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86 results for “COI gene”
FIGURE 2 Bayesian consensus single gene trees for COI, 16S, 28S and ITS2 in The role of allopatric speciation and ancient origins of Bathynellidae (Crustacea) in the Pilbara (Western Australia): two new genera from the De Grey River catchment
FIGURE 2 Bayesian consensus single gene trees for COI, 16S, 28S and ITS2. Numbers on branches represent Bayesian posterior probabilities followed by maximum likelihood bootstrap percentage. ABGD and PTP results are reported next to the trees. ABGD method: major partitions are showed; PTP: partitions with the highest support for each group are represented.
Figure 1. - Bayesian phylogeny of Euptychia based on one mitochondrial (COI) and one nuclear (EF1-a) gene. Posterior probabilities are listed above and bootstrap values below branches. A dash denotes bootstrap support lower than 50%. (Euptychiaattenboroughi is not included in the analysis – see text for details.)
Figure 1. - Bayesian phylogeny of Euptychia based on one mitochondrial (COI) and one nuclear (EF1-a) gene. Posterior probabilities are listed above and bootstrap values below branches. A dash denotes bootstrap support lower than 50%. (Euptychiaattenboroughi is not included in the analysis – see text for details.)
Figure 10. - Maximum-likelihood phylogeny of Epicephala species based on sequences of the COI, ArgK and EF1α genes. Numbers above nodes are maximum-likelihood bootstrap support values based on 1,000 replications. The Japanese Epicephala species are marked in blue. Symbols right to species names donate ovipositor morphology: inverted U-shape, rounded apically; inverted V-shape, acute apically.
Figure 10. - Maximum-likelihood phylogeny of Epicephala species based on sequences of the COI, ArgK and EF1α genes. Numbers above nodes are maximum-likelihood bootstrap support values based on 1,000 replications. The Japanese Epicephala species are marked in blue. Symbols right to species names donate ovipositor morphology: inverted U-shape, rounded apically; inverted V-shape, acute apically.
Fig. 1 in Mitochondrial DNA diversity in the acanthocephalan Prosthenorchis elegans in Colombia based on cytochrome c oxidase I (COI) gene sequence
Fig. 1. Photo showing the characteristic external morphology of Prosthenorchis elegans.
Sepiola COI and Vibrio gapA gene sequences
Open the record for dataset details and reuse information.
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
Evaluating the genetic variation of the COI gene of Insecta: Implications for DNA barcoding, metabarcoding and species delimitation studies
<p>The genetic variation of the COI gene has a great effect on the final results of the species delimitation studies. However, little research has comprehensively investigated the genetic divergence in COI among Insecta. The fast-growing COI data in BOLD provide an opportunity for comprehensively appraising the genetic variation in COI among Insecta. We calculated the K2P distance of 64,414 insect species downloaded from BOLD. The match ratios of the clustering analysis based on different thresholds were compared among 4,288 genera (35,068 species). Besides, we also compared the match ratios obtained from two species delimitation methods: the clustering analysis (distance-based method) and the bPTP analysis (tree-based method). Furthermore, the effectiveness of two different results of the bPTP analysis: bPTP_h and bPTP_ml was also tested. Approximately one-quarter of the species of Insecta showed high intraspecific genetic variation (> 3%), and a conservative estimate of this value is 12.05-22.58%. The application of empirical thresholds (e.g., 2% and 3%) in the clustering analysis may result in the overestimation of species diversity. In metabarcoding studies, a threshold of 3% can only be used to estimate the insect diversity roughly. As for the clustering analysis, the "threshOpt" or "localMinima" algorithms can provide a priori value for the researcher. Nevertheless, if the minimum interspecific genetic distance of congeneric species was greater than or equal to 2%, it is possible to avoid overestimating the species diversity based on the empirical thresholds. Besides, the match ratios of the bPTP_ml results were higher than those of the bPTP_h results. As for the bPTP analysis, the bPTP_ml results were recommended. If a proper threshold was selected, the clustering analysis may outperform the bPTP analysis.</p>
FIGURE 2 in The first phylogenetic study of sword-tail crickets from China inferred from COI, 18S and 28S genes, with the establishment of two new genera and description of one new species (Orthoptera: Grylloidea: Trigonidiidae)
FIGURE 2. Emerasoma curvicerca sp. nov. A. male in dorsal view, B. female in dorsal view, C. male head in dorsal view, D. female head in dorsal view, E. palpus, F. tympana (1. outside, 2. inner side), G. cercus, H. ovipositor, I. male genitalia in dorsal view, J. male genitalia in ventral view.
FIGURE 1 in The first phylogenetic study of sword-tail crickets from China inferred from COI, 18S and 28S genes, with the establishment of two new genera and description of one new species (Orthoptera: Grylloidea: Trigonidiidae)
FIGURE 1. Phylogenetic tree of Trigonidiidae species distributed in China. The topology of the tree was constructed inferred from 18S-28S-COI concatenated sequences using ML method. Two Nemobiinae species comprises Po. taprobanensis and Di. fascipes are regarded as the outgroup. Bootstrap values and posterior probabilities are indicated above each branch. The representative species of each lineage is shown in right in this order top to down: Ho. nigripes, An. brevisparamerus, Na. matsuurai, Em. curvicerca, Me. minor, Se. fujianensis, Sv. bifasciata, Am. fulvus, Pa. nitidum, Tr. cicindeloides, Ab. Chloropodum (photos by He Z.-Q.)
Data from: Identification of Swedish mosquitoes based on molecular barcoding of the COI gene and SNP analysis
Mosquito-borne infectious diseases are emerging in many regions of the world. Consequently, surveillance of mosquitoes and concomitant infectious agents is of great importance for prediction and prevention of mosquito-borne infectious diseases. Currently, morphological identification of mosquitoes is the traditional procedure. However, sequencing of specified genes or standard genomic regions, DNA barcoding, has recently been suggested as a global standard for identification and classification of many different species. Our aim was to develop a genetic method to identify mosquitoes and to study their relationship. Mosquitoes were captured at collection sites in northern Sweden and identified morphologically before the cytochrome c oxidase subunit I (COI) gene sequences of 14 of the most common mosquito species were determined. The sequences obtained were then used for phylogenetic placement, for validation and benchmarking of phenetic classifications, and finally to develop a hierarchical PCR-based typing scheme based on single nucleotide polymorphism sites (SNPs) to enable rapid genetic identification, circumventing the need for morphological characterization. The results showed that exact phylogenetic relationships between mosquito taxa were preserved at shorter evolutionary distances, but at deeper levels they could not be inferred with confidence by using COI gene sequence data alone. Fourteen of the most common mosquito species in Sweden were identified by the SNP/PCR-based typing scheme, demonstrating that genetic typing using SNPs of the COI gene is a useful method for identification of mosquitoes with potential for worldwide application.
FIGURE 1. Neighbour joining COI gene tree using uncorrected p in Description of two final stadium platystictid larvae from Borneo, including that of Drepanosticta? attala Lieftinck, identified using DNA barcoding (Odonata: Zygoptera: Platystictidae)
FIGURE 1. Neighbour joining COI gene tree using uncorrected p–distance for Drepanosticta attala and D. barbatula adults and larva plus related platystictid taxa with Sinosticta hainanense as outgroup. All voucher specimens except that of D. barbatula have a six digit collection number with an RMNH.INS. prefix; this prefix is omitted in the figure for clarity.
FIGURE 1. Neighbour-joining COI gene tree using uncorrected p in Description of the final stadium larvae of Onychargia atrocyana Selys, 1865 from Sarawak, identified using DNA barcoding (Odonata: Zygoptera: Platycnemididae), with an overview of larval characters in the Platycnemididae
FIGURE 1. Neighbour-joining COI gene tree using uncorrected p-distance for Onychargia atrocyana using Paracnemis alluaudi and Podolestes harrissoni as outgroups. All voucher specimens have a six-digit collection number with an RMNH.INS. prefix; this prefix is omitted in the figure for clarity.
FIGURE 2. COI gene tree for the 33 in Revision of the genus Devadatta Kirby, 1890 in Borneo based on molecular and morphological methods, with descriptions of four new species (Odonata: Zygoptera: Devadattidae)
FIGURE 2. COI gene tree for the 33 specimens of Devadatta also used in the analysis with other markers and one outgroup taxon. Posterior probability values are shown (as percentages) if less than 100%. RMNH collection codes are shown for each specimen, with the RMNH.INS. prefix omitted for clarity.
FIGURE 1. COI gene tree for 73 in Revision of the genus Devadatta Kirby, 1890 in Borneo based on molecular and morphological methods, with descriptions of four new species (Odonata: Zygoptera: Devadattidae)
FIGURE 1. COI gene tree for 73 specimens of Devadatta and one outgroup taxon, from Bayesian Inference analysis. Posterior probability values are shown (as percentages) if less than 100%. RMNH collection codes are shown for each specimen, with the RMNH.INS. prefix omitted for clarity.
Figure 1. Neighbour joining COI gene tree using uncorrected p in Description of larvae of two species of Coeliccia Selys, 1865 from Sarawak, identified using DNA barcoding (Odonata: Platycnemididae)
Figure 1. Neighbour joining COI gene tree using uncorrected p-distance for species of the Coeliccia borneensis-group, including both adults and larvae of C. campioni and C.flavostriata, and their sampling sites (except for Lestes dissimulans all from Sarawak, East Malaysia). Coeliccia didyma and Lestes dissimulans are used as outgroups.
FIGURE 2. Overview tree for the COI gene fragment. Bayesian inference tree using MrBayes 3.2.7a in The Oracle of Delphi-a molecular phylogenetic approach to Greek Cordulegaster Leach in Brewster, 1815 (Odonata: Anisoptera: Cordulegastridae)
FIGURE 2. Overview tree for the COI gene fragment. Bayesian inference tree using MrBayes 3.2.7a using the best-fit model (GTR+I+G) identified with JModeltest 2.1.10. Bayesian posterior probabilities values are depicted at the nodes. Included are our own sequences (PCR number next to the name) and those retrieved from GenBank (accession numbers next to the name), if specimens identify different taxa in the COI and ITS analysis they are considered hybrids. Haplotype analysis (TCS-network made in PopART 1.7) is shown in Figs. 5 and 6.
FIGURE 1. Neighbour joining COI gene tree using uncorrected p in Description of the final instar larva of Orthetrum borneense Kimmins, 1936 (Odonata, Libellulidae), using rearing and molecular methods
FIGURE 1. Neighbour joining COI gene tree using uncorrected p–distance for adults of nine species and subspecies of Orthetrum plus two outgroup taXa, and a larva of O. borneense.
FIGURE 1. COI gene tree for 29 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURE 1. COI gene tree for 29 specimens of Leptogomphus and three outgroup taxon. The best Maximum Likelihood tree is shown, with posterior probabilities from the Bayesian Inference analysis also depicted on the branches. Bootstrap values and posterior probabilities are shown if less than 100 or 1.0 respectively. RMNH collection codes are shown for each specimen, as well as the sex of the specimen and an indication of where it was collected.
Figure 7 in Molecular characterisation of leeches (Clitellata, Annelida) based on the mitochondrial cytochrome oxidase I (COI) gene region for Turkish fauna
Figure 7. Bayesian tree analysis of the COI (629 positions) data set of Hirudo species, with MrBayes v. 3.2.7.
Figure 8 in Molecular characterisation of leeches (Clitellata, Annelida) based on the mitochondrial cytochrome oxidase I (COI) gene region for Turkish fauna
Figure 8. Maximum likelihood phylogeny for Limnatis species based on COI sequences. Bootstrap values are shown for 1000 replicates.
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