Concatenated amino acid sequences of all the 13 protein coding genes in mitochondria recovered a known phylogeny of 11 vertebrate species with statistical significance, even though some of the ...phylogenetic trees generated for each mitochondrial gene did not have the correct tree topology. However, when this tree was rooted by lamprey and sea urchin, the root was placed between a cluster of chicken, frog and fish, and a cluster of mammals and marsupial. This clustering pattern is apparently incorrect in a biological sense, but it was again supported with statistical significance. In this study, we investigated the possible causes of this reconstruction of the incorrect phylogeny. Our analysis showed that there is an extensive rate variation among amino acid sites and that substitutions seem to have saturated at sites with high rate. When the sites with a large number of substitutions were excluded, the biologically correct tree was constructed. Further, under the assumption of an extensive rate variation among sites, the correct tree can be reconstructed without excluding the sites with a large number of substitutions. It appears that because there is an extensive rate difference between fish lineage and others, it is important to consider an appropriate model of substitution in reconstructing a phylogenetic tree.
Allelic frequencies at the three most polymorphic loci of the HLA class II region (DRB1, DQA1, and DQB1) were determined in 24 Nganasans and 17 Kets, the remnants of the two most ancient groups of ...the Lower Yenisey River/Taimyr Peninsula region in northern Siberia. By single-stranded conformational polymorphism typing, verified by sequencing the corresponding segments of genomic DNA, 19 HLA-DRB1-DQA1-DQB1 haplotypes and 15 HLA-DRB1, 7 DQA1, and 11 DQB1 alleles were found. The most frequent alleles were DRB1*1301(23.5%), DQA1*0103 (29.4%), *0501/03/05 (29.4%), and DQB1*0301/0309 (32.4%) in the Kets, and DRB1*0901 (25%), DQA1*0301 (39.6%), and DQB1 *0301/0309 (37.5%) in the Nganasans. The distribution patterns and comprehensive phylogenic analysis based on the haplotype frequencies of 17 Siberian populations suggest that the founders of both Kets and Nganasans came from Paleolithic populations in the Altai-Sayan Upland. The high frequency of the DRB1*0901 allele in the Uralic-speaking Nganasans may be the result of a relatively recent gene flow from the northwardly-expanding Tungus-speaking Evenki who originated in the Baikal area.
Two species of the subfamily Murinae, Diplothrix legata and Tokudaia osimensis have their own genera and are presented in a limited distribution on three small islands (Amamioshima, Tokunoshima, and ...Okinawa) which are located at the center of the Nansei Islands, southern part of Japan in contrast to the wide distribution of the four main genera of Murinae, Apodemus, Micromys, Mus, and Rattus throughout almost all of Palaearctic region. We examined the phylogenetic relationships of the six lineages of Murinae with an analysis of mitochondrial cytochrome b gene (1140 bp) and nuclear IRBP gene (782 bp) sequences. The results indicate that not only the four main Murinae genera but also Tokudaia diverged at similar evolutionary tines, namely at the time of the radiation of Murinae, 14 or 40 million years ago, depending on different concepts for the divergent times of Rattus and Mus. By contrast, our findings indicate that Diplothrix was separated from the lineage of the Rattus group more recently. Our results indicated that D. legate and the Rattus group diverged at 20-30% the divergent time of Rattus and Mus under the assumption of the molecular clock, suggesting that D. legata established its lineage at least by the beginning of the Pleistocene era. It is thus evident that the Okinawa area preserves rare indigenous species with various levels of genetic endemicity.
Reconstruction of phylogenetic trees of genes or populations is an important subject in the study of evolution. However, statistical methods for reconstructing phylogenetic relationships and for ...estimating the times of divergence between genes or populations are not well established. I therefore studied three problems concerning the methods for constructing phylogenetic trees and estimating the times of divergence between genes or populations by using molecular sequences and allele frequency data. They are as follows. (1) It is well known that the maximum parsimony method may choose an incorrect tree when the evolutionary rate varies from branch to branch extensively, even if an infinite number of nucleotides are examined. However, this statistical inconsistency of the parsimony method can occur even when the sequences evolve with a constant rate. I have therefore studied the reason and condition for this to happen by considering the cases of five to seven DNA sequences. (2) Molecular data are useful for estimating the divergence time of species. In practice, however, the evolutionary rate may vary with evolutionary lineage. Therefore, I have developed methods for testing the molecular clock and for estimating the times of divergence of species or species groups after elimination of excessively fast or slowly evolving sequences. These methods can also be applied to phylogenetic trees for different populations with allele frequency data. (3) Microsatellite DNA loci are highly polymorphic and thus useful for studying the evolutionary relationships of closely related populations or species. Some new genetic distance measures have been proposed specifically for these loci, but their efficiencies of constructing reliable phylogenetic trees are unclear. I have therefore investigated these efficiencies by computer simulation. The results have indicated that the new distance measures designed for microsatellite DNA loci have a large variance and are generally less efficient than traditional distance measures that are used for classical genetic markers such as electrophoretic and blood group loci.
Background: Improving diets requires an awareness of the need to limit foods for which excessive consumption is a health problem. Since there are limited reports on the link between this awareness ...and mortality risk, we examined the association between awareness of limiting food intake (energy, fat, and sweets) and all-cause mortality in a Japanese cohort study.Methods: Participants comprised 58,772 residents (27,294 men; 31,478 women) aged 35–69 years who completed baseline surveys of the Japan Multi-Institutional Collaborative Cohort Study from 2004 to 2014. Hazard ratios (HRs) for all-cause mortality and 95% confidence intervals (CIs) were estimated by sex using a Cox proportional hazard model, with adjustment for related factors. Mediation analysis with fat intake as a mediator was also conducted.Results: The mean follow-up period was 11 years, and 2,516 people died. Estimated energy and fat intakes according to the Food Frequency Questionnaire were lower in those with awareness of limiting food intake than in those without this awareness. Women with awareness of limiting fat intake showed a significant decrease in mortality risk (HR 0.73; 95% CI, 0.55–0.94). Mediation analysis revealed that this association was due to the direct effect of the awareness of limiting fat intake and that the total effect was not mediated by actual fat intake. Awareness of limiting energy or sweets intake was not related to mortality risk reduction.Conclusion: Awareness of limiting food intake had a limited effect on reducing all-cause mortality risk.
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FFLJ, NUK, ODKLJ, UL, UM, UPUK
The association between nutrient patterns and metabolic syndrome (MetS) has not been examined in a Japanese population. A cross-sectional study was performed on 30,108 participants (aged 35-69 years) ...in the baseline survey of the Japan Multi-Institutional Collaborative Cohort Study. Dietary intake was assessed using a 46-item food frequency questionnaire. MetS was diagnosed according to the Joint Interim Statement Criteria of 2009, using body mass index instead of waist circumference. Factor analysis was applied to energy-adjusted intake of 21 nutrients, and three nutrient patterns were extracted: Factor 1 (fiber, potassium and vitamins pattern); Factor 2 (fats and fat-soluble vitamins pattern); and Factor 3 (saturated fatty acids, calcium and vitamin B
pattern). In multiple logistic regression analysis adjusted for sex, age, and other potential confounders, Factor 1 scores were associated with a significantly reduced odds ratio (OR) of MetS and all five components. Factor 2 scores were associated with significantly increased prevalence of MetS, obesity, and high blood pressure. Factor 3 scores were significantly associated with lower OR of MetS, high blood pressure, high serum triglycerides and low HDL cholesterol levels. Analysis of nutrient patterns may be useful to assess the overall quality of diet and its association with MetS.
Although socioeconomic status (SES) may affect food and nutrient intakes, few studies have reported on sodium (Na) and potassium (K) intakes among individuals with various SESs in Japan. We ...investigated associations of SES with Na and K intake levels using urinary specimens in a representative Japanese population.
This was a cross-sectional study of 2,560 men and women (the NIPPON DATA2010 cohort) who participated in the National Health and Nutrition Survey Japan in 2010. Casual urine was used to calculate estimated excretion in 24-hour urinary Na (E24hr-Na) and K (E24hr-K). The urinary sodium-to-potassium (Na/K) ratio was calculated from casual urinary electrolyte values. An analysis of covariance was performed to investigate associations of aspects of SES, including equivalent household expenditure (EHE), educational attainment, and job category, with E24hr-Na, E24hr-K, and the Na/K ratio for men and women separately. A stratified analysis was performed on educational attainment and the job category for younger (<65 years) and older (≥65 years) participants.
In men and women, average E24hr-Na was 176.2 mmol/day and 172.3, average E24hr-K was 42.5 and 41.3, and the average Na/K ratio was 3.61 and 3.68, respectively. Lower EHE was associated with a higher Na/K ratio in women and lower E24hr-K in men and women. A shorter education was associated with a higher Na/K ratio in women and younger men, and lower E24hr-K in older men and women.
Lower EHE and a shorter education were associated with a lower K intake and higher Na/K ratio estimated from casual urine specimens in Japanese men and women.
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FFLJ, GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, ODKLJ, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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