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21 results for “NGS barcodes”
Fig. 11 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 11. Haplotype network of Ngirhaphium sivasothii. Thailand: Krabi, Phangnga, Satun; Singapore: Sarimbun, Pulau Tekong, Pulau Ubin, Labrador, Semakau Island, and Sungei Buloh.
Fig. 10 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 10. Haplotype network of Ngirhaphium murphyi. Singapore: Pulau Ubin, Mandai Sungei Buloh; Thailand: Satun and Krabi.
Fig. 12 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 12. Compilation of male terminalia of Ngirhaphium in lateral view. A, Ngirhaphium sivasothii left side with ventral surstylus removed; cerci dorsally; B, Ngirhaphium murphyi left side with ventral surstylus removed; cerci and dorsal surstyli dorsally; C, Ngirhaphium caeruleum left side with ventral surstylus removed; cerci and dorsal surstyli dorsally; D, Ngirhaphium meieri, new species left side with ventral surstylus removed; E, Ngirhaphium chutamasae left side with ventral surstylus removed; F, Ngirhaphium thaicum, new species right side. Scale = 0.1 mm.
Fig. 8 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 8. Ngirhaphium meieri, new species, holotype male terminalia: A, Lateral view of genital capsule with left ventral surstylus removed; B, Cerci dorsally; C. Left ventral surstylus; D, Ventral view of genital capsule. Abbreviations: ae = aedeagus; c = cercus; ds = dorsal surstylus; hy = hypandrium; sp = sperm pump; vs = ventral surstylus. Scale = 0.1 mm.
Fig. 5 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 5. Ngirhaphium thaicum, new species male terminalia (27_009) A, epandrium left side; B, cerci dorsal view; C, left surstylus inside view. Scale = 0.1 mm.
Fig. 2 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 2. Ngirhaphium caeruleum-complex. View of inside of the dorsal surstylus of the left side and the fused dorsal and ventral surstyli of the right side. Scale = 0.1mm. A, green caeruleum from Tutong, Brunei (ZRCBDP0066395) at 1.6 % from the Semakau population; B, green caeruleum from Pulau Tekong, Singapore (ZRCBDP0001462) at 0.6% from the Semakau population; C, green caeruleum from Pulau Ubin, Singapore (ZRC_BDP_0084430) at 0.6% from the Semakau population; D, blue caeruleum from the type locality on Semakau Island, Singapore (ZRCBDP0118762); E, green thaicum, new species from Surat Thani, Thailand (24-018) at 4.2% from the Semakau population; F, green thaicum, new species from Cambodia (JP3C_Ngi-cambodiensis_Misc002) within the variability of the southern Thailand populations.
Fig. 1 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 1. Haplotype network of the Ngirhaphium caeruleum-complex. Brunei: Berambang, Tutong, Labu; Singapore: Pulau Ubin, Pulau Tekong, Semakau Island; Thailand: Chumphon, Surat Thani, and Cambodia.
Fig. 13 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 13. Distribution map of Ngirhaphium in Southeast Asia
Fig. 9 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 9. Distribution map of Ngirhaphium meieri, new species and Ngirhaphium thaicum, new species.
Fig. 7 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 7. Ngirhaphium meieri, new species, female habitus. Scale = 1 mm.
Fig. 6 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 6. Ngirhaphium meieri, new species, male habitus (photo: Abdulloh Samoh). Scale = 1 mm.
Fig. 3 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 3. Ngirhaphium thaicum, new species male habitus. Scale = 1 mm.
Fig. 4 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 4. Ngirhaphium thaicum, new species habitus female. Scale = 1 mm.
Morphology and mini-barcodes: The inclusion of larval sampling and NGS-based barcoding improves robustness of ecological analyses of mosquito communities
<p class="Normal0">A significant proportion of vector-borne diseases are transmitted by blood-sucking dipterans, including mosquitoes. Understanding transmission risks requires accurate identification of species across heterogenous habitats, but many cryptic and polymorphic species are overlooked when using morphological identification. Estimates of mosquito diversity are typically based on adult female trapping methods which tend to target host-seeking species and may represent a biased snapshot of community structure. Unfortunately, diversity estimates based on larval data are rarely included in mosquito ecological analyses. We carried out adult and larval sampling over six months in Singapore using an integrative approach of morphological identification and molecular delineation with mini-barcodes (313 bp) generated on a Next Generation Sequencing platform to obtain species estimates. We collected 3201 mosquitoes across 58 species (14 genera). Notably, 16 species were collected only through larval sampling and 22 species were only resolved using mini-barcodes. Of the latter we identified three morphologically similar species groups and documented several intraspecific polymorphisms. We compared adult-only data against a full dataset (adult + larval + mini-barcode). The species accumulation curves reached an asymptote for all but one site when using the latter; non-metric multidimensional scaling (NMDS) revealed that mosquito communities were only well separated when using the full dataset. Overall, the latter reflects a more defined and accurate community structure across all sites. We find that several mosquito species were generally influenced by tree cover, rainfall and presence of large water bodies, further supporting the idea that many species are niche-specific. <i>Synthesis and applications</i>. We report the first successful use of mini-barcodes on mosquitoes and demonstrate its utility in delineating multiple challenging species groups. We recommend the use of both morphological and molecular identification methods for ecological studies and vector surveillance. Misidentification in species estimation, especially for medically relevant insect groups can lead to conflicting reports and slows down vector control efforts. We provide evidence that varying sampling techniques, particularly of the larval stages for holometabolous insects, is important in generating a robust dataset for downstream analyses. Together with DNA barcoding, this integrative approach helps to minimize error cascades when designing management strategies.</p>
Morphology and mini-barcodes: The inclusion of larval sampling and NGS-based barcoding improves robustness of ecological analyses of mosquito communities
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Data from: Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies
Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.
Data from: Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies
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Data from: Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: validating a reverse workflow for specimen processing
Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an NGS barcoding pipeline that allows for cost-effective high throughput generation of short specimen-specific barcodes (313 bp of COI; lab cost <$0.50 per specimen) through Next Generation Sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3290 of 4032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88-90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases, and yields precise abundance information.
Fig. 14 in NGS-barcodes, haplotype networks combined to external morphology help to identify new species in the mangrove genus Ngirhaphium Evenhuis & Grootaert, 2002 (Diptera: Dolichopodidae: Rhaphiinae) in Southeast Asia
Fig. 14. Maximum likelihood tree of Ngirhaphium based on NGS barcodes (COI, 313bp).
Data from: Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: validating a reverse workflow for specimen processing
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