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724 results for “COI”
COI and 18S metabarcoding data from Hidden Lake (Banff National Park, Canada) over two rotenone applications between 2018 and 2020.
Water samples were taken in Hidden Lake at five different time points around two rotenone applications: (i) five weeks prior to the first rotenone application, on July 12 2018; (ii) approximately three weeks after the first application of rotenone, on 7 September 2018; (iii) approximately 10 months after the first rotenone application, on 10 July 2019; (iv) four weeks following the final treatment of rotenone on the 17 September 2019; and (v) one year after the final rotenone treatment, on 19 August 2020. For each time point there is a pelagic, a littoral and a profundal sample. COI and 18S metabarcoding methods were used to produce community data. The objective of this study was to assess the non-target effect of rotenone application (in summer 2018 and 2019) on aquatic communities (i.e. phytoplankton, fungi, zooplankton and benthic macroinvertebrates).
FIG. 1 in Beyond shells: first detailed morphological description of the mangrove-associated gastropod Haminoea cf. fusca (A. Adams, 1850) (Cephalaspidea, Haminoeidae), with a COI phylogenetic analysis
FIG. 1. — Bayesian phylogenetic tree based on partial sequences of the COI gene. Figures on nodes are posterior probabilities, scale bar refer to branch lengths. Coloured squares refer to species that are Indo West Pacific in origin, whereas grey squares to Atlantic and eastern Pacific species. PP, 1. The specimen here used from the Philippines is depicted in Gosliner et al. 2015: 30, lower right.
Figure 2. D in Neotypification of Drawida hattamimizu Hatai, 1930 (Annelida, Oligochaeta, Megadrili, Moniligastridae) as a model linking mtDNA (COI) sequences to an earthworm type, with a response to the 'Can of Worms' theory of cryptic species
Figure 2. D. hattamimizu unscaled habitus (from Watanabe, 2005, fig. 1 after Hatai's 1931 original).
Fig. 27. Maximum likelihood tree from the concatenated data set with COI, 28S and 18S in Revision of the Merodon bombiformis group (Diptera: Syrphidae) - rare and endemic African hoverflies
Fig. 27. Maximum likelihood tree from the concatenated data set with COI, 28S and 18S rRNA gene sequences.
COI sequences dataset of Dicronocephalus species in this study.
Explanation note: This COI data includes 50 individual sequences of the examined Dicronocephalus species and subspecies in this study
The combined dataset of COI and 16S rRNA of Dicronocephalus species in this study.
Explanation note: There is the concatenated sequences of COI and 16S rRNA genes correspondence with each sample.
COI phylogeny of Epicephala
Explanation note: Maximum-likelihood phylogeny of Epicephala moths based on 582 base pairs of the mitochondrial COI gene.
Raw data used for COI delineation of the Eupolybothrus species: Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
<p>Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar</p>
COInr a comprehensive, non-redundant COI database from NCBI-nt and BOLD
<p>COInr is a non-redundant, comprehensive database of COI sequences extracted from NCBI-nt and BOLD. It is not limited to a taxon, a gene region, or a taxonomic resolution. Sequences are dereplicated between databases and within taxa.</p> <p>Each taxon has a unique taxonomic Identifier (taxID), fundamental to avoid ambiguous associations of homonyms and synonyms in the source database. TaxIDs form a coherent hierarchical system fully compatible with the NCBI taxIDs allowing creating their full or ranked linages.<br> <br> COInr is a good starting point to create custom databases according to the users’ needs using mkCOInr scripts available at <a href="https://github.com/meglecz/mkCOInr">https://github.com/meglecz/mkCOInr</a> <br> It is possible to select/eliminate sequences for a list of taxa, select a specific gene region, select for minimum taxonomic resolution, add new custom sequences, and format the database for BLAST, QIIME, RDP classifiers.</p> <p> </p>
COI metabarcoding data from arthropod pollinator communities in burned and unburned sites of California
<p>Novel wildfire regimes are rapidly changing global ecosystems and pose significant challenges for biodiversity conservation and ecosystem management. In this study, we used DNA metabarcoding to assess the response of arthropod pollinator communities to large-scale wildfires across diverse habitat types in California. We sampled six reserves within the University of California Natural Reserve System (UCNRS), each of which was partially burned in the 2020 Lightning Complex wildfires in California. Using yellow pan traps to target pollinators, we collected arthropods from burned and unburned sites across multiple habitat types including oak woodland, redwood, scrub, chamise, grassland, forest, and serpentine habitats. We found no significant difference in alpha diversity values between burned and unburned sites; instead, seasonal variations played a significant role in arthropod community dynamics, with the emergence of plant species in Spring promoting increased pollinator richness at all sites. When comparing all sites, we found that burn status was not a significant grouping factor. Instead, compositional differences were largely explained by geographic differences, with distinct communities within each reserve. Within a geographic area, the response of arthropods to fire was dependent on habitat type. While communities in grasslands and oak woodlands exhibited recovery following burn, scrublands experienced substantial changes in community composition. Our study highlights the importance of examining community responses to wildfires across broad spatial scales and diverse habitat types. By understanding the nuanced dynamics of arthropod communities in response to fire disturbances, we can develop effective conservation strategies that promote resilience and maintain biodiversity in the face of increasing wildfire frequency and severity driven by climate change.</p>
Fig. 3. Cytochrome c oxidase subunit I in Analysis of COI gene, prevalence, and intensity of the bat fly Cyclopodia greeffi on roosting straw-coloured fruit bat Eidolon helvum in Southwest Nigeria
Fig. 3. Cytochrome c oxidase subunit I (COI) gene sequence phylogeny showing the relationship between Cyclopodia greeffi and other species of the same and different genera. Values obtained from Bayesian posterior are presented as supports at the nodes. BI – Bayesian posterior probability value.
Fig. 2. Cyclopodia greeffi. a in Analysis of COI gene, prevalence, and intensity of the bat fly Cyclopodia greeffi on roosting straw-coloured fruit bat Eidolon helvum in Southwest Nigeria
Fig. 2. Cyclopodia greeffi. a. Thorax, dorsal: ctenidia with thick blunt teeth. b, c, d. Abdomen ventral: b. sternite 1–2 bearing ctenidium, with about 40–44 blunt teeth; c. male, claspers long and slender, pigmented at the apex, fifth sternite with 8 spines; d. female, truncate abdomen, sternite with two curved rows of spine.
Fig. 6 in Analysis of COI gene, prevalence, and intensity of the bat fly Cyclopodia greeffi on roosting straw-coloured fruit bat Eidolon helvum in Southwest Nigeria
Fig. 6. Regression distribution plot of Cyclopodia greeffi infestation intensity on Eidolon helvum weight for both sexes and seasons.
Fig. 1. a, b, c. C in Analysis of COI gene, prevalence, and intensity of the bat fly Cyclopodia greeffi on roosting straw-coloured fruit bat Eidolon helvum in Southwest Nigeria
Fig. 1. a, b, c. C. greeffi parasites on the straw-coloured fruit bat Eidolon helvum. a. fur around the right side of shoulder and neck region; b. ventral side of the wing (patagium) region below the right forearm; c. ventral side of the abdominal region. Arrows are pointing to the location of the bat flies.
Fig. 5 in Analysis of COI gene, prevalence, and intensity of the bat fly Cyclopodia greeffi on roosting straw-coloured fruit bat Eidolon helvum in Southwest Nigeria
Fig. 5. Density distribution plot of intensity of infestation of Cyclopodia greeffi on Eidolon helvum showing seasonal bimodal distribution.
Fig. 4 in Analysis of COI gene, prevalence, and intensity of the bat fly Cyclopodia greeffi on roosting straw-coloured fruit bat Eidolon helvum in Southwest Nigeria
Fig. 4. Density distribution plot of intensity of Cyclopodia greeffi infestation on Eidolon helvum for sexes and seasons.
Fig. 36 in COI mtDNA barcoding and morphology for the description of a new species of ricinuleid of the genus Pseudocellus (Arachnida: Ricinulei: Ricinoididae) from El Triunfo Biosphere Reserve, Chiapas, Mexico
Fig. 36. Species of the genus Pseudocellus Platnick, 1980 described from Chiapas, Mexico, including the new species described herein. Star: El Triunfo Biosphere Reserve, El Quetzal Camp, Angel Albino Corzo Municipality. Red circle: Cerro Boquerón, Ejido Boquerón, Motozintla Municipality. Orange circle: Sumidero del Camino, 16 km NE of Comitán. Pink circle: Kolem-chen Cave "Cueva Grande", Chan-kin Reserve, Ocosingo Municipality. Blue circle: San Francisco Cave, La Trinitaria Municipality. Purple circle: Finca Guatimoc, south slope of the Tacaná volcano, 32 km north of Tapachula, near Cacahuatán. Green circle: Las Abejas Cave, San Fernando Municipality.
Fig. 1 in COI mtDNA barcoding and morphology for the description of a new species of ricinuleid of the genus Pseudocellus (Arachnida: Ricinulei: Ricinoididae) from El Triunfo Biosphere Reserve, Chiapas, Mexico
Fig. 1. Neighbour-Joining (NJ) tree with p-distances constructed with COI barcode sequences from different specimens and species of Pseudocellus Platnick, 1980. Colors of the branches indicate species of Pseudocellus already described, red branches indicate the new species. Numbers on the branches represent Bootstrap support values (>50% significant).
Figs 32–35 in COI mtDNA barcoding and morphology for the description of a new species of ricinuleid of the genus Pseudocellus (Arachnida: Ricinulei: Ricinoididae) from El Triunfo Biosphere Reserve, Chiapas, Mexico
Figs 32–35. Pseudocellus giribeti sp. nov. Paratypes (MCZ 80010). 32–33. Deutonymph, habitus, dorsal and ventral views. 34–35. Tritonymph, habitus, dorsal and ventral views. Scale bars = 2 mm.
Figs 20–26 in COI mtDNA barcoding and morphology for the description of a new species of ricinuleid of the genus Pseudocellus (Arachnida: Ricinulei: Ricinoididae) from El Triunfo Biosphere Reserve, Chiapas, Mexico
Figs 20–26. Pseudocellus giribeti sp. nov. Holotype, ♂ (MCZ 80010). 20–22. Right leg III (copulatory apparatus), retrolateral, prolateral and dorsal views. 23. Copulatory apparatus extended, prolateral view. 24. Copulatory apparatus, dorsal view. 25. Copulatory apparatus, prolateral view. 26. Tarsal process, distal half, prodorsal view. Scale bars: 20–22 = 0.5 mm; 23–25 = 0.2 mm; 26 = 0.1 mm.
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Allen Brain Atlas
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