Local wildlife enthusiasts drive DNA barcode library building in the UK

Local wildlife enthusiasts drive DNA barcode library building in the UK

Local wildlife enthusiasts drive DNA barcode library building in the UK

Researchers in the UK are spearheading a number of high-profile initiatives designed to populate and fill gaps in the national DNA barcode library

Distribution of DNA barcode records for the United Kingdom.

IMAGE: BOLD Sytems 2020-03-10

Despite some notable achievements, such as a complete DNA barcode library for the native plants of Wales, the UK has lagged behind other European countries when it comes to growing its DNA barcode library. On BOLD there are 24,555 DNA barcode records for specimens collected in the UK (from 5,484 species) which is very similar to Austria (24,513 records, from 5,375 species), a landlocked country with roughly one third the land area and one seventh the human population. Germany leads Europe with 167,458 records from 14,805 species.

    The UK is working to catch-up through a number of high-profile initiatives designed to populate and fill gaps in the UK’s DNA barcode library and, in particular, bring BIOSCAN to UK insects.

    Distribution of DNA barcodes records for the United Kingdom.
    IMAGE: BOLD Systems from 2020-03-10

    The Darwin Tree of Life project is being led by the Wellcome Sanger Institute and involves a consortium of institutes, universities, museums, and agencies, including the Natural History Museum and Royal Botanical Gardens Kew. The project aims to deliver public DNA barcodes for 10,000 species by 2023 and ultimately sequence the genomes of all 66,000 species of plants, fungi, protozoa, and animals that are found in the UK.

    DEFRA (the Department for Environment, Food & Rural Affairs) has established a Centre of Excellence for Environmental Genomic Applications. This virtual centre recognises the absolute necessity of DNA barcode libraries to meet its aims of “applying genomics methods (eDNA and metabarcoding) to detect rare and invasive species, evaluate the effectiveness of conservation interventions, monitor the status and trends for key assemblages and taxa, and assess ecosystem health, functioning, and resilience”1.

    What is special about these initiatives is that they capitalize on the UK’s large community of local wildlife enthusiasts. A recent workshop organised by BugLife (the Invertebrate Conservation Trust) and Natural England (the UK government’s adviser for the natural environment in England) to examine “gaps” in BOLD for “key English invertebrates” brought together members of the Caddisfly Recording Scheme, Cranefly Recording Scheme, the British Dragonfly Society, the Amateur Entomologists’ Society, amongst others. The UK’s exceptional network of dedicated volunteer wildlife recorders already contribute thousands of records to taxon-focussed databases such as the UK Butterfly Monitoring Scheme (UKBMS), Local Record Centres, and through apps such as iSpot and iRecord which transmit data to the NBN (National Biodiversity Network) Atlas.

    Ainsdale Sand Dunes National Nature Reserve, one of the most important wildlife sites in England.
    PHOTO CREDIT: Gary Hedges

    The Darwin Tree of Life project kicked off last summer about 25 km north of Liverpool at Ainsdale Sand Dunes National Nature Reserve with a DNA Bioblitz attended by a team of local recorders including National Museums Liverpool entomologists. These local experts are passionate, driven and keen to contribute to DNA barcode libraries, but don’t necessarily have background knowledge in molecular biology or a basic skill set in “wet” lab techniques.

    Participants during the World Museum DNA Barcoding Workshop in February 2020.
    PHOTO CREDIT: Leanna Dixon

    To address this we recently ran a DNA barcoding workshop at World Museum Liverpool for eleven prominent local recorders connected with the Tanyptera Project. The Tanyptera Project is a seven-year initiative funded by the Tanyptera Trust to promote the study and conservation of insects and other invertebrates in the Lancashire and Cheshire region of Northwest England. To our knowledge this was one of the first DNA barcoding workshops run solely for non-professional scientists.

    Sphecodes ferruginatus female blood bee collected in Cheshire, England.
    PHOTO CREDIT: Chloe Aldridge

    The 1.5-day workshop covered the key steps in DNA barcoding from lab to BOLD2. Participants brought along their own invertebrates collected during recent local fieldwork and all successfully produced DNA barcodes for their specimens, which included springtails, bees, a cranefly, other flies, beetles, and spiders. The specimens have been vouchered into World Museum Liverpool’s National Entomology Collection which includes over 1 million specimens, and the sequences have been submitted to BOLD. One participant was able to confirm the first record of a Nationally Scarce blood bee in Cheshire – Sphecodes ferruginatus – raising interesting hypotheses about its potential host species.

    At National Museums Liverpool, together with the Tanyptera Project, we are committed to continue developing our DNA barcoding educational offering for local wildlife enthusiasts and supporting their work driving forward national initiatives to get more UK barcodes onto BOLD.

    References:

    1. Nelson M, Woodcock P, Maggs C (2018) Using eDNA and metabarcoding for nature conservation. Joint Nature Conservation Committee (JNCC 18 25). Available at http://data.jncc.gov.uk/data/99e1f69f-c438-439f-8401-dd8a6ce17320/JNCC18-25-Using-eDNA-and-Metabarcoding-for-Nature-Conservation.pdf

    2. Wilson JJ, Sing KW, Jaturas N (2019) DNA barcoding: Bioinformatics workflows for beginners. In Bioinformatics and Computational Biology. The A to Z of Bioinformatics. Ranganathan S, Nakai K, Gribskov M & Schönbach C, Eds. Elsevier Ltd., Oxford.

    Written by

    John-James Wilson

    John-James Wilson

    Vertebrate Zoology at World Museum, National Museums Liverpool, United Kingdom

    Leanna Dixon

    Leanna Dixon

    Tanyptera Project, National Museums Liverpool, United Kingdom

    Gary Hedges

    Gary Hedges

    Tanyptera Project, National Museums Liverpool, United Kingdom

    March 20, 2020

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    Assessing herbarium material with novel molecular techniques reveals a wealth of new data from old treasure troves

    Assessing herbarium material with novel molecular techniques reveals a wealth of new data from old treasure troves

    Assessing herbarium material with novel molecular techniques reveals a wealth of new data from old treasure troves

    Using large-scale genome skimming to build a resilient resource for the future
    Hamersley Range, Pilbara, Western Australia

    PHOTO CREDIT: Stephen van Leeuwen

    Herbaria are valuable sources of extensive curated plant material that are important reference specimens for plant identification. These plant materials are now also accessible to genetic studies because of advances in high-throughput, next-generation sequencing (NGS) methods.

    In our study, we conducted a large-scale applied assessment of one such NGS approach – genome skimming – and its ability to recover plastid and ribosomal genome sequences from a broad taxonomic sampling of herbarium material for the Western Australian flora. We sequenced 672 samples covering 21 families, 142 genera, and 530 named and proposed named species, and explored the impact of sample age, DNA concentration and quality, read depth and fragment length on plastid assembly error.

    We demonstrate that herbaria are a valuable source of plant material for building a comprehensive DNA sequence database which serves various applications from modernizing plant surveys to improving the resolution of plant phylogenies.

    Gastrolobium grandiflorum, Pilbara, Western Australia

    PHOTO CREDIT: Stephen van Leeuwen

    Genome skimming1 was effective at producing genomic information at large scale. Substantial sequence information on the chloroplast genome was obtained from 96.1% of samples, and complete or near-complete sequences of the nuclear ribosomal RNA gene repeat were obtained from 93.3% of samples.

    Eucalyptus kingsmillii, Pilbara, Western Australia

    PHOTO CREDIT: Stephen van Leeuwen

    Grevillea wickhamii, Pilbara, Western Australia

    PHOTO CREDIT: Stephen van Leeuwen

    We extracted sequences for plastid markers rbcL and matK – the core DNA barcode regions – from 96.4% and 93.3% of samples, respectively. Read quality and DNA fragment length had significant effects on sequencing outcomes and error correction of reads proved essential. Assembly problems were specific to certain taxa with low GC and high repeat content (e.g. Goodenia, Scaevola, Cyperus, Bulbostylis, Fimbristylis), suggesting the influence of biological rather than technical factors. The structure of related genomes was needed to guide the assembly of repeats that exceeded the read length. DNA-based matching proved highly effective and showed that the efficacy for species identification declined in the following order: total chloroplast DNA >> ribosomal DNA > matK >> rbcL.

    Ptilotus rotundifolius, Pilbara, Western Australia

    PHOTO CREDIT: Stephen van Leeuwen

    Our success is important as it demonstrates that herbaria can be used as a source of plant material for building a comprehensive DNA sequence database. These data form the basis of development of a molecular identification system for the Western Australian flora. This will enable identification of specimens throughout the year (e.g., non-flowering times) and for hard-to-identify species (e.g., those with constrained or reduced morphological characters) or for specimens where only fragments of non-diagnostic material are available. The availability of this technology will modernize plant surveys by reducing constraints on survey effort through moderating sampling timing restrictions and seasonal effects, as well as enabling rapid verifiable identification. It will also have practical applications in a wide range of ecological contexts using eDNA metabarcoding, such as gut and scat analysis of animals to determine dietary preferences of threatened species and livestock, and checking the integrity of seed collections for seed banking and use in land restoration/revegetation programs. Other potential uses of extensive plastid sequence data, beyond species identification, include improving the resolution of plant phylogenies and studies on the evolution of plastid genome function, including understanding adaptive changes.

    References:

    1. Straub S, Parks M, Weitemier K, Fishbein M, Cronn R, Liston A (2012) Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics. American Journal of Botany 99(2), 349-364. https://dx.doi.org/10.3732/ajb.1100335

    For full details, please refer to the publication in BMC Plant Methods.

    Written by

    Paul Nevill

    Paul Nevill

    Curtin University, School of Molecular and Life Sciences, ARC Centre for Mine Site Restoration

    & Trace and Environmental DNA (TrEnD) Lab, Perth, Western Australia

    February 4, 2020
    https://doi.org/10.21083/ibol.v10i1.5934 

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    The celebrities of the microcosmos aren’t always easy to find: detecting tardigrades in environmental DNA

    The celebrities of the microcosmos aren’t always easy to find: detecting tardigrades in environmental DNA

    The celebrities of the microcosmos aren’t always easy to find: detecting tardigrades in environmental DNA

    The hidden diversity of tardigrades is being uncovered in Norwegian forests using DNA barcoding and metabarcoding

    Scanning electron microscopy image of Diploechiniscus oihonnae

    PHOTO CREDIT: Lasse Topstad

    Found across every continent on Earth, to now potentially living on our moon, tardigrades are some of the most resilient microorganisms we know of. But despite our fascination with these microscopic water bears, there is still much to discover. Our study is exploring the applicability of using environmental DNA to facilitate the examination of tardigrade diversity.

    The popular narrative that tardigrades can withstand anything – from -272 degrees Celsius to as high as 150 degrees Celsius, 6,000 times the atmospheric pressure, extreme radiation, and vacuum – has earned them celebrity status of the microcosmos. However, tardigrades are more than just superstars. They constitute their own phylum of life, ranked at the same taxonomic level as arthropods (insects and spiders), and currently hold around 1,270 described species. Many of these species fulfill ecologically important roles related to the breakdown of organic material in the soil. Other species are found in freshwater streams, sediments, mosses, lichens, and leaf-litter, occurring in most ecosystems throughout the world. As with other tiny taxa, telling tardigrade species apart can be challenging. Confident identifications of many species depend on the presence of both adult specimens and eggs. Additionally, tardigrade taxonomy is traditionally based on a limited set of morphological traits. This has resulted in several complex species groups, comprising morphologically inseparable, but genetically distinct species.

    The claws of one of the species in the Macrobiotus hufelandi group. These species are often inseparable based on morphology, but clearly distinct species based on the COI gene.

    PHOTO CREDIT: Lasse Topstad

    DNA barcodes offer a solution to these impediments by generating unique genetic characteristics for each of these species. In recent years, there has been an increase in the use of molecular tools on tardigrades, but currently, only a small portion of the known species have barcodes deposited in public databases. Such reference sequences are essential if tardigrades are to be included in large-scale biomonitoring methods such as metabarcoding of environmental DNA (eDNA). Our study is the first to compare the applicability of eDNA-based metabarcoding of tardigrade diversity with morphologically identified communities.

    Collection of lichen samples during fieldwork in Southern Norway

    PHOTO CREDIT: Torbjørn Ekrem

    We extracted tardigrades and eggs from samples of moss, lichens, and leaf-litter and identified them using morphology. The 3,788 recorded tardigrade specimens and eggs were identified as 40 morphologically distinct species, of which 24 were successfully sequenced for the gene cytochrome c oxidase I (COI). These were represented by 151 successfully sequenced individuals. Interestingly, the barcodes revealed 32 genetically distinct linages among the 24 morpho-species, showing high levels of hidden diversity.

    Figure 1. Overlap in species recovery by the different methods.

    Next, we extracted eDNA from the same environmental samples and sequenced two fragments of the COI marker and one fragment of the 18S marker using the Illumina MiSeq next-generation sequencing platform. This method recovered 57 species of tardigrades compared to the 40 species detected by conventional methods. Mostly, the two methods identified the same species (Figure 1), yet, metabarcoding detected cryptic species elusive to morphological identification. This indicates that metabarcoding of eDNA successfully captures tardigrade diversity.

    However, the credibility of such records needs to be evaluated thoroughly. While the COI marker distinguishes well between tardigrade species, the 18S marker might not be as useful as there is not sufficient sequence variation between species (a so-called barcode gap). Furthermore, the 18S marker detected Acutuncus antarcticus in two of the samples, a species endemic to Antarctica. This species is likely not found in Norway and highlights the danger of blindly trusting marker-based identifications without carefully evaluating taxonomic assignments and possibilities of contamination.

    Our findings were dependent on our barcode reference library of locally sampled species and the use of multiple markers. As only a small portion of tardigrade species are deposited with reference sequences in public databases, both the COI and 18S markers are limited in their ability to detect species of tardigrades as most sequences will go unmatched. We demonstrate that metabarcoding is applicable for large-scale biomonitoring of tardigrades, but highlight the need for better reference libraries for tardigrade species.

    Aknowledgements:

    This research is part of a Master thesis at the NTNU University Museum and the project ‘Tardigrades in Norwegian Forests’ funded by the Norwegian Taxonomy Initiative and NorBOL. Special thanks to Roberto Guidetti at University of Modena and Reggio Emilia for his supervision during my stay in Italy.

    Written by

    Lasse Topstad

    Lasse Topstad

    Norwegian University of Science and Technology University Museum, Department of Natural History

    September 18, 2019
    https://doi.org/10.21083/ibol.v9i1.5722

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    DNA Barcoding Wild Flora in Pakistan’s Forests

    DNA Barcoding Wild Flora in Pakistan’s Forests

    DNA Barcoding Wild Flora in Pakistan’s Forests

    Preserving voucher specimens and creating a virtual herbarium to understand and protect some of the oldest living trees on the planet.
    Juniper Forest of Ziarat, Balochistan, Pakistan.
    PHOTO CREDIT: Nazeer Ahmed
    Balochistan, the largest province of Pakistan, is endowed with a variety of natural forests. Juniper (Juniperus excelsa), Pinus (Pinus gerardiana), wild Olive (Olea sp.) and mangroves are the predominant forest ecosystems of the province. The versatility of life forms in these forests support dynamic ecosystems and provide several important ‘ecosystem services’ like food, medicines, climate regulation, genetic resources, recreation facilities, etc. Biodiversity conservation, in the face of such benefits, becomes imperative. Comprehensive cataloguing of flora and fauna is, by all means, at the heart of such conservation endeavours.

    The Juniper forest of Ziarat, Balochistan, declared a UNESCO Man and Biosphere Reserve, is considered one of the world’s largest compact forests of its kind spreading over an area of 100,000 ha. Being some of the oldest living trees on earth, they are termed “Living Fossils”. The Chilgoza (Pinus gerardiana), also known as the Chilgoza Pine, on the other hand, are listed as lower risk, near threatened forest. Anthropogenic interferences have further aggravated the situation in this ecosystem and a more focused study about their current status is needed.

    Juniper Forest of Ziarat, Balochistan, Pakistan.
    PHOTO CREDIT: Nazeer Ahmed

    Fragmented studies exist attempting to document the associated flora of these forests; however, a more comprehensive approach is needed. The use of DNA barcoding techniques, duly augmented by classical taxonomy, is necessary for the creation of a reference library to inventory, assess, and describe the biodiversity of these forests. To fill this gap, a study was designed to provide a foundation for future biodiversity assessment and conservation efforts.

     

    Funded by Pakistan Agricultural Research Council and Higher Education Commission of Pakistan, our research group at the Balochistan University of Information Technology, Engineering & Management Sciences, Quetta is expecting to barcode and acquire samples of approximately 1,000 wild plant species. 

    To date, 730 samples of 525 different species have been collected and 29% (150 of 525) have been barcoded. Besides maintaining voucher specimens, a virtual herbarium will be made available to the global scientific community interested in the flora of these forest ecosystems.

    Read more about Pakistan:

    SMALL STEPS LEAD TO BIG INITIATIVES: PAKISTAN REAFFIRMS SUPPORT FOR IBOL BY LAUNCHING PAKBOL

    From economically important insect species to plants to food security, Pakistani researchers are working to barcode all life in their country through a national initiative – PakBOL.

    UNIVERSITY OF SINDH JAMSHORO BARCODES GRASSHOPPERS IN PAKISTAN’S THAR DESERT

    Tracking the shift of non-pests to crop pests, a phenomenon accelerated by anthropogenic pressures in the Thar Desert.

    Written by

    Nazeer Ahmed

    Nazeer Ahmed

    Balochistan University of Information Technology, Quetta, Pakistan

    April 7, 2019
    PDF
    https://doi.org/10.21083/ibol.v9i1.5476

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    Scat Raiders Unravel Animal-Plant Interactions in Lebanon Using DNA Barcoding Tools

    Scat Raiders Unravel Animal-Plant Interactions in Lebanon Using DNA Barcoding Tools

    Scat Raiders Unravel Animal-Plant Interactions in Lebanon Using DNA Barcoding Tools

    Using DNA dietary analysis on Eastern Mediterranean wildlife to explore the role of animals in ecological restoration processes.
    Plant collection in Ehden Nature Reserve – north Lebanon. PHOTO CREDIT: Saint Joseph University

    Lebanon is considered a hotspot for biodiversity in the Mediterranean basin likely due to its geographic position at the transition of two major landmasses (that is Eurasia and Africa). The Lebanese territory is divided between mountainous slopes with fertile valleys separating the two mountain chains that run parallel with the sea and the steppe areas in the north-east. Deep canyons and numerous rivers characterize this mountainous landscape.

    These geomorphological regions give rise to many bio-climatic zones and several habitat types that are home to more than 9,116 described species (4,486 for fauna and 4,630 for flora from which 91 are endemic). However, major taxonomic groups like insects and fungi are understudied and taxa are underrepresented within public data platforms. For example, according to the Barcode of Life Data System (BOLD), only 345 Lebanese specimens with sequences are published, forming 151 BINs and, of these records, only 108 have species names.

    In September 2018, the Faculty of Science at Saint Joseph University of Beirut joined the iBOL Consortium providing us with the opportunity to unravel Lebanese biodiversity by DNA barcoding both small and large mammals as well as the main trees and shrubs used in reforestation programs. We will also target endemic plant species.

    Animals are a crucial component for the resilience of forest ecosystems and an important factor in forest restoration projects as they promote the sustainability of reintroduced plants, as well as seed dispersal. However, we still need to identify the animals present in restored areas.

    Animal scat collection. PHOTO CREDIT: Saint Joseph University

    In addition, knowing what each animal eats and which plant seeds are being dispersed is crucial for reforestation schemes that promote wildlife and ensure ecosystem sustainability. The information needed to study the diets of animals can be found hidden in their scat which contains not only the animal’s DNA, but also what that animal has eaten. With the powerful technique of DNA metabarcoding, we now have the necessary tool to efficiently unravel the genetic information hidden in animal scat. The DNA sequences obtained from such material are identified by comparison to a reference library of animals and plants of the Eastern Mediterranean countries.

     

    Constructing the Reference Library – DNA isolation. PHOTO CREDIT: Saint Joseph University
    This reference library was prepared from leaves collected in the wild and from DNA isolated from dead animals found along roads or from private museums. Thus, we have generated sequences for 51 plants and 18 mammals. This study conducted in collaboration with the Smithsonian Conservation Biology Institute and the University of Otago is the first to employ a DNA dietary analysis on wildlife in the Eastern Mediterranean Region and explicitly considering the role of wildlife in ecological restoration processes. Our results will inform management strategies to help with the conservation efforts of these imperiled species.

    Written by

    Carole Saliba

    Carole Saliba

    Faculty of Science, Saint-Joseph University

    Liliane Boukhdoud

    Liliane Boukhdoud

    Faculty of Science, Saint-Joseph University

    Magda Bou Dagher Kharrat

    Magda Bou Dagher Kharrat

    Faculty of Science, Saint-Joseph University

    April 7, 2019
    PDF
    https://doi.org/10.21083/ibol.v9i1.5489

    Read more about Lebanon:

    HOW BIOSCAN IS INSPIRING THE NEXT GENERATION OF RESEARCHERS

    They were enlightened by the idea of discovering new species and by the possibility of doing so using DNA barcoding tools.”

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