Mitochondrial COI Gene Sequences Research Articles

Single nucleotide polymorphism‐based species phylogeny of greater fritillary butterflies (Lepidoptera: Nymphalidae: Speyeria) demonstrates widespread mitonuclear discordance

AbstractThe systematics of Speyeria butterflies has historically been complicated by intraspecific variability that has challenged efforts to delimit species and reconstruct phylogenies. Our study presents a phylogenetic comparison of genomic single nucleotide polymorphisms (SNPs) and mitochondrial COI gene sequences, with comprehensive taxon sampling that includes 15 species and 46 subspecies. Increased sampling of genetic markers and taxa improved the match between genetic clusters, obtained with both phylogenetic and cluster‐based analyses, and species previously detected using morphology, as well as showing two species delimitations that may need revision. We also recovered extensive mitonuclear discordance between genomic SNPs and the COI gene, confirming that mitochondrial DNA does not reliably identify several species at broad geographic scales. Resolution of the relationships of Speyeria species demonstrates the importance of sampling variation across the whole genome, and provides an essential foundation for understanding the evolution of this charismatic clade of North American butterflies.

Genetic variation among the geographic population of Cassava mealybug Phenacoccus manihoti (Hemiptera: Pseudococcidae) in Indonesia inferred from mitochondrial COI gene sequence

Abstract. Nopriawansyah N, Rauf A, Kusumah YM, Nurmansyah A, Koesmaryono Y. 2019. Genetic variation among the geographic population of Cassava mealybug Phenacoccus manihoti (Hemiptera: Pseudococcidae) in Indonesia inferred from mitochondrial COI gene sequence. Biodiversitas 20: 2685-2692. Cassava mealybug, Phenacoccus manihoti Matile-Ferrero (Hemiptera: Pseudococcidae) is an invasive pest native to South America. Research was conducted with the objective to study genetic variation of cassava mealybug from different geographic areas in Indonesia. Thirty-six samples of cassava mealybugs were collected from eight different population locations. Genomic DNA was extracted from individual specimens of P. manihoti using gSYNC DNA Extraction Kit from Geneaid Lot No. FB221707. PCR amplification using primary CO1 gene showed the target position as long as 518 bp. Analysis of homology from eight populations revealed eight haplotypes in Indonesia with different variable sites. Genetic distance analysis was done by calculating base pair differences in each population. The percentage of genetic distance between populations was 0.0000% -0.00409%. The results of the analyst using the Kimura-2 parameter showed that the population was divided into 2 clusters. The highest haplotype (Hd) diversity value was 0.8333, while the lowest was zero (Hd = 0). The highest nucleotide diversity (π) was 0.00225 and the lowest was 0.000000. The genetic distance and nucleotide diversity were low because P. manihoti was thelytoky parthenogenesis.

SNP barcoding based on decision tree algorithm: A new tool for identification of mosquito species with special reference to Anopheles

Molecular taxonomy based identification of species in the form of DNA barcodes are extensively used in evolutionary systematics. Almost all the DNA barcodes contain detailed information of the barcoding gene along with uninformative sequences of a particular species. Therefore, a technique is highly essential to remove or to reduce the number of uninformative sequences and ought to create species-specific barcodes for differentiation. The actual variation in genetic sequences, called single nucleotide polymorphism (SNP) genotyping, can be utilized to develop a new tool for rapid, reliable, and high-throughput assay to distinguish the known species. SNPs act as important hereditary markers for uncovering the evolutionary history and normal genetic polymorphisms. Keeping in mind, we propose a decision tree-based barcoding (DTB) algorithm for generating SNP barcodes from the DNA barcoding sequence of several evolutionarily related species to accurately identify a single species. To address this issue, we analyzed mitochondrial COI gene sequences of 64 species of Anopheles mosquitoes. After alignment and truncating, 32 SNPs were discovered in COI gene sequences of Anopheles mosquitoes and then computed to set up the decision rule for constructing the decision tree. The decision tree based barcoding algorithm generates 126 nodes and 32 loci for discriminating 64 Anopheles mosquito species. Finally, we concluded that the DTB method is useful and effective for generating sequence tags for Anopheles mosquito species identification.

<p class="Body">First pentasetacid mite from Australasian Araucariaceae: morphological description and molecular phylogenetic position of Pentasetacus novozelandicus n. sp. (Eriophyoidea, Pentasetacidae) and remarks on anal lobes in eriophyoid mites

A new vagrant eriophyoid mite species of the archaic genus Pentasetacus (Schliesske 1985), P. novozelandicus n. sp., is described with the aid of conventional microscopy, confocal laser scanning microscopy and scanning electron microscopy. It was found on Araucaria heterophylla, which is an araucarian that is endemic to Norfolk Island and introduced to New Zealand. Partial sequences of mitochondrial barcode COI gene and D1–D2 domains of nuclear rDNA of two pentasetacid mites, P. araucariae (MK903025 and MK898944) and P. novozelandicus n. sp. (MK903024 and MK898943) are provided. Molecular phylogenetic analyses of full-length D1–D2 eriophyoid sequences, including GenBank sequences and newly generated sequences of pentasetacids, confirmed the monophyly of Pentasetacidae but failed to resolve the basal phylogeny of Eriophyoidea. This may be because the D1–D2 domains of 28S are hypervariable in Eriophyoidea. Moreover, in pentasetacids D1–D2 sequences are about 20% shorter than in other eriophyoids, and thus harder to align. Two types of anal lobes are described in Eriophyoidea: (1) Eriophyidae s.l. and Phytoptidae s.l. have bilaterally symmetric lobes; (2) pentasetacids have non-divided lobes. The presence of an anal secretory apparatus, comprising internal structures that have previously been described in Eriophyidae s.l. and Phytoptidae s.l., is confirmed in pentasetacid genera. The phylogeny of pentasetacids is also discussed in the context of the paleobiography of Araucariaceae.

A New Vent Limpet in the Genus Lepetodrilus (Gastropoda: Lepetodrilidae) From Southern Ocean Hydrothermal Vent Fields Showing High Phenotypic Plasticity

The recently discovered hydrothermal vent ecosystems in the Southern Ocean host a suite of vent-endemic species, including lepetodrilid limpets dominating in abundance. Limpets were collected from the chimneys, basalts and megafauna of the East Scotia Ridge segments E2 and E9 and the Kemp Caldera at the southern end of the South Sandwich Island arc. The limpets varied in size and shell morphology between vent fields and displayed a high degree of phenotypic plasticity. Size frequency analyses between vent fields suggests continuous reproduction in the limpet and irregular colonisation events. Phylogenetic reconstructions and comparisons of mitochondrial COI gene sequences revealed a level of genetic similarity between individuals from the three vent fields consistent with their belonging to a single molecular operational taxonomic unit. Here we describe Lepetodrilus concentricus n. sp., and evaluate its genetic distinctness and pylogenetic position with congeners based on the mitochondrial COI gene. Results indicate that L. concentricus n. sp. is a sister species towith the two species estimated to have diverged within the last ~5 million years.

Production of specific pathogen free larvae from genetically characterized populations of Anadara tuberculosa (Bivalvia), for stock enhancement and aquaculture in the Peru Northeast Biosphere Reserve

The pustulose ark, Anadara tuberculosa , is considered as an emblematic species of the east Pacific mangrove ecosystem. The decline of its populations is of increasing preoccupation, in particular in Peru. The use of hatchery-produced larvae for stock enhancement or aquaculture is attractive but raises strong criticisms from an ecological point of view, as it could conduce to loss of genetic diversity in wild populations and favor the disease spreading from hatcheries to the environment. In this works, spat production through traditional aquaculture/biotechnology technologies was associated with pathogen molecular diagnostics and with genetic diversity estimation to produce specific pathogen-free (SPF) larvae from genetically characterized populations. All PCR and nested-PCR diagnostics of common bivalve pathogens, such as Bonamia , Martelia , Perkinsus and OsHV1, led to negative results for healthy or moribund adults and spat samples. Microbiological and molecular analyses realized during mortalities led to identifying a pathogenic Pseudomonas strain present on culture tank walls, in moribund spats and adults´ blood. Population genetic variation was assessed by mitochondrial COI gene sequences which showed 36.7% haplotype diversity. This study with hatchery production, pathology and genetic components for an overexploited native bivalve represents an original model for successful mollusk stock enhancement or/and innovative aquaculture programs. Normal 0 21 false false false ES-EC X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:Tabla normal; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0cm; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:Calibri,sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-ansi-language:ES-MX; mso-fareast-language:ES-MX;}

Genetic variation of reef-building polychaete Sabellaria chandraae in the south-eastern Arabian Sea based on mitochondrial COI gene sequences

The honeycomb worm Sabellaria chandraae is the most common reef-building polychaete in the intertidal area along the south-eastern Arabian Sea. We used the mitochondrial cytochrome c oxidase subunit I (mtCOI) gene to examine the levels of genetic variation the population. The samples were collected from seven intertidal areas along the south-eastern Arabian Sea. The hierarchical Analysis of Molecular Variance (AMOVA) and conventional population statistics (FST) showed a low level of genetic differentiation (FST = 0.0864, p < .05), indicating no geographical patterning among seven populations. The present results were able to provide a reference for the single stock population along the south-eastern Arabian Sea.

Integrative taxonomy reveals phenotypic plasticity in the freshwater mussel Contradens contradens (Bivalvia: Unionidae) in Thailand, with a description of a new species

The freshwater mussel Contradens contradens (Lea, 1838) occurs in most types of freshwater habitats throughout Thailand. The species shows extensive variation in shell morphology, which has led to the recognition of six different subspecies. In this study, the validity of these six subspecies plus one unknown species was assessed using an integrative taxonomic approach. Geometric morphometric analyses revealed significant differences in shell shapes among these six nominal morphological subspecies, although a considerable degree of overlap was detected in some groups. In contrast, the phylogenetic tree obtained from the concatenated data of mitochondrial COI and nuclear H3 gene sequences and molecular species delimitation analyses revealed only three supported clades. These clades are proposed herein as three distinct species, and strongly corresponded to the biogeographically disjunct drainage systems in Thailand. They consisted of the (i) C. contradens clade found in the Chao Phraya Basin and other rivers that drain into the Gulf of Thailand, (ii) C. crossei clade that is restricted to the Middle Mekong Basin, and (iii) a clade containing only the newly discovered species from Huai Luang River in the north-east of Thailand, which is described herein as Contradens rolfbrandti Jeratthitikul & Panha, sp. nov. Speciation among these congeners was probably caused by the restriction of gene flow due to the past geomorphology of the river systems. The intraspecific variation in the shell shape detected here does not reflect the evolution of the mussel, but rather is evidence of phenotypic plasticity.http://zoobank.org/urn:lsid:zoobank.org:pub:649B6093-E1DD-4FD8-8185-A4696C43AD36; http://zoobank.org/urn:lsid:zoobank.org:act:777DDE86-8397-4FF3-AA78-0BE0F34611F4

Description of new species of algal-boring Limnoria (Crustacea, Isopoda,Limnoriidae) from Japan and redescription of Limnoria segnoides Menzies, 1957 and L. nagatai Nunomura, 2012.

Previous research on the mitochondrial COI gene sequences of several populations of Limnoria nagatai Nunomura suggested a cryptic species from the Sea of Japan. A new species of algal-boring limnoriid is here described. Limnoria furca sp. nov. was collected from the holdfasts of Eisenia bicyclis on the Oki Islands and the Sea of Japan coast of Honshu and Kyushu Islands, Japan. L. furca sp. nov. is diagnosed morphologically by lacking a mandibular palp, faint subparallel carinae on the pleotelson, faint Y-shaped carinae on pereonite 5, the bifid lacinia mobilis of right mandible and the shapes of the secondary unguis on the pereopods. Similar species, L. segnoides Menzies, 1957 and L. nagatai Nunomura, 2012, are redescribed on the basis of the holotypes.

Genetic diversity of Northern snakehead (Channa argus) based on complete mitochondrial COI gene sequences

White type Channa argus, which has the common name of the great northern snakehead, has an uncertain classification for many years. In the present study, mitochondrial COI gene has been used to analyze the relationships and genetic diversity of nine kinds of Channa. For the Chnannidae family, the average of the inter-species genetic distance was 0.156 (ranged: 0.000–0.245). And the intra-species genetic distances were ranged from 0.000 to 0.002. For the haplotypes of two-colour morphs of Channa argus, the mean of the pair-wise genetic distances was estimated as 0.0009. This value was within the intra-species genetic distance interval, indicating that two-colour morphs of Channa argus are not subspecies of white type at the molecular level. Moreover, take Lateolabrax maculates and Epinephelus coioides as outgroups, molecular phylogenetic tree showed that all the haploids gather together as a branch and crossing each other. These indicated that the white type Channa argus should be regarded as an albino of bio colour type.

Phylogeographic investigation on the spiny frog Quasipaa shini (Amphibia: Anura: Dicroglossidae) using mitochondrial DNA: cryptic species and species complex

The spiny-flanked frog Quasipaa shini is distributed in southcentral China. Here, phylogenetic relationships and diversification of the species were examined using mitochondrial COI gene sequences of 70 individuals from eight populations. Phylogenetic analyses revealed that the species contained two deeply divergent clades (Clades I and II) and five subclades in Clade II. Haplotype network, AMOVA and genetic distance estimations also supported the separations of the six phylogroups. Based on the results, we proposed that at least the Clade I should represent a cryptic species. Neutrality tests indicated that all populations and clades have been probably suffered bottleneck effects or subdivisions.

Genetic analysis reveals Finnish Formica fennica populations do not form a separate genetic entity from F. exsecta.

Coptoformica Müller, 1923 is a subgenus of Formica Linnaeus, 1758 that consists of c. a dozen species of ants that typically inhabit open grassy habitats and build small nest mounds. The most recent addition to the group is Formica fennica Seifert, 2000. The description was based on morphological characters, but the species status has not been confirmed by molecular methods. In this study, we use thirteen DNA microsatellite markers and a partial mitochondrial COI gene sequence to assess the species status of F. fennica, by comparing the genetic variation among samples identified as F. fennica and six other boreal Formica (Coptoformica) species. Most of the species studied form separate, discontinuous clusters in phylogenetic and spatial analyses with only little intraspecific genetic variation. However, both nuclear and mitochondrial markers fail to separate the species pair F. exsecta Nylander, 1846 and F. fennica despite established morphological differences. The genetic variation within the F. exsecta/fennica group is extensive, but reflects spatial rather than morphological differences. Finnish F. fennica populations studied so far should not be considered a separate species, but merely a morph of F. exsecta.

Population genetic diversity of an odorous frog Odorrana grahami (Amphibia: Anura: Ranidae) in relation to conservation based on mitochondrial DNA

The diskless-fingered odorous frog Odorrana grahami is widely distributed in the high-altitude mountains in the southwestern China and northern Indochina regions. In this study, a comparative analysis of the mitochondrial COI gene sequences was performed to examine the population genetic diversity of 76 individuals from 10 localities across the distributional range of the species. Haplotype diversity and nucleotide diversity were 0.605 and 0.00199, respectively, in the total population. An AMOVA indicated that 47.3% of the total variation originated from variation within individual populations and 52.7% came from variation between the 10 geographic populations. Tests of neutral evolution indicated that a recent expansion occurred in total population. The findings provide useful information for the conservation of this species.

Genetic variation analysis of the cosmopolitan chaetognath Sagitta enflata in the northern South China Sea based on mitochondrial COI gene sequences

In this study, genetic diversity and population genetic structure of Sagitta enflata in the northern South China Sea were investigated by 623 bp fragment of mtDNA COI gene sequence. A total of 146 individuals were collected from nine stations and 92 different haplotypes were obtained. 485 variable sites (210 were parsimony informative and 275 were singleton variable sites), and no insertion or deletion was found. An analysis of molecular variance (AMOVA) and conventional population statistics (FST) revealed a low level of genetic differentiation among nine populations (FST = 0.14794, p < .05), indicating no geographical patterning among nine populations. The present results were able to provide a reference for the phylogenetic relationships and assessment of the genetic structure of S. enflata in the northern South China Sea.

Thriving populations with low genetic diversity in giant clam species, Tridacna maxima and Tridacna noae, at Dongsha Atoll, South China Sea

Giant clams provide valuable functions to the coral reefs and traditional fisheries in the South China Sea (SCS), but many populations face escalating threats of overexploitation and habitat loss. To provide critical biodiversity data for development of protection and sustainable utilisation strategies, we examine the status of wild tridacnine population at Dongsha Atoll, the largest northernmost atoll of the SCS. This study also examines the genetic patterns of Tridacna maxima and Tridacna noae, based on partial mitochondrial COI gene sequences. We found four species at Dongsha Atoll with an overall density of 3.14 per 100 m2. Over-harvesting may have depleted populations of T. squamosa and Hippopus hippopus, and they may no longer be reproductively viable. Populations of T. maxima and T. noae appear to be thriving and replenished by recruits, but species showed low levels of mitochondrial genetic diversity that could reduce its adaptability and may become further impacted by exploitation and global warming. Haplotype networks for T. maxima and T. noae showed strong significant population structuring consistent with contemporary geographic boundaries: Dongsha Atoll, Taiwan and Philippines—likely established by the intrusion of the Kuroshio Current. Given the contrasting species status and genetic diversity, conservation strategies need to be tailored to increase success of these efforts.

Exploring taxonomic and phylogenetic relationships to predict radiocaesium transfer to marine biota

One potentially useful approach to fill data gaps for concentration ratios, CRs, is based upon the hypothesis that an underlying taxonomic and/or phylogenetic relationship exists for radionuclide transfer. The objective of this study was to explore whether these relationships could be used to explain variation in the transfer of radiocaesium to a wide range of marine organisms. CR data for 137Cs were classified in relation to taxonomic family, order, class and phylum. A Residual Maximum Likelihood (REML) mixed-model regression modelling approach was adopted. The existence of any patterns were then explored using phylogenetic trees constructed with mitochondrial COI gene sequences from various biota groups and mapping the REML residual means onto these trees. A comparison of the predictions made using REML with blind datasets allowed the efficacy of the procedure to be tested. The only significant correlation between predicted and measured activity concentrations was revealed at the taxonomic level of order when comparing REML analysis output with data from the Barents Sea Region. For this single case a correlation 0.80 (Spearman rank) was derived which was significant at the 0.01 level (1-tailed test) although this was not the case once a (Bonferroni) correction was applied. The application of the REML approach to marine datasets has met with limited success, and the phylogenetic trees illustrate complications of using predictions based on values from different levels of taxonomic organization, where predicted values for the order level can mask the values at lower taxonomic levels. Any influence of taxonomy and phylogeny on transfer is not immediately conspicuous and categorizing marine organisms in this way is limited in providing a potentially robust prognostic extrapolation tool. Other factors may plausibly affect transfer to a much greater degree in marine systems, such as quite diverse life histories and different diets, which may confound any phylogenetic pattern.

A Combined Molecular and Morphological Approach to Explore the Higher Phylogeny of Entimine Weevils (Coleoptera: Curculionidae), with Special Reference to South American Taxa

The Entiminae are broad-nosed weevils constituting the most diverse subfamily of Curculionidae, with over 50 tribes. We performed Bayesian and Maximum Parsimony combined phylogenetic analyses with the main objective of testing higher-level relationships and the naturalness of the major Neotropical and Southern South American (Patagonia and Andes) tribes, including some members from other regions. We compiled a data matrix of 67 terminal units with 63 Entiminae species, as well as four outgroup taxa from Cyclominae, by 3522 molecular (from nuclear 18S rDNA and 28S rDNA, and mitochondrial 16S rDNA and COI gene sequences) and 70 morphological characters. The resulting trees recover a clade Entiminae with a monophyletic Cylydrorhinini and Premnotrypes branching off early. The tree resulting from parsimony analysis shows a clade of Leptopiini from the Australian region and another clade including taxa mainly distributed in the Palaearctic and Neotropical regions, but in the Bayesian tree the South American and Australian Leptopiini are grouped together. The mainly Palaearctic Entiminae (e.g., Brachyderini, Laparocerini, Otiorhynchini, Peritelini, Polydrusini, Phyllobiini and Sciaphylini) form a subclade separated from Southern Hemisphere taxa. Among the latter, the well-supported Naupactini are the sister group of the South American Tanymecini, excluding Platyaspistes, herein transferred to Leptopiini (new placement). Another well-justified clade is Eustylini–Geonemini, which also includes the enigmatic Galapagonotus, and the genus Artipus, thus corroborating its recent exclusion from Naupactini.

Morphological and molecular evidence for a new shrimp species, Atyaephyra vladoi sp. nov. (Decapoda, Atyidae) in the ancient Skadar Lake system, Balkan Peninsula – its evolutionary relationships and demographic history

The Balkan Lake Skadar used to be recognized as potentially ancient. Recent studies revealed that, although the present lake is of post-Pleistocene origin, its hydrological system is of at least Pliocene origin. The basin of this lake is characterized by rich biodiversity and high endemism, particularly in the local spring areas. Our study upon freshwater shrimps from the family Atyidae conducted in the Skadar Lake as well as adjacent springs and rivers led to the description of a new species Atyaephyra vladoi, on the basis of morphological features and molecular data. Phylogenetic investigation using mitochondrial COI gene sequences revealed that this new species is most closely related to the south-Balkan A. thyamisensis, from which it diverged in Late Miocene. Population of A. vladoi has expanded both in demographic and spatial terms during the last major interglacial period before the Holocene, i.e. Marine Isotope Stage 5 or Eemian. Combining this evidence with occurrence of A. vladoi mainly in the areas under influence of spring and riverine waters, we can conclude that the species is probably a relic of the old marshlands occupying the basin before the present lake. This supports the supposedly ancient, pre-Holocene, origins of Lake Skadar hydrological system.

Effects of habitat fragmentation on the genetic diversity and differentiation of Dendrolimus punctatus (Lepidoptera: Lasiocampidae) in Thousand Island Lake, China, based on mitochondrial COI gene sequences.

Thousand Island Lake (TIL) is a typical fragmented landscape and an ideal model to study ecological effects of fragmentation. Partial fragments of the mitochondrial cytochrome oxidase subunit I gene of 23 island populations of Dendrolimus punctatus in TIL were sequenced, 141 haplotypes being identified. The number of haplotypes increased significantly with the increase in island area and shape index, whereas no significant correlation was detected between three island attributes (area, shape and isolation) and haplotype diversity. However, the correlation with number of haplotypes was no longer significant when the 'outlier' island JSD (the largest island) was not included. Additionally, we found no significant relationship between geographic distance and genetic distance. Geographic isolation did not obstruct the gene flow among D. punctatus populations, which might be because of the high dispersal capacity of this pine moth. Fragmentation resulted in the conversion of large and continuous habitats into isolated, small and insular patches, which was the primary effect on the genetic diversity of D. punctatus in TIL. The conclusion to emphasize from our research is that habitat fragmentation reduced the biological genetic diversity to some extent, further demonstrating the importance of habitat continuity in biodiversity protection.

Two new species of the crangonid genus Metacrangon Zarenkov, 1965 (Crustacea: Decapoda: Caridea) from the Okinawa Trough, Japan.

Two new species of the crangonid shrimp genus Metacrangon Zarenkov, 1965, are described and illustrated on the basis of materials collected from the Okinawa Trough, Ryukyu Islands, southern Japan, during diving operations of remotely operated vehicles (ROVs): M. ryukyu n. sp. from off Iheya Island, at depth of 986 m; and Metacrangon kaiko n. sp. from NE of Yonaguni Island, at depth of 2205 m. The two new species resemble members of the M. munita (Dana, 1852) species group, but are both characteristic in having setose dactyli on pereopods 4 and 5. Some minor differences in morphology and genetic analysis using partial sequences of the barcoding mitochondrial COI gene support the recognition of the two new species. Holotypes of the two new species were collected from hydrothermally influenced areas, representing a previously unknown habitat for species of Metacrangon.