Peering into the Darkness: DNA Barcoding Reveals Surprisingly High Diversity of Unknown Species of Diptera (Insecta) in Germany

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.

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Larval morphology and DNA barcodes as valuable tools in early detection of marine invaders: a new pea crab found in European waters

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315417000996 ◽

2017 ◽

Vol 98 (7) ◽

pp. 1675-1683 ◽

Cited By ~ 6

Author(s):

Elena Marco-Herrero ◽

Pilar Drake ◽

Jose A. Cuesta

Keyword(s):

Early Detection ◽

Iberian Peninsula ◽

Dna Barcoding ◽

Dna Markers ◽

Larval Morphology ◽

Dna Barcodes ◽

Marine Waters ◽

Larval Stages ◽

Unknown Species ◽

Pea Crab

Four species of Pinnotheridae inhabit European marine waters,Afropinnotheres monodi,Nepinnotheres pinnotheres,Pinnotheres pectunculiandPinnotheres pisum. For these four species there are data available on the morphology of their larval stages as well as DNA markers. This information has allowed us to detect some larvae in plankton samples from the Gulf of Cadiz (SW Iberian Peninsula) that do not belong to any of these European pinnotherid species and to be confirmed by DNA barcoding. In this study these findings are shown as a case of early detection of a newly introduced and unknown species in European marine waters.

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Diversity of Ophioniformes wasps (Hymenoptera: Ichneumonidae) in a Central-West Brazilian Savanna area

Papéis Avulsos de Zoologia ◽

10.11606/1807-0205/2021.61.45 ◽

2021 ◽

Vol 61 ◽

pp. e20216145

Author(s):

Alvaro Doria dos Santos ◽

Helena Carolina Onody ◽

Carlos Roberto Ferreira Brandão

Keyword(s):

Species Richness ◽

Relative Humidity ◽

Abundant Species ◽

Brazilian Savanna ◽

Mato Grosso ◽

Unknown Species ◽

Taxonomic Studies ◽

First Time ◽

Mato Grosso Do Sul ◽

Malaise Traps

This study aimed to assess the diversity, abundance and seasonal dynamics of Ophioniformes wasps collected throughout a year, as recorded in Malaise traps set at the Reserva Ecológica da Universidade Estadual do Mato Grosso do Sul, a Brazilian Savanna area in Aquidauana city, MS. A total of 621 specimens of Ophioniformes belonging to 11 subfamilies, 30 genera and 106 species were sampled. Despite the impressive number of species found, in a pattern of a few relatively abundant species and many rare ones, our data estimate even higher richness, probably between 125 to 165 species in the studied area. The genera Diadegma, Nonnus, Diradops, Meniscomorpha, Syzeuctus, Ophiopterus and Thyreodon are recorded for the first time in Mato Grosso do Sul State. Among the climatic variables evaluated, mean temperature and relative humidity were positively and significantly correlated with richness and abundance. Our data highlights the huge unknown species richness of these parasitoids in Brazil and the need of taxonomic studies efforts in the future.

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Identification of Nepeta olgae Regel and phylogenetic status of some genera in subtribe Nepetinae (Lamiaceae) using DNA markers

BIO Web of Conferences ◽

10.1051/bioconf/20213800087 ◽

2021 ◽

Vol 38 ◽

pp. 00087

Author(s):

Elena Nikitina ◽

Abdurashid Rakhmatov

Keyword(s):

Dna Barcoding ◽

Large Scale ◽

Dna Barcode ◽

Dna Barcodes ◽

Biodiversity Monitoring ◽

Reference Library ◽

Accurate Identification ◽

Unknown Species ◽

Phylogenetic Status ◽

Nuclear Its

The species level diversity is the reference unit for biodiversity accounting, should be systematized and include full information about the species. Reliable identification of any species is critical for a large-scale biodiversity monitoring and conservation. A DNA barcode is a DNA sequence that identifies a species by comparing the sequence of an unknown species with barcodes of a known species sequence database. Accurate identification of important plants is essential for their conservation, inventory. The species diversity assessing exampled on the subtribe Nepetinae (Lamiaceae) representatives, growing in Uzbekistan is given, using DNA barcoding method. The study was aimed to identify indigenous important plants with the nuclear (ITS) and plastid (matK, rbcL, trnL-F) genomes. This work demonstrates the phylogenetic relationships of some genera within the subtribe Nepetinae Coss. & Germ. (Lamiaceae), based on ITS locus gene. All results indicate that the DNA barcoding tool can be successfully used to reliably identify important plants, to inventory the botanical resources of Uzbekistan and to create a reference library of DNA barcodes. So, the combination of three-four locus gene is a good candidate for this approach.

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The diversity of terrestrial arthropods in Canada

ZooKeys ◽

10.3897/zookeys.819.31947 ◽

2019 ◽

Vol 819 ◽

pp. 9-40 ◽

Cited By ~ 6

Author(s):

David W. Langor

Keyword(s):

Species Richness ◽

Dna Barcoding ◽

Native Species ◽

Dna Barcodes ◽

Special Issue ◽

Additional Species ◽

Index Numbers ◽

Strategic Investment ◽

Terrestrial Arthropods ◽

Diverse Groups

Based on data presented in 29 papers published in theBiota of CanadaSpecial Issue of ZooKeys and data provided herein about Zygentoma, more than 44,100 described species of terrestrial arthropods (Arachnida, Myriapoda, Insecta, Entognatha) are now known from Canada. This represents more than a 34% increase in the number of described species reported 40 years ago (Danks 1979a). The most speciose groups are Diptera (9620 spp.), Hymenoptera (8757), and Coleoptera (8302). Less than 5% of the fauna has a natural Holarctic distribution and an additional 5.1% are non-native species. A conservatively estimated 27,000–42,600 additional species are expected to be eventually discovered in Canada, meaning that the total national species richness is ca. 71,100–86,700 and that currently 51–62% of the fauna is known. Of the most diverse groups, those that are least known, in terms of percent of the Canadian fauna that is documented, are Acari (31%), Thysanoptera (37%), Hymenoptera (46%), and Diptera (32–65%). All groups but Pauropoda have DNA barcodes based on Canadian material. More than 75,600 Barcode Index Numbers have been assigned to Canadian terrestrial arthropods, 63.5% of which are Diptera and Hymenoptera. Much work remains before the Canadian fauna is fully documented, and this will require decades to achieve. In particular, greater and more strategic investment in surveys and taxonomy (including DNA barcoding) is needed to adequately document the fauna.

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Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding

PeerJ ◽

10.7717/peerj.5811 ◽

2018 ◽

Vol 6 ◽

pp. e5811

Author(s):

Kam-Cheng Yeong ◽

Haruo Takizawa ◽

Thor-Seng Liew

Keyword(s):

Species Richness ◽

Dna Barcoding ◽

West Coast ◽

Dna Barcode ◽

Operational Taxonomic Unit ◽

Leaf Beetle ◽

Dna Barcodes ◽

The West ◽

Leaf Beetles ◽

Island Habitats

Sabah is a province of Malaysia located on the northern part of the island of Borneo. Most of the leaf beetle fauna studies from this region conducted over the past 15 years have focussed on the mainland habitats while the leaf beetle fauna from island habitats (ca. 500 islands) have largely been overlooked. This study looks into the leaf beetle fauna of 13 small satellite islands off the west coast of Sabah. All specimens were first sorted into morpho-species operational taxonomic unit (OTU) before being identified to species rank where possible based on morphological characters and species names assigned when the specimens fitted the description of species in the literature. We collected 75 OTUs from 35 genera and five subfamilies according to morphology, 12 of which were identifiable to species level. In addition, the DNA barcode for each OTU was cross checked with records in GenBank and Barcoding of Life Data system (BOLD) to verify their identity. The number of species recorded was reduced from 12 species and 63 OTUs (total 75 OTUs) to 12 species and 56 OTUs (total 68 OTUs) after removal of the colour polymorphic species based on DNA barcode analyses. Pulau Gaya has the highest species richness and Pulau Sulug has the lowest species richness. A total of 64 Barcode Index Numbers consisting of 101 DNA barcodes were obtained from the 12 leaf beetle species and 48 OTUs. Based on the DNA barcode analyses, it was possible to confirm several polymorphic OTUs and cryptic species. The mean intraspecific and interspecific genetic divergence were determined as 0.77% and 16.11%, respectively. DNA barcodes of this study show a low similarity with records in GenBank and BOLD, highlighting the lack of representation and the urgency of studying leaf beetles from this region. The study provides the first documentation of leaf beetle fauna from island habitats of Sabah and the first DNA barcoding data for leaf beetles from this part of the world, with the next steps being larger scale sampling over a wider geographical scale for a better understanding of tropical arthropod diversity.

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Counting animal species with DNA barcodes: Canadian insects

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2015.0333 ◽

2016 ◽

Vol 371 (1702) ◽

pp. 20150333 ◽

Cited By ~ 109

Author(s):

Paul D. N. Hebert ◽

Sujeevan Ratnasingham ◽

Evgeny V. Zakharov ◽

Angela C. Telfer ◽

Valerie Levesque-Beaudin ◽

...

Keyword(s):

Dna Barcoding ◽

Animal Species ◽

Fold Increase ◽

Dna Barcodes ◽

Animal Kingdom ◽

Insect Fauna ◽

Substantial Impact ◽

Geographical Regions ◽

Prior Estimate ◽

Diverse Groups

Recent estimates suggest that the global insect fauna includes fewer than six million species, but this projection is very uncertain because taxonomic work has been limited on some highly diverse groups. Validation of current estimates minimally requires the investigation of all lineages that are diverse enough to have a substantial impact on the final species count. This study represents a first step in this direction; it employs DNA barcoding to evaluate patterns of species richness in 27 orders of Canadian insects. The analysis of over one million specimens revealed species counts congruent with earlier results for most orders. However, Diptera and Hymenoptera were unexpectedly diverse, representing two-thirds of the 46 937 barcode index numbers (=species) detected. Correspondence checks between known species and barcoded taxa showed that sampling was incomplete, a result confirmed by extrapolations from the barcode results which suggest the occurrence of at least 94 000 species of insects in Canada, a near doubling from the prior estimate of 54 000 species. One dipteran family, the Cecidomyiidae, was extraordinarily diverse with an estimated 16 000 species, a 10-fold increase from its predicted diversity. If Canada possesses about 1% of the global fauna, as it does for known taxa, the results of this study suggest the presence of 10 million insect species with about 1.8 million of these taxa in the Cecidomyiidae. If so, the global species count for this fly family may exceed the combined total for all 142 beetle families. If extended to more geographical regions and to all hyperdiverse groups, DNA barcoding can rapidly resolve the current uncertainty surrounding a species count for the animal kingdom. A newly detailed understanding of species diversity may illuminate processes important in speciation, as suggested by the discovery that the most diverse insect lineages in Canada employ an unusual mode of reproduction, haplodiploidy. This article is part of the themed issue ‘From DNA barcodes to biomes’.

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Assemblage Patterns of Hymenoptera at Different Elevations of Gunung Datuk, Rembau

Scientific Research Journal ◽

10.24191/srj.v14i2.9358 ◽

2017 ◽

Vol 14 (2) ◽

pp. 1 ◽

Cited By ~ 1

Author(s):

Noor Nasuha Abd Aziz ◽

Siti Khairiyah Mohd Hatta ◽

Idris Abd Ghani ◽

Saiyid Jalaluddin Saiyid Shaifuddin

Keyword(s):

Species Richness ◽

Diversity Index ◽

High Elevation ◽

Significant Difference ◽

Index Site ◽

Evenness Index ◽

Abundance And Diversity ◽

Richness Index ◽

Paired T Test ◽

Malaise Traps

A study on abundance and diversity of Hymenoptera was conducted in Gunung Datuk, Rembau. Samplings were conducted from November 2014 to February 2015 using six Malaise traps. Three traps were placed at Site 1 at 700m height for high elevation and the remaining traps were placed at Site 2 at 200m height for low elevation. A total number of 221 Hymenopteran were collected which consist of nine families namely Ichneumonidae, Formicidae, Braconidae, Bethylidae, Evaniidae, Tiphiidae, Vespidae, Pompilidae and Apidae. In this study, 93 individuals were obtained from Site 1, comprising nine families and 43 morphospecies while 127 individuals were obtained from Site 2 with nine families and 45 morphospecies. Formicidae was the most dominant family collected from both sites with a total of 104 individuals while the least family recorded was Apidae with only one individual. Shannon’s Weiner Diversity Index (H’) showed Site 1 had the higher diversity value with H’ = 3.17 compared to Site 2 with value H’ = 3.12. For Evenness Index, Site 1 had higher value compared to Site 2 with E’ = 0.84 and E’ = 0.82 respectively. Moreover, for Margalef Richness Index, Site 1 recorded R’ = 9.24 while site two recorded R’ = 9.08 which concluded that Site 1 had higher species richness compared to Site 2. Paired t-test showed that both sites had no significant difference with p>0.05. Overall study showed that the diversity and abundance of Hymenoptera in Gunung Datuk were low since the value of H’ is less than 3.50.

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Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽

10.1139/g06-025 ◽

2006 ◽

Vol 49 (7) ◽

pp. 851-854 ◽

Cited By ~ 48

Author(s):

Mehrdad Hajibabaei ◽

Gregory AC Singer ◽

Donal A Hickey

Keyword(s):

New Species ◽

Cryptic Species ◽

Dna Barcoding ◽

Species Identification ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Primate Species ◽

Dna Barcodes ◽

Global Biodiversity ◽

Efficient Sequence

DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms—the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships. Our conclusion is that these short DNA sequences do not contain enough information to build reliable molecular phylogenies or define new species, but that they can provide efficient sequence tags for assigning unknown specimens to known species. As such, DNA barcoding provides enormous potential for use in global biodiversity studies.Key words: DNA barcoding, species identification, primate, biodiversity.

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Baseline Assessments of Wildlife Biodiversity Within Selected Areas of Central Visayas, Philippines

Journal of Biodiversity Conservation and Bioresource Management ◽

10.3329/jbcbm.v6i2.55244 ◽

2021 ◽

Vol 6 (2) ◽

pp. 27-34

Author(s):

RP Jose ◽

WA Aureo ◽

CI Narido ◽

TD Reyes Jr ◽

MB Sarnowski

Keyword(s):

Species Richness ◽

Species Diversity ◽

Diversity Index ◽

Population Trends ◽

Species Richness And Diversity ◽

Natural Park ◽

Biodiversity Inventories ◽

Baseline Information ◽

High Diversity ◽

Areas Of Protection

A comprehensive inventory of faunal biodiversity was conducted within three Key Biodiversity Areas of Central Visayas. Mt. Bandilaan Natural Park (MBNP), Balinsasayao Twin Lakes Natural Park (BTLNP), and Rajah Sikatuna Protected Landscape (RSPL). Three primary wildlife groups were surveyed: bats, birds and amphibians. Species diversity and population trends were then analyzed to assess areas of biodiversity importance. RSPL generally had the highest species richness and diversity index while MBNP consistently had the lowest. When pooled. The surveyed areas resulted in a high diversity index and rate of endemicity showing the importance of multiple areas of protection. These findings can be utilized to prioritize habitat protection as well as to serve as a baseline information for future biodiversity inventories. J. Biodivers. Conserv. Bioresour. Manag. 2020, 6(2): 27-34

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Effects of Malaise trap spacing on species richness and composition of terrestrial arthropod bulk samples

10.1101/2020.09.30.321430 ◽

2020 ◽

Author(s):

D Steinke ◽

TWA Braukmann ◽

L Manerus ◽

A Woodhouse ◽

V Elbrecht

Keyword(s):

Species Richness ◽

Field Experiments ◽

Collection Efficiency ◽

Malaise Trap ◽

Number Of Factors ◽

Large Numbers ◽

Set Up ◽

Taxonomic Groups ◽

A Site ◽

Malaise Traps

AbstractThe Malaise trap has gained popularity for assessing diverse terrestrial arthropod communities because it collects large samples with modest effort. A number of factors that influence collection efficiency, placement being one of them. For instance, when designing larger biotic surveys using arrays of Malaise traps we need to know the optimal distance between individual traps that maximises observable species richness and community composition. We examined the influence of spacing between Malaise traps by metabarcoding samples from two field experiments at a site in Waterloo, Ontario, Canada. For one experiment, we used two trap pairs deployed at weekly increasing distance (3m increments from 3 to 27 m). The second experiment involved a total of 10 traps set up in a row at 3m distance intervals for three consecutive weeks.Results show that community similarity of samples decreases over distance between traps. The amount of species shared between trap pairs shows drops considerably at about 15m trap-to-trap distance. This change can be observed across all major taxonomic groups and for two different habitat types (grassland and forest). Large numbers of OTUs found only once within samples cause rather large dissimilarity between distance pairs even at close proximity. This could be caused by a large number of transient species from adjacent habitat which arrive at the trap through passive transport, as well as capture of rare taxa, which end up in different traps by chance.

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