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PubMed2001

Self-organized dynamics in spatially structured populations.

Self-organization and pattern formation represent the emergence of order in temporal and spatial processes. Self-organization in population ecology is gaining attention due to the recent advances concerning temporal fluctuations in the population size of dispersal-linked subunits. We shall report that spatially structured models of population renewal promote the emergence of a complex power law order in spatial population dynamics. We analyse a variety of population models showing that self-organization can be identified as a temporal match in population dynamics among local units, and how the synchrony changes in time. Our theoretical results are concordant with analyses of population data on the Canada lynx.

Animals↗
PubMed2007

Population structure and resistance genes in antibiotic-resistant bacteria from a remote community with minimal antibiotic exposure.

In a previous study, we detected unexpectedly high levels of acquired antibiotic resistance in commensal Escherichia coli isolates from a remote Guaraní Indian (Bolivia) community with very low levels of antibiotic exposure and limited exchanges with the exterior. Here we analyzed the structure of the resistant E. coli population from that community and the resistance mechanisms. The E. coli population (113 isolates from 72 inhabitants) showed a high degree of genetic heterogeneity, as evidenced by phylogenetic grouping (77% group A, 10% group B1, 8% group D, 5% group B2) and genotyping by randomly amplified polymorphic DNA (RAPD) analysis (44 different RAPD types). The acquired resistance genes were always of the same types as those found in antibiotic-exposed settings [blaTEM, blaPSE-1, catI, cmlA6, tet(A), tet(B), dfrA1, dfrA7, dfrA8, dfrA17, sul1, sul2, aphA1, aadA1, aadA2, aadA5, aadB, and sat-1]. Class 1 and class 2 integrons were found in 12% and 4% of the isolates, respectively, and harbored arrays of gene cassettes similar to those already described. The cotransferability of multiple-resistance traits was observed from selected isolates and was found to be associated with resistance conjugative plasmids of the F, P, and N types. Overall, these data suggest that the resistance observed in this remote community is likely the consequence of the dissemination of resistant bacteria and resistance genes from antibiotic-exposed settings (rather than of an independent in situ selection) which involved both the clonal expansion of resistant strains and the horizontal transfer/recombination of mobile genetic elements harboring resistance genes.

Anti-Bacterial Agents↗
PubMed2006

Ancestral genomes, sex, and the population structure of Trypanosoma cruzi.

Acquisition of detailed knowledge of the structure and evolution of Trypanosoma cruzi populations is essential for control of Chagas disease. We profiled 75 strains of the parasite with five nuclear microsatellite loci, 24Salpha RNA genes, and sequence polymorphisms in the mitochondrial cytochrome oxidase subunit II gene. We also used sequences available in GenBank for the mitochondrial genes cytochrome B and NADH dehydrogenase subunit 1. A multidimensional scaling plot (MDS) based in microsatellite data divided the parasites into four clusters corresponding to T. cruzi I (MDS-cluster A), T. cruzi II (MDS-cluster C), a third group of T. cruzi strains (MDS-cluster B), and hybrid strains (MDS-cluster BH). The first two clusters matched respectively mitochondrial clades A and C, while the other two belonged to mitochondrial clade B. The 24Salpha rDNA and microsatellite profiling data were combined into multilocus genotypes that were analyzed by the haplotype reconstruction program PHASE. We identified 141 haplotypes that were clearly distributed into three haplogroups (X, Y, and Z). All strains belonging to T. cruzi I (MDS-cluster A) were Z/Z, the T. cruzi II strains (MDS-cluster C) were Y/Y, and those belonging to MDS-cluster B (unclassified T. cruzi) had X/X haplogroup genotypes. The strains grouped in the MDS-cluster BH were X/Y, confirming their hybrid character. Based on these results we propose the following minimal scenario for T. cruzi evolution. In a distant past there were at a minimum three ancestral lineages that we may call, respectively, T. cruzi I, T. cruzi II, and T. cruzi III. At least two hybridization events involving T. cruzi II and T. cruzi III produced evolutionarily viable progeny. In both events, the mitochondrial recipient (as identified by the mitochondrial clade of the hybrid strains) was T. cruzi II and the mitochondrial donor was T. cruzi III.

Animals↗
PubMed2000

Effects of local geographic barriers and latitude on population structure in Anopheles punctipennis (Diptera: Culicidae).

We sampled Anopheles punctipennis (Say) from 11 localities throughout Vermont to examine the effects of latitude and two local geographical boundaries, Lake Champlain and the Green Mountains, on the population genetic structure of this species. Thirty-five mitochondrial haplotypes were detected in 104 individuals using a variable region of the COI gene. When latitude was examined, we detected significant structure within localities and among localities within latitudinal regions. For geographic analysis, significant genetic structure was detected only within localities. Estimates of gene flow across geographic regions indicate that the Green Mountains, but not Lake Champlain, is a barrier to dispersal for this species. We found no correlation between genetic and geographic distances for An. punctipennis.

Animals↗
PubMed2005

Temporal variation of the population structure and genetic diversity of Farfantepenaeus notialis assessed by allozyme loci.

Population genetic studies carried out on penaeid shrimps have disclosed different patterns of population subdivision, revealing new aspects of shrimp biology as well as the effects of historical contingency molding those patterns. However, the stability of observed allele frequencies over time still remains untested. The objective of this article is to show the analysis of the temporal variation of allozymes in a shrimp species inhabiting Cuba which proves that the genetic structure of this species could significantly change in time. The study involves four populations of Farfantepenaeus notialis sampled in a period of 8 years. The significant statistics obtained from partitions observed in 1995 were not detected in 2003 (as suggested by AMOVA and F(ST)), whereas temporal genetic differentiation and heterozygosity became highly significant. The results strongly suggest that the effect of migrations could be the cause for the loss of F. notialis genetic structure in 2003. It is therefore imperative to call attention on the vulnerability of these populations when facing unstable environmental and habitat conditions.

Alleles↗
PubMed2002

Land barriers and open oceans: effects on gene diversity and population structure in Avicennia germinans L. (Avicenniaceae).

Avicennia germinans L. is a widespread mangrove species occupying the west coast of Africa and the Atlantic and Pacific coasts of the Americas from the Bahamas to Brazil and Baja California to Peru. An amplified fragment length polymorphism (AFLP) molecular analysis was carried out to assess genetic architecture within this species and to evaluate the effects of the Atlantic Ocean and the Central American Isthmus (CAI) on population and regional genetic diversity and differentiation. In total, 349 polymorphic AFLP fragments were identified among 144 individuals from 14 populations from the east Atlantic, west Atlantic and east Pacific. Levels of genetic diversity varied considerably among populations, but were generally higher in populations from the east Atlantic. Regional differentiation between the Pacific coast and Atlantic populations was greater than between east and west Atlantic populations, suggesting that the CAI has had an important influence on population genetic structure in this species. The lower level of divergence of east Atlantic from west Atlantic populations suggests some dispersal across the Atlantic Ocean, although migration rates are probably low; Nm from GST equal to 0.41 and accumulation of private and rare alleles in the east Atlantic. Population differentiation did not appear to follow an isolation by distance model and has probably resulted from complex patterns of population bottlenecks, and founder events due to landscape changes during the Pleistocene, particularly in the west Atlantic. The molecular data provide no support for the treatment of east Atlantic populations as a separate species A. africana.

Genes, Plant↗
PubMed2006

Species-specific population structure in rock-specialized sympatric cichlid species in Lake Tanganyika, East Africa.

Species richness and geographical phenotypic variation in East African lacustrine cichlids are often correlated with ecological specializations and limited dispersal. This study compares mitochondrial and microsatellite genetic diversity and structure among three sympatric rock-dwelling cichlids of Lake Tanganyika, Eretmodus cyanostictus, Tropheus moorii, and Ophthalmotilapia ventralis. The species represent three endemic, phylogenetically distinct tribes (Eretmodini, Tropheini, and Ectodini), and display divergent ecomorphological and behavioral specialization. Sample locations span both continuous, rocky shoreline and a potential dispersal barrier in the form of a muddy bay. High genetic diversity and population differentiation were detected in T. moorii and E. cyanostictus, whereas much lower variation and structure were found in O. ventralis. In particular, while a 7-km-wide muddy bay curtails dispersal in all three species to a similar extent, gene flow along mostly continuous habitat appeared to be controlled by distance in E. cyanostictus, further restricted by site philopatry and/or minor habitat discontinuities in T. moorii, and unrestrained in O. ventralis. In contrast to the general pattern of high gene flow along continuous shorelines in rock-dwelling cichlids of Lake Malawi, our study identifies differences in population structure among stenotopic Lake Tanganyika species. The amount of genetic differentiation among populations was not related to the degree of geographical variation of body color, especially since more phenotypic variation is observed in O. ventralis than in the genetically highly structured E. cyanostictus.

Animals↗
PubMed1998

Genetic variation and population structure of the Japanese sika deer (Cervus nippon) in Hokkaido Island, based on mitochondrial D-loop sequences.

Mitochondrial DNA (mtDNA) D-loop region sequences (602 bp) from 141 samples of the sika deer Cervus nippon collected from Hokkaido Island of Japan were investigated to elucidate population genetic structure. All animals possessed seven repeat units (38 or 39 bp each) in the sequences. Comparison of the 602-bp sequences showed four sites of transitional mutations (A<-->G or C<-->T). Based on combination of the substitutions, six D-loop haplotypes (a-f types) were identified in the Hokkaido population, suggesting the occurrence of at least six maternal lineages. Distribution maps of the haplotypes constructed using the Geographic Information System showed that the distribution of the major three types differed from haplotype to haplotype. In particular, distribution of the major three types (a-, b-, and c-types) almost overlapped with three main areas of coniferous forests in Hokkaido. These results suggest that expansion of the sika deer population could have occurred through the habitat of coniferous forests after the historical bottleneck in Hokkaido.

Animals↗
PubMedDate not supplied

[Death in the milieu of homeless persons. A comparative retrospective analysis of an autopsy sample of different regional population structures (Middle Hessia/Hamburg)].

For an evaluation concerning different regional population and community characteristics, 23 fatalities of homeless individuals were selected from the current autopsy series of the Institutes of Legal Medicine of Giessen/Germany and Hamburg/Germany from 1990 to 1996. The outcome of this retrospective analysis enables to overcome the deficiency of knowledge of causes, manners and circumstances of death among homeless individuals.

Accidents↗
PubMed2006

Genetic variation, population structure, and phylogenetic relationships of Triatoma rubida and T. recurva (Hemiptera: Reduviidae: Triatominae) from the Sonoran Desert, insect vectors of the Chagas' disease parasite Trypanosoma cruzi.

Nucleotide and amino acid sequence data from the mitochondrial cytochrome b (Cytb) and cytochrome c oxidase subunit I (COI) gene segments were used to gain insights into the population biology and phylogenetic relationships of two species of hematophagous kissing bugs (Hemiptera: Reduviidae: Triatominae) from the Sonoran Desert of northwestern Mexico and southern Arizona, USA, Triatoma rubida (Uhler, 1894) and T. recurva (Stål, 1868), both of which are vectors of the protozoan parasite Trypanosoma cruzi responsible for Chagas' disease. Analysis of molecular variance of gene sequences indicated significant structure among populations of both species from widely separated geographic localities. Phylogenetic analyses of gene and amino acid sequences employing both Bayesian and parsimony methods showed that T. recurva clustered within the phyllosoma complex of Triatoma species from central and southern Mexico with high statistical support, and that it was closely related to T. longipennis. Triatoma dimidiata also was shown to be closely related to the phyllosoma complex, as was T. sanguisuga which has historically been assigned to the lecticularia complex. Analyses of gene sequences were unable to confidently resolve relationships of T. rubida, although weak support for a T. nitida+T. rubida clade was seen under certain conditions. A provisional calibration of a mitochondrial DNA molecular clock for T. rubida, based on geological dates for the vicariant separation of the Baja California peninsula from mainland Mexico, suggested that pairwise sequence divergences for the Cytb and COI genes were 1.1-1.8% and 0.6-1.0% per million years, respectively. Two highly supported sympatric lineages of T. rubida uhleri from southern Arizona, which are hypothesized to have diverged approximately 550,000-900,000 years ago, were detected in the Cytb gene trees.

Amino Acid Sequence↗
PubMed1999

Analysis of population structure of the chestnut blight fungus based on vegetative incompatibility genotypes.

Vegetative incompatibility is a self/nonself-recognition system in fungi that has often been used for describing phenotypic diversity in fungal populations. A common hypothesis is that vegetative incompatibility polymorphisms are maintained by balancing selection. However, understanding the evolutionary significance of vegetative incompatibility and the factors that maintain these polymorphisms has been limited by a lack of knowledge of the underlying genetics of vegetative compatibility (vc) types. Genotypes of 64 vc types, controlled by six unlinked vegetative incompatibility (vic) loci, have been identified in the chestnut blight fungus, Cryphonectria parasitica. By interpreting vc type survey data in terms of vic genotypes, we estimated vic-allele frequencies and analyzed the multilocus genetic structure of 13 populations in Europe and 3 populations in the U.S. European populations have less vc type diversity than the US populations because of a combination of lower vic-allele diversity and limited recombination. Genotypic diversity of 10 populations in Italy correlated to the abundance of sexual structures; however, significant deviations from random mating suggest that either sexual reproduction may not contribute many offspring in these populations or that vic genes (or vic genotypes) are under selection. Most vic-allele frequencies deviated from 0.5, the equilibrium frequency predicted under frequency-dependent selection, providing no evidence for selection acting on these loci.

Journal Article↗
PubMed2004

Multilocus microsatellite typing system for Penicillium marneffei reveals spatially structured populations.

For eukaryotic pathogens that have low levels of genetic variation, multilocus microsatellite typing (MLMT) offers an accurate and reproducible method of characterizing genetic diversity. Here, we describe the application of an MLMT system to the emerging pathogenic fungus Penicillium marneffei. Isolates used for this study were those held in the culture collections of the Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands, and the Chiang Mai University Department of Microbiology, Chang Mai, Thailand. High genetic diversity and extensive spatial structure were observed among clinical isolates, with the geographical area of origin for each isolate strongly correlating with the occurrence of two deeply divided clades. Within each clade, multilocus linkage associations were highly significant and could be explained by genetically differentiated populations or by an exclusively clonal reproductive mode, or both. Our results show that southeast Asian penicilliosis is caused by a fungus with a complex population genetic structure. Furthermore, this MLMT system generates digital data that can be easily queried against a centrally held database via the internet (http://pmarneffei.multilocus.net/); this provides a powerful epidemiological tool for analyzing the underlying parameters that are responsible for the emergence of P. marneffei in human immunodeficiency virus-positive populations.

AIDS-Related Opportunistic Infections↗
PubMed1978

Sex-linked genes in age-structured populations.

We study the progress towards equilibrium of the frequencies of sex-linked genes in elementary discrete time models of age-structured, overlapping generation populations. It is found that, if a finite upper age limit is assumed, the difference in the frequencies of an allele in males and females will oscillate as in the familiar non-overlapping generation models, although the oscillations may be irregular. Monotonic convergence of that difference, as found by Nagylaki (1975) in continuous-time overlapping generation models without age-structure, occurs in the models considered here only when there is no upper age limit and when there is "sufficient" overlap of generations.

Age Factors↗
PubMed2005

Local genetic population structure in an endangered plant species, Silene tatarica (Caryophyllaceae).

Genetic substructuring in plant populations may evolve as a consequence of sampling events that occur when the population is founded or regenerated, or if gene dispersal by pollen and seeds is restricted within a population. Silene tatarica is an endangered, perennial plant species growing along periodically disturbed riverbanks in northern Finland. We investigated the mechanism behind the microspatial genetic structure of S. tatarica in four subpopulations using amplified fragment length polymorphism markers. Spatial autocorrelation revealed clear spatial genetic structure in each subpopulation, even though the pattern diminished in older subpopulations. Parentage analysis in an isolated island subpopulation indicated a very low level of selfing and avoidance of breeding between close relatives. The mean estimated pollen dispersal distance (24.10 m; SD = 10.5) was significantly longer and the mean seed dispersal distance (9.07 m; SD = 9.23) was considerably shorter than the mean distance between the individuals (19.20 m; SD = 13.80). The estimated indirect and direct estimates of neighbourhood sizes in this subpopulation were very similar, 32.1 and 37.6, respectively. Our results suggested that the local spatial genetic structure in S. tatarica was attributed merely to the isolation-by-distance process rather than founder effect, and despite free pollen movement across population, restricted seed dispersal maintains local genetic structure in this species.

DNA, Plant↗
PubMed2000

Evolution of nitrogen fixation in spatially structured populations of Rhizobium.

Symbiosis between legumes and nitrogen-fixing bacteria is thought to bring mutual benefit to each participant. However, it is not known how rhizobia benefit from nodulation of legume hosts because they fix nitrogen only after differentiating into bacteroids, terminally differentiated cells that cannot reproduce. Because free-living rhizobia can reproduce, and may benefit from the increase of plant root exudates stimulated by nodulation, evolution of symbiotic nitrogen fixation may depend upon kin selection. However, unrelated nonmutualists may also benefit from increased plant exudates and nitrogen-fixing populations are therefore vulnerable to invasion by nonfixing, saprophytic Rhizobium. The access of nonfixing Rhizobium to the plant exudates associated with nodules depends upon the spatial structure of the Rhizobium populations within the soil. We investigate the influence of spatial structure on the evolution of N-fixation within a Rhizobium population using a mathematical model. Our model demonstrates that spatial structure is necessary for the evolution of N-fixation and that N-fixation is more likely to evolve with increasing degrees of spatial structure. In fact, we identify three dynamic outcomes that depend upon the relative strength of the costs of N-fixation relative to the degree of spatial structure and benefits resulting from nodulations. If the costs are relatively high, N-fixation will not evolve; if the costs are relatively low, N-fixing genes will fix in the population, but at intermediate conditions, a stable mixture of N-fixing bacteria and nonfixing bacteria will be maintained. The conditions for coexistence of N-fixing bacteria and nonfixing bacteria expand under a saturating relationship between nodule numbers and N-fixing genotype frequency.

Biological Evolution↗
PubMed2004

Population structure of the large Japanese field mouse, Apodemus speciosus (Rodentia: Muridae), in suburban landscape, based on mitochondrial D-loop sequences.

Genetic structure of the large Japanese field mouse populations in suburban landscape of West Tokyo, Japan was determined using mitochondrial DNA control region sequence. Samples were collected from six habitats linked by forests and green tract along the Tama River, and from two forests segregated by urban areas from those continuous habitats. Thirty-five haplotypes were detected in 221 animals. Four to eight haplotypes were found within each local population belonging to the continuous landscape. Some haplotypes were shared by two or three adjacent local populations. On the other hand, two isolated habitats were occupied by one or two indigenous haplotypes. Significant genetic differentiation between all pairs of local populations, except for one pair in the continuous habitats, was found by analysis of molecular variance (amova). The geographical distance between habitats did not explain the large variance of pairwise F(ST)-values among local populations. F(ST)-values between local populations segregated by urban areas were higher than those between local populations in the continuous habitat, regardless of geographical distance. The results of this study demonstrated quantitatively that urban areas inhibit the migration of Apodemus speciosus, whereas a linear green tract along a river functions as a corridor. Moreover, it preserves the metapopulation structure of A. speciosus as well as the corridors in suburban landscape.

Animals↗