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PubMed2001

Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila.

Selection acting on codon usage can cause patterns of synonymous evolution to deviate considerably from those expected under neutrality. To investigate the quantitative relationship between parameters of mutation, selection, and demography, and patterns of synonymous site divergence, we have developed a novel combination of population genetic models and likelihood methods of phylogenetic sequence analysis. Comparing 50 orthologous gene pairs from Drosophila melanogaster and D. virilis and 27 from D. melanogaster and D. simulans, we show considerable variation between amino acids and genes in the strength of selection acting on codon usage and find evidence for both long-term and short-term changes in the strength of selection between species. Remarkably, D. melanogaster shows no evidence of current selection on codon usage, while its sister species D. simulans experiences only half the selection pressure for codon usage of their common ancestor. We also find evidence for considerable base asymmetries in the rate of mutation, such that the average synonymous mutation rate is 20-30% higher than in noncoding regions. A Bayesian approach is adopted to investigate how accounting for selection on codon usage influences estimates of the parameters of mutation.

Animals↗
PubMed2002

Testing models of selection and demography in Drosophila simulans.

We analyze patterns of nucleotide variability at 15 X-linked loci and 14 autosomal loci from a North American population of Drosophila simulans. We show that there is significantly more linkage disequilibrium on the X chromosome than on chromosome arm 3R and much more linkage disequilibrium on both chromosomes than expected from estimates of recombination rates, mutation rates, and levels of diversity. To explore what types of evolutionary models might explain this observation, we examine a model of recurrent, nonoverlapping selective sweeps and a model of a recent drastic bottleneck (e.g., founder event) in the demographic history of North American populations of D. simulans. The simple sweep model is not consistent with the observed patterns of linkage disequilibrium nor with the observed frequencies of segregating mutations. Under a restricted range of parameter values, a simple bottleneck model is consistent with multiple facets of the data. While our results do not exclude some influence of selection on X vs. autosome variability levels, they suggest that demography alone may account for patterns of linkage disequilibrium and the frequency spectrum of segregating mutations in this population of D. simulans.

Animals↗
PubMed2003

Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach.

Demography and selection have been recognized for their important roles in shaping patterns of nucleotide variability. To investigate the relative effects of these forces in the genome of Drosophila melanogaster, we used a multi-locus scan (105 fragments) of X-linked DNA sequence variation in a putatively ancestral African and a derived European population. Surprisingly, we found evidence for a recent size expansion in the African population, i.e., a significant excess of singletons at a chromosome-wide level. In the European population, such an excess was not detected. In contrast to the African population, we found evidence for positive natural selection in the European sample: (i) a large number of loci with low levels of variation and (ii) a significant excess of derived variants at the low-variation loci that are fixed in the European sample but rare in the African population. These results are consistent with the hypothesis that the European population has experienced frequent selective sweeps in the recent past during its adaptation to new habitats. Our study shows the advantages of a genomic approach (over a locus-specific analysis) in disentangling demographic and selective forces.

Animals↗
PubMed1999

Genomic demography: a life-history analysis of transposable element evolution.

Retrotransposons are ubiquitous mobile genetic elements that have played a significant role in shaping eukaryotic genome evolution. The genome of the yeast Saccharomyces cerevisiae harbours five families of retrotransposons, Ty1-Ty5. With the publication of the S. cerevisiae genome sequence, for the first time a full genomic complement of retrotransposon sequences is available. Analysis of these sequences promises to yield insight into the nature of host--transposon coevolution. Evolutionary change in Ty elements depends on their replication and excision rates, which have been determined in the laboratory. Rates measured in the laboratory may differ from those that have operated over evolutionary time. Based on an analysis of sequence data for the Ty1, Ty2 and hybrid Ty1/2 families, we develop a novel 'genomic demography' model to estimate long-term transposition and excision rates and to estimate how long ago these elements entered the yeast genome. We find that rates of excision and transposition have averaged 7.2-8.7 x 10(-8) per generation over evolutionary time. Two separate models provide upper- and lower-bound estimates for the age of the system, suggesting that the first elements entered the genome between approximately 50 million and 250 million generations ago.

Evolution, Molecular↗
PubMed2002

The irreducible uncertainty of the demography-environment interaction in ecology.

The interpretation of ecological data has been greatly improved by bridging the gap between ecological and statistical models. The major challenge is to separate competing hypotheses concerning demography, or other ecological relationships, and environmental variability (noise). In this paper we demonstrate that this may be an arduous, if not impossible, task. It is the lack of adequate ecological theory, rather than statistical sophistication, which leads to this problem. A reconstruction of underlying ecological processes can only be done if we are certain of either the demographic or the noise model, which is something that can only be achieved by an improved theory of stochastic ecological processes. Ignoring the fact that this is a real problem may mislead ecologists and result in erroneous conclusions about the relative importance of endogenous and exogenous factors in natural ecosystems. The lack of correct model identification may also have far-reaching consequences for population management and conservation.

Animals↗
PubMed1997

The epidemiology of BSE in cattle herds in Great Britain. I. Epidemiological processes, demography of cattle and approaches to control by culling.

This paper explores the key epidemiological processes and demographic factors that determined the pattern of transmission of the aetiological agent of bovine spongiform encephalopathy (BSE) in cattle herds in Great Britain (GB). The analyses presented utilize data from published and unpublished experimental studies and from the GB central database of confirmed BSE cases. We review the experimental and epidemiological evidence that has both confirmed indirect horizontal transmission via the consumption of infectious material as the major transmission route and provided information on the duration and variability of the dose-dependent incubation period of BSE in cattle. The epidemiological and genetic data pertaining to the possible existence of maternal transmission and/or genetically variable susceptibility to infection is discussed. The demography of British cattle is characterized and the impacts of key demographic features on the observed epidemic profile are discussed. In the main BSE case database, analyses reveal that BSE cases cluster significantly at both the holding and county scale. Furthermore, analysis of longitudinal patterns reveal substantial temporal within-holding correlation. Such clustering of cases suggests a highly heterogeneous infection process. The paper ends with a discussion of how analyses of spatio-temporal clustering inform the design of targeted culling programmes aimed at reducing future disease incidence. We show how the retrospective implementation of culling policies on the BSE case database allows the qualitative evaluation of policy performance, but that model predictions of future trends in case incidence are required to estimate the precise impact of any current or future programme.

Age Factors↗
PubMed2005

Measuring marine fishes biodiversity: temporal changes in abundance, life history and demography.

Patterns in marine fishes biodiversity can be assessed by quantifying temporal variation in rate of population change, abundance, life history and demography concomitant with long-term reductions in abundance. Based on data for 178 populations (62 species) from four north-temperate oceanic regions (Northeast Atlantic and Pacific, Northwest Atlantic, North mid-Atlantic), 81% of the populations in decline prior to 1992 experienced reductions in their rate of loss thereafter; species whose rate of population decline accelerated after 1992 were predominantly top predators such as Atlantic cod (Gadus morhua), sole (Solea solea) and pelagic sharks. Combining population data across regions and species, marine fishes have declined 35% since 1978 and are currently less than 70% of recorded maxima; demersal species are generally at historic lows, pelagic species are generally stable or increasing in abundance. Declines by demersal species have been associated with substantive increases in pelagic species, a pattern consistent with the hypothesis that increases in the latter may be largely attributable to reduced predation mortality. There is a need to determine the consequences to population growth effected by the reductions in age and size at maturity, and in mean age and size of spawners, concomitant with population decline. We conclude that reductions in the rate of population decline, in the absence of targets for population increase, will be insufficient to effect a recovery of marine fishes biodiversity, and that great care must be exercised when interpreting multi-species patterns in abundance. Of fundamental importance is the need to explain the geographical, species-specific and habitat biases that pervade patterns of marine fishes recovery and biodiversity.

Age Factors↗
PubMed1997

Demography of assault in a provincial Victorian population.

The study examined the frequency and patterns of assault within a large regional population of Victoria. The records of 860 victims of physical assault who presented to the Geelong Hospital emergency department during 1993 and 1994 were analysed retrospectively. The policy data on 1427 reported cases of physical assault, from the same catchment area and over a similar period of time, were also examined. The hospital data revealed that 65 per cent of assault victims were males aged from 15 to 34 years, that 58 per cent of presentations were within four hours of midnight, and 68 per cent were on Friday, Saturday or Sunday. Most assaults occurred on the streets, on footpaths, in open spaces or within dwellings, and the highest incidence was during the summer months. The police data showed similar patterns but from a different population of victims. It also showed an upward trend in the rates of assault in Victorian regional areas. The award-winning Geelong 'Local Industry Accord', a police and community intervention program, may have contributed to the decline in violence, particularly within the Geelong city centre, and has been suggested as a model for other community-based intervention programs. For intervention programs to be successful, the demography of assault within communities must be established and target groups identified. Hospital, police and victim surveys data do not identify accurately the population of assault victims. Improved methods of data collection and compatibility between databases already in existence may provide more accurate statistics upon which intervention programs may be based and their success evaluated.

Adolescent↗
PubMed2006

Habitat change and demography of Primula veris: identification of management targets.

Although the effects of deterministic factors on population viability often are more important than stochasticity, few researchers have dealt with the effect of deterministic habitat changes on plant population demography. We assessed population viability for the perennial herb Primula veris L. and identified targets for management based on demographic data from five different habitat types representing different degrees of canopy closure. We conducted replicate studies at the border of the distribution area and in more central parts. Demographic patterns were similar between the two regions. Most study populations had a positive population growth, and only populations in late phases of forest succession showed consistently negative trends. The populations of open habitats had high seedling recruitment, and the populations of early and middle forest succession had high seed production. The importance of survival for population growth rate increased with increasing habitat closure, whereas the importance of growth and reproduction decreased. Results of the elasticity analysis suggested that the best method to manage decreasing late-successional populations is to increase survival of the largest individuals. The life-table response experiment (LTRE) analysis, however showed that survival of the largest individuals contributed little to differences in population growth rates of different habitats, whereas seed production and growth of small individuals were more important. Moreover direct perturbation of the performance of the largest stages showed that late-successional populations would not attain positive population growth even if the largest stages had no mortality at all. We conclude that restoration of recruitment is the only possibility for positive population growth in late-successional populations of P. veris, although the elasticities of recruitment transitions are low. Our results also suggest that retrospective demographic methods such as LTRE constitute an important and necessary complement to prospective methods such as elasticities in identifying management targets.

Conservation of Energy Resources↗
PubMed2006

Demography, hunting ecology, and pathogen exposure of domestic dogs in the Isoso of Bolivia.

Disease is increasingly recognized as a threat to the conservation of wildlife, and in many cases the source of disease outbreaks in wild carnivores is the domestic dog. For disease to spill over from a domestic to a wild population, three conditions must be satisfied: susceptibility of the wild species, presence of the disease agent in the domestic population, and contact between the two populations of interest. We investigated the potential for disease spillover from the domestic dog population to the wild carnivore population in the Isoso of Bolivia, an area of tropical dry forest contiguous with a national park. Using questionnaires and discussions with residents, we gathered data on the demography of dogs in the Isoso, including adult and neonatal mortality, litter size, and hunting frequency. We analyzed a large data set containing self-recorded information on hunting in various communities of the Isoso to determine the extent of dog participation in hunting and the duration of hunting trips. Finally, we took blood samples from dogs in the Isoso for a serosurvey of common canine pathogens. More than 95% of dogs had positive titers to canine distemper virus and canine parvovirus. There was also a high seroprevalence in dogs for other pathogens, a high population turnover of dogs (which may allow diseases to be maintained endemically), and frequent opportunities for contact between domestic and wild carnivores. Based on our results and the susceptibility of wild species previously reported in the literature, domestic dogs represent a disease risk for wildlife in the Bolivian Isoso.

Animals↗
PubMed1986

Symptomatic depression in elderly medical outpatients. I. Prevalence, demography, and health service utilization.

The authors assessed the prevalence and demography of depressive symptoms, their association with specific chronic diseases, and their influence on health service use in a large sample of elderly men seen in a primary care setting. Twenty-four percent of respondents reported clinically significant depressive symptoms; the prevalence of major depressive disorders was estimated at 10%, but only 1% reported receiving mental health treatment by a specialist. Self-reported marital separation or divorce and physical disability affecting employment were strongly associated with high depression scores, whereas the normative stresses of aging (widowhood, retirement, social isolation) were not. Only chronic lung disease was differentially associated with high depression scores, and this effect was weak. The authors discuss the implications of these findings for the design of comprehensive health services for the elderly with chronic disease.

Aged↗
PubMed1993

Demography, auxology and response to recombinant human growth hormone treatment in girls with Turner's syndrome in the Kabi Pharmacia International Growth Study. International Board of the Kabi Pharmacia International Growth Study.

Demographic and auxological data were analysed from 818 girls with Turner's syndrome treated with recombinant human growth hormone (GH) and entered into the Kabi Pharmacia International Growth Study. Size at birth was low and correlated with the heights of both parents. The median age at start of GH treatment was 11.4 years and the parents had a median height SDS of -2.9. Height SDS at the start of treatment correlated with parental heights. Height velocities conformed to Turner-specific standards. The weight-for-height index increased sharply above 9 years of age. The frequency of spontaneous appearance of Tanner breast stage 2 was high (34.1% of girls > 10 years of age). Bone age (Greulich and Pyle) data were described by the equation: bone age = 1.61(chronological age) - 0.04(chronological age)2 - 3.61. This equation was used to correct adult height predictions. The median initial dose of GH was 0.8 IU/kg/week and was maintained during the first 3 years of treatment. The median frequency of injections was six/week. Height velocity increased from 4.1 to 6.8 cm/year in the first year, and height velocity SDS for chronological age remained positive for 4 years. The height prediction corrected for bone age increased over the first 2 years only. Differences in demography and auxology were described according to karyotype and country of origin. A greater height velocity SDS was observed at higher GH doses and when oxandrolone was used concomitantly.

Age Determination by Skeleton↗
PubMed1993

Demography and dental needs, an international perspective.

The population of the world is changing and the science dealing with the study of these changes in human populations, in terms of disease, health and mortality has been called demography. It can be understood to include the evaluation of the size, density, and distribution of populations including the influence of a variety of factors such as age and economics. This paper will review the distribution of the world's population with regard to age and utilization of dental care with particular emphasis on the older cohorts.

Adolescent↗
PubMed1988

Genetics and demography in biological conservation.

Predicting the extinction of single populations or species requires ecological and evolutionary information. Primary demographic factors affecting population dynamics include social structure, life history variation caused by environmental fluctuation, dispersal in spatially heterogeneous environments, and local extinction and colonization. In small populations, inbreeding can greatly reduce the average individual fitness, and loss of genetic variability from random genetic drift can diminish future adaptability to a changing environment. Theory and empirical examples suggest that demography is usually of more immediate importance than population genetics in determining the minimum viable sizes of wild populations. The practical need in biological conservation for understanding the interaction of demographic and genetic factors in extinction may provide a focus for fundamental advances at the interface of ecology and evolution.

Animals↗
PubMed1992

The Scottish Motor Neuron Disease Register: a prospective study of adult onset motor neuron disease in Scotland. Methodology, demography and clinical features of incident cases in 1989.

The Scottish Motor Neuron Disease Register (SMNDR) is a prospective, collaborative, population based study of motor neuron disease (MND) in Scotland. The register started in January 1989 with the aim of studying the clinical and epidemiological features of MND by prospectively identifying incident patients. It is based on a system of registration by recruitment from multiple sources, followed by the collection of complete clinical data and follow up, mainly through general practitioners. In this report the register's methodology and the demography and incidence data for the first year of study are presented. One hundred and fourteen newly diagnosed patients were identified in 1989 giving a crude incidence for Scotland of 2.24/100,000/year. Standardised incidence ratios showed a non-significant trend towards lower rates in north eastern regions and island areas.

Adult↗
PubMed1998

Demography of family households.

A profile of the demography of individuals with mental retardation and related developmental disabilities (MR/DD) was developed from the Survey of Income and Program Participation, a national household survey. We estimated a total 1991 population of 2.97 million Americans with MR/DD, with 2.63 million living outside the formal long-term care system. Observations suggest that (a) families are the dominant form of support and, thus, a key constituency in disability policy; (b) a large cohort currently live in households headed by aging family members; and (c) there are significant economic disparities between subgroups of families, defined primarily along gender and racial lines.

Adult↗
PubMed2006

Intracellular demography and the dynamics of Salmonella enterica infections.

An understanding of within-host dynamics of pathogen interactions with eukaryotic cells can shape the development of effective preventive measures and drug regimes. Such investigations have been hampered by the difficulty of identifying and observing directly, within live tissues, the multiple key variables that underlay infection processes. Fluorescence microscopy data on intracellular distributions of Salmonella enterica serovar Typhimurium (S. Typhimurium) show that, while the number of infected cells increases with time, the distribution of bacteria between cells is stationary (though highly skewed). Here, we report a simple model framework for the intensity of intracellular infection that links the quasi-stationary distribution of bacteria to bacterial and cellular demography. This enables us to reject the hypothesis that the skewed distribution is generated by intrinsic cellular heterogeneities, and to derive specific predictions on the within-cell dynamics of Salmonella division and host-cell lysis. For within-cell pathogens in general, we show that within-cell dynamics have implications across pathogen dynamics, evolution, and control, and we develop novel generic guidelines for the design of antibacterial combination therapies and the management of antibiotic resistance.

Animals↗
PubMed2006

Male demography in East Asia: a north-south contrast in human population expansion times.

The human population has increased greatly in size in the last 100,000 years, but the initial stimuli to growth, the times when expansion started, and their variation between different parts of the world are poorly understood. We have investigated male demography in East Asia, applying a Bayesian full-likelihood analysis to data from 988 men representing 27 populations from China, Mongolia, Korea, and Japan typed with 45 binary and 16 STR markers from the Y chromosome. According to our analysis, the northern populations examined all started to expand in number between 34 (18-68) and 22 (12-39) thousand years ago (KYA), before the last glacial maximum at 21-18 KYA, while the southern populations all started to expand between 18 (6-47) and 12 (1-45) KYA, but then grew faster. We suggest that the northern populations expanded earlier because they could exploit the abundant megafauna of the "Mammoth Steppe," while the southern populations could increase in number only when a warmer and more stable climate led to more plentiful plant resources such as tubers.

Asian People↗