Genetic hemochromatosis and HLA linkage

Summary We previously reported five families with primary, genetic (idiopathic) hemochromatosis in whom HLA typing of subjects indicated that a homozygous-heterozygous mating had almost certainly occurred and in whom inheritance of the disease trait was best explained by an autosomal recessive mode of inheritance. However, in one family, two children apparently homozygous for hemochromatosis did not manifest overt evidence of the disease, and alternative explanations were postulated, including autosomal dominant inheritance in this family. Subsequent study of the family members, including repeat HLA-DR serology with more recently defined antisera and DNA genotyping at the HLA-DR locus has, we believe, provided the true explanation for the previous apparent anomaly and adds further evidence for the tight linkage of the disease to the HLA-A locus.     

Genetic Loads in Heterogeneous Environments

A model of population structure in heterogeneous environments is described with attention focused on genetic variation at a single locus. The existence of equilibria at which there is no genetic load is examined.--The absolute fitness of any genotype is regarded as a function of location in the niche space and the population density at that location. It is assumed that each organism chooses to live in that habitat in which it is most fit ("optimal habitat selection").--Equilibria at which there is no segregation load ("loadless equilibria") may exist. Necessary and sufficient conditions for the existence of such equilibria are very weak. If there is a sufficient amount of dominance or area in which the alleles are selectively neutral, then there exist equilibria without segregational loads. In the N2p phase plane defined by population size, N, and gene frequency, p, these equilibria generally consist of a line segment which is parallel to the p axis. These equilibria are frequently stable.     

Genetic Variation in Heterogeneous Environments

A model of population structure in heterogeneous environments is described and conditions sufficient for maintaining a polymorphism are derived.

The absolute fitness of any genotype is regarded as a function of location in the niche space and the population density at that location. Two modes of habitat selection are examined: (1) organisms are distributed uniformly over the environment; and (2) each organism selects to occupy that habitat in which it is most fit ("optimal habitant selection").—Sufficient conditions for maintenance of genetic polymorphisms are derived for both models. In populations which do not practice habitat selection heterozygote superiority averaged over the environment is sufficient to guarantee the existence of polymorphisms. Comparable conditions for populations which practice optimal habitat selection are much less restrictive. If the heterozygotes are superior to one homozygote in any one part of the niche and to the other homozygote in any other part of the niche then a polymorphism will be defined.—A positive correlation between genetic and environmental variation follows from the model with habitat selection, but not from the other. The adaptive significance of polymorphisms thus depends on how animals behave.

     

羊驼种群内亲缘关系的研究

应用RAPD技术对羊驼群体进行亲缘关系检测。在所采用的40条随机引物中筛选出10条,优化了RAPD的反应条件,确立了适合于羊驼基因组RAPD分析的最佳反应体系和反应程序。计算出个体间之间的带纹相似系数及遗传距离指数,带纹相似系数位于0.3901~0.7851之间,平均为0.5374;彼此间的遗传距离最小为0.2149,最大为0.6099,平均为0.4626,并绘制出个体间亲缘关系树状聚类图。结果显示羊驼种群内遗传基础广泛,证明其个体间的血缘关系较远,这将有利于羊驼种群的正常生长、发育、繁殖和快速扩群。     

人类群体遗传空间结构对应分析中的“蹄型效应”及其遗传学解释

探讨了人类群体遗传结构对应分析中“蹄型效应”的产生机制及其遗传学解释。从分析基因频率矩阵的结构特点入手,以实例验证和比较了对应分析中散点图的结构特征。发现当基因频率矩阵的结构不同时,其对应分析中散点图的分布模式不同;当基因频率矩阵中存在稀有基因时,其对应分析的散点图则呈现明显的“蹄型效应”。“蹄型效应”经常会歪曲潜在遗传结构的真实形态,其产生主要是因为对应分析中的c2距离不相似测度高估了稀有基因的作用。在人类群体遗传结构对应分析中,当出现“蹄型效应”效应时,需认真分析基因频率矩阵的结构,寻找“蹄型效应”产生原因并给出合理的遗传学解释,以免做出错误结论。     

The Performance of Mixture Models in Heterogeneous Closed Population Capture–Recapture

Summary .   Dorazio and Royle (2003, Biometrics 59, 351–364) investigated the behavior of three mixture models for closed population capture–recapture analysis in the presence of individual heterogeneity of capture probability. Their simulations were from the beta-binomial distribution, with analyses from the beta-binomial, the logit-normal, and the finite mixture (latent class) models. In this response, simulations from many different distributions give a broader picture of the relative value of the beta-binomial and the finite mixture models, and provide some preliminary insights into the situations in which these models are useful.     

Distribution of HLA Antigens in the Armenian Population of Nagornyi Karabakh

Characteristics of the distribution of 31 HLA antigens of classes I (A, B, and Cw) and II (DR) in Nagornyi Karabakh Armenians are reported for the first time. It has been found that the antigens most common in this population are A2, A3, A9, B5, B7, B12, Cw4, DR4, DR2, and DR3; the least common antigens are B15, B16, and B40. The results are compared with the data for Armenians living in Armenia and those for major ethnic groups. The frequencies of HLA antigens in Nagornyi Karabakh Armenians match those in Armenians living in Armenia. In the HLA-antigen distribution, Armenians are generally close to Caucasoids.     

HLA Genes in Mayos Population from Northeast Mexico

HLA class I and class II alleles have been studied in 60 unrelated people belonging to Mayos ethnic group, which lives in the Mexican Pacific Sinaloa State. Mayos HLA profile was compared to other Amerindians and worldwide populations’ profile. A total of 14,896 chromosomes were used for comparisons. Genetic distances between populations, Neigbour-Joining dendrograms and correspondence analyses were performed to determine the genetic relationship among population. The new specific Mayo HLA haplotypes found are: HLA-A*02-B*35-DRB1*1406-DQB1*0301; HLA-A*02-B*48-DRB1*0404-DQB1*0302; HLA-A*24-B*51-DRB1*0407-DQB1*0302 and HLA-A*02-B*08-DRB1*0407-DQB1*0302. However, the typical Meso American HLADRB1*0407 represents a 40% of all DRB1 alleles. While common HLA characteristics are found in Amerindian distant ethnic groups, still new group specific HLA haplotypes are being found, suggesting that a common founder effect (i.e. high DRB1*0407) is noticed. Moreover, new HLA haplotypes are almost certainly appearing along time probably due to specific pathogen (?) selection for diversity. Mayo language is close to the Tarahumara one (another geographically close group); notwithstanding both groups are not genetically close according to our results, showing again the different evolution of genes and languages, which do not correlate. Finally, Sinaloa is one of the Mexican States in which more European genes are found. However, the results presented in this paper, where no European HLA genes are seen in Mayos, should have a bearing in establishing transplant programs and in HLA and disease studies.Key Words: Amerindians, HLA, mayos, mexica, nahua, transplant.     

江浙沪地区汉族人群HLA单体型研究

利用HLA血清学和分子生物学分型方法对江浙沪地区汉族人群166对夫妻进行HLA-A,B和DR B1单体型调查,并分析HLA单体型的分布特征.结果显示,江浙沪地区汉族人群HLA-A2,A11,A24,B13,B46,B60,DRB104,DRB108,DRB109,DRB112和DRB115有较高的频率分布(＞10%).研究中发现HLA-A-B,B-DRB1单体型分别有128条和182条,占理论单体型总数的19.28%(128/664)和27.41%(182/664).其中有18种A-B单体型频率大于0.5%(连锁不平衡参数△＞0),有23种B-DRB1单体型频率大于0.5%(△＞0).A-B-DRB1单体型有351条,占理论单体型总数的52.86%(351/664),其中8种单体型频率大于0.5%(△＞0),A 30-B13-DRB107(4.22 %),A2-B46-DRB109(3.77%),A33-B58-DRB117(3.01%),A33-B58-DRB113.1(1.81%)和A11-B75-DRB112(1.51%)是最常见单体型.江浙沪地区汉族人群HLA单体型有其自身分布特点,遗传特征介于南北汉族之间,在东亚人群中中国汉族群体HLA多态性较为丰富.     

Risk Factors for Whole Carcass Condemnations in the Swiss Slaughter Cattle Population

We used meat-inspection data collected over a period of three years in Switzerland to evaluate slaughterhouse-level, farm-level and animal-level factors that may be associated with whole carcass condemnation (WCC) in cattle after slaughter. The objective of this study was to identify WCC risk factors so they can be communicated to, and managed by, the slaughter industry and veterinary services. During meat inspection, there were three main important predictors of the risk of WCC; the slaughtered animal''s sex, age, and the size of the slaughterhouse it was processed in. WCC for injuries and significant weight loss (visible welfare indicators) were almost exclusive to smaller slaughterhouses. Cattle exhibiting clinical syndromes that were not externally visible (e.g. pneumonia lesions) and that are associated with fattening of cattle, end up in larger slaughterhouses. For this reason, it is important for animal health surveillance to collect data from both types of slaughterhouses. Other important risk factors for WCC were on-farm mortality rate and the number of cattle on the farm of origin. This study highlights the fact that the many risk factors for WCC are as complex as the production system itself, with risk factors interacting with one another in ways which are sometimes difficult to interpret biologically. Risk-based surveillance aimed at farms with reoccurring health problems (e.g. a history of above average condemnation rates) may be more appropriate than the selection, of higher-risk animals arriving at slaughter. In Switzerland, the introduction of a benchmarking system that would provide feedback to the farmer with information on condemnation reasons, and his/her performance compared to the national/regional average could be a first step towards improving herd-management and financial returns for producers.     

Reconstructing the Population Genetic History of the Caribbean

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse—which today is reflected by shorter, older ancestry tracts—consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse—reflected by longer, younger tracts—is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source populations with far greater resolution than previously thought, even when limited pre-Columbian Caribbean haplotypes have survived.     

Genetic Hitchhiking under Heterogeneous Spatial Selection Pressures

During adaptive evolutionary processes substantial heterogeneity in selective pressure might act across local habitats in sympatry. Examples are selection for drug resistance in malaria or herbicide resistance in weeds. In such setups standard population-genetic assumptions (homogeneous constant selection pressures, random mating etc.) are likely to be violated. To avoid misinferences on the strength and pattern of natural selection it is therefore necessary to adjust population-genetic theory to meet the specifics driving adaptive processes in particular organisms. We introduce a deterministic model in which selection acts heterogeneously on a population of haploid individuals across different patches over which the population randomly disperses every generation. A fixed proportion of individuals mates exclusively within patches, whereas the rest mates randomly across all patches. We study how the allele frequencies at neutral markers are affected by the spread of a beneficial mutation at a closely linked locus (genetic hitchhiking). We provide an analytical solution for the frequency change and the expected heterozygosity at the neutral locus after a single copy of a beneficial mutation became fixed. We furthermore provide approximations of these solutions which allow for more obvious interpretations. In addition, we validate the results by stochastic simulations. Our results show that the application of standard population-genetic theory is accurate as long as differences across selective environments are moderate. However, if selective differences are substantial, as for drug resistance in malaria, herbicide resistance in weeds, or insecticide resistance in agriculture, it is necessary to adapt available theory to the specifics of particular organisms.     

Trypanosoma cruzi: Analysis of the Population Dynamics of Heterogeneous Mixtures1

Utilizing the previously reported inter-clonal differences in total DNA/organism, flow cytometry was used to analyze the population dynamics of Trypanosoma cruzi clone mixtures growing in liquid medium or vertebrate cells. The growth of clone mixtures in liquid medium can be described by unique parameters reflecting exponential growth rate (r), stationary phase population density (1/k), and the interaction between the clones (h). The relative numbers of each clone in the population change rapidly with time and the results arc in quantitative agreement with mathematical models of competitive population growth. The relationship between the parameters for T. cruzi is such that, in general, there is no dynamic equilibrium with coexistence of clones with different growth rates; under all culture protocols, the faster growing clone will prevail. A computer simulation of the vertebrate cell cycle of T. cruzi suggests that clone mixtures grow relatively independently; the basic attributes of the model were substantiated experimentally. Although wide fluctuations in the proportion of each clone released occurred, the faster growing clone again predominated. Finally, these results underline the importance of working with well-defined clones in the laboratory to avoid inconsistencies and paradoxical results and stress the importance of the rapid isolation of single cell clones from clinical specimens when studying the relationship of the parasite to human disease.