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Results for “variable gene flow”

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PubMed1989

Limited diversity of T-cell receptor gamma-chain expression of murine Thy-1+ dendritic epidermal cells revealed by V gamma 3-specific monoclonal antibody.

To study the origin of and the degree of T-cell antigen receptor (TCR) diversity of Thy-1+ dendritic epidermal cells (Thy-1+ dECs) in mice, we have developed a monoclonal antibody (mAb 536) to the gamma delta TCR. mAb 536 binds to and stimulates interleukin 2 secretion from Thy-1+ dEC but not cells that express TCR composed of alpha and beta chains. mAb 536 precipitates CD3-associated gamma and delta chains from lysates of radioiodinated Thy-1+ dECs. Analysis of a panel of hybridomas that express gamma delta TCR indicated that mAb 536 defines an epitope of the variable region (V gamma 3) gene product. Flow cytometric analysis revealed that expression of V gamma 3 in the adult mouse is restricted to cells in the epidermis, where essentially all Thy-1+ cells are V gamma 3+. The majority of CD3+ cells in the 14-day fetal thymus also express V gamma 3. These results indicate that the T-cell complement in epidermis are cells that express gamma delta TCR and that the diversity of antigens recognized by the cells might be restricted by the use of a single V gamma gene segment. Finally, the data raise the intriguing possibility that Thy-1+ dECs may arise from precursors that are among the first to emerge from the developing thymus. This suggests that V gene usage during thymocyte development is highly regulated and has important consequences on the tissue localization and function of the emerging cells. As in other developing tissues, it appears that programmed and transient gene expression determines the fate of the emerging cells.

Animals↗

PubMed2002

Gene flow among Calomys musculinus (Rodentia, Muridae) populations in Argentina.

Calomys musculinus is a Sigmodontinae rodent inhabiting periodically disturbed habitats in the central eastern plains of Argentina. It is the natural reservoir host of Junin virus, the etiological agent of Argentine Hemorrhagic Fever (AHF). In order to analyze the levels of gene flow among populations of this species, allozymic variability at 26 loci was studied in 291 individuals from the endemic zone of AHF and localities outside it. All populations showed high levels of polymorphism (He between 0.107 and 0.144; P95% between 38 and 54%). Individual loci f values were in most cases negative, although not significantly different from zero. Mean genetic differentiation among populations was low, but statistically significant (theta = 0.020; P < 0.01). There was no correlation between genetic and geographic distances between pairs of populations, and scatter of the pairwise points suggests that, at the regional scale, genetic drift is more influential than gene flow. This result can be interpreted as indicative of a relatively recent expansion of C. musculinus habitat and restricted on-going gene flow, which would be compatible with a relatively slow expansion rate of AHF.

Alleles↗

PubMed1995

Identification of malignant cells in multiple myeloma bone marrow with immunoglobulin VH gene probes by fluorescent in situ hybridization and flow cytometry.

Because it has been difficult to identify and separate malignant cells in human lymphoid malignancies, we have developed a flow cytometry-based fluorescent in situ hybridization (FISH) technique using immunoglobulin (Ig) heavy chain variable region (VH) gene probes. After obtaining the specific VH gene sequence expressed by the multiple myeloma IM-9 cell line and the malignant cells in five multiple myeloma patients, sense and antisense biotinylated single-stranded RNA probes were prepared by transcription from the malignant clone's VH DNA sequences. The cells from the IM-9 cell line and from the mononuclear bone marrow cells of multiple myeloma patients were fixed, hybridized with the above biotinylated RNA probes, incubated with streptavidin-phycoerythrin, and analyzed by FACS analysis. The myeloma cells stained positive with their own specific antisense VH biotinylated RNa probes, whereas sense and irrelevant antisense biotinylated probes demonstrated only background staining. Dilutional concentrations of the IM-9 cell line with normal bone marrow cells were also accurately quantitated by this procedure. The application of this technique will allow a more accurate assessment of tumor burden in patients with multiple myeloma and should permit an accurate method of tumor cell purification for clinical as well as biological studies. Furthermore, this technological advance should be equally effective at identifying specific VH gene-expressing cells in other lymphoid malignancies, as well as in nonmalignant B cell disorders.

Bacterial Proteins↗

PubMed1998

Mitochondrial control region polymorphism reveal high amount of gene flow in Fennoscandian willow tits (Parus montanus borealis).

We studied the genetic variability and differentiation of two Fennoscandian willow tit (Parus montanus borealis) populations located ca. 1000 km apart in Finland and Sweden by using the control region sequences of the mitochondrial DNA. Individual variation in the control region was extensive since all the 13 Finnish and the 12 Swedish individuals had unique haplotypes and the mean pairwise genetic distance resulted in 0.0052 (range 0.0008-0.0109). In the minimum spanning network connecting the genotypes, the two populations were completely intermingled. The mismatch distribution of the combined data set was very close to expected distribution of an expanding population. This result was supported by a significantly negative Tajima's D value. The sequence data indicate that (1) the long-term effective population size of the breeding willow tits has been large (122,000 and 110,000 females for the Finnish and the Swedish populations, respectively); and that (2) the gene exchange between distant localities is/has been extensive. Dispersal area for the Finnish females was estimated to be about 19,000-30,000 km2 and for the Swedish, 22,000-28,000 km2. Thus, the whole Fennoscandian population can be regarded as one panmictic unit, without any subdivisions to local demes. The amount of gene flow is remarkable because the willow tit has been considered a highly sedentary species. Provided that adult birds are site-tenacious, the gene flow must occur through juvenile summer dispersal, or irruptive autumn invasions, or both.

Animals↗

PubMed2003

Electrophysiology and ocular blood flow in a family with dominant optic nerve atrophy and a mutation in the OPA1 gene.

OBJECTIVE: To characterize the clinical phenotype, with emphasis on electrophysiology and blood flow measurements, of a family with dominant optic nerve atrophy and an identified mutation in the OPA1 gene. METHODS: Seven family members were examined. Ophthalmological evaluation included testing of visual acuity, ophthalmolscopy, kinetic perimetry, color vision testing, full-field electroretinography (ERG), multifocal electroretinography (MERG), and multifocal visual evoked potential (MVEP). Retrobulbar arterial blood flow and retinal capillary perfusion was measured in three patients using scanning laser Doppler flowmetry (SLDF) and color Doppler imaging techniques. PCR-SSCP and DNA sequencing determined the presence of a mutation in exon 18 of the OPA1 gene. RESULTS: The clinical characteristics varied considerably in the family. The ERG and the MERG demonstrated normal retinal function, while the MVEP was abnormal in all examined patients. Retinal and optic nerve head capillary perfusion was significantly decreased in the three patients examined with SLDF. Retrobulbar blood flow velocities were significantly decreased in the central retinal and ophthalmic arteries. In all seven examined subjects, a microdeletion (1756-1767del(12 bp)) in the OPA1 gene was identified. CONCLUSION: Patients with a mutation in the OPA1 gene have a very variable phenotype. MVEP and blood flow measurements are two new objective methods for an easier detection of this specific genetic optic nerve atrophy.

Adolescent↗

PubMed1996

Detection of CD8 T-cell expansions with restricted T-cell receptor V gene usage in infants vertically infected by HIV-1.

OBJECTIVE: To investigate the T-cell receptor (TCR) repertoire usage in infants born to mothers infected with HIV-1 in order to discern possible perturbations in TCR usage as a consequence of HIV-1 infection. DESIGN: Blood samples from five HIV-1-infected and six non-infected children born to HIV-1-seropositive mothers were collected at two to three timepoints during the first and second year of life and the TCR variable gene usage was determined. METHODS: Triple staining flow cytometry analysis using a panel of monoclonal antibodies (MAb) to TCR V alpha and V beta gene products and antibodies to CD4 and CD8 was performed. RESULTS: Frequent large expansions of CD8+ lymphocyte subpopulations bearing distinct V alpha and V beta gene products was seen in HIV-1-infected children (four out of five) but was rarely detected in uninfected children. CONCLUSION: The study demonstrated the frequent occurrence of persistent and clonal expansions of CD8+ T cells bearing distinct V alpha/V beta gene products in some HIV-1 vertically infected infants similar to those observed during primary infection in adults.

CD8-Positive T-Lymphocytes↗

PubMed2005

Phenotypic divergence despite high levels of gene flow in Galápagos lava lizards (Microlophus albemarlensis).

The extent of evolutionary divergence of phenotypes between habitats is predominantly the result of the balance of differential natural selection and gene flow. Lava lizards (Microlophus albemarlensis) on the small island of Plaza Sur in the Galápagos archipelago inhabit contrasting habitats: dense vegetation on the western end of the island thins rapidly in a transitional area, before becoming absent on the eastern half. Associated with these habitats are phenotypic differences in traits linked to predator avoidance (increased wariness, sprint speed, and endurance in lizards from the sparsely vegetated habitat). This population provides an opportunity to test the hypothesis that reduced gene flow is necessary for phenotypic differentiation. There was no evidence of any differences among habitats in allele frequencies at six out of seven microsatellite loci examined, nor was there any indication of congruence between patterns of genetic variability and the change in vegetation regime. We infer that gene flow between the habitats on Plaza Sur must be sufficiently high to overcome genetic drift within habitats but that it does not preclude phenotypic differentiation.

Analysis of Variance↗

PubMed1998

Gene expression in rod shaped cardiac myocytes, sorted by flow cytometry.

OBJECTIVE: Primary cardiac myocyte cultures are usually contaminated with variable parts of different cell types, such as fibroblasts, endothelial cells and smooth muscle cells. Thus, the objective of our study was to analyse the gene expression in a pure population. METHODS: To obtain an homogeneous population, cardiac myocytes from adult rats were fixed with ethanol and sorted by flow cytometry. This approach is suitable for isolating either single cells or up to several thousand cells. To measure the messenger ribonucleic acid (mRNA) expression of different genes at the level of a few rod-shaped myocytes, a cDNA library was created by polymerase chain reaction (PCR). RESULTS: Sorting by a fluorescence-activated cell sorter (FACS) resulted in pure rod-shaped cardiac myocytes and isolated RNA from these cells is undegraded, as shown by Northern blotting. We demonstrated both the expression of housekeeping genes, such as beta-actin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as well as the myocyte-specific transcripts, alpha-cardiac myosin heavy chain (alpha-MHC) and beta-MHC. Furthermore, we showed the induction of the immediately early gene c-fos at the level of ten sorted cells. CONCLUSIONS: This method allows one to study gene expression in different cell types within the heart, in tissue samples or to tackle the problem of heterogeneity within a cell population.

Animals↗

PubMed2001

Genetic diversity of Iberian populations of Bemisia tabaci (Hemiptera: Aleyrodidae) based on random amplified polymorphic DNA-polymerase chain reaction.

The genetic structure of six Iberian populations of the whitefly Bemisia tabaci, two of them biotype Q, one biotype B, and the other three a mixture of both, has been studied using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). A total of 336 individuals was completely discriminated by means of 234 scored bands. Separate analyses of molecular variance of haploid males and diploid females using the pairwise number of differences between haplotypes showed that biotypes contribute significantly more to the observed variability than populations within biotypes. On average, gene flow between two biotypes of the same population is lower than between populations of identical biotypes. On the basis of these results and the nondetection under natural conditions of a single hybrid, we consider that both biotypes are genetically isolated under the ecological conditions prevailing in the south Iberian Peninsula. All populations of biotype Q presented similar values of intrapopulational diversity, which were higher than the values shown by populations of biotype B.

Animals↗

PubMed2002

Postglacial dispersal of the European rabbit (Oryctolagus cuniculus) on the Iberian peninsula reconstructed from nested clade and mismatch analyses of mitochondrial DNA genetic variation.

Nested clade analysis was applied to cytochrome b restriction site data previously obtained on 20 natural populations of the European rabbit across the Iberian Peninsula to test the hypothesis of postglacial dispersal from two main refugia, one in the northeast and the other in the southwest. Apart from historical fragmentation that resulted in geographic discontinuity of two distinct mitochondrial DNA (mtDNA) clades A and B, patterns of haplotype genetic variability have been shaped mostly by restricted gene flow via isolation by distance. The distribution of tip versus interior haplotypes suggests that dispersal occurred from both the southwestern and northeastern groups. Dispersal from the southwest had a north and northwest direction, whereas from the northeast it had mostly a western and southern orientation, with subsequent overlap in a southeastern-northwestern axis across the Iberian Peninsula. The analysis of the pairwise mismatch distribution of a 179-181-bp fragment of the mtDNA control region, for seven of those populations, further supports the idea that major patterns of dispersal were in the direction of central Iberia. Additionally, rabbit populations do not show signs of any significant loss of genetic diversity in the recent past, implying that they maintained large population sizes and structure throughout the ice ages. This is congruent with the fact that the Iberian Peninsula was itself a glacial refugium during Quaternary ice ages. Nonetheless, climatic oscillations of this period, although certainly milder than in northern Europe, were sufficient to affect the range distributions of Iberian organisms.

Animals↗

PubMedDate not supplied

Extensive gene flow in human populations as revealed by protein and microsatellite DNA markers.

Population genetic studies are mainly based on the description of genetic variability and on interpopulational comparisons using genetic distance measures. The evolutionary dynamics of the populations are inferred from these parameters and accurate estimates of gene flow may be critical. The present study reevaluates the role of gene flow in human populations by different statistical methods from a number of microsatellite and protein polymorphism data. The estimated number of individuals exchanged per generation (Nm) was greater than 1 in all data sets with all statistical methods. The correlation between geographic and genetic distances suggests a pattern of isolation by distance, characteristic of demographic and genetic equilibrium conditions among populations worldwide. Thus the high values of Nm may be interpreted as a reflection of high gene flow between geographically close populations. As expected, gene flow appears to exert a pivotal role in the genetic history of humans.

Gene Frequency↗

PubMed2004

Global population genetic structure and male-mediated gene flow in the green sea turtle (Chelonia mydas): analysis of microsatellite loci.

We assessed the degree of population subdivision among global populations of green sea turtles, Chelonia mydas, using four microsatellite loci. Previously, a single-copy nuclear DNA study indicated significant male-mediated gene flow among populations alternately fixed for different mitochondrial DNA haplotypes and that genetic divergence between populations in the Atlantic and Pacific Oceans was more common than subdivisions among populations within ocean basins. Even so, overall levels of variation at single-copy loci were low and inferences were limited. Here, the markedly more variable microsatellite loci confirm the presence of male-mediated gene flow among populations within ocean basins. This analysis generally confirms the genetic divergence between the Atlantic and Pacific. As with the previous study, phylogenetic analyses of genetic distances based on the microsatellite loci indicate a close genetic relationship among eastern Atlantic and Indian Ocean populations. Unlike the single-copy study, however, the results here cannot be attributed to an artifact of general low variability and likely represent recent or ongoing migration between ocean basins. Sequence analyses of regions flanking the microsatellite repeat reveal considerable amounts of cryptic variation and homoplasy and significantly aid in our understanding of population connectivity. Assessment of the allele frequency distributions indicates that at least some of the loci may not be evolving by the stepwise mutation model.

Animals↗

PubMed2004

Low levels of allozyme variability in the threatened species Antirrhinum subbaeticum and A. pertegasii (Scrophulariaceae): implications for conservation of the species.

AIMS: This study was designed to compare levels of genetic variation and its partitioning in three related species of Antirrhinum, A. subbaeticum, A. pertegasii and A. pulverulentum, and to check the hypothesis that species with small total population size have lower levels of genetic variability than those with bigger ones. This information should contribute to the development of conservation strategies of rare endemic species of Antirrhinum. METHODS: One hundred and seventy-seven plants were screened for variability at 14 allozyme loci by means of horizontal starch gel. Parameters of genetic diversity, and its partitioning, were calculated. An indirect estimate of gene flow was based on the equation: Nm = (1 - GST)/4GST. KEY RESULTS: Genetic variabilities in A. subbaeticum and A. pertegasii were found to be the lowest known for the genus, the within-population genetic diversity being correlated with population size in both species. The distribution of genetic diversity is strikingly different among species, with 85 % of the total variation distributed among populations in A. subbaeticum, 6 % in A. pertegasii and 23 % in A. pulverulentum. Estimated levels of gene flow were negligible for A. subbaeticum (0.04), high for A. pertegasii (3.92), and substantial for A. pulverulentum (0.83). Genetic and geographic distances were negatively correlated in A. pertegasii, whereas no significant correlation was found in the other two species. CONCLUSIONS: Levels of total genetic diversity agree with the hypothesis that species with small total population size have lower levels of genetic variability than those with bigger ones. Strategies for the conservation of the species are recommended, such as preservation of natural populations and avoidance of possible causes of threat, as well as ex situ preservation of seeds, reinforcement of small populations of A. subbaeticum with plants or seeds from the same population, and avoidance of translocations among populations.

Antirrhinum↗

PubMed2005

Comparison of quantitative and molecular variation in agroforestry populations of the shea tree (Vitellaria paradoxa C.F. Gaertn) in Mali.

In this study we investigated the within- and between-population genetic variation using microsatellite markers and quantitative traits of the shea tree, Vitellaria paradoxa, an important agroforestry tree species of the Sudano-Sahelian region in Africa. Eleven populations were sampled across Mali and in northern Côte d'Ivoire. Leaf size and form and growth traits were measured in a progeny test at the nursery stage. Eight microsatellites were used to assess neutral genetic variation. Low levels of heterozygosity were recorded (1.6-3.0 alleles/locus; H(E) = 0.25-0.42) and the fixation index (F(IS) = -0.227-0.186) was not significantly different from zero suggesting that Hardy-Weinberg equilibrium is encountered in all populations sampled. Quantitative traits exhibited a strong genetic variation between populations and between families within populations. The degree of population differentiation of the quantitative traits (Q(ST) = 0.055-0.283, Q(STmean) = 0.189) strongly exceeds that in eight microsatellite loci (F(ST) = -0.011-0.142, F(STmean) = 0.047). Global and pairwise F(ST) values were very low and not significantly different from zero suggesting agroforestry practices are amplifying gene flow (Nm = 5.07). The population means for quantitative traits and the rainfall variable were not correlated, showing variation was not linked with this climatic cline. It is suggested that this marked differentiation for quantitative traits, independent of environmental clines and despite a high gene flow, is a result of local adaptation and human selection of shea trees. This process has induced high linkage disequilibrium between underlying loci of polygenic characters.

Cote d'Ivoire↗

PubMed2003

The phylogeography of dusky dolphins (Lagenorhynchus obscurus): a critical examination of network methods and rooting procedures.

We investigated the phylogeography and evolutionary history of dusky dolphins (Lagenorhynchus obscurus) using DNA sequences of the full mitochondrial cytochrome b gene in 124 individuals from the putative stocks off Peru, Argentina and Southwest Africa. While genetic differentiation within oceans is surprisingly low, there is no evidence for recent female gene flow between Atlantic and Pacific waters. Highest genetic variability in terms of sequence divergence and number of haplotypes is found in the Atlantic. Our analyses also indicate that the eastern South Pacific dusky dolphins stock should be considered a separate management unit. Given the high level of mortality experienced by the Peruvian dusky dolphin in local fishery activities, these findings have important implications for an objective management of the species. Furthermore, we analysed our mitochondrial sequence data with several widely used network estimation and rooting methods. The resulting intraspecific gene genealogies and rooting inferences exhibited substantial differences, underlying the limitations of some algorithms. Given that scientific hypotheses and management decisions depend strongly on inferred tree or network topologies, there is a clear need for a systematic comparative analysis of available methods. Finally, the present study indicates that (i) the dusky and the Pacific white-sided dolphins are sister species and (ii) not only the Westwind Drift hypothesis but also other models of dispersion are compatible with the current geographical distribution of dusky dolphins.

Animals↗

PubMed2000

Population genetics of Chrysomela tremulae: a first step towards management of transgenic Bacillus thuringiensis poplars Populus tremula x .P. tremuloides.

Many strategies have been proposed for delaying the development of insect resistance to Bacillus thuringiensis (Bt). The current paradigm for Bt resistance management is the high dose-refuge strategy. For this strategy to be successful: (i) heterozygotes must be killed in treated areas, (ii) resistant alleles must be rare (frequency < 10-3), and (iii) there must be a high level of gene flow between populations to ensure random mating. We studied gene flow within and between populations with a view to managing the resistance of Chrysomela tremulae (Coleoptera: Chrysomelidae) to new transgenic, highly toxic poplars expressing a synthetic Bt gene. In this study, we assessed the extent of gene flow in C. tremulae within and between 16 sites in France and Belgium, using allozyme markers. We found a high level of genetic variability in C. tremulae, with a mean of 0.206 +/- 0.16. There were no obvious limitations to gene flow between populations of C. tremulae over large geographical distances (several hundreds of kilometres). Nevertheless, a very low level of genetic differentiation was observed between a site located in the south of France and the sampled sites from the Centre region.

Animals↗

PubMed2000

RAPD variation among and within small and large populations of the rare clonal plant Ranunculus reptans (Ranunculaceae).

In the pre-alpine region of Europe numbers and sizes of populations of the clonal lake shore plant Ranunculus reptans have declined because of the regulation of lake water levels. We investigated genetic variation among and within 17 populations of different size (cover 1-10 000 m) in R. reptans with RAPD (random amplified polymorphic DNA) profiles. We sampled 127 rosettes in 14 populations at Lake Constance and three populations at or near Lake Como. There was significant genetic variation between plants from the two lake regions (5.9%, analysis of molecular variance [AMOVA], P < 0.001), among populations within lake regions (20.4%, P < 0.001), and within populations (73.7%, P < 0.001). Under the assumptions of Wright's island model the variation among populations corresponds to a gene flow of N(e)m = 0.70. Within the 14 Lake Constance populations we detected significant genetic variation among subpopulations separated by only a few metres (4.0% of the within-population variation; P < 0.05). Molecular variance was 24% smaller in small populations covering <100 m area than in larger ones (P < 0.03), indicating that samples from large populations were genetically more variable than samples representing comparable areas of smaller populations. We conclude that gene flow among populations is very limited and that genetic drift has caused reduced genetic variability of smaller populations. Conservation of genetic variability in R. reptans requires persistence of large and also of small populations (because of population differentiation), and it could be enhanced by increasing the size of small populations (to counter genetic drift).

Journal Article↗

PubMed1992

Effects of demographic and ethnohistorical factors on average heterozygosities of South Amerindians.

Recent investigations have shown that average within-Tupi genetic distances differ from within-Carib distances, which is possibly due to differences in effective size of the populations belonging to these two linguistic stocks of South American tribes. The aim of this paper is to verify the influence of demographic factors and of interpopulation contacts on the degree of intragroup genetic variability of 18 South American native groups (eight Carib, seven Tupi, and three Gê). The mean per locus per individual heterozygosity (Hm) was studied for seven polymorphic systems and the distance from the centroid rii on Hm was evaluated with regression analysis according to Harpending and Ward's model. Data on intergroup contacts among the populations since the end of the eighteenth century were collected from an extensive review of the ethnohistorical literature. The level of Hm of the three linguistic stocks did not differ, which suggests a homogeneous within-group variation for these groups. In addition, there was no association between gene diversity and population size. On the other hand, demographic size correlated with rii, which suggest that gene frequencies in groups of larger populations more closely resemble the average gene frequencies of native South Americans. Values of rii differed between the stocks, and the average distance from the centroid of the Carib was about 2.6 times greater than that of the Tupi, in accordance with previous genetic distance analysis. It should also be emphasized that there was an important correlation between mean heterozygosity and the degree of historical intertribal contacts. This constitutes a particularly significant finding, suggesting the basic role of intertribal gene flow of the past two centuries on the level of present genetic variability of South American tribes.

Gene Frequency↗