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1.
Implementing cost‐effective monitoring programs for wild bees remains challenging due to the high costs of sampling and specimen identification. To reduce costs, next‐generation sequencing (NGS)‐based methods have lately been suggested as alternatives to morphology‐based identifications. To provide a comprehensive presentation of the advantages and weaknesses of different NGS‐based identification methods, we assessed three of the most promising ones, namely metabarcoding, mitogenomics and NGS barcoding. Using a regular monitoring data set (723 specimens identified using morphology), we found that NGS barcoding performed best for both species presence/absence and abundance data, producing only few false positives (3.4%) and no false negatives. In contrast, the proportion of false positives and false negatives was higher using metabarcoding and mitogenomics. Although strong correlations were found between biomass and read numbers, abundance estimates significantly skewed the communities' composition in these two techniques. NGS barcoding recovered the same ecological patterns as morphology. Ecological conclusions based on metabarcoding and mitogenomics were similar to those based on morphology when using presence/absence data, but different when using abundance data. In terms of workload and cost, we show that metabarcoding and NGS barcoding can compete with morphology, but not mitogenomics which was consistently more expensive. Based on these results, we advocate that NGS barcoding is currently the seemliest NGS method for monitoring of wild bees. Furthermore, this method has the advantage of potentially linking DNA sequences with preserved voucher specimens, which enable morphological re‐examination and will thus produce verifiable records which can be fed into faunistic databases.  相似文献   

2.
Mitochondrial genomes can be assembled readily from shotgun‐sequenced DNA mixtures of mass‐trapped arthropods (“mitochondrial metagenomics”), speeding up the taxonomic characterization. Bulk sequencing was conducted on some 800 individuals of Diptera obtained by canopy fogging of a single tree in Borneo dominated by small (<1.5 mm) individuals. Specimens were split into five body size classes for DNA extraction, to equalize read numbers across specimens and to study how body size, a key ecological trait, interacts with species and phylogenetic diversity. Genome assembly produced 304 orthologous mitochondrial contigs presumed to each represent a different species. The small‐bodied fraction was the by far most species‐rich (187 contigs). Identification of contigs was through phylogenetic analysis together with 56 reference mitogenomes, which placed most of the Bornean community into seven clades of small‐bodied species, indicating phylogenetic conservation of body size. Mapping of shotgun reads against the mitogenomes showed wide ranges of read abundances within each size class. Ranked read abundance plots were largely log‐linear, indicating a uniformly filled abundance spectrum, especially for small‐bodied species. Small‐bodied species differed greatly from other size classes in neutral metacommunity parameters, exhibiting greater levels of immigration, besides greater total community size. We suggest that the established uses of mitochondrial metagenomics for analysis of species and phylogenetic diversity can be extended to parameterize recent theories of community ecology and biodiversity, and by focusing on the number mitochondria, rather than individuals, a new theoretical framework for analysis of mitochondrial abundance spectra can be developed that incorporates metabolic activity approximated by the count of mitochondria.  相似文献   

3.
This study examines the utility of morphology and DNA barcoding in species identification of freshwater fishes from north‐central Nigeria. We compared molecular data (mitochondrial cytochrome c oxidase subunit I (COI) sequences) of 136 de novo samples from 53 morphologically identified species alongside others in GenBank and BOLD databases. Using DNA sequence similarity‐based (≥97% cutoff) identification technique, 50 (94.30%) and 24 (45.30%) species were identified to species level using GenBank and BOLD databases, respectively. Furthermore, we identified cases of taxonomic problems in 26 (49.00%) morphologically identified species. There were also four (7.10%) cases of mismatch in DNA barcoding in which our query sequence in GenBank and BOLD showed a sequence match with different species names. Using DNA barcode reference data, we also identified four unknown fish samples collected from fishermen to species level. Our Neighbor‐joining (NJ) tree analysis recovers several intraspecific species clusters with strong bootstrap support (≥95%). Analysis uncovers two well‐supported lineages within Schilbe intermedius. The Bayesian phylogenetic analyses of Nigerian S. intermedius with others from GenBank recover four lineages. Evidence of genetic structuring is consistent with geographic regions of sub‐Saharan Africa. Thus, cryptic lineage diversity may illustrate species’ adaptive responses to local environmental conditions. Finally, our study underscores the importance of incorporating morphology and DNA barcoding in species identification. Although developing a complete DNA barcode reference library for Nigerian ichthyofauna will facilitate species identification and diversity studies, taxonomic revisions of DNA sequences submitted in databases alongside voucher specimens are necessary for a reliable taxonomic and diversity inventory.  相似文献   

4.
As the globally dominant group of pollinators, bees provide a key ecosystem service for natural and agricultural landscapes. Their corresponding global decline thus poses an important threat to plant populations and the ecosystems they support. Bee conservation requires rapid and effective tools to identify and delineate species. Here, we apply DNA barcoding to Irish solitary bees as the first step towards a DNA barcode library for European solitary bees. Using the standard barcoding sequence, we were able to identify 51 of 55 species. Potential problems included a suite of species in the genus Andrena, which were recalcitrant to sequencing, mitochondrial heteroplasmy and parasitic flies, which led to the production of erroneous sequences from DNA extracts. DNA barcoding enabled the assignment of morphologically unidentifiable females of the parasitic genus Sphecodes to their nominal taxa. It also enabled correction of the Irish bee list for morphologically inaccurately identified specimens. However, the standard COI barcode was unable to differentiate the recently diverged taxa Sphecodes ferruginatus and S. hyalinatus. Overall, our results show that DNA barcoding provides an excellent identification tool for Irish solitary bees and should be rolled out to provide a database for solitary bees globally.  相似文献   

5.
6.
The interplay between insect and plant traits outlines the patterns of pollen transfer and the subsequent plant reproductive fitness. We studied the factors that affect the pollination efficiency of a pollinator community of Dictamnus albus L. by evaluating insect behaviour and morphological characteristics in relation to flowering phenology. In order to extrapolate the pollinator importance of single taxa and of the whole pollinator guild, we calculated an index distinguishing between potential (PPI) and realized (RPI) pollinator importance. Although the pollinator species spectrum appeared rather constant, we found high intra‐ and inter‐annual variability of pollinator frequency and importance within the insect community. Flower visitation rate strictly depended on insect abundance and on the overlap between their flying period and flower blooming. All the pollinators visited flowers from the bottom to the top of the racemes, excluding intra‐plant geitonogamous pollination, and most of them showed high pollen fidelity. Only medium large‐sized bees could contact the upward bending stiles while feeding on nectar, highlighting a specialisation of the plant towards bigger pollinators. Moreover, we found evidence of functional specialisation, since all pollinators were restricted to a single taxonomic group (order: Hymenoptera; superfamily: Apoidea). Both the PPI and RPI indices indicate Habropoda tarsata as the most important pollinator of D. albus. Following hand cross‐pollination experiments we revealed the presence of pollination limitation in 1 of the 3 years of field study. We discuss this result in relation to flowering abundance and to possible mismatches of phenological periods between plants and insects.  相似文献   

7.
Native vegetation is frequently replaced by alien plants on isolated oceanic islands. The effects of such replacements by invasive plants on the diversity and temporal dynamics of island-endemic insects remain unclear. We examined flying insect communities using Malaise traps on the small island of Nishi-jima in the oceanic Ogasawara Archipelago in the northwestern Pacific. On the island, an alien tree, Casuarina equisetifolia, has become dominant, occupying 57.3?% of the vegetation area. The species richness, composition, and abundance of pollinators (bees), predators (wasps), and wood-boring beetles (cerambycids, mordellids, and elaterids) were compared in each summer season of 4?years among three vegetation types: C. equisetifolia forest, natural forest, and grassland. In the traps, 82.3?% of species captured were endemic to the archipelago. The grassland harbored the highest species richness of native bees and wasps, whereas the natural forest had the highest species richness of native wood-boring beetles. The C. equisetifolia forest had the poorest species richness for most insect groups. Principal response curves indicated that differences in species composition among the three vegetation types were consistent through time for all insect groups. Most insect species were more abundant in natural forest or grassland than in C. equisetifolia forest. Standard deviations in both the numbers of individuals and species estimated under a Bayesian framework suggested that annual fluctuations of abundance and species density were similar among vegetation types (except for elaterid abundance). Therefore, replacement by C. equisetifolia has likely altered insect species composition but has not necessarily dramatically affected the temporal dynamics of insect assemblages on the island.  相似文献   

8.
  1. Bees are prolific, vital pollinators in agricultural and natural settings, but some taxa are declining. Surveying bees is crucial to understand the needs of these taxa; however, we lack a fine-grained understanding of assemblages associated with different sampling methods that would enable us to analyse data range-wide.
  2. Here we examine the difference in abundance and richness of bees (bee bowls and vane traps only) and bumble bees (genus Bombus; bee bowls, blue vane traps and target netting) sampled with these methods from mixed-grass prairie to alpine habitats in Wyoming, USA.
  3. We collected four times more bees and twice as many genera of bees in vane traps than bee bowls. Vane traps captured more individuals of abundant genera than bee bowls.
  4. Bombus species abundance did not vary between vane traps and target netting; however, richness was higher in vane traps. Bee bowls captured few Bombus species.
  5. Overall, we recommend using vane traps to sample most bees, and a combination of vane traps and target netting to collect bumble bees. We evaluated how three sampling techniques perform when surveying for wild bees, which will aid in identifying declining species as well as monitoring species of conservation concern.
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9.
The bees (Hymenoptera: Apiformes) are important pollinators in many ecosystems, but their diversity has declined in Europe during the past century, mainly due to habitat loss. However, some of the habitat requirements of wild bees are met in anthropogenic landscape elements, such as road sides, power-line strips and field edges. Moreover, as the bee species assemblages change throughout the season the habitat requirements of the bee fauna may change accordingly. Understanding such seasonally distinct responses of solitary bees with different phenologies may be of high value for local conservation planning. The purpose of this study was to examine if the habitat quality of field edges for solitary bees change throughout the season, and how this temporal variation relates to local habitat and landscape conditions. By sampling solitary bees in 18 field edges in southeast Norway throughout the season we found that the species richness and abundance of bees was highest in sun exposed field edges, independently of the season. However, we found phenologically distinct responses to the landscape context. Moreover, field edges situated in landscapes with a high proportion of forests and semi-natural landscape elements hosted the most phenologically diverse bee species assemblages. We conclude that in order to fulfil the habitat requirements of bee species assemblages throughout the season, one should conserve and direct habitat restoration schemes towards increasing sun exposure at field edges with a diverse flora and a high proportion of semi-natural areas in the vicinity.  相似文献   

10.
Pan and Malaise traps have been used widely to sample insect abundance and diversity, but no studies have compared their performance for sampling pollinators in forested ecosystems. Malaise trap design and color of pan traps are important parameters that influence insect pollinator catches. We compared pan trap (blue, yellow, white, and red) and Malaise trap catches from forests in three physiographic provinces (Piedmont, Coastal Plain, and Blue Ridge) of the southeastern United States. Similarities in trap performance between sites were observed with blue pan traps being most effective overall. Our results showed that various pollinator groups preferred certain pan trap colors and that adding color to Malaise traps influenced insect pollinator catches. However, pan traps generally caught more pollinators than Malaise traps. Because of their low cost and simplicity, using several colors of pan traps is an effective way to sample relative abundance and species richness of flower-visiting insects.  相似文献   

11.
Natural vegetation is often replaced by invasive alien plants on isolated oceanic islands. To determine how invasive alien plants affect insect diversity, we compared flying insects captured using Malaise traps among different vegetation types on a small island (Nishijima; 0.49 km2) in the oceanic Ogasawara (Bonin) Islands in the north‐western Pacific. The numbers of individuals and species, and the species composition of pollinators (bees), predators (wasps) and wood borers (cerambycid, mordellid and elaterid beetles) were compared among three vegetation types: Casuarina equisetifolia (an invasive alien tree) forest, natural forest and natural grassland (forest edge), during two seasons (June and October–November 2005). In traps, 80.0, 66.7, 87.5, 85.7 and 100.0% of bee, wasp, cerambycid, mordellid and elaterid beetle species, respectively, were endemic to the Ogasawara Islands. Grassland had the highest wasp and bee species richness, whereas natural forest had the highest species richness of wood‐boring beetles. The C. equisetifolia forest had the poorest species richness for most insect groups (except mordellid beetles). More individuals of most insect groups (except bees) were captured in June than in October–November. More individual bees and wasps were captured in grassland than in forests, whereas more individual mordellid and elaterid beetles were captured in forests than in grassland. The number of cerambycid individuals did not differ among vegetation types. Redundancy analysis suggested that most insect species preferred natural forest or grassland to alien forest. Therefore, further invasion of natural grassland and forest by the alien tree C. equisetifolia may negatively affect the endemic insect fauna of Nishijima.  相似文献   

12.
Introduced plants may be important foraging resources for honey bees and wild pollinators, but how often and why pollinators visit introduced plants across an entire plant community is not well understood. Understanding the importance of introduced plants for pollinators could help guide management of these plants and conservation of pollinator habitat. We assessed how floral abundance and pollinator preference influence pollinator visitation rate and diversity on 30 introduced versus 24 native plants in central New York. Honey bees visited introduced and native plants at similar rates regardless of floral abundance. In contrast, as floral abundance increased, wild pollinator visitation rate decreased more strongly for introduced plants than native plants. Introduced plants as a group and native plants as a group did not differ in bee diversity or preference, but honey bees and wild pollinators preferred different plant species. As a case study, we then focused on knapweed (Centaurea spp.), an introduced plant that was the most preferred plant by honey bees, and that beekeepers value as a late‐summer foraging resource. We compared the extent to which honey bees versus wild pollinators visited knapweed relative to coflowering plants, and we quantified knapweed pollen and nectar collection by honey bees across 22 New York apiaries. Honey bees visited knapweed more frequently than coflowering plants and at a similar rate as all wild pollinators combined. All apiaries contained knapweed pollen in nectar, 86% of apiaries contained knapweed pollen in bee bread, and knapweed was sometimes a main pollen or nectar source for honey bees in late summer. Our results suggest that because of diverging responses to floral abundance and preferences for different plants, honey bees and wild pollinators differ in their use of introduced plants. Depending on the plant and its abundance, removing an introduced plant may impact honey bees more than wild pollinators.  相似文献   

13.
Accurate identification of aquatic species is fundamental to freshwater research. In this paper, we targeted Ephemeroptera, a key taxonomic insect group for biomonitoring of water bodies and present an overview on the efficacy of the DNA barcoding approach to document species identity in the Mediterranean region. We sequenced the mitochondrial cytochrome c oxidase (COI) in 39 nominal species. Sample discrimination and species identification were investigated by evaluating haplotype identity and similarity, intra-/interspecific genetic distances, optimal identification of barcoding gap thresholds, estimates of species monophyly and comparative species matches on available reference libraries. The resolving power of the obtained data was discussed in the light of statistical tools such as Spider R-package and Poisson Tree Processes. High levels of species identification were achieved with all the used methodologies, and the occurrence of cryptic species was suggested. We conclude that DNA barcoding is a powerful tool for taxonomic research in Mediterranean mayflies, with great promise to ameliorate biodiversity inventories of freshwater ecosystems and to provide the necessary accuracy for water quality assessment programs. Our results further indicated we need to upgrade the current regional mayfly diversity knowledge. The development of a Mediterranean reference library could integrate this new information system.  相似文献   

14.
Wildflower strips (WFS) are amongst the most commonly applied measures to promote pollinators and natural enemies of crop pests in agroecosystems. Their potential to enhance these functionally important insect groups may vary substantially with time since establishment of WFS. However, knowledge on their temporal dynamics remains scarce, hampering recommendations for optimized design and management. We therefore examined temporal dynamics of taxonomic and functional groups of bees and hoverflies in perennial WFS ranging from one to ≥6 years since sowing with a standardized species-rich seed mixture of flowering plants in 18 agricultural landscapes in Switzerland. The abundance of wild bees, honeybees and hoverflies declined after the second year by 89%, 62% and 72%, respectively. Declines in bee abundance and hoverfly species richness were linear and those of aphidophagous hoverflies exponential, while wild bee species richness peaked in the third year. Declines over time generally paralleled decreases in flower abundance (-83%) and flowering species richness (-61%) and an increase in grass cover (+70%) in WFS. Flowering plant species richness showed strong positive relationships with dominant crop-visiting wild bees and aphidophagous hoverflies. Furthermore, dominant crop-visiting wild bees, but not aphidophagous hoverflies, were positively related to the proportion of (semi-)open semi-natural habitat in the surrounding landscape (500 m radius), but negatively with forest. We conclude that the effectiveness of perennial WFS to promote pollinator diversity, crop-pollinating bees and aphidophagous hoverflies through foraging resources decreases after the first two to three years, probably due to a decline of diverse and abundant floral resources. Although older perennial WFS may still provide valuable nesting and overwintering opportunities for pollinators and natural enemies, our findings indicate that regular re-sowing of perennial WFS may be necessary to maintain adequate floral resource provisioning for effective pollinator conservation and promotion of crop pollination and natural pest control services in agricultural landscapes.  相似文献   

15.
Automated species identification based on data produced with metabarcoding offers an alternative for assessing biodiversity of bulk insect samples obtained with traps. We used a standard two‐step PCR approach to amplify a 313 bp fragment of the barcoding region of the mitochondrial COI gene. The PCR products were sequenced on an Illumina MiSeq platform, and the OTUs production and taxonomic identifications were performed with a customized pipeline and database. The DNA used in the PCR procedures was extracted directly from the preservative ethanol of bulk insect samples obtained with automatic light traps in 12 sampling areas located in different biomes of Brazil, during wet and dry seasons. Agricultural field and forest edge habitats were collected for all sampling areas. A total of 119 insect OTUs and nine additional OTUs assigned to other arthropod taxa were obtained at a ≥97% sequence similarity level. The alpha and beta diversity analyses comparing biomes, habitats, and seasons were mostly inconclusive, except for a significant difference in beta diversity between biomes. In this study, we were able to metabarcode and HTS adult insects from their preservative medium. Notwithstanding, our results underrepresent the true magnitude of insect diversity expected from samples obtained with automatic light traps in Brazil. Although biological and technical factors might have impacted our results, measures to optimize and standardize eDNA HTS should be in place to improve taxonomic coverage of samples of unknown diversity and stored in suboptimal conditions, which is the case of most eDNA samples.  相似文献   

16.
DNA barcoding has become a promising means for identifying organisms of all life stages. Currently, phenetic approaches and tree-building methods have been used to define species boundaries and discover 'cryptic species'. However, a universal threshold of genetic distance values to distinguish taxonomic groups cannot be determined. As an alternative, DNA barcoding approaches can be 'character based', whereby species are identified through the presence or absence of discrete nucleotide substitutions (character states) within a DNA sequence. We demonstrate the potential of character-based DNA barcodes by analysing 833 odonate specimens from 103 localities belonging to 64 species. A total of 54 species and 22 genera could be discriminated reliably through unique combinations of character states within only one mitochondrial gene region (NADH dehydrogenase 1). Character-based DNA barcodes were further successfully established at a population level discriminating seven population-specific entities out of a total of 19 populations belonging to three species. Thus, for the first time, DNA barcodes have been found to identify entities below the species level that may constitute separate conservation units or even species units. Our findings suggest that character-based DNA barcoding can be a rapid and reliable means for (i) the assignment of unknown specimens to a taxonomic group, (ii) the exploration of diagnosability of conservation units, and (iii) complementing taxonomic identification systems.  相似文献   

17.
One common goal of habitat restoration and reconstruction is to reinstate the biodiversity found at intact reference sites. However, few researchers have examined whether these practices reinstate communities of flower‐visiting insects. This is unfortunate, as anthropogenically mediated declines in flower visitors, including bees (the primary pollinators for most terrestrial ecosystems), beetles, flies, and butterflies, have been reported worldwide. Biodiversity declines may be especially severe in North America's tallgrass prairie, a once‐vast grassland that has experienced severe destruction and degradation due to agricultural conversion. As such, we assessed the structure of forb and flower‐visiting insect communities as a whole and two subsets of the flower visitor community—bees and phytophagous beetles—across five tallgrass prairie remnants and five reconstructed prairies (former crop fields) in Kansas from 2013 to 2015. Remnant prairies had significantly higher forb diversity and differed significantly in forb composition, compared to reconstructed prairies. Despite the dissimilarities in forb community structure, there were no differences in flower visitor diversity or abundance between remnants and reconstructed prairies. However, when considered separately, bee communities exhibited significantly greater variability in composition on reconstructed prairies, likely due to the abundance of generalist bee species visiting non‐native legumes at two reconstructed prairies. Our work provides evidence that prairie habitat reconstruction is a valuable tool for reestablishing flower‐visiting insect communities and also emphasizes the considerable role that non‐native species may play in structuring grassland plant–bee interactions.  相似文献   

18.
Intensification of inland fisheries and aquatic landscape conversion led to a drastic decline of fish populations in the Yangtze River (YR) during the last decades. This situation urges for the development of a large‐scale molecular assessment of YR ichthyofauna to further develop standardized methods of molecular identification for conservation and fisheries management purposes. We present here the results of a large‐scale campaign to DNA barcode YR freshwater fishes that succeeded in producing 1,424 new DNA barcodes for 123 species. Together with 1,406 sequences mined from BOLD and GenBank, a reference library including 2,830 DNA barcodes for 238 species was compiled. By using four DNA‐based species delimitation methods, RESL, ABGD, mPTP and mGMYC, 230 operational taxonomic units (OTUs) were identified and 195 species displayed OTUs that tightly match species boundaries. No barcoding gap was observed; however, and conflicting cases of species and OTU delimitation were identified. A total of 23 species with maximum intraspecific distances above 2% were detected and null genetic distances to the nearest phylogenetic relatives were detected in 11 species. Among those 23 species, 16 were represented by multiple OTUs amounting to 40 OTUs delineated. Several cases of multiple OTUs confined to species boundaries were detected suggesting the presence of overlooked species. A total of 18 OTUs, however, were shared by several species and particularly so for the Qinghai‐Tibet plateau endemic species. These results are discussed with reference to previous large‐scale DNA barcoding campaign and compared to previous phylogeographic studies in the YR.  相似文献   

19.
20.
We present the findings of a DNA barcoding study of the UK tree flora, implemented as part of an innovative, research‐based science education programme called ‘Tree School’. The UK tree flora comprises native and introduced species, and is a taxonomically diverse study group for the exploration of the potential and limitations of DNA barcoding. The children participating in the project collected voucher specimens and generated DNA barcode sequences from trees and shrubs found in the grounds and surrounding woodlands of a residential field centre in Dorset, UK. We assessed the potential of rbcL and matK markers for amplification and DNA sequencing success and for species discrimination among the 67 tree and shrub species included in this study. Although we achieved 100% PCR amplification and sequencing success for rbcL and matK, mononucleotide repeats affected sequence quality in matK for some taxonomic groups (e.g. Rosaceae). Species discrimination success ranged from 65% to 71% using tree‐based methods to 86% using BLASTN. The occurrence of known hybrids (diploid and polyploid) and their progenitors on the study site reduced the overall species discrimination success for both loci. This study demonstrates that, even in a floristic context, rbcL and matK alone are insufficient for the discrimination of UK tree species, especially where taxonomically complex groups are present. From a science education perspective, DNA barcoding represents a compelling and accessible platform for the engagement of non‐experts in ongoing research, providing an opportunity for them to contribute authentic scientific data to an international research campaign.  相似文献   

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