 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Brucella canis infectivity rates in stray and pet dog populations

A serological survey of 200 healthy, mature dogs was made to determine Brucella canis infectivity rates. The 9 per cent rate reported in the stray dogs was significantly higher (0.05 less than P greater than 0.025) than the 1 per cent rate found in pet dogs. These rates coupled with a predictably growing stray dog population have patent zoonotic implications.     

Linkage analysis of susceptibility to ozone-induced lung inflammation in inbred mice

Through a survey of all departments of pediatrics, neurology and neuropathology in Germany, we calculated the incidence of all major forms of leukodystrophy. Only diagnoses based on specific biochemical tests in association with typical findings and/or neuroradiologically proven white matter involvement were accepted. In accordance with these strict criteria, 617 cases of leukodystrophy were found (incidence of all forms: app. 2.0/100,000). Minimal incidence was estimated at 0.8/100,000 for adrenoleukodystrophy/adrenomyeloneuropathy (ALD/AMN), 0.6/100,000 for metachromatic leukodystrophy (MLD), and 0.6/100,000 for Krabbe disease. Thus ALD/AMN is apparently underdiagnosed in Germany. A considerable proportion of leukodystrophies could not be classified in spite of adequate diagnostic procedures in experienced centers.