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PubMed1989

An interpretation and proof of the Fundamental Theorem of Natural Selection.

Fisher's "Fundamental Theorem of Natural Selection" has long caused controversy in population genetics theory. Viewed as a statement about the increase, or rate of increase, of mean fitness over time, it encounters difficulties with cases arising in a multi-locus system for which mean fitness can decrease. An interpretation of the theorem is put forward here which implies that it is correct as a mathematical statement, but of less biological value than was claimed by Fisher.

Gene Frequency↗
PubMed1985

A threshold model for punctuated gradualism.

A model for continuous and discontinuous evolutionary change is proposed that accommodates both punctuated equilibrium and phyletic gradualism. Natural selection operating on a gaussian distribution of phenotypes subjected to severe stress will result in a skewing of the normal distribution in the direction of the favoured phenotype. If a reproductive isolation threshold is imposed upon this model, rapid crossing of the threshold by large numbers of individuals within the skewed distribution will result in the sudden achievement of a critical descendant population mass. Mild directional selection however, will result in gentle shifts of the gaussian mean thus leading us to suggest that stasis and incipient speciatior are extremes of the same spectrum, defined by the rates of mean-shift in response to varying severities of selection pressure. Both punctuated and gradualistic evolution as accommodated in our model may further be described within Thom's cusp catastrophe theory.

Biological Evolution↗
PubMed2003

C-106T polymorphism of AKR1B1 is associated with diabetic nephropathy and erythrocyte aldose reductase content in Japanese subjects with type 2 diabetes mellitus.

BACKGROUND: The C-106T polymorphism of AKR1B1, which encodes aldose reductase (AR), was reported to be associated with diabetic nephropathy (DN). However, this association in Japanese patients with type 2 diabetes mellitus and its potential role as a clinical marker remain unclear. METHODS: The C-106T polymorphism was genotyped in 228 cases (microalbuminuria or overt proteinuria) and 220 controls (normoalbuminuria with diabetes duration > or =10 years) for a case-control comparison, and the association with erythrocyte AR content was investigated. In addition, a new C-11G polymorphism in the promoter region of AKR1B1 was genotyped. RESULTS: The distribution of genotypes of the C-106T polymorphism in cases was significantly different from that in controls (P = 0.031). Carriers of the TT genotype at the C-106T polymorphism were more frequent in cases than controls, with an odds ratio of 4.7 (95% confidence interval, 1.3 to 17). Erythrocyte AR content was significantly elevated in TT carriers in comparison to non-TT carriers (13.1 +/- 1.2 versus 10.2 +/- 1.2 ng/mg hemoglobin [Hb]; P < 0.001) and in cases in comparison to controls (10.6 +/- 1.3 versus 10.1 +/- 1.2 ng/mg Hb; P = 0.041). However, distribution of genotypes of the C-11G polymorphism and estimated frequencies of haplotypes defined by these 2 polymorphisms did not differ between cases and controls. CONCLUSION: The TT genotype of the C-106T polymorphism of AKR1B1 increases the risk for DN in Japanese subjects with type 2 diabetes mellitus, which could be linked in part to greater expression of AR.

Aged↗
PubMed2005

Twenty-three generations of mice bidirectionally selected for open-field thigmotaxis: selection response and repeated exposure to the open field.

We examined: (a) the response to bidirectional selection for open-field (OF) thigmotaxis in mice for 23 generations and (b) the effects of repeated exposure (during 5 days) on different OF behaviors in the selectively bred high OF thigmotaxis (HOFT) and low OF thigmotaxis (LOFT) mice. A total of 2049 mice were used in the study. Prior to the testing in the selection experiment, the mice were exposed to the OF apparatus for approximately 2 min on each of 4 consecutive days. Thus, the selection was based on the scores registered on the 5th day after the four habituation periods. The HOFT mice were more thigmotactic than the LOFT mice in almost each generation. The HOFT mice also tended to rear less than the LOFT mice, which was explained by the inverse relationship between emotionality and exploratory tendencies. The lines did not generally differ in ambulation. Sex differences were found in thigmotaxis, ambulation, and rearing. In the repeated exposure experiment, the development of nine different OF behaviors across the 5 days of testing was addressed. Both lines ambulated, explored, and reared most on the 1st, 4th, and 5th days. Grooming and radial latency decreased and thigmotaxis increased linearly across the testing days. Line differences were found in ambulation, exploration, grooming, and rearing, while sex differences were manifested in ambulation and exploration. The line difference in thigmotaxis was evident only on the 5th day. Temporal changes were partially at variance with the general assumptions. OF thigmotaxis was found to be a powerful characteristic for producing two diverging lines of mice.

Animals↗
PubMed2006

Neuropsychological assessment, quantitative MRI and ApoE gene polymorphisms in a series of MS patients treated with IFN beta-1b.

Few trials issued the effect of disease-modifying medications on cognitive functions in multiple sclerosis. We designed an open-label longitudinal study to evaluate, during 2 years, cognitive performance and its relationship with MRI data and ApoE polymorphism findings in a group of relapsing-remitting (RR) multiple sclerosis (MS) Interferon (IFN) beta-1b-treated patients (median age 30 years, median disease duration 3.4 years). Complete neuropsychological battery was grouped into attention, information learning/memory, language and visuo-spatial functions. Fifty-two patients (33 females) were enrolled in the study. Six patients (11.5%) dropped out, mainly due to side effects. At baseline neuropsychological evaluation, we found 54% normal, 42% mildly impaired and 4% moderately impaired patients. At 2 years follow-up, cognitive status was stable in 65%, improved in 33% and worsened in 2% of patients. No significant relations were found between global cognitive outcome vs. EDSS change, clinical disease activity, MRI data or ApoE gene polymorphisms over the 2 years follow-up. EDSS and MRI fractional volumes were found to correlate with the performance at single tests. Twenty-one patients (45.6%) showed active MRI scans throughout the study, without any worsening at the corresponding neuropsychological examination. This ongoing trial suggests a possible beneficial effect of IFN beta-1b treatment on cognitive functions in RRMS patients. Extension of follow-up and further data analyses are needed to confirm and clarify these findings.

Adolescent↗
PubMed2005

A polymorphism in plasma platelet-activating factor acetylhydrolase is involved in resistance to immunoglobulin treatment in Kawasaki disease.

OBJECTIVE: To investigate whether reduced levels of plasma platelet-activating factor acetylhydrolase (PAF-AH) as a result of a genetic polymorphism are involved in the pathogenesis of Kawasaki disease (KD). STUDY DESIGN: The frequency of a V279F polymorphism (G/T transversion) in the PAF-AH gene was quantified in 76 Japanese children with KD and 112 healthy Japanese adults using the allele-specific polymerase chain reaction (PCR). Associations between genotype, clinical features, and resistance to intravenous immunoglobulin (IVIG) were investigated in the patients with KD. Plasma PAF-AH activity was measured by using [3H]-acetyl-PAF. RESULTS: There were no significant differences in genotype frequency between patients and controls (P = .51). Compared with the GG (normal genotype) group, significantly more patients in the GT (heterozygous) +TT (homozygous deficient) group required additional IVIG (52% vs 14%, P = .001). The duration of fever and maximum serum C-reactive protein (CRP) levels also were significantly increased in the GT+TT group (P = .012 and .036, respectively), whereas plasma PAF-AH activity was significantly lower (P <.0001). CONCLUSION: We conclude that the V279F polymorphism in the plasma PAF-AH gene and consequent enzymatic deficiency is one of the factors for IVIG nonresponse in Japanese patients with acute KD.

1-Alkyl-2-acetylglycerophosphocholine Esterase↗
PubMed2005

The evolution of a Müllerian mimic in a spatially distributed community.

Strong positive density-dependence should lead to a loss of diversity, but warning-colour and Müllerian mimicry systems show extraordinary levels of diversity. Here, we propose an analytical model to explore the dynamics of two forms of a Müllerian mimic in a heterogeneous environment with two alternative model species. Two connected populations of a dimorphic, chemically defended mimic are allowed to evolve and disperse. The proportions of the respective model species vary spatially. We use a nonlinear approximation of Müller's number-dependent equations to model a situation where the mortality for either form of the mimic decreases hyberbolically when its local density increases. A first non-spatial analysis confirms that the positive density-dependence makes coexistence of mimetic forms unstable in a single isolated patch, but shows that mimicry of the rarer model can be stable once established. The two-patch analysis shows that when models have different abundance in different places, local mimetic diversity in the mimic is maintained only if spatial heterogeneity is strong, or, more interestingly, if the mimic is not too strongly distasteful. Therefore, mildly toxic species can become polymorphic in a wider range of ecological settings. Spatial dynamics thus reveal a region of Müllerian polymorphism separating classical Batesian polymorphism and Müllerian monomorphism along the mimic's palatability spectrum. Such polymorphism-palatability relationship in a spatial environment provides a parsimonious hypothesis accounting for the observed Müllerian polymorphism that does not require quasi-Batesian dynamics. While the stability of coexistence depends on all factors, only the migration rate and strength of selection appear to affect the level of diversity at the polymorphic equilibrium. Local adaptation is predicted in most polymorphic cases. These results are in very good accordance with recent empirical findings on the polymorphic butterflies Heliconius numata and H. cydno.

Adaptation, Physiological↗
PubMed2006

A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility.

Detecting, characterizing, and interpreting gene-gene interactions or epistasis in studies of human disease susceptibility is both a mathematical and a computational challenge. To address this problem, we have previously developed a multifactor dimensionality reduction (MDR) method for collapsing high-dimensional genetic data into a single dimension (i.e. constructive induction) thus permitting interactions to be detected in relatively small sample sizes. In this paper, we describe a comprehensive and flexible framework for detecting and interpreting gene-gene interactions that utilizes advances in information theory for selecting interesting single-nucleotide polymorphisms (SNPs), MDR for constructive induction, machine learning methods for classification, and finally graphical models for interpretation. We illustrate the usefulness of this strategy using artificial datasets simulated from several different two-locus and three-locus epistasis models. We show that the accuracy, sensitivity, specificity, and precision of a naïve Bayes classifier are significantly improved when SNPs are selected based on their information gain (i.e. class entropy removed) and reduced to a single attribute using MDR. We then apply this strategy to detecting, characterizing, and interpreting epistatic models in a genetic study (n = 500) of atrial fibrillation and show that both classification and model interpretation are significantly improved.

Atrial Fibrillation↗
PubMed2003

Heparan sulfate proteoglycan 2 polymorphism in Alzheimer's disease and correlation with neuropathology.

A genetic association of an intronic single nucleotide polymorphism site of heparan sulfate proteoglycan 2 (HSPG2) with Alzheimer's disease (AD) was investigated among Finnish AD patients (n=213) and controls (n=269). No association of the HSPG2 polymorphism alone was observed with AD. However, an association of HSPG2 A allele with AD was detected in apolipoprotein (APOE) epsilon4 allele carriers. The odds ratio for AD was doubled in subjects carrying both epsilon4 and HSPG2 A alleles (OR=6.6) when compared to subjects with epsilon4 allele alone (OR=3.1). The impact of HSPG2 polymorphism on beta amyloid and tau pathology was studied using immunohistochemistry. Paired helical filament labeling was significantly more pronounced in AD patients carrying both epsilon4 and HSPG A alleles when compared to epsilon4 carriers lacking the HSPG2 A allele. In conclusion, HSPG2 A allele may possess an additive risk effect among the APOE epsilon4 carriers in AD.

Adult↗
PubMed2003

False discoveries and models for gene discovery.

In the search for genes underlying complex traits, there is a tendency to impose increasingly stringent criteria to avoid false discoveries. These stringent criteria make it hard to find true effects, and we argue that it might be better to optimize our procedures for eliminating and controlling false discoveries. Focusing on achieving an acceptable ratio of true- and false-positives, we show that false discoveries could be eliminated much more efficiently using a stepwise approach. To avoid a relatively high false discovery rate, corrections for 'multiple testing' might also be needed in candidate gene studies. If the appropriate methods are used, detecting the proportion of true effects appears to be a more important determinant of the genotyping burden than the desired false discovery rate. This raises the question of whether current models for gene discovery are shaped excessively by a fear of false discoveries.

Data Interpretation, Statistical↗
PubMed2005

Multiallelic selection polymorphism.

The existence and stability of an internal (i.e., completely polymorphic) equilibrium for viability selection at a single multiallelic locus is investigated. Generations are discrete and nonoverlapping; the population is panmictic, monoecious, and diploid. Various necessary and sufficient conditions for the existence of an internal equilibrium are established and applied to the loss of alleles. Some necessary conditions for the existence of an asymptotically stable internal equilibrium are also established. All these conditions are simpler and yield general biological conclusions more easily than the classical necessary and sufficient conditions.

Alleles↗
PubMed2006

On the evolution of epistasis II: a generalized Wright-Kimura framework.

The evolution of fitness interactions between genes at two major loci is studied where the alleles at a third locus modify the epistatic interaction between the two major loci. The epistasis is defined by a parameter epsilon and a matrix structure that specifies the nature of the interactions. When epsilon=0 the two major loci have additive fitnesses, and when these are symmetric the interaction matrices studied here produce symmetric viabilities of the Wright [1952. The genetics of quantitative variability. In: Reeve, E.C.R., Waddington, C.H. (Eds.), Quantitative Inheritance. Her Majesty's Stationary Office, London]-Kimura [1956. A model of a genetic system which leads to closer linkage by natural selection. Evolution 10, 278-281] form. Two such interaction matrices are studied, for one of which epistasis as measured by |epsilon| always increases, and for the other it increases when the linkage between the major loci is tight enough and there is initial linkage disequilibrium. Increase of epistasis does not necessarily coincide with increase in equilibrium mean fitness.

Alleles↗