On a population genetic model by S. Karlin

Summary One of the basic models in population genetics by S. Karlin is the model for a population of haploid individuals with several types and mutation and fixed population size. Mathematically the model is a derived multitype branching process. In order to estimate the approach to homozygosity of the population one has to compute the eigenvalues of the finite transition matrix of the corresponding Markov chain. Karlin (1968) gave explicit expressions for these eigenvalues. The idea of his proof is to transform the transition matrix into triangular form. Starting from the same idea the paper establishes a somewhat simpler and more elaborate proof.     

Contribution of A.S. Serebrovski? to population genetics]

The article commemorates Professor Alexander Sergeevich Serebrovsky (1892-1948), a prominent Russian geneticist, the founder of the Department of Genetics of Moscow University. A thorough analysis of his publications written in the 20s and 30s demonstrates that A.S. Serebrovsky: 1) developed the principles of such original fields of population genetics as gene geography and the theory of gene pools; 2) specified the significance of random genetic drift for neutral evolution in small populations; 3) showed that subdivision of an isolated population is essential for long-term conservation of its genetic composition. A.S. Serebrovsky's contribution into population genetics is viewed as an achievement of the Russian scientific school, always distinguished by historic and geographical approach to natural phenomena and processes.     

Forecasting the obesity epidemic in the aging U.S. population

Objective: The objective was to forecast BMI distribution in the U.S. population along with demographic changes based on past race‐, sex‐, and birth cohort‐specific secular trends. Research Methods and Procedures: We compiled data from 44,184 subjects from 4 National Health and Nutrition Examination Surveys (NHANES; 1971 to 2004). By race and sex, we fit regression models to create smoothed mean BMI curves by age for 1970 to 2010. Linking corresponding birth cohorts across age‐ and year‐specific mean BMI projections, we estimated the trajectory of relative BMI throughout each cohort's lifetime. These projections were validated using actual cohorts in the Nurses’ Health Study and Health Professionals Follow‐up Study. Combined with U.S. census, we predicted BMI distributions in 2010 and examined the joint impact of the obesity epidemic and population aging. Results: BMI secular trends in the past 3 decades differ significantly by birth cohort, sex, and race. If these trends continue, the prevalence of obesity is expected to reach 35%, 36%, 33%, and 55% in 2010 among white men, white women, black men, and black women, respectively, far from the Healthy People 2010 goal of 15%. Such forecasts translate into 9.3 million more obese adults 20 to 74 years of age than in 2000, 8.3 million of whom would be 50 years of age or older, and 8.5 million of whom would be white. The mean age among obese men and women is also expected to rise from 47 to 49 years among whites and from 43 to 44 years among blacks. Discussion: As the baby boom generation approaches retirement age, the continuing obesity epidemic signals a likely expansion in the population with obesity‐related comorbidities. A framework to combine BMI and demographic trends is essential in evaluating the burden and disparity associated with the epidemic in the aging U.S. population.     

Statin use and risk of hepatocellular carcinoma in a U.S. population

PurposeStatins (3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors) are medications widely prescribed to reduce cholesterol levels. Observational studies in high-risk populations, mostly in Asia, have suggested that statins are associated with a reduced risk of hepatocellular carcinoma (HCC). The current study sought to evaluate the association of statin use and HCC in a U.S.-based, low-risk, general population.MethodsA nested case–control study was conducted among members of the Health Alliance Plan HMO of the Henry Ford Health System enrolled between 1999 and 2010. Electronic pharmacy records of statin use were compared among tumor registry-confirmed cases of HCC (n = 94) and controls (n = 468) matched on age, sex, diagnosis date, and length of HMO enrolment.ResultsIn multivariate analyses, ever-use of statins was significantly inversely associated with development of HCC (Odds ratio (OR): 0.32, 95%CI: 0.15–0.67). No clear dose–response relationship was evident as statin use for <2 years (OR = 0.32, 95%CI = 0.13–0.83) and >2 years (OR = 0.31, 95CI% = 0.12–9.81) resulted in very similar ORs.ConclusionsThe use of statins among populations in low-risk HCC areas may be associated with decreased risk of HCC.     

Association of the DTNBP1 locus with schizophrenia in a U.S. population

Linkage and association studies have recently implicated dystrobrevin-binding protein 1 (DTNBP1) in the etiology of schizophrenia. We analyzed seven previously tested DTNBP1 single-nucleotide polymorphisms (SNPs) in a cohort of 524 individuals with schizophrenia or schizoaffective disorder and 573 control subjects. The minor alleles of three SNPs (P1578, P1763, and P1765) were positively associated with the diagnosis of schizophrenia or schizoaffective disorder in the white subset of the study cohort (258 cases, 467 controls), with P1578 showing the most significant association (odds ratio 1.76, P =.0026). The same three SNPs were also associated in a smaller Hispanic subset (51 cases, 32 controls). No association was observed in the African American subset (215 cases, 74 controls). A stratified analysis of the white and Hispanic subsets showed association with the minor alleles of four SNPs (P1578, P1763, P1320, and P1765). Again, the most significant association was observed for P1578 (P =.0006). Haplotype analysis supported these findings, with a single risk haplotype significantly overrepresented in the white sample (P =.005). Our study provides further evidence for a role of the DTNBP1 gene in the genetic etiology of schizophrenia.     

Weedy adaptation in Setaria spp. II. Genetic diversity and population genetic structure in S. glauca,S. geniculata,and S. faberii (Poaceae)

Setaria glauca (yellow foxtail), S. geniculata (knotroot foxtail), and S. faberii (giant foxtail) are important cosmopolitan weeds of temperate and tropical regions. Isozyme markers were used to investigate genetic diversity and population genetic structure in 94 accessions of yellow foxtail, 24 accessions of knotroot foxtail, and 51 accessions of giant foxtail, collected mainly from North America and Eurasia. Giant foxtail populations were nearly identical genetically, with only one population exhibiting isozyme polymorphism. Yellow and knotroot foxtail populations had low genetic diversity but marked population differentiation. Although the latter species are similar morphologically, they are readily distinguished electrophoretically, with Nei's genetic identity being 0.83. In both species, genetic divergence between accessions from Eurasia and North America was minimal. Populations from the native ranges had slightly greater genetic diversity than those from the respective introduced ranges. Yellow foxtail populations genetically clustered into Asian, European, and North American groups. Within North America, yellow foxtail populations from Iowa were genetically diverse whereas populations collected from other North American locations were nearly monomorphic for the same multilocus genotype. Knotroot foxtail populations in North America were genetically differentiated into northern and southern groups on either side of a line at ≈37° N latitude. No genetic patterning was evident in knotroot foxtail populations from Eurasia. In both yellow and knotroot foxtail, patterns of population genetic structure have been influenced by several factors, including genetic bottlenecks associated with founder events, genetic drift, and natural selection.     

Associations between organochlorine pesticides and vitamin D deficiency in the U.S. population

Background

Recently low dose organochlorine (OC) pesticides have been strongly linked to various chronic diseases including diabetes and cardiovascular diseases. Both field and animal studies have suggested a possibility that persistent lipophilic chemicals like OC pesticides can cause vitamin D deficiency, but there have been no human studies of exposure to any chemical as a possible cause of vitamin D deficiency. This study was performed to examine if serum concentrations of OC pesticides were associated with serum concentrations of 25-hydroxyvitamin D (25(OH)D) in the U.S. general population.

Methodology/Principal Findings

Cross-sectional associations of serum OC pesticides with serum 25(OH)D were investigated in 1,275 subjects aged ≥20 in the National Health and Nutrition Examination Survey(NHANES), 2003–2004. We selected 7 OC pesticides detectable in ≥80% of participants. Among the 7 OC pesticides, p,p′-DDT (β = −0.022, P<0.01), p,p′-DDE (β = −0.018, P = 0.04), and β-hexachlorocyclohexane (β = −0.022, P = 0.02) showed significant inverse associations with serum 25(OH)D levels. When study subjects were stratified by age, race, and the presence of various chronic diseases, p,p′-DDT showed consistent inverse associations in all subgroups, although stronger associations tended to be observed among subjects with old age, white race, or chronic diseases.

Conclusion/Significance

The current study suggests that the background exposure to some OC pesticides leads to vitamin D deficiency in human. Considering the importance of vitamin D deficiency in the development of chronic diseases, chemical exposure as a possible cause of vitamin D deficiency should be evaluated in prospective and experimental studies.     

Subspecies composition and founder contribution of the captive U.S. chimpanzee (Pan troglodytes) population

Chimpanzees are presently classified into three subspecies: Pan troglodytes verus from west Africa, P.t. troglodytes from central Africa, and P.t. schweinfurthii from east Africa. A fourth subspecies (P.t. vellerosus), from Cameroon and northern Nigeria, has been proposed. These taxonomic designations are based on geographical origins and are reflected in sequence variation in the first hypervariable region (HVR-I) of the mtDNA D-loop. Although advances have been made in our understanding of chimpanzee phylogenetics, little has been known regarding the subspecies composition of captive chimpanzees. We sequenced part of the mtDNA HVR-I region in 218 African-born population founders and performed a phylogenetic analysis with previously characterized African sequences of known provenance to infer subspecies affiliations. Most founders were P.t. verus (95.0%), distantly followed by the troglodytes schweinfurthii clade (4.6%), and a single P.t. vellerosus (0.4%). Pedigree-based estimates of genomic representation in the descendant population revealed that troglodytes schweinfurthii founder representation was reduced in captivity, vellerosus representation increased due to prolific breeding by a single male, and reproductive variance resulted in uneven representation among male P.t.verus founders. No increase in mortality was evident from between-subspecies interbreeding, indicating a lack of outbreeding depression. Knowledge of subspecies and their genomic representation can form the basis for phylogenetically informed genetic management of extant chimpanzees to preserve rare genetic variation for research, conservation, or possible future breeding.     

Overweight and fatness in Dalmatia, Croatia: comparison with the U.S. population reference

Subscapular skinfold, elbow breadth and upper arm indicators of nutritional status were studied in the population of Dalmatia in Croatia. Age- and sex-specific percentiles were obtained from 4373 subjects, 18 to 74 years of age, and compared to the U.S. NHANES I and II reference data. There were significant differences between these data sets in all studied variables. The results complement those reported previously for BMI and triceps skinfold and indicate that high prevalence of overweight in Dalmatians largely reflects their muscularity and skeletal robustness rather than excess body fatness. The findings suggest that the U.S. upper percentiles of BMI and skinfolds are inadequate for the assessment of excess body fatness in Dalmatian population. The obtained population-specific percentile distributions should be used provisionally as the reference data for group comparisons in the Dalmatian region.     

What people believe about how memory works: a representative survey of the U.S. population

Incorrect beliefs about the properties of memory have broad implications: the media conflate normal forgetting and inadvertent memory distortion with intentional deceit, juries issue verdicts based on flawed intuitions about the accuracy and confidence of testimony, and students misunderstand the role of memory in learning. We conducted a large representative telephone survey of the U.S. population to assess common beliefs about the properties of memory. Substantial numbers of respondents agreed with propositions that conflict with expert consensus: Amnesia results in the inability to remember one's own identity (83% of respondents agreed), unexpected objects generally grab attention (78%), memory works like a video camera (63%), memory can be enhanced through hypnosis (55%), memory is permanent (48%), and the testimony of a single confident eyewitness should be enough to convict a criminal defendant (37%). This discrepancy between popular belief and scientific consensus has implications from the classroom to the courtroom.     

群落演替对夏蜡梅种群分布和数量的影响

对夏蜡梅(Sinocalycanthus chinensis(Cheng et S.Y.Chang)Cheng et S.Y.Chang)所有分布地(浙江临安、天台和安徽绩溪)进行了详细调查,分析夏蜡梅种群面积、密度、结构和群落特征等,并与前人调查结果对比,阐明群落演替对夏蜡梅种群的影响。10余年来,由于国家相关政策的实施(退耕还林、天然林保护以及自然保护区的建立等)以及夏蜡梅分布地林地经营模式的改变,不同夏蜡梅群落呈现发展演替的不同状态,从而对夏蜡梅种群产生了显著影响。从群落类型来看,较为稳定的种群为大明山、西坑、白水坞、捣臼孔种群,种群结构为增长型或稳定型,群落处于乔木或顶级乔木阶段,原生植被保存较好,生境相对稳定,各物种在长期竞争中趋于稳定;直源种群为严重衰退的种群,群落经历了从灌丛阶段向灌乔阶段演化,原来同层次的常绿乔木逐渐形成密集的乔木层,郁闭度高,造成夏蜡梅生长不良甚至死亡,幼苗缺少或数量少,更新困难,此区域的夏蜡梅呈逐渐退化消亡趋势;而溪古坪、龙塘山种群所处群落正是属于这种群落演替的早期阶段,处于衰退过程中种群,不加人工干预也会逐渐退化;而双石边、经过坪等种群虽目前数量多,分布集中,更新良好,但变数最大,一旦人工干扰加剧或消除,则种群结构将快速发生变化,走向消亡的几率极大。该研究结果可为夏蜡梅保护提供科学依据。     

Genetic population structure of spotted seatrout Cynoscion nebulosus along the south‐eastern U.S.A.

Analyses of the genetic population structure of spotted seatrout Cynoscion nebulosus along the south‐eastern U.S. coast using 13 microsatellites suggest significant population differentiation between fish in North Carolina (NC) compared with South Carolina (SC) and Georgia (GA), with New River, NC, serving as an area of integration between northern and southern C. nebulosus. Although there is a significant break in gene flow between these areas, the overall pattern throughout the sampling range represents a gradient in genetic diversification with the degree of geographic separation. Latitudinal distance and estuarine density appear to be main drivers in the genetic differentiation of C. nebulosus along the south‐eastern U.S. coast. The isolation‐by‐distance gene‐flow pattern creates fine‐scale differences in the genetic composition of proximal estuaries and dictates that stocking must be confined to within 100 km of the location of broodstock collection in order to maintain the natural gradient of genetic variation along the south‐eastern U.S. coast.     

Geographical patterns in the population genetics of Atlantic salmon, Salmo salar L., on U.S.S.R. territory, as evidence for colonization routes

From data on interpopulation genetic structure of the Atlantic salmon from the rivers of the Barents, White and Baltic Sea basins on U.S.S.R. territory, it is suggested that salmon colonized the Onega and Pechora River basins from the Baltic drainage as the last ice-sheet receded, and that the Kola Peninsula rivers were colonized separately from the Barents Sea area.