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PubMed2006

Population structure of the boll weevil in cotton fields and subtropical forests of South America: a bayesian approach.

The main goal of this contribution is to investigate the genetic structure of boll weevil populations from South America (Argentina and Brazil) and to make further comparisons with a putative source population from USA. Samples were collected in a Paranaense forest under reserve protection, cotton fields and non-cultivated areas. Data from anonymous molecular markers were analysed using both traditional methods of population genetics and Bayesian approaches. Results help to support a previous hypothesis on the presence of two lineages of boll weevil populations in South America: one with characteristics of recent invaders and the other with characteristics of ancient populations. The sample from Urugua-í Provincial Park (Misiones, Argentina) shows the highest percentage of polymorphic loci, the highest values of mean heterozigosity, and the largest number of population-specific alleles, all being typical features of ancient populations. Furthermore, the Urugua-í sample shows two gene pools occurring in sympatry, probably as a consequence of a secondary contact. The remaining samples reveal not only lower percentages of polymorphic loci and heterozygosity values, but also an almost negligible presence of specific alleles. Bayesian methods also suggest the occasional migration of some individuals of ancient lineages from their natural habitats in fragments of the Paranaense forest into cotton fields, and vice versa.

Animals↗
PubMed1994

Population structure of a predatory beetle: the importance of gene flow for intertrophic level interactions.

Migration and gene flow of natural enemies play an important role in the stability of predator-prey interactions and community organization in both natural and managed systems. Yet, relative to that of their herbivorous insect prey, the genetic structure of natural enemy populations has been little studied. We present evidence that populations of the predatory coccinellid beetle Coleomegilla maculata (Coleoptera: Coccinellidae), are not genetically subdivided and that levels of gene flow among these populations are extremely high. Furthermore, in the same geographical area, gene flow of C. maculata was significantly (one order of magnitude) greater than that of an abundant prey species, the Colorado potato beetle Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). The high mobility of this natural enemy relative to the insect herbivores on which it feeds may contribute to its effectiveness as a biological control agent in agricultural systems.

Alleles↗
PubMed2003

Fine-scaled geographical population structuring in a highly mobile marine species: the Atlantic cod.

Compared with many terrestrial and freshwater environments, dispersal and interbreeding is generally much less restricted in the marine environment. We studied the tendency for a marine species, the Atlantic cod, to be sub-structured into genetically differentiated populations on a fine geographical scale. We selected a coastal area free of any obvious physical barriers and restricted sampling to a 300-km region, well within the dispersal ability of this species. Screening 10 polymorphic microsatellite loci in 6 samples we detected a weak, but consistent, differentiation at all 10 loci. The average FST over loci was small (0.0023) but highly significant statistically, demonstrating that genetically differentiated populations can arise and persist in the absence of physical barriers or great distance. We found no geographical pattern in the genetic differentiation and there was no apparent trend of isolation by distance along the coastline. These findings lend support to the notion that low levels of differentiation are due to passive transport of eggs or larvae by the ocean currents rather than to adult dispersal, the latter being strongly dependent on distance.

Animals↗
PubMed2007

Genetic diversity and population structure of Mycobacterium tuberculosis in HIV-1-infected compared with uninfected individuals in Burkina Faso.

HIV-1 infection and HIV-1-induced immune deficiency may play a role in selecting particular Mycobacterium tuberculosis (MTB) strains (i.e. genotypes). We compared 43 MTB isolates obtained from HIV-1-infected patients with 77 MTB isolates obtained from HIV-1-uninfected patients in Burkina Faso, by means of DNA fingerprinting methods (MIRU-VNTR plus spoligotyping). This study suggests a lack of structure of the MTB population caused by HIV-1 infection and a similar genetic diversity of MTB in HIV-1-infected compared with uninfected individuals.

AIDS-Related Opportunistic Infections↗
PubMed2004

Regional population structure of a widely introduced estuarine invertebrate: Nematostella vectensis Stephenson in New England.

Nematostella vectensis is an infaunal anemone occurring in salt marshes, lagoons and other estuarine habitats in North America and the United Kingdom. Although it is considered rare and receives protection in England, it is widely distributed and abundant in the United States, particularly along the Atlantic coast. Recent studies suggest that both anthropogenic dispersal and reproductive plasticity may significantly influence the genetic structure of N. vectensis populations. Amplified fragment length polymorphism (AFLP) fingerprinting of individuals from nine populations in the northeastern United States indicates that stable populations are maintained by both asexual and sexual reproduction; in some cases asexually reproducing lineages exist within sexually reproducing populations. F statistics reveal extraordinarily high degrees of genetic differentiation between populations, even those separated by very short distances (less than 100 m). Genetic distances show little to no correlation with geographical distances, consistent with a role for sporadic, geographically discontinuous dispersal coupled with limited gene flow. No single genotype was found at more than one site, despite apparent homogeneity of habitat. In contrast with reported genotypic distributions for Nematostella in the United Kingdom, where a single clonal genotype dominates at multiple sites through southern England, our data thus fail to support the hypothesis of a general-purpose genotype in the northeastern United States. However, they are consistent with important roles for reproductive plasticity, sporadic introductions and complex local population dynamics in determining the global and regional distribution of this species.

Analysis of Variance↗
PubMed1998

Sequence polymorphism in the beta-tubulin gene reveals heterogeneous and variable population structures in Cryptosporidium parvum.

Restriction fragment length polymorphism (RFLP) analysis of isolates of Cryptosporidium parvum has revealed two subgroups, termed H and C. The limited resolution of the RFLP method precludes an in-depth study of the genetic structure of C. parvum populations. Published C. parvum restriction polymorphisms lie within protein-coding regions known to be more homogeneous than noncoding sequences. To better assess the degrees of heterogeneity between and within C. parvum isolates, sequence polymorphism in the beta-tubulin intron, the only C. parvum intron described to date, was investigated. In contrast to the two genotypes distinguished by multilocus RFLP, several alleles were detected by sequence and RFLP analysis of the beta-tubulin intron and adjacent exon 2. Isolates carrying different beta-tubulin alleles were found. Significantly, one of the beta-tubulin alleles present in two geographically unrelated isolates combined features of C- and H-type isolates, suggesting that it might have arisen from a recombination event. A comparison of multiple samples of a calf-propagated laboratory isolate showed that the ratio of different beta-tubulin alleles fluctuated during serial passage.

Animals↗
PubMed2006

Population structure analysis of Plasmodium vivax in areas of iran with different malaria endemicity.

To obtain the genetic structure of Plasmodium vivax populations in the northern and southern malaria-endemic areas in Iran, which differ in endemicity, sequence diversity in the variable block 5 and the C-terminal part of P. vivax merozoite surface protein 1 (Pvmsp 1) was analyzed. The variable block 5 fragment from 52 northern and 94 southern isolates was amplified and sequenced. Type 1, type 2, and recombinant type 3 allelic variants were found in both northern and southern isolates, with type 1 predominant in parasites from the north and type 2 in those from the south. A total of 7 and 27 distinct variants were detected among northern and southern isolates, respectively. A single variant predominated (71%) in the northern isolates, whereas variants were evenly distributed among southern isolates, with only two exceeding 10%. Thus, parasites from the southern malaria-endemic area were more polymorphic than those circulating in the northern area, where malaria is a re-emerging disease. Sequence alignments showed that although some variants were found only in northern or southern isolates, some were common to both and had also been observed in parasites from Azerbaijan, Turkey, Thailand, Bangladesh, and China. The Pvmsp 1 fragment corresponding to the C-terminal region was also amplified and the sequences derived from 20 northern and 50 southern isolates were identical. This high degree of conservation reinforces the potential of this polypeptide fragment for inclusion in synthetic vaccines being developed against P. vivax.

Adult↗
PubMed1999

Population structure and dynamics of Magnaporthe grisea in the Indian Himalayas.

The population genetics of Magnaporthe grisea, the rice blast pathogen, were analyzed in a center of rice diversity (the Uttar Pradesh hills of the Indian Himalayas) using multilocus and single-, or low-copy, DNA markers. Based on DNA fingerprinting with the multilocus probe MGR586 and single-locus probes, 157 haplotypes clustered into 56 lineages (at >/=70% MGR586 band similarity, each with unique single-locus profiles) and high diversity indices were detected among 458 isolates collected from 29 sites during 1992-1995. Most valleys sampled had distinct populations (73% of the lineages were site specific) with some containing one or a few lineages, confirming the importance of clonal propagation, and others were very diverse. Widely distributed lineages suggested that migration occurs across the region and into the Indo-Gangetic plains. Repeated sampling at one site, Matli, (170 isolates, 1992-1995) yielded 19 lineages and diversity significantly greater than that reported from similar samples from Colombia and the Philippines. Analysis of allelic associations using pairwise comparisons and multilocus variance analysis failed to reject the hypothesis of gametic phase equilibrium. The Matli population shifted from highly diverse in 1992 to almost complete dominance by one lineage in 1995. Such population dynamics are consistent with recombination followed by differential survival of clonal descendants of recombinant progeny. At another site, Ranichauri, population (n = 84) composition changed from 2 to 11 lineages over 2 yr and yielded additional evidence for equilibrium. Sexually fertile and hermaphrodite isolates of both mating types were recovered from rice in both Matli and Ranichauri. We demonstrate that Himalayan M. grisea populations are diverse and dynamic and conclude that the structure of some populations may be affected to some extent by sexual recombination.

Crosses, Genetic↗
PubMed2004

Microsatellite variation reveals high levels of genetic variability and population structure in the gorgonian coral Pseudopterogorgia elisabethae across the Bahamas.

The primary mechanism of gene flow in marine sessile invertebrates is larval dispersal. In Pseudopterogorgia elisabethae, a commercially important Caribbean gorgonian coral, a proportion of the larvae drop to the substratum within close proximity to the maternal colony, and most matings occur between individuals in close proximity to each other. Such limited dispersal of reproductive propagules suggests that gene flow is limited in this gorgonian. In this study, we characterized the population genetic structure of P. elisabethae across the Bahamas using six microsatellite loci. P. elisabethae was collected from 18 sites across the Bahamas. Significant deviations from Hardy-Weinberg equilibrium due to deficits of heterozygotes within populations were detected for all 18 populations in at least one of the six screened loci. Levels of genetic structure among populations of P. elisabethae were high and significant. A distance analysis placed populations within three groups, one formed by populations located within Exuma Sound, a semi-isolated basin, another consisting of populations located outside the basin and a third group comprising two populations from San Salvador Island. The patterns of genetic variation found in this study are concordant with the life-history traits of the species and in part with the geography of the Bahamas. Conservation and management plans developed for P. elisabethae should considered the high degree of genetic structure observed among populations of the species, as well as the high genetic diversity found in the San Salvador and the Exuma Sound populations.

Animals↗
PubMed2005

"Clonal" population structure of the malaria agent Plasmodium falciparum in high-infection regions.

The population genetic structure of Plasmodium falciparum, the agent of malignant malaria, has been shown to be predominantly "clonal" (i.e., highly inbred) in regions of low infectivity; in high-infectivity regions, it is often thought to be panmictic, or nearly so, although there is little supporting evidence for this. The matter can be settled by investigating the parasite's genetic makeup in the midgut oocysts of the mosquito vector, where the products of meiosis can directly be observed. The developmental stages of P. falciparum are haploid, except in the oocysts of infected mosquito vectors, where two gametes fuse, diploidy occurs, and meiosis ensues. We have investigated genetic polymorphisms at seven microsatellite loci located on five chromosomes by assaying 613 oocysts in 145 mosquitoes sampled from 11 localities of Kenya, where malignant malaria is perennial and intense. There is considerable allelic variation, 16.3 +/- 2.1 alleles per locus, and considerable inbreeding, approximately 50% on the average. The inbreeding is caused by selfing (approximately 25%) and nonrandom genotype distribution of oocysts among mosquito guts (35%). The observed frequency of heterozygotes is 0.43 +/- 0.03; the expected frequency, assuming random mating, is 0.80 +/- 0.05. Linkage disequilibrium is statistically significant for all 21 pairwise comparisons between loci, even though 19 comparisons are between loci in different chromosomes, which is consistent with strong deviation from panmixia and the consequent reproduction of genomes as clones, without recombination between gene loci. This is of considerable evolutionary significance and of epidemiological consequence, concerning the spread of multilocus drug and vaccine resistance.

Animals↗
PubMed2004

Genetic variation and population structure of the mosquito Anopheles jeyporiensis in southern China.

Genetic differentiation among populations of Anopheles jeyporiensis was examined using 76 mtDNA COII sequences from 16 sites throughout southern China and northern Vietnam. The COII sequences are AT-rich (74.58%) and reveal high levels of diversity with 39 of 685 sites polymorphic and 50 different haplotypes present. Genetic variation is high within populations and significant geographical structure was detected at both population and regional levels. In the larger samples, the distributions of haplotypes suggest recent population expansion.

Analysis of Variance↗
PubMed2006

Comparative population structure of Cynopterus fruit bats in peninsular Malaysia and southern Thailand.

The extent to which response to environmental change is mediated by species-specific ecology is an important aspect of the population histories of tropical taxa. During the Pleistocene glacial cycles and associated sea level fluctuations, the Sunda region in Southeast Asia experienced concurrent changes in landmass area and the ratio of forest to open habitat, providing an ideal setting to test the expectation that habitat associations played an important role in determining species' response to the opportunity for geographic expansion. We used mitochondrial control region sequences and six microsatellite loci to compare the phylogeographic structure and demographic histories of four broadly sympatric species of Old World fruit bats in the genus, Cynopterus. Two forest-associated species and two open-habitat generalists were sampled along a latitudinal transect in Singapore, peninsular Malaysia, and southern Thailand. Contrary to expectations based on habitat associations, the geographic scale of population structure was not concordant across ecologically similar species. We found evidence for long and relatively stable demographic history in one forest and one open-habitat species, and inferred non-coincident demographic expansions in the second forest and open-habitat species. Thus, while these results indicate that Pleistocene climate change did not have a single effect on population structure across species, a correlation between habitat association and response to environmental change was supported in only two of four species. We conclude that interactions between multiple factors, including historical and contemporary environmental change, species-specific ecology and interspecific interactions, have shaped the recent evolutionary histories of Cynopterus fruit bats in Southeast Asia.

Animals↗
PubMed1998

On the theory of partially inbreeding finite populations. V. The effective size of a partially selfing age-structured population.

Consider a large population, with the same age distribution at times 0, 1, 2, ..., in which there is reproduction by selfing with probability beta and by random mating with probability 1-beta. An individual between i and i + 1 units of age at time t is said to be in age group i at that time. Let L be the mean, among copies of an allele A in genotypes of offspring in age group 0, of ages of parents when the inbreeding coefficient has attained an equilibrium value. Then if there is no selection and allele A is originally present in one heterozygote, the probability that it is ultimately fixed is 1/(2N0L), where N0 is the number of individuals in age group 0 at any time. The effective population size can then be derived. It turns out to be the same as for a population with discrete generations having the same mean and variance of the number of successful gametes produced during a lifetime and the same number of individuals entering the population per generation.

Age Distribution↗
PubMed1989

Genetic heterogeneity and population structure in eastern India: red cell enzyme variability in ten Assamese populations.

This paper is a part of the genetic study of the people of Assam (eastern India), initiated by the Anthropometry and Human Genetics Unit, Indian Statistical Institute, Calcutta, India, and the Dept. of Human Biology/Physical Anthropology, University of Bremen, W. Germany. The results of 1. allele distribution of five red cell enzyme polymorphisms in ten Assamese populations, 2. heterogeneity of allele frequencies and extent of gene differentiation among these populations, and 3. standard genetic distances are presented here. A total of 1024 blood samples was screened for aP, E D, AK, ADA and LDH enzyme systems for Brahmins, Kalitas, Kaibartas, Rajbanshis, Muslims, Ahoms, Chutiyas, Kacharis, Karbis (Mikirs) and Sonowals, of which the latter three are tribes. The gene diversity (FST) is smallest (0.0035) for pa and highest (0.1604) for HbE. The total FST value (0.0399 +/- 0.0141) appears to be statistically significant. From distance analysis two major clusters with sub-clusters in each are visible, which are in conformity with the ethnohistory of these populations.

Asian People↗
PubMed2004

Dynamical consequences of harvest in discrete age-structured population models.

The role of harvest in discrete age-structured one-population models has been explored. Considering a few age classes only, together with the overcompensatory Ricker recruitment function, we show that harvest acts as a weak destabilizing effect in case of small values of the year-to-year survival probability P and as a strong stabilizing effect whenever the survival probability approaches unity. In the latter case, assuming n = 2 age classes, we find that harvest may transfer a population from the chaotic regime to a state where the equilibrium point ( x(1)*, x(2)*) becomes stable. However, as the number of age classes increases (which acts as a stabilizing effect in non-exploited models), we find that harvest acts more and more destabilizing, in fact, when the number of age classes has been increased to n = 10, our finding is that in case of large values of the survival probabilities, harvest may transfer a population from a state where the equilibrium is stable to the chaotic regime, thus exactly the opposite of what was found in case of n = 2. On the other hand, if we replace the Ricker relation with the generalized Beverton and Holt recruitment function with abruptness parameter larger than 2, several of the conclusions derived above are changed. For example, when n is large and the survival probabilities exceed a certain threshold, the equilibrium will always be stable.

Age Factors↗
PubMed2001

Two-generation analysis of pollen flow across a landscape. III. Impact of adult population structure.

The rate and distance of instantaneous pollen flow in a population are parameters of considerable current interest for plant population geneticists and conservation biologists. We have recently developed an estimator (phi ft) of differentiation between the inferred pollen clouds that fertilize several females, sampled within a single population. We have shown that there is a simple relation between phi ft and the average pollen dispersal distance (delta) for the case of a population with no geographic structure. Though forest trees usually show considerable pollen flow, assuming an absence of spatially distributed genetic structure is not always wise. Here, we develop analytical theory for the relation between phi ft and delta, for the case where the probability of Identity by Descent (IBD) for two individuals decreases with the physical distance between them. This analytical theory allows us to provide an effective method for estimating pollen dispersal distance in a population with adult genetic structure. Using real examples, we show that estimation errors can be large if genetic structure is not taken into account, so it is wise to evaluate adult genetic structure simultaneously with estimation of phi ft for the pollen clouds. We show that the results are only moderately affected by changes in the decay function, a result of some importance since no completely established theory is available for this function.

Genetics, Population↗