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140 results for “COI sequences”
Potential new species of pseudaliid lung nematode (Metastrongyloidea) from two stranded neonatal orcas (Orcinus orca) characterised by ITS-2 and COI sequences
<p class="MsoNormal"><span>Knowledge about parasite species of orcas, their prevalence and impact on the health status is scarce. Only two records of lungworm infections in orca exist from male neonatal orcas stranded in Germany and Norway. The nematodes were identified as <em>Halocercus</em> sp. (Pseudaliidae), which have been described in the respiratory tract of multiple odontocete species, but morphological identification to species level remained impossible due to the fragile structure and ambiguous morphological features. Pseudaliid nematodes (Metastrongyloidea) are specific to the respiratory tract of toothed whales and are hypothesized to have become almost extinct in terrestrial mammals. Severe lungworm infections can cause secondary bacterial infections and bronchopneumonia and are a common cause of mortality in odontocetes. DNA isolations and subsequent sequencing of the rDNA ITS-2 and mtDNA COI revealed nucleotide differences between previously described <em>Halocercus</em> species from common dolphin (<em>H. delphini</em>) and harbour porpoises (<em>H. invaginatus</em>) that were comparatively analysed, pointing towards a potentially new species of pseudaliid lungworm in orcas. New COI sequences of six additional metastrongyloid lungworms of seals and porpoises were derived to elucidate phylogenetic relationships and differences between nine species of Metastrongyloidea.</span></p>
COI Barcode sequences for arthropod species from the high Appalachian Mountains, USA
<p>Developing systematic conservation plans depends on a wealth of information on a region's biodiversity. For 'dark taxa' such as arthropods, such data is usually very incomplete and in most cases left out from assessments.</p> <p>Sky islands are important and often fragile biodiversity hotspots. Southern Appalachian high-elevation spruce-fir forests represent a particularly threatened sky-island ecosystem, hosting numerous endemic and threatened species, but their arthropods remain understudied.</p> <p>Here we use voucher-based megabarcoding to explore genetic differentiation among leaf-litter arthropod communities of these highlands, and to examine the extent to which they represent dispersed communities of more or less coherent species, manageable as a distributed unit. We assembled a dataset comprising >6000 COI sequences representing diverse arthropod groups to assess species richness and sharing across peaks and ranges. Comparisons were standardized across taxa using automated species delimitation, measuring endemism levels by putative species.</p> <p>Species-richness was high, with sites hosting from 86-199 litter arthropod species (not including mites or myriapods). Community profiles suggest that around one-fourth of these species are unique to single sky islands and more than one-third of all species are limited to a particular range. Across major taxa, endemicity was lowest in Araneae, and highest in neglected groups like Isopoda, Pseudoscorpionida, Protura, and Diplura.</p> <p>Southern Appalachian sky islands of spruce-fir habitat host significantly distinct leaf litter arthropod communities, with high levels of local endemicity. This is the first work to provide such a clear picture of peak and range uniqueness for a taxonomically broad sample. Ensuring the protection of a sizeable fraction of high-elevation litter species richness will therefore require attention at a relatively fine spatial scale.</p>
Sepiola COI and Vibrio gapA gene sequences
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Potential new species of pseudaliid lung nematode (Metastrongyloidea) from two stranded neonatal orcas (Orcinus orca) characterised by ITS-2 and COI sequences
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COI Barcode sequences for arthropod species from the high Appalachian Mountains, USA
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FIGURE5. Maximum likelihood tree based on the Kimura 2-parameter model of the COI sequences from the Siphamia species with P. kauderni as the outgroup. Tree shown here has the highest log likelihood following 10 000 replications. The percentage of trees in which the associated taxa clustered together is shown next to the branches, branch lengths are measured in the number of substitutions per site and all positions containing gaps and missing data have been eliminated. in Redescription and distributional range extension of the Speckled Siphonfish, Siphamia guttulata (Pisces: Apogonidae)
FIGURE5. Maximum likelihood tree based on the Kimura 2-parameter model of the COI sequences from the Siphamia species with P. kauderni as the outgroup. Tree shown here has the highest log likelihood following 10 000 replications. The percentage of trees in which the associated taxa clustered together is shown next to the branches, branch lengths are measured in the number of substitutions per site and all positions containing gaps and missing data have been eliminated.
III Average nucleotide distances (%) based on the Kimura 2-parameter (K2P) model between Aselliscus spp., and associated outgroups based on complete mitochondrial Cytb (1,140 bp, below the diagonal) and COI (657 bp, above the diagonal) gene sequences in Description of a new species of the genus Aselliscus (Chiroptera, Hipposideridae) from Vietnam
III Average nucleotide distances (%) based on the Kimura 2-parameter (K2P) model between Aselliscus spp., and associated outgroups based on complete mitochondrial Cytb (1,140 bp, below the diagonal) and COI (657 bp, above the diagonal) gene sequences
Mitochondrial DNA tree for COI sequences (DNA barcode) of the goby genus Trimma.
<p>Mitochondrial DNA tree for COI sequences (DNA barcode) of the goby genus Trimma</p>
FIGURE 6. Bayesian tree from mitochondrial COI sequences for the Alpheus bouvieri A in Description of cryptic taxa within the Alpheus bouvieri A. Milne-Edwards, 1878 and A. hebes Kim and Abele, 1988 species complexes (Crustacea: Decapoda: Alpheidae)
FIGURE 6. Bayesian tree from mitochondrial COI sequences for the Alpheus bouvieri A. Milne-Edwards, 1878 and A. hebes Kim and Abele, 1988 species complexes. Numbers at nodes indicate posterior probability values. Results from maximum likelihood and neighbor-joining analyses produced very similar trees (not shown). Field collection numbers (numbers associated with each terminal) correspond to specimens from various localities on the Pacific coast of Panama (EP), Atlantic (Caribbean) coast of Panama (WA), Atol das Rocas, Brazil (WA-Br), and São Tomé (EA). The tree is rooted with three species of Alpheus not closely related to the species of Clade L.
FIGURES 1–6 in The cosmopolitan spider Cryptachaea blattea (Urquhart 1886) (Araneae: Theridiidae): Redescription, including COI sequence, and new synonymy
FIGURES 1–6. Cryptachaea blattea (Urquhart 1886). 1. Habitus of female, dorsal view; 2. Female abdomen, lateral view, small tubercle arrowed; 3. Epigynum, ventral view; 4. Internal genitalia, dorsal view; 5. Male pedipalp, ventral view; 6. Male abdomen, dorsal view. Scale bars for figures 1, 2, 6 = 1.0 mm, 3–5 = 0.1 mm. Abbreviations used: E, embolus; C, conductor; T, tegulum; Cy, cymbium; S, spermathecae.
FIGURE 2. Phylogenetic results. A, Maximum likelihood tree from COI dataset rooted with Ophelia limacina. B, Maximum likelihood tree from ITS1 in Validation of three sympatric Thoracophelia species (Annelida: Opheliidae) from Dillon Beach, California using mitochondrial and nuclear DNA sequence data
FIGURE 2. Phylogenetic results. A, Maximum likelihood tree from COI dataset rooted with Ophelia limacina. B, Maximum likelihood tree from ITS1 dataset rooted according to the result for the COI dataset. Support values are shown as jackknife from parsimony analysis and bootstrap from maximum likelihood respectively separated by /. * indicates 100% values for each support measure.
FIGURE 5. Circular maximum parsimony phylogenetic tree with all sequenced recognised Thai Aleiodes species with a in A turbo-taxonomic study of Thai Aleiodes (Aleiodes) and Aleiodes (Arcaleiodes) (Hymenoptera: Braconidae: Rogadinae) based largely on COI barcoded specimens, with rapid descriptions of 179 new species
FIGURE 5. Circular maximum parsimony phylogenetic tree with all sequenced recognised Thai Aleiodes species with a number of named, primarily Palaearctic taxa included. Species groups that are characterizable morphologically and discussed are indicated in different colours. The tree is rooted using Heterogamus species.
Integrative taxonomic analysis to reveal the species status of Bombus flavidus, combining COI and nuclear sequencing, wing morphometrics and secretions used for mate attraction as well as patterns of color polymorphism
<p>Bumble bees, due to their morphological monotony and color diversity, have presented difficulties with species delimitation. Recent bumble bee declines have made it ever more imperative to resolve the status of species to address conservation concerns. Some of the taxa found to be most threatened are the often-rare socially parasitic bumble bees, which have additional trophic requirements. Among the socially parasitic bumble bees,<i> Bombus flavidus</i> Eversmann has contentious species status. While multiple separate species allied with <i>Bombus flavidus</i> have been suggested, until recently, recognition of two species, a Nearctic <i>Bombus fernaldae</i> (Franklin) and Palearctic <i>B. flavidus,</i> was favoured. Limited genetic data, however, suggested that even these could be a single widespread species, <i>B. flavidus</i>. We addressed the species status of this lineage using an integrative taxonomic approach, combining <i>COI</i> and nuclear sequencing, wing morphometrics and secretions used for mate attraction. We also explore patterns of color polymorphism that have previously confounded taxonomy in this lineage. Our results support the conspecific status of <i>Bombus fernaldae</i> and <i>Bombus flavidus,</i> however, sampling specimens from across the range of these two taxa revealed a distinct population within this broader species confined to eastern North America. This makes the distribution of the social parasite <i>B. flavidus</i> the broadest of any bumble bee, broader than the known distribution of any non-parasitic bumble bee species. Analysis of color phenotypes revealed that color polymorphisms are retained across the range of the species, but may be influenced by local mimicry complexes. Following these results, <i>Bombus flavidus</i> Eversmann, 1852<i> </i>is synonymized with <i>Bombus fernaldae </i>(Franklin, 1911) <b>syn. nov.</b> and a subspecific status, <i>Bombus flavidus </i><i>appalachiensis</i> <b>ssp. nov.</b>, is assigned to the distinct lineage ranging from the Appalachians to the eastern boreal regions of the United States and far southeastern Canada.</p>
Supplementary material 1 from: Colihueque N, Gantz A, Rau JR, Parraguez M (2015) Genetic divergence analysis of the Common Barn Owl Tyto alba (Scopoli, 1769) and the Short-eared Owl Asio flammeus (Pontoppidan, 1763) from southern Chile using COI sequence. ZooKeys 534: 135-146. https://doi.org/10.3897/zookeys.534.5953
Pictures of external morphology of specimens of Tyto alba and Asio flammeus collected in southern Chile: Explanation note: Pictures of ventral and dorsal views of specimens showing plumage color and overall appearance. Data on body mass of these specimens are also provided.
FIGURE 20. Phylogenetic relationship among selected Dryocosmus and Chilaspis species based COI sequences resolved using with MrBayes 3.2.6 in Discovery of a new species of Dryocosmus Giraud, 1859 (Hymenoptera: Cynipidae: Cynipini) on Castanopsis tibetana from China
FIGURE 20. Phylogenetic relationship among selected Dryocosmus and Chilaspis species based COI sequences resolved using with MrBayes 3.2.6 (Ronquist et al. 2012). Two independent MCMC runs were run with the following parameters: 10 million gens, nst = 6, rates = gamma, sample frequency = 1/1,000, burn-in = 30%, and otherwise default. The length of the branches is drawn to scale of genetic distance and the number over branches is posterior probability. (Generic name abbreviations: A. = Andricus, Ch. = Chilaspis, D. = Dryocosmus)
FIGURE 6. Maximum likelihood tree constructed using COI sequences with GenBank accession numbers. Bootstrap support values were calculated with a rapid bootstrapping algorithm for 1000 in Branchinotogluma bipapillata n. sp., a new branchiate scale worm (Annelida: Polynoidae) from two hydrothermal fields on the Southwest Indian Ridge
FIGURE 6. Maximum likelihood tree constructed using COI sequences with GenBank accession numbers. Bootstrap support values were calculated with a rapid bootstrapping algorithm for 1000 replicates in Raxml, and only those higher than 50 were shown.
FIGURE 2. Maximum Likelihood tree for Acanthephyra COI sequences with 1000 in First record of deep-sea caridean shrimp Acanthephyra fimbriata Alcock & Anderson, 1894 (Crustacea: Decapoda: Acanthephyridae) from southwest coast of India
FIGURE 2. Maximum Likelihood tree for Acanthephyra COI sequences with 1000 bootstrap showing the relationship of the specimen with other related species.
Data from: Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the Northern Red Sea
High-Throughput Sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs of the Gulf of Aqaba, a semi-enclosed system in the Northern Red Sea. Samples were obtained from standardized sampling devices [Autonomous Reef Monitoring Structures (ARMS)] deployed for 18 months. DNA barcoding of non-sessile specimens >2mm revealed 83 OTUs in six phyla, of which only 25% matched a reference sequence in public databases. Metabarcoding of the 2mm-500μm and sessile bulk fractions revealed 1197 OTUs in 15 animal phyla, of which only 4.9% matched reference barcodes. These results highlight the scarcity of COI data for cryptobenthic organisms of the Red Sea. Compared with data obtained using similar methods, our results suggest that Gulf of Aqaba reefs are less diverse than two Pacific coral reefs but much more diverse than an Atlantic oyster reef at a similar latitude. The standardized approaches used here show promise for establishing baseline data on biodiversity, monitoring the impacts of environmental change, and quantifying patterns of diversity at regional and global scales.
FIGURE 20 in Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)
FIGURE 20. Phylogram of a maximum likelihood analysis of the DNA sequence data (Appendix 4) using the general time reversible model. The analysis includes the subaptera – group taxa and one outgroup.
FIGURE 19 in Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)
FIGURE 19. Strict consensus tree (length 374 steps, CI 0.94, RI 0.90) of a maximum parsimony analysis of the DNA sequence data (Appendix 4). Maximum parsimony bootstrap values> 50 % are shown above branches (2000 replications). The analysis includes the subaptera – group taxa and one outgroup.
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