Nucleotide Sequence Of Mitochondrial DNA Research Articles

Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence.

All mitochondrial-encoded proteins and RNAs function through interactions with nuclear-encoded proteins, which are critical for mitochondrial performance and eukaryotic fitness. Coevolution maintains inter-genomic (i.e., mitonuclear) compatibility within a taxon, but hybridization can disrupt coevolved interactions, resulting in hybrid breakdown. Thus, mitonuclear incompatibilities may be important mechanisms underlying reproductive isolation and, potentially, speciation. Here we utilize Pool-seq to assess the effects of mitochondrial genotype on nuclear allele frequencies in fast- and slow-developing reciprocal inter-population F2 hybrids between relatively low-divergence populations of the intertidal copepod Tigriopus californicus. We show that mitonuclear interactions lead to elevated frequencies of coevolved (i.e., maternal) nuclear alleles on two chromosomes in crosses between populations with 1.5% or 9.6% fixed differences in mitochondrial DNA nucleotide sequence. However, we also find evidence of excess mismatched (i.e., noncoevolved) alleles on three or four chromosomes per cross, respectively, and of allele frequency differences consistent with effects involving only nuclear loci (i.e., unaffected by mitochondrial genotype). Thus, our results for low-divergence crosses suggest an underlying role for mitonuclear interactions in variation in hybrid developmental rate, but despite substantial effects of mitonuclear coevolution on individual chromosomes, no clear bias favoring coevolved interactions overall.

Phylogenetic relationships and historical population reconstruction of Asian members of the genus Epischura (Copepoda, Calanoida)

We have reconstructed major demographic and phylogenetic events for two closely related copepod species: Epischura baikalensis Sars, 1900 (Copepoda, Calanoida), a key endemic species of the plankton community from Lake Baikal, and E. chankensis Rylov, 1928, a key zooplankton species from Lake Khanka. The reconstructions were based on the nucleotide sequences of mitochondrial DNA (mtDNA) cytochrome oxidase subunit 1 (CO1) using the BEAST software package and recently identified calibrations for the Baikal amphipods Gmelinoides fasciatus. The time span to a common ancestor for E. baikalensis and E. chankensis is 13.7 million years (95% confidence interval is 8.3–21.4 million years. Both species studied have experienced abrupt changes in the effective population size in the past. These changes are likely associated with climate and geological shifts in their habitat areas. For E.baikalensis, these changes can be associated with alternating glacier and interglacial periods as well as an increase in depth of Lake Baikal; for E. chankensis with formation and increase in the area of Lake Khanka, which was also due to climate and geological shifts in the Khanka basin.

Distribution, Composition and Relationships of Phylogenetic Groups of Arctic Charr Salvelinus alpinus (L.) (Salmoniformes, Salmonidae) in the European part of Russia and in Siberia as Revealed by the Analysis of Nucleotide Sequences of Mitochondrial DNA

In order to extend the geography of genetic studies at the broad circumpolar range of Arctic charr we analyzed sequence variation of mtDNA control region (537–547 b.p.) in 25 populations of the European part of Russia and Siberia. In most of them, haplotypes of the Atlantic or of the Siberia phylogenetic groups were found. The results of phylogenetic analysis indicate low segregation between these groups, for that reason they are considered as two subgroups of a single Eurasian group; the composition and ranges of these subgroups are specified. Charr with haplotypes of the Atlantic subgroup were found in Karelia, at Kola Peninsula, Polar Urals, Novaya Zemlya archipelago, Taimyr; charr with haplotypes of the Atlantic subgroup, in Transbaikalia, in mountainous upper reaches of the Yana and the Indigirka basins and in the lower reaches of the Anabar. Both subgroups reveal weak geographical structuring at large geographic scale. Besides, in the lower Anabar basin Arctic charr bearing a haplotype of the Bering group, which introgressed in their genome from the northern form of Dolly Varden were recorded. Our results evidence a wide-scale post-Pleistocene dispersal of the anadromous form of the Atlantic subgroup charr throughout the Atlantic and Arctic Oceans drainage basins; common origin and close phylogenetic relationships of Arctic charr of the Siberian subgroup from different regions of Siberia and their possible migrations between these regions during the Pleistocene glacial maxima. They also confirm the participation of charr from Beringia in the colonization of Siberian Arctic coasts and indicate that they dispersed further to the west than previously known.

Genetic characterization of Vietnamese Yellow cattle using mitochondrial DNA and Y-chromosomal haplotypes and genes associated with economical traits.

Vietnamese Yellow cattle are native cattle well adapted to local tropical environment. The aim of this study was to investigate genetic characteristics of the Yellow cattle using molecular markers. We investigated the nucleotide sequences of mitochondrial DNA and SRY gene on Y chromosome, and genotyped SREBP-1, SCD1, EDG1, NCAPG, DGAT1, MC1R, and HSP70 genes in the Yellow cattle population. The sequence analysis of the mitochondrial DNA showed that most of the cattle possesses zebu (Bos indicus) type I1 haplotype, suggesting relatively low genetic diversity in maternal lineage. The sequence analysis of the SRY gene indicates that while most of the males possess zebu type haplotype, taurine (Bos taurus) type haplotype was also observed, suggesting gene-flow from taurine cattle. The results of the genotyping of the functional genes showed that the NCAPG, SCD, MC1R, and HsSP70 genes are polymorphic in the population, whereas the SREBP-1, EDG1, and DGAT1 genes are monomorphic. Particularly, the presence of the desirable and undesirable alleles of the NCAPG and HSP70 genes, respectively, will be important for the selection of animals by potential performances in meat productivity and fertility. The present findings will be informative for future conservation and breeding of the Vietnamese Yellow cattle.

First record of Triops strenuus Wolf, 1911 (Branchiopoda, Notostraca), a tadpole shrimp of Australian origin, from Japan

Three species of tadpole shrimp, i.e.,Triops granarius(Lucas, 1864),Triops longicaudatus(LeConte, 1846) andTriops cancriformis(Bosc, 1801-1802), have been known from Japan. In this paper the author describes a fourthTriopsspecies (= Triops strenuusWolf, 1911) living in the rice paddies of a southern area of Honshu, the largest of the four main islands of Japan. This species was probably endemic to the Australian continent, and no habitat distribution outside Australia has been reported so far. The impact on the existing ecosystem of Japan is quite unknown, and therefore, it is necessary to announce this intrusion into Japan in order to clarify the invasion route, habitat ecology, and the future measures against this new alien species. This invasion is considered to be caused by the resting eggs brought together with silica sand (imported from Western Australia into Japan for the large-scale beach improvement). The results presented here also describe the phylogenetic relationship with all the Australian species described so far, but also all the knownTriopsspecies of the world, based on the nucleotide sequences of mitochondrial DNA.

Molecular identification of four Panonychus species (Acari: Tetranychidae) in Korea, including new records of P. caglei and P. mori

AbstractFour species of the genus Panonychus are identified in Korea including two previously known species P. citri (McGregor) and P. ulmi (Koch) and two newly identified species P. mori Yokoyama and P. caglei Mellot. Morphological diagnostics were observed among the four species in the color of dorsal tubercles and in the shape of male aedeagus. The dorsal tubercles of P. citri, P. ulmi, P. mori and P. caglei are red, white, whitish red and light red, respectively. The aedeagi of male adults are diagnostic in sigmoid‐shaped at the distal end and its shape and length was different among four species. Molecular comparison of the internal transcribed spacer 2 (ITS2) sequence of nuclear DNA and cytochrome‐c oxidase subunit I (COI) nucleotide sequence of mitochondrial DNA among the four species showed divergences 8–12% and 9–12%, respectively. Molecular analysis of the ITS2 and COI sequences revealed their divergences were slightly different among four species. In addition, species‐specific primer sets were designed at the base on ITS2 sequences to precisely diagnose these four species at the molecular level.

Comparative analysis of the complete nucleotide sequences of mitochondrial DNA of rat strains Wistar and oxys of the institute of cytology and genetics, Siberian Branch, Russian Academy of Sciences

Complete nucleotide sequences of the mitochondrial DNA of Wistar rats and premature aging rats OXYS, sensitive to cataractogenic effect of galactose, from the Center for collective usage «Gene pool of laboratory animals» of the Institute of Cytology and Genetics (ICG), Siberian Branch, Russian Academy of Sciences, were investigated (nucleotide sequences were submitted to GenBank). It was shown that two additional unique nucleotide substitutions between rats OXYS (ICG) and Wistar (ICG) are not found in other known nucleotide sequences of mitochondrial DNA of rats and do not result in amino acid substitutions, so that all differences in phenotypic data of these lines are determined only by differences in the genomic DNA. Comparative analysis showed that Wistar (ICG) rats have a significant number of nucleotide substitutions compared to rat strains derived from outbred rat Wistar colony, which contradicts possible relationship of Wistar (ICG) rats to baseline Wistar rat line or its descendants. It was assumed that the Sprague Dawley rat line is the progenitor of Wistar (ICG) rats.

Complete mitochondrial genome of the Southern catfish (Silurus meridionalis Chen) and Chinese catfish (S. asotus Linnaeus): Structure, phylogeny, and intraspecific variation.

The complete mitochondrial genome of the Southern catfish (Silurus meridionalis) and the Chinese catfish (S. asotus), was determined using the long and accurate polymerase chain reaction (LA-PCR) method. The mitochondrial DNA nucleotide sequences of S. meridionalis and S. asotus were compared with those of 47 other catfish species in the same order. The total length of mitochondrial DNA for S. meridionalis and S. asotus was 16,526 and 16,525 bp, respectively, and included 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region. This mitochondrial gene arrangement is identical to that observed in other Siluriformes. To determine the relative phylogenetic positions of S. meridionalis and S. asotus, and to discover phylogenetic relationships among 24 families of Siluriformes, analyses were conducted, based on mitochondrial DNA, 12S ribosomal RNA, 16S ribosomal RNA, and 13 protein-coding gene sequence data sets. Phylogenetic analyses were congruent with a basal split of the order into Clupeiformes, Characiformes, Cypriniformes, and Siluriformes, and supported a closer relationship of the Southern catfish (family Siluridae) and the Chinese catfish (family Siluridae) to Pimelodidae than to Bagridae. We concluded that these two species are part of a molecular clade that is different from that proposed in recent studies, in which Amblycipitidae appears as a sister group. Our results showed Amblycipitidae appearing as the most basal extant, and Bagridae appearing as a sister group of Cranoglanididae and Pangasiidae. The Siluriformes showed close phylogenetic relationship to the Characiformes.

Origin of a White-tailed Eagle Wintering on Tsushima Island, Japan, Established by Mitochondrial and Nuclear DNA Analyses

The White-tailed Eagle breeds and winters on Hokkaido, the northern island of Japan. It is not known whether wintering eagles occasionally observed in southern Japan migrate there from the Hokkaido population or arrive from an Asian continental population. To further our understanding of their migration, we examined a nucleotide sequence of mitochondrial DNA and a multilocus genotype from the nuclear DNA of an eagle found wintering on Tsushima Island, southern Japan. Our results revealed that the eagle had originated from a continental population.

On the record of Fedorov’s eelpout (Zoarces fedorovi, Zoarcidae), off western Kamchatka

is also found in the same areas; it isdistinguished from Fedorov’s eelpout by many morphological characters, osteological parameters, andlevel of variation in mitochondrial DNA nucleotidesequences (Radchenko et al., 2010; Voskoboinikovaet al., 2010; Chereshnev and PoezzhalovaChegodaeva, 2011). The most vivid feature of coloration,unambiguously separating these species, is the presence on the dorsal fin in Fedorov’s eelpout of inclineddark stripes with upper ends shifted anteriorly and alarge oval spot in the anterior part. A similar colorationpattern is found in another species of the genus,Andriashev’s eelpout (

Two Distinct mtDNA Lineages among Captive African Penguins in Japan

ABSTRACTThe African penguin (Spheniscus demersus) is one of the world’s most endangered seabirds. In Japan, although the number of African penguins in captivity continues to increase, genetic data have not been collected for either wild or captive populations. To reveal genetic diversity and characterization in captive African penguins, we analyzed the nucleotide sequences of mitochondrial DNA (mtDNA) from a sample of 236 African penguins. Analysis of 433 bp of the control region and 1,140 bp of cytochrome b sequences revealed the existence of two mtDNA clades. Control region haplotypes were much more divergent (d=3.39%) between the two clades than within each clade. The divergence of these clades may reflect differences at the subspecies or geographical population level in African penguins. These findings suggest that at least two distinct maternal lineages exist in the wild populations of the African penguin.

Sequence Diversity at Cyt-b and Co-1 mtDNA Genes in Animal Taxa Proved Neo-Darwinism

Nucleotide sequences of mitochondrial DNA (mtDNA) depict the process of molecular evolution and speciation in animals. A dataset of about twenty three thousand sequences of 2 genes, Cyt-b and Co-1, among different species was analyzed at 5 taxa ranks across the Animal Kingdom. The results support the prevalence of a geographic or allopatric speciation and suggest that Darwin’s gradual evolution in animals also prevails at the molecular level. The approach suggested allows recognize the geographic and other speciation modes, using the set theory equations and genetic terms as their components. The suggested approach may solve a key problem of the Biological Species Concept, i.e. the inability of evolutionary studies to monitor the reproductive isolation among species in nature, by defining a species rank with measurable estimates of genetic parameters.

Population genetic structure and geographical differentiation of burbot (Lota lota) in China.

The burbot (Lota lota Linnaeus, 1758) is the only freshwater species of the family Gadidae. There is a long-standing controversy about taxonomic status of the burbot from the Amur River basin. It is necessary to investigate population genetic structure and geographical differentiation among burbot populations from the Irtysh River basin and Amur River basin by mitochondrial DNA nucleotide sequence analysis. A 572 bp segment of cytochrome b and 425 bp segment of control region gene were sequenced from 4 populations. The results showed that there was lower genetic diversity of burbot in China and highly significant genetic difference between populations in the Amur Riverbasin (P < 0.01). Demographic analysis indicated that the burbot from the Amur River basin experienced population expansion (Cytb: F(s) = -0.912 (P = 0.287), D = -0.399 (P = 0.375); CR: F(s) = -4.771 (P = 0.015), D = -1.523 (P = 0.03 )). The data of 4 populations in China combining with the published data representing the Eurasian and North American burbot, revealed three distinct phylogenetic lineages (labelled EB, NA, Amur).

О ПОПУЛЯЦИОННОЙ ДИФФЕРЕНЦИАЦИИ ГУМЕННИКА (Anser fabalis) ПРИ МИГРАЦИОННЫХ ПЕРЕРАСПРЕДЕЛЕНИЯХ НА ЮГЕ РОССИИ

In the paper, an ecomorphism, a geographic variability and population origin of bean gooses during their migration in the South of Russia are discussed. A few genetic features of the bean goose populations were considered. On the basis of analysis of nucleotide sequences of mitochondrial DNA (mtDNA) haplotypes the authors estimated the genetic differentiation in forms (subspecies) of bean goose. The problems of conservation of the bean goose species in whole, and a methodological validity of regulation of goose hunting are under consideration.

Complete nucleotide sequences of mitochondrial DNA of long-finned squid Loligo edulis

The complete nucleotide sequence of the mitochondrial genome of long-finned squid Loligo edulis forma kensaki (L. edulis f. kensaki, Teuthida: Myopsida) was determined. It contains 13 protein-coding genes, 12SrRNA, 16SrRNA, and the 22 tRNA genes, and three long noncoding regions. We also determined the mitochondrial genome nucleotide sequence of seasonal brood samples of L. edulis f. budo collected from the western part of the Sea of Japan in the autumn to winter seasons, which showed morphologic discrepancies with L. edulis f. kensaki. Comparison of the two complete sets of mitochondrial DNA data showed that the similarity of the two sequences was as high as 99.9 %, with only eight nucleotide substitutions in coding regions. The complete mitochondrial genome of Loligo edulis f. kensaki from Nagasaki Pref. is 17360 bp and L. edulis f. budo from the Shimane Pref. is 17351 bp. The nucleotide sequences and haplotype patterns in ND1 suggest that L. edulis f. kensaki and L. edulis f. budo share a single genetic background.

Species identification method for marine products of Seriola and related species

The complete nucleotide sequences of mitochondrial DNA (mtDNA) from four Seriola spp. (S. quinqueradiata, S. lalandi, S. dumerili, and S.rivoliana) were determined with the aim of developing a species identification analysis method for discriminating between commercially important Seriola spp. and other related species. In addition, the nucleotide sequences of the mitochondrial cytochrome b gene (Cytb) from five related but less expensive species in terms of market value (Seriolella brama, S. caerulea, S. punctata, Hyperoglyphejaponica, and Rachycentroncanadum), which are often used as substitutes for Seriola spp., were determined. Restriction enzyme sites were examined by comparing the nucleotide sequences, and species-specific primers were designed for PCR-based restriction fragment length polymorphism (RFLP) analysis. Based on the results of the PCR amplification studies, the four Seriola spp. and the five related species tested could be categorized into three groups according to their PCR product pattern: a 373-bp product from the four Seriola spp., a 513-bp product from three Seriolella spp. and H. japonica, and a 204-bp product from R. canadum. In addition, RFLP analysis of the PCR products was able to differentiate these fish species.

Genetic variation of the white-spotted longicorn beetle Anoplophora spp. (Coleoptera: Cerambycidae) in Japan detected by mitochondrial DNA sequence

Genetic variation of the white-spotted longicorn beetle Anoplophora spp., distributed on the Japanese mainland and the Ryukyu Islands, was examined using nucleotide sequences of mitochondrial DNA. Two fragments, a 1.2-kb-long fragment containing portions of the cytochrome oxidase subunit I and II genes and a 1.4-kb-long fragment containing portions of 16S and 12S rDNAs, were sequenced. In phylogenetic analyses based on the sequences, 294 individuals collected at 75 localities were divided into two major groups (groups A and B) and then split into seven subgroups (A1–A4 and B1–B3). In group A, the closely related subgroups A1, A2, and A3 were mainly distributed on the Japanese mainland and were roughly separated among geographic areas, although the range of A3 spread significantly from Kyushu to the Central Ryukyu Islands. The sequence of A4, detected from one individual collected in eastern Honshu, was almost the same as that reported for A. chinensis (Forster) on the Chinese continent. In group B, subgroups B1 and B2 were restricted to the Central and Southern Ryukyu Islands, respectively, while B3 was distributed widely in both regions. Based on the results, we discuss the geographic origin of the haplotypes and movement of the insects between geographic areas.

Genetic relatedness in different Medicago sativa lines based on polymorphism of mitochondrial DNA specific sequences

Two synthetic populations (Syn-5 and Syn-7), four inbred lines and four landraces of alfalfa (Medicago sativa L.) were studied for genetic relatedness. These forms were characterized by different amount of seeds set and green mass yield. Two primer pairs of specific nucleotide sequences of mitochondrial DNA isolated from soybean were used. The mtDNA revealed the existence of significant polymorphism among the investigated forms of alfalfa. The genetic similarity (Dice coefficient) among studied forms of alfalfa ranged from 20.1 to 96.1. The greatest resemblances were noticed between D5 inbred line and the population of Syn-5. The lowest resemblances were noticed between Syn-7 and E1/2. The UPGMA dendrogram split investigated forms of alfalfa into two groups: first group include three landraces, the second consist of the rest analyzed forms. There are two landraces distinct with the highest seed set and yield of green mass: one in the first group, another one in the second group.

Phylogeny and phylogeography of the sword-tailed newt, Cynops ensicauda (Amphibia: Caudata), as revealed by nucleotide sequences of mitochondrial DNA

We investigated the phylogenetic relationships and phylogeography among individuals of the endemic newt (Cynops ensicauda) of the Central Ryukyus, Japan based on the mitochondrial cytochrome b gene. The results of phylogenetic analyses showed the presence of remarkable differentiation between assemblages from the Amami and Okinawa Island Groups, supporting the validity of the subspecies C. e. popei described from the latter on morphological grounds. The group of individuals from Okinawa Island Group was further divided into two distinct subgroups unlike the results of previous morphological and allozyme studies. Geographic ranges of these subgroups overlapped in the northern part of Okinawajima Island. The phylogeographic pattern within the Okinawa Island Group suggests an initial division into two geographically isolated population lineages and subsequent secondary sympatry before formation of reproductive isolation. It is also likely that within the Okinawa Island Group emigration occurred from the central and northern parts of Okinawajima Island to its southern part, as well as to several small islets off its western coast. Within the Amami Island Group, recurring restricted gene flow with isolation by distance seems to have occurred around the southwestern region including three islets southwest of Amamioshima Island.

Distinct taxonomic position of the Madagascar stonechat (Saxicola torquatus sibilla) revealed by nucleotide sequences of mitochondrial DNA

Abstract Stonechats (genus Saxicola) are passerine birds with an extraordinarily large breeding distribution. Recent studies provide strong evidence that the taxon shows far greater geographic differentiation than originally suspected, with African, Siberian and European stonechats forming distinct, monophyletic groups that have been suggested to be species in their own right. Here, we present additional data on the geographic differentiation among African stonechats, Saxicola torquatus. Nucleotide sequences of the mitochondrial NADH dehydrogenase subunit 2 and cytochrome b genes indicate that the stonechats from Eastern Madagascar (Saxicola t. sibilla) form a distinct clade and that they constitute a monophyletic group with stonechats from mainland eastern Africa (Saxicola t. axillaris) and La Réunion (Saxicola tectes). The genetic and morphological data suggest that the Madagascar stonechat is very likely to be a distinct species, Saxicola sibilla (Linnaeus 1766). However, further studies are needed to verify this. A detailed description of the plumage and various external body measurements is given.