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PubMed2004

Population structure of the Bacillus cereus group as determined by sequence analysis of six housekeeping genes and the plcR Gene.

The population structure of the Bacillus cereus group (52 strains of B. anthracis, B. cereus, and B. thuringiensis) was investigated by sequencing seven gene fragments (rpoB, gyrB, pycA, mdh, mbl, mutS, and plcR). Most of the strains were classifiable into two large subgroups in six housekeeping gene trees but not in the plcR tree. In addition, several consistent clusters were identified, which were unrelated to species distinction. Moreover, interrelationships among these clusters were incongruent in each gene tree. The incongruence length difference test and split decomposition analyses also showed incongruences between genes, suggesting horizontal gene transfer. The plcR gene was observed to have characteristics that differed from those of the other genes in terms of phylogenetic topology and pattern of sequence diversity. Thus, we suggest that the evolutionary history of the PlcR regulon differs from those of the other chromosomal genes and that recombination of the plcR gene may be frequent. The homogeneity of B. anthracis, which is depicted as an independent lineage in phylogenetic trees, is suggested to be of recent origin or to be due to the narrow taxonomic definition of species.

Animals↗
PubMed2006

Strain typing and determination of population structure of Candida krusei by multilocus sequence typing.

A multilocus sequence typing (MLST) scheme for Candida krusei was devised, based on sequencing of six gene fragments of the species. The existence of heterozygous results for each of the six fragments sequenced confirms that C. krusei is diploid for at least part of its genome. The C. krusei MLST scheme had a discriminatory index of 0.998, making this system ideal for strain typing of C. krusei clinical isolates. MLST data for 122 independent C. krusei isolates from a range of geographical sources were analyzed by eBURST, structure, and the unweighted-pair group method using average linkages to derive a population structure comprising four subtype strain clusters. There was no evidence of geographical associations with particular subtypes. Data for pairs of isolates from seven patients showed that each patient was colonized and/or infected with strain types that were indistinguishable by MLST. The C. krusei MLST database can be accessed online at http://pubmlst.org/ckrusei/.

Blood↗
PubMed1997

Current views on the population structure of plasmodium falciparum: Implications for control.

In recent years there has been a considerable debate on the population genetic structure of malaria parasites. Work on this subject has been revolutionized by the advent of the polymerase chain reaction (PCR) technique, which has made it feasible to study the genetic diversity of parasites in small samples of infected blood, allowing extensive surveys of natural parasite populations to be made. In addition, the technique can be applied to the mosquito stages of the malaria parasite, allowing direct assessments to be trade of the frequency of crossing between parasite clones in Nature. Studies on Plasmodium falcjparum in a wide range of malaria-endemic regions are now revealing the relationship between parasite population structure and malaria epidemiology. In this article, Hamza Babiker and David Walliker review recent work in this field, and discuss how such knowledge might be used to advise on the future deployment of control measures such as antimalarial drugs and possible malaria vaccines.

Journal Article↗
PubMed2005

Population structure in Ascaris suum (Nematoda) among domestic swine in Denmark as measured by whole genome DNA fingerprinting.

We here analyze the population structure in the pig roundworm, Ascaris suum, among domestic pigs in Denmark using a whole-genome DNA fingerprinting technique, "amplified fragment length polymorphism" (AFLP) analysis. With these data, we can extract absolute gene frequency variance components and G-statistics for 135 independent nucleotide polymorphisms. The average proportion of total variance partitioned between Jutland and Zealand is less than 3% of the total variance, implying no restriction in gene flow between worms from different regions in Denmark. The average gene frequency difference between two farms widely separated in Jutland represents 5% of the total genetic variance of these two farms combined. Conversely, worms from different hosts within these two farms are more subdivided, with an average of 12% of the total variance in gene frequencies within farms being distributed between hosts. This result implies substantial single generation inbreeding due to founder effects in the establishment of adult worms in single hosts. Absolute variance components extracted from the gene diversities also showed significant differences, with the among-host variance being greater that the between-farm and between-region values. This little geographical variation is discussed in relation to the hierarchic structure of the Danish swine production system. Comparison of our results with other studies on parasitic roundworms, suggests that patterns of host dispersal effectively control patterns of worm gene flow. Furthermore, the potential spread of anthelminth resistance among A. suum may thus be rapid, due to the flow of infected hosts within the domestic swine stocks in Denmark.

Animals↗
PubMed2004

Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene.

Phylogeographical studies are emerging as a powerful tool for understanding the population structure and evolution of wild relatives of crop species. Because of their value as genetic resources, there is great interest in exploring the distribution of variation in wild relatives of cultivated plants. In this study, we use sequence variation from the nuclear gene, fruit vacuolar invertase (Vac), to investigate the population history of Solanum pimpinellifolium. Solanum pimpinellifolium is a close relative of the cultivated tomato and has repeatedly served as a source of valuable traits for crop improvement. We sequenced the second intron of the Vac gene in 129 individuals, representing 16 populations from the northern half of Peru. Patterns of haplotype sharing among populations indicate that there is isolation by distance. However, there is no congruence between the geographical distribution of haplotypes and their genealogical relationships. Levels of outcrossing decrease towards the southernmost populations, as previously observed in an allozyme study. The geographical pattern of Vac variation supports a centre of origin in northern Peru for S. pimpinellifolium and a gradual colonization along the Pacific coast. This implies that inbreeding populations are derived from outcrossing ones and that variation present at the Vac locus predates the spread of S. pimpinellifolium. The expansion of cities and human agricultural activity in the habitat of S. pimpinellifolium currently pose a threat to the species.

Analysis of Variance↗
PubMed1999

Population structure of pathogens: the role of immune selection.

Sunetra Gupta and Roy Anderson discuss how the balance between host immune responses against conserved and variable antigens shapes the population structure of pathogens. At one extreme, immune selection against polymorphic determinants can cause pathogen populations to self-organize spontaneously into discrete antigenic types that may either be maintained over long periods or undergo cyclical or chaotic fluctuations. At the other extreme, diversity may be drastically reduced by competition induced by a strong immune response against a conserved determinant. Where does each pathogen lie along this continuum? How would this knowledge influence our attempts to control an infectious disease?

Alleles↗
PubMed2006

Global patterns reveal strong population structure in Haemonchus contortus, a nematode parasite of domesticated ruminants.

We have examined the global population genetic structure of Haemonchus contortus. The genetic variability was studied using both amplified fragment length polymorphism (AFLP) and nad4 sequences of the mitochondrial genome. To examine the performance and information content of the two different marker systems, comparative assessment of population genetic diversity was undertaken in 19 isolates of H. contortus, a parasitic nematode of small ruminants. A total of 150 individual adult worms representing 14 countries from all inhabited continents were analysed. Altogether 1,429 informative AFLP markers were generated using four different primer combinations. Also, the genetic variation was high, which agrees with results from previous AFLP studies of nematode parasites of livestock. The genetic structure was high, indicating limited gene flow between the different isolates and populations from each continent mostly formed monophyletic groups in the phylogenetic analysis. However, for isolates representing Australia, Greece and one laboratory strain that originated from South Africa (WRS), there was no clear genetic relationship between the isolates and the distance between their geographical origins. Basically the same pattern was observed for the mitochondrial marker, although the phylogenetic analysis was less resolved than for AFLP. In contrast with previous findings on the population genetic structure of H. contortus, the calculation of population structure gave high values (Nst=0.59). The strong structure was present also for the four Swedish isolates (Nst=0.16) representing a small geographical area.

Animals↗
PubMed2002

Population structure of a lodgepole pine (Pinus contorta) and jack pine (P. banksiana) complex as revealed by random amplified polymorphic DNA.

We studied the population structure of a lodgepole (Pinus contorta Dougl.) and jack pine (Pinus banksiana Lamb.) complex in west central Alberta and neighboring areas by assessing random amplified polymorphic DNA (RAPD) variability in 23 lodgepole pine, 9 jack pine, and 8 putative hybrid populations. Of 200 random primers screened, 10 that amplified 39 sharp and reproducible RAPDs were chosen for the study. None of the 39 RAPDs were unique to the parental species. RAPD diversity ranged from 0.085 to 0.190 among populations and averaged 0.143 for lodgepole pine, 0.156 for jack pine, 0.152 for hybrids, and 0.148 for all 40 populations. The estimated population differentiation based on G(ST) was 0.168 for hybrids, 0.162 for lodgepole pine, 0.155 for jack pine, and 0.247 across all 40 populations. Cluster analysis of genetic distances generally separated jack pine from lodgepole pine and hybrids, but no division could be identified that further separated lodgepole pine from hybrids. The observed weak to mild trend of "introgression by distance" in the complex and neighbouring areas was consistent with the view that introgressive hybridization between lodgepole and jack pines within and outside the hybrid zone may have been through secondary contact and primary intergradation, respectively.

Genetic Variation↗
PubMed2001

Differences in population structure of the anther smut fungus Microbotryum violaceum on two closely related host species, Silene latifolia and S. dioica.

We investigated the genetic population structure of the sexually transmitted plant pathogen, the fungus Microbotryum violaceum, on the two closely related host species Silene latifolia and S. dioica using microsatellite markers. We found strong deviations from Hardy-Weinberg expectations, with significant heterozygote deficiency in almost all populations. Fungal strains from the two host species were differentiated, and these host races differed in amount of variation within populations and differentiation among populations. Anther smut from S. latifolia harboured significantly less microsatellite diversity and were more genetically differentiated from each other than those from S. dioica. Small effective population sizes, rapid population turnover, and less gene flow among populations could lead to this higher population differentiation and lower within population genetic diversity for anther smut populations on S. latifolia than on S. dioica. These results are in concordance with host ecology because S. latifolia grows in more disturbed habitats than S. dioica and may provide a shorter-lived host environment.

Alleles↗
PubMed2001

Deconstructing maize population structure.

Association studies have rarely been used in plant genetics, in part because of the risk of false positives caused by population structure. A study of flowering time in maize makes the first use of recent 'structured association' methods-statistical approaches that use independent loci to control for the effects of structure and admixture.

Genes, Plant↗
PubMed2004

BAPS 2: enhanced possibilities for the analysis of genetic population structure.

UNLABELLED: Bayesian statistical methods based on simulation techniques have recently been shown to provide powerful tools for the analysis of genetic population structure. We have previously developed a Markov chain Monte Carlo (MCMC) algorithm for characterizing genetically divergent groups based on molecular markers and geographical sampling design of the dataset. However, for large-scale datasets such algorithms may get stuck to local maxima in the parameter space. Therefore, we have modified our earlier algorithm to support multiple parallel MCMC chains, with enhanced features that enable considerably faster and more reliable estimation compared to the earlier version of the algorithm. We consider also a hierarchical tree representation, from which a Bayesian model-averaged structure estimate can be extracted. The algorithm is implemented in a computer program that features a user-friendly interface and built-in graphics. The enhanced features are illustrated by analyses of simulated data and an extensive human molecular dataset. AVAILABILITY: Freely available at http://www.rni.helsinki.fi/~jic/bapspage.html.

Algorithms↗
PubMed2006

Stability analysis of age-structured population equations by pseudospectral differencing methods.

In this paper a numerical scheme to investigate the stability of linear models of age-structured population dynamics is studied. The method is based on the discretization of the infinitesimal generator associated to the semigroup of the solution operator by using pseudospectral differencing techniques, hence following the approach recently proposed in Breda et al. [SIAM J Sci Comput 27(2): 482-495, 2005] for delay differential equations. The method computes the rightmost characteristic roots and it is shown to converge with spectral accuracy behavior.

Age Factors↗
PubMed1989

Stability effects of a juvenile period in age-structured populations.

Prior theoretical studies have shown that the juvenile period's length is an important determinant of local stability in age-structured population dynamics. For example, both short and long periods produce stability, but intermediate lengths can cause instability. Short juvenile periods significantly increase stability (compared to no juvenile period) if fecundity is independent of adult age. Here I re-examine these and other patterns, using a model which includes a variable juvenile period, juvenile mortality, density-dependent fecundity and adult mortality, and age-dependence is adult fecundity. Among other things, the results confirm the stable-unstable-stable pattern with increasing juvenile period length, but show that the stabilizing effect of short periods disappears when fecundity varies with adult age. Broadly speaking, the results suggest that age-dependence in adult fecundity has important dynamical consequences, and that models assuming that fecundity is independent of adult age may be unreliable guides to the dynamics of populations for which this assumption is not reasonably accurate.

Animals↗
PubMed2006

Population structure of the malaria vector Anopheles funestus (Diptera: Culicidae) in Madagascar and Comoros.

Microsatellites were used as markers for a study of the population structure of Anopheles funestus on Madagascar and Comoros. Mosquitoes were collected in four different localities on Madagascar and one on Comoros. There was a significant genetic differentiation between all samples from Madagascar and that from Comoros (P<0.05). With respect to the Madagascar mosquito samples, it was found that there were no significant genetic differences between samples that were collected at the east coast, and in the highlands, respectively. By contrast, the west coast sample exhibited significant genetic differences (with regard to all Madagascar samples). The results are discussed with respect to population distribution and migration of A. funestus from mainland Africa and the islands east of the mainland.

Animals↗
PubMed1995

Flightless brown kiwis of New Zealand possess extremely subdivided population structure and cryptic species like small mammals.

Using allozymes and mtDNA sequences from the cytochrome b gene, we report that the brown kiwi has the highest levels of genetic structuring observed in birds. Moreover, the mtDNA sequences are, with two minor exceptions, diagnostic genetic markers for each population investigated, even though they are among the more slowly evolving coding regions in this genome. A major unexpected finding was the concordant split in molecular phylogenies between brown kiwis in the southern South Island and elsewhere in New Zealand. This basic phylogeographic boundary halfway down the South Island coincides with a fixed allele difference in the Hb nuclear locus and strongly suggests that two morphologically cryptic species are currently merged under one polytypic species. This is another striking example of how molecular genetic assays can detect phylogenetic discontinuities that are not reflected in traditional morphologically based taxonomies. However, reanalysis of the morphological characters by using phylogenetic methods revealed that the reason for this discordance is that most are primitive and thus are phylogenetically uninformative. Shared-derived morphological characters support the same relationships evident in the molecular phylogenies and, in concert with the molecular data, suggest that as brown kiwis colonized northward from the southern South Island, they retained many primitive characters that confounded earlier systematists. Strong subdivided population structure and cryptic species in brown kiwis seem to have evolved relatively recently as a consequence of Pleistocene range disjunctions, low dispersal power, and genetic drift in small populations.

Animals↗
PubMed2003

Molecular investigation on strain genetic relatedness and population structure of Beauveria bassiana.

Triplicate molecular methods, i.e. polymerase chain reaction-restriction fragment length polymorphism of the pr1 gene, microsatellite markers and 28S rDNA haplotyping by detecting the presence or absence of group I introns, were used for population study of the entomopathogenic fungus, Beauveria bassiana. The findings showed that the average genetic diversity index of geographical populations was significantly smaller than that of populations derived from insect host orders, indicating that the genetic relatedness of B. bassiana strains was highly associated with geographical locality rather than insect host species. The reproductive style of all the B. bassiana populations was found to be non-clonal. Population structure analysis revealed that the average divergent coefficient among populations of B. bassiana was far below 1 (0.1112), which indicated that there was no significant genetic differentiation between populations, and that the overall genetic diversity mainly resulted from the genetic variations within geographical populations. Statistically, genetic distances between populations were positively correlated with geographical distances, suggesting that geographical separation poses an obstacle to the possibility and frequency of genetic exchanges between populations. On the other hand, gene flow was indirectly established to occur between B. bassiana populations.

Animals↗
PubMed1974

A Markov process of gene frequency change in a geographically structured population.

A Markov process (chain) of gene frequency change is derived for a geographically-structured model of a population. The population consists of colonies which are connected by migration. Selection operates in each colony independently. It is shown that there exists a stochastic clock that transforms the originally complicated process of gene frequency change to a random walk which is independent of the geographical structure of the population. The time parameter is a local random time that is dependent on the sample path. In fact, if the alleles are selectively neutral, the time parameter is exactly equal to the sum of the average local genetic variation appearing in the population, and otherwise they are approximately equal. The Kolmogorov forward and backward equations of the process are obtained. As a limit of large population size, a diffusion process is derived. The transition probabilities of the Markov chain and of the diffusion process are obtained explicitly. Certain quantities of biological interest are shown to be independent of the population structure. The quantities are the fixation probability of a mutant, the sum of the average local genetic variation and the variation summed over the generations in which the gene frequency in the whole population assumes a specified value.

Alleles↗
PubMed2002

Population structure in the endangered Blanca Cacereña bovine breed demonstrated by RAPD analyses.

RAPD analyses have been used to determine the genetic diversity and the population structure of the endangered Blanca Cacereña bovine breed. Genetic variability was evaluated on the basis of 1048 loci produced by 71 primers. RAPD produced a number of polymorphic loci (30.44%), and it has been proved to be a useful method for evaluating polymorphisms in this breed. The dendrograms based on simililarity indexes and on Nei's genetic distances between 60 animals and the value of genetic differentiation among subpopulations (F(ST)) showed a clear population substructure defined by herds and a scarce genetic flow among herds. Analysis of molecular variance (AMOVA) showed that 32.4% of the total variance was due to differences among herds and confirmed the clustering found. The results of the present study allow us to plan more adequate mating in order to maintain the genetic diversity and to improve the efficiency of conservation for the Blanca Cacereña bovine breed.

Animals↗