Genetic polymorphisms of blood proteins in the troops of Japanese macaques,Macaca fuscata: V. Erythrocyte phosphohexose isomerase polymorphism

The electrophoretic variations of erythrocyte phosphohexose isomerase (PHI) were examined in 1433 blood samples from 37 troops of Japanese macaques in order to clarify the gene dynamics of this species. The genetic polymorphisms were observed in several troops. The troops showing the variation of PHI were Fukushima, Shiga A, Shiga C, Ryozenyama, Mikata I and II, Kawara, Takasakiyama A, B, and C, Itsuki, Koshima and Kushima. The variant alleles found in these troops were PHI ₂ ^mac , PHI ₇ ^mac , PHI ₈ ^mac , and PHI ₁₀ ^mac alleles, and the PHI ₁₀ ^mac allele was newly found in the present work.     

Genetic polymorphisms of blood proteins in the troops of Japanese macaques,Macaca fuscata: VI. Serum transferrin polymorphism

As the serum transferrin polymorphism was observed in several macaque species, we considered it as one of the best markers for the study of population genetics of Japanese macaques,Macaca fuscata. In this work the genetic variants of transferrin (Tf) of 1,451 blood samples from 37 troops of this species were tested. The troops showing the variation of Tf were Fukushima, Yugawara T, Ihama, Ryozenyama, Mikata I and II, Takahama, Takahama (Otomi), Arashiyama A, Minoh A and B, Kohchi, Mihara, Shimane, and Tomogashima. The wild-type allele of this species was Tf F, and the variant alleles detected in these troops were E, G⁻, G, and H′. The alleles E, G and H′ were probably identical with those reported in several macaque species byIshimoto (1972), but the identification of allele G⁻ could not be done.     

Intraspecies variation in dominance style of Macaca fuscata

Knowledge of intraspecific variation is important to test the evolutionary basis of covariation in primate social systems, yet few reports have focused on it, even in the best-studied species of the Macaca genus. We conducted a comparative study of the dominance styles among three provisioned, free-ranging groups of Japanese macaques at Shodoshima Island, Takasakiyama Mountain and Shiga Heights, and collected standard data on aggressive and affiliative behavior during a period of 5 years. Our data in the Takasakiyama and Shiga groups support previous studies showing that Japanese macaques typically have despotic social relations; nevertheless, our data in the Shodoshima group are inconsistent with the norm. The social traits of Shodoshima monkeys suggested that: (1) their dominance style is neither despotic nor tolerant but is intermediate between the two traits; (2) some measures of dominance style, e.g., frequency and duration of social interactions, covary as a set of tolerant traits in Shodoshima monkeys. This study suggests broad intraspecific variation of dominance style in Japanese macaques as can be seen in some other primate species.     

Genetic polymorphism of blood proteins in the troops of Japanese macaques,Macaca fuscata: II. Erythrocyte lactate dehydrogenase polymorphism inMacaca fuscata

In investigating the genetic marker for population genetics of Japanese macaques by electrophoresis, the author found the erythrocyte lacate dehydrogenase (LDH) polymorphism existing in some troops. There were four kinds of variations which seemed to be controlled by two loci, controlling A and B subunits of this enzyme. The variant phenotypes were named LDH-A_mac2-1 LDH-B_mac1-1, LDH-A_mac3-1 LDH-B_mac1-1, LDH-A_mac 1-1 LDH-B_mac2-1, and LDH-A_mac1-1 LDH-B_mac2-2. The two former types seemed to be heterozygote of a mutation controlling subunit A; the third was heterozygote, and the last homozygote, a mutation controlling subunit B. LDH-A_mac2-1 LDH-B_mac1-1 was found in Takasakiyama A, Takasakiyama B, Takasakiyama C, and Kamae troops; LDH-A_mac3-1 LDH-B_mac1-1 was in an individual of the unknown group. LDH-A_mac1-1 LDH-B_mac2-1 and LDH-A_mac1-1 LDH-B_mac2-2 were found in the Kohchi troop. All other troops were found to be monomorphic.     

Sampling for Microsatellite-Based Population Genetic Studies: 25 to 30 Individuals per Population Is Enough to Accurately Estimate Allele Frequencies

One of the most common questions asked before starting a new population genetic study using microsatellite allele frequencies is “how many individuals do I need to sample from each population?” This question has previously been answered by addressing how many individuals are needed to detect all of the alleles present in a population (i.e. rarefaction based analyses). However, we argue that obtaining accurate allele frequencies and accurate estimates of diversity are much more important than detecting all of the alleles, given that very rare alleles (i.e. new mutations) are not very informative for assessing genetic diversity within a population or genetic structure among populations. Here we present a comparison of allele frequencies, expected heterozygosities and genetic distances between real and simulated populations by randomly subsampling 5–100 individuals from four empirical microsatellite genotype datasets (Formica lugubris, Sciurus vulgaris, Thalassarche melanophris, and Himantopus novaezelandia) to create 100 replicate datasets at each sample size. Despite differences in taxon (two birds, one mammal, one insect), population size, number of loci and polymorphism across loci, the degree of differences between simulated and empirical dataset allele frequencies, expected heterozygosities and pairwise F_ST values were almost identical among the four datasets at each sample size. Variability in allele frequency and expected heterozygosity among replicates decreased with increasing sample size, but these decreases were minimal above sample sizes of 25 to 30. Therefore, there appears to be little benefit in sampling more than 25 to 30 individuals per population for population genetic studies based on microsatellite allele frequencies.     

Biochemical polymorphic systems in inbred lines of chickens: A survey

Biochemical polymorphic gene frequency profiles from blood samples of two outbred and seven inbred lines of chickens were studied for hemoglobin, albumin, transferrin, alkaline phosphatase, esterase II, and leucine aminopeptidase, and from egg samples of these lines for ovoalbumen, ovoglobulin (G₂ and G₃), and conalbumen. Complete gene fixation was found for hemoglobin, albumin, transferrin, ovalbumin, ovoglobulin, and conalbumin. The same alleles were fixed in each system in each line. For four systems, a particular allele within a system predominated in seven populations; gene frequencies ranged from 0.60 to 0.98. For esterases I and II, the genes Es-I ^B and Es-II ^S ranged in frequency between 0.82 and 0.97, and between 0.64 and 0.93, respectively. For ovoglobulin, G ₂ B ranged between 0.75 and 1.00 with four lines fixed for this allele. The rather remarkable similarity of gene frequency profiles among lines, several of which are only remotely related, suggests that certain characteristic polymorphic frequencies for these biochemical polymorphisms possess higher adaptive values in an evolutionary sense.     

A healthy Bifidobacterium dentium caramel cocktail

β-d-fructofuranosyl glycosidases are enzymes that produce health-beneficial fructooligosaccharides from natural fructans. In a recent issue of JBC, Kashima et al. identified a novel α-d-fructofuranosyl-active enzyme, αFFase1, from the caries-associated bacterium Bifidobacterium dentium. αFFase1 reversibly forms a potential prebiotic also found in caramel, difructose dianhydride I, via intramolecular condensation of the substrate inulobiose. Kashima et al. elegantly combine NMR, X-ray crystallography, and molecular dynamics to describe an original mechanism for the reversible reactions catalyzed by αFFase1 that establishes the new glycoside hydrolase family GH172.     

Genetic variations within and between troops of the crab-eating macaque (Macaca fascicularis) on Sumatra,Java, Bali,Lombok and Sumbawa,Indonesia

Genetic variations within and between troops of the Indonesian crab-eating macaque (Macaca fascicularis) were studied. A total of 456 blood samples were collected from 29 free-ranging troops in 19 different localities on Sumatra, Java, Bali, Lombok and Sumbawa. Blood protein polymorphisms were examined electrophoretically. Mean genetic variability within troops was estimated to be P_poly=12.22% and =3.84%. Troops inhabiting small islands showed lower variability. Genetic differences were more marked between troops on different islands than between troops on the same island. Additionally, clinal variations of allelic frequencies at some loci were detected. The genetic features and socio-ecological and evolutionary implications are discussed.     

Genetic variability within and between the troops of toque macaque,Macaca sinica,in Sri Lanka

Genetic variability within and between the troops of toque macaque in Sri Lanka was studied from a population genetical perspective. Studies were made using electrophoretical blood protein variations as markers in order to clarify the genetic characteristics of the population of this species. A total of 256 samples from 20 troops which were collected in the field in 1981 to 1982 and 1983 to 1984 were examined for 32 blood protein loci. Eleven loci, that is, Tf, Alb, TBPA, Hb-α, PHI, PGM-II, CA-I, IDH, AK, ADA, and Ch-E showed the polymorphism in one or more troops. Of these 11 loci, 7 loci, that is, Tf, TBPA, Hb-α, PHI, PGM-II, CA-I, and IDH were highly polymorphic in most troops. The genetic variability within troops were quantified as H=0.0782 in average and this value was on higher level than other primates and comparable with that of continental macaques,Macaca fascicularis, in Thailand. The genetic differentiation between troops was quantified byG _ST andF _ST and these values were relatively smaller than those of other insular macaques.     

Analysis of STAT5A/AvaI Gene Polymorphism in Four Italian Cattle Breeds

The STAT5A/AvaI polymorphism was investigated with PCR-RFLP in a sample of 339 cattle belonging to four breeds: Italian Friesian, Jersey, Italian Brown, and Podolica reared in south Italy. All three possible genotypes for the C/T polymorphism were identified. In these breeds, PCR-RFLP showed the predominance of the TT genotype in Italian Brown and Jersey cows; in Podolica and Italian Friesian CT is the most frequent genotype. The frequency of the T allele ranged from 0.55 to 0.81 in the analyzed populations. The distribution of genotypic and allelic frequencies at this locus was significantly different among the four populations based on a χ² test (P < 0.001), suggesting that the molecular characteristics of the STAT5A gene could be significantly affected by the breed selection. Gene heterozygosity, gene homozygosity, effective allele number, fixation index, and polymorphism information content (PIC) were calculated. The observed heterozygosity, as well as the N _e and PIC values, indicates high genetic variability in the Podolica breed. Podolica could be considered an interesting reservoir of genetic diversity for a species under high selective pressure elsewhere.     

Genetic polymorphisms of blood proteins in the troops of Japanese macaques,Macaca fuscata: IV. Erythrocyte esterase polymorphism inMacaca fuscata

Genetic variation at the locus controlling A₁ band of erythrocyte esterase was found in the Japanese macaque,Macaca fuscata. Existence of four alleles,Es-A ₁ ¹ ,Es-A ₁ ² ,Es-A ₁ ³ , andEs-A ₁ ⁴ , controlling the mobility of the band and codominance relation between them were postulated. A majority of the troops examined were monomorphic inEs-A ₁ 1-1 phenotype, and the variant phenotypes were observed to occur only in Yugawara-Ihama, Arashiyama, and Koshima areas.     

Genetic Linkage between the AH Locus and a Major Gene That Inhibits Susceptibility to Audiogenic Seizures in Mice

Mice of the DBA/2 (D2) strain are highly susceptible to sound-induced seizures at 21 days of age; whereas, mice of the C57BL/6 (B6) strain are resistant to these seizures. Although the difference in susceptibility to audiogenic seizures (ASs) between these two strains is inherited as a multiple-factor trait, an association was observed between susceptibility to ASs and the Ah locus. The Ah locus controls the inducibility of aryl hydrocarbon hydroxylase (AHH) activity by a number of aromatic hydrocarbons. B6 mice carry the Ah^b allele and have inducible AHH activity; whereas, D2 mice carry the Ah^d allele and have noninducible activity. Inducibility is inherited as a Mendelian dominant trait in crosses between these strains. Mice carrying the Ah^b allele are generally less susceptible to ASs at 21 days of age than are mice carrying the Ah^d allele. The combined results from B6 x D2 recombinant inbred strains, congenic strains (where the Ah^b allele was placed into the D2 genome and the Ah^d allele placed into the B6 genome), the B6D2F₁ x D2 backcross generation, and a random survey of various inbred strains, suggest that the association between these two traits is due to genetic linkage, rather than to pleiotrophy or to chance. A major gene that inhibits susceptibility to ASs appears to be closely linked to the Ah locus. This gene has been designated Ias, for inhibition of ASs. A large portion of the genetic variability of AS susceptibility may be due to the segregation of Ias.     

Single nucleotide polymorphisms of NR3C1 gene and recurrent depressive disorder in population of Poland

Depressive disorder is a disease characterized by disturbances in the hypothalamo–pituitary–adrenal axis. Abnormalities include the increased level of glucocorticoids (GC) and changes in sensitivity to these hormones. The changes are related to glucocorticoid receptors gene (NR3C1) variants. The NR3C1 gene is suggested to be a candidate gene affecting depressive disorder risk and management. The aim of this study was to investigate polymorphisms within the NR3C1 gene and their role in the susceptibility to recurrent depressive disorder (rDD). 181 depressive patients and 149 healthy ethnically matched controls were included in the study. Single nucleotide polymorphisms were assessed using polymerase chain reaction/restriction fragment length polymorphism method. Statistical significance between rDD patients and controls was observed for the allele and genotype frequencies at three loci: BclI, N363S, and ER22/23EK. The presence of C allele, CC, and GC genotype of BclI polymorphism, G allele and GA genotype for N363S and ER22/23EK variants respectively were associated with increased rDD risk. Two haplotypes indicated higher susceptibility for rDD, while haplotype GAG played a protective role with OR_dis 0.29 [95 % confidence interval (CI) = 0.13–0.64]. Data generated from this study support the earlier results that genetic variants of the NR3C1 gene are associated with rDD and suggest further consideration on the possible involvement of these variants in etiology of the disease.     

Genetic variation of five blood group polymorphisms in ten populations of Assam,India

Six Mongoloid and four Caucasoid populations of Assam, India, were examined for A₁A₂BO, Rhesus, Duffy and Diego blood groups. The distribution of their phenotypes and allele frequencies are presented. In the perspective of the ethnographic background, the results have been discussed in terms of genetic variability among these populations and probable reasons for its existence. The major groups, namely Caucasoids and Mongoloids, appear to form two separate groups in terms of these blood groups, though evidence is there to suggest intermixture.     

Molecular characterization of a novel vernalization allele <Emphasis Type="Italic">Vrn-B1d</Emphasis> and its effect on heading time in Chinese wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) landrace Hongchunmai

Flowering time of wheat cultivars contributes greatly to the adaptability to environmental conditions and it is largely controlled by vernalization genes. In this study, 262 Chinese mini-core wheat cultivars were used to identify the allelic variation at VRN-B1 locus. A novel dominant allele Vrn-B1d was found in Chinese spring wheat landrace cultivar Hongchunmai. This allele contained several genetic divergence within the first intron comparing to the recessive allele vrn-B1, including one large 6850-bp deletion (670–7519 bp), one small 187-bp deletion (7851–8037 bp), one unique SNP (T to C, 7845 bp), and one 4-bp mutation (TTTT to ACAA, 7847–7850 bp). Meanwhile, it was also different from the three known dominant alleles at VRN-B1 locus. Two pairs of primers were designed to identify the novel allele Vrn-B1d and other four known alleles of VRN-B1. A multiplex PCR was established to discriminate all five alleles simultaneously. The greenhouse experiment with high temperature (non-vernalizing condition) and long light showed that F₂ plants containing Vrn-B1d allele headed significantly earlier than those with recessive vrn-B1 allele, suggesting that Vrn-B1d is a dominant allele conferring the spring growth habit. This study provides a useful germplasm and molecular markers for wheat breeding.     

Temporal Stability of Genetic Variability and Differentiation in the Three-Spined Stickleback (Gasterosteus aculeatus)

Temporal variation in allele frequencies, whether caused by deterministic or stochastic forces, can inform us about interesting demographic and evolutionary phenomena occurring in wild populations. In spite of the continued surge of interest in the genetics of three-spined stickleback (Gasterosteus aculeatus) populations, little attention has been paid towards the temporal stability of allele frequency distributions, and whether there are consistent differences in effective size (N_e) of local populations. We investigated temporal stability of genetic variability and differentiation in 15 microsatellite loci within and among eight collection sites of varying habitat type, surveyed twice over a six-year time period. In addition, N_es were estimated with the expectation that they would be lowest in isolated ponds, intermediate in larger lakes and largest in open marine sites. In spite of the marked differences in genetic variability and differentiation among the study sites, the temporal differences in allele frequencies, as well as measures of genetic diversity and differentiation, were negligible. Accordingly, the N_e estimates were temporally stable, but tended to be lower in ponds than in lake or marine habitats. Hence, we conclude that allele frequencies in putatively neutral markers in three-spined sticklebacks seem to be temporally stable – at least over periods of few generations – across a wide range of habitat types differing markedly in levels of genetic variability, effective population size and gene flow.     

Risk conferred by FokI polymorphism of vitamin D receptor (VDR) gene for essential hypertension

BACKGROUND:

The vitamin D receptor (VDR) gene serves as a good candidate gene for susceptibility to several diseases. The gene has a critical role in regulating the renin-angiotensin system (RAS) influencing the regulation of blood pressure. Hence determining the association of VDR polymorphisms with essential hypertension is expected to help in the evaluation of risk for the condition.

AIM:

The aim of this study was to evaluate association between VDRFok I polymorphism and genetic susceptibility to essential hypertension.

MATERIALS AND METHODS:

Two hundred and eighty clinically diagnosed hypertensive patients and 200 normotensive healthy controls were analyzed for Fok I (T/C) [rs2228570] polymorphism by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) analysis. Genotype distribution and allele frequencies in patients and controls, and odds ratios (ORs) were calculated to predict the risk for developing hypertension by the individuals of different genotypes.

RESULTS:

The genotype distribution and allele frequencies of Fok I (T/C) [rs2228570] VDR polymorphism differed significantly between patients and controls (χ² of 18.0; 2 degrees of freedom; P = 0.000). FF genotype and allele F were at significantly greater risk for developing hypertension and the risk was elevated for both the sexes, cases with positive family history and habit of smoking.

CONCLUSIONS:

Our data suggest that VDR gene Fok I polymorphism is associated with the risk of developing essential hypertension     

Empirical Distributions of F ST from Large-Scale Human Polymorphism Data

Studies of the apportionment of human genetic variation have long established that most human variation is within population groups and that the additional variation between population groups is small but greatest when comparing different continental populations. These studies often used Wright’s F _ST that apportions the standardized variance in allele frequencies within and between population groups. Because local adaptations increase population differentiation, high-F _ST may be found at closely linked loci under selection and used to identify genes undergoing directional or heterotic selection. We re-examined these processes using HapMap data. We analyzed 3 million SNPs on 602 samples from eight worldwide populations and a consensus subset of 1 million SNPs found in all populations. We identified four major features of the data: First, a hierarchically F _ST analysis showed that only a paucity (12%) of the total genetic variation is distributed between continental populations and even a lesser genetic variation (1%) is found between intra-continental populations. Second, the global F _ST distribution closely follows an exponential distribution. Third, although the overall F _ST distribution is similarly shaped (inverse J), F _ST distributions varies markedly by allele frequency when divided into non-overlapping groups by allele frequency range. Because the mean allele frequency is a crude indicator of allele age, these distributions mark the time-dependent change in genetic differentiation. Finally, the change in mean-F _ST of these groups is linear in allele frequency. These results suggest that investigating the extremes of the F _ST distribution for each allele frequency group is more efficient for detecting selection. Consequently, we demonstrate that such extreme SNPs are more clustered along the chromosomes than expected from linkage disequilibrium for each allele frequency group. These genomic regions are therefore likely candidates for natural selection.     

MHC influences infection with parasites and winter survival in the root vole Microtus oeconomus

Selective pressure from parasites is thought to maintain the polymorphism of major histocompatibility complex (MHC) genes. Although a number of studies have shown a relationship between the MHC and parasitic infections, the fitness consequences of such associations are less well documented. In the present paper, we characterised the variation in exon 2 of MHC class II DRB gene in the root vole and examined the effects of that gene on parasite prevalence and winter survival. We identified 18 unique exon 2 sequences, which translated into 10 unique amino acid sequences. Phylogenetic analysis revealed the presence of three distinct clusters, and allele distributions among these individuals suggested that the clusters correspond to three different loci. Although the rate of synonymous substitutions (d_S) exceeded the rate of nonsynonymous substitutions (d_N) across sequences, implying purifying selection, d_N was significantly elevated at antigen-binding sites, suggesting that these sites could be under positive selection. Screening for parasites revealed a moderate prevalence of infection with gastrointestinal parasites (24 % infected), but a high infection rate for blood parasites (56 % infected). Infection with the blood parasite Babesia ssp. decreased survival almost twofold (25.7 vs. 13.9 %). Animals possessing the amino acid sequence AA*08 survived better than others (44.9 vs. 22 %), and they were infected with Babesia ssp. less often (13.9 vs 25.7 %). In contrast, individuals carrying allele AA*05 were infected more often (31.7 vs. 15.3 %). Heterozygosity at one of the putative loci was associated with a lower probability of infection with Babesia ssp., but at the other locus, the association was reversed. The unexpected latter result could be at least partly explained by the increased frequency of the susceptible allele AA*05 among heterozygotes. Overall, we demonstrate that infection with Babesia ssp. is a strong predictor of winter survival and that MHC genes are important predictors of infection status as well as survival in the root vole.     

Genetic Integrity and Microgeographic Population Structure of Westslope Cutthroat Trout, Oncorhynchus clarki lewisi, in the Pend Oreille Basin in Washington

Five microsatellite DNA loci (Ots-101 ^*,Ots-107 ^*,Oki-10 ^*, Ogo-3 ^*, and FGT-3 ^*) were screened to evaluate the genetic characteristics and population structure for cutthroat trout from eight tributaries of the Pend Oreille River in northeastern Washington and to compare these collections with two hatchery stocks of westslope cutthroat trout, Oncorhynchus clarki lewisi, Yellowstone cutthroat trout, Oncorhynchus clarki bouvieri and a hatchery rainbow trout, Oncorhynchus mykiss, strain that have been stocked in northeastern Washington. Relatively high levels of variation (numbers of alleles and heterozygosity) were observed in all collections and allele frequencies were quite variable among collections. Evidence of limited introgression by rainbow and/or Yellowstone cutthroat was found at several locations. Both F_ST values and tests of genetic differentiation indicated the existence of numerous, reproductively isolated populations. The population in Slate Creek was very similar to the Kings Lake Hatchery strain, and we conclude that this similarity is the result of historical introductions of this hatchery strain into what was presumably a stream without a native cutthroat population. In one stream, differences in introgression and allele frequencies were found above and below a barrier falls. Because of the substantial level of population differentiation observed among the various collections, we recommend that management and conservation actions be focused at the level of individual streams in order to maintain the productivity and genetic character of the existing populations of cutthroat trout.