Analysis of population genetic structure of ten district populations of the Rostov oblast by means of an extended isonymic method of Barrai and colleagues

Parameters suggested by Barrai et al. (1992), including the random isonymy (I _r), surname diversity (α), migration index (v), and entropy (H) and redundancy (R) of surname distribution have been estimated in ten district populations of the Rostov oblast. Their weighted mean values are the following: I _r = 0.000813, v = 0.048, α = 1334.9, H = 11.30, R = 22.52.     

The age-sex structure of the slave population in Harris County, Texas: 1850 and 1860

The effect of the slave system on demography can be revealed by examining the age-sex structure of slave populations. The age-sex structure of slaves in Harris County, Texas is investigated using the 1850 and 1860 slave schedules. Median ages for black and mulatto slaves suggest that the population was young. Population pyramids exhibit a narrow base and top with a broad middle. The high proportion of slaves between 10 and 30 years of age and the increase in population size between 1850 and 1860 were mainly related to the importation of slaves and only partly due to natural increase. The data also show that black slaves were older on small plantations while mulattoes were older on larger farms. It is suggested that differential treatment in terms of purchase practices, assignment of tasks, food allocation, and/or differential susceptibility to infectious diseases may account for this pattern.     

2008年永福县早稻田稻纵卷叶螟发生动态及虫源性质

2008年通过调查和雌蛾卵巢解剖研究广西区永福县早稻田稻纵卷叶螟Cnaphalocrocis medinalis(Guenée)的发生动态和田间种群的虫源性质。结果表明,稻纵卷叶螟在永福县早稻田可发生4代。稻纵卷叶螟第1、2代属于基本迁入型;第3代性质较为复杂,属于本地繁殖型,既有迁入又有迁出;第4代为本地繁殖、大部分迁出型。对暴雨期间稻纵卷叶螟田间蛾量消长的研究表明,短时期的暴雨水淹对全县稻纵卷叶螟的田间蛾量消长总的影响不明显,但不同水淹情况的田块间虫量存在显著差异。还分析讨论2008年永福县早稻田稻纵卷叶螟暴发成灾的原因。     

Clines, clusters, and the effect of study design on the inference of human population structure

Previously, we observed that without using prior information about individual sampling locations, a clustering algorithm applied to multilocus genotypes from worldwide human populations produced genetic clusters largely coincident with major geographic regions. It has been argued, however, that the degree of clustering is diminished by use of samples with greater uniformity in geographic distribution, and that the clusters we identified were a consequence of uneven sampling along genetic clines. Expanding our earlier dataset from 377 to 993 markers, we systematically examine the influence of several study design variables—sample size, number of loci, number of clusters, assumptions about correlations in allele frequencies across populations, and the geographic dispersion of the sample—on the “clusteredness” of individuals. With all other variables held constant, geographic dispersion is seen to have comparatively little effect on the degree of clustering. Examination of the relationship between genetic and geographic distance supports a view in which the clusters arise not as an artifact of the sampling scheme, but from small discontinuous jumps in genetic distance for most population pairs on opposite sides of geographic barriers, in comparison with genetic distance for pairs on the same side. Thus, analysis of the 993-locus dataset corroborates our earlier results: if enough markers are used with a sufficiently large worldwide sample, individuals can be partitioned into genetic clusters that match major geographic subdivisions of the globe, with some individuals from intermediate geographic locations having mixed membership in the clusters that correspond to neighboring regions.     

An instantaneous coalescent method insensitive to population structure

Conventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic. However, most populations are structured. This complicates the prevailing coalescent analyses and sometimes leads to inaccurate estimates. To develop a coalescent method unhampered by population structure, we perform two analyses. First, we demonstrate that the coalescent probability of two randomly sampled alleles from the immediate preceding generation(one generation back)is independent of population structure. Second, motivated by this finding, we propose a new coalescent method: i-coalescent analysis. The i-coalescent analysis computes the instantaneous coalescent rate by using a phylogenetic tree of sampled alleles. Using simulated data, we broadly demonstrate the capability of i-coalescent analysis to accurately reconstruct population size dynamics of highly structured populations, although we find this method often requires larger sample sizes for structured populations than for panmictic populations. Overall, our results indicate i-coalescent analysis to be a useful tool, especially for the inference of population histories with intractable structure such as the developmental history of cell populations in the organs of complex organisms.     

Genetic diversity, population structure, effective population size and demographic history of the Finnish wolf population

The Finnish wolf population (Canis lupus) was sampled during three different periods (1996-1998, 1999-2001 and 2002-2004), and 118 individuals were genotyped with 10 microsatellite markers. Large genetic variation was found in the population despite a recent demographic bottleneck. No spatial population subdivision was found even though a significant negative relationship between genetic relatedness and geographic distance suggested isolation by distance. Very few individuals did not belong to the local wolf population as determined by assignment analyses, suggesting a low level of immigration in the population. We used the temporal approach and several statistical methods to estimate the variance effective size of the population. All methods gave similar estimates of effective population size, approximately 40 wolves. These estimates were slightly larger than the estimated census size of breeding individuals. A Bayesian model based on Markov chain Monte Carlo simulations indicated strong evidence for a long-term population decline. These results suggest that the contemporary wolf population size is roughly 8% of its historical size, and that the population decline dates back to late 19th century or early 20th century. Despite an increase of over 50% in the census size of the population during the whole study period, there was only weak evidence that the effective population size during the last period was higher than during the first. This may be caused by increased inbreeding, diminished dispersal within the population, and decreased immigration to the population during the last study period.     

Self-reported ethnicity, genetic structure and the impact of population stratification in a multiethnic study

It is well-known that population substructure may lead to confounding in case–control association studies. Here, we examined genetic structure in a large racially and ethnically diverse sample consisting of five ethnic groups of the Multiethnic Cohort study (African Americans, Japanese Americans, Latinos, European Americans and Native Hawaiians) using 2,509 SNPs distributed across the genome. Principal component analysis on 6,213 study participants, 18 Native Americans and 11 HapMap III populations revealed four important principal components (PCs): the first two separated Asians, Europeans and Africans, and the third and fourth corresponded to Native American and Native Hawaiian (Polynesian) ancestry, respectively. Individual ethnic composition derived from self-reported parental information matched well to genetic ancestry for Japanese and European Americans. STRUCTURE-estimated individual ancestral proportions for African Americans and Latinos are consistent with previous reports. We quantified the East Asian (mean 27%), European (mean 27%) and Polynesian (mean 46%) ancestral proportions for the first time, to our knowledge, for Native Hawaiians. Simulations based on realistic settings of case–control studies nested in the Multiethnic Cohort found that the effect of population stratification was modest and readily corrected by adjusting for race/ethnicity or by adjusting for top PCs derived from all SNPs or from ancestry informative markers; the power of these approaches was similar when averaged across causal variants simulated based on allele frequencies of the 2,509 genotyped markers. The bias may be large in case-only analysis of gene by gene interactions but it can be corrected by top PCs derived from all SNPs.     

An anthropometric study of the ear in an adult population

A sample of 539 individuals, 188 males and 351 females from 35 to 93 years, from a rural area, were studied in order to show ear variability according to age and sex. The characters analyzed were: maximum length and breadth, lobe type, and their possible asymmetries. The individuals were also searched for Darwin’s tubercle. Paper presented at the 4^th congress of the European Anthropology Association (Florence, Sept. 1984).     

An early Indian cranium from the Medicine Crow site, (39BF2), Buffalo County,South Dakota

Artifacts of Paleoindians have been found in most if not all of the Plains states; however, documented human skeletal remains from this early period are rare. The Medicine Crow cranium dates by stratigraphy and by the amount of absorbed alpha and beta radiation at between 5,000 and 2,000 B.C. This places this young adult male in the Archaic period and represents the earliest documented human skeletal material from South Dakota. It compares favorably in age with other well documented human skeletons from the Plains area, such as Lansing Man (Kansas) (3579 B.C.). Metrically, (with a cranial index of 76.7) and morphologically the Medicine Crow cranium falls well within the range of other early or middle Archaic skeletons.     

The use of quantitative traits in the study of human population structure

Studies of human population structure and history have tended to use demographic and/or serological data for analysis. This paper reviews the methods and studies that incorporate quantitative traits (usually polygenic traits) in such analyses. Methods of assessing the degree and pattern of among-group variation are discussed, and are characterized as being model-free or model-bound. Model-free methods deal with the measure of overall populational differentiation and with comparative methods for describing the pattern of differentiation. Model-bound methods are used for direct incorporation into theoretical models of population structure in order to estimate genetic parameters, such as those in admixture and isolation by distance models. To date, studies have indicated that quantitative traits may often be used successfully in studies of human population structure, and show effects of microevolutionary forces on quantitative variation among populations.     

Inbreeding and ecological change: An isonymic analysis of secular trends in a tyneside parish over three centuries

Abstract

Marriage entries in the parish records of Whickham, near Newcastle in the North of England, are analyzed by isonomy. Over the three centuries (1566–1866), a period including the arrival of the industrial revolution in the region, secular changes occur in the level of inbreeding. There is a general relationship of inbreeding level with demographic change and particularly with socioeconomic pattern.     

Dispersal, gene flow, and population structure

The accuracy of gene flow estimates is unknown in most natural populations because direct estimates of dispersal are often not possible. These estimates can be highly imprecise or even biased because population genetic structure reflects more than a simple balance between genetic drift and gene flow. Most of the models used to estimate gene flow also assume very simple patterns of movement. As a result, multiple interpretations of population structure involving contemporary gene flow, departures from equilibrium, and other factors are almost always possible. One way to isolate the relative contribution of gene flow to population genetic differentiation is to utilize comparative methods. Population genetic statistics such as FST, heterozygosity and Nei's D can be compared between species with differing dispersal abilities if these species are otherwise phylogenetically, geographically and demographically comparable. Accordingly, the available literature was searched for all groups that meet these criteria to determine whether broad conclusions regarding the relationships between dispersal, population genetic structure, and gene flow estimates are possible. Allozyme and mtDNA data were summarized for 27 animal groups in which dispersal differences can be characterized. In total, genetic data were obtained for 333 species of vertebrates and invertebrates from terrestrial, freshwater and marine habitats. Across these groups, dispersal ability was consistently related to population structure, with a mean rank correlation of -0.72 between ranked dispersal ability and FST. Gene flow estimates derived from private alleles were also correlated with dispersal ability, but were less widely available. Direct-count heterozygosity and average values of Nei's D showed moderate degrees of correlation with dispersal ability. Thus, despite regional, taxonomic and methodological differences among the groups of species surveyed, available data demonstrate that dispersal makes a measurable contribution to population genetic differentiation in the majority of animal species in nature, and that gene flow estimates are rarely so overwhelmed by population history, departures from equilibrium, or other microevolutionary forces as to be uninformative.