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25 results for “ND2”
DNA sequence data generated using non-invasive feather and eggshell samples from the Grenada Dove for two gene regions: Cyt b and ND2
<p>As an island endemic with a decreasing population, the Critically Endangered Grenada Dove <em>Leptotila wellsi</em> is threatened by accelerated loss of genetic diversity resulting from ongoing habitat fragmentation. Small, threatened populations are difficult to sample directly but advances in molecular methods mean that non-invasive samples can be used. We performed the first assessment of genetic diversity of populations of Grenada Dove by a) assessing mtDNA genetic diversity in the only two areas of occupancy on Grenada, b) defining the number of haplotypes present at each site and c) evaluating evidence of isolation between sites. We used non-invasively collected samples from two locations: Mt Hartman (n=18) and Perseverance (n=12). DNA extraction and PCR were used to amplify 1,751 bps of mtDNA from two mitochondrial markers: NADH dehydrogenase 2 (<em>ND2</em>) and Cytochrome b (<em>Cyt b</em>). Haplotype diversity (<em>h</em>) of 0.4, a nucleotide diversity (π) of 0.00023 and two unique haplotypes were identified within the <em>ND2</em> sequences; a single haplotype was identified within the <em>Cyt b </em>sequences. Of the two haplotypes identified; the most common haplotype (haplotype A = 73.9%) was observed at both sites and the other (haplotype B = 26.1%) was unique to Perseverance. Our results show low mitochondrial genetic diversity and clear evidence for genetically isolated populations. The Grenada Dove needs urgent conservation action, including habitat protection and potential augmentation of gene flow by translocation in order to increase genetic resilience and diversity with the ultimate aim of securing the long-term survival of this Critically Endangered species. </p>
Example ND2 file for testing issues with bioformats metadata extraction
<p>This upload is to assist diagnosis of timestamp issues in new version of Nikon Elements ND2 file formats </p>
20230315 ImageJ bio-format importer multi-channel ND2 bug
<p>A bug wherein ND2 images taken with different camera settings are read incorrectly by ImageJ's bio-format importer</p> <p>imageJ_test.nd2 - The ND2 file produced by NIS Elements AR on a Nikon LV100 microscope. 11 time steps, 2 channels (images taken with different filter blocks).</p> <p>test_image_ImageJ.jpg - A screenshot of Fiji/ImageJ after opening the ND2 with bio-formats importer. The number of dimensions is correct (11 time steps, two channels) but each channel is mono rather than an rgb image and the images are badly jumbled.</p> <p>test_image_metadata_ImageJ.jpg - The OME metadata of the ND2.</p> <p>test_image_movie_imageJ.avi - The ImageJ output exported as an AVI.</p> <p>test_image_NIS.jpg - A screenshot of the ND2 opened in Nikon's NIS Elements Viewer.</p> <p> </p> <p> </p> <p> </p>
Example dataset for Bioformats issue with Nikon ND2 file format
<p>This is an example dataset to help troubleshoot issues with opening ND2 files in the current version of Fiji (latest Bioformats installed). The dataset opens fine in NIS Elements including the free Viewer version. There should be 4 separate images/channels. Three of the images are fluorescence (DAPI, GFP, Texas Red) and the last is DIC (transmitted light). They were taken with a Nikon DS-Ri2 colour camera. However, the data set opens as a 4 channel set where the first image is not recognisable and the subsequent 3 have vertical stripes (missing information?) but look a bit like the DIC image.</p>
Mitochondrial ND2 sequences from 40 specimens of six Onychorhynchus coronatus lineages: swainsoni, coronatus, castelnaui, mexicanus, occidentalis, and fraterculus
<p>We examined phylogeographic patterns and cryptic diversity within the royal flycatcher, <em>Onychorhynchus coronatus</em> (Aves: Onychorhynchidae), a widespread Neotropical lowland forest tyrant flycatcher. A phylogeny of the six recognized subspecies was constructed from mtDNA sequence data of the NADH dehydrogenase subunit two gene, using Bayesian Inference and Maximum Likelihood methods. Phylogenetic analyses revealed high levels of intraspecific divergence within <em>O. coronatus</em>, supporting the existence of at least six independent lineages. The phylogenetic results uncovered the following relationships: (<em>O. c. swainsoni</em> [Southern Atlantic Forest], (<em>O. c. coronatus</em> [western Amazonia], (<em>O. c. castelnaui </em>[eastern Amazonia], (<em>O. c. mexicanus</em> [Central America], (<em>O. c. occidentalis</em> [Tumbesian], <em>O. c. fraterculus </em>[extreme northwestern South America])))). Biogeographic and dating analyses suggest that vicariant and dispersal events acted across approximately six million years to influence lineage diversification within this genus. Some of those events include the formation of the Amazon River and its tributaries, Andean uplift, and climatically induced vegetational shifts. Phylogenetic and biogeographic analyses of <em>O. coronatus</em> lineages support a hypothesis of area relationships in which the first divergence event isolated the Southern Atlantic Forest from Amazonia during the Late Miocene/Early Pliocene. This event was followed by the split of western and eastern Amazonia at the Early/Late Pliocene, the divergence of cis- and trans-Andean lowland regions also at the Early/Late Pliocene, the split between Central America and the extreme northwestern South America/Tumbes at the Early/Middle Pleistocene, and the split between extreme northwestern South America and Tumbes at Middle/Late Pleistocene. Subsequent divergence of the southern and northern populations in the western and eastern <em>Onychorhynchus </em>lineages took place during the Pleistocene. Comparison of phylogenetic trees and patterns in <em>Onychorhynchus </em>with those from published work suggests that across large New World radiations such as the Suboscines, some co-distributed lineages began to diverge long before others, which exemplifies the complexity of their evolutionary history.</p>
Partial NADH dehydrogenase subunit 2 (ND2) gene sequences for Trochilidae hummingbirds
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DNA sequence data generated using non-invasive feather and eggshell samples from the Grenada Dove for two gene regions: Cyt b and ND2
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Mitochondrial ND2 sequences from 40 specimens of six Onychorhynchus coronatus lineages: swainsoni, coronatus, castelnaui, mexicanus, occidentalis, and fraterculus
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Nikon Ri2 colour image nd2 file
<p>Cells with blue counterstain imaged using a Nikon Ti2 microscope and Nikon Ri2 camera</p>
Cytb + ND2 Prinia gracilis complex
<p>Prinias (Cisticolidae: Prinia) are resident warblers of open areas across Africa and Asia and include many polytypic species whose species limits have not been seriously reevaluated recently. Based on an integrative taxonomic analysis of morphology, song, and mitochondrial DNA (mtDNA), we suggest that 2 species should be recognized in the Graceful Prinia (<em>Prinia gracilis</em>) complex. In addition, our morphological analyses show the existence of a well-marked undescribed form in southeastern Somalia, which we name herein as a new subspecies. <em>Prinia gracilis</em> is a small, drab, long-tailed species with streaking above and plain pale underparts that has been suggested to fall into 2 groups: the southwestern nominate group (from Egypt to Oman) and the northeastern <em>lepida </em>group (from Turkey through India). However, the characters presented to justify this grouping are variable and show a mosaic pattern, and whether genetic and vocal differences exist is unknown. We found consistent between-group song differences, with the nominate group giving consistently longer inter-phrase intervals, whereas the members of the <em>lepida </em>group sing an essentially continuous reel. An mtDNA tree suggests a deep split between the nominate and <em>lepida </em>groups, with a coalescence time between these clades of ~ 2.2 million years ago. Vocal and mtDNA analyses provided evidence that the northeastern Arabian Peninsula taxon <em>carpenteri </em>belongs to the <em>lepida </em>group. We found that, of all the morphological characters proposed, only proportions and tail barring and spotting relatively consistently distinguish the 2 groups. However, these characters strongly suggest that the eastern Arabian Peninsula is populated by taxa of both the <em>gracilis </em>and <em>lepida </em>groups, in different areas, but we lack genetic and bioacoustic data to corroborate this. Although further study is needed in potential contact zones, we suggest that 2 species should be recognized in the <em>P. gracilis</em> complex, and we propose the retention of the English name Graceful Prinia for <em>P. gracilis </em>sensu stricto, while we suggest that <em>P. lepida</em> be known as Delicate Prinia.</p>
DS-Fi3 nd2 RGB Image Import Issue
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FIGURE. 1 in Two new Cnemaspis Strauch, 1887 (Squamata: Gekkonidae) from the Shevaroy massif, Tamil Nadu, India, with a preliminary ND2 phylogeny of Indian Cnemaspis
FIGURE. 1. Relief map showing distribution of four divergent Cnemaspis lineages in the Shevaroy massif and Kollimalai. Inset map of India shows location of study area (black rectangle).
FIGURE 11 in Two new Cnemaspis Strauch, 1887 (Squamata: Gekkonidae) from the Shevaroy massif, Tamil Nadu, India, with a preliminary ND2 phylogeny of Indian Cnemaspis
FIGURE 11. Habitat photos of (A) Cnemaspis yercaudensis, (B) Cnemaspis thackerayi sp. nov., and (C) Cnemaspis shevaroyenesis sp. nov., from the Shevaroy massif, Salem district, Tamil Nadu, India.
FIGURE 10 in Two new Cnemaspis Strauch, 1887 (Squamata: Gekkonidae) from the Shevaroy massif, Tamil Nadu, India, with a preliminary ND2 phylogeny of Indian Cnemaspis
FIGURE 10. Type series of Cnemaspis shevaroyensis sp. nov. (from left to right, NCBS-BH675, NCBS-BH676, BNHS 2529, BNHS 2530 and BNHS 2531). Scale bar 10 mm.
FIGURE 7 in Two new Cnemaspis Strauch, 1887 (Squamata: Gekkonidae) from the Shevaroy massif, Tamil Nadu, India, with a preliminary ND2 phylogeny of Indian Cnemaspis
FIGURE 7. Details of dorsal pholidosis at midbody of (A) Cnemaspis thackerayi sp. nov., holotype, NCBS-BH670, (C) Cnemaspis shevaroyensis sp. nov., holotype, NCBS-BH674 and details of ventral scales at midbody (B) Cnemaspis thackerayi sp. nov., holotype, NCBS-BH670, and (D) Cnemaspis shevaroyensis sp. nov., holotype, NCBS-BH674. Scale bars 5 mm.
FIGURE 6 in Two new Cnemaspis Strauch, 1887 (Squamata: Gekkonidae) from the Shevaroy massif, Tamil Nadu, India, with a preliminary ND2 phylogeny of Indian Cnemaspis
FIGURE 6. Photos in life of (A) Cnemaspis yercaudensis, male NCBS-BH678, (B) Cnemaspis yercaudensis, female BNHS 2534, (C) Cnemaspis thackerayi sp. nov., holotype male NCBS-BH670, (D) Cnemaspis thackerayi sp. nov., female, uncollected individual, (E) Cnemaspis shevaroyensis sp. nov., holotype male NCBS-BH674, (F) Cnemaspis shevaroyensis sp. nov., paratype female BNHS 2529; all from Yercaud on the Shevaroy massif, Salem district, Tamil Nadu, India.
FIGURE 8 in Two new Cnemaspis Strauch, 1887 (Squamata: Gekkonidae) from the Shevaroy massif, Tamil Nadu, India, with a preliminary ND2 phylogeny of Indian Cnemaspis
FIGURE 8. Cnemaspis shevaroyensis sp. nov. (holotype, NCBS-BH674), dorsal view (A), ventral view (B), dorsal view of tail (C), and ventral view of tail (D). Scale bars 10 mm.
FIGURE 2 in Two new Cnemaspis Strauch, 1887 (Squamata: Gekkonidae) from the Shevaroy massif, Tamil Nadu, India, with a preliminary ND2 phylogeny of Indian Cnemaspis
FIGURE 2. Maximum likelihood tree of South Asian Cnemaspis based on ND2. Solid circles at nodes indicate bootstrap support>90% and hollow circles 80–90%. Major clades are marked with a vertical line, outgroups not shown.
FIGURE 5 in Two new Cnemaspis Strauch, 1887 (Squamata: Gekkonidae) from the Shevaroy massif, Tamil Nadu, India, with a preliminary ND2 phylogeny of Indian Cnemaspis
FIGURE 5. Type series of Cnemaspis thackerayi sp. nov. (from left to right, NCBS-BH671, NCBS-BH672, NCBS-BH673, BNHS 2526, BNHS 2527, BNHS 2528). Scale bar 10 mm.
FIGURE 4 in Two new Cnemaspis Strauch, 1887 (Squamata: Gekkonidae) from the Shevaroy massif, Tamil Nadu, India, with a preliminary ND2 phylogeny of Indian Cnemaspis
FIGURE 4. Cnemaspis thackerayi sp. nov. (holotype, NCBS-BH670), dorsal view of head (A), ventral view of head (B), lateral view of head (C), view of cloacal region showing precloacal and femoral pores (D), ventral view of right manus (E), and ventral view of right pes (F). Scale bars 5 mm.
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