Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach.
(17/4953)
A new method for the estimation of migration rates and effective population sizes is described. It uses a maximum-likelihood framework based on coalescence theory. The parameters are estimated by Metropolis-Hastings importance sampling. In a two-population model this method estimates four parameters: the effective population size and the immigration rate for each population relative to the mutation rate. Summarizing over loci can be done by assuming either that the mutation rate is the same for all loci or that the mutation rates are gamma distributed among loci but the same for all sites of a locus. The estimates are as good as or better than those from an optimized FST-based measure. The program is available on the World Wide Web at http://evolution.genetics. washington.edu/lamarc.html/. (+info)
Overdominant alleles in a population of variable size.
(18/4953)
An approximate method is developed to predict the number of strongly overdominant alleles in a population of which the size varies with time. The approximation relies on the strong-selection weak-mutation (SSWM) method introduced by J. H. Gillespie and leads to a Markov chain model that describes the number of common alleles in the population. The parameters of the transition matrix of the Markov chain depend in a simple way on the population size. For a population of constant size, the Markov chain leads to results that are nearly the same as those of N. Takahata. The Markov chain allows the prediction of the numbers of common alleles during and after a population bottleneck and the numbers of alleles surviving from before a bottleneck. This method is also adapted to modeling the case in which there are two classes of alleles, with one class causing a reduction in fitness relative to the other class. Very slight selection against one class can strongly affect the relative frequencies of the two classes and the relative ages of alleles in each class. (+info)
Gene genealogies in geographically structured populations.
(19/4953)
Population genetics theory has dealt only with the spatial or geographic pattern of degrees of relatedness or genetic similarity separately for each point in time. However, a frequent goal of experimental studies is to infer migration patterns that occurred in the past or over extended periods of time. To fully understand how a present geographic pattern of genetic variation reflects one in the past, it is necessary to build genealogy models that directly relate the two. For the first time, space-time probabilities of identity by descent and coalescence probabilities are formulated and characterized in this article. Formulations for general migration processes are developed and applied to specific types of systems. The results can be used to determine the level of certainty that genes found in present populations are descended from ancient genes in the same population or nearby populations vs. geographically distant populations. Some parameter combinations result in past populations that are quite distant geographically being essentially as likely to contain ancestors of genes at a given population as the past population located at the same place. This has implications for the geographic point of origin of ancestral, "Eve," genes. The results also form the first model for emerging "space-time" molecular genetic data. (+info)
Population dynamics of scrapie in a sheep flock.
(20/4953)
A detailed analysis of an outbreak of natural scrapie in a flock of Cheviot sheep is described. A total of 137 cases was reported over 13 years among 1307 sheep born into the flock. The epidemiology of scrapie can only be understood with reference to sheep demography, the population genetics of susceptibility to scrapie, pathogenesis during a long incubation period, and the rate of transmission (by both vertical and horizontal routes), all of which interact in complex ways. A mathematical model incorporating these features is described, parameter values and model inputs are derived from available information from the flock and from independent sources, and model outputs are compared with the field data. The model is able to reproduce key features of the outbreak, including its long duration and the ages of cases. The analysis supports earlier work suggesting that many infected sheep do not survive to show clinical signs, that most cases arise through horizontal transmission, and that there is strong selection against susceptible genotypes. However, important aspects of scrapie epidemiology remain poorly understood, including the possible role of carrier genotypes and of an environmental reservoir of infectivity, and the mechanisms maintaining alleles giving susceptibility to scrapie in the sheep population. (+info)
Population biology of human onchocerciasis.
(21/4953)
Human onchocerciasis (river blindness) is the filarial infection caused by Onchocerca volvulus and transmitted among people through the bites of the Simulium vector. Some 86 million people around the world are at risk of acquiring the nematode, with 18 million people infected and 600,000 visually impaired, half of them partially or totally blind. 99% of cases occur in tropical Africa; scattered foci exist in Latin America. Until recently control programmes, in operation since 1975, have consisted of antivectorial measures. With the introduction of ivermectin in 1988, safe and effective chemotherapy is now available. With the original Onchocerciasis Control Programme of West Africa coming to an end, both the new African Programme for Onchocerciasis Control and the Onchocerciasis Elimination Programme for the Americas, rely heavily on ivermectin self-sustained mass delivery. In consequence, the need for understanding the processes regulating parasite abundance in human and simuliid populations is of utmost importance. We present a simple mathematical framework built around recent analyses of exposure- and density-dependent processes operating, respectively, within the human and vector hosts. An expression for the basic reproductive ratio, R0, is derived and related to the minimum vector density required for parasite persistence in localities of West Africa in general and northern Cameroon in particular. Model outputs suggest that constraints acting against parasite establishment in both humans and vectors are necessary to reproduce field observations, but those in humans may not fully protect against reinfection. Analyses of host age-profiles of infection prevalence, intensity, and aggregation for increasing levels of endemicity and intensity of transmission in the Vina valley of northern Cameroon are in agreement with these results and discussed in light of novel work on onchocerciasis immunology. (+info)
Migration patterns of children with cancer in Britain.
(22/4953)
OBJECTIVES: To investigate the early migration patterns of children who later developed cancer. To test a prior hypothesis that some cancers are initiated by early exposures to toxic atmospheric pollutants from point sources. DESIGN: Address changes in children dying from cancer are examined in relation to potentially hazardous sites of several different types. The relative proximities of birth addresses and death addresses to these sites, are compared. The approach is based upon the premise that a local exposure, effective only at an early age, must be preferentially linked with an early address. SETTING AND SUBJECTS: Records of 22,458 children dying from leukaemia or other cancer under the age of 16 years in Great Britain between 1953 and 1980: including 9224 who moved house between birth and death. The migration analysis was based upon birth and death addresses, converted first to postcodes and thence to map coordinates. The geographical locations of potentially toxic industrial sites were obtained through direct map searches and from commercial directories. RESULTS: Systematic asymmetries were found between measured distances from birth and death addresses to sources emitting volatile organic compounds, or using large scale combustion processes. The children had more often moved away from these hazards than towards them. Many of the sources had already been identified as hazardous using other methods. There was also a birth association with areas of dense habitation; possibly because of unidentified toxic sources contained within them. All forms of cancer were involved although some effluents were associated preferentially with specific types. CONCLUSIONS: The main findings of an earlier study, based upon a different and independent method, were confirmed. Proximities to several types of industrial source, around the time of birth, were followed by a raised risk of childhood cancer. Combustion products and volatile organic compounds were especially implicated. Within the 16 year limit of the study, the increased risk did not decay with advancing age. Low atmospheric concentrations of many carcinogenic substances suggest that the mother acts as a cumulative filter and passes them to the fetus across the placenta or in breast milk. (+info)
Who are "the homeless"? Reconsidering the stability and composition of the homeless population.
(23/4953)
OBJECTIVES: This study assessed the extent to which the use of point-prevalence samples biases conclusions drawn about homeless people. METHODS: Three data sets and published research were used to examine the degree to which conditions leading to point-prevalence bias (turnover in the homeless population, variability in the persistence of homelessness, and associations between personal characteristics and persistence) characterize the homeless population. Results were compared from point-prevalence studies concerning persistence of homelessness and characteristics of homeless people with those from a study of formerly homeless people. RESULTS: Conditions leading to point-prevalence bias strongly characterize the homeless population. Moreover, profiles of homeless people differed dramatically between point-prevalence studies and the study of formerly homeless people. In the former, average duration of homelessness was longer, and samples included higher proportions of men, minorities, non-high school graduates, and people with histories of psychiatric hospitalization, incarceration, and detoxification. CONCLUSIONS: Reliance on point-prevalence samples, when such samples are generalized beyond the currently homeless population, leads to overestimations of the persistence of homelessness, the demographic distinctiveness of the homeless population, and the prevalence of personal disabilities and deviant lifestyles among homeless people. (+info)
Venereal syphilis in tropical Africa.
(24/4953)
A steady decline in the incidence of positive results to the Kahn test is reported in Malawian patients during the period 1968-75. Other studies have shown that the incidence of early and late syphilis in sub-Saharan Africa has dropped considerably over the past few decades. The number of reported cases of early syphilis in certain urban areas, however, appears to be high. It is suggested that the downward trend in the incidence of syphilis in Africa is related to the increased and often indiscriminate use of penicillin. (+info)