Polymorphism of mitochondrial genome noncoding regions in the three Kazakh populations inhabited different areas of Kazakhstan and in the samples of DNA from ancient people of Kazakhstan Altai

Polymorphism of major noncoding region of mitochondrial DNA (mtDNA D-loop, 528 bp in length) from the three modem kazakh populations and from DNA samples of ancient people inhabited modern Kazakhstani Altai were studied. PCR and RFLP analysis of 13 sites of restriction--BamHI, EcoRV, Sau3AI (1 restriction site), KpnI (2 sites), HaeIII (3 sites), RsaI (5 restriction sites), were carried out. The distribution of each site frequencies was determined. Nucleotide diversity (h) and genetic distance between different kazakh population and other populations of world were estimated. The same RFLP analysis of the mitochondrial DNA control region was carried out for the paleogenomic samples. It was shown that two samples of ancient mitochondrial DNA were monomorphous throughout all analyzed restriction sites.     

Insertion-deletion polymorphism of mitochondrial DNA region V in Kazakh populations from different regions of Kazakhstan

Insertion-deletion polymorphism of the mitochondrial DNA (mtDNA) region V was examined in three Kazakh populations inhabiting different regions of Kazakhstan. The 9-bp deletion was revealed in all three populations examined. In Altai population the 4-bp insertion was also found. The presence of these polymorphic variants was confirmed by DNA sequencing.     

Mitochondrial DNA Polymorphism in Natural Populations of the Drosophila virilis Species Group

Restriction fragment length polymorphism (RFLP) analysis has been used to evaluate mitochondrial DNA (mtDNA) variation in 12 sibling species forming the Drosophila virilis species group. The variation thresholds corresponding to the interspecific and interstrain levels have been determined. The results indicate that interspecific hybridization has significantly contributed to the evolutionary history of the virilis species group.     

Insertion–Deletion Polymorphism of Mitochondrial DNA Region V in Kazakh Populations from Different Regions of Kazakhstan

Insertion–deletion polymorphism of the mitochondrial DNA (mtDNA) region V was examined in three Kazakh populations inhabiting different regions of Kazakhstan. The 9-bp deletion was revealed in all three populations examined. In Altai population the 4-bp insertion was also found. The presence of these polymorphic variants was confirmed by DNA sequencing.     

Polymerase chain reaction analysis of mitochondrial DNA polymorphism in N'Dama and Zebu cattle

A study of polymorphisms of mitochondrial DNA (mtDNA) of West African N'Dama (Bos taurus) and East African Zebu (B. indicus) cattle was carried out to obtain information on maternal phylogenetic relationships between these breeds. A relatively large sample size was made possible by using polymerase chain reaction (PCR) amplification of DNA prepared from small blood samples to generate fragments of two known polymorphic mtDNA regions, one within the gene encoding subunit 5 of NADH dehydrogenase and one encompassing the entire D-loop. This approach allowed us to achieve a higher resolution restriction analysis on mtDNA from more animals than would have been possible by conventional methods. PCR-amplified mtDNA of 58 animals from five populations was examined at 26 restriction sites by 16 enzymes. In this way 154 nucleotides of mtDNA were scanned for polymorphism. Six polymorphic sites were located by this means, five of which were within the D-loop and one of which was within the NADH dehydrogenase 5 gene. None of the polymorphisms observed could be con sidered typical of breed or type.     

Phylogeographic Analysis of Chum Salmon Oncorhynchus keta Walbaum in Asian Populations Based on mtDNA Variation

We used restriction length polymorphism (RFLP) analysis of PCR-amplified fragments of mtDNA to study the genetic structure of chum salmon populations sampled in 1993–2000 during a spawning run in five rivers: Narva (Southern Primorye), Naiba (Sakhalin Island), Sernovodnaya (Kunashir Island, Southern Kuril Islands), Ola (northwestern coast of the Sea of Okhotsk), and Anadyr' (Chukotka Peninsula). In total, 49 haplotypes were identified in 193 fish. Heterogeneity tests showed highly significant (P = 0) differences among all sample pairs. The estimated time of independent divergence of the populations or population groups is in good agreement with the time of Pleistocene glaciations. This result suggests that it is cyclic global changes during this time period that were crucial in determining the within-species divergence in chum salmon. The types of mtDNA genetic variability and mismatch distribution between haplotypes in the populations indicate that the southern regions of the Sea of Okhotsk and Sea of Japan served as refugia for chum salmon during glaciation periods.     

The Divergence of the Dolly Varden Char Salvelinus malma in the Asian Northern Pacific Populations Inferred from the PCR–RFLP Analysis of Mitochondrial DNA

Genetic differentiation of the Dolly Varden char Salvelinus malmaWalbaum was studied in five populations from the western part of the Northern Pacific. Using restriction analysis (RFLP), we examined polymorphism of three mitochondrial DNA (mtDNA) fragments amplified in polymerase chain reaction (PCR). MtDNA haplotypes were shown to fall into two phylogenetic groups, which probably reflect the existence of two previously described subspecies of Asian Dolly Varden,S. malma malma and S. malma krascheninnikovi. The divergence of mtDNA nucleotide sequences in the Dolly Varden subspecies (about 4%) corresponds to the differences between the valid char species from the genus Salvelinus.     

MITOCHONDRIAL DNA HOMOGENEITY IN THE PHENOTYPICALLY DIVERSE REDPOLL FINCH COMPLEX (AVES: CARDUELINAE: CARDUELIS FLAMMEA-HORNEMANNI)

Breeding redpoll finches (Aves: Carduelinae) show extensive plumage and size variability and, in many cases, a plumage polymorphism that is not related to age or sex. This has been ascribed to extreme phenotypic variation within a single taxon or to moderate variability within distinct taxa coupled with hybridization. The predominant view favors the recognition of two largely sympatric species: Carduelis flammea, comprised of four well-marked subspecies—flammea, cabaret, islandica, and rostrata; and C. hornemanni, comprised of two subspecies—hornemanni and exilipes. We studied representative samples of these putative subspecies (except islandica) for variation in mitochondrial DNA (mtDNA). Using 20 informative restriction enzymes that recognized 124 sites (642 base pairs [bp] of sequence or ≈ 3.7% of the molecule), we identified 17 RFLP haplotypes in the 31 individuals surveyed. The haplotypes formed a simple phylogenetic network with most clones diverging by a single site difference from a common haplotype found in almost half of the individuals. Within populations and taxa, levels of mtDNA diversity were similar to those observed in other avian species. The pattern of mtDNA divergence among populations was statistically unrelated to their geographic or traditional taxonomic relationships, and the estimated distance between the two traditionally recognized species was very small relative to those typically observed among avian sister species.     

Congruence in genetic markers used to describe Mediterranean and Atlantic populations of European hake (Merluccius merluccius L. 1758)

Eight samples of the hake, Merluccius merluccius L., from the Mediterranean basin (370 fishes total) and one from the Atlantic ocean (50 fishes) were analysed in order to assess genetic variability and describe genetic population structure. Five polymorphic protein coding loci were scored (ADH*, PGI‐1*, PGI‐2*, PGM* and SOD‐1*) in eight samples, together with a haplotype variation of four samples, obtained from polymerase chain reaction/restriction fragment length polymorphism (PCR–RFLP) analysis on the mitochondrial DNA control region. The average value for observed heterozygosity was typically higher than expected (showing an excess of heterozygotes among the samples) whereas the haplotype diversity at mtDNA was very low. Samples originating from inside the Mediterranean basin appeared genetically homogeneous but the sample originating from the Atlantic was heterogeneous compared with the Mediterranean populations. Nuclear and mitochondrial gene analysis showed similar results supporting that the Strait of Gibraltar may be considered as a breakpoint area to gene flow.     

Mitochondrial DNA diversity in Siberian Tatars of the Tobol-Irtysh basin

Data on the variation of the nucleotide sequence of hypervariable segment I (HVSI) and restriction fragment length polymorphism (RFLP) of the coding region of mitochondrial DNA (mtDNA) have been used to characterize the mitochondrial gene pool of Siberian Tatars of the Tobol-Irtysh basin (N = 218), one of three geographic/linguistic groups of Siberian Tatars. The gene pool of Siberian Tatars has been shown to contain both Asian and European mtDNA lineages at a ratio of 1.0 : 1.5. The mtDNA diversity of Siberian Tatars is substantially higher than that of other Turkic-speaking populations of North and Central Asia. The position of the mitochondrial gene pool of Tatars of the Tobol-Irtysh basin in the genetic space of northern Eurasia populations has been determined.     

Microsatellite Markers Reveal Genetic Variation within Sclerotinia sclerotiorum Populations in Irrigated Dry Bean Crops in Brazil

Microsatellites are powerful markers to infer population genetic parameters. We used 10 microsatellite loci to characterize the genetic diversity and structure of 79 samples of Sclerotinia sclerotiorum isolated from four Brazilian dry bean populations and observed that eight of them were polymorphic within populations. We identified 102 different haplotypes ranging from 6 to 18 per locus. Analyses based on genetic diversity and fixation indices indicated variability among and within populations of 28.79% (F_ST = 28793) and 71.21%, respectively. To examine genetic relatedness among S. sclerotiorum isolates, we used internal spacer (ITS1‐5.8S‐ITS2) restriction fragment length polymorphism (PCR‐RFLP) and sequencing analysis. PCR‐RFLP analysis of these regions failed to show any genetic differences among isolates. However, we detected variability within the sequence, which does not support the hypothesis of clonal populations within each population. High variability within and among populations may indicate the introduction of new genotypes in the areas analysed, in addition to the occurrence of clonal and sexual reproduction in the populations of S. sclerotiorum in the Brazilian Cerrado.     

Mitochondrial DNA Diversity in Three Populations of the Giant Tiger Shrimp Penaeus monodon

Mitochondrial DNA restriction fragment length polymorphism (mtDNA-RFLP) was utilized for determination of genetic variation and population structure in Penaeus monodon collected from Satun (the Andaman Sea) and Surat and Trat (the Gulf of Thailand). Twenty-eight composite haplotypes were generated from 52 restriction profiles of P. monodon mtDNA digested with 11 restriction endonucleases. The size of the entire P. monodon mitochondrial genome was estimated to be 15.913 ± 0.177 kb. The average haplotype diversity in P. monodon was 0.864, whereas the mean nucleotide diversity within populations was 2.51%, 2.22%, and 1.91% for Satun, Trat, and Surat, respectively. Geographic heterogeneity analysis indicated population differentiation between P. monodon from the Andaman Sea and P. monodon from the Gulf of Thailand (p < .0001). On the basis of the high genetic diversity level of P. monodon in Thailand, the Satun and Trat P. monodon populations from the west and east of the pennisula were selected to be founder stocks in our selective breeding program. Received February 23, 1998; accepted September 30, 1998.     

Mitochondrial DNA restriction map for the mediterranean fruit fly,Ceratitis capitata

Molecular genetic research on the Mediterranean fruit fly,Ceratitis capitata, will provide tools to permit determination of source populations for new pest infestations. Restriction fragment length polymorphism (RFLP) of mitochondrial DNA provides some interpopulation discrimination. A restriction map, including the informative variableEcoRV andXbaI restriction sites, is constructed for the Mediterranean fruit fly, and several restriction sites are associated with specific gene regions based on polymerase chain reaction-RFLP and sequence analyses. A partial sequence of the mitochondrial 16S ribosomal RNA gene is reported.     

Identification of Japanese Lymantria species (Lepidoptera: Lymantriidae) based on PCR–RFLP analysis of mitochondrial DNA

A polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP)-based method for species identification was applied to seven Japanese Lymantria species, including four Asian gypsy moth (AGM) species. We sequenced the partial end of the cytochrome c oxidase I (COI) gene, tRNA leucine, COII gene, and partial end of the tRNA lysine in mitochondrial DNA (mtDNA) for one individual of each of the seven species. We analyzed the recognition sites of three restriction endonucleases and constructed a scheme for Lymantria species identification using PCR–RFLP. We then applied the scheme to 291 individuals from 45 populations of seven species. We found that all seven species were correctly identified using PCR–RFLP. These results suggest that PCR–RFLP is useful for identifying Japanese Lymantria species, which may be detected at Japanese ports.     

Rapid polymerase chain reaction-restriction fragment length polymorphism method for discrimination of the two Atlantic cryptic deep-sea species of scabbardfish

The present investigation provides an efficient diagnostic method based on polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis to discriminate between two cryptic species of scabbardfish, Aphanopus carbo and A. intermedius, with commercial relevance in several European fish markets. Two DNA fragments from the mtDNA, including control region and partial cytochrome oxidase subunit I genes of about 1100 bp and 700 bp, respectively, were isolated by PCR amplification. Digestion of the amplicon including the control region with HaeII and the amplicon including the COI gene with Sau3AI restriction enzymes allowed an unequivocal discrimination between the two scabbardfish species. This PCR–RFLP method allowed a clear and rapid discrimination of the trichiurid species studied.     

Molecular analysis of the gene for the human vitamin-D-binding protein (group-specific component): allelic differences of the common genetic GC types

Summary DNA sequence analysis of the polymerase chain reaction products, including the coding region for amino acids 416 and 420, of the vitamin-D-binding protein (DBP, group-specific component, GC) shows allelespecific differences. The GC2 and GC1F phenotypes have an aspartic acid residue at amino acid position 416, whereas the GC1S phenotype has a glutamic acid at this position. In the GC2 phenotype, amino acid 420 is a lysine residue, and in the both common GC1 phenotypes, it is a threonine residue. The nucleotide exchanges involve a HaeIII (position 416) and a StyI (position 420) restriction site: the HaeIII restriction site is specific for the GC^*1S allele and the StyI restriction site is specific for the GC^*2 allele. We have tested 140 individual genomic DNA samples for the HaeIII site and 148 samples for the StyI site by restriction fragment length polymorphism (RFLP) analysis with a DBP-specific direct genomic DNA probe, and have compared these findings with the GC phenotype classification, by isoelectric focusing (IEF) of the corresponding plasma. The results of the HaeIII RFLP analysis and the IEF typing were in complete agreement. By using our DNA probe, we could disclose, in addition to the StyI site at amino acid position 420, two further StyI site downstream: one was specific for the GC^*1S allele and another for the GC^*1F allele. In 147 samples, there was agreement between the IEF GC typing and the analysis of the StyI restriction sites. In a single case, the observed result of the StyI-digest differed from the result expected after IEF classification: homozygous GC 1F-1F by IEF and heterozygous by StyI RFLP analysis. We discuss this finding as a recombination event or a possible silent allele in IEF typing. The GC polymorphism revealed by Southern blot analysis of StyI-digests provides an informative DNA marker system for chromosome 4q11–q13.     

Restriction polymorphism of the major non-decoding region of mitochondrial DNA in human populations from the Volga-Ural region]

The restriction fragment length polymorphism (RFLP) of the major noncoding region of mitochondrial DNA (mtDNA) was studied in the Bashkir (N = 217), Tatar (N = 57), Chuvash (N = 44), Mari (N = 52), Mordovian (N = 55), Udmurt (N = 62), and Komi (N = 45) populations. Of seven polymorphic AvaII, BamHI, EcoRV, KpnI, and RsaI restriction sites, five were found in Bashkirs and Tatars, and four were found in each of the other populations. In total, 13 mitotypes were detected, and only three of them were common to all populations from the Volga-Ural region. The parameters of gene diversity were calculated with respect to the polymorphic sites and mitotypes. Comparison with published data revealed both Mongoloid and Caucasoid components in the gene pool of the modern populations from the Volga-Ural region. The Mongoloid component was prevalent in the mitochondrial gene pool, which is consistent with historical, anthropological, and ethnographic data.     

Origin and differentiation of human mitochondrial DNA.

A recent study of mitochondrial DNA (mtDNA) polymorphism has generated much debate about modern human origins by proposing the existence of an "African Eve" living 200,000 years ago somewhere in Africa. In an attempt to synthesize information concerning human mtDNA genetic polymorphism, all available data on mtDNA RFLP have been gathered. A phylogeny of the mtDNA types found in 10 populations reveals that all types could have issued from a single common ancestral type. The distribution of shared types between continental groups indicates that caucasoid populations could be the closest to an ancestral population from which all other continental groups would have diverged. A partial phylogeny of the types found in five other populations also demonstrates that the myth of an African Eden was based on an incorrect "genealogical tree" of mtDNA types. Two measures of molecular diversity have been computed on all samples on the basis of mtDNA type frequencies, on one hand, and on the basis of the number of polymorphic sites in the samples, on the other. A large discrepancy is found between the two measures except in African populations; this suggests the existence of some differential selective mechanisms. The lapse of time necessary for creating the observed molecular diversity from an ancestral monomorphic population has been calculated and is found generally greater in Oriental and caucasoid populations. Implications concerning human mtDNA evolution are discussed.     

Plastid DNA diversity in natural populations of Beta maritima showing additional variation in sexual phenotype and mitochondrial DNA

Summary Plants of two natural populations of Beta maritima, characterized by high percentages of male-sterile plants, have been investigated for organelle DNA polymorphism. We confirm the two classes of mitochondrial DNA variation previously described: (i) mitochondrial DNA (mtDNA) type N is associated with male fertility, whereas mtDNA type S can cause cytoplasmic male sterility (CMS); (ii) the 10.4-kb linear plasmid is observed in both types of mitochondria and is not correlated with the cytoplasmic male sterility occurring in this plant material. A third polymorphism is now described for chloroplast DNA (ctDNA). This polymorphism occurs within single populations of Beta maritima. Three different ctDNA types have been identified by HindIII restriction analysis. Among the plants studied, ctDNA type 1 is associated with N mitochondria and type 2 with S mitochondria. Chloroplast DNA type 3 has been found both in a fertile N plant and in a sterile S plant. This finding suggests that the chloroplast DNA polymorphism reported is not involved in the expression of male sterility. A comparison with Beta vulgaris indicates that ctDNA type 3 of Beta maritima corresponds to the ctDNA of fertile sugar beet maintainer lines. The three types of Beta maritima ctDNA described in this study differ from the ctDNA of male-sterile sugar beet.     

Discrimination of cassava-associated Bemisia tabaci in Africa from polyphagous populations, by PCR–RFLP of the internal transcribed spacer regions of ribosomal DNA

Restriction fragment length polymorphism (RFLP) analysis of the ribosomal DNA internal transcribed spacer regions of Bemisia tabaci was used to distinguish cassava‐associated populations from other host‐associated populations. Endonuclease restriction profile analysis indicated that cassava‐associated populations from Africa represent a distinct group, with a significant level of separation into subgroups that were not linked to geographical origin. Analysis of molecular variance (amova ) revealed that a high proportion of the total genetic variation (47%) was attributable to among‐population differences within the host‐associated groups. Principal coordinate analysis supported the differentiation between the cassava and the non‐cassava group, a result which was in agreement with the cluster analysis of the restriction fragment profile. Internal transcribed spacer RFLP markers, especially SmaI, identified in this study can be used to monitor the spread of B. tabaci biotypes, especially of the more virulent biotype B that has so far not been reported in the cassava‐growing belt of Africa.