Human mitochondrial DNA types in Finland

Summary Variation in mitochondrial DNA (mtDNA) in a sample of 110 Finns was analyzed with six restriction enzymes, AvaII, BamHI, HaeII, HinII, HpaI, and MspI, by using total blood cell DNA probed with mouse mtDNA. Two new enzyme morphs were observed, one for HaeII and one for HindII. Double-digestion experiments indicated that the BamHI morphs 2 and 3 result from base changes leading to AvaII morphs 3 and 9, respectively. Of the ten different mtDNA types observed, defined by restriction fragment patterns, seven have been previously described in Caucasoid populations. The three new Finnish mtDNA types can be derived from Caucasoid lineages by single restriction site changes. The results were used to reconstruct a phylogenetic tree for Caucasoid mtDNA types defined by the enzymes used. The frequencies of mtDNA types were used to compute genetic distances between Finns, Italians, and Israeli Jews. The frequencies of both enzyme morphs and mtDNA types show that the Finnish population is highly homogeneous.     

Mitochondrial DNA diversity among four sympatric morphs of Arctic charr, Salvelinus alpinus L., from Thingvallavatn, Iceland

Restriction fragment length polymorphisms in mitochondrial DNA (mtDNA) were examined in progeny of four sympatric morphs of Arctic charr ( Salvelinus alpinus L.) from Thingvallavatn, Iceland. The mtDNA analysis with 46 hexanucleotide restriction enzymes indicates that the Thingvallavatn morphs are very closely related. Sequence divergence was less than 0.2% between any of the five clones detected. Although not significant, the topology of the mtDNA UPGMA dendogram was similar to that from a previous allozyme survey. Icelandic Arctic charr show greater affinity to charr from the British Isles than those from North America supporting their current taxonomic distinction.     

Genetic studies on the Tharu population of Nepal: restriction endonuclease polymorphisms of mitochondrial DNA.

The mitochondrial DNAs (mtDNAs) of 91 Tharus from Nepal were screened for restriction fragment length polymorphisms (RFLPs) using six highly informative restriction endonucleases. One pattern (morph) was found for BamHI, two for HpaI and HincII, three for HaeII, four for AvaII, and six for MspI. Two of the AvaII and four of the MspI morphs were "new" (not previously described). Virtually all of the "old" morphs found in the Tharus were previously observed in Orientals. The Oriental HaeII morph (HaeII-5) previously observed at a frequency of 5% was present in 25% of the Tharus. Of the 13 Tharu mtDNA types (defined by the six restriction endonuclease morphs) observed, five had previously been described ("old" types), all in Orientals. Three of these were unique for Orientals. All of the remaining eight "new" Tharu mtDNAs were all closely related to Oriental mtDNAs. Two of the "old" Tharu mtDNA types included the HpaI/HincII morph 1, a morph possibly indicative of the earliest human mtDNA types. From these data we have concluded that the Tharu mtDNAs are closely related to those of other Oriental populations. Further, our data support the hypothesis that human mtDNAs radiated from Asia.     

Molecular genetic examination of the polymorphic Arctic charr Salvelinus alpinus of Thingvallavatn, Iceland

Thingvallavatn, Iceland contains two sympatric morphotypes (benthic and limnetic) of Arctic charr Salvelinus alpinus. Each morphotype is composed of two morphs and these differ markedly in ecology, behaviour and life history. We used molecular genetic approaches to test whether (i) genetic heterogeneity exists among morphs and (ii) if morphs arose in allopatry and came into secondary contact or arose sympatrically within the lake through genetic segregation and/or phenotypic plasticity. Direct sequencing of 275 bp of the mitochondrial DNA (mtDNA) control region, mtDNA restriction fragment length polymorphisms and single locus minisatellite analyses detected insufficient variation to test our hypotheses. Analysis of multilocus minisatellite band sharing detected no significant differences between morphs within the same morphotype. However, significant differences among morphs belonging to different morphotypes suggest some genetic heterogeneity in Thingvallavatn charr. Limnetic charr from Thingvallavatn were more similar to sympatric benthic charr than to allopatric limnetics from two other Icelandic lakes. This suggests that the Thingvallavatn morphs arose sympatrically within the lake rather than in allopatry followed by secondary contact.     

Phylogeography of lateral plate dimorphism in the freshwater type of ninespine sticklebacks, genus Pungitius

The freshwater type of ninespine sticklebacks, genus Pungitius, is widely distributed in northern Japan and reproductively isolated from other genetically divergent types endemic to small regions in Japan. This type expresses dimorphism in its lateral plate morphology: complete and partial row morphs. The two morphs show a parapatric distribution in Japan. To clarify the process involving the distribution of these two morphs, we examined their phylogeography based on restriction fragment length polymorphism of an entire mitochondrial DNA (mtDNA). The survey was carried out with seven restriction enzymes on the populations of the freshwater type collected from 41 localities across the distribution range in Japan, and 6 further Pungitius populations from the Okhotsk Sea coast of Russia were appended. An unweighted pair-group method with arithmetic averages (UPGMA) tree among 54 mtDNA haplotypes resolved eight clustering groups that differed in sequence divergence by approximately 1.3%–2.1%. Two of the eight groups were found only in Russia. mtDNA phylogenies constructed by neighbor-joining and Wagner parsimony methods suggested that the haplotypes of each plate morph were polyphyletic. The geographic distribution pattern of these groups suggests that they should be classified into two broad categories, one with extensive distribution and the other with localized distribution of the constituent haplotypes within a group. The former groups were found mainly in the populations with the completely plated morph and the latter groups with the partially plated morph. It is supposed that twice dispersals of dimorphic or complete plated ancestors and genetic differentiation during the interglacial played an important role in the formation of the present distribution of the two morphs in Japan. Received: March 28, 2000 / Revised: November 3, 2000 / Accepted: January 16, 2001     

Mitochondrial DNA polymorphism in Japanese

Summary The mitochondrial DNA (mtDNA) from 120 Japanese was analysed with 15 restriction enzymes that recognize six base pairs, of which 11 enzymes showed at least one atypical cleavage pattern. Digestion patterns with HincII and HaeII were highly polymorphic. The observed restriction enzyme morphs were classified into 22 types of distinct cleavage patterns. By pairwise comparison of each restriction type, the average number of nucleotide substitutions per nucleotide site () was estimated at 0.00417, which agreed with the values obtained from other human populations in previous studies. There were 11 site gains, of which seven were transitions and four were transversions. Phylogenetic analysis of the present data suggested that the Japanese population conceals a considerably high degree of mtDNA diversity.     

Mitochondrial DNA polymorphism among five Asian populations

Mitochondrial DNA (mtDNA) polymorphisms were detected using 13 restriction enzymes on the total DNA obtained from blood samples of five Asian populations: Japanese and Ainu of northern Japan, Korean, Negrito (Aeta) of the Philippines, and Vedda of Sri Lanka. Of a total of 28 restriction-enzyme morphs detected, eight had not been reported previously. By combining the morphs, we were able to classify mtDNAs of 243 individuals into 20 mtDNA types. Phylogenetic analyses using maximum parsimony and genetic distance methods both showed that the Japanese, Ainu, and Korean populations were closely related to each other. Aeta was found to show a relatively close relationship to these three populations, confirming the conclusion from previous studies of blood markers. In contrast, Vedda was quite different from the other four populations.     

Comparison between the Polish population and European populations on the basis of mitochondrial morphs and haplogroups

Polymorphisms in mitochondrial DNA (mtDNA) were analyzed in 152 samples from the Polish population using restriction enzymes AvaI, BamHI, HaeII, HpaI and PstI. Additionally, each sample was classified into the appropriate haplogroup. When required, appropriate fragments were sequenced to establish the exact polymorphic sites. We found one new morph for PstI and six new morphs for AvaII. Some detected morphs have previously been described as population specific morphs in different regions of the world. All polymorphisms were classified into 31 different haplotypes. 21 of them were detected in single individuals. The Polish population was compared with other populations from different regions. Moreover, we have obtained evidence for mutation hot spots in the mtDNA coding region. Our results indicate that AvaII morph and haplogroup composition of the Polish population is similar to other European populations and has a distribution typical for this part of the world. However, statistically significant differences in haplogroup composition were found between the Polish population and Italian and Finnish populations.     

Human mitochondrial DNA types in two Israeli populations--a comparative study at the DNA level.

Variations in human mtDNA restriction endonuclease fragment patterns were investigated in a sample number of 81 Israelis--Jews and Arabs--using total blood cell DNA. Eight new morphs were observed using five enzymes: HpaI, BamHI, HaeII, MspI, and AvaII. Of the 18 different combinations of fragment patterns (mtDNA types), only three were shared by both groups, but with striking frequency differences. The Arab sample disclosed "African" characteristics and was found to be slightly more polymorphic than the Israeli sample. One of the new types filled a "missing link" originally postulated in a phylogeny of mtDNA human types.     

Mitochondrial DNA polymorphism in Japanese

Summary Mitochondrial DNA (mtDNA) from 116 Japanese was analyzed with nine restriction enzymes that recognize a four or five base pair sequence. The sizes of the mtDNA fragments produced by digestion by each enzyme were compared after gel electrophoresis. Double digestion experiments indicated that, in the coding region from URF2 (unidentified reading frame) to tRNA^Asn (bp 5274–5691), there is an insertion of about 60 base pairs (bp) compared with the published mtDNA sequence, which is common to all individuals in the present sample. A total of 95 different morphs were detected with the nine enzymes, 60 of which have not been documented previously. Based on a comparison of the cleavage maps of all individuals, 62 different combinations of restriction types were observed. By pairwise comparison of each restriction type, the average number of nucleotide substitutions per nucleotide site () was estimated to be 0.0026. Phylogenetic analysis of the present data indicates that at least two distinct lineages exist in the Japanese population.     

Mitochondrial DNA differentiation between two sympatric morphs of striped jack near Japan

Two sympatric morphs (type A with a vertebral number of 25 and type B with a vertebral number of 24) of striped jack Pseudocaranx dentex (Bloch & Schneider) were analysed genetically. A part of the 16S–rRNA region of mtDNA was amplified with polymerase chain reaction for 24 specimens, and a restriction enzyme fragment polymorphism showed significant differences between the two types. While all specimens sampled in Ogasawara were identified as type B, about 90% of striped jack in Oita were type A and 10% were type B. Although the spawning areas of these two types are still unknown, significant genetic differences between the two sympatric morphs show that recruitment and migration patterns might differ from each other. The current system suggests the possibility that the juveniles of type B in Oita may migrate from the Ogasawara Islands.     

Mitochondrial DNA polymorphisms in a sample of Albanian population (Tirana)

RFLPs of mtDNA for HpaI, BamHI, HaeII, MspI, AvaII and HincII were analysed in a sample of 100 from collected in Tirana (Albania). Eighteen mtDNA types were identified, four of which are new: two because of new morphs for Hpa/HincII (HpaI-9^Tir/HincII-17^Tir) and AvaII (AvaII-35Tir), and two because of new associations between morphs which were already known. Albanian data were compared with corresponding ones from Calabrians (Southern Italians) and Arbreshes (people of Albanian ancestry living in Calabria). Even though the examined mtDNA markers do not reveal important differences among the three groups, the analysis of both morphs and types shows a trend which places Arbreshes closer to Calabrians than to Albanians.     

Mitochondrial DNA variation in cattle of South China: origin and introgression

Ten restriction endonucleases were used to investigate the mitochondrial DNA restriction fragment length polymorphism (mtDNA RFLP) of 11 native cattle breeds and one cultivated cattle breed in South China. Twenty-three restriction morphs were detected, which can be sorted into five haplotypes. A phylogenetic tree of the haplotypes was constructed by using the 'upgMa' method. Our study showed that haplotype I and II are identical to the zebu (Bos indicus) and taurine (Bos taurus) haplotypes, respectively. Zebu and taurine were the two major origins of cattle populations in South China, and the zebu probably had more influence on the native cattle population than taurine did. Haplotype III is identical to haplotype I of yak (Bos grunniens), which was only detected in the Diqing cattle breed. Haplotype IV was detected for the first time. This haplotype, found only in Dehong cattle, might be from an independent domestication event, probably from another Bos indicus population. Divergence of haplotypes I and IV occurred about 268,000-535,000 years ago, much earlier than the 10,000-year history of cattle husbandry. Our results also suggest a secondary introgession of mtDNA from yak to Diqing cattle.     

Genetic variation of the mitochondrial DNA genome in American Indians is at mutation-drift equilibrium.

Several surveys have found evidence for founder effects in Amerindian mitochondrial DNA because of the existence of rare Asian morphs in high frequencies in some Amerindian populations and the occurrence of several new morphs not seen elsewhere in the world. These reports, however, do not address whether or not the present genetic variation in the mtDNA genome in Amerindians has reached the steady-state distribution predicted by the mutation-drift theory of population genetics. The present work suggests that in three Amerindian populations (Pima, Maya, and Ticuna) a steady state has apparently been reached, and hence the initial founder effect has probably dissipated during the evolution of Amerindians in the New World. This result is consistent with the genetic variation in nuclear genes in similar populations, shown through surveys of protein variation in earlier work and, more recently, in studies of restriction fragment length polymorphisms.     

Genetic studies on the Senegal population. I. Mitochondrial DNA polymorphisms.

The mtDNA of 186 Senegalese, mainly Wolof and Peuls, were analyzed by means of six restriction enzymes: HpaI, BamHI, HaeII, MspI, AvaII, and HincII. Two of the HpaI, one of the HaeII, two of the MspI, and one of the AvaII morphs had not been described before. The only enzymes which enabled Wolof and Peuls to be differentiated were HincII and, to a lesser extent, HaeII. Important differences emerge in the comparison of Senegalese with Bantu of South Africa and with Bushmen, the only other Africans who, as far as we know, were studied for the same genetic markers. Though Senegalese mtDNAs display typical African features (presence and frequency of HpaI morph 3 and high incidence of AvaII morph 3), the distribution of MspI and AvaII patterns markedly differentiates Senegalese from the others. The phylogeny of mtDNA types in Africa well portrays how the three African groups are clearly distinguishable genetic entities. Bushmen lie at one end of the range of variability, Senegalese being at the other end but still fairly closely related to Bantu. The information provided by individual restriction enzymes to the distinction among the three major ethnic groups is reviewed and discussed.     

Mitochondrial DNA polymorphism reveals hidden heterogeneity within some Asian populations.

Use of data on mtDNA morph distributions from six Asian populations has shown that the observed number of different mtDNA morphs is too large when compared with the number expected on the basis of the observed gene diversity in the mtDNA genome. This excess number of morphs mainly occurs through an excess of rare morphs, and this discrepancy is more pronounced in a pooled sample of five Asian populations. It is suggested that this discrepancy is probably due to internal heterogeneity in each of the anthropologically defined populations. This analysis demonstrates the utility that population data for a single locus, such as the mtDNA genome, have for detecting hidden heterogeneity in populations, provided that the locus has substantial genetic variability, so that many variant alleles can be detected.     

Lack of mitochondrial genetic structure in hamlets (Hypoplectrus spp.): recent speciation or ongoing hybridization?

Species in the genus Hypoplectrus (hamlet fish) have been recognized primarily on the basis of colour morphology, which varies substantially. Limited differentiation in other morphological characters, however, has led to ongoing debate about their taxonomy. Our analysis of mtDNA sequences demonstrates neither reciprocal monophyly nor significant genetic differentiation among hamlet colour morphs. These data are potentially consistent with a model of recent speciation due to sexual selection on colour morphology. The presence within hamlets of two divergent mtDNA clades, however, suggests a longer history during which hybridization and gene flow have prevented the differentiation of hamlet colour morphs, at least in neutral genetic markers.     

RACE FORMATION,SPECIATION, AND INTROGRESSION WITHIN DROSOPHILA SIMULANS,D. MAURITIANA,AND D. SECHELLIA INFERRED FROM MITOCHONDRIAL DNA ANALYSIS

Mitochondrial DNA cleavage maps from three chromosomally homosequential species Drosophila simulans, D. mauritiana, and D. sechellia, were established for 12 restriction enzymes. One isofemale strain was studied in D. sechellia (se), 13 in D. simulans, and 17 in D. mauritiana: in the last two species, respectively, three (siI, II, and III) and two (maI and II) cleavage morphs were found. The evolutionary relationships based on mtDNA cleavage map comparisons show that the maI and se mtDNAs are internal branches of the phylogenetic tree of the D. simulans mtDNA. D. mauritiana and D. sechellia species appear to be derived from a population of D. simulans which carried an ancestral form of the current siI mtDNA type. In addition, two cleavage morphs (siIII [only present in D. simulans from Madagascar] and maI) appeared to be identical, although found in different species. We present a speculative interpretation of data on biogeography and hybridization which is consistent with the hypothesis of a recent introgression of mitochondrial DNA of D. simulans from Madagascar into D. mauritiana.     

EVIDENCE OF A BIOGEOGRAPHIC BREAK BETWEEN POPULATIONS OF A HIGH DISPERSAL STARFISH: CONGRUENT REGIONS WITHIN THE INDO-WEST PACIFIC DEFINED BY COLOR MORPHS,mtDNA, AND ALLOZYME DATA

Both mtDNA variation and allozyme data demonstrate that geographic groupings of different color morphs of the starfish Linckia laevigata are congruent with a genetic discontinuity between the Indian and Pacific Oceans. Populations of L. laevigata sampled from Thailand and South Africa, where an orange color morph predominates, were surveyed using seven polymorphic enzyme loci and restriction fragment analysis of a portion of the mtDNA including the control region. Both allozyme and DNA data demonstrated that these populations were significantly genetically differentiated from each other and to a greater degree from 23 populations throughout the West Pacific Ocean, where a blue color morph is predominant. The genetic structure observed in L. laevigata is consistent with traditional ideas of a biogeographic boundary between the Indian and Pacific Oceans except that populations several hundreds kilometers off the coast of north Western Australia (Indian Ocean) were genetically similar to and had the same color morphs as Pacific populations. It is suggested that gene flow may have continued (possibly at a reduced rate) between these offshore reefs in Western Australia and the West Pacific during Pleistocene falls in sea level, but at the same time gene flow was restricted between these Western Australian populations and those in both Thailand and South Africa, possibly by upwellings. The molecular data in this study suggest that vicariant events have played an important role in shaping the broadscale genetic structure of L. laevigata. Additionally, greater genetic structure was observed among Indian Ocean populations than among Pacific Ocean populations, probably because there are fewer reefs and island archipelagos in the Indian Ocean than in the Pacific, and because present-day surface ocean currents do not facilitate long-distance dispersal.     

Some physicochemical properties of rice mitochondrial DNA

Summary Certain physicochemical properties of rice mitochondrial DNA (mtDNA) were determined. Certain low-molecular-weight mtDNA bands were found in addition to the major mtDNA band. Rice mtDNA appeared in the electron microscope as a collection of linear molecules with heterogeneous length in the range of 1–156 kb. The major distribution area was 60–105 kb. A small fraction (less than 5%) of rice mtDNA was found in the form of a circular molecule. Some molecules had the appearance of being supercoiled. Replication fork structures were found in both circular and linear mtDNA molecules. In one rice species, Jin Nante, 15 different circular molecules were found. Rice mtDNA was digested with different restriction enzymes. The total molecular weight of rice mtDNA was calculated to be about 300 kb according to the data of restriction enzyme digestion and electron microscopy.