DNA POLYMORPHISM DETECTABLE BY RESTRICTION ENDONUCLEASES

ABSTRACT Data on DNA polymorphisms detected by restriction endonucleases are rapidly accumulating. With the aim of analyzing these data, several different measures of nucleon (DNA segment) diversity within and between populations are proposed, and statistical methods for estimating these quantities are developed. These statistical methods are applicable to both nuclear and non-nuclear DNAs. When evolutionary change of nucleons occurs mainly by mutation and genetic drift, all the measures can be expressed in terms of the product of mutation rate per nucleon and effective population size. A method for estimating nucleotide diversity from nucleon diversity is also presented under certain assumptions. It is shown that DNA divergence between two populations can be studied either by the average number of restriction site differences or by the average number of nucleotide differences. In either case, a large number of different restriction enzymes should be used for studying phylogenetic relationships among related organisms, since the effect of stochastic factors on these quantities is very large. The statistical methods developed have been applied to data of Shah and Langley on mitochondrial (mt)DNA from Drosophila melanogaster, simulans and virilis. This application has suggested that the evolutionary change of mtDNA in higher animals occurs mainly by nucleotide substitution rather than by deletion and insertion. The evolutionary distances among the three species have also been estimated.

Download Full-text

The genetic structure of natural populations of Drosophila melanogaster. XXII. Comparative study of DNA polymorphisms in northern and southern natural populations.

Genetics ◽

10.1093/genetics/129.3.753 ◽

1991 ◽

Vol 129 (3) ◽

pp. 753-761

Author(s):

T S Takano ◽

S Kusakabe ◽

T Mukai

Keyword(s):

Drosophila Melanogaster ◽

Genetic Drift ◽

Nucleotide Diversity ◽

Restriction Site ◽

Natural Populations ◽

Dna Polymorphisms ◽

Restriction Map ◽

Random Genetic Drift ◽

Two Populations ◽

Restriction Site Polymorphisms

Abstract Restriction map variation in four gene regions (Adh, Amy, Pu and Gpdh) was surveyed for 86 second chromosomes from northern (Aomori) and southern (Ogasawara) Japanese populations of Drosophila melanogaster (43 chromosomes from each population). The regions examined cover a total of 62 kilobases. Estimates of nucleotide diversity (pi) were approximately constant across the gene regions and populations examined. The distribution of restriction site polymorphisms was compatible with the expectation from the neutral mutation-random genetic drift hypothesis, but insertion/deletion polymorphisms were not consistent with it. While the two populations shared a majority of restriction site polymorphisms, frequencies of individual restriction site variants were significantly different between the two populations at 7 out of 35 segregating sites. In addition, an insertion in the Amy region was found in 15 chromosomes from the Ogasawara sample but absent in the Aomori sample. A considerable difference was observed in the number of rare insertions and deletions between the two populations. The numbers of aberrations uniquely represented were 16 in the Ogasawara sample and only 3 in the Aomori sample. These findings suggest that the two populations were differentiated from each other to some degree by means of random genetic drift and/or other factors.

Download Full-text

Chloroplast DNA diversity among trees, populations and species in the California closed-cone pines (Pinus radiata, Pinus muricata and Pinus attenuata).

Genetics ◽

10.1093/genetics/135.4.1187 ◽

1993 ◽

Vol 135 (4) ◽

pp. 1187-1196

Author(s):

Y P Hong ◽

V D Hipkins ◽

S H Strauss

Keyword(s):

Genetic Variation ◽

Chloroplast Dna ◽

Pinus Radiata ◽

Nucleotide Diversity ◽

Restriction Enzymes ◽

Dna Polymorphisms ◽

Pinus Muricata ◽

Monterey Pine ◽

Haplotypic Diversity ◽

Closed Cone

Abstract The amount, distribution and mutational nature of chloroplast DNA polymorphisms were studied via analysis of restriction fragment length polymorphisms in three closely related species of conifers, the California closed-cone pines-knobcone pine: Pinus attenuata Lemm.; bishop pine: Pinus muricata D. Don; and Monterey pine: Pinus radiata D. Don. Genomic DNA from 384 trees representing 19 populations were digested with 9-20 restriction enzymes and probed with cloned cpDNA fragments from Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] that comprise 82% chloroplast genome. Up to 313 restriction sites were surveyed, and 25 of these were observed to be polymorphic among or within species. Differences among species accounted for the majority of genetic (haplotypic) diversity observed [Gst = 84(+/- 13)%]; nucleotide diversity among species was estimated to be 0.3(+/- 0.1)%. Knobcone pine and Monterey pine displayed almost no genetic variation within or among populations. Bishop pine also showed little variability within populations, but did display strong population differences [Gst = 87(+/- 8)%] that were a result of three distinct geographic groups. Mean nucleotide diversity within populations was 0.003(+/- 0.002)%; intrapopulation polymorphisms were found in only five populations. This pattern of genetic variation contrasts strongly with findings from study of nuclear genes (allozymes) in the group, where most genetic diversity resides within populations rather than among populations or species. Regions of the genome subject to frequent length mutations were identified; estimates of subdivision based on length variant frequencies in one region differed strikingly from those based on site mutations or allozymes. Two trees were identified with a major chloroplast DNA inversion that closely resembled one documented between Pinus and Pseudotsuga.

Download Full-text

Reduced levels of DNA polymorphism and fixed between-population differences in the centromeric region of Drosophila ananassae.

Genetics ◽

10.1093/genetics/132.4.1039 ◽

1992 ◽

Vol 132 (4) ◽

pp. 1039-1045 ◽

Cited By ~ 3

Author(s):

W Stephan ◽

S J Mitchell

Keyword(s):

Dna Polymorphism ◽

Restriction Site ◽

Total Sample ◽

Dna Polymorphisms ◽

Drosophila Ananassae ◽

Site Variation ◽

V Region ◽

Two Populations ◽

Distal Gene

Abstract We have estimated DNA sequence variation within and between two populations of Drosophila ananassae, using six-cutter restriction site variation at vermilion (v) and furrowed (fw). These two gene regions are located close to the centromere on the left and right X chromosome arms, respectively. In the fw region, no DNA polymorphism was detected within each population. In the v region, average heterozygosity per nucleotide was very low in both populations (pi = 0.0005 in the Burma population, and 0.0009 in the India population). These estimates are significantly lower than those from loci in more distal gene regions. The distribution of DNA polymorphisms between both populations was also striking. At fw, three fixed differences between the Burma and India populations were detected (two restriction site differences and one insertion/deletion of approximately 2 kb). At v, each DNA polymorphism in high frequency in the total sample was nearly fixed in one or the other population, although none of them reached complete fixation. The observed pattern of reduced variation within populations and fixed differences between populations appears to correlate with recombination rate. We conclude that recent hitchhiking associated with directional selection is the best explanation for this pattern. The data indicate that different selective sweeps have occurred in the two populations. The possible role of genetic hitchhiking in rapid population differentiation in gene regions of restricted recombination is discussed.

Download Full-text

No variation is detected in the chloroplast genome of Pinustorreyana

Canadian Journal of Forest Research ◽

10.1139/x91-253 ◽

1991 ◽

Vol 21 (12) ◽

pp. 1832-1835 ◽

Cited By ~ 12

Author(s):

Elizabeth R. Waters ◽

Barbara A. Schaal

Keyword(s):

Genetic Differentiation ◽

San Diego ◽

Restriction Site ◽

Restriction Enzymes ◽

San Diego County ◽

Length Variation ◽

Random Genetic Drift ◽

Length Polymorphisms ◽

Restriction Sites ◽

Two Populations

Pinustorreyana Parry ex Carrière has only two extant populations, containing less than 10 000 individuals in total. The two populations are in California, in San Diego County and on the island Santa Rosa. They are separated by 280 km and have been isolated for more than 8000 years. Random genetic drift over this period of time should have resulted in genetic differentiation between the two populations. We surveyed the chloroplast DNA of 24 individuals of P. torreyana for both restriction site and length polymorphisms with 26 restriction enzymes. The San Diego and Santa Rosa populations were monomorphic at over 150 restriction sites. Moreover, there was no detectable length variation. The results of this study suggest that P. torreyana has been monomorphic at these sites since before the two populations were isolated.

Download Full-text

Variation in natural populations of Drosophila as revealed by four-cutter analysis

Genome ◽

10.1139/g89-138 ◽

1989 ◽

Vol 31 (2) ◽

pp. 784-787 ◽

Cited By ~ 1

Author(s):

Montserrat Aguadé

Keyword(s):

Restriction Site ◽

Natural Populations ◽

Restriction Enzymes ◽

Dna Polymorphisms ◽

Enzyme Analysis ◽

Restriction Enzyme Analysis ◽

Molecular Variation ◽

Deletion Polymorphism ◽

Isolated Populations ◽

Chromosome Arrangements

Four-cutter restriction enzyme analysis, a recently developed electroblotting technique, enables the survey of restriction site and insertion–deletion polymorphism in natural populations at a fine level of resolution. Using this technique, the distribution of polymorphism among geographically isolated populations of Drosophila melanogaster and in different structural–functional domains of the genome has been studied. A summary of these results is presented and discussed. Recent investigations of molecular variation within and between different chromosome arrangements in Drosophila are presented. Levels of variation in different regions of the X chromosome of D. melanogaster are also discussed.Key words: populations, DNA polymorphisms, Drosophila, restriction enzymes.

Download Full-text

Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽

10.1093/genetics/164.4.1511 ◽

2003 ◽

Vol 164 (4) ◽

pp. 1511-1518 ◽

Cited By ~ 1

Author(s):

Ning Yu ◽

Michael I Jensen-Seaman ◽

Leona Chemnick ◽

Judith R Kidd ◽

Amos S Deinard ◽

...

Keyword(s):

Nucleotide Diversity ◽

Nuclear Dna ◽

Demographic History ◽

Nuclear Genome ◽

Limited Data ◽

Effective Population ◽

East Central ◽

Dna Diversity ◽

History Of ◽

Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

Download Full-text

Hierarchical Analysis of Nucleotide Diversity in Geographically Structured Populations

Genetics ◽

10.1093/genetics/142.2.629 ◽

1996 ◽

Vol 142 (2) ◽

pp. 629-639 ◽

Cited By ~ 4

Author(s):

Kent E Holsinger ◽

Roberta J Mason-Gamer

Keyword(s):

Nucleotide Diversity ◽

Restriction Site ◽

Rooted Tree ◽

Structured Populations ◽

Hierarchical Analysis ◽

Restriction Site Variation ◽

Hierarchical Levels ◽

Site Variation ◽

The Mean ◽

Mean Time

Abstract Existing methods for analyzing nucleotide diversity require investigators to identify relevant hierarchical levels before beginning the analysis. We describe a method that partitions diversity into hierarchical components while allowing any structure present in the data to emerge naturally. We present an unbiased version of Nei's nucleotide diversity statistics and show that our modification has the same properties as Wright's F ST. We compare its statistical properties with several other F ST estimators, and we describe how to use these statistics to produce a rooted tree of relationships among the sampled populations in which the mean time to coalescence of haplotypes drawn from populations belonging to the same node is smaller than the mean time to coalescence of haplotypes drawn from populations belonging to different nodes. We illustrate the method by applying it to data from a recent survey of restriction site variation in the chloroplast genome of Coreopsis grandiflora.

Download Full-text

Low genetic diversity in the endangered Taxus yunnanensis following a population bottleneck, a low effective population size and increased inbreeding

Silvae Genetica ◽

10.1515/sg-2016-0008 ◽

2016 ◽

Vol 65 (1) ◽

pp. 59-66 ◽

Cited By ~ 3

Author(s):

Y. C. Miao ◽

Z. J. Zhang ◽

J. R. Su

Keyword(s):

Genetic Diversity ◽

Habitat Fragmentation ◽

Population Size ◽

Effective Population Size ◽

Spatial Genetic Structure ◽

Population Bottleneck ◽

Effective Population ◽

Taxus Yunnanensis ◽

Low Genetic Diversity ◽

Two Populations

Abstract Taxus yunnanensis, which is an endangered tree that is considered valuable because it contains the effective natural anticancer metabolite taxol and heteropolysaccharides, has long suffered from severe habitat fragmentation. In this study, the levels of genetic diversity in two populations of 136 individuals were analyzed based on eleven polymorphic microsatellite loci. Our results suggested that these two populations were characterized by low genetic diversity (NE = 2.303/2.557; HO = 0.168/0.142; HE = 0.453/0.517), a population bottleneck, a low effective population size (Ne = 7/9), a high level of inbreeding (FIS = 0.596/0.702), and a weak, but significant spatial genetic structure (Sp = 0.001, b = −0.001*). Habitat fragmentation, seed shadow overlap and limited seed and pollen dispersal and potential selfing may have contributed to the observed gene tic structure. The results of the present study will enable development of practical conservation measures to effectively conserve the valuable genetic resources of this endangered plant.

Download Full-text

Identification of restriction enzyme in the FSHR gene of indonesian local cattle

IOP Conference Series Earth and Environmental Science ◽

10.1088/1755-1315/888/1/012024 ◽

2021 ◽

Vol 888 (1) ◽

pp. 012024

Author(s):

P W Prihandini ◽

A Primasari ◽

M Luthfi ◽

D Pamungkas ◽

A P Z N L Sari ◽

...

Keyword(s):

Restriction Enzyme ◽

Restriction Site ◽

Follicle Stimulating Hormone ◽

Restriction Enzymes ◽

Future Studies ◽

Fshr Gene ◽

Pcr Rflp ◽

Mapping Analysis ◽

Pcr Products ◽

Enzyme Mapping

Abstract The restriction enzyme is important for genotyping using the PCR-RFLP technique. Therefore, this study aims to identify the restriction enzyme mapping in the partial sequence of the follicle-stimulating hormone receptor (FSHR) gene in Indonesian local cattle. A total of 29 samples sized 306 bp, were aligned with Genbank sequence acc no. NC_032660, resulting three polymorphic sites, namely g.193G>C, g.227T>C, and g.275A>C. Furthermore, the restriction mapping analysis using the NEBcutter program V2.0 showed that no enzyme recognized the SNP g.275A>C, while the SNP g.193G>C and g.227T>C were identified by the AluI and MscI enzymes, respectively. The AluI enzyme cuts at two positions (193 bp and 243 bp) in the G allele sample producing three fragments namely 50 bp, 63 bp, and 193 bp, meanwhile, in the C allele, the AluI cuts only in position 243 bp, hence, the fragment products are 63 bp and 243 bp. In contrast, the MscI enzyme was only recognized in the T allele, producing fragments sized 77 bp and 229 bp but failed to identify the restriction site along with the PCR products in the C allele. Based on the results, the SNPs (g.193G>C and g.227T>C) and restriction enzymes (AluI and MscI) are applicable for genotyping local Indonesian cattle using the PCR-RFLP technique in future studies.

Download Full-text

Genetic divergence in mitochondrial DNA of Anopheles nuneztovari (Diptera: Culicidae) from Brazil and Colombia

Genetics and Molecular Biology ◽

10.1590/s1415-47572000000100013 ◽

2000 ◽

Vol 23 (1) ◽

pp. 71-78 ◽

Cited By ~ 13

Author(s):

Vera Margarete Scarpassa ◽

Silvia Geurgas ◽

Ana Maria L. Azeredo-Espin ◽

Wanderli Pedro Tadei

Keyword(s):

Mitochondrial Dna ◽

Genetic Divergence ◽

Nucleotide Diversity ◽

Haplotype Diversity ◽

Sequence Divergence ◽

Brazilian Amazon ◽

Restriction Endonucleases ◽

Separate Species ◽

Geographic Populations

In the present study, we have examined the variability in Anopheles nuneztovari mitochondrial DNA of three populations from the Brazilian Amazon and one from western Colombia (Sitronela), using four restriction endonucleases (BclI, ClaI, HindIII, SstI). The haplotype diversity (h) was slightly elevated in all populations (0.5000 to 0.6765), whereas the nucleotide diversity (pi) was lower in the Sitronela population (0.0029) and higher in populations from the Brazilian Amazon (0.0056 to 0.0098). The degree of sequence divergence (delta) estimated within the Brazilian Amazon and that in Sitronela (0.0329 to 0.0371) suggests that these geographic populations of A. nuneztovari may eventually constitute separate species. The low sequence divergence values among the three Brazilian Amazon populations (0.0012 to 0.0031) indicate that these populations are genetically similar. These results are consistent with those recently reported for allozymes of these same populations.

Download Full-text