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PubMed1996

Genetic variation in the population of Ibiza (Spain): genetic structure, geography, and language.

A sample of 203 individuals from Ibiza (Balearic Islands, Spain) were tested for blood group and serum protein genetic variation and compared with other circum-Mediterranean populations. Allele frequencies were calculated for the following blood group and serum systems: ABO, Rh, MNSs, P, Lewis, Duffy, Kell, ORM, GC, TF, PI, and HP. The allele frequencies from Ibiza were compared with those from other Balearic Islands (Majorca and Minorca) and with related European and North African groups using an assortment of analytical methods (genetic distances, R matrix analysis, and Mantel tests). R matrix analysis revealed that Ibiza is genetically different from the other Balearic populations and, because of gene flow from Spain, clusters with European groups. The level of genetic microdifferentiation of the Mediterranean populations, measured by RST (average of the R matrix diagonal elements, rii), is 0.028. An examination of the relationship between genetic, geographic, and linguistic distances by Mantel tests revealed that genetic distances are significantly correlated with linguistic distances, whereas the genetic distances are not significantly correlated with geographic distances. The plot of mean per locus heterozygosity versus the genetic distance from the centroid of distribution revealed that all three Balearic Islands have experienced considerable gene flow but that Ibiza has been most affected by the action of stochastic processes.

Blood Group Antigens↗
PubMed2025

Genetic structure and demographic history of house mice in western Europe inferred using whole-genome sequences.

The western house mouse, Mus musculus domesticus, is a human commensal and an outstanding model organism for studying a wide variety of traits and diseases. However, we have few genomic resources for wild mice and only a rudimentary understanding of the demographic history of house mice in Europe. Here, we sequenced 59 whole genomes of mice collected from England, Scotland, Wales, Guernsey, northern France, Italy, Portugal and Spain. We combined this dataset with 24 previously published sequences from southern France, Germany and Iran and compared patterns of population structure and inferred demographic parameters for house mice in western Europe to patterns seen in humans. Principal component and phylogenetic analyses identified three genetic clusters in western European mice. Admixture and f-branch statistics identified historical gene flow between these genetic clusters. Demographic analyses suggest a shared history of population bottlenecks prior to 20 000 years ago. Estimated divergence times between populations of house mice from western Europe ranged from 1500 to 5500 years ago, in general agreement with the zooarchaeological record. These results correspond well with key aspects of contemporary human population structure and the history of migration in western Europe, highlighting the commensal relationship of this important genetic model.

Animals↗
PubMed2006

Population genetic structuring in Acanthopagrus butcheri (Pisces: Sparidae): does low gene flow among estuaries apply to both sexes?

Acanthopagrus butcheri completes its entire life history within estuaries and coastal lakes of southern Australia, although adults occasionally move between estuaries via the sea. Consequently, it is expected that populations of A. butcheri in different estuaries will be genetically distinct, with the magnitude of genetic divergence increasing with geographic isolation. However, previous genetic studies of A. butcheri from southeast Australia yielded conflicting results; allozyme variation exhibited minimal spatial structuring (theta = 0.012), whereas mitochondrial DNA distinguished the majority of populations analyzed (theta = 0.263) and genetic divergence was positively correlated with geographic isolation. This discrepancy could reflect high male gene flow, which impacts nuclear but not mitochondrial markers. Here we estimated allele frequencies at five nuclear microsatellite loci across 11 southeast Australian populations (595 individuals). Overall structuring of microsatellite variation was weaker (theta = 0.088) than that observed for mitochondrial DNA, but was able to distinguish a greater number of populations and was positively correlated with geographic distance. Therefore, we reject high male gene flow and invoke a stepping-stone model of infrequent gene flow among estuaries for both sexes. Likewise, management of A. butcheri within the study range should be conducted at the scale of individual or geographically proximate estuaries for both sexes. The lack of allozyme structuring in southeast Australia reflects either the large variance in structuring expected among loci under neutral conditions and the low number of allozymes surveyed or a recent colonization of estuaries such that some but not all nuclear loci have approached migration-drift equilibrium.

Animals↗
PubMed2005

Genetic structure of a Cuban population based on nine short tandem repeat loci.

Cuba is a multiethnic and multiracial society. Here we describe the genetic variation of a sample of the Cuban population, which include the three most common racial groups, Caucasians, Negroids and Mestizos, by means of a set of nine microsatellites (HUMTH01, HUMTPOX, HUMCFS1PO, HUMVWA, HUMFESFPS, HUMF13A, HUMF13B, HUMLPL and HUMHPRTB). The analysis presented here indicates that these STR loci are highly informative for forensic purposes. The genetic data on the major racial groups is in good agreement with current demographic tendencies and with historic events that took place during the formation of the Cuban population.

Cuba↗
PubMed1998

The roles of the bacteriophage T4 r genes in lysis inhibition and fine-structure genetics: a new perspective.

Seldom has the study of a set of genes contributed more to our understanding of molecular genetics than has the characterization of the rapid-lysis genes of bacteriophage T4. For example, T4 rII mutants were used to define gene structure and mutagen effects at the molecular level and to help unravel the genetic code. The large-plaque morphology of these mutants reflects a block in expressing lysis inhibition (LIN), the ability to delay lysis for several hours in response to sensing external related phages attacking the cell, which is a unique and highly adaptive attribute of the T4 family of phages. However, surprisingly little is known about the mechanism of LIN, or how the various r genes affect its expression. Here, we review the extensive old literature about the r genes and the lysis process and try to sort out the major players affecting lysis inhibition. We confirm that superinfection can induce lysis inhibition even while infected cells are lysing, suggesting that the signal response is virtually instantaneous and thus probably the result of post-translational regulation. We identify the rI gene as ORF tk.-2, based on sequence analysis of canonical rI mutants. The rI gene encodes a peptide of 97 amino acids (Mr = 11.1 kD; pI = 4.8) that probably is secreted into the periplasmic space. This gene is widely conserved among T-even phage. We then present a model for LIN, postulating that rI is largely responsible for regulating the gpt holin protein in response to superinfection. The evidence suggests that the rIIA and B genes are not directly involved in lysis inhibition; rather, when they are absent, an alternate pathway for lysis develops which depends on the presence of genes from any of several possible prophages and is not sensitive to lysis inhibition.

Amino Acid Sequence↗
PubMed2003

Spatial ecological and genetic structure of a mixed population of sexual diploid and apomictic triploid dandelions.

Ecological differentiation is widely seen as an important factor enabling the stable coexistence of closely related plants of different ploidy levels. We studied ecological and genetic differentiation between co-occurring sexual diploid and apomictic triploid Taraxacum section Ruderalia by analysing spatial patterns both in the distribution of cytotypes and in the distribution of genetic variation within and between the cytotypes. A significant relationship between ploidy level and elevation was found. This mode of ecological differentiation however, was not sufficient to explain the significant spatial structure in the distribution of diploids and triploids within the population. Strong congruence was found between the spatial genetic patterns within the diploids and within the triploids. We argue that this congruence is an indication of gene flow between neighbouring plants of different ploidy levels.

Demography↗
PubMed2004

Evidence for fine-scale genetic structure and estuarine colonisation in a potential high gene flow marine goby (Pomatoschistus minutus).

Marine fish seem to experience evolutionary processes that are expected to produce genetically homogeneous populations. We have assessed genetic diversity and differentiation in 15 samples of the sand goby Pomatoschistus minutus (Pallas, 1770) (Gobiidae, Teleostei) from four major habitats within the Southern Bight of the North Sea, using seven microsatellite and 13 allozyme loci. Despite its high dispersal potential, microsatellite loci revealed a moderate level of differentiation (overall F(ST)=0.026; overall R(ST)=0.058). Both hierarchical analysis of molecular variance and multivariate analysis revealed significant differentiation (P<0.01) between estuarine, coastal and marine samples with microsatellites, but not with allozymes. Comparison among the different estimators of differentiation (F(ST) and R(ST)) pointed to possible historical events and contemporary habitat fragmentation. Samples were assigned to two breeding units in the estuary and coastal region. Despite this classification, there were indications of a complex and dynamic spatiotemporal structure, which is, most likely, determined by historical events and local oceanic currents.

Alleles↗
PubMed2004

Genetic structure and population dynamics of Xanthomonas axonopodis pv. manihotis in Colombia from 1995 to 1999.

Restriction fragment length polymorphisms (RFLPs) were used to study the population genetics and temporal dynamics of the cassava bacterial pathogen Xanthomonas axonopodis pv. manihotis. The population dynamics were addressed by comparing samples collected from 1995 to 1999 from six locations, spanning four different edaphoclimatic zones (ECZs). Forty-five different X. axonopodis pv. manihotis RFLP types or haplotypes were identified between 1995 and 1999. High genetic diversity of the X. axonopodis pv. manihotis strains was evident within most of the fields sampled. In all but one site, diversity decreased over time within fields. Haplotype frequencies significantly differed over the years in all but one location. Studies of the rate of change of X. axonopodis pv. manihotis populations during the cropping cycle in two sites showed significant changes in the haplotype frequencies but not composition. However, variations in pathotype composition were observed from one year to the next at a single site in ECZs 1 and 2 and new pathotypes were described after 1997 in these ECZs, thus revealing the dramatic change in the pathogen population structure of X. axonopodis pv. manihotis. Disease incidence was used to show the progress of cassava bacterial blight in Colombia during the 5-year period in different ecosystems. Low disease incidence values were correlated with low rainfall in 1997 in ECZ 1.

Bacterial Proteins↗
PubMed1990

LINKERS: a simulation programming system for generating populations with genetic structure.

Significant features are described of a Monte Carlo simulation system, LINKERS, that generates nuclear family data conforming to one locus and two loci genetic models. Software engineering techniques help to produce a user friendly environment for studies of genetic ascertainment. LINKERS' 39 code modules are maintained and optimized using VAXset. Within a VAX/VMS workstation environment LINKERS generates a useful population of 10,000 families in 1 min. An example is presented to illustrate the use of LINKERS. Generated data were analysed using the segregation program POINTER. Likelihood ratio tests showed the effects of multiple alleles, gene frequency and incorrect specification of disease prevalence.

Computer Simulation↗
PubMed2006

Genetic structure of the dopamine receptor D4 gene (DRD4) and lack of association with schizophrenia in Japanese patients.

In order to investigate the contribution of genetic variation in the human dopamine receptor D4 gene (DRD4) to the risk of developing schizophrenia, we carried out a genetic analysis of 27 polymorphisms in 216 schizophrenic patients and 243 healthy controls from the Kyushu region of Japan. Twenty-two single nucleotide polymorphisms (SNPs) and five insertion/deletion polymorphisms were analyzed in this study, including four novel SNPs and a novel mononucleotide repeat. Linkage disequilibrium (LD) and haplotype analyses reveal weak LD across the DRD4 gene. In univariate analysis female individuals with allele -521C had a higher risk for schizophrenia. However, this finding was not significant after correction for multiple hypothesis testing. No other polymorphisms or haplotypes differed between schizophrenic patients and controls. Likewise, multivariate analyses did not reveal any statistically significant associations.

Adolescent↗
PubMed2006

Population genetic structure of Anopheles maculatus in Thailand.

Anopheles (Cellia) maculatus Theobald is a major malaria vector in southern Thailand and peninsular Malaysia, and previous population genetic studies suggested that mountain ranges act as barriers to gene flow. In this study, we examine the genetic variance among 12 collections of natural populations in southern Thailand by analyzing 7 microsatellite loci. Based on analysis of molecular variance (AMOVA), three geographic populations of An. maculatus are suggested. The southern population exists in western Thailand north of 12 degrees north latitude. Mosquitoes to the south fall into two genetic populations: 1) the middle southern collections located on the west side of the Phuket mountain range between 8 degrees and 10 degrees north latitude, and 2) the southern collections located on the east of the Phuket mountain range located between approximately 6.5 degrees and 11.5 degrees north latitude. AMOVA revealed significant genetic differentiation between northern and middle southern and southern populations. The middle southern population was moderately differentiated from the southern population. Furthermore, gene flow was restricted between proximal collections located on different sides of the Phuket mountain range. Collections separated by 50 km exhibited restriction of gene flow when separated by geographic barriers, whereas greater gene flow was evident among collections 650 km apart but without geographic barriers.

Animals↗
PubMed2000

Genetic structure of Native Andean populations from Argentina inhabiting different altitudes.

On the basis of erythrocyte and serum protein polymorphisms, we investigated the level of genetic differentiation among 3 Argentinian native populations sharing ethnic and morphological characteristics but inhabiting different altitudes in the Andes. Of the 15 loci studied, 8 are monomorphic. Phenotype distribution of the polymorphic systems are in agreement with Hardy-Weinberg equilibrium, except for malic enzyme (MOD), where a silent allele was found. The 2 highland populations exhibit a close genetic similarity, probably as a result of intense gene flow. The lowland population shows reduced genetic diversity, which suggests the influence of stochastic phenomena such as the founder effect.

Alleles↗