GBOL III: Dark Taxa

GBOL III: Dark Taxa

GBOL III: Dark Taxa

Researchers launch new BIOSCAN project that aims to illuminate thousands of new insect species on Germany's doorstep.

A “pixelated” Diptera.

Currently, around 1.4 million species of animals are known. For tropical regions, many species are still unknown, with estimates of global biodiversity ranging from five to 30 or even 100 million species. More recent studies suggest that there are about 10 million species on our planet. In contrast to the tropics, the Central European fauna is considered to be very well studied. However, specialists have mostly concentrated on less diverse and easy-to-study organisms, neglecting the species-rich, often taxonomically difficult groups, like many Diptera and Hymenoptera. This led to a mismatch between high species numbers and a small number of researchers, often referred to as the ‘taxonomic impediment’. This is most prominent for the megadiverse faunas of tropical regions. Less known is that this also applies, to some extent, for countries with a long history of taxonomic research like Germany, covering 200 or more years. For example, for the compilation of the German checklist of Hymenoptera, 32 specialists were available for 247 species of digger wasps (Crabronidae), while for parasitoid wasps of the family Ichneumonidae one specialist had to deal with 3,332 species.

In Germany, about 48,000 species of animals have been documented, including about 33,300 species of insects. In little-studied groups such as insects and arachnids, preliminary results of earlier DNA barcoding initiatives indicate the presence of thousands of species that are still awaiting discovery. Among the groups with a particularly large suspected number of unknown species are the Diptera (flies) and the Hymenoptera (in particular, the parasitoid wasps). With almost 10,000 known species each, these two insect orders account for two-thirds of the German insect fauna, underlining their importance.

Bar Graph depicting availability of taxonomic expertise for major insects orders in Germany.

“Dark taxa” are, as a rule, small-sized and rich in species, and have therefore been largely ignored by taxonomists. This is reflected by the number of undescribed species in these taxa, combined with a low chance to get specimens identified by specialists.

The insight that there are not only a few but many unknown species in Germany is a result of the earlier German Barcode of Life projects GBOL I and II, both supported by the Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, BMBF) and the Bavarian Ministry of Science (project Barcoding Fauna Bavarica). The projects aimed at making all German species reliably, quickly and inexpensively identifiable by DNA barcodes. Since the first project was launched about ten years ago, more than 25,000 animal species have been barcoded, in collaboration with national and international partners. Among them are mostly well-known groups such as butterflies, moths, beetles, grasshoppers, spiders, bees and wasps.

Two scatterplots demonstrating relationship between body size (top) and species richness (bottom) in German Diptera

Relationship between body size (top) and species richness (bottom) in German Diptera1

Despite their popularity, these groups represent only a fraction of the total inventory of German insects. In Germany there are 170 butterfly species, 81 dragonfly and damselfly species, 87 species of grasshoppers, katydids and crickets, and 580 species of ground beetles, all of which are well-studied. Taken together, these 918 species stand for only a small fraction (2.8%) of the German insect fauna. They are morphologically well identifiable, have manageable species numbers, can easily be monitored during daytime and are therefore regarded as relevant in nature conservation and often used for monitoring species diversity. Conversely, however, this means that the vast majority of the native species diversity has been largely ignored in nature conservation and in general and applied research.

Circular tree depicting Nematocera (midges) and Brachycera (flies)
A circular neighbour‐joining tree for the two suborders of flies, Nematocera and Brachycera1. Each line in the tree corresponds to a distinct Barcode Index Number (BIN). Whereas for two of the “big four” insect orders, the Lepidoptera and Coleoptera, the number of German species are very precisely known, the numbers for the Diptera and Hymenoptera must rely on rough estimates. 

This applies in particular to the Diptera (flies). The observation that estimates of the number of species of native Diptera have been far too low was not only a result of the DNA barcoding projects at the ZSM, but became clear in a recent study by Paul Hebert and his team2. In this large-scale study, DNA barcodes of about one million insects were analyzed. Based on this study, Canada’s gall midges alone are estimated to include about 16,000 species, suggesting the existence of at least two million species on earth. That would be more species of gall midges worldwide than all previously described animal species combined.

The little-known or unknown species, referred to as ‘dark taxa’, are the subject of another BMBF-funded DNA barcoding project that is being carried out at the ZSM in collaboration with other German natural history museums and institutions. The project focuses on Diptera and Hymenoptera (in particular, parasitoid wasps), each with a large proportion of ‘dark taxa’. The new project, funded by a grant of 5.3 million Euro, starts July 1st 2020, with 12 PhD students at three major natural history institutions in Bonn (Zoological Research Museum Alexander Koenig), Munich (SNSB – Zoologische Staatssammlung München) and Stuttgart (State Museum of Natural History Stuttgart), to address a range of questions related to the taxonomy of German ‘dark taxa’, targeting selected groups of Diptera and parasitoid Hymenoptera.

Detailed photo of a Eulophidae specimen
Yellow Mymaridae specimen

Small parasitoid wasps of the families Eulophidae (top) and Mymaridae (bottom), both group with possibly hundreds of new species in Germany that still await discovery.

Among the major aims of GBOL III is assessing of the performance of DNA barcoding for species identification of ‘dark taxa’, and assessing the species detection ability of DNA barcodes in mass samples that are obtained from metabarcoding studies. Other aims of the project include the development of a platform for managing OTU-based taxonomic data, developing a pipeline for reliable and fast barcoding of small and poor-quality samples, and training of the next generation of taxonomists.

GBOL III is designed to make an important contribution to the global BIOSCAN initiative of the Centre for Biodiversity Genomics. It helps to lay the foundations for a global biomonitoring system to record the biodiversity of our planet on a large geographical scale in times of rising temperatures, increasing weather extremes and receding ice, and to track its changes as a result of global environmental changes.

References:

1. Morinière J, Balke M, Doczkal D, Geiger MF, Hardulak LA, Haszprunar G, Hausmann A, Hendrich L, Regalado L, Rulik B, Schmidt S, Wägele J, Hebert PDN (2019) A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding‐based biomonitoring. Molecular Ecology Resources 19: 900–928. https://doi.org/10.1111/1755-0998.13022

2. Hebert PDN, Ratnasingham S, Zakharov EV, Telfer AC, Levesque-Beaudin V, Milton MA, Pedersen S, Jannetta P, deWaard JR (2016) Counting animal species with DNA barcodes: Canadian insects. Philosophical Transactions of the Royal Society B: Biological Sciences 371: 20150333. https://doi.org/10.1098/rstb.2015.0333

Written by

Axel Hausmann

Axel Hausmann

SNSB - Zoologische Staatssammlung München, Munich, Germany

Lars Krogmann

Lars Krogmann

State Museum of Natural History Stuttgart, Stuttgart, Germany

Ralph S. Peters

Ralph S. Peters

Zoological Research Museum Alexander Koenig, Bonn, Germany

Vera Rduch

Vera Rduch

Zoological Research Museum Alexander Koenig, Bonn, Germany

Stefan Schmidt

Stefan Schmidt

SNSB - Zoologische Staatssammlung München, Munich, Germany

July 10, 2020

doi: 10.21083/ibol.v10i1.6242

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Discovering Fiji’s native bees: hidden secrets in a biodiversity hotspot

Discovering Fiji’s native bees: hidden secrets in a biodiversity hotspot

Discovering Fiji’s native bees: hidden secrets in a biodiversity hotspot

Researchers provide new insights into biodiversity using DNA barcoding in Fiji's topographically complex archipelago.

Homalictus hadrander, one of the four described species previously known from Fiji.
PHOTO CREDIT: James Dorey

Fiji’s entomological diversity has historically been considered depauperate. Recent widespread DNA barcoding efforts, however, from the South Australian Museum, Flinders University, and University of South Australia, along with a flurry of undergraduate, honours, and PhD students, have helped to uncover some of the hidden secrets of biodiversity within this topographically complex archipelago. Since 2010, funding from the Australian & Pacific Science Foundation and Australian Commonwealth New Colombo Plan, along with support from students, has enabled fieldwork focused on collecting bees, wasps, and butterflies across all the major Fijian islands. Trekking up the tallest mountains, four-wheel driving across challenging terrain, and following the meandering rivers of inland Fiji has revealed that initial estimations of Fiji’s entomological fauna have been severely underestimated. DNA barcoding over 1,000 bee specimens has increased species richness estimates from 4 species (known since 1979) up to 26 endemic species in the genus Homalictus. Interestingly, 60% of these new species are only found above 800 m elevation which comprise a mere 2% of land area of Fiji, and they are often restricted to single mountain tops (Figure 1). From extensive DNA barcoding, mitochondrial haplotype diversity was used to explore the level of intraspecific gene flow in the widespread species of the genus (Figure 2).

Figure 1: (a) The number of species (species richness) plotted against land area available at each elevational gradient. (b) Map of Fiji showing the land area available. Colours correspond to those used in (a).

CREATED BY: Cale Matthews

These results also indicate that gene flow is being restricted within highland localities of the most widespread Homalictus species. Dispersal from a species home range does not appear to be occurring in Fiji, which may be presenting a contemporary model of speciation that is predominantly influenced by past climatic fluctuations. There is an estimated crown age of 400 ka for the initial Fijian Homalictus colonisation, which would result in the genus being present for several glacial cycles. During glacial maxima, cooler climates would be ubiquitous throughout Fiji, however during glacial minima and interglacial periods there is a distinction between cool highland and warm lowland climate. DNA barcoding results indicate that the largest diversification of this genus is concordant with the most recent glacial minima, as species that were freely dispersing during glacial maxima are forced to retreat into highland refugia. Combined with the inferred haplotype networks, these results indicate that restriction due to low thermal tolerance of lowland climate is driving the extraordinary highland species richness in Fiji.

 

Figure 2: (a) Haplotype network of all sequenced Homalictus fijiensis (N=358) coloured by sampling locality. Hash marks represent nucleotide changes between each haplotype. Shared haplotypes represented by circles with multiple colours. Circle outline representing highland or lowland sampling. (b) Sampling map of H. fijiensis coloured by geographic sampling locality.

CREATED BY: Cale Matthews

Further to the work on bees, we have also started barcoding Fiji’s butterfly fauna, along with the first-ever species of Gasteruption, a parasitoid wasp genus, found in Fiji. The species, Gasteruption tomanivi (Published in Zootaxa by PhD student Ben Parslow), was found at the peak of Fiji’s highest mountain. These discoveries have highlighted how little is known about the entomofauna of Fiji and how the use of DNA barcoding has helped to uncover Fiji’s hidden secrets of biodiversity.

 

Written by

Cale Matthews

Cale Matthews

School of Biological Sciences, Flinders University, Adelaide, Australia

James Dorey

James Dorey

School of Biological Sciences, Flinders University, Adelaide, Australia

Scott Groom

Scott Groom

School of Agriculture, University of Adelaide, Australia

Olivia Davies

School of Biological Sciences, Flinders University, Adelaide, Australia

Elisha Freedman

Elisha Freedman

School of Biological Sciences, Flinders University, Adelaide, Australia

Justin Holder

School of Biological Sciences, Flinders University, Adelaide, Australia

Ben Parslow

School of Biological Sciences, Flinders University, Adelaide, Australia

Michael Schwarz

School of Biological Sciences, Flinders University, Adelaide, Australia

Mark Stevens

Mark Stevens

School of Biological Sciences, Flinders University, Adelaide, Australia

April 7, 2019
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https://doi.org/10.21083/ibol.v9i1.5482

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A DNA Barcoding Review of the Entomofauna of Egypt

A DNA Barcoding Review of the Entomofauna of Egypt

A DNA Barcoding Review of the Entomofauna of Egypt

From insect diversity to pests to forensics, DNA barcoding plays a vital role in Egyptian biodiversity conservation and legislative protection efforts.
Egyptian hornet wasp (Vespa orientalis) predating on Dermaptera (Labidura sp.). PHOTO CREDIT: Mohamed Gamal

Egypt has more than 23,587 identified plant and animal species in addition to thousands of algae, bacteria, and viruses1, and this unique biodiversity contributes to Egypt’s economy and supports the welfare of its citizens. Agricultural production accounts for more than 10 per cent of Egypt’s GDP while tourism revenues from marine activities on the Red Sea represent more than 30 billion LE annually. Protecting threatened species such as dolphins, sharks, and dugong contribute by more than 61 million LE per year and the marine fish production is estimated to be worth 5 billion LE2. Therefore, Egypt has paid particular attention to the conservation and legislative protection of its natural heritage.

Joining its International Barcode of Life (iBOL) partners, Egypt has been using DNA barcoding to better understand and plan for protection of biodiversity. So far, Egypt has published 20,980 DNA barcode sequence records, 25 per cent (5,368) of which have species names that represent 695 species.

In this review, we present an overview of the DNA barcoding carried out on the Egyptian entomofauna and introduce current advances of this promising technique. This review focuses on three main areas that highlight studies investigating insect diversity and distribution, insects in forensic applications as well as pest and parasite dynamics.

Insect diversity and distribution: DNA barcoding has been used to investigate the genetic diversity of Egyptian wasp populations with a wide geographical range3. Three species, Vespa orientalis, Polistes bucharensis, and Polistes mongolicus were accurately identified by their DNA barcodes with the COI phylogenetic signal revealing interesting insights across Jordan, Giza, Cyprus, and Greece. Despite the wide geographical range, only minor genetic diversity was observed among populations of the three wasp species, indicating unrestricted gene flow. 

DNA barcoding has also been used in a larger-scale insect diversity investigation in the understudied Saharo-Arabian zoogeographic region, revealing significant heterogeneity between Egypt, Pakistan, and Saudi Arabia4. The year-long deployment of Malaise traps in these countries collected 53,092 specimens, including 18,391 from Egypt. The DNA barcode sequences revealed the occurrence of 3,682 BINs belonging to 254 families. These results reflect the high species richness of the area, encouraging further research into biodiversity monitoring for the region.

Insects in forensic applications: The Egyptian Forensic Medicine Authority, the leading authority on forensic medicine in Egypt, handles a relatively large number of cases annually and relies on laboratories for assistance with molecular techniques to ensure fast and reliable identification of species of forensic interest (e.g. necrophagous insects). To date, few studies in Egypt have evaluated the use of DNA barcoding in the identification and establishment of reference libraries for insect species of important post-mortem interval indication.

PHOTO CREDIT: Samy Zalat

Egyptian records of blow flies (Calliphoridae). Maggots (larva) are scavengers and adults are plant visitors.

PHOTO CREDIT: Ramadan Mounir

Aly & Wen5 studied the applicability of a 296-bp cytochrome c oxidase I (COI) sequence as a reliable mitochondrial genetic marker for the identification of forensically important flies following previous research showing the efficacy of a short COI marker in this group6. The study analyzed 16 species of blowflies (Calliphoridae), flesh flies (Sarcophagidae), and house flies (Muscidae) originating from Egypt and China and concluded that a shorter COI fragment is simple, cheap, and reproducible but lacks agreement with traditional morphological classification. In a follow-up investigation, Aly7 examined the reliability of long (1173-bp) vs. short (272-bp) COI markers for 18 species of the same 3 dipteran families from Egypt and China. The results indicated that the longer COI marker performed better than the shorter marker for dipterous identification due to better monophyletic separation and concordance with taxonomic classifications. A more in-depth survey of the genetic diversity of forensically important blowflies (Calliphoridae) revealed numerous haplotypes among 158 specimens collected from four locations in Egypt (Giza, Dayrout, Minya, and North Sinai)8. Three particularly important species (Chrysomya albiceps, Chrysomya , Chrysomya marginalis) were well-differentiated using COI supporting its use for subfamily-, genera-, and species-level identification of blowflies. Most importantly for forensics use, COI is highly effective at identifying different developmental stages of forensically important flies, including larvae, pupae, and even empty, otherwise difficult to identify morphologically. Five different species of Diptera and their immature stages from Alexandria, Egypt including Chrysomya albiceps, Chrysomya megacephala, Calliphora vicina, Lucilia sericata, and Ophyra capensis, were correctly identified using mitochondrial DNA markers9. Pest and parasite dynamics: DNA barcoding has also played an important role in the identification of pests and parasites. Seventeen species of mealybug pests (Hemiptera: Pseudococcidae) have been identified by DNA barcoding specimens collected from populations infesting various crops and ornamental plants in Egypt and France10. The genetic variation found between populations of the same species using a combination of three markers (28S-D2, COI, and ITS2) and morphological examination indicated cryptic taxa that might respond differently to management strategies. High diversity and rapid diversification were found in the head louse, Pediculus humanus (Pediculidae: Phthiraptera)11. P. humanus includes two morphologically indistinguishable subspecies: the head louse, P. humanus and the body louse, P. humanus. By analyzing sequence diversity of two mitochondrial genes (COI, cytb) in 837 specimens of Pediculus humanus from Egypt, Pakistan, and South Africa, high diversity and the occurrence of five mitochondrial lineages was revealed with implications for the spread of disease. Conclusion: DNA barcoding of crop pests and pollinators, in addition to disease-carrying insect-vectors, will continue to be the top priority for the Egyptian government. Egypt actively enacts laws, carries out research, increases public awareness, engages local communities in the management of protected areas, and implements projects funded by Egypt and other international donors to protect biodiversity. These motivations place Egypt in a valuable position among other countries joining iBOL in support of BIOSCAN, a project that will build a global monitoring system for the planet.

References:

1. Egypt’s Fifth Biodiversity National Report (2014). Ministry of Environmental Affairs, Cairo, Egypt.

2. Coastal and marine biodiversity in Egypt (2018). United Nations Convention on Biological Diversity Conference (CBD COP14), Sharm El Sheikh. Ministry of Environment.

3. Abdel-Samie E, ElKafrawy I, Osama M, Ageez A (2018) Molecular phylogeny and identification of the Egyptian wasps (Hymenoptera: Vespidae) based on COI mitochondrial gene sequences. Egyptian Journal of Biological Pest Control. 28: 36. https://doi.org/10.1186/s41938-018-0038-z

4. Ashfaq M, Sabir JSM, El-Ansary HO, Perez K, Levesque-Beaudin V, Khan AM, Rasool A, Gallant C, Addesi Jo, Hebert PDN (2018) Insect diversity in the Saharo-Arabian region: revealing a little-studied fauna by DNA barcoding. PLoS ONE 13(7). https://doi.org/10.1371/journal.pone.0199965

5. Aly SM, Wen J (2013) Molecular identification of forensically relevant Diptera inferred from short mitochondrial genetic marker. Libyan Journal of Medicine 8:10. https://doi.org/10.3402/ljm.v8i0.20954

6. Zehner R, Amendt J, Schutt S, Sauer J, Krettek R, Povolny D. (2004) Genetic identification of forensically important flesh flies (Diptera: Sarcophagidae). International Journal of Legal Medicine 118(4): 245–247. https://doi.org/10.1007/s00414-004-0445-4

7. Aly SM (2014) Reliability of long vs short COI markers in identification of forensically important flies. Croatian Medical Journal. 55(1): 19–26. https://doi.org/10.3325/cmj.2014.55.19

8. Salem A, Adham F, Picard C (2015) Survey of the genetic diversity of forensically important Chrysomya (Diptera: Calliphoridae). Journal of Medical Entomology 52(3):320–328. https://doi.org/10.1093/jme/tjv013

9. Abdel Ghaffar HA, Moftah MZ, Favereaux A, Swidan M, Shalaby O, El Ramah S, Gamal R (2018) Mitochondrial DNA-based identification of developmental stages and empty puparia of forensically important flies (Diptera) in Egypt. Journal of Forensic Science & Medicine 4(3): 129–134. http://www.jfsmonline.com/text.asp?2018/4/3/129/242508

10. Abd-Rabou S, Shalaby H, Germain J, Ris N (2012) Identification of mealybut pest species (Hemiptera: Pseudococcidae) in Egypt and France, using a DNA barcoding approach. Bulletin of Entomological Research 102(5):515–523. https://doi.org/10.1017/S0007485312000041

11. Ashfaq M, Prosser S, Nasir S, Masood M, Ratnasingham S, Hebert PDN (2015) High diversity and rapid diversification in the head louse, Pediculus humanus (Pediculidae: Phthiraptera). Scientific Reports, 14188. https://doi.org/10.1038/srep14188

Written by

Samy Zalat

Samy Zalat

Zoology Department, Faculty of Science, Suez Canal University, Ismailia, Egypt.

Mona Mahmoud

Mona Mahmoud

Nature & Science Foundation, Cairo, Egypt.

April 7, 2019
doi:10.21083/ibol.v9i1.5515

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Finland Takes a Leap into the BIOSCAN Age

Finland Takes a Leap into the BIOSCAN Age

Finland Takes a Leap into the BIOSCAN Age

With remarkable governmental support, FinBOL aims to add thousands of species to the DNA barcode library by the end of 2022.
Six thousand specimens of sawflies recently processed for DNA barcoding as part of the FinBOL project. PHOTO CREDIT: Vlad Dinca

Written by

Marko Mutanen

Marko Mutanen

Ecology and Genetics Research Unit, University of Oulu, Finland

April 7, 2019

DNA barcoding first gained momentum in Finland in 2011 with the launch of the national Finnish Barcode of Life (FinBOL) initiative, initially funded by three major national funders – the Kone Foundation, the Finnish Cultural Foundation as well as the University of Oulu. FinBOL’s main goal is to build a DNA barcode reference library for the species of Finland.

Since 2015, the Academy of Finland has funded barcoding activities through the Finnish Biodiversity Information Facility (FinBIF) which brings together all information about Finnish species under the Laji.fi portal, including links to the DNA barcodes available on the Barcode of Life Database (BOLD).

With approximately 40,000 species known and 48,000 estimated, Finland’s biodiversity is relatively modest in comparison to most other countries. The fauna and flora are, however, among the best investigated globally, and roughly one-half of the species are presently represented with sequence data on BOLD. Some major groups, such as butterflies, moths, and caddisflies, already have barcode sequences for virtually all species. Many experts have been closely engaged with the project and this continued collaboration will be integral to reaching our goal.

Recently, the Academy of Finland provided €2.7M to FinBIF 2.0 to further strengthen the national biodiversity infrastructure. With this remarkable governmental support, we aim to add thousands of species to the DNA barcode library by the end of 2022. To reach this goal, we take advantage of the unprecedented progress in high-throughput sequencing technology that also facilitates the recovery of full barcode sequences from old museum specimens when fresh specimens are not available.

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