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Results for “Genetic Variation”

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PubMed1990

Frequency-dependent selection: the high potential for permanent genetic variation in the diallelic, pairwise interaction model.

A detailed analytic and numerical study is made of the potential for permanent genetic variation in frequency-dependent models based on pairwise interactions among genotypes at a single diallelic locus. The full equilibrium structure and qualitative gene-frequency dynamics are derived analytically for a symmetric model, in which pairwise fitnesses are chiefly determined by the genetic similarity of the individuals involved. This is supplemented by an extensive numerical investigation of the general model, the symmetric model, and nine other special cases. Together the results show that there is a high potential for permanent genetic diversity in the pairwise interaction model, and provide insight into the extent to which various forms of genotypic interactions enhance or reduce this potential. Technically, although two stable polymorphic equilibria are possible, the increased likelihood of maintaining both alleles, and the poor performance of protected polymorphism conditions as a measure of this likelihood, are primarily due to a greater variety and frequency of equilibrium patterns with one stable polymorphic equilibrium, in conjunction with a disproportionately large domain of attraction for stable internal equilibria.

Alleles↗

PubMed2002

Statistics of selectively neutral genetic variation.

Random models of evolution are instrumental in extracting rates of microscopic evolutionary mechanisms from empirical observations on genetic variation in genome sequences. In this context it is necessary to know the statistical properties of empirical observables (such as the local homozygosity, for instance). Previous work relies on numerical results or assumes Gaussian approximations for the corresponding distributions. In this paper we give an analytical derivation of the statistical properties of the local homozygosity and other empirical observables assuming selective neutrality. We find that such distributions can be very non-Gaussian.

Alleles↗

PubMed2000

Reconciling patterns of genetic variation with stream structure, earth history and biology in the Australian freshwater fish Craterocephalus stercusmuscarum (Atherinidae).

We examined the consequences of barriers, stream architecture and putative dispersal capability on levels of genetic differentiation among populations of the freshwater fish Craterocephalus stercusmuscarum. Seven polymorphic allozyme loci and sequences of a 498-bp fragment of the ATPase 6 mitochondrial DNA (mtDNA) gene were used to assess patterns of genetic variation among 16 populations from upland and lowland streams of five drainages in northern Queensland, Australia. Concordant patterns at both genetic markers revealed that there were significant levels of genetic subdivision among all populations, while an analysis of molecular variation showed that the distribution of genetic diversity was not consistent with contemporary drainage structure. There were reciprocally monophyletic mtDNA clades and fixed or large frequency differences at allozyme loci either side of instream barriers such as waterfalls. This implied barriers were effective in restricting gene flow between upland and lowland populations separated by waterfalls. However, there were two genetically distinct groups in upland areas, even within the same subcatchment, as well as high levels of genetic subdivision among lowland populations, suggesting barriers alone do not explain the patterns of genetic diversity. The data revealed a complex phylogeographic pattern, which we interpreted to be the result of one or more invasion events of independent lineages to different sections of each drainage, possibly mediated by well documented geomorphological changes. Our results highlight the importance of earth structure and history in shaping population genetic structure in stream organisms where dispersal capability may be limited, and reveal that the contemporary structure of drainages is not necessarily a good indicator of genetic relationships among populations.

Adenosine Triphosphatases↗

PubMed1994

Biomphalaria glabrata: extensive genetic variation in Brazilian isolates revealed by random amplified polymorphic DNA analysis.

To examine the extent of genetic variation in Biomphalaria glabrata, the intermediate host of Schistosoma mansoni, specimens from seven Brazilian isolates were studied. Regions of genomic DNA were amplified using short, arbitrarily selected oligonucleotide primers under low-stringency conditions (random amplified polymorphic DNAs--RAPDs) and analyzed by polyacrylamide gel electrophoresis followed by silver staining. The RAPD profiles of snails of the same isolate were relatively homogeneous, with the majority of bands being common to all individuals studied. In contrast, the profiles of snails from different isolates were quite distinct, with less than 10% of amplified DNA fragments being common to all of the specimens studied. This was found to be true irrespective of the primer, indicating that B. glabrata is remarkably genetically heterogeneous. The data are consistent with the view that genetic drift plays a major role in the genetic structure of populations of B. glabrata due to their ability to reconstitute populations from very small numbers of individuals by self-fertilization. The great variety of polymorphic genetic markers identified in this restricted survey indicates that RAPD analysis may make a major contribution to the study of the genetics of Biomphalaria.

Animals↗

PubMed1992

Genetic variation of human sex hormone-binding globulin: evidence for a worldwide bi-allelic gene.

Genetic variation of human sex hormone-binding globulin (SHBG) has been investigated on 1690 unrelated neuraminidase-treated serum samples using isoelectric focusing followed by transfer to nitrocellulose membranes and immunostaining. Three clearly distinct isoelectric focusing patterns, consistent with the expression of an autosomal genetic system, were identified. Using allele frequencies, calculated on the basis of a bi-allelic gene, an excellent agreement between observed and expected phenotype numbers was obtained in every examined population sample. Family data along with the observed distribution of the three SHBG phenotypes among racially different groups and sexes indicate that SHBG is worldwide encoded by two autosomal codominant alleles. Compared with healthy Belgian blood donors no statistically significant differences were noted for the allele frequencies among 399 patients and 70 hirsute women of Belgian origin. Evidence is also presented that the subunit produced by the variant allele (SHBG2) has a higher molecular mass than the one produced by the regular allele (SHBG1) and that the three SHBG genotypes have identical binding characteristics for 5 alpha-dihydrotestosterone.

Alleles↗

PubMed2006

Genetic variations of 13 indigenous Chinese goat breeds based on cytochrome B gene sequences.

Phylogenetic relationships among and genetic variability within 13 Chinese indigenous goat breeds and Boer goat were analyzed using cytochrome b gene sequences. There were 44 variable sites found in a 642 bp sequence, and 46 Cyt b haplotypes were subsequently defined. The phylogeny analysis of haplotypes in combination with goat Cyt b sequences from GenBank shows that Chinese goats are obviously separated from wild goats and might come from Capra aegagrus. Further analysis indicated that indigenous Chinese goats might descend from at least two lineages; most of the individuals analyzed could be classified into lineage A as defined by Luikart, but five other goats were of uncertain lineage. The Tibet plateau is a possible place of origin for Chinese goats. The neighbor-joining tree based on pairwise differences among populations shows that most Tibetan goats, except the Middle Tibet type, cluster closely with North China goats, and then with South China goats. This result confirms that differences in genetic structure exist among goats in different geographic locations. Nucleotide diversity varied among populations. Tibet and North China goats had higher genetic diversity than South China goats. The fixation index (F (st)=87.72%) suggested that most of the total genetic variation was due to variation within populations. In addition, the results indicate that Cyt b gene sequence information alone might not be enough for phylogeny analysis among breeds within species, as shown by fewer polymorphic sites and lower bootstrap values on the neighbor-joining tree.

Animals↗

PubMed2000

Cryptic genetic variation and paraphyly in ravens.

Widespread species that are morphologically uniform may be likely to harbour cryptic genetic variation. Common ravens (Corvus corax) have an extensive range covering nearly the entire Northern Hemisphere, but show little discrete phenotypic variation. We obtained tissue samples from throughout much of this range and collected mitochondrial sequence and nuclear microsatellite data. Our study revealed a deep genetic break between ravens from the western United States and ravens from throughout the rest of the world. These two groups, the 'California clade' and the 'Holarctic clade' are well supported and over 4% divergent in mitochondrial coding sequence. Microsatellites also reveal significant differentiation between these two groups. Ravens from Minnesota, Maine and Alaska are more similar to ravens from Asia and Europe than they are to ravens from California. The two clades come in contact over a huge area of the western United States, with mixtures of the two mitochondrial groups present in Washington, Idaho and California. In addition, the restricted range Chihuahuan raven (Corvus cryptoleucus) of the south-west United States and Mexico is genetically nested within the paraphyletic common raven. Our findings suggest that the common raven may have formerly consisted of two allopatric groups that may be in the process of remerging.

Animals↗

PubMed1988

Genetic variation in the Aleuts of the Pribilof Islands and the Eskimos of Kodiak Island.

A sample of Aleuts residing in the Pribilof Islands of St. Paul (N = 163) and St. George (N = 62) and Eskimo residents of Kodiak Island (N = 294) have been typed for genetic variation at 31 discrete genetic markers. Of these, 16 were polymorphic and 15 were monomorphic. Several private polymorphisms previously reported in Eskimo or Alaskan Amerindian populations were absent in both the Aleuts and Kodiak Island Eskimos. Genetic distance analysis shows considerable genetic differentiation between Aleuts and Kodiak Island Eskimos.

Alaska↗

PubMed2000

Genetic variation and structure in six Rhododendron species (Ericaceae) with contrasting local distribution patterns in Hong Kong, China.

Genetic variability of six rhododendrons with contrasting local distribution patterns in Hong Kong was assessed by starch gel electrophoresis. Rhododendron championiae, R. hongkongense and R. simiarum are locally rare with disjunct distributions, R. moulmainense is restricted and R. farrerae and R. simsii are common. For each species, 13-18 allozyme loci representing 12-16 enzyme systems were scored. The six species showed similar levels of genetic variations (HT ranged from 0.209 to 0.386 and AT ranged from 2.4 to 4.1) which are high compared to plants with similar life history traits. Genetic structure, in contrast, varied greatly between species, with FST ranging from 0.056 to 0.393. The three rarest species had high genetic differentiation (FST and FPT) and distinct geographical patterns, while the other three had low differentiation and little or no geographical structure. These differences are attributed to both present distributions and historical changes following deforestation within the last 1000 years. The conservation implications of these results are discussed.

Alleles↗

PubMed2006

Genetic variation in Hippophae rhamnoides ssp. sinensis (Elaeagnaceae) revealed by RAPD markers.

Hippophae rhamnoides ssp. sinensis is endemic to China, and it is a dioecious, outcrossing plant. Although many studies have been undertaken mainly on its agricultural, nutritional, medical, and ornamental value, little is known about its population genetics. This study uses random amplified polymorphic DNA to investigate the genetic diversity and population genetic structure of 13 natural populations of the subspecies sinensis. Fifteen primers amplified 107 reproducible bands, with 95 (88.79%) being polymorphic. The gene diversity within population was 0.168, considerably lower than that of tree species and most perennial, outcrossing species, but higher than that of annual or short-lived, selfing species. The Gst value showed that 18.3% of the total genetic variation resided among populations, a little lower than that of outcrossing species. The present results are quite similar to those previously reported in another subspecies, H ssp. . rhamnoides rhamnoides. The low genetic differentiation among populations in ssp. sinensis may be attributed to the long-distance dispersal of seeds facilitated by birds, in addition to its characteristics of outcrossing, wind pollination, and widespread distribution. No association between genetic distance and geographical distribution was found. The population relationships revealed by the UPGMA dendrogram parallel this result, in that genetic distance did not increase with geographic separation. This pattern of population differentiation may imply the adaptation of ssp. s populations to the local environment, given that its habitats vary greatly across its distribution.

China↗

PubMed2003

Genetic variation and gene flow of broadcast spawning and planula brooding coral, Goniastrea aspera (Scleractinia) in the Ryukyu Archipelago, southern Japan.

The scleractinian coral Goniastrea aspera (Verrill) undergoes both broadcast spawning and planulae brooding in the Ryukyu Archipelago of southern Japan. Genetic variation and gene flow in G. aspera were studied using allozyme electrophoresis. We tested the hypothesis that gene flow is determined by the competency period of the planulae. We also assessed the relative contributions of sexual and asexual reproduction to recruitment. For the five staining systems surveyed, G. aspera encoded five polymorphic loci and one monomorphic locus. The genotype frequencies in each population significantly differed from the expected Hardy-Weinberg equilibrium (HWE), indicating that the local populations of G. aspera are not fully panmictic. The high ratio of the observed number of genotypes to the number of individuals (0.90 +/- 0.07, mean NG:N +/- SD) and the observed to expected genotypic diversity (0.84 +/- 0.11, mean GO:GE +/- SD) suggested that each population is likely maintained by sexual reproduction. The genetic differentiation (FST) and value of average number of migrants per generation (Nem) among and within regions ranged from 0.025 to 0.104 and 2.2 to 9.6, respectively. Comparisons with other species demonstrated that larva survival rates also influence gene flow. In addition, gene flow on distant reefs by planulae originating from spawning might prevent divergence by planulae originating from brooding for short-distant dispersal among and within populations of G. aspera in the Ryukyu Archipelago.

Animals↗

PubMed1999

Genetic variation in geographical populations of western and Mexican corn rootworm.

Genetic variation in the nuclear rDNA ITS1 region of western corn rootworm, Diabrotica virgifera virgifera (WCR), and Mexican corn rootworm, D. v. zeae (MCR) was studied. Two sites were detected which differentiated WCR and MCR in the 642-base sequence. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the first internal transcribed spacer region (ITS1) sequence revealed no variation within or among the twelve WCR and two MCR populations. PCR-RFLP of 75% of the mitochondrial DNA genome detected one significant polymorphic site out of the approximately 190 restriction sizes observed in WCR. The polymorphism did not differentiate geographical populations of WCR and is not diagnostic for the subspecies. The low levels of variation observed in WCR suggests either high levels of gene flow or a recent geographical expansion from a relatively small base. Gene flow would facilitate the rapid spread of traits that could compromise control programmes, such as insecticide resistance or behavioural modifications. The minimal genetic differentiation between WCR and MCR raises questions about the evolutionary history of these subspecies and how the distinct phenotypes are maintained.

Animals↗

PubMed2003

Genetic variations observed in arterial and venous thromboembolism--relevance for therapy, risk prevention and prognosis.

We undertook genetic and biochemical assays in patients with arterial (n = 146) and venous (n = 199) thromboembolism and survivors of pulmonary embolism (n = 58) to study causation and gene-life style interactions. In the clinical material from North Western Russia, factor V Leiden was found to be a risk factor in venous thrombosis (OR = 3.6), while the methylenetetrahydrofolate reductase (MTHFR) C677T mutation was a significant variable in both venous (p = 0.03) and arterial thrombosis (p = 0.004). Homocysteine levels were determined (n = 84) and hyperhomocysteinemia correlated with the T allele of the MTHFR gene, and with smoking and coffee consumption. Vitamin supplementation reduced homocysteine levels dependent on MTHFR genotype (36% TT, 25% CT, 22% CC). In pulmonary embolism patients, frequency of the -455G/A beta-fibrinogen dimorphism was studied. Carriers of this allele were significantly underrepresented (p < 0.02) among pulmonary embolism survivors (34.5%) compared to controls (56.7%). Additionally, -455AA homozygotes were found in 11.7% controls but only 1.7% of pulmonary embolism patients (p = 0.006). In venous and arterial thrombosis cases, MTHFR and homocysteine data led to effective dietary supplementation with a reduced risk of disease progression. Results from the pulmonary embolism study may indicate that screening tests for the -455G/A beta-fibrinogen genetic variation could be of prognostic value, and may point the way for novel anticoagulation strategies.

Adult↗

PubMed1999

High population differentiation and genetic variation in the endangered Mexican pine Pinus Rzedowskii (Pinaceae).

Pinus rzedowskii is an endangered pine species from Michoacán (central México), which has been previously reported from only three localities. Classified within the subgenus Strobus, it exhibits intermediate morphological characters between subgenera Strobus and Pinus. We analyzed genetic aspects that could shed light on the evolution and conservation of this species. The genetic structure of nine populations was examined using 14 isozyme loci. Pinus rzedowskii has a relatively high level of genetic variation with 46.8% of the loci assayed being polymorphic, a total of 35 alleles, and a mean heterozygosity per population of 0.219. We calculated Wright's F(ST) statistic to estimate gene flow indirectly and to evaluate whether or not there was genetic structuring among populations. We found a marked differentiation among populations (F(ST) = 0.175) and significant inbreeding (F(IS) = 0.247). No pattern of isolation by distance was found. We also constructed a dendrogram based on a genetic distance matrix to obtain an overview of the possible historical relationships among populations. Finally, we found a convex relationship between the genetic distance among populations and the number of ancestral lineages, suggesting that demographically this species has not been at risk recently. Although endangered, with small and fragmented populations, P. rzedowskii shows higher levels of genetic variation than other conifer species with larger populations or similar conservation status.

Journal Article↗

PubMed2000

Detection of genetic variation in Indian population groups using a novel minisatellite probe and finding relationships through tree construction.

Genetic variation in HaeIII-digested genomic DNA samples from different individuals belonging to population groups from Bengal, Uttar Pradesh (UP), Punjab, and South India was assessed at hypervariable loci, using a minisatellite probe, pBA1.2 (accession number, AF 157691), the repeat unit of which was 24 mer long and rich in G-bases. Comparison of DNA profiles between individuals showed a very low probability of band sharing, which ranged from 0.18 to 0.24. A dendrogram, based on Nei's genetic distance, constructed by the neighbor-joining method, showed the formation of separate clusters by both South Indian and non-Indian samples, whereas the construction of a dendrogram based on the Unweighted pair group method arithmetic average (UPGMA) method with Jaccard's similarity coefficient at the individual level led to the formation of several small clusters which were interleaved; also, the subgroups for each of the populations were intermingled with the subgroups for the other populations. A separate analysis was carried out to check the consistency of the proximity between different individuals forming a cluster and between those individuals who were in the vicinity of two clusters. The dendrograms thus obtained did not change the relationship between the individuals from all the populations studied. Despite the distinct clustering observed in the population group comparison, a probable admixture was reflected in the finding that some individuals belonging to one population group were dispersed or embedded within a cluster generated by the individuals of another population group, when a minute dissection of the data for generating a tree at the individual level was carried out.

DNA Fingerprinting↗

PubMed2004

Evaluation of the ARMD1 locus on 1q25-31 in patients with age-related maculopathy: genetic variation in laminin genes and in exon 104 of HEMICENTIN-1.

The age-related maculopathy (ARM) genetics program at Columbia University utilizes comprehensive genetic analysis of candidate genes in large case-control studies to determine genotypes associated with the ARM complex trait. Genes encoding laminins, a class of extracellular matrix proteins, represent attractive candidates for two reasons. First, the presence of laminins in the basal lamina of the retinal pigment epithelium (RPE), Bruch's membrane, and choriocapillaris suggests a possible role in the pathophysiology of ARM. Second, three laminin genes, LAMC1, LAMC2, and LAMB3, are located in the 1q25-31 region, within the previously mapped ARMD1 locus. The entire open reading frame of the three laminin genes was screened for variants by denaturing high-performance liquid chromatography (DHPLC) and direct sequencing in at least 92, and up to 368 ARM patients and matched unaffected controls. Sixty-nine sequence variants were detected in the 69 exons of the LAMC1, LAMC2, and LAMB3 genes. Screening of exon 104 of the recently proposed ARMD1 gene, HEMICENTIN-1, residing in the 1q25-31 locus, did not detect the suggested causal variant, Q5345R, in 632 study subjects. Overall, we did not find statistically significant differences in the frequency of variants between ARM-affected individuals and age-matched controls. Four rare, non-synonymous, variants were detected in single cases of ARM patients. Our data on relatively limited numbers of study subjects do not suggest a significant role for genetic variation in the three laminin genes and in exon 104 of HEMICENTIN-1 in predisposing individuals to ARM. However, as in many instances in similar studies, involvement of rare amino acid-changing variants in a fraction of ARM cannot be ruled out.

Aged↗

PubMed2000

Amount and structure of intra- and interspecific genetic variation in the moss genus Polytrichum.

Allozyme electrophoresis was used to determine amount and structure of genetic variation within and between five congeneric haploid moss species: Polytrichum formosum, P. commune, P. uliginosum, P. piliferum and P. juniperinum. For the different species, gene diversity within populations (HS) ranged from very low (0.025) to moderate values (0.127), being, on average, lower than those observed for vascular plants and many other moss species. Polytrichum piliferum and P. juniperinum showed significantly higher levels of HS than the other species examined, which possibly might be explained by sexual reproduction being more prevalent in these two species, that often live in more dynamic habitats, where turnover of individuals is more frequent. Genetic variability was observed to be structured in contrasting ways at different levels. At the intraspecific level genetic differentiation among populations of most Polytrichum species was low, FST </= 0.1, indicating a considerable degree of gene flow by wind-dispersed spores over substantial distances. At the interspecific level strong divergence, genetic identities being on average I=0.222, was observed between most species studied, despite low levels of divergence at the morphological level. These I-values are significantly lower than observed for congeneric vascular plant species and most congeneric bryophyte species. This suggests that the morphological conservatism is not due to lack of genetic variability and evolutionary potential.

Genetic Variation↗

PubMed1995

Random amplified polymorphic DNA in cattle and sheep: application for detecting genetic variation.

The present study investigated the use of the random amplified polymorphic DNA (RAPD) method to detect genetic variation in cattle and sheep. The animals studied consisted of samples from five Finnish cattle breeds: native Eastern (18 animals), Northern (24), Western Finncattle (24), Finnish Ayrshire (24), and Finnish Friesian (18); as well as a white (6 animals) and a grey (9) colour type of Finnsheep. The cattle and sheep populations were analysed with 11 and 13 RAPD primers demonstrating the most repeatable amplification pattern. Two out of ten RAPD fragments tested by cross hybridization showed homology between the two species. The RAPD method did not prove efficient for finding new polymorphisms in either species, because we found only three polymorphic RAPD markers for cattle and seven markers for sheep with different allele frequencies between the breeds. Although there is a greater presence of polymorphic RAPD markers in sheep, according to the similarity indices the sheep populations showed a higher degree of homogeneity than the cattle breeds. However, the interbreed and intrabreed similarity indices for cattle did not suggest any significant differentiation of the Finnish breeds, contrary to earlier results based on blood group and protein polymorphism.

Animals↗