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PubMed1999

The Red Queen and Fluctuating Epistasis: A Population Genetic Analysis of Antagonistic Coevolution.

Host-parasite coevolution has been shown to provide an advantage to recombination, but the selective mechanism underlying this advantage is unclear. One possibility is that recombination increases the frequency of advantageous genotypes that are disproportionately rare because of fluctuating epistasis. However, for this mechanism to work, epistasis for fitness must fluctuate over a very narrow timescale: two to five generations. Alternatively, recombination may speed up the response to directional selection by breaking up linkage disequilibria that decrease additive genetic variance. Here we analyze the results of a numerical simulation of host-parasite coevolution to assess the importance of these two mechanisms. We find that linkage disequilibria may tend to increase, rather than decrease, additive genetic variance. In addition, the sign of epistasis changes every two to five generations under several of the parameter values investigated, and epistasis and linkage disequilibrium are frequently of opposite signs. These results are consistent with the idea that selection for recombination is mediated by fluctuating epistasis. Finally, we explore the conditions under which an allele causing free recombination can spread in a nonrecombining host population and find general agreement between the predictions of a population genetic model of fluctuating epistasis and our simulation model.

Red Queen↗
PubMed2003

Molecular population genetic analysis of the spectacled bear (Tremarctos ornatus) in the northern Andean area.

Eighty-two Andean bear samples obtained in three South American Andean countries were analyzed using five hypervariable microsatellite markers. Neither the overall sample nor the samples coming from each of the countries analyzed were in Hardy-Weinberg equilibrium. This is attributable to the Wahlund effect caused by a fragmentation of the bear populations. The genetic variability levels found were in general low for this kind of molecular markers (H = 0.38 for the global population). The situation of the Ecuadorian bear population seems to be endangered (H = 0.24). This is the lowest level recorded for any bear population. The genetic heterogeneity among the three populations was large and highly significant (F(ST) = 0.39; R(ST) = 0.32-0.49). Likewise, the gene flow estimates were remarkably low among these populations (Nm = 0.2-0.3). This means that the populations are strongly isolated. Different methods were applied to determine the effective numbers in these populations. A significant spatial structure of the genotypes was analyzed with different procedures. In all cases, an isolation-by-distance structure was detected. This could be a consequence of the original South America colonization. There was no evidence for a recent genetic bottleneck. This could mean that the low heterozygosity and the population fragmentation could be explained by ancient events related to the bear colonization, with the arrival of humans beings in the Americas, and/or with the glacial maximum, 16.000-30.000 years ago.

Animals↗
PubMedDate not supplied

Male/female ratio in centenarians: a possible role played by population genetic structure.

All the demographic surveys on the centenarians have highlighted that females outnumber males. The centenarians' male/female (M/F) ratio reported by most studies ranges between 1:4 and 1:7. A puzzling 1:2 ratio was observed in Calabria, a Southern Italian region. To our knowledge only in Sardinia a similar phenomenon had been previously observed. We have therefore used the data of the Italian Institute of Statistics to figure out the centenarians' M/F ratio in the Italian regions. We found that this ratio gradually decreases from South to North. Such a result is certainly due to many factors. Thus, we have explored the possibility, it is also influenced by the genetic structure of the Italian population. In fact, the distribution of the centenarians' M/F ratio turned out to be significantly correlated with the genetic structure of the Italian population as outlined by the principal component analysis.

Aged↗
PubMed2001

Population genetic structure and competence as a vector for dengue type 2 virus of Aedes aegypti and Aedes albopictus from Madagascar.

Starch gel electrophoresis was used to assess the polymorphism of 7 isoenzymes in single mosquitoes (field-collected F0 or F1 generation) for Aedes albopictus (8 strains) from northern Madagascar. Mosquitoes of the F2 generation (3 strains of Aedes aegypti and 10 strains of Ae. albopictus) were tested for oral susceptibility to dengue type 2 virus. Aedes aegypti was less susceptible to viral infection than Ae. albopictus. The genetic differentiation was less high between Ae. albopictus populations collected in agglomerations connected by highly frequented roads, indicating that human ground transportation favors mosquito dispersal. These results have implications for the ecology, pattern of migration, and relative importance in epidemic transmission of dengue viruses between the 2 Aedes species.

Aedes↗
PubMed1998

Non-genetic population heterogeneity studied by in situ polymerase chain reaction.

Expression of a lac operon in Salmonella typhimurium single cells was monitored using lac mRNA targeting in situ reverse transcription-polymerase chain reaction (RT-PCR). It is demonstrated that suboptimal induction of the lac operon in a culture of S. typhimuriuml/F'lac+ cells generates a subpopulation in which transcription of the lac operon occurs and another subpopulation in which transcription of the lac operon is repressed, whereas suboptimal induction of the lac operon in a culture of S. typhimuriuml/F'lacY cells generates a population with uniform levels of lac mRNA. The outcome of the single-cell lac mRNA detection assay was compared with the outcome of a single-cell beta-galactosidase assay. In cultures grown under different suboptimal lac induction conditions, the fraction of cells in which transcription of the lac operon occurred was concurrent with the fraction of cells showing beta-galactosidase activity. Besides supporting the hypothesis that the lactose permease has a role in generating non-genetic heterogeneity in suboptimally induced cultures of Lac+ cells, these results demonstrate the usefulness of in situ RT-PCR for the study of non-genetic population heterogeneities.

Escherichia coli Proteins↗
PubMed1978

Sequence variability of immunoglobulins considered from the standpoint of population genetics.

The probability of gene identity between members of a multigene family was investigated, assuming mutation, random genetic drift, and unequal crossing-over. The theoretical results on the equilibrium and transient behavior of the identity probability were applied to the analyses of sequence variability in the variable regions of immunoglobulins. The probability of amino acid identity between corresponding residue sites at different but homologous immunoglobulin sequences was computed both within and between species from data reported by other workers. The average probability of amino acid identity was obtained for the hypervariable regions and also for the framework regions. From statistical analyses based on population genetics theory it is concluded that somatic mutations cannot be the major cause of hypervariability and that the results can readily be explained by the germ line theory.

Journal Article↗
PubMedDate not supplied

[Population-genetic study of the polymorphism of structural genes and ISSR-PCR markers in some cattle breeds].

The comparative analysis of genetic structures of five cattle breeds has been carried out using polymorphism of two different types of molecular-genetic markers--20 structural genes and 128 DNA loci (the DNA fragments flanked by inverted microsatellite loci repetitions--ISSR-PCR method). In spite of availability of breed-specific singularities of genotype distribution detected by the both methods the level of mean heterozygosity of structural genes was similar in all the investigated breeds. A part of polymorphic loci and the average value of the polymorphic information contents (PIC) of ISSR-PCR markers has appeared much higher in commercial breeds with high effective number in comparison with Ukrainian autochthonous breeds. The population-genetic processes detected by different methods are discussed.

Animals↗
PubMed2004

Populational genetic structure of free-living maned wolves (Chrysocyon brachyurus) determined by proteic markers.

Electrophoretic analysis of presumptive twenty gene loci products was conducted in hemolisates and plasma samples of twenty-eight maned wolves (Chrysocyon brachyurus) from an area in northeastern São Paulo State, Brazil. The area sampled was divided into three sub-areas, with the Mogi-Guaçu and Pardo rivers regarded as barriers to the gene flow. The polymorphism degree and heterozygosity level (intralocus and average) estimated in this study were similar to those detected by other authors for maned wolves and other species of wild free-living canids. The samples of each sub-area and the total sample exhibited genotype frequencies consistent with the genetic equilibrium model. The values of the F-statistics evidenced absence of inbreeding and population subdivision and, consequently, low genetic distances were found among the samples of each area.

Animals↗
PubMed2003

Spatial and demographic population genetic structure in Catasetum viridiflavum across a human-disturbed habitat.

Spatial and temporal genetic structures were examined across sites on islands and mainland (continuous forest) populations of an epiphytic orchid, Catasetum viridiflavum, using 17 polymorphic allozyme loci. I tested whether patches on islands or at mainland sites comprised small local populations or a large population. Low among population differentiation was observed across the landscape suggesting that the species-specific pollinator and tiny wind-dispersed seeds maintain interconnections among distant patches. Temporal genetic structure among stage classes, and among breeding individuals are important components of the maintenance of genetic variation in this orchid. The natural history of this species including small breeding populations, probable high frequency of mating among relatives, and the high rates of seed movement among sites contribute to the high FIS. These data show that physically isolated patches in this epiphytic orchid comprise a single larger genetic population, which is independent of the physical distances among sites. Although quite different in ecological and life history characteristics, the genetic structure of this orchid demonstrates a pattern similar to temperate and tropical trees in fragmented landscapes.

Ecology↗
PubMed2001

Population genetics of the schistosome intermediate host Biomphalaria pfeifferi in the Zimbabwean highveld: implications for co-evolutionary theory.

Co-evolutionary theory proposes that polymorphisms in co-evolved traits may be maintained through differential selection in spatially heterogeneous environments. Spatial heterogeneity of the schistosome intermediate host, Biomphalaria pfeifferi, was investigated here, using RAPD markers. Overall, 256 individuals, collected at 32 sites on 13 rivers in the Chiweshe region of Zimbabwe, were analysed. Significant genetic differentiation was demonstrated, both between populations from the different rivers and between populations collected at different sites on each of several of the rivers investigated. However, the presence of spatial differentiation between populations from individual rivers varied with river type. It was not apparent in permanent, deep, fast-flowing rivers, where high levels of migration, through passive dispersal along the rivers, are likely. The snails collected from shallow, semi-permanent rivers not only showed relatively high levels of population subdivision but also high levels of within-site genetic diversity, consistent with the existence of 'co-evolutionary hot-spots' where schistosome infection may be prevalent. These results are discussed with reference to the population biology of B. pfeifferi and to host-parasite co-evolution.

Analysis of Variance↗
PubMed2002

Population genetics and dynamics at short spatial scale in Bulinus truncatus, the intermediate host of Schistosoma haematobium, in Morocco.

The population biology of the schistosome-vector snail Bulinus truncatus was studied in an irrigation system near Marrakech, Morocco using both genetic and demographic approaches. The population genetic survey was conducted in 4 sites, 2 sites being sampled on 2 separate occasions. Individuals were genotyped at 6 microsatellite loci. No variability was found at 4 loci, and the 2 other loci had less than 4 alleles. The differentiation, both spatial and temporal, among populations was extremely weak. The demographic survey was conducted using 2 capture-mark-recapture analyses in 2 separate sites, the first in 1999 and the second in 2000. The second analysis permitted the estimation of parameters based on recent methodological developments (multisite models). Although these studies provided information on several traits, we report here on dispersal only. Both analyses showed that individual dispersal is of the order of a few hundreds of metres per reproductive life, that is the scale of the whole irrigation area. Both the genetic and demographic studies indicated that this area harbours a single--or no more than a few--populations of B. truncatus. This has implications for our understanding of the coevolutionary process between snails and flukes.

Animals↗
PubMed2006

Population genetics and linkage analysis of loci within the FCT region of Streptococcus pyogenes.

The FCT regions of Streptococcus pyogenes strains encode a variety of cell wall-anchored surface proteins that bind the extracellular matrix of the human host and/or give rise to pilus-like appendages. Strong linkage is evident between transcription-regulatory loci positioned within the FCT and emm regions and the emm pattern genotype marker for preferred infection of the throat or skin. These findings provide a basis for the hypothesis that FCT region gene products contribute to tissue-specific infection. In an initial series of steps to address this possibility, the FCT regions of 13 strains underwent comparative sequence analysis, the gene content of the FCT region was characterized for 113 strains via PCR, and genetic linkage was assessed. A history of extensive recombination within FCT regions was evident. The emm pattern D-defined skin specialist strains were highly homogenous in their FCT region gene contents, whereas the emm pattern A-C-defined throat specialist strains displayed a greater variety of forms. Most pattern A-C strains harbored prtF1 (75%) but lacked cpa (75%). In contrast, the majority of emm pattern D strains had cpa (92%) but lacked prtF1 (79%). Models based on FCT and emm region genotypes revealed the most parsimonious pathways of evolution. Using niche-determining candidate genes to infer phylogeny, emm pattern E strains--the so-called generalists, which lack a strong tissue site preference--occupied a transition zone separating most throat specialists from skin specialists. Overall, population genetic analysis supports the possibility that the FCT region gives rise to surface proteins that are largely necessary, but not always sufficient, to confer tissue site preference for infection.

Evolution, Molecular↗
PubMed2001

Population genetics of ten STR loci (AmpFlSTR SGM plus) in Austria.

A population study on the ten short tandem repeat (STR) loci D3S1358, VWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01 and FGA was performed on 204 unrelated Austrian Caucasians. The DNA was amplified by multiplex PCR using the AmpF/STR SGM plus kit. All loci met Hardy-Weinberg expectations. The combined power of exclusion for the ten STR loci was 0.999976. The results show that these loci are very useful for forensic purposes.

Austria↗
PubMed1999

Molecular population genetics of the primary neotropical malaria vector Anopheles darlingi using mtDNA.

Samples of the neotropical malaria vector Anopheles darlingi from Bolivia, Brazil, and Venezuela were analyzed to test for differences in mitochondrial haplotype frequencies. With the use of molecular variance components and F-statistics, significant genetic variability of An. darlingi was found apportioned primarily among populations within regions or within populations, with regions defined either as biomes (n = 5) or ecoregions (n = 2). The Mantel analysis resulted in a significant correlation [Prob (r) = 0.009] between genetic and geographic distances, evidence that these populations are genetically isolated by distance. Such isolation could reflect differences in phenotypes for factors affecting vector capacity.

Animals↗
PubMed1989

Genetic studies of low-abundance human plasma proteins. XI. Linkage analysis and population genetics of the C1S subcomponent of the first complement component.

Although subcomponents C1r and C1s of the first complement component, C1, have been established to be in the same linkage group as the proline-rich protein gene cluster on chromosome 12p13.2, no direct analysis of linkage between the C1R and C1S structural gene loci has been available. We have detected through a population screening study 5 families which are heterozygous at the structural loci for both C1R and C1S. Three of the 5 families, 21 individuals, were informative for linkage. A maximum lod score of 1.505 at theta = 0.00 was found in a two-point analysis between C1R and C1S. Ten populations were screened for structural variation at the C1S locus. Only US Whites and a Kodiak Island Eskimo group expressed heterogeneity. The frequencies of the designated alleles, C1S*1 and C1S*2, were 0.992 and 0.007, respectively, in the US White population and 0.998 and 0.002, respectively, in the Kodiak Island Eskimo population. In addition, the product of a putative new allele, designated C1S*4, was observed in a single US White individual but segregation of this variant was not observed in the limited family data available.

Blood Proteins↗
PubMed2006

Genetic population structure as indirect measure of dispersal ability in a Lake Tanganyika cichlid.

Diversification and speciation processes are influenced by intrinsic (ecological specialization, dispersal) and extrinsic (habitat structure and instability) factors, but the effect of ecological characteristics on dispersal is difficult to assess. This study uses mitochondrial control region sequences to investigate the population structure and demographic history of the endemic Lake Tanganyika cichlid Neolamprologus caudopunctatus with a preference for the rock-sand interface along two stretches of continuous, rocky shoreline, and across a sandy bay representing a potential dispersal barrier. Populations along uninterrupted habitat were not differentiated; whereas, the sandy bay separated two reciprocally monophyletic clades. The split between the two clades between 170,000 and 260,000 years BP coincides with a period of rising water level following a major lowstand, and indicates that clades remained isolated throughout subsequent lake level fluctuations. Low long-term effective population sizes were inferred from modest genetic diversity estimates, and may be due to recent population expansions starting from small population sizes 45,000-60,000 years BP. Comparisons with available data from specialized rock-dwelling species of the same area suggest that habitat structure and lake level fluctuations determine phylogeographic patterns on large scales, while fine-scale population structure and demography are modulated by species-specific ecologies.

Africa, Eastern↗