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16 results for “community barcoding”
Data from: Using full-length metabarcoding and DNA barcoding to infer community assembly for speciose taxonomic groups: a case study
<p>How insect communities are assembled in nature remains largely unknown. In particular, whether habitat filtering or competition serves as the main mechanism in forming insect communities is rarely subject to an in-depth investigation. One bottleneck lies in the difficulty of species identification when dealing with a large number of diverse insects. However, High-Throughput Sequencing (HTS) technology coupled with classic DNA barcoding offers a great opportunity to infer community assembly for this speciose group. In this study, using 13,909 full-length barcodes obtained by Sanger sequencing or the SOAPBarcode metabarcoding method, we showed that competition was the main assembly mechanism for the moth communities studied in temperate forests of China. The two sequencing methods showed highly consistent results with regards to both diversity composition and community assembly mechanism. Significant phylogenetic signals and structure suggested that the focal moth communities were the result of the non-neutral assembly process, which was further confirmed by results of neutral assembly test that accounted for immigration and speciation rates. In conclusion, HTS coupled with a well-curated DNA barcode library can facilitate community assembly inferences, especially for speciose taxonomic groups.</p>
Data from: Life cycle matters: DNA barcoding reveals contrasting community structure between fern sporophytes and gametophytes
Ferns are the only major lineage of vascular plants that have nutritionally independent sporophyte (diploid) and gametophyte (haploid) life stages. However, the implications of this unique life cycle for fern community ecology have rarely been considered. To compare patterns of community structure between fern sporophytes and gametophytes, we conducted a survey of the ferns of the islands of Moorea and Tahiti (French Polynesia). We first constructed a DNA barcode library (plastid rbcL and trnH–psbA) for the two island floras including 145 fern species. We then used these DNA barcodes to identify more than 1300 field-collected gametophytes from 25 plots spanning an elevational gradient from 200 to 2000 m. We found that species richness of fern sporophytes conforms to the well-known unimodal (i.e., mid-elevation peak) pattern, reaching a maximum at ca. 1000 – 1200 m. Moreover, we found that fern sporophyte communities become increasingly phylogenetically clustered at high elevations. In contrast, species richness of fern gametophytes was consistent across sites, and gametophytes showed no correlation of phylogenetic community structure with elevation. Turnover of sporophyte and gametophyte communities was closely linked with elevation at shallow phylogenetic levels, but not at deeper nodes in the tree. Finally, we found several species for which gametophytes had broader ranges than sporophytes, including a vittarioid fern with abundant gametophytes but extremely rare sporophytes. Our study highlights the importance of including diverse life history stages in surveys of community structure, and has implications for the possible impacts of climate change on the distribution of fern diversity.
Data from: Establishing community-wide DNA barcode references for conserving mangrove forests in China
<p><b>Background:</b> Mangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering 'blue carbon'. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring naturally along the country's coasts. Mangrove ecosystems, however, are widely threatened by intensifying human disturbances and rising sea levels. The urgent need to protect mangrove ecosystems could be assisted by using barcoding technology, which provides rapid species identification. </p> <p><b>Results</b>: To investigate this potential, 898 plant specimens were collected from 33 of the major mangrove sites in China. Based on the morphologic diagnosis, the specimens were assigned to 72 species, including all 28 true mangrove species and all 12 mangrove associate species recorded in China. Three chloroplast DNA markers <i>rbcL</i>, <i>trnH-psbA</i>, <i>matK</i>, and one nuclear marker <i>ITS2</i> were chosen to investigate the utility of using barcoding to identify these species. According to the criteria of barcoding gaps in genetic distance, sequence similarity and phylogenetic monophyly, we propose that a single marker, <i>ITS2</i>, is sufficient to barcode the species of mangroves and their associates in China. Furthermore, <i>rbcL</i> or <i>trnH-psbA</i> can also be used to gather supplement confirming data. In using these barcodes, we revealed a very low level of genetic variation among geographic locations in the mangrove species, which is an alert to their vulnerability to climate and anthropogenic disturbances. </p> <p><strong>Conclusion:</strong> We suggest to use <em>ITS2</em> to barcode mangrove species and terrestrial coastal plants in South China. The DNA barcode sequences we obtained would be valuable in monitoring biodiversity and the restoration of ecosystems, which are essential for mangrove conservation.</p>
Toward understanding insect species introduction and establishment: a community-level barcoding approach using island beetles
<p>Since Darwin put forward his opposing hypotheses to explain the successful establishment of species in areas outside their native ranges, the preadaptation and competition-relatedness hypotheses, known as Darwin's naturalisation conundrum, numerous studies have sought to understand the relative importance of each. Here we take advantage of well-characterised beetle communities across laurel forests of the Canary Islands for a first evaluation of the relative support for Darwin's two hypotheses within arthropods. We generated a mitogenome backbone tree comprising nearly half of the beetle genera recorded within the Canary Islands for the phylogenetic placement of native and introduced species sampled in laurel forests, using cytochrome c oxidase I (COI) sequences. For comparative purposes, we also assembled and phylogenetically placed a data set of COI sequences for introduced beetle species that were not sampled within laurel forests. Our results suggest a stronger effect of species preadaptation over resource competition, while also revealing an underappreciated shortfall in arthropod biodiversity data – knowledge of endemic species. We name this the Humboldtean shortfall, and suggest that similar studies using arthropods should incorporate DNA barcode sequencing to mitigate this problem.</p>
Data from: Establishing community-wide DNA barcode references for conserving mangrove forests in China
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Leaf beetle community data for 20 Iberian localities and associated genetic barcodes (cox1)
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Data from: Life cycle matters: DNA barcoding reveals contrasting community structure between fern sporophytes and gametophytes
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Data from: Using full-length metabarcoding and DNA barcoding to infer community assembly for speciose taxonomic groups: a case study
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Toward understanding insect species introduction and establishment: a community-level barcoding approach using island beetles
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Data from: Establishing a community-wide DNA barcode library as a new tool for arctic research
DNA sequences offer powerful tools for describing the members and interactions of natural communities. In this study, we establish the to-date most comprehensive library of DNA barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively studied area of the High Arctic, the Zackenberg Valley in Northeast Greenland. To demonstrate its utility, we apply the library to identify nearly 20 000 arthropod individuals from two Malaise traps, each operated for two summers. Drawing on this material, we estimate the coverage of previous morphology-based species inventories, derive a snapshot of faunal turnover in space and time and describe the abundance and phenology of species in the rapidly changing arctic environment. Overall, 403 terrestrial animal and 160 vascular plant species were recorded by morphology-based techniques. DNA barcodes (CO1) offered high resolution in discriminating among the local animal taxa, with 92% of morphologically distinguishable taxa assigned to unique Barcode Index Numbers (BINs) and 93% to monophyletic clusters. For vascular plants, resolution was lower, with 54% of species forming monophyletic clusters based on barcode regions rbcLa and ITS2. Malaise catches revealed 122 BINs not detected by previous sampling and DNA barcoding. The insect community was dominated by a few highly abundant taxa. Even closely related taxa differed in phenology, emphasizing the need for species-level resolution when describing ongoing shifts in arctic communities and ecosystems. The DNA barcode library now established for Zackenberg offers new scope for such explorations, and for the detailed dissection of interspecific interactions throughout the community.
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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Rapid and cost-effective generation of single specimen multilocus barcoding data from whole arthropod communities by multiple levels of multiplexing
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Data from: Effects of long term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach
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Data from: Plant DNA-barcode library and community phylogeny for a semi-arid East African savanna
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Data from: Establishing a community-wide DNA barcode library as a new tool for arctic research
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