Mitochondrial Cytochrome Oxidase I Gene Research Articles

Comparative Study of Two Himalayan Snow Trouts, Schizothorax esocinus and Schizothorax curvifrons Within the Schizothoracinae and Other Nearest Relatives of Cyprinidae, Inferred from Mitochondrial Sequences of Cytochrome b (Cyt-b) and Cytochrome Oxidase I (Co-I) Gene.

The Himalayan region encompasses varied aquatic ecosystems, characterized by the presence of diverse ichthyofauna, particularly represented by members of the Schizothorax genus, commonly referred to as snow trout. The primary objective of this work was to examine the molecular phylogeny of Schizothoracinae, specifically focusing on the two species, Schizothorax esocinus and Schizothorax curvifrons, which are known to inhabit the northern and north-eastern regions of the Himalayas. This investigation was conducted by analyzing the entire mitochondrial Cyt-b and Co-I gene sequences. The aligned Cyt-b and Co-I sequences for S. esocinus, S. curvifrons, and related members within the subfamily Schizothoracinae, spanned 1130 to 1141 and 1536 to 1551 base pairs, respectively. Using these gene, phylogenetic trees were created to compare Schizothoracinae species to other subfamilies of the family Cyprinidae (Barbinae, Alburninae, Leuciscinae, Xenocyprinae, Cyprininae, and Cultrinae). Genetic distances for Cyt-b and Co-I sequence at three hierarchical levels shows significant disparities in their average score. For Cyt-b, average p-distances for intraspecies, intragenus, and intrafamily were 2.13%, 4.1%, and 15.23%, respectively. Similarly, for Co-I, average p-distances were 1.19%, 3.6%, and 13.8% for intraspecies, intragenus, and intrafamily, respectively. Total number of haplotypes (h) based on Cyt-b and Co-I gene were 6 and 12 within the target Schizothorax spp. In the present study, the observed range of haplotype diversity (hd) for the Cyt-b gene varied from 0.00 to 0.847, with an average haplotype diversity of 0.847 ± 0.034. Similarly, for the Co-I gene, the observed haplotype diversity ranged from 0.00 to 0.931, with an average value of haplotype diversity estimated to be 0.931 ± 0.024. The results of the present study clearly shows that the representative species exhibited close affinities with members of Barbinae and Cyprininae, while other subfamilies formed distinct groups. The findings of the study also indicated that the Cyt-b and Co-I gene exhibits polymorphism and has the potential to serve as a marker for identifying genetic differentiation among populations based on ecological habitats. Mitochondrial Cyt-b and Co-I have been established as a universally accepted and validated genetic marker within a comprehensive bio-identification system at the species level.

No mitochondrial DNA variation in COI gene among widely distributed populations of a parthenogenetic praying mantid: a biogeographic puzzle

Abstract The endemic North American praying mantid, Brunneria borealis Scudder (1896), is obligatorily parthenogenic and wingless. The species is both geographically widespread, distributed over an essentially continuous pericoastal range of more than 2,400 km from eastern Texas to central North Carolina, and abundant in early-stage successional old fields. We used mitochondrial cytochrome oxidase I (COI) analysis to examine the genetic similarities among specimens of this insect and collected from 7 states along this range of distribution. We found no variations in the mitochondrial COI gene, which suggests that this wide geographic distribution of the species is surprisingly recent. We hypothesize that its obligatory parthenogenic status may be an accident of colonization of North America by a single facultative parthenogenic female, and the subsequent distribution was most likely achieved by inadvertent human transport.

DNA Barcoding of Cardinalfish (Apogonidae) in Gilimanuk Bay, Bali, Indonesia

Highlight Research Eight species of cardinalfish in Gilimanuk Bay were delineated using the barcoding method. This study provides the first nucleotide sequence for Ostorhinchus hartzfeldii in GenBank online database. The phylogenetic tree showed that each sample resided in a distinct cluster, indicating that the barcoding method efficiently differentiated at the species level. The mean genetic distance between genera within the family was 31.8-fold higher than the mean genetic distance within species. Abstract The Apogonidae is estimated to consist of nearly 300 fish species, most of which inhabit coral reef areas. The lack of distinctive body markings and overlapping species distribution makes species assignment challenging. Therefore, this study aimed to delineate species and establish barcoding reference databases of Apogonidae in Gilimanuk Bay (Bali, Indonesia) using the Cytochrome Oxidase I (COI) gene of the mitochondrial DNA. A total of 22 fish tissue samples were extracted with 10% Chelex solution. BLAST analysis was performed and genetic differentiation between species was calculated. The phylogenetic tree was constructed using the Maximum Likelihood method and tree visualization was generated using iTOL V5. The morphology and genetic identification results based on the mitochondrial COI gene revealed eight species of seven genera, and one species was new to GenBank online database. This study was the first-ever addition of COI sequence for Ostorhinchus hartzfeldii into the GenBank database. The average K2P genetic distance within species and K2P distance between genera within the family were 0.60% and 19.10%, respectively. The mean genetic distance between genera within the family was 31.8-fold higher than the mean genetic distance within species. The phylogenetic tree showed that each sample resided in a distinct cluster, which indicates that DNA barcoding is a reliable and effective approach for species delimitation in Apogonidae fishes.

Cytochrome oxidase I (COI) revealed differentiation among populations of Atule mate in the coastal waters of Persian Gulf and Sea of Oman (Bushehr, Bandar Abbas, Chabahar)

This study investigated the genetic structure of the yellowtail scad (Atule mate) population based on the mitochondrial cytochrome oxidase subunit I gene sequences by collecting 90 specimens of Atule mate from Bushehr, Bandar Abbas and Chabahar in Iran. Mitochondrial DNA was extracted using ammonium acetate method. The PCR reaction was performed using a primer pair of the nucleotide sequences of the mitochondrial COI gene and its PCR products were sequenced. Out of the 13 haplotypes identified through evaluating the sequences, one haplotype was common within the sampling areas. The mean haplotype diversity was high (0.762±0.044) and the mean nucleotide diversity was low (0.003±0.0003). The longest genetic distance of 0.243 (P<0.05) was observed between the samples collected from Chabahar and Bushehr and the lowest of −0.048 (P>0.05) between the samples collected from Bandar Abbas and Bushehr. The mean values of Tajima’s D and Fu’s Fs were respectively calculated as −0.232 and 0.485 (P>0.05). Analysis of molecular variance (AMOVA) showed a high intra-population genetic diversity and a low inter-population diversity, which suggested a high gene flow among the study areas. The present findings suggested, probably the population of yellowtail scad in Chabahar constitutes a independent gene pool of other regions, and despite the unity of the populations of Bandar Abbas and Bushehr, their molecular diversity is acceptable. These results can help genetically manage Atule mate populations in the study areas and manage stocks and monitor genetic variations in this species.

Molecular phylogeny of grouper of Epinephelus genus in Jayapura, Papua, Indonesia inferred from Cytochrome Oxidase I (COI) gene

Abstract. Dwifajri S, Tapilatu RF, Pranata B, Kusuma AB. 2022. Molecular phylogeny of grouper of Epinephelusgenus in Jayapura, Papua, Indonesiainferred from Cytochrome Oxidase I (COI) gene. Biodiversitas 23: 1449-1456. Grouper (Serranidae: Epinephelinae: Epinephelus) fish have high economic value, and are relatively overfis hed, yet have not received serious attention to determine conservation status by the International Union for Conservation of Nature (IUCN). DNA barcoding is an important molecular approach to identify Papua's grouper species. The objective of the present study was to analyze species diversity and molecular phylogeny of Epinephelus grouper based on DNA sequences of mitochondrial control region COI gene. Samples of grouper fish were collected from Hamadi, Sentani, and Youtefa local fish markets in Jayapura, Papua during August 2020. Grouper was morphologically identified, photographed and its fin was clipped and preserved for molecular analysis. Present study used primers, i.e., Fish R1 5'TAGACTTCTGGCCAAGAATCA3' and Fish F1 5'TCAACCAACCACAAAGACATTGGCA3'. Based on gene bank comparison at the sequence length 689 base pairs, the present study obtained seven species of grouper (Serranidae: Epinephelinae), namely Epinephelus areolatus, Epinephelus coioides, Epinephelus episictus, Epinephelus kupangensis, Epinephelus macrospilos, Epinephelus melanostigma and Epinephelus merra. The phylogenetic tree was composed of seven clades, where each grouper species represented each clade. The genetic distance between Epinephelus kupangensis and Epinephelus melanostigma was determined as the closest genetic distance (0.123) in the present study, while the farthest one was found between Epinephelus episictus and Epinephelus merra (0.161).

Exploring the fish assemblage structure in the process of ecological stocking: A case study of Daye Lake

As human activities cause water eutrophication and overfishing, which had a serious impact on fish resources, fish diversity showed a downward trend. In order to understand the changes of fish assemblage structure in the process of ecological stocking and effectively, the existing fish community in Daye Lake which was divided into 9 sites was evaluated in the summer of 2019 and 2020, and fish resources were investigated by traditional fishing and eDNA metabarcoding technology. The results showed that 33 species belonging to 18 genera, 6 families and 4 orders of fish were investigated in Daye Lake based on traditional fishing methods. Among them, Hypophthalmichthys molitrix and Hypophthalmichthys nobilis were the dominant species in Daye Lake all year round, and the dominant group was omnivorous, middle-lower fish. And the fish communities at the same point at different times were similar, the separation degree of fish communities was relatively high among different locations. Based on eDNA metabarcoding technology, the mitochondrial COI (cytochrome oxidase I) and 12S rRNA gene regions of eDNA were amplified respectively. A total of 10 species of freshwater lake fish were detected, of which 7 were detected together with traditional methods. Alpha and Beta diversity analysis showed that GJQ had the lowest species diversity, DW and LJH had the highest species diversity, and the biodiversity of adjacent sites was relatively similar. This study proved that ecological stocking will not have a great impact on the diversity of fish populations in lakes. At the same time, it proved the effectiveness of eDNA metabarcoding technology in fish diversity investigation.

Strategy for DNA extraction and detection from insect pests in stored home grain samples RESEARCH

Stored grains are subjected to infestations with more than 60 species of insects, that responsible for millions of dollars’ loss and cause several health problems including allergies and gastrointestinal disorders. Traditional detection techniques are laborious, expensive and not sensitive to detect insect contamination at the egg and larvae stages. Therefore, alternative methods are needed for rapid and sensitive detection. One obvious approach is to develop a molecular approach utilizing genetic information of the potential insect species that infest grains for amplification of specific target gene fragment utilizing polymerase chain reaction [PCR]. In the present study, a number of known infested grain samples were used in standardizing a method to isolate larvae and adult insects that were based on centrifugation washing method and a filtration washing method. The isolated insects were subjected to DNA extraction and PCR amplification of defined regions of cytochrome oxidase I (COI) gene followed by sequencing to identify the di"erent pest species. For PCR amplification new primers were designed and for this purpose the obtained COI sequences from di"erent insects were aligned to design two sets of primers (named: COI-PCR4 and COI-PCR5) specific for the indicated insect mitochondrial COI gene. The designed primers were tested for their specificity and sensitivity. The suitability of PCR primers and DNA extraction methods were evaluated on eleven samples of commercial grains utilizing each primer set with the two extraction methods.

Phylogenetic Analysis of Rasbora spp. Based on the Mitochondrial DNA COI gene in Harapan Forest

Harapan forest is the remaining lowland tropical forest in Sumatra which represents about 20 percent of the biodiversity on the island of Sumatra. There are several Rasbora species found in the Sungai Kapas Tengah River Refuge in the Harapan Jambi Forest that the relationship is not yet known.This research aims to know kinship and genetic distance several species of Rasbora from Sungai Kapas Tengah, Hutan Harapan Jambi. The method in this research using secondary data from the NCBI website ((National Center for Biotechnology Information). The data taken, namelynucleotide sequence from the Cytochrome Oxidase I (COI) gene in mitochondrial DNA. The Rasbora species analyzed were Rasbora from identification results in the Sungai Kapas Tengah River Refuge, Harapan Jambi Forest, consisting of, Rasbora bankanensis, R. caudimaculata, R. cf. sumatrana, R. dusonensis, R. elegans, R. sumatrana, and R. trilineata. Based on phylogenetic analysis, the location of the branch length in each Rasbora species, the closest kinship is owned byR. sumatrana and R. elegans species. Based on the results of genetic distance analysis, the closest genetic distance was the species R. elegans and R. sumatrana, with a distance value of 0.023 (2.3%). While the farthest genetic distance between R. bankanensis and R. caudimaculata, with a distance value of 0.172 (17.2%).Based on research results It can be concluded that R. bankanensis has a greater kinship and genetic distance value than other Rasbora species, so that this species forms a separate group. Meanwhile, 5 other species have kinship and the value of close genetic distance so that these species are united in the same group. For future researchers, it is hoped that some additional families of fish species will be analyzed for phylogenetic analysis in Sungai Kapas, Hutan Harapan Jambi, so that they can find out the relationship of several other species.

Species identification of zooplankton resting eggs based on DNA barcode technology: A case study of Lake Liuye (Changde), Lake Dongting Basin

以洞庭湖流域的典型城市湖泊常德柳叶湖表层沉积物中浮游动物休眠卵为研究对象，采用DNA条形码技术进行种类鉴定，从191个休眠卵中成功获得101条有效序列，鉴定成功率约为53%.根据NCBI数据库比对成功鉴定休眠卵9科12属11种，另有6个样品鉴定到属或科；3个类群的种间遗传距离平均为种内遗传距离的68倍，表明可以利用线粒体细胞色素c氧化酶第一亚基编码基因（COⅠ）对休眠卵进行有效物种鉴定.通过Neighbor-Joining树进行系统发育分析，发现所鉴定的物种与其参比序列聚类为一支，所有物种分别聚为独立的一个支系，不同物种可有效区分.研究结果均表明，COⅠ基因作为DNA条形码可以实现沉积物中浮游动物休眠卵的物种鉴定.;With the rapid development of modern molecular biology tools, especially DNA barcoding technology, a rapid, accurate and efficient identification method for species of zooplankton resting eggs is possible. In this study, zooplankton resting eggs, including copepods,cladocerans and rotifers in the surface sediments of Lake Liuye (Changde), a typical urban lake in Lake Dongting Basin, were studied. Using DNA barcode technology for species identification, 101 valid DNA sequences were successfully obtained from 191 resting eggs, and the identification success rate was 53%. According to the NCBI database comparison, 9 families, 12 genera and 11 species of resting eggs were successfully identified, and 6 samples were only identified to the genus or family level. The inter-species genetic distance of the three taxa was 68 times that of the intra-species genetic distance, indicating that the cytochrome oxidase Ⅰ (COⅠ) gene could be used for effective species identification of zooplankton resting eggs. Through the phylogenetic analysis by Neighbour-Joining tree, it was found that the identified species and their reference sequences were clustered into one branch, and all different species were clustered into independent branches respective. Therefore, different species could be effectively distinguished. The above results all indicate that the mitochondrial COⅠ gene, as a DNA barcode, can be used to identify the species of zooplankton resting eggs in sediment of lakes.

Mitochondrial COI gene is valid to delimitate Tylenchidae (Nematoda: Tylenchomorpha) species.

Tylenchidae is a widely distributed soil-inhabiting nematode family. Regardless their abundance, molecular phylogeny based on rRNA genes is problematic, and the delimitation of taxa in this group remains poorly documented and highly uncertain. Mitochondrial Cytochrome Oxidase I (COI) gene is an important barcoding gene that has been widely used species identifications and phylogenetic analyses. However, currently COI data are only available for one species in Tylenchidae. In present study, we newly obtained 27 COI sequences from 12 species and 26 sequences from rRNA genes. The results suggest that the COI gene is valid to delimitate Tylenchidae species but fails to resolve phylogenetic relationships.

Population genetic analysis of trematode Parasaccocoelium mugili Zhukov, 1971 (Haploporidae Nicoll, 1914) from the Russian Far East and Vietnam based on ribosomal ITS and mitochondrial COI gene partial sequence data.

Intraspecific variation of Parasaccocoelium mugili collected from mullet fish of the south of Russian Far East and Vietnam has previously been estimated on the basis of two molecular markers: ribosomal internal transcribed spacer 1 (ITS1) rDNA and mitochondrial cytochrome oxidase I (COI) gene sequences. In the present study, molecular identification of this species from the Kievka River, Primorye and from Vietnam was performed by analysis of 28S rDNA sequences. Analysis of ITS1 rDNA sequences variation revealed two highly differentiated main groups, representing trematode specimens from the two regions. Genetic variation within each region was relatively low. Mitochondrial COI gene sequence data analysis revealed fixed nucleotide and amino acid substitutions, and supported the existence of two genetically different groups associated with geographical origin. Analysis of the COI gene fragments showed extremely high variation within Russian and Vietnamese P. mugili samples. Our results for P. mugili most probably represent a case of initial step of allopotric speciation for this trematode, caused by living strategy of its definitive host at evolutionary scale. Mitochondrial DNA sequence data show that existence of gene flow between local populations of P. mugili in the Primorye Region caused by definitive hosts can be proposed.

Phylogenetic analysis of goat warble fly (Przhevalskiana silenus) based on mitochondrial COI gene.

The larvae of the genus Przhevalskiana (Diptera: Oestridae) are the causative agents of subcutaneous myiasis in goats. Several species have been grouped under this genus based on the morphology of different larval stages, albeit with a lot of uncertainties. Thus, application of genetic tools seems to be helpful for taxonomy. During this study, the cytochrome oxidase I (COI) gene was targeted for the characterization of larval stages of goat warble fly. Fragments of 606bp were amplified for all the specimens. Based on the COI gene analysis, all the recovered specimens were identified as larvae of Przhevalskiana silenus. Molecular data on the genus is relatively rare but present isolates revealed about 87-89% identity with previous isolates of P. silenus. According to the phylogenetic data, the present isolates branched (as a sister group) with a number of Hypoderma spp. including H. bovis, H. diana, H. lineatum and H. sinense. The present findings confirmed that the COI gene could be a suitable marker for genetic characterization and identification of larvae up to the species level.

Genetic diversity of Culicoides species within the Pulicaris complex (Diptera: Ceratopogonidae) in Turkey inferred from mitochondrial COI gene sequences

Identification of Culicoides (Diptera: Ceratopogonidae) biting midges to species has become important due to their potential role in the transmission of arboviruses such as bluetongue virus, bovine ephemeral fever virus, Akabane virus, African horse sickness virus, epizootic haemorrhagic disease virus and Schmallenberg virus. In several studies, molecular tools, used for the identification of biting midges, revealed the presence of cryptic and undescribed species especially within Pulicaris complex. The presence of cryptic species within species complexes raise questions about their role in viral disease transmission as there are apparent differences in the vectorial capacity between closely related species. In this study, we analyzed the mitochondrial DNA cytochrome oxidase I (COI) gene sequences of species within the Pulicaris complex present in Turkey and determined their phylogenetic relationships. Twenty-one haplotypes within the already described species C. pulicaris P1, C. lupicaris, C. lupicaris L2, C. newsteadi, C. newsteadi N1, C. punctatus, C. fagineus F2 and C. flavipulicaris were determined from the study areas. The molecular analysis revealed further two haplotypes belonging to new non-described cryptic species named as C. lupicaris L3 and Culicoides WBS corresponding to C. lupicaris and Fagineus complex which diverged by 17.9% to 25.7% and 18.7% to 31.8%, respectively from other species in the subgenus Culicoides. Genetic divergence within species was <2.0% and phylogenetic analyses of the COI dataset revealed 22 different monophyletic separate clades within two major cluster. The results of this study emphasize the applicability of COI sequences as a diagnostic marker for differentiating Culicoides species and revealing cryptic species.

Phylogenetic Analysis of Duck Species from Tegal Indonesia Using 18S Ribosomal RNA and Mitochondrial COI Gene

Background and Objective: Tegal duck is a domestic waterfowl species known as a major producer of eggs that is traditionally used for making the famous salted egg by the local people. This study aimed to analyze the phylogenetic relationship of the Tegal duck through the gene encoding 18S ribosomal RNA (rRNA) and mitochondrial cytochrome oxidase I (COI). Methodology: We amplified and sequenced part of the 18S rRNA and COI gene of Tegal duck. These data were used to determine their similarity with other Anas species retrieved from GenBank and analyzing phylogenetic relationship. Results: The size of the PCR product of partial 18S rRNA was approximately 485 bp, whereas the size of the partial mitochondrial DNA (mtDNA) of the COI gene sequence was 751 bp. The 18S rRNA data showed that the Tegal duck is closely related to A. platyrhynchos (84.4% similarity). The COI gene data of the Tegal duck confirmed this relationship, with 99% homology with A. platyrhynchos voucher NHMO-BC399. However, the COI gene fragment of the Tegal duck also showed 99% homology with A. poecilorhyncha. Conclusion: Tegal duck has a close phylogenetic relationship with not only A. platyrhynchos but also A. poecilorhyncha.

Molecular Detection of Chevon and Mutton Adulteration by Species-specific PCR Assay Targeting Mitochondrial COI Gene

A highly species-specific polymerase chain reaction (PCR) was developed for authentic identification of raw and processed meat products of chevon and mutton. To achieve this, four species-specific primers for mitochondrial cytochrome oxidase I (COI) gene were selected from previous reports. The assay generated PCR products of 157, 157, 268, 251, and 177 bp for chevon, mutton, pork, chicken and duck, respectively. The sensitivity for the detection of adulteration was established to be 0.1% (w/w), while the DNA limit for detection was as low as 0.001 ng. The adulteration was found in all meat product types including raw frozen meat, cold cuts, ground meats and cooked foods. These findings showed that species-specific PCR are potentially reliable method in detection of meat products of chevon and mutton authentication.

Concordant patterns of mtDNA and nuclear phylogeographic structure reveal Pleistocene vicariant event in the green crab Carcinus aestuarii across the Siculo-Tunisian Strait

This study focuses on the population genetic structure of the green crab Carcinus aestuarii along part of the African Mediterranean coast, with the main target to confirm genetic subdivision across the well documented genetic boundary of the Siculo-Tunisian Strait. For this purpose, the mitochondrial COI (cytochrome oxidase I) gene and five polymorphic microsatellite loci were analysed in 144 and 120 specimens, respectively. Our results show the existence of two distinct haplogroups, separated by 16 mutational steps and revealed a non random distribution of the genetic variation along the African Mediterranean coast. Dating analyses, based on the use of different molecular clock models and rates, placed the divergence among both haplogroups at 1.91 Myr (95% HPD: 1.11–2.68 Myr) to 0.69 Myr (95% HPD: 0.44–0.98 Myr). This range of divergence time estimation corresponds to the Early Pleistocene. The particular pattern of genetic divergence among Eastern and Western African Mediterranean populations of C. aestuarii, detected by 2-level AMOVA at the mitochondrial level, was consistent with that inferred from microsatellite analysis and suggests a vicariant event in C. aestuarii. Demographic reconstruction, inferred from mismatch distribution and BSP analyses, yielded different patterns of demographic history between both African Mediterranean groups. The distribution pattern of the two haplogroups across the African Mediterranean coast, along with results of Bayesian analysis of genetic structure revealing an intermediate geographic group between the two divergent groups of the African coast, support the hypothesis of a secondary contact between two historically isolated groups. Although this hypothetical contact zone, thought to be located near the Siculo-Tunisian Strait, still needs to be verified, the asymmetric gene flow from Western to Eastern African Mediterranean, as inferred by the results of a MIGRATE analysis, reinforces the previously mentioned results.

Demographic history and population structure of Anopheles pseudopunctipennis in Argentina based on the mitochondrial COI gene.

BackgroundAnopheles pseudopunctipennis is an important malaria vector in the Neotropical region and the only species involved in Plasmodium transmission in the Andean foothills. Its wide geographical distribution in America, high preference for biting humans and capacity to rest inside dwellings after feeding, are attributes contributing to its vector status. Previous reports have tried to elucidate its taxonomic status, distinguishing populations from North, Central and South America. In the present study we used a mitochondrial marker to examine the demographic history of An. pseudopunctipennis in northwestern Argentina.MethodsTwelve localities were selected across 550 km of the distribution of this species in Argentina, including two near the Bolivian border and several in South Tucumán, for sampling. A fragment of the cytochrome oxidase I (COI) gene was sequenced and haplotype relationships were analyzed by a statistical parsimony network and a Neighbor-Joining (NJ) tree. Genetic differentiation was estimated with FST. Historical demographic processes were evaluated using diversity measures, neutrality tests and mismatch distribution.ResultsForty-one haplotypes were identified, of which haplotype A was the most common and widely distributed. Neither the network nor the NJ tree showed any geographic differentiation between northern and southern populations. Haplotype diversities, Tajima’s DT and Fu & Li’s F and D neutrality tests and mismatch distribution supported a scenario of Holocene demographic expansion.ConclusionThe demographic pattern suggests that An. pseudopunctipennis has undergone a single colonization process, and the ancestral haplotype is shared by specimens from all localities, indicating mitochondrial gene flow. Genetic differentiation was minimal, observed only between one northern and one southern locality. The estimated time of the population expansion of this species was during the Holocene. These data suggest that regional vector control measures would be equally effective in both northern and southern localities sampled, but also that insecticide resistant genes may spread rapidly within this region.

Mitochondrial COI gene transfers to the nuclear genome of Dendroctonus valens and its implications

Mitochondrial gene transfer to the nuclear genome could affect the accuracy of results in population genetics and evolutionary studies using mitochondrial gene markers. In a population genetics study of the red turpentine beetle (Dendroctonus valens), an invasive species in China, we found numerous ambiguous sites existing in the Cytochrome Oxidase I (COI) gene sequences obtained directly from polymerase chain reaction (PCR) products amplified from total genomic DNA using universal primers. By comparing the profiles of restriction endonuclease digestions and the sequences of PCR products amplified from mitochondrial DNA and nuclear DNA of the same individuals, we confirmed it was a phenomenon of mitochondrial gene transfer to the nuclear genome. Large numbers of COI pseudogenes were detected in this species. According to different levels of condon position bias and phylogenetic analysis, these should have originated from independent integration events. The impact of nuclear mitochondrial DNA sequences on population genetics analyses was discussed.

Intraspecific variations and phylogenetic relationships of steinernematids isolated from Japan based on the sequences of the ITS region of the nuclear rRNA gene and the partial mitochondrial COI gene

DNA sequences of the internal transcribed spacer (ITS) region of the nuclear rRNA gene and mitochondrial cytochrome oxidase I (COI) gene were used to analyze intraspecific variations and infer phylogenetic relationships of steinernematids isolated from Japan. DNA fragment lengths of the amplified ITS region obtained from 19 Japanese steinernematid isolates ranged from 914-1,067 bp and varied considerably among the species. A few intraspecific variations were detected in Steinernema litorale, Steinernema spp. MY6 and MY8, and no variation was observed in S. monticolum and Steinernema sp. MY5 in the sequences of the ITS region. The fragment length of the amplified partial COI gene was 397 bp for all species. The intraspecific variations of the sequences ranged from 0.3%-7.8% (0-42 nucleotide differences) for S. monticolum, S. litorale, Steinernema spp. MY5, MY6, and MY8. Sequence comparisons and phylogenetic analyses reveal that the sequence of the COI region can distinguish the isolates within a species but is not as effective as the ITS region in elucidating the relationship among species.

DNA sequences of the mitochondrial COI gene have low levels of divergence among deep-sea octocorals (Cnidaria: Anthozoa)

We are analyzing genetic diversity in deep-seamount octocorals with the ultimate goal of studying the effect of retention and dispersal of larvae on genetic population structure. Here we report on the sequence diversity of the mitochondrial cytochrome oxidase I (COI) gene among 11 species. Uncorrected pairwise sequence divergences ranged from 0.4–10.3% for comparisons among species spanning the intrageneric to interordinal levels. Relative to other invertebrates, these divergences are very low, suggesting that COI may not be useful as a genetic marker for studying dispersal among deep-sea octocoral populations. Possible explanations for the reduced rates of divergence observed include a lower rate of evolution for octocoral mitochondrial genomes and the presence of a gene, mtMSH, which may code for a mitochondrial DNA mismatch-repair system. We report the finding of mtMSH in three deep-sea octocorals (Acanthogorgia sp., Corallium ducale, and Paramuricea sp.), which brings the total published observations of this gene to six species, all in the subclass Octocorallia.