Restriction Fragment Length Polymorphism Alleles Research Articles

Distribution of a Human RFLP in the ACTG2 (ACTA3) Gene Among African-American and Caucasian populations

Abstract. Restriction fragment length polymorphisms (RFLPs) are variations in DNA sequences that can be detected by digestion with restriction enzymes. RFLPs are used to study variation and evolution within populations. This study focused on a specific PvFLP occurring within the human ACTG2 (formerly ACTA3) gene. ACTG2 encodes a γ-actin specifically expressed in mammalian enteric muscle. The RFLP occurs within the first intron and, while not a linkage marker for any genetic condition, has implications as a marker in human evolution. Humans normally have two copies of each chromosome. Each chromosome contributes one allele towards the pair examined using Mendelian genetics. An earlier study of the RFLP, conducted among Japanese and Caucasian populations, published the finding that the RFLP allele occurred twenty-one times more frequently in Caucasian populations. This study expanded analysis on this RFLP by surveying allelic frequencies in African Americans. Two hypotheses to explain earlier allelic result...

A porcine genomic glucosephosphate isomerase probe detects a multiallelic restriction fragment length polymorphism assigned to chromosome 10pter in horse

A porcine genomic GPI probe has been shown to detect an equine six allele restriction fragment length polymorphism, which was localized to chromosome 10pter by in situ hybridization.

Molecular and phenotypic description of the widespread root symbiont Acephala applanata gen. et sp. nov., formerly known as dark-septate endophyte Type 1

Acephala applanata gen. et sp. nov. is described. A. applanata is a dark-septate endophyte (DSE) of conifer roots and belongs to the Phialocephala fortinii species complex. Several genetic markers, including isozymes, inter-simple-sequence-repeat (ISSR) fingerprints, single-copy restriction fragment length polymorphisms (RFLP) and sequences of the internal transcribed spacers (ITS), let us unambiguously separate isolates of A. applanata from isolates of P. fortinii s.l. and other dark-septate endophytes. Alleles at four RFLP loci and two fixed nucleotides in the ITS region were diagnostic for A. applanata. One of the fixed nucleotides resulted in the addition of an Afa I restriction site. PCR amplification with primers prITS4 and the newly developed primer PF_ITS_F (ACT CTG AAT GTT AGT GAT GTC TGA GT) and restriction digestion with Afa I yielded three fragments (203 bp, 117 bp, 56 bp) in A. applanata but only two (260 bp and 117 bp) in P. fortinii s.l. Population differentiation (GST) between A. applanata and other cryptic species of P. fortinii was pronounced, and the index of association (IA) did not deviate significantly from zero, showing that recombination occurs or had occurred in A. applanata. Although isolates of A. applanata never were observed to sporulate, it can be distinguished morphologically from P. fortinii s.l. by the scarcity of aerial mycelium, significantly slower growth and denser mycelium on cellophane overlaid on water agar. These phenotypic characteristics, combined with diagnostic RFLP alleles and/or PCR-RFLP of the ITS fragment with the fixed Afa I restriction site, unequivocally allow identification of A. applanata.

Differential chromosome pairing affinities at meiosis in polyploid sugarcane revealed by molecular markers.

Chromosome pairing at meiosis is an essential feature in cell biology, which determines trait inheritance and species evolution. Complex polyploids may display diverse pairing affinities and offer favorable situations for studying meiosis. The genus Saccharum encompasses diverse forms of polyploids with predominantly bivalent pairing. We have focused on a modern cultivar of sugarcane, R570, and taken advantage of a particular single copy probe (BNL 12.06) revealing 11 alleles by restriction fragment length polymorphism (RFLP). As for other cultivars, R570 is highly polyploid (2n=ca. 115) and indirectly derived from interspecific hybridization between Saccharum officinarum (2n=80, x=10) and S. spontaneum (2n=40-128, x=8). Here we determined the doses of the various BNL12.06 RFLP alleles among 282 progeny of R570 and estimated the mutual pairing frequencies among the corresponding homo- or homoeologous chromosomes using a maximum likelihood method. The result is an atypical picture, with pairing frequencies ranging from 0 to 40% and differential affinities leading to the identification of several chromosome subsets. This example illustrates the unsystematic meiotic behavior in a complex polyploid. It highlights a continuous range of pairing affinities between chromosomes and pinpoints a strong role of individual chromosome features, partly related to their ancestral origin, in the determination of these affinities.

RFLP diversity within and between major groups of barley in Europe

AbstractRestriction fragment length polymorphism (RFLP) diversity has been determined and analyzed as expressed by 33 single‐ or low‐copy clone/ enzyme combinations at 32 loci distributed over all chromosomes of the barley genome within a sample of 223 European barley accessions comprised of pure line (single‐head progenies) genotypes. The accessions have been selected to include landraces and widely grown cultivars derived from crossbreeding during the 20th century in North‐, West‐ and Central European countries. Genetic diversity obtained from 83 alleles across all accessions is characterized by the diversity index H = 0.385. The diversity indices determined for landraces and cultivars were almost equal, with the difference between spring (H = 0.260) and winter (H = 0.415) barley approaching statistical significance, while comparisons of other groupings only revealed statistically insignificant trends. A more detailed analysis based on differences in allele frequency distributions at each locus (clone/enzyme combinations resp.) revealed very clear differences related to the existence, continuity and dynamics of changes in group‐specific RFLP profiles. With the majority (69%) of RFLP alleles at 23 out of 32 loci on all barley chromosomes involved, contributions from chromosomes 1H, 3H, 4H and 5H seem to be of special importance. Differences in the overall average of abundance indicate higher levels of genetic diversity within both groups of winter barley compared with both groups of spring barley, from which the most frequent alleles at 15 (2‐rowed spring barley) and 17 (6‐rowed spring barley) RFLP loci approach fixation. The results of this study are discussed in relation to the history of barley cultivation and barley breeding in Europe, and possible explanations for group‐specific differences in the RFLP profiles of landraces and cultivars as well as for the high levels of (nearly) fixed alleles of both subsets of spring barley, and with respect to progress in barley breeding that it has been possible to obtain within the rather narrow RFLP profiles.

The global genetic structure of the wheat pathogen Mycosphaerella graminicola is characterized by high nuclear diversity, low mitochondrial diversity, regular recombination, and gene flow

A total of 1673 Mycosphaerella graminicola strains were assayed for DNA fingerprints and restriction fragment length polymorphism (RFLP) markers in the nuclear and mitochondrial genomes. The isolates were collected from 17 wheat fields located in 11 countries on five continents over a six year period (1989–1995). Our results indicate that genetic diversity in the nuclear genome of this fungus was high for all but three of the field populations surveyed and that populations sampled from different continents had similar frequencies for the most common RFLP alleles. Hierarchical analysis revealed that more than 90% of global gene diversity was distributed within a wheat field, while ∼5% of gene diversity was distributed among fields within regions and ∼3% was distributed among regions on different continents. These findings suggest that gene flow has occurred on a global scale. On average, each leaf was colonized by a different nuclear genotype. In contrast, only seven mtDNA haplotypes were detected among the 1673 isolates and the two most common mtDNA haplotypes represented approximately 93% of the world population, consistent with a selective sweep. Analysis of multilocus associations indicated that all field populations were in gametic equilibrium, suggesting that sexual recombination is a regular occurrence globally.

Aluminum Tolerance Associated with Quantitative Trait Loci Derived from Soybean PI 416937 in Hydroponics

Acid soils with high levels of Al impede root growth, causing increased crop sensitivity to drought and decreased nutrient acquisition. Development of Al‐tolerant cultivars may be a cost effective response to the problem. In previous investigations, we identified an Al‐tolerant soybean [Glycine max (L.) Merr.] plant introduction from Japan (PI 416937), and subsequently determined the heritability of the trait in a cross with Young, a highly productive Al‐sensitive cultivar. The objective of the present study was to identify quantitative trait loci (QTL) which condition Al tolerance by a genetic linkage map of 155 restriction fragment length polymorphism (RFLP) marker loci and a hydroponics‐based Al response. The 120 F4‐derived progeny from Young × PI 416937 were divided into four sets and evaluated with the parents for tap root extension in 0 and 2 μM Al3+ activity solutions (NOAL and HIAL, respectively) employing Al levels as whole plots in a split‐plot experimental design. Aluminum tolerance was defined as (i) root extension under HIAL conditions, and (ii) root extension as a percentage of control [PC = (HIAL/NOAL) × 100]. Multiple regression analysis revealed five QTL from independent linkage groups which conditioned root extension under HIAL stress. Three of the five QTL were also detected by PC as the expression of Al tolerance. While most alleles for Al tolerance were derived from the Al‐tolerant parent, PI 416937, a RFLP allele from Young (for marker EV2‐1) improved Al tolerance expressed as PC and exhibited a similar trend under HIAL stress. At present, it is not known whether the Al tolerance gene from Young, in combination with those from PI 416937, will raise Al tolerance beyond that now observed in the PI. One allele for Al tolerance from PI 416937 (for marker B122‐1) may be difficult to capitalize upon, agronomically, because of its association with a detrimental pod dehiscence factor. Further experimentation is needed to distinguish between linkage and pleiotropic effects near this marker. A favorable epistatic effect for Al tolerance was detected between two alleles from the PI 416937. The relationships revealed by marker analysis indicated that marker‐facilitated selection may be a viable approach in the breeding of Al‐tolerant soybean.

Single-locus inheritance in the allotetraploid Coffea arabica L. and interspecific hybrid C. arabica x C. canephora.

Molecular cytogenetic analysis has indicated that Coffea arabica is an amphidiploid formed from the hybridization between two closely related diploid progenitor species, C. canephora and C. eugenioides. Our aim was to determine the mode of inheritance in C. arabica and in a tetraploid interspecific hybrid (called arabusta) between C. arabica and C. canephora as revealed by segregation analyses of restriction fragment length polymorphism (RFLP) loci markers. The observed RFLP allele segregations in an F(2) progeny of C. arabica conform to disomic inheritance as expected, with regular bivalent pairing of homologous chromosomes in the F1 hybrid. In contrast, RFLP loci followed tetrasomic inheritance in the arabusta interspecific hybrid, although bivalents have been reported to predominate greatly at meiosis in its hybrid. These results suggest that homologous chromosomes do not pair in C. arabica, not as a consequence of structural differentiation, but because of the functioning of pairing regulating factors. Moreover, the arabusta hybrid seems to offer the possibility of gene exchange between the homologous genomes.

Association of fatty acid synthase gene and malic enzyme gene polymorphisms with fatness in turkeys

A candidate gene approach was carried out on a commercial line of turkeys to assess the association between fatness variability and polymorphisms of genes involved in lipid metabolism. Four restriction fragment length polymorphisms (RFLP) were typed on the fatty acid synthase gene (MspI/pF5), on the malic enzyme gene (HindIII/em), as well as on the acetyl coenzyme A carboxylase and delta9 desaturase genes. Fatness level was estimated in vivo by an ultrasonic instrument. Fat yield was assessed after slaughter by calculating the ratio of the leg skin plus subcutaneous fat weight to the whole leg weight. Finally, the lipid content was determined by extraction from the boneless leg. The 84 female turkeys sampled were full and half-sibs born from eight sires, seven of which were heterozygous for MspI/pF5 or HindIII/em RFLP and one of which was double homozygous at these loci. The analyses of variance used to compare the genotypes at each RFLP suggested a major role associated with the fatty acid synthase gene polymorphism in the explanation of fatness variability. One homozygous genotype for MspI/pF5 was about 1.5 standard deviations leaner than the other two homozygous genotypes. An analysis of the average effects of gene substitution confirmed the association between leanness and one allele of the fatty acid synthase polymorphism. It also identified a significant association between leanness and one malic enzyme RFLP allele, congruent with a strictly additive determinism for the effect associated with this polymorphism. This experiment provided new evidence of the association between both fatty acid synthase and malic enzyme gene polymorphisms and fatness variability in turkeys.

Gene and genotypic diversity of Phytophthora cinnamomi in South Africa and Australia revealed by DNA polymorphisms

Phytophthora cinnamomiisolates from South Africa and Australia were compared to assess genetic differentiation between the two populations. These two populations were analysed for levels of phenotypic diversity using random amplified polymorphic DNAs (RAPDs) and gene and genotypic diversity using restriction fragment length polymorphisms (RFLPs). Sixteen RAPD markers from four decanucleotide Operon primers and 34 RFLP alleles from 15 putative loci were used. A few isolates from Papua New Guinea known to posses alleles different from Australian isolates were also included for comparative purposes. South African and Australian P. cinnamomipopulations were almost identical with an extremely low level of genetic distance between them (DmD 0:003). Common features for the two populations include shared alleles, low levels of phenotypic/genotypic diversity, high clonality, and low observed and expected levels of heterozygosity. Furthermore, relatively high levels of genetic differentiation between mating type populations (Dm South AfricaD 0:020 andDm AustraliaD 0:025 respectively), negative fixation indices, and significant deviations from Hardy‐Weinberg equilibrium, all provided evidence for the lack of frequent sexual reproduction in both populations. The data strongly suggest that both the South African and Australian P. cinnamomipopulations are introduced.

Polymorphisms in IL-1 β and IL-1 receptor antagonist genes are associated with myasthenia gravis

Interleukin 1 (IL-1) β Taq I restriction fragment length polymorphism (RFLP) in exon 5 and IL-1 receptor antagonist (IL-1Ra) polymorphism, variable numbers of an 86-bp tandem repeat (VNTR), were analysed in 107 patients with myasthenia gravis (MG) and 82 ethnically matched healthy control (HC) individuals. Positive association was found with IL-1 β Taq I RFLP allele 2 carriage in MG (OR=2.007), while allele 1 was negatively associated with MG (OR=0.498). When homozygous individuals for allele 2 were considered, the association was stronger (OR=4.630), indicating a dose effect of allele 2. Analysis of IL-1 β Taq I RFLP in relation to HLA-B8 demonstrated that the allelic association was more pronounced in patients without HLA-B8 (OR=2.813). There was no difference in IL-1Ra VNTR allelic distribution in MG patients compared with HC. However, MG patients who were noncarriers of IL-Ra allele 2 had a significantly higher percentage of IL-1 β Taq I RFLP allele 2 carriage (OR=3.085), while there was no such difference in IL-1Ra allele 2 carriers. Our results demonstrate a new genetic marker in MG, which exerts its maximum effect in patients with the lowest MHC-associated susceptibility. We propose a possible pathogenetic role of IL-1 β and a possible intrinsic dyregulation of IL-1 in MG.

Characterization of the bovine epsilon gene.

Immunoglobulin E is quantitatively a minor immunoglobulin class in serum, but nevertheless the major class of antibody mediating type I hypersensitivity reactions and hence, type I allergic phenomena. The bovine epsilon gene is one of the as yet uncharacterized mammalian immunoglobulin genes. We have therefore cloned and determined the cDNA sequence and genomic organization of the gene. It contains four constant region domain-encoding exons (CH1 to CH4) with a high homology to sheep C epsilon (87%) and to a lower degree to dog (62%), horse (58%), chimpanzee, orangutan, human (55%), mouse (52%) and rat (52%) C epsilon genes. Southern blot analysis of bovine genomic DNA, revealed the existence of a single C epsilon gene with a presence of allelic restriction fragment length polymorphism (RFLP).

Gene Flow and Sexual Reproduction in the Wheat Glume Blotch Pathogen Phaeosphaeria nodorum (Anamorph Stagonospora nodorum)

ABSTRACT Restriction fragment length polymorphisms (RFLPs) were used to characterize the genetic structures of three field populations of Phaeosphaeria nodorum from Texas, Oregon, and Switzerland. Data from seven nuclear RFLP loci were used to estimate gene diversity and genetic distances and to make indirect measures of gene flow between populations. Three of the seven RFLP loci differed significantly in allele frequencies across populations. On average, 96% of the total gene diversity was found within populations. There was little evidence for population subdivision, suggesting that gene flow was not restricted among populations. Based on an average population differentiation of 0.04, we estimated that the exchange of 11 migrants among populations per generation would be needed to account for the present level of population subdivision. Genotype diversity based on DNA fingerprints was at a maximum for the Swiss population, whereas populations in Texas and Oregon had lower genotype diversities. Many multilocus haplotypes were found in each population. Ninety-five percent of RFLP allele pairs were in gametic equilibrium. The data were consistent with random mating within each population.

Allelic association between D2 but not D1 dopamine receptor gene and alcoholism in Finland.

We studied the relationship of D2 and D1 receptor gene polymorphisms and alcoholism in male Finnish alcoholics and assessed male controls. Seventy alcoholics entering a detoxification programme and 50 control individuals were recruited. Forty-three per cent of the alcoholic patients, but only 22% of controls, had the D2 receptor gene TaqI A restriction fragment length polymorphism A1 allele. The frequency of the A1 allele was significantly higher in alcoholics (p = 0.039). In comparison, no association between alcoholism and the D1 receptor gene EcoRI restriction fragment length polymorphism alleles was found. A logistic regression analysis of the alcoholic population failed to support the idea that the presence of the A1 allele would be linked to estimates of alcohol dependence severity rated with the Severity of Alcohol Dependence Questionnaire or the Michigan Alcoholism Screening Test. In conclusion, allelic association between the D2 but not D1 receptor gene and alcoholism in a genetically relatively homogenous population of male Finns was found. The results are in agreement with the view that the D2 receptor locus is involved in genetic susceptibility to alcoholism but does not give support to a special association of severe alcohol dependence and the A1 allele of the D2 receptor gene.

Intercontinental population structure of the chestnut blight fungus,Cryphonectria parasitica

The population structure of the chestnut blight fungus, Cryphonectria parasitica was analyzed using restriction fragment length polymorphisms (RFLPs). A total of 791 isolates were sampled from four regions, China, Japan, North America and Europe, and assayed for alleles at eight RFLP loci. Alleles at all eight loci segregated in simple Mendelian ratios, and most loci were unlinked. Gene diversity was decomposed hierarchically: 56% of gene diversity was attributable to diversity within subpopulations, compared to 7% among subpopulations within regions, and 37% among regions. Subpopulations of C. parasitica in China have distinctly different allele frequencies from subpopulations in other regions, including Japan. DNA fingerprint genotypes in China were also significandy different from those in the other regions. There was an average of 3.2 restriction fragments hybridizing to a DNA fingerprinting probe in Chinese isolates from 11 subpopulations compared to 8.6 in isolates from Japan; the exception was in one subpopulation in northeastern China where there was an average of 11.1 fragments per isolate. North American and European subpopulations were similar to each other, and more similar to Japan than to China, for both RFLP allele frequencies and DNA fingerprints. The results suggest that C. parasitica was introduced into North America from Japan, not China. The origin of C. parasitica for European subpopulations cannot be determined from these results, but eastern China was not a likely source. Analysis of population structure within China showed moderate differentiation, with 11% of gene diversity attributable to differences among subpopulations (ĜST = 0.11). Pairwise estimates of gene flow between sub-populations were negatively correlated to geographic distances between subpopulations in China. This result suggests that Chinese populations are in equilibrium, and that restricted gene flow and genetic drift shape these populations.

Intercontinental Population Structure of the Chestnut Blight Fungus, Cryphonectria parasitica

The population structure of the chestnut blight fungus, Cryphonectria parasitica was analyzed using restriction fragment length polymorphisms (RFLPs). A total of 791 isolates were sampled from four regions, China, Japan, North America and Europe, and assayed for alleles at eight RFLP loci. Alleles at all eight loci segregated in simple Mendelian ratios, and most loci were unlinked. Gene diversity was decomposed hierarchically: 56% of gene diversity was attributable to diversity within subpopulations, compared to 7% among subpopulations within regions, and 37% among regions. Subpopulations of C. parasitica in China have distinctly different allele frequencies from subpopulations in other regions, including Japan. DNA fingerprint genotypes in China were also significandy different from those in the other regions. There was an average of 3.2 restriction fragments hybridizing to a DNA fingerprinting probe in Chinese isolates from 11 subpopulations compared to 8.6 in isolates from Japan; the exception was in one subpopulation in northeastern China where there was an average of 11.1 fragments per isolate. North American and European subpopulations were similar to each other, and more similar to Japan than to China, for both RFLP allele frequencies and DNA fingerprints. The results suggest that C. parasitica was introduced into North America from Japan, not China. The origin of C. parasitica for European subpopulations cannot be determined from these results, but eastern China was not a likely source. Analysis of population structure within China showed moderate differentiation, with 11% of gene diversity attributable to differences among subpopulations (ĜST = 0.11). Pairwise estimates of gene flow between sub-populations were negatively correlated to geographic distances between subpopulations in China. This result suggests that Chinese populations are in equilibrium, and that restricted gene flow and genetic drift shape these populations.

Morphological Trait QTL Mapping in Tomato Recombinant Inbred Line Population

Quantitative trait loci influencing morphological traits were identified by restriction fragment length polymorphism (RFLP) analysis in a population of recombinant inbred lines (RIL) derived from a cross of the cultivated tomato (Lycopersicon esculentum) with a related wild species (L. cheesmanii). One-hundred-thirty-two polymorphic RFLP loci spaced throughout the tomato genome were scored for 97 RIL families. Morphological traits, including plant height, fresh weight, node number, first flower-bearing node, leaf length at nodes three and four, and number of branches, were measured in replicated trials during 1991, 1992, and 1993. Significant (P ≤ 0.01 level) quantitative trait locus (QTL) associations of marker loci were identified for each trait. Lower plant height, more branches, and shorter internode length were generally associated with RFLP alleles from the L. cheesmanii parent. QTL with large effects on a majority of the morphological traits measured were detected at chromosomes 2, 3, and 4. Large additive effects were measured at significant marker loci for many of the traits measured. Several marker loci exhibited significant associations with numerous morphological traits, suggesting their possible linkage to genes controlling growth and development processes in Lycopersicon.

Quantitative trait locus analysis of a recombinant inbred line population derived from a Lycopersicon esculentum x Lycopersicon cheesmanii cross

Quantitative trait loci influencing fruit traits were identified by restriction fragment length polymorphism (RFLP) analysis in a population of recombinant inbred lines (RIL) derived from a cross of the cultivated tomato, Lycopersicon esculentum with a related wild species Lycopersicon cheesmanii. One hundred thirty-two polymorphic RFLP loci spaced throughout the tomato genome were scored for 97 F8 RIL families. Fruit weight and soluble solids were measured in replicated trials during 1991 and 1992. Seed weight was measured in 1992. Significant (P<0.01 level) quantitative trait locus (QTL) associations of marker loci were identified for each trait. A total of 73 significant marker locus-trait associations were detected for the three traits measured. Fifty-three of these associations were for fruit weight and soluble solids, many of which involved marker loci signficantly associated with both traits. QTL with large effects on all three traits were detected on chromosome 6. Greater homozygosity at many loci in the RIL population as compared to F2 populations and greater genomic coverage resulted in increased precision in the estimation of QTL effects, and large proportions of the total phenotypic variance were explained by marker class variation at significant marker loci for many traits. The RIL population was effective in detecting and discriminating among QTL for these traits previously identified in other investigations despite skewed segregation ratios at many marker loci. Large additive effects were measured at significant marker loci. Lower fruit weight, higher soluble solids, and lower seed weight were generally associated with RFLP alleles from theL. cheesmanii parent.

Nrs1, a repetitive element linked to pisatin demethylase genes on a dispensable chromosome of Nectria haematococca.

We have identified a repetitive DNA element in Nectria haematococca mating population VI, isolate T-2. This repetitive sequence has been called Nrs1. DNA hybridization analysis indicates the sequence is found in several isolates of the fungus pathogenic to Pisum sativum. A 2,027-bp clone containing the Nrs1-2 allele contains a long polyA sequence, imperfect RNA polymerase III promoter sequences, multiple inverted repeats, and the potential for extensive secondary structure similar to known RNA polymerase III transcripts and related retroelements. Ten of the 11 HindIII restriction fragments from isolate T-2 DNA that hybridize to Nrs1-2 segregate in a manner consistent with a 1:1 ratio for random ascospore progeny. The 10 restriction fragment length polymorphism (RFLP) loci define three linkage groups and correspond to three chromosome-sized DNAs from T-2 separated by pulsed field gel electrophoresis. Three RFLP loci defined by hybridization to the gene for pisatin demethylase and localized on the 1.6 million base pair (Mb) chromosome were genetically linked to each other and to several Nrs1 loci. These sequences recombined despite the fact that no obvious homolog exists for the 1.6-Mb chromosome in one parent strain. Allelic RFLPs corresponding to the gene sequence of cutinase were unlinked to Nrs1 loci.

Genetic population structure and gene flow in the Atlantic cod Gadus morhua: a comparison of allozyme and nuclear RFLP loci.

High levels of gene flow have been implicated in producing uniform patterns of allozyme variation among populations of many marine fish species. We have examined whether gene flow is responsible for the limited population structure in the Atlantic cod, Gadus morhua L., by comparing the previously published patterns of variation at 10 allozyme loci to 17 nuclear restriction fragment length polymorphism (RFLP) loci scored by 11 anonymous cDNA clones. Unlike the allozyme loci, highly significant differences were observed among all populations at the DNA markers in a pattern consistent with an isolation-by-distance model of population structure. The magnitude of allele frequency variation at the nuclear RFLP loci significantly exceeded that observed at the protein loci (chi 2 = 24.6, d.f. = 5, P < 0.001). Estimates of gene flow from the private alleles method were similar for the allozymes and nuclear RFLPs. From the infinite island model, however, estimates of gene flow from the DNA markers were fivefold lower than indicated by the proteins. The discrepancy between gene flow estimates, combined with the observation of a large excess of rare RFLP alleles, suggests that the Atlantic cod has undergone a recent expansion in population size and that populations are significantly displaced from equilibrium. Because gene flow is a process that affects all loci equally, the heterogeneity observed among populations at the DNA level eliminates gene flow as the explanation for the homogeneous allozyme patterns. Our results suggest that a recent origin of cod populations has acted to constrain the extent of population differentiation observed at weakly polymorphic loci and implicate a role for selection in affecting the distribution of protein variation among natural populations in this species.