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Genetic population structure of Italy. II. Physical and cultural barriers to gene flow.

Three approaches were employed to evaluate the relative importance of geographic and linguistic factors in maintaining genetic differentiation of Italian populations as shown by blood groups and erythrocyte and serum markers. Genetic distances are closer to linguistic than to geographic distances. Gene-frequency change across 12 linguistic boundaries is significantly more rapid than at random locations. The zones of sharp genetic variation correspond to physical barriers to gene flow and to boundaries between dialect families, which overlap widely. However, two linguistically differentiated populations appear genetically differentiated despite the absence of physical obstacles to gene flow around them. The Po River is associated with abrupt genetic change only in the area where it corresponds to a dialect boundary. At most loci the genetic population structure seems affected by linguistic rather than geographic factors; exceptions are the systems that were subject to malarial selection in geographically close but linguistically heterogeneous localities. Gene flow appears to homogenize gene frequencies within regions corresponding to dialect families but not between them, leading to the patchy distributions of allele frequencies that were detected in an earlier study.

Alleles↗

Genetic drift and gene flow in post-famine Ireland.

This study examines the genetic impact of the Great Famine (1846-1851) on the regional genetic structure of Ireland. The Great Famine resulted in a rapid decrease in population size throughout Ireland in a short period of time, increasing the possibility of genetic drift. Our study is based on migration and anthropometric data collected originally in the 1930s from 7211 adult Irish males. These data were subdivided into three time periods defined by year of birth: 1861-1880, 1881-1900, and 1901-1920. Within each time period the data were further subdivided into six geographic regions of Ireland. Estimates of Wright's FST were calculated from parent-offspring migration data and from 17 anthropometric variables (10 head measures, 7 body measures). Over time, the average population size decreased, but average rates of migration increased. The estimates of FST at equilibrium from migration matrix analysis suggest that the net effect of these opposite effects is a reduction in among-group variation. Closer examination shows that within each time period the rate of convergence to equilibrium is slow, meaning that the expected levels of genetic homogeneity revealed from migration matrix analysis are not likely to be seen over short intervals of time. Estimates of FST from anthropometric data show either relatively little change in microdifferentiation or some increase, depending on which variables are analyzed. Investigation of a simple model of demographic and genetic change shows that, given the demographic changes in post-Famine Ireland, FST could in theory increase, decrease, or remain the same over short intervals of time. Overall, the Great Famine appears to have had minimal impact on the genetic structure of Ireland on a regional level. Comparison with studies focusing on local genetic structure shows the opposite. It appears that the level of genetic impact depends strongly on the level of analysis; local populations are affected to a greater extent by demographic shifts than regional populations. We also provide formulas for the standard errors of FST from metric traits and related statistics.

Adolescent↗

[The study of the distribution of Chinese surnames and the diversity of genetic population structure in the Song dynasty].

Surname in China, as a cultural genetic factor, is a very huge and remarkable human population study resource. The transmission feature of surname has been proved to be similar to that of the genetic markers on Y chromosome of males. It, therefore, has been applied in the population genetic studies since 1965's. In the present study, we have analyzed a group of Chinese surname data of the Song dynasty (AD. 960-1179). The distribution of the present surname data is corresponded with the Karlin-McGregor's neutral allele model. The surname abundance alpha and the migration rate parameter v in the Song dynasty in 16 provincial regions reflected degrees of migration and admixture at that time. Surname phylogenetic dendrogram analysis demonstrated that the Han Chinese had been segregated into North and South two parts in Song dynasty of 1000 years ago. Wuyi and Nanling Mountains divided Northern and Southern Han populations into the two major parts of Han Chinese. The results also showed that the surname distribution of Song dynasty 1000 years ago was quite similar to the present model. The 100 high frequency surnames in Song dynasty were well corresponded with the current surname distribution. This phenomenon suggests that Chinese surnames have been steadily transmitted from ancient to the present. The present study improved that the Chinese surname is a very important genetic resource for the studies of structure of the Chinese populations, migration, and affinities among different populations.

China↗

Genetic covariance structure of growth in the salamander Ambystoma macrodactylum.

The size of an organism at any point during ontogeny often has fitness consequences through either direct selection on size or through selection on size-related morphological, performance, or life history traits. However, the evolutionary response to selection on size across ontogeny (a growth trajectory) may be limited by genetic correlations across ages. Here we characterize the phenotypic and genetic covariance structure of length and mass growth trajectories in a natural population of larval Ambystoma macrodactylum using function-valued quantitative genetic analyses and principal component decomposition. Most of the phenotypic and genetic variation in both growth trajectories appears to be confined to a single principal component describing a pattern of positive covariation among sizes across all ages. Higher order principal components with no significant associated genetic variation were identified for both trajectories, suggesting that evolution towards certain patterns of negative covariation between sizes across ages is constrained. The well-characterized positive relationship between size at metamorphosis and fitness in pond-breeding amphibians predicts that the across-age covariance structure will strongly limit evolution only if there is negative selection on size prior to metamorphosis. The pattern of genetic covariation observed in this study is similar to that observed in other vertebrate taxa, indicating that size may often be highly genetically and phenotypically integrated across ontogeny. Additionally, we find that phenotypic and genetic analyses of growth trajectories can yield qualitatively similar patterns of covariance structure.

Animals↗

A study of Cryptosporidium parvum genotypes and population structure.

Genetic evidence for the occurrence of two Cryptosporidium parvum subgroups is presented. This evidence is based on restriction fragment length polymorphism analysis of several independent loci. Sequence analysis of the beta-tubulin intron revealed additional polymorphism. The stability of the genetic profiles following passage of C. parvum isolates between different hosts was investigated.

Animals↗

Genetic variation and migration in the Mexican free-tailed bat (Tadarida brasiliensis mexicana).

Incomplete lineage sorting can genetically link populations long after they have diverged, and will exert a more powerful influence on larger populations. The effects of this stochastic process can easily be confounded with those of gene flow, potentially leading to inaccurate estimates of dispersal capabilities or erroneous designation of evolutionarily significant units (ESUs). We have used phylogenetic, population genetic, and coalescent methods to examine genetic structuring in large populations of a widely dispersing bat species and to test hypotheses concerning the influences of coalescent stochasticity vs. gene flow. The Mexican free-tailed bat, Tadarida brasiliensis mexicana, exhibits variation in both migratory tendency and route over its range. Observations of the species' migratory behaviour have led to the description of behaviourally and geographically defined migratory groups, with the prediction that these groups compose structured gene pools. Here, we used mtDNA sequence analyses coupled with existing information from allozyme, banding, and natural history studies to evaluate hypotheses regarding the relationship between migration and genetic structure. Analyses of molecular variance revealed no significant genetic structuring of behaviourally distinct migratory groups. Demographic analyses were consistent with population growth, although the timing of population expansion events differs between migratory and nonmigratory populations. Hypotheses concerning the role of gene flow vs. incomplete lineage sorting on these data are explored using coalescent simulations. Our study demonstrates the importance of accounting for coalescent stochasticity in formulating phylogeographical hypotheses, and indicates that analyses that do not take such processes into account can lead to false conclusions regarding a species' phylogeographical history.

Analysis of Variance↗

Structural and genetic diversity of group B streptococcus capsular polysaccharides.

Group B Streptococcus (GBS) is an important pathogen of neonates, pregnant women, and immunocompromised individuals. GBS isolates associated with human infection produce one of nine antigenically distinct capsular polysaccharides which are thought to play a key role in virulence. A comparison of GBS polysaccharide structures of all nine known GBS serotypes together with the predicted amino acid sequences of the proteins that direct their synthesis suggests that the evolution of serotype-specific capsular polysaccharides has proceeded through en bloc replacement of individual glycosyltransferase genes with DNA sequences that encode enzymes with new linkage specificities. We found striking heterogeneity in amino acid sequences of synthetic enzymes with very similar functions, an observation that supports horizontal gene transfer rather than stepwise mutagenesis as a mechanism for capsule variation. Eight of the nine serotypes appear to be closely related both structurally and genetically, whereas serotype VIII is more distantly related. This similarity in polysaccharide structure strongly suggests that the evolutionary pressure toward antigenic variation exerted by acquired immunity is counterbalanced by a survival advantage conferred by conserved structural motifs of the GBS polysaccharides.

Bacterial Capsules↗

Scheduling of water distribution system rehabilitation using structured messy genetic algorithms.

A methodology is presented for the optimal design and scheduling of investment for the rehabilitation of water distribution networks. Based on the evolutionary programming technique known as Structured Messy Genetic Algorithms, the methodology utilizes a multi-objective formulation which improves the evolutionary process and provides nondominated optimal solutions over a range of costs and benefits. The model is applied to an example-a small artificial network of fifteen pipes. The effects on the optimal solutions of varying parameters such as interest rate and inflation rate are also investigated.

Algorithms↗

Microsatellite genetic variation in small and isolated populations of Magnolia sieboldii ssp. japonica.

Magnolia sieboldii ssp. japonica, distributed mainly in western Japan, is restricted to high elevation areas (1000-2000 m above sea level) and usually forms small isolated populations. Four microsatellite loci were assayed for 19 populations from six regions spanning the range of distribution, and the levels and distribution of genetic variation were estimated. All four loci were variable, with a total of 39 alleles, but the overall level of microsatellite genetic variation was low, especially compared with a related species, M. obovata. Genetic structure in M. sieboldii was characterised by low intrapopulational genetic variation (A = 3.74 and H(o) = 0.366 on average) and high genetic differentiation even among regional populations. Highly significant isolation-by-distance (IBD) models at the short distance were detected. Genetic drift and limited gene flow was considered to be important in determining the genetic structure within regions. Total genetic differentiation was remarkably high (F(ST) = 0.488 and R(ST) = 0.538), suggesting genetic barriers among regions. Neighbour-joining dendrograms relating the 19 populations, and further analysis on the IBD models, revealed that a stepwise mutation model was more suited than an infinite allele model to explain the genetic differentiation among regions. It is suggested that mutation at microsatellite loci might be influential in generating the genetic differentiation among regions. These results showed the potential of hypervariable microsatellite loci to evaluate the effects of genetic drift and population isolation within regions, and to detect genetic distinctiveness, in spite of the loss of overall genetic variation in M. sieboldii.

DNA Primers↗

Molecular epidemiology of pneumococcal colonization in response to pneumococcal conjugate vaccination in children with recurrent acute otitis media.

A randomized double-blind trial with a 7-valent pneumococcal conjugate vaccine was conducted in The Netherlands among 383 children, aged 1 to 7 years, with a history of recurrent acute otitis media. No effect of vaccination on the pneumococcal colonization rate was found. However, a shift in serotype distribution was clearly observed (R. Veenhoven et al., Lancet 361:2189-2195, 2003). We investigated the molecular epidemiology of 921 pneumococcal isolates retrieved from both the pneumococcal vaccine (PV) and control vaccine (CV) groups during the vaccination study. Within individuals a high turnover rate of pneumococcal restriction fragment end labeling genotypes, which was unaffected by vaccination, was observed. Comparison of the genetic structures before and after completion of the vaccination scheme revealed that, despite a shift in serotypes, there was clustering of 70% of the pneumococcal populations. The remaining isolates (30%) were equally observed in the PV and CV groups. In addition, the degree of genetic clustering was unaffected by vaccination. However, within the population genetic structure, nonvaccine serotype clusters with the serotypes 11, 15, and 23B became predominant over vaccine-type clusters after vaccination. Finally, overall pneumococcal resistance was low (14%), and, albeit not significant, a reduction in pneumococcal resistance as a result of pneumococcal vaccination was observed. Molecular surveillance of colonization in Dutch children shows no effect of pneumococcal conjugate vaccination on the degree of genetic clustering and the genetic structure of the pneumococcal population. However, within the genetic pneumococcal population structure, a clear shift toward nonvaccine serotype clusters was observed.

Acute Disease↗

Isolation by distance in a continuous population: reconciliation between spatial autocorrelation analysis and population genetics models.

Analysis of the spatial genetic structure within continuous populations in their natural habitat can reveal acting evolutionary processes. Spatial autocorrelation statistics are often used for this purpose, but their relationships with population genetics models have not been thoroughly established. Moreover, it has been argued that the dependency of these statistics on variation in mutation rates among loci strongly limits their interest for inferential purposes. In the context of an isolation by distance process, we describe relationships between a descriptor of the spatial genetic structure used in empirical studies, Moran's I statistic and population genetics parameters. In particular, we point out that, when Moran's I statistic is used to describe correlation in allele frequencies at the individual level, it provides an estimator of Wright's coefficient of relationship. We also show that the latter parameter, as a descriptor of genetic structure, is not influenced by selfing rate or ploidy level. Under specific finite population models, numerical simulations show that values of Moran's I statistic can be predicted from analytical theory. These simulations are also used to estimate the time taken to approach a structure at equilibrium. Finally, we discuss the conditions under which spatial autocorrelation statistics are little influenced by variation in mutation rates, so that they could be used to estimate gene dispersal parameters.

Genetics, Population↗

[Peptide thermostable enterobacterial toxins (genetic control, structure, mechanism of action, testing)].

The structure and functional specificity of thermostable toxins, their genetic determination, mechanisms of action and testing are reviewed. Amino acid sequences of the peptide toxins with the common amino acid residues on the C-end of their molecules are presented as well as the sequences of the functional groups underlying the biological activity. The data on the structure of precursors of enterotoxins, the genetic control of toxin production and location of the est-genes in the genome of bacteria are demonstrated. The nature of receptors binding enterotoxins, their effect on the guanylate-cyclase system are also described. The possibility of enterotoxins testing by different techniques (genetic, biological, immunological) are discussed.

Amino Acid Sequence↗

Genetic evidence against panmixia in the European eel.

The panmixia hypothesis--that all European eel (Anguilla anguilla) migrate to the Sargasso Sea for reproduction and comprise a single, randomly mating population--is widely accepted. If true, then this peculiar life history strategy would directly impact the population genetics of this species, and eels from European and north African rivers should belong to the same breeding population through the random dispersal of larvae. To date, the panmixia hypothesis has remained unchallenged: genetic studies realized on eel's mitochondrial DNA failed to detect any genetic structure; and a similar lack of structure was found using allozymes, with the exception of clinal variation imposed by selection. Here we have used highly polymorphic genetic markers that provide better resolution to investigate genetic structure in European eel. Analysis of seven microsatellite loci among 13 samples from the north Atlantic, the Baltic Sea and the Mediterranean Sea basins reveals that there is global genetic differentiation. Moreover, pairwise Cavalli-Sforza and Edwards chord distances correlate significantly with coastal geographical distance. This pattern of genetic structure implies non-random mating and restricted gene flow among eels from different sampled locations, which therefore refute the hypothesis of panmixia. Consequently, the reproductive biology of European eel must be reconsidered.

Animals↗

Large artery stiffness: structural and genetic aspects.

1. Large artery stiffness is a principal determinant of pulse pressure and both are related to cardiovascular mortality independently of other major risk factors. A clearer understanding of the structural and genetic processes that contribute to large artery properties may provide novel approaches to therapy. 2. Age, atherosclerosis and gender are three important factors that contribute to large artery stiffening. Each influences the artery elastic matrix and its relationship to medial smooth muscle cells. Genetic and hormonal modulation of the extracellular matrix proteins and their regulators, including matrix metalloproteinases (MMPs), may account for some interindividual differences. 3. In a study of 213 healthy individuals and 105 patients with coronary artery disease (CAD), we examined whether stromelysin-1 (MMP-3) genotype, determined by the 5A/6A promoter polymorphism, influences large artery stiffening. In healthy individuals, the 5A/5A genotype was linked with stiffer large arteries and higher systolic blood pressure compared with other genotypes. 4. Genetic variation in the extracellular matrix protein fibrillin-1, using a pentanucleotide repeat polymorphism, was assessed as a potential determinant of large artery stiffness in patients with CAD. The 2-3 genotype was associated with stiffer large arteries, higher pulse pressure and more severe CAD than other genotypes. 5. Females experience a greater increase in large artery stiffness with age than males, with a time-course suggestive of sex steroid modulation. The mechanisms mediating such gender differences have not been established, but the known regulatory role of sex steroids with respect to MMPs likely contributes. 6. The demonstration that genetic and hormonal modulation of extracellular matrix components and MMPs contributes to age, atherosclerotic and gender-related differences in large artery mechanical properties suggests these proteins may be important targets for therapy.

Age Factors↗

Multi-resistant Gram-negative bacilli: from epidemics to endemics.

PURPOSE OF REVIEW: Infections due to multi-drug resistant Gram-negative bacilli represent a worrying situation for the management of hospitalized patients. In addition, these bacteria are increasingly involved in epidemics throughout the world. This review focuses on recent data that may help to understand the emergence and dissemination of multi-drug resistant bacilli and the current trend from epidemic to endemic situations. RECENT FINDINGS: Well-established clones enhance their resistance phenotype by the acquisition of new resistant genes, via gene capture genetic units (plasmids, transposons or integrons), thus facilitating the co-selective process under different antimicrobial selective pressures and therefore the long-term persistence of organisms in selective environments. Not only resistant bacterial clones are selected, but also their genetic structures carrying resistance genes. Therefore, current epidemiology of multi-drug resistant bacilli is not only focused on bacterial clones but also on any kind of resistance gene capture units. In this scenario a multiclonal population structure of bacterial organisms corresponds to a collection of different strains sharing resistance genes carried by horizontally transferred genetic structures. As different strains tend to prefer different environments, this concept helps understand why the epidemiology of multi-drug resistant Gram-negative bacilli is moving from epidemics to endemics. SUMMARY: The emergence and spread of multi-drug resistant bacilli in the nosocomial setting should be understood in terms of a complex interplay of bacterial clonality, resistance genes and genetic structures promoting rapid dissemination of antimicrobial resistance. Intervention strategies in the forthcoming scenario should identify existing epidemic and/or endemic situations involving clonal organisms or resistance genes carried by epidemic gene capture units.

Cross Infection↗

No apparent reduction of gene flow in a hybrid zone between the West and North European karyotypic groups of the common shrew, Sorex araneus.

The common shrew, Sorex araneus, exhibits an unusually high level of karyotypic variation. Populations with identical or similar karyotypes are defined as chromosome races, which are, in turn, grouped into larger evolutionary units, karyotypic groups. Using six microsatellite markers, we investigated the genetic structure of a hybrid zone between the Sidensjö and Abisko chromosome races, representatives of two distinct karyotypic groups believed to have been separated during the last glacial maximum, the West European karyotypic group (western group) and the North European karyotypic group (northern group), respectively. Significant FST values among populations suggest some weak genetic structure. All hierarchical levels show similar levels of genetic differentiation, equivalent to levels of genetic structure in several intraracial studies of common shrew populations from central Europe. Notably, genetic differentiation was of the same order of magnitude between and within karyotypic groups. Although the genetic differentiation was weak, the correlation between genetic and geographical distance was positive and significant, suggesting that the genetic variation observed between populations is a function of geographical distance rather than racial origin. Hence, considerable chromosomal differences do not seem to prevent extensive gene flow.

Animals↗

Development of microsatellite markers for Japanese scallop (Mizuhopecten yessoensis) and their application to a population genetic study.

The Japanese scallop (Mizuhopecten yessoensis) is one of the main fishery products in Japan, but with the expansion of culture operations of the Japanese scallop, various problems have been encountered including high mortality, poor growth, poor seed production, and so on. Moreover, there is concern that many years of cultivation may have affected the genetic structure of the scallop population. To approach these problems and concerns, we developed microsatellite markers as a molecular tool for population genetic studies. By using 4 microsatellite markers as well as a mitochondrial marker, we investigated the genetic structure of samples from the islands of Hokkaido (14 populations) and Honshu (Tohoku, 3 populations) in Japan, and south Primorye (4 populations) in Russia. All the populations sampled had high genetic diversity (average expected heterozygosity, 0.7011 to 0.7622; haplotype diversity, 0.6090 to 0.8848), and almost all showed a tendency of homozygote excess, which was significant in 2 populations. Hierarchical analysis of molecular variance tests based on the microsatellite and mitochondrial markers indicated that the 3 geographic regions were genetically divergent from one another, with little evidence of divergence within regions. Homogeneity in allele frequency distributions between natural and cultured scallops and allele frequency stability over a period of 2 decades indicated that the culturing operations have probably not had a substantial effect on the genetic structure of the populations.

Animals↗

Molecular epidemiology of Cucumber mosaic virus and its satellite RNA.

Molecular analysis of viral isolates can yield information that facilitates an understanding of virus epidemiology and has been termed molecular epidemiology. This approach has only recently been applied to plant viruses. Results on the molecular epidemiology of Cucumber mosaic virus (CMV) and its satellite RNA (satRNA) in Spain, where CMV is endemic in vegetable crops are presented here. To characterise the genetic structure of CMV populations, c. 300 isolates, representing 17 outbreaks (i.e. sub-populations) in different crops, regions and years, were compared. Genetic analyses of CMV isolates were done by ribonuclease protection assay of cRNA probes representing RNA1, RNA2 and the two open reading frames in RNA3. All isolates belonged to one of three genetic types: Sub-group II and two types of Sub-group I. The genetic structure of the 17 sub-populations varied randomly, without correlation with location, year, or host plant species. Thus, CMV in Spain shows a metapopulation structure with local extinction and random recolonisation from local or distant virus reservoirs. The frequency of mixed infections and of new genetic types generated by reassortment of genomic segments or by recombination was also estimated. Results indicate that heterologous genetic combinations are not favoured. About 30% of CMV isolates were supporting a satRNA. The frequency of CMV isolates with a satRNA differed for each sub-population, being c. 1 in eastern Spain in 1990 and decreasing to c. 0 in distant regions and in subsequent years. Molecular analyses of CMV-satRNA isolates show high genetic diversity, due both to the accumulation of point mutations and to recombination. The CMV-satRNA population is a single, unstructured one. Thus, the CMV-satRNA population has a genetic structure and dynamics different from those of its helper virus. This indicates that CMV-satRNA has spread epidemically on the extant virus population from an original reservoir in eastern Spain. The relevance of these results for the control of CMV infections is discussed.

Cucumber Mosaic Virus Satellite↗