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PubMed2004

Genetic diversity and population structure of Mycobacterium tuberculosis in Casablanca, a Moroccan city with high incidence of tuberculosis.

Although lower-resource countries have by far the highest burden of tuberculosis, knowledge of Mycobacterium tuberculosis population structure and genetic diversity in these regions remains almost nonexistent. In this paper, 150 Moroccan M. tuberculosis isolates circulating in Casablanca were genotyped by random amplified polymorphic DNA analysis using 10 different primers and by mycobacterial interspersed repetitive units-variable number of tandem repeats typing at 12 loci. The population genetic tests revealed a basically clonal structure for this population, without excluding rare genetic exchanges. Genetic analysis also showed a notable genetic polymorphism for the species M. tuberculosis, a weak cluster individualization, and an unexpected genetic diversity for a population in such a high-incidence community. Phylogenetic analyses of this Moroccan sample also supported that these isolates are genetically heterogeneous.

Genetic Variation↗
PubMed2003

Population structure analysis of Burkholderia cepacia genomovar III: varying degrees of genetic recombination characterize major clonal complexes.

Infection with bacterial species belonging to the Burkholderia cepacia complex contribute significantly to morbidity and mortality in persons with cystic fibrosis (CF). The majority of isolates recovered from CF patients belong to B. cepacia genomovar III and several distinct 'epidemic' strains have been described. This study examined the population structure of B. cepacia genomovar III by using multilocus restriction typing, indexing allelic variation at five chromosomal genes by restriction analysis of PCR-amplified genes. A collection of 375 isolates, recovered from CF and non-CF patients and natural environments in North America, Europe and Australia, was examined. Among these isolates 144 different restriction types were found. Overall, the population is at linkage disequilibrium, indicating that it has a clonal structure. The majority (86.7 %) of restriction types grouped into three major clonal complexes, comprising the epidemic ET12, PHDC and Midwest clonal lineages. The analysis indicates that these complexes are geographically widespread and demonstrate varying degrees of genetic recombination. These differences in population structure among major clonal complexes within the same species are likely related to differences in evolutionary history and ecology. The observation that genetic recombination is frequent within some B. cepacia genomovar III populations has important implications for the biotechnological use of B. cepacia complex species.

Alleles↗
PubMed1978

[Population structure and consaguinity in Dota, Costa Rica, 1888-1962].

A study of consanguinity and population structure was carried out in a sample of 498 consanguineous (MC) and 570 non-consanguineous matings (MNC) in the Parrish of Dota, Costa Rica, during a period of 75 years. The inbreeding coefficient (F) shows fluctuations in time (476 to 194 x 10(-5) with an increase from 1888 to 1917, followed by a decrease in the last years but remains high in nonmigrant marriages. There is a high frequency of unions among second cousins. The endogamy percentage is high, greater in MC (80%) than in MNC (61%). Exogamy tends to diminish with time among both types of union. Effects of age distributions in the groups was not found. Marital and migrational distances are short and tend to become shorter in the final periods. There is a positive correlation (r = 0.71; p less than 0.05) between these distances in MC but not in MNC; distances are shorter in MC. Immigration is minimal and reduced to short distances. Post-marital movement is intense (37%) and involves greater distances. Emigratory behavior is identical in MC and MNC.

Consanguinity↗
PubMed2006

Endemic threshold results in an age-duration-structured population model for HIV infection.

In this paper we consider an age-duration-structured population model for HIV infection in a homosexual community. First we investigate the invasion problem to establish the basic reproduction ratio R(0) for the HIV/AIDS epidemic by which we can state the threshold criteria: The disease can invade into the completely susceptible population if R(0)>1, whereas it cannot if R(0)<1. Subsequently, we examine existence and uniqueness of endemic steady states. We will show sufficient conditions for a backward or a forward bifurcation to occur when the basic reproduction ratio crosses unity. That is, in contrast with classical epidemic models, for our HIV model there could exist multiple endemic steady states even if R(0) is less than one. Finally, we show sufficient conditions for the local stability of the endemic steady states.

Age Factors↗
PubMed1992

Phenotypic evolution under gene-culture transmission in structured populations.

I consider a simple model for the evolution of a quantitative character is structured populations when an offspring's phenotype is determined partly by his or her genetic constitution and partly by cultural transmission of the parental phenotype. Analysis of the model indicates that when individual and group selection are in the same direction, phenotypic evolution always proceeds faster under gene-culture vs. purely genetic transmission. When individual and group selection are countervailing, altruistic characters evolve faster under gene-culture transmission when individual selection is weak and migration among groups is limited, with increased individual selection and migration tending to decrease the advantage of gene-culture transmission over purely genetic transmission. Given the prevalence of cultural transmission in higher species, these results suggest that contrary to what is often assumed, group selection may indeed by a potent evolutionary force in the evolution of altruistic characters.

Altruism↗
PubMed1989

Time delays in age-structured populations.

A combination of analytical and computational techniques is employed to investigate age-structured populations in which the life cycle consists of two sequential demographic phases. Individuals within each phase have identical demographic rates that are functions of population size, but these rates may differ between phases. A model consisting of a system of delay ordinary differential equations is derived, and existence and stability of equilibria are discussed. Analysis reveals how equilibrium abundances depend on all demographic variables and, in particular, on the lengths of the demographic phases.

Aging↗
PubMed2003

Phylogeography and population structure of the Japanese wild boar Sus scrofa leucomystax: mitochondrial DNA variation.

Phylogeographic characteristics and population structure of Japanese wild boar (Sus scrofa leucomystax) were investigated using mitochondrial DNA (mtDNA) sequence data. Sixteen Japanese wild boar haplotypes detected from partial sequences of the mtDNA control region (574-bp) from 180 Japanese wild boar specimens from 10 local populations on Honshu, Shikoku, and Kyushu islands and 41 haplotypes from other S. scrofa were analyzed using the neighbor-joining method. The Japanese wild boars were more closely related to Northeast Asian wild boars from Mongolia than to the other Asian continental S. scrofa. The Japanese and Northeast Asian wild boars were not significantly distinguished by corrected average pairwise difference analysis. The ancestors of Japanese wild boars are suggested to have been part of the continental S. scrofa population that spread from Southeast to Northeast Asia during the Middle to Late Pleistocene. The Japanese wild boar mtDNA haplotype cladogram shows 95% parsimoniously plausible branch connections supporting three sympatric clades. Nested clade analysis indicates that these three clades are the result of distinct historical events or gene flow. The present population of Japanese wild boars may have been formed by a few independent migrations of distinct clades from the continent with subsequent mixing on the Japanese Islands.

Analysis of Variance↗
PubMed1996

Individual Energetics and the Equilibrium Demography of Structured Populations

This paper considers the relationship between the demographic mechanisms of population control and the energetics of the individuals who comprise the population. We examine the equilibrium properties of a class of structured population models in which individuals compete for some environmental resource (such as food) and demonstrate that population demography is independent of the nature of the feedback loop which establishes the equilibrium state. We thus derive general insights into the influence exerted by individual energetic and allocation strategies on population average demographic characteristics. We show that models of individual energetics which produce apparently very similar predictions at the individual level can result in very different behaviour at the population level. In addition, we observe that different models of individual mortality can imply marked differences in population demography and that the common assumption of constant mortality can be responsible for potentially unrealistic model behaviour. Our results emphasise the substantial data requirements for parameterising and testing individual-based models.

Journal Article↗
PubMed2006

A simple persistence condition for structured populations.

The fundamental question in both basic and applied population biology of whether a species will increase in numbers is often investigated by finding the population growth rate as the largest eigenvalue of a deterministic matrix model. For a population classified only by age, and not stage or size, a simpler biologically interpretable condition can be used, namely whether R0, the mean number of offspring per newborn, is greater than one. However, for the many populations not easily described using only age classes, stage-structured models must be used for which there is currently no quantity like R0. We determine analogous quantities that must be greater than one for persistence of a general structured population model that have a similar useful biological interpretation. Our approach can be used immediately to determine the magnitude of changes and interactions that would either allow population persistence or would ensure control of an undesirable species.

Animals↗
PubMed1997

Evolutionary constraints on population structure: the parasites of Fundulus zebrinus (Pisces:Cyprinodontidae) in the South Platte River of Nebraska.

Population and community descriptor values (parasites per host, prevalence per parasite species, variance/mean ratios, species density, and diversity indices) for the 7-species parasite community of 61 relatively homogeneous samples of Fundulus zebrinus (Pisces: Cyprinodontidae) in the South Platte River of Nebraska, U.S.A., taken over a 14-yr period, are reported. South Platte River streamflow fluctuates over 2 orders of magnitude on several time scales-monthly, annually, and over multiple year wet-dry cycles. Relatively homogeneous sampling of a single host species with several parasite species provided a system that allowed assessment of the contribution of evolved parasite life cycles to population structure in an everchanging environment. No significant negative species-to-species associations were observed. Species abundance, order of abundance, and diversity were affected most strongly by streamflow, with high water reducing prevalence and abundance of larval trematode parasites. Each parasite species had its characteristic long- and short-term patterns of variation in population descriptor values, with mostly long-term stability superimposed on sometimes extreme short-term fluctuations of descriptor values. The differences in these characteristic patterns were considered products primarily of the evolved life cycle traits and transmission mechanisms operating in the common fluctuating environment. The parasite community as a whole showed resilience, returning to preperturbation diversity following extended periods of high water.

Animals↗
PubMed1998

Population structure of nuclear and mitochondrial DNA variation among humpback whales in the North Pacific.

The population structure of variation in a nuclear actin intron and the control region of mitochondrial DNA is described for humpback whales from eight regions in the North Pacific Ocean: central California, Baja Peninsula, nearshore Mexico (Bahia Banderas), offshore Mexico (Socorro Island), southeastern Alaska, central Alaska (Prince Williams Sound), Hawaii and Japan (Ogasawara Islands). Primary mtDNA haplotypes and intron alleles were identified using selected restriction fragment length polymorphisms of target sequences amplified by the polymerase chain reaction (PCR-RFLP). There was little evidence of heterogeneity in the frequencies of mtDNA haplotypes or actin intron alleles due to the year or sex composition of the sample. However, frequencies of four mtDNA haplotypes showed marked regional differences in their distributions (phi ST = 0.277; P < 0.001; n = 205 individuals) while the two alleles showed significant, but less marked, regional differences (phi ST = 0.033; P < 0.013; n = 400 chromosomes). An hierarchical analysis of variance in frequencies of haplotypes and alleles supported the grouping of six regions into a central and eastern stock with further partitioning of variance among regions within stocks for haplotypes but not for alleles. Based on available genetic and demographic evidence, the southeastern Alaska and central California feeding grounds were selected for additional analyses of nuclear differentiation using allelic variation at four microsatellite loci. All four loci showed significant differences in allele frequencies (overall FST = 0.043; P < 0.001; average n = 139 chromosomes per locus), indicating at least partial reproductive isolation between the two regions as well as the segregation of mtDNA lineages. Although the two feeding grounds were not panmictic for nuclear or mitochondrial loci, estimates of long-term migration rates suggested that male-mediated gene flow was several-fold greater than female gene flow. These results include and extend the range and sample size of previously published work, providing additional evidence for the significance of genetic management units within oceanic populations of humpback whales.

Alleles↗
PubMed2005

Population structure of Anopheles arabiensis on La Réunion island, Indian Ocean.

Anopheles arabiensis, together with Anopheles gambiae sensu stricto, are the most important vectors of human malaria in sub-Saharan Africa. The malaria situation keeps worsening, with 1 to 3 million deaths a year, and alternative strategies are needed to decrease malaria transmission intensity. In this paper, we studied the population structure of An. arabiensis from three sample sites on the remote Indian Ocean island of La Réunion. Our results showed strong genetic structuring between An. arabiensis populations on La Réunion, indicating the presence of barriers to gene flow. Reasons for such a high genetic differentiation are discussed, including the role of intensive control measures that have maintained reduced effective population size as well as a putative genetic adaptation to the environment. This strong structuring situation on the island represents an ideal framework for the prospect of genetic-based control trials.

Animals↗
PubMed1999

The population structure of Trypanosoma cruzi: expanded analysis of 54 strains using eight polymorphic CA-repeat microsatellites.

Recently we cloned and sequenced the first eight Trypanosoma cruzi polymorphic microsatellite loci and studied 31 clones and strains to obtain valuable information about the population structure of the parasite. We have now studied 23 further strains, increasing from 11 to 31 the number of strains obtained from patients with chronic Chagas disease. This expanded set of 54 strains and clones analyzed with the eight microsatellites markers confirmed the previously observed diploidy, clonal population organization and very high polymorphism of T. cruzi. Moreover, this new study disclosed two new features of the population genetic structure of T. cruzi. The first was the discovery that, similarly to what we had previously shown for strains isolated from insect vectors, mammals and humans with acute disease, isolates from patients in the chronic phase of Chagas disease could also be multiclonal, albeit at a reduced proportion. Second, when we used parsimony to display the genetic relationship among the clonal lineages in an unrooted Wagner network we observed, like before, a good correlation of the tree topography with the classification in three clusters on the basis of single locus analysis of the ribosomal RNA genes. However, a significant new finding was that now the strains belonging to cluster 2 split in two distant sub-clusters. This observation suggests that the evolutionary history of T. cruzi may be more complex than we previously thought.

Animals↗
PubMed1994

Threshold conditions for the spread of the HIV infection in age-structured populations of homosexual men.

The age-structure of a population, and the distribution of sexual behavior according to age, are significant factors determining the spread of the AIDS epidemic. The threshold conditions for age-structured models account for life-history information, and thus differ significantly from their age-independent counterparts. We examine the threshold conditions for four general age-structured models of the spread of HIV in a homosexual population: three with random partner selection and one with biased partner selection. We consider both discrete and continuous risk groups, and the duration of infection. Susceptibility and infectiousness are treated separately, and the infectivity varies with duration of infection. Through specific examples, we examine the sensitivity of the threshold conditions to the population age-structure and the shape of the infectivity profile. The effects of each are of the same order of magnitude.

Adult↗
PubMed2003

Population structure and recruitment of the ectoparasite Argulus coregoni Thorell (Crustacea: Branchiura) on a fish farm.

The population structure and recruitment of Argulus coregoni was monitored at a Finnish fish farm during the open water periods of 1999 and 2001 by weekly sampling of attached argulids. In 2001 the numbers of rainbow trout examined increased in the autumn when the A. coregoni population was declining. When the water temperature exceeded 10 degrees C, at the end of May, A. coregoni egg hatching commenced. A mean number of 98 (S.D. +/- 5.4) juvenile A. coregoni was recorded on each fish, before the start of female egg laying in July 1999. The abundance of lice was lower in 2001. The main recruitment of A. coregoni juveniles occurred in early summer, but the hatching of eggs continued until September. However, no pulses of hatching were recorded later in the summer and the numbers of lice on fish substantially decreased after mid-July in both years. On average, only 0.6 (S.D. +/- 0.72) parasites/fish were found between August and late October 2001 and none in November. We suggest that there is 1 main A. coregoni generation annually in Central Finland. Environmental conditions, especially temperature, affects the population cycle of A. coregoni: we found a more synchronous and intense population cycle during the summer 1999, when the early summer was warmer than in 2001. The overall sex ratio (female:male) of A. coregoni was nearly 1:1 in June 1999, but was male biased (1:1.4) in June 2001. It was also shown that from July onwards, many females detached from the fish host in order to lay their eggs on the bottom of the pond. Large males were often bigger than the largest females between mid-July and early September 2001, when as many as 3.7 (s.r. +/- 1.48) times more males than females were present in the lice samples.

Animals↗
PubMed2005

Unfolding of population structure in Baltic sheep breeds using microsatellite analysis.

Studies of domestic animals are performed on breeds, but a breed does not necessarily equate to a genetically defined population. The division of sheep from three native and four modern Baltic sheep breeds was studied using 21 microsatellite loci and applying a Bayesian clustering method. A traditional breed-wise approach was compared to that relying on the pattern of molecular diversity. In this study, a breed was found to be inconsistent with a distinct genetic population for three reasons: (i) a lack of differentiation between modern Baltic breeds, since the majority of the studied sheep formed a single population; (ii) the presence of individuals of foreign ancestry within the breed; and (iii) an undefined local Saaremaa sheep was referred to as a breed, but was shown to consist of separate populations. In the breed-wise approach, only the clearly distinct Ruhnu sheep demonstrated low within-breed variation, although the newly identified Saaremaa populations also have low variability. Providing adequate management recommendations for the Saaremaa sheep is not possible without further studies, but the potential harmful effects of inbreeding in the Ruhnu sheep could be reduced through the use of two genetically related Saaremaa populations. In other breeds, excessive crossing appears to be a larger concern than inbreeding. Assigning individuals into populations based on the pattern of genetic diversity offers potentially unbiased means of elucidating the genetic population structure of species. Combining these genetic populations with phenotypic and aetiological data will enable formulation of the most informed recommendations for gene resource management.

Animals↗
PubMed2002

Population structure of Candida albicans, a member of the human flora, as determined by microsatellite loci.

This study examines the macrogeographic population structure of Candida albicans, a yeast commensal of humans, through a population genetic analysis of 5 microsatellite loci in 13 cities. The populations were predominantly clonal with some recombination. About 5% of the genetic variation is between populations and the overall pattern is one of intermediate differentiation. We did not find a single widespread genotype but instead found high, macrogeographic gene flow in these clinical populations; the most common genotype was limited to Atlanta and San Francisco. Homogeneity is evident within large geographic regions, such as Europe, Asia, and the USA, and isolation by distance accounted for 39% of the variation observed. Overall gene flow for a member of the human flora is variable but can be extensive, with an average of 4.5 migrants per generation (N(m)). Eastern hemisphere populations were less divergent than those of the Americas and Caribbean, consistent with the expansion of humans out of the eastern hemisphere.

Alleles↗
PubMedDate not supplied

[Seasonal dynamics of the population structure of Sphaerostomum globiporum (Trematoda: Opecoelidae) maritae in Ladoga Lake].

Data on the seasonal dynamics of population structure is obtained for the first time for the Trematode species Sphaerostomum globiporum from roach Rutilus rutilus (L) in Ladoga Lake, which situates in the northern limit of the distribution range of this species. The parasites infest the host in October and leave it from the end of July to the beginning of August. The maximum of the magnitude of the Trematode population falls on spring, and the minimum is observed in summer. In August and September roach is free of the parasites. It is established that the period of maturing occupies 10 months for S. globiporum from roach in Ladoga Lake. The prereproductive period takes 5 months and comes to the end in February. The reproductive period occupies 5 months too. Although these two periods of the parasite's life cycle do not separated from each other clearly, an overlapping of two generations was not observed, unlike the case of more southern water bodies.

Animals↗