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Wang H, Meng FM, Jin SJ, Gao JW, Tong XR, Liu ZC. A new species of medicinal leech in the genus Hirudo Linnaeus, 1758 (Hirudiniformes, Hirudinidae) from Tianjin City, China. Zookeys 2022; 1095:83-96. [PMID: 35836684 PMCID: PMC9021146 DOI: 10.3897/zookeys.1095.74071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/24/2022] [Indexed: 11/12/2022] Open
Abstract
Medicinal leeches in the genus Hirudo have been utilized for therapeutic procedures for thousands of years. To date, six known species of Hirudo are widely distributed in different regions of the Eurasian continent. In this study, a new medicinal leech species Hirudotianjinensis Liu, sp. nov. is described based upon specimens collected from Tianjin City, China. The new species can be distinguished from its congeners by a combination of characters: blackish green dorsum with five continuous yellow longitudinal stripes; six sensillae on dorsal annulus a2 of segments VIII–XXV; greyish green ventrum with irregular bilateral dark brown spots; dorsum and abdomen separated by a pair of pale yellow stripes; front half atrium wrapped by white prostate; apparent albumen gland; epididymis massive in relation to ejaculatory bulb. The phylogenetic tree based upon COI implies a sister relationship to H.nipponia Whitman, 1886. A key to the known species is provided.
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Jovanović M, Haring E, Sattmann H, Grosser C, Pesic V. DNA barcoding for species delimitation of the freshwater leech genus Glossiphonia from the Western Balkan (Hirudinea, Glossiphoniidae). Biodivers Data J 2021; 9:e66347. [PMID: 34616211 PMCID: PMC8458266 DOI: 10.3897/bdj.9.e66347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
Glossiphoniid leeches are a diverse group and sometimes abundant elements of the aquatic fauna inhabiting various types of freshwater habitats. In this study, we sampled leeches of the genus Glossiphonia from the Western Balkan in order to test the suitability of the mitochondrial cytochrome c oxidase subunit 1 (COI) marker sequence for species delimitation. Morphological analysis revealed the presence of four taxa, G.complanata with two subspecies, G.c.complanata and G.c.maculosa, the latter an endemic of Ohrid Lake, G.nebulosa and endemic G.balcanica. In total, 29 new barcodes of Glossiphonia were sequenced in the course of this study and compared with the available molecular dataset of the latter genus from GenBank/BOLD databases. The applied ASAP distance-based species delimitation method for the analysed dataset revealed an interspecific threshold between 4-8% K2P distance as suitable for species identification purposes of the Western Balkan Glossiphonia species. Our study revealed that morphologically identified taxa as G.nebulosa and G.concolor each consists of more than one clearly different phylogenetic clade. This study contributes to a better knowledge of the taxonomy of glossiphoniid leeches and emphasises future work on the revision of this genus using a standard molecular COI marker in species identification.
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Affiliation(s)
- Milica Jovanović
- Department of Biology, Faculty of Natural Science and Mathematics, University of Montenegro, Džordža Vašingtona bb, 81000, Podgorica, Montenegro Department of Biology, Faculty of Natural Science and Mathematics, University of Montenegro, Džordža Vašingtona bb, 81000 Podgorica Montenegro
| | - Elisabeth Haring
- Department of Evolutionary Biology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria Department of Evolutionary Biology, University of Vienna, Althanstraße 14, 1090 Vienna Austria.,Central Research Laboratories, Natural History Museum Vienna, Burgring 7, 1010, Vienna, Austria Central Research Laboratories, Natural History Museum Vienna, Burgring 7, 1010 Vienna Austria
| | - Helmut Sattmann
- 3rd Zoological Department, Natural History Museum Vienna, Burgring 7, Vienna, Austria 3rd Zoological Department, Natural History Museum Vienna, Burgring 7 Vienna Austria
| | - Clemens Grosser
- 4 Bernd-Blindow-Schule Leipzig, Comeniusstraße 17, 04315, Leipzig, Germany 4 Bernd-Blindow-Schule Leipzig, Comeniusstraße 17, 04315 Leipzig Germany
| | - Vladimir Pesic
- Department of Biology, Faculty of Natural Science and Mathematics, University of Montenegro, Džordža Vašingtona bb, 81000, Podgorica, Montenegro Department of Biology, Faculty of Natural Science and Mathematics, University of Montenegro, Džordža Vašingtona bb, 81000 Podgorica Montenegro
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Cryptic Clitellata: Molecular Species Delimitation of Clitellate Worms (Annelida): An Overview. DIVERSITY-BASEL 2021. [DOI: 10.3390/d13020036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Methods for species delimitation using molecular data have developed greatly and have become a staple in systematic studies of clitellate worms. Here we give a historical overview of the data and methods used to delimit clitellates from the mid-1970s to today. We also discuss the taxonomical treatment of the cryptic species, including the recommendation that cryptic species, as far as possible, should be described and named. Finally, we discuss the prospects and further development of the field.
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Draft genome of the European medicinal leech Hirudo medicinalis (Annelida, Clitellata, Hirudiniformes) with emphasis on anticoagulants. Sci Rep 2020; 10:9885. [PMID: 32555498 PMCID: PMC7303139 DOI: 10.1038/s41598-020-66749-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023] Open
Abstract
The European medicinal leech has been used for medicinal purposes for millennia, and continues to be used today in modern hospital settings. Its utility is granted by the extremely potent anticoagulation factors that the leech secretes into the incision wound during feeding and, although a handful of studies have targeted certain anticoagulants, the full range of anticoagulation factors expressed by this species remains unknown. Here, we present the first draft genome of the European medicinal leech, Hirudo medicinalis, and estimate that we have sequenced between 79–94% of the full genome. Leveraging these data, we searched for anticoagulation factors across the genome of H. medicinalis. Following orthology determination through a series of BLAST searches, as well as phylogenetic analyses, we estimate that fully 15 different known anticoagulation factors are utilized by the species, and that 17 other proteins that have been linked to antihemostasis are also present in the genome. We underscore the utility of the draft genome for comparative studies of leeches and discuss our results in an evolutionary context.
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Kaygorodova I, Bolbat N, Bolbat A. Species delimitation through DNA barcoding of freshwater leeches of theGlossiphoniagenus (Hirudinea: Glossiphoniidae) from Eastern Siberia, Russia. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12385] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Irina Kaygorodova
- Limnological Institute of Siberian Branch of Russian Academy of Sciences Irkutsk Russia
| | - Nadezhda Bolbat
- Limnological Institute of Siberian Branch of Russian Academy of Sciences Irkutsk Russia
- Department of Plant Physiology, Cell Biology and Genetics Irkutsk State University Irkutsk Russia
| | - Alexander Bolbat
- Limnological Institute of Siberian Branch of Russian Academy of Sciences Irkutsk Russia
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Guggolz T, Meißner K, Schwentner M, Dahlgren TG, Wiklund H, Bonifácio P, Brandt A. High diversity and pan-oceanic distribution of deep-sea polychaetes: Prionospio and Aurospio (Annelida: Spionidae) in the Atlantic and Pacific Ocean. ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-020-00430-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractPrionospio Malmgren 1867 and Aurospio Maciolek 1981 (Annelida: Spionidae) are polychaete genera commonly found in the deep sea. Both genera belong to the Prionospio complex, whose members are known to have limited distinguishing characters. Morphological identification of specimens from the deep sea is challenging, as fragmentation and other damages are common during sampling. These issues impede investigations into the distribution patterns of these genera in the deep sea. In this study, we employ two molecular markers (16S rRNA and 18S) to study the diversity and the distribution patterns of Prionospio and Aurospio from the tropical North Atlantic, the Puerto Rico Trench and the central Pacific. Based on different molecular analyses (Automated Barcode Gap Discovery, GMYC, pairwise genetic distances, phylogenetics, haplotype networks), we were able to identify and differentiate 21 lineages (three lineages composed solely of GenBank entries) that represent putative species. Seven of these lineages exhibited pan-oceanic distributions (occurring in the Atlantic as well as the Pacific) in some cases even sharing identical 16S rRNA haplotypes in both oceans. Even the lineages found to be restricted to one of the oceans were distributed over large regional scales as for example across the Mid-Atlantic Ridge from the Caribbean to the eastern Atlantic (> 3389 km). Our results suggest that members of Prionospio and Aurospio may have the potential to disperse across large geographic distances, largely unaffected by topographic barriers and possibly even between oceans. Their high dispersal capacities are probably explained by their free-swimming long-lived planktonic larvae.
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Jiménez-Armenta J, Oceguera-Figueroa A. Leeches from Mexico City, remnants of the ancient lake. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:632-642. [PMID: 31072187 DOI: 10.1080/24701394.2019.1606217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Genetic barcodes (partial sequences of the mitochondrial cytochrome c oxidase subunit I) were generated for freshwater leeches that inhabit the Mexico Basin, upon which Mexico City and its metropolitan area have developed. Once a continuous lake, the basin has passed through continuous events of artificial desiccation in the last 500 years so that it is currently conformed by a few and highly modified and polluted isolated freshwater bodies. Six species of leeches from three families were collected in five localities. Current sequence databases were able to determine five of the six species collected for this study with the only exception of Haemopis caballeroi, for which no sequence data are available in public repositories. Taxonomic assignment of cocoons was possible via comparison of barcode sequences. We discuss the presence of a population of Erpobdella ochoterenai in Tecocomulco Lake that bares high genetic divergence from its conspecifics, which may indicate it is an undescribed species.
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Affiliation(s)
- J Jiménez-Armenta
- a Departamento de Zoología, Instituto de Biología , Universidad Nacional Autónoma de México , Mexico City , Mexico.,b Posgrado en Ciencias Biológicas , Universidad Nacional Autónoma de México, Avenida Universidad, Ciudad Universitaria , Coyoacán , México
| | - A Oceguera-Figueroa
- a Departamento de Zoología, Instituto de Biología , Universidad Nacional Autónoma de México , Mexico City , Mexico
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Young MK, Smith RJ, Pilgrim KL, Fairchild MP, Schwartz MK. Integrative taxonomy refutes a species hypothesis: The asymmetric hybrid origin of Arsapnia arapahoe (Plecoptera, Capniidae). Ecol Evol 2019; 9:1364-1377. [PMID: 30805166 PMCID: PMC6374720 DOI: 10.1002/ece3.4852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/02/2018] [Accepted: 11/29/2018] [Indexed: 11/23/2022] Open
Abstract
Molecular tools are commonly directed at refining taxonomies and the species that constitute their fundamental units. This has been especially insightful for groups for which species hypotheses are ambiguous and have largely been based on morphological differences between certain life stages or sexes, and has added importance when taxa are a focus of conservation efforts. Here, we examine the taxonomic status of Arsapnia arapahoe, a winter stonefly in the family Capniidae that is a species of conservation concern because of its limited abundance and restricted range in northern Colorado, USA. Phylogenetic analyses of sequences of mitochondrial and nuclear genes of this and other capniid stoneflies from this region and elsewhere in western North America indicated extensive haplotype sharing, limited genetic differences, and a lack of reciprocal monophyly between A. arapahoe and the sympatric A. decepta, despite distinctive and consistent morphological differences in the sexual apparatus of males of both species. Analyses of autosomal and sex-linked single nucleotide polymorphisms detected using genotyping by sequencing indicated that all individuals of A. arapahoe consisted of F1 hybrids between female A. decepta and males of another sympatric stonefly, Capnia gracilaria. Rather than constitute a self-sustaining evolutionary lineage, A. arapahoe appears to represent the product of nonintrogressive hybridization in the limited area of syntopy between two widely distributed taxa. This offers a cautionary tale for taxonomists and conservation biologists working on the less-studied components of the global fauna.
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Affiliation(s)
- Michael K. Young
- U.S. Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontana
| | - Rebecca J. Smith
- U.S. Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontana
| | - Kristine L. Pilgrim
- U.S. Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontana
| | | | - Michael K. Schwartz
- U.S. Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontana
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9
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Kambestad M, Kirkendall LR, Knutsen IL, Jordal BH. Cryptic and pseudo-cryptic diversity in the world’s most common bark beetle—Hypothenemus eruditus. ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-017-0334-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Schäffer S, Zachos FE, Koblmüller S. Opening the treasure chest: A DNA-barcoding primer set for most higher taxa of Central European birds and mammals from museum collections. PLoS One 2017; 12:e0174449. [PMID: 28358863 PMCID: PMC5373577 DOI: 10.1371/journal.pone.0174449] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/09/2017] [Indexed: 11/19/2022] Open
Abstract
DNA-barcoding is a rapidly developing method for efficiently identifying samples to species level by means of short standard DNA sequences. However, reliable species assignment requires the availability of a comprehensive DNA barcode reference library, and hence numerous initiatives aim at generating such barcode databases for particular taxa or geographic regions. Historical museum collections represent a potentially invaluable source for the DNA-barcoding of many taxa. This is particularly true for birds and mammals, for which collecting fresh (voucher) material is often very difficult to (nearly) impossible due to the special animal welfare and conservation regulations that apply to vertebrates in general, and birds and mammals in particular. Moreover, even great efforts might not guarantee sufficiently complete sampling of fresh material in a short period of time. DNA extracted from historical samples is usually degraded, such that only short fragments can be amplified, rendering the recovery of the barcoding region as a single fragment impossible. Here, we present a new set of primers that allows the efficient amplification and sequencing of the entire barcoding region in most higher taxa of Central European birds and mammals in six overlapping fragments, thus greatly increasing the value of historical museum collections for generating DNA barcode reference libraries. Applying our new primer set in recently established NGS protocols promises to further increase the efficiency of barcoding old bird and mammal specimens.
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Affiliation(s)
- Sylvia Schäffer
- Institute of Zoology, University of Graz, Universitätsplatz 2, Graz, Austria
| | | | - Stephan Koblmüller
- Institute of Zoology, University of Graz, Universitätsplatz 2, Graz, Austria
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11
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Sundberg P, Kvist S, Strand M. Evaluating the Utility of Single-Locus DNA Barcoding for the Identification of Ribbon Worms (Phylum Nemertea). PLoS One 2016; 11:e0155541. [PMID: 27171471 PMCID: PMC4865114 DOI: 10.1371/journal.pone.0155541] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 04/29/2016] [Indexed: 11/22/2022] Open
Abstract
Whereas many nemerteans (ribbon worms; phylum Nemertea) can be identified from external characters if observed alive, many are still problematic. When it comes to preserved specimens (as in e.g. marine inventories), there is a particular need for specimen identifier alternatives. Here, we evaluate the utility of COI (cytochrome c oxidase subunit I) as a single-locus barcoding gene. We sequenced, data mined, and compared gene fragments of COI for 915 individuals representing 161 unique taxonomic labels for 71 genera, and subjected different constellations of these to both distance-based and character-based DNA barcoding approaches, as well as species delimitation analyses. We searched for the presence or absence of a barcoding gap at different taxonomic levels (phylum, subclass, family and genus) in an attempt to understand at what level a putative barcoding gap presents itself. This was performed both using the taxonomic labels as species predictors and using objectively inferred species boundaries recovered from our species delimitation analyses. Our data suggest that COI works as a species identifier for most groups within the phylum, but also that COI data are obscured by misidentifications in sequence databases. Further, our results suggest that the number of predicted species within the dataset is (in some cases substantially) higher than the number of unique taxonomic labels-this highlights the presence of several cryptic lineages within well-established taxa and underscores the urgency of an updated taxonomic backbone for the phylum.
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Affiliation(s)
- Per Sundberg
- Department of Marine Science, University of Gothenburg, Box 463, SE-405 30, Gothenburg, Sweden
| | - Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, ON, M5S 2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 2B4, Canada
| | - Malin Strand
- Swedish Species Information Center, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
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12
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Prosser SWJ, deWaard JR, Miller SE, Hebert PDN. DNA barcodes from century-old type specimens using next-generation sequencing. Mol Ecol Resour 2015; 16:487-97. [PMID: 26426290 DOI: 10.1111/1755-0998.12474] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 09/14/2015] [Accepted: 09/25/2015] [Indexed: 02/05/2023]
Abstract
Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are often more than a century old and have experienced conditions unfavourable for DNA preservation, success in sequence recovery has been uncertain. This study addresses this challenge by employing next-generation sequencing (NGS) to recover sequences for the barcode region of the cytochrome c oxidase 1 gene from small amounts of template DNA. DNA quality was first screened in more than 1800 century-old type specimens of Lepidoptera by attempting to recover 164-bp and 94-bp reads via Sanger sequencing. This analysis permitted the assignment of each specimen to one of three DNA quality categories--high (164-bp sequence), medium (94-bp sequence) or low (no sequence). Ten specimens from each category were subsequently analysed via a PCR-based NGS protocol requiring very little template DNA. It recovered sequence information from all specimens with average read lengths ranging from 458 bp to 610 bp for the three DNA categories. By sequencing ten specimens in each NGS run, costs were similar to Sanger analysis. Future increases in the number of specimens processed in each run promise substantial reductions in cost, making it possible to anticipate a future where barcode sequences are available from most type specimens.
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Affiliation(s)
- Sean W J Prosser
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
| | - Jeremy R deWaard
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
| | - Scott E Miller
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Paul D N Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
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13
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Shokralla S, Porter TM, Gibson JF, Dobosz R, Janzen DH, Hallwachs W, Golding GB, Hajibabaei M. Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Sci Rep 2015; 5:9687. [PMID: 25884109 PMCID: PMC4401116 DOI: 10.1038/srep09687] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/16/2015] [Indexed: 01/26/2023] Open
Abstract
Genetic information is a valuable component of biosystematics, especially specimen identification through the use of species-specific DNA barcodes. Although many genomics applications have shifted to High-Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies, sample identification (e.g., via DNA barcoding) is still most often done with Sanger sequencing. Here, we present a scalable double dual-indexing approach using an Illumina Miseq platform to sequence DNA barcode markers. We achieved 97.3% success by using half of an Illumina Miseq flowcell to obtain 658 base pairs of the cytochrome c oxidase I DNA barcode in 1,010 specimens from eleven orders of arthropods. Our approach recovers a greater proportion of DNA barcode sequences from individuals than does conventional Sanger sequencing, while at the same time reducing both per specimen costs and labor time by nearly 80%. In addition, the use of HTS allows the recovery of multiple sequences per specimen, for deeper analysis of genetic variation in target gene regions.
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Affiliation(s)
- Shadi Shokralla
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
| | - Teresita M Porter
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1
| | - Joel F Gibson
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
| | - Rafal Dobosz
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
| | - Daniel H Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA 19104
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA 19104
| | - G Brian Golding
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1
| | - Mehrdad Hajibabaei
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
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14
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Lago-Barcia D, Fernández-Álvarez FA, Negrete L, Brusa F, Damborenea C, Grande C, Noreña C. Morphology and DNA barcodes reveal the presence of the non-native land planarian Obama marmorata (Platyhelminthes : Geoplanidae) in Europe. INVERTEBR SYST 2015. [DOI: 10.1071/is14033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We report for the first time the occurrence of Obama marmorata in the Iberian Peninsula as an introduced species from the Neotropical Region. The species is also reported for the first time in Argentina. The identification was made on the basis of morphological evidence. The divergence levels of a fragment of the mitochondrial cytochromec oxidaseI gene from Argentinean and Iberian samples were studied. The morphology of samples from the two regions was the same and matched the original description of the species. A DNA barcoding matrix was constructed using new sequences from O. marmorata and sequences of related species taken from GenBank. Among the Geoplanidae, interspecific divergence ranged between 3.3 and 14.4%, while intraspecific divergence percentages were 0–1.2%, signalling the presence of a DNA barcoding gap. All O. marmorata sequences, irrespective of their geographic origin, form a well supported clade with an intraspecific divergence of 0–0.9 (average = 0.4%). These results indicate the utility of DNA barcoding to discover allochthonous species in this group of organisms.
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15
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Abstract
Accurate identification of unknown specimens by means of DNA barcoding is contingent on the presence of a DNA barcoding gap, among other factors, as its absence may result in dubious specimen identifications - false negatives or positives. Whereas the utility of DNA barcoding would be greatly reduced in the absence of a distinct and sufficiently sized barcoding gap, the limits of intraspecific and interspecific distances are seldom thoroughly inspected across comprehensive sampling. The present study aims to illuminate this aspect of barcoding in a comprehensive manner for the animal phylum Annelida. All cytochrome c oxidase subunit I sequences (cox1 gene; the chosen region for zoological DNA barcoding) present in GenBank for Annelida, as well as for "Polychaeta", "Oligochaeta", and Hirudinea separately, were downloaded and curated for length, coverage and potential contaminations. The final datasets consisted of 9782 (Annelida), 5545 ("Polychaeta"), 3639 ("Oligochaeta"), and 598 (Hirudinea) cox1 sequences and these were either (i) used as is in an automated global barcoding gap detection analysis or (ii) further analyzed for genetic distances, separated into bins containing intraspecific and interspecific comparisons and plotted in a graph to visualize any potential global barcoding gap. Over 70 million pairwise genetic comparisons were made and results suggest that although there is a tendency towards separation, no distinct or sufficiently sized global barcoding gap exists in either of the datasets rendering future barcoding efforts at risk of erroneous specimen identifications (but local barcoding gaps may still exist allowing for the identification of specimens at lower taxonomic ranks). This seems to be especially true for earthworm taxa, which account for fully 35% of the total number of interspecific comparisons that show 0% divergence.
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Affiliation(s)
- Sebastian Kvist
- a Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University , Cambridge , MA , USA
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16
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Kutschera U, Elliott J. The European medicinal leech Hirudo medicinalis L.: Morphology and occurrence of an endangered species. ZOOSYST EVOL 2014. [DOI: 10.3897/zse.90.8715] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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17
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Status and prospects of DNA barcoding in medically important parasites and vectors. Trends Parasitol 2014; 30:582-91. [PMID: 25447202 DOI: 10.1016/j.pt.2014.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 11/23/2022]
Abstract
For over 10 years, DNA barcoding has been used to identify specimens and discern species. Its potential benefits in parasitology were recognized early, but its utility and uptake remain unclear. Here we review studies using DNA barcoding in parasites and vectors affecting humans and find that the technique is accurate (accords with author identifications based on morphology or other markers) in 94-95% of cases, although aspects of DNA barcoding (vouchering, marker implicated) have often been misunderstood. In a newly compiled checklist of parasites, vectors, and hazards, barcodes are available for 43% of all 1403 species and for more than half of 429 species of greater medical importance. This is encouraging coverage that would improve with an active campaign targeting parasites and vectors.
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18
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Kvist S, Laumer CE, Junoy J, Giribet G. New insights into the phylogeny, systematics and DNA barcoding of Nemertea. INVERTEBR SYST 2014. [DOI: 10.1071/is13061] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Although some clades of ribbon worms (phylum Nemertea) are consistently recovered with high support in molecular phylogenies, the placement and inter-relationships of some taxa have proven problematic. Herein, we performed molecular phylogenetic analyses aimed at resolving these recalcitrant splits, using six loci (nuclear 18S rRNA, 28S rRNA, histones H3 and H4, and mitochondrial 16S rRNA and COI) for 133 terminals, with particular emphasis on the problematic families Hubrechtidae and Plectonemertidae. Three different datasets were used for phylogenetic analyses and both maximum likelihood and maximum parsimony methodologies were applied. All but one of the resulting tree topologies agree on the paraphyly of the class Palaeonemertea, whereas Heteronemertea, Hoplonemertea, Polystilifera, Monostilifera and Hubrechtidae are always recovered as reciprocally monophyletic. Hubrechtidae is sister group to Heteronemertea (the Pilidiophora hypothesis) only when length variable regions of 18S rRNA and 28S rRNA are excluded. Moreover, the terrestrial and freshwater family Plectonemertidae is recovered with high support and the implications of this finding are further discussed. Finally, we evaluate the utility of DNA barcoding for specimen identification within Nemertea using an extended dataset containing 394 COI sequences. Results suggest that DNA barcoding may work for Nemertea, insofar as a distinct barcoding gap (the gap between the maximum intraspecific variation and the minimum interspecific divergence) may exist, but its recognition is regularly hampered by low accuracy in species level identifications.
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Kvist S. Barcoding in the dark?: A critical view of the sufficiency of zoological DNA barcoding databases and a plea for broader integration of taxonomic knowledge. Mol Phylogenet Evol 2013; 69:39-45. [DOI: 10.1016/j.ympev.2013.05.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 12/16/2022]
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Young MK, McKelvey KS, Pilgrim KL, Schwartz MK. DNA
barcoding at riverscape scales: assessing biodiversity among fishes of the genus
C
ottus
(
T
eleostei) in northern
R
ocky
M
ountain streams. Mol Ecol Resour 2013; 13:583-95. [DOI: 10.1111/1755-0998.12091] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 01/24/2013] [Accepted: 02/06/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Michael K. Young
- U.S. Forest Service Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
| | - Kevin S. McKelvey
- U.S. Forest Service Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
| | - Kristine L. Pilgrim
- U.S. Forest Service Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
| | - Michael K. Schwartz
- U.S. Forest Service Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
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Trontelj P, Utevsky SY. Phylogeny and phylogeography of medicinal leeches (genus Hirudo): Fast dispersal and shallow genetic structure. Mol Phylogenet Evol 2012; 63:475-85. [DOI: 10.1016/j.ympev.2012.01.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 01/10/2012] [Accepted: 01/28/2012] [Indexed: 10/14/2022]
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Siddall ME, Kvist S, Phillips A, Oceguera-Figuero A. DNA barcoding of parasitic nematodes: is it kosher? J Parasitol 2012; 98:692-4. [PMID: 22300283 DOI: 10.1645/ge-2994.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Nematode parasites were encountered in kosher-certified fish meat and roe, and the question was raised as to whether or not these food products were kosher as concerns food preparation standards-a matter that pertains to the identity and, by extension, the life cycle of the parasites. To ascertain the identities of parasitic nematodes, given the distorted or damaged nature of the specimens, molecular techniques were applied in the form of DNA barcoding. To our knowledge, this is the first application of this technique to an obviously cultural concern as opposed to one of health or economic significance. Results, based both on cytochrome c oxidase subunits I and II, suggested that the parasite species found in the fish products are anisakine species that do not inhabit the intestinal lumen of the fish hosts examined. Thus, there was no evidence of failure to adhere to food preparation practices consistent with the proscriptions of Orthodox Judaism. Notwithstanding the success of DNA barcoding in determining at least the higher taxonomic identities of the parasites, some shortcomings of the DNA barcoding pipeline as it pertains to nematode parasites were encountered; specifically, the paucity of data available for the DNA barcoding locus, even for very common nematode taxa.
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Affiliation(s)
- Mark E Siddall
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA.
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