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1.
Zookeys ; 1188: 305-386, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38250474

RESUMO

Substantial parts of the European and German insect fauna still remain largely unexplored, the so-called "dark taxa". In particular, midges (Diptera) and parasitoid wasps (Hymenoptera) are abundant and species-rich throughout Europe, yet are often neglected in biodiversity research. One such dark taxon is Microgastrinae wasps (Hymenoptera: Braconidae), a group of parasitoids of lepidopteran caterpillars with 252 species reported in Germany so far. As part of the German Barcode of Life Project GBOL III: Dark Taxa, reverse DNA barcoding and integrative taxonomic approaches were used to shed some light on the German Fauna of Microgastrinae wasps. In our workflow, DNA barcoding was used for molecular clustering of our specimens in a first step, morphological examination of the voucher specimens in a second step, and host data compared in a third step. Here, 30 species are reported for the first time in Germany, adding more than 10% to the known German fauna. Information for four species is provided in a new Holarctic context, reporting them for the Nearctic or, respectively, Palaearctic region, and 26 additional country records are added from sequenced material available in the collections accessible to us. Molecular clusters that show signs of discrepancies are discussed. Results show that we are just scratching the tip of the iceberg of the unexplored Microgastrinae diversity in Germany.

2.
Front Zool ; 10(1): 37, 2013 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-23809165

RESUMO

BACKGROUND: Gastropods are among the most diverse animal clades, and have successfully colonized special habitats such as the marine sand interstitial. Specialized meiofaunal snails and slugs are tiny and worm-shaped. They combine regressive features - argued to be due to progenetic tendencies - with convergent adaptations. Microscopic size and concerted convergences make morphological examination non-trivial and hamper phylogenetic reconstructions. The enigmatic turbellarian-like Rhodopemorpha are a small group that has puzzled systematists for over a century. A preliminary molecular framework places the group far closer to the root of Heterobranchia - one of the major gastropod groups - than previously suggested. The poorly known meiofaunal Helminthope psammobionta Salvini-Plawen, 1991 from Bermuda is the most worm-shaped free-living gastropod and shows apparently aberrant aspects of anatomy. Its study may give important clues to understand the evolution of rhodopemorphs among basal heterobranchs versus their previously thought origin among 'higher' euthyneuran taxa. RESULTS: We describe the 3D-microanatomy of H. psammobionta using three-dimensional digital reconstruction based on serial semithin histological sections. The new dataset expands upon the original description and corrects several aspects. Helminthope shows a set of typical adaptations and regressive characters present in other mesopsammic slugs (called 'meiofaunal syndrome' herein). The taxonomically important presence of five separate visceral loop ganglia is confirmed, but considerable further detail of the complex nervous system are corrected and revealed. The digestive and reproductive systems are simple and modified to the thread-like morphology of the animal; the anus is far posterior. There is no heart; the kidney resembles a protonephridium. Data on all organ systems are compiled and compared to Rhodope. CONCLUSIONS: Helminthope is related to Rhodope sharing unique apomorphies. We argue that the peculiar kidney, configuration of the visceral loop and simplicity or lack of other organs in Rhodopemorpha are results of progenesis. The posterior shift of the anus in Helminthope is interpreted as a peramorphy, i.e. hypertrophy of body length early in ontogeny. Our review of morphological and molecular evidence is consistent with an origin of Rhodopemorpha slugs among shelled 'lower Heterobranchia'. Previously thought shared 'diagnostic' features such as five visceral ganglia are either plesiomorphic or convergent, while euthyneury and a double-rooted cerebral nerve likely evolved independently in Rhodopemorpha and Euthyneura.

3.
Front Zool ; 9(1): 23, 2012 Sep 14.
Artigo em Inglês | MEDLINE | ID: mdl-22973977

RESUMO

BACKGROUND: Two types of excretory systems, protonephridia and metanephridial systems are common among bilaterians. The homology of protonephridia of lophotrochozoan taxa has been widely accepted. In contrast, the homology of metanephridial systems - including coelomic cavities as functional units - among taxa as well as the homology between the two excretory systems is a matter of ongoing discussion. This particularly concerns the molluscan kidneys, which are mostly regarded as being derived convergently to the metanephridia of e.g. annelids because of different ontogenetic origin. A reinvestigation of nephrogenesis in polyplacophorans, which carry many primitive traits within molluscs, could shed light on these questions. RESULTS: The metanephridial system of Lepidochitona corrugata develops rapidly in the early juvenile phase. It is formed from a coelomic anlage that soon achieves endothelial organization. The pericardium and heart are formed from the central portion of the anlage. The nephridial components are formed by outgrowth from lateral differentiations of the anlage. Simultaneously with formation of the heart, podocytes appear in the atrial wall of the pericardium. In addition, renopericardial ducts, kidneys and efferent nephroducts, all showing downstream ciliation towards the internal lumen, become differentiated (specimen length: 0.62 mm). Further development consists of elongation of the kidney and reinforcement of filtration and reabsorptive structures. CONCLUSIONS: During development and in fully formed condition the metanephridial system of Lepidochitona corrugata shares many detailed traits (cellular and overall organization) with the protonephridia of the same species. Accordingly, we suggest a serial homology of various cell types and between the two excretory systems and the organs as a whole. The formation of the metanephridial system varies significantly within Mollusca, thus the mode of formation cannot be used as a homology criterion. Because of similarities in overall organization, we conclude that the molluscan metanephridial system is homologous with that of the annelids not only at the cellular but also at the organ level.

4.
Zookeys ; 1092: 147-194, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35586297

RESUMO

This contribution is an update to the 2014 compilation of all supra- and (infra-) specific taxa of extant and fossil Valvatidae, a group of freshwater operculate snails near the base of Heterobranchia with a nearly worldwide distribution. This update includes corrections and many additions (two replacement taxon names, 21 mainly fossil taxa previously overlooked, and 37 invalid names) to the 2014 contribution and adds all newly described species (11) during the past eight years. The extensive reference list is directly linked, where possible, to the available electronic source of the cited papers.

5.
Zootaxa ; 5209(3): 379-393, 2022 Nov 17.
Artigo em Inglês | MEDLINE | ID: mdl-37045384

RESUMO

A new species of crown-of-thorns sea star (CoTS), Acanthaster benziei sp. nov., is described based on four specimens collected from Saudi Arabia's Red Sea coast where it inhabits coral reefs. Species delimitation from congeners in the species complex, i.e., Acanthaster planci, Acanthaster mauritiensis and Acanthaster cf. solaris, is primarily based on distinct and diagnostic mitochondrial DNA sequence regions. Species separation of Acanthaster benziei is additionally justified due to diagnostic morphological characters: fewer arms; narrower and thinner spines; fanned spine tips in primary and latero-oral spines; a wider tip or tapering shape in circumoral spines; and rhombus-shaped oral pedicellariae.


Assuntos
Recifes de Corais , Estrelas-do-Mar , Animais , Oceano Índico
6.
Insects ; 13(1)2022 Jan 12.
Artigo em Inglês | MEDLINE | ID: mdl-35055925

RESUMO

Determining the size of the German insect fauna requires better knowledge of several megadiverse families of Diptera and Hymenoptera that are taxonomically challenging. This study takes the first step in assessing these "dark taxa" families and provides species estimates for four challenging groups of Diptera (Cecidomyiidae, Chironomidae, Phoridae, and Sciaridae). These estimates are based on more than 48,000 DNA barcodes (COI) from Diptera collected by Malaise traps that were deployed in southern Germany. We assessed the fraction of German species belonging to 11 fly families with well-studied taxonomy in these samples. The resultant ratios were then used to estimate the species richness of the four "dark taxa" families (DT families hereafter). Our results suggest a surprisingly high proportion of undetected biodiversity in a supposedly well-investigated country: at least 1800-2200 species await discovery in Germany in these four families. As this estimate is based on collections from one region of Germany, the species count will likely increase with expanded geographic sampling.

7.
Front Zool ; 8(1): 25, 2011 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-22029904

RESUMO

BACKGROUND: Taxonomy or biological systematics is the basic scientific discipline of biology, postulating hypotheses of identity and relationships, on which all other natural sciences dealing with organisms relies. However, the scientific contributions of taxonomists have been largely neglected when using species names in scientific publications by not citing the authority on which they are based. DISCUSSION: Consequences of this neglect is reduced recognition of the importance of taxonomy, which in turn results in diminished funding, lower interest from journals in publishing taxonomic research, and a reduced number of young scientists entering the field. This has lead to the so-called taxonomic impediment at a time when biodiversity studies are of critical importance.Here we emphasize a practical and obvious solution to this dilemma. We propose that whenever a species name is used, the author(s) of the species hypothesis be included and the original literature source cited, including taxonomic revisions and identification literature - nothing more than what is done for every other hypothesis or assumption included in a scientific publication. In addition, we postulate that journals primarily publishing taxonomic studies should be indexed in ISISM. SUMMARY: The proposal outlined above would make visible the true contribution of taxonomists within the scientific community, and would provide a more accurate assessment for funding agencies impact and importance of taxonomy, and help in the recruitment of young scientists into the field, thus helping to alleviate the taxonomic impediment. In addition, it would also make much of the biological literature more robust by reducing or alleviating taxonomic uncertainty.

9.
PLoS One ; 15(1): e0224188, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31999713

RESUMO

The present study aimed to perform molecular identification of lepidopteran larvae from canopy fogging including gut-content analyses. A total of 130 lepidopteran larvae were selected from 37 fogging samples at the Panguana station, district Yuyapichis, province Puerto Inca, department Huánuco, Peru. Target trees were pre-identified and subsequently submitted to molecular confirmation of identity with three markers (rbcL, psbA and trnL-F). The COI gene of 119 lepidopteran larvae was successfully sequenced and found to belong to 92 species: Comparison of DNA barcodes with the reference database of adult moths resulted in 65 (55%) matches at species level, 32 (27%) at genus level, 19 (16%) at subfamily or family level, three just to order level. Three larvae could not be assigned to a family. For these larvae the fogged target tree now suggests a potential host-plant relationship. Molecular gut content analysis, based on High-Throughput-Sequencing was successfully tested for ten larvae corroborating feeding on the target plant in some cases but elucidating several other cases of potential 'alternative feeding'. We propose a larger-scale approach using this rapid and efficient method including molecular gut-content analyses for comprehensively testing the ratio of 'alternative feeders' and pitfalls caused by collateral fogging of larvae from neighboring trees.


Assuntos
Código de Barras de DNA Taxonômico/métodos , Mariposas/genética , Filogenia , Animais , DNA/genética , Sequenciamento de Nucleotídeos em Larga Escala , Insetos/classificação , Insetos/genética , Larva/genética , Mariposas/classificação , Peru , Plantas/classificação , Plantas/genética , Especificidade da Espécie , Clima Tropical
10.
Mol Ecol Resour ; 20(6): 1542-1557, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32559020

RESUMO

DNA metabarcoding was utilized for a large-scale, multiyear assessment of biodiversity in Malaise trap collections from the Bavarian Forest National Park (Germany, Bavaria). Principal component analysis of read count-based biodiversities revealed clustering in concordance with whether collection sites were located inside or outside of the National Park. Jaccard distance matrices of the presences of barcode index numbers (BINs) at collection sites in the two survey years (2016 and 2018) were significantly correlated. Overall similar patterns in the presence of total arthropod BINs, as well as BINs belonging to four major arthropod orders across the study area, were observed in both survey years, and are also comparable with results of a previous study based on DNA barcoding of Sanger-sequenced specimens. A custom reference sequence library was assembled from publicly available data to screen for pest or invasive arthropods among the specimens or from the preservative ethanol. A single 98.6% match to the invasive bark beetle Ips duplicatus was detected in an ethanol sample. This species has not previously been detected in the National Park.


Assuntos
Artrópodes , Biodiversidade , Código de Barras de DNA Taxonômico , Animais , Artrópodes/classificação , Alemanha , Parques Recreativos
11.
J Forensic Sci ; 64(2): 593-601, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-29995972

RESUMO

Throughout the years, DNA barcoding has gained in importance in forensic entomology as it leads to fast and reliable species determination. High-quality results, however, can only be achieved with a comprehensive DNA barcode reference database at hand. In collaboration with the Bavarian State Criminal Police Office, we have initiated at the Bavarian State Collection of Zoology the establishment of a reference library containing arthropods of potential forensic relevance to be used for DNA barcoding applications. CO1-5P' DNA barcode sequences of hundreds of arthropods were obtained via DNA extraction, PCR and Sanger Sequencing, leading to the establishment of a database containing 502 high-quality sequences which provide coverage for 88 arthropod species. Furthermore, we demonstrate an application example of this library using it as a backbone to a high throughput sequencing analysis of arthropod bulk samples collected from human corpses, which enabled the identification of 31 different arthropod Barcode Index Numbers.


Assuntos
Artrópodes/genética , Código de Barras de DNA Taxonômico , Bases de Dados de Ácidos Nucleicos , Ciências Forenses , Animais , Complexo IV da Cadeia de Transporte de Elétrons/genética , Entomologia , Sequenciamento de Nucleotídeos em Larga Escala , Reação em Cadeia da Polimerase , Análise de Sequência de DNA
12.
Mol Ecol Resour ; 19(4): 900-928, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-30977972

RESUMO

This study summarizes results of a DNA barcoding campaign on German Diptera, involving analysis of 45,040 specimens. The resultant DNA barcode library includes records for 2,453 named species comprising a total of 5,200 barcode index numbers (BINs), including 2,700 COI haplotype clusters without species-level assignment, so called "dark taxa." Overall, 88 out of 117 families (75%) recorded from Germany were covered, representing more than 50% of the 9,544 known species of German Diptera. Until now, most of these families, especially the most diverse, have been taxonomically inaccessible. By contrast, within a few years this study provided an intermediate taxonomic system for half of the German Dipteran fauna, which will provide a useful foundation for subsequent detailed, integrative taxonomic studies. Using DNA extracts derived from bulk collections made by Malaise traps, we further demonstrate that species delineation using BINs and operational taxonomic units (OTUs) constitutes an effective method for biodiversity studies using DNA metabarcoding. As the reference libraries continue to grow, and gaps in the species catalogue are filled, BIN lists assembled by metabarcoding will provide greater taxonomic resolution. The present study has three main goals: (a) to provide a DNA barcode library for 5,200 BINs of Diptera; (b) to demonstrate, based on the example of bulk extractions from a Malaise trap experiment, that DNA barcode clusters, labelled with globally unique identifiers (such as OTUs and/or BINs), provide a pragmatic, accurate solution to the "taxonomic impediment"; and (c) to demonstrate that interim names based on BINs and OTUs obtained through metabarcoding provide an effective method for studies on species-rich groups that are usually neglected in biodiversity research projects because of their unresolved taxonomy.


Assuntos
Ceratopogonidae/classificação , Ceratopogonidae/genética , Chironomidae/classificação , Chironomidae/genética , Código de Barras de DNA Taxonômico , Dípteros/classificação , Dípteros/genética , Animais , Monitorização de Parâmetros Ecológicos/métodos , Alemanha
13.
J Morphol ; 269(6): 762-74, 2008 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-18431810

RESUMO

The strongly modified mode of development of the small and brooding galeommatoid bivalve Lasaea adansonii (Gmelin, 1791) [syn. Lasaea rubra (Montagu, 1803)] has been studied by means of transmission and scanning electron microscopy and by fluorescent staining of the muscular system and of two neurotracers, FMRFamide and serotonin. In addition, two developmental stages were visualized using computer-aided 3D-reconstruction. All larval stages of L. adansonii lack ciliary rings. The apical organ appears invaginated: the base of the duct contacts the cerebral ganglia and opens on the preoral region. Larval protonephridia are lacking. The adult kidneys develop independently of the pericardial cavity and contain a protonephridial part that enables excretory function until the pericardium is formed. The larval muscular system is composed of smooth muscle fibers; striated fibers are lacking. Posteriorly and immediately below the ligament, a paired cell of unknown function is present that contains serotonin and FMRFamide. In summary, L. adansonii exhibits the direct mode of development. Only few truly larval structures (e.g., the modified apical organ) are elaborated.


Assuntos
Bivalves , Animais , Bivalves/anatomia & histologia , Bivalves/embriologia , Larva/ultraestrutura
14.
Biol Bull ; 213(2): 122-34, 2007 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-17928519

RESUMO

The organization of the central nervous system of an "aplacophoran" mollusc, Chaetoderma japonicum, is described as a means to understand a primitive condition in highly diversified molluscan animals. This histological and immunocytochemical study revealed that C. japonicum still retains a conservative molluscan tetra-neural plan similar to those of neomenioids, polyplacophorans, and tryblidiids. However, the ventral and lateral nerve cords of C. japonicum are obviously ganglionated to various degrees, and the cerebral cord-like ganglia display a lobular structure. The putative chemosensory networks are developed, being composed of sensory cells of the oral shield, eight precerebral ganglia, and eight neuropil compartments that form distinct masses of neurites. In the cerebral cord-like ganglia, three anterior, posterior, and dorsal lobes are distinguished with well-fasciculated tracts in their neuropils. Most neuronal somata are uniform in size, and no small globuli-like cell clusters are found; however, localized serotonin-like immunoreactivity and acetylated tubulin-containing tracts suggest the presence of functional subdivisions. These complicated morphological features may be adaptive structures related to the specialized foraminiferan food in muddy bottoms. Based on a comparative scheme in basal molluscan groups, we characterize an independent evolutionary process for the unique characters of the central nervous systems of chaetoderms.


Assuntos
Evolução Biológica , Gânglios dos Invertebrados/anatomia & histologia , Moluscos/anatomia & histologia , Animais , Biomarcadores/análise , Sistema Nervoso Central/anatomia & histologia , Feminino , Imuno-Histoquímica
15.
Mol Ecol Resour ; 17(6): 1293-1307, 2017 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-28449274

RESUMO

Mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) are prominent representatives of aquatic macroinvertebrates, commonly used as indicator organisms for water quality and ecosystem assessments. However, unambiguous morphological identification of EPT species, especially their immature life stages, is a challenging, yet fundamental task. A comprehensive DNA barcode library based upon taxonomically well-curated specimens is needed to overcome the problematic identification. Once available, this library will support the implementation of fast, cost-efficient and reliable DNA-based identifications and assessments of ecological status. This study represents a major step towards a DNA barcode reference library as it covers for two-thirds of Germany's EPT species including 2,613 individuals belonging to 363 identified species. As such, it provides coverage for 38 of 44 families (86%) and practically all major bioindicator species. DNA barcode compliant sequences (≥500 bp) were recovered from 98.74% of the analysed specimens. Whereas most species (325, i.e., 89.53%) were unambiguously assigned to a single Barcode Index Number (BIN) by its COI sequence, 38 species (18 Ephemeroptera, nine Plecoptera and 11 Trichoptera) were assigned to a total of 89 BINs. Most of these additional BINs formed nearest neighbour clusters, reflecting the discrimination of geographical subclades of a currently recognized species. BIN sharing was uncommon, involving only two species pairs of Ephemeroptera. Interestingly, both maximum pairwise and nearest neighbour distances were substantially higher for Ephemeroptera compared to Plecoptera and Trichoptera, possibly indicating older speciation events, stronger positive selection or faster rate of molecular evolution.


Assuntos
Código de Barras de DNA Taxonômico/métodos , Bases de Dados Genéticas , Ephemeroptera/classificação , Ephemeroptera/genética , Holometábolos/classificação , Holometábolos/genética , Animais , Alemanha
16.
J Morphol ; 267(2): 231-47, 2006 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-16292773

RESUMO

Phylogenetic analysis of the highly enigmatic and aberrant acochlidian opisthobranch gastropods is mainly hindered by the lack of reliable anatomical data. Due to their small size, marine interstitial acochlidian species are not suitable for anatomical investigations by dissecting. The tinyness and complexity of, e.g., opisthobranch central nervous and reproductive systems make data derived from older paraffin-based histology and interpretation by hand-based graphical reconstruction questionable. In a former study, a hermaphroditic member of the basal acochlidian genus Hedylopsis ("Hedylopsacea") has been examined in detail. The present study uses the gonochoric Microhedyle remanei (Microhedylidae) as a model organism of the other traditional major acochlidian subgroup, the "Microhedylacea." More than 20 specimens with up to 2 mm body length were extracted from coarse subtidal sand near Castle Roads, Bermuda Islands. Their central nervous, digestive, circulatory, excretory, and genital systems were reconstructed three-dimensionally from serial semithin histological sections using AMIRA software. The radula was analyzed by SEM. Our specimens closely resemble the original description of M. remanei (Marcus, 1953; as Unela) from Brazil; apparent differences regarding the number of visceral loop ganglia or details of male genitalia are assumed to be due to oversights by the former author or because of different ontogenetic stages. Microhedyle remanei differs from all congeners due to the lack (vs. presence) of eyes; further distinguishing features are discussed. In contrast to members of the hedylopsacean Hedylopsidae, Acochlidiidae, and Tantulidae, M. remanei shows a nervous system with numerous precerebral accessory "ganglia" that are not differentiated into cortex and medulla. While all Microhedylidae previously were thought to lack a heart, M. remanei shows a two-chambered heart, as is usual for opisthobranchs. The oocytes of M. remanei are yolky and large in relation to body size and suggest intracapsular larval development. A comparative microanatomical discussion and the distribution of characters within acochlidian taxa indicate that the current classification of the Acochlidia does not reflect phylogenetic relationships. Detailed structural investigations on further poorly known species are required; the computer-based 3D reconstruction of semithin serial sections with AMIRA is shown to be an ideal tool for efficient analysis and presentation of the microanatomy of small specimens.


Assuntos
Gastrópodes/anatomia & histologia , Imageamento Tridimensional , Animais , Bermudas , Sistema Digestório/anatomia & histologia , Genitália/anatomia & histologia , Modelos Anatômicos , Sistema Nervoso/anatomia & histologia
17.
Biodivers Data J ; (4): e10671, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27932930

RESUMO

BACKGROUND: Biodiversity patterns are inherently complex and difficult to comprehensively assess. Yet, deciphering shifts in species composition through time and space are crucial for efficient and successful management of ecosystem services, as well as for predicting change. To better understand species diversity patterns, Germany participated in the Global Malaise Trap Program, a world-wide collection program for arthropods using this sampling method followed by their DNA barcode analysis. Traps were deployed at two localities: "Nationalpark Bayerischer Wald" in Bavaria, the largest terrestrial Natura 2000 area in Germany, and the nature conservation area Landskrone, an EU habitats directive site in the Rhine Valley. Arthropods were collected from May to September to track shifts in the taxonomic composition and temporal succession at these locations. NEW INFORMATION: In total, 37,274 specimens were sorted and DNA barcoded, resulting in 5,301 different genetic clusters (BINs, Barcode Index Numbers, proxy for species) with just 7.6% of their BINs shared. Accumulation curves for the BIN count versus the number of specimens analyzed suggest that about 63% of the potential diversity at these sites was recovered with this single season of sampling. Diversity at both sites rose from May (496 & 565 BINs) to July (1,236 & 1,522 BINs) before decreasing in September (572 & 504 BINs). Unambiguous species names were assigned to 35% of the BINs (1,868) which represented 12,640 specimens. Another 7% of the BINs (386) with 1,988 specimens were assigned to genus, while 26% (1,390) with 12,092 specimens were only placed to a family. These results illustrate how a comprehensive DNA barcode reference library can identify unknown specimens, but also reveal how this potential is constrained by gaps in the quantity and quality of records in BOLD, especially for Hymenoptera and Diptera. As voucher specimens are available for morphological study, we invite taxonomic experts to assist in the identification of unnamed BINs.

18.
PLoS One ; 11(5): e0155497, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27191722

RESUMO

The German Barcoding initiatives BFB and GBOL have generated a reference library of more than 16,000 metazoan species, which is now ready for applications concerning next generation molecular biodiversity assessments. To streamline the barcoding process, we have developed a meta-barcoding pipeline: We pre-sorted a single malaise trap sample (obtained during one week in August 2014, southern Germany) into 12 arthropod orders and extracted DNA from pooled individuals of each order separately, in order to facilitate DNA extraction and avoid time consuming single specimen selection. Aliquots of each ordinal-level DNA extract were combined to roughly simulate a DNA extract from a non-sorted malaise sample. Each DNA extract was amplified using four primer sets targeting the CO1-5' fragment. The resulting PCR products (150-400bp) were sequenced separately on an Illumina Mi-SEQ platform, resulting in 1.5 million sequences and 5,500 clusters (coverage ≥10; CD-HIT-EST, 98%). Using a total of 120,000 DNA barcodes of identified, Central European Hymenoptera, Coleoptera, Diptera, and Lepidoptera downloaded from BOLD we established a reference sequence database for a local CUSTOM BLAST. This allowed us to identify 529 Barcode Index Numbers (BINs) from our sequence clusters derived from pooled Malaise trap samples. We introduce a scoring matrix based on the sequence match percentages of each amplicon in order to gain plausibility for each detected BIN, leading to 390 high score BINs in the sorted samples; whereas 268 of these high score BINs (69%) could be identified in the combined sample. The results indicate that a time consuming presorting process will yield approximately 30% more high score BINs compared to the non-sorted sample in our case. These promising results indicate that a fast, efficient and reliable analysis of next generation data from malaise trap samples can be achieved using this pipeline.


Assuntos
Código de Barras de DNA Taxonômico , Sequenciamento de Nucleotídeos em Larga Escala , Insetos/classificação , Insetos/genética , Animais , Artrópodes/classificação , Artrópodes/genética , Biodiversidade , Análise por Conglomerados , Citocromos c/genética , Código de Barras de DNA Taxonômico/métodos , Bases de Dados de Ácidos Nucleicos , Alemanha , Fluxo de Trabalho
19.
Mol Ecol Resour ; 15(4): 795-818, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25469559

RESUMO

Beetles are the most diverse group of animals and are crucial for ecosystem functioning. In many countries, they are well established for environmental impact assessment, but even in the well-studied Central European fauna, species identification can be very difficult. A comprehensive and taxonomically well-curated DNA barcode library could remedy this deficit and could also link hundreds of years of traditional knowledge with next generation sequencing technology. However, such a beetle library is missing to date. This study provides the globally largest DNA barcode reference library for Coleoptera for 15 948 individuals belonging to 3514 well-identified species (53% of the German fauna) with representatives from 97 of 103 families (94%). This study is the first comprehensive regional test of the efficiency of DNA barcoding for beetles with a focus on Germany. Sequences ≥500 bp were recovered from 63% of the specimens analysed (15 948 of 25 294) with short sequences from another 997 specimens. Whereas most specimens (92.2%) could be unambiguously assigned to a single known species by sequence diversity at CO1, 1089 specimens (6.8%) were assigned to more than one Barcode Index Number (BIN), creating 395 BINs which need further study to ascertain if they represent cryptic species, mitochondrial introgression, or simply regional variation in widespread species. We found 409 specimens (2.6%) that shared a BIN assignment with another species, most involving a pair of closely allied species as 43 BINs were involved. Most of these taxa were separated by barcodes although sequence divergences were low. Only 155 specimens (0.97%) show identical or overlapping clusters.


Assuntos
Besouros/classificação , Besouros/genética , Código de Barras de DNA Taxonômico , Bases de Dados de Ácidos Nucleicos , Animais , DNA Mitocondrial/química , DNA Mitocondrial/genética , Alemanha , Dados de Sequência Molecular , Análise de Sequência de DNA
20.
Mol Ecol Resour ; 15(4): 985-1000, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25588628

RESUMO

This study presents DNA barcode records for 4118 specimens representing 561 species of bees belonging to the six families of Apoidea (Andrenidae, Apidae, Colletidae, Halictidae, Megachilidae and Melittidae) found in Central Europe. These records provide fully compliant barcode sequences for 503 of the 571 bee species in the German fauna and partial sequences for 43 more. The barcode results are largely congruent with traditional taxonomy as only five closely allied pairs of species could not be discriminated by barcodes. As well, 90% of the species possessed sufficiently deep sequence divergence to be assigned to a different Barcode Index Number (BIN). In fact, 56 species (11%) were assigned to two or more BINs reflecting the high levels of intraspecific divergence among their component specimens. Fifty other species (9.7%) shared the same Barcode Index Number with one or more species, but most of these species belonged to a distinct barcode cluster within a particular BIN. The barcode data contributed to clarifying the status of nearly half the examined taxonomically problematic species of bees in the German fauna. Based on these results, the role of DNA barcoding as a tool for current and future taxonomic work is discussed.


Assuntos
Abelhas/classificação , Abelhas/genética , Classificação/métodos , Código de Barras de DNA Taxonômico/métodos , Animais , Abelhas/anatomia & histologia , Alemanha , Dados de Sequência Molecular , Análise de Sequência de DNA
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