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Phylogenetic Diversity of the Red Swamp Crayfish Procambarus clarkii and Its Dispersal Pattern in Northern and Central Italy. BIOLOGY 2023; 12:biology12020313. [PMID: 36829588 PMCID: PMC9953125 DOI: 10.3390/biology12020313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/05/2023] [Accepted: 02/11/2023] [Indexed: 02/17/2023]
Abstract
The red swamp crayfish Procambarus clarkii is one of the most threatening freshwater species in the world. The aim of this study is to provide a better understanding of the phylogeography and the invasion routes of P. clarkii populations in the Italian Peninsula through the analysis of mitochondrial phylogeny. Mitochondrial control region and cytochrome c oxidase subunit I (COI) sequences of 153 samples collected from six Italian basins were analyzed and compared to worldwide data. Except for the lakes Bolsena and Posta Fibreno, a high genetic variability was found in the other basins. The mitochondrial DNA pattern of P. clarkii from the lakes Candia and Massaciuccoli confirmed the hypothesis of double introduction events. Another entry point could be represented by Lake Trasimeno, which shows haplotypes originating from Louisiana and not shared with other Italian basins. Moreover, unique lineages were also found in the Stella River, thus enhancing the hypothesis that multiple introductions of P. clarkii occurred in northern and Central Italy and strengthening the idea that knowledge about the dispersion routes of this alien species can be useful to predict its invasiveness and elaborate control strategies to preserve biodiversity.
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Park E, Poulin R. Extremely divergent COI sequences within an amphipod species complex: A possible role for endosymbionts? Ecol Evol 2022; 12:e9448. [PMID: 36311398 PMCID: PMC9609454 DOI: 10.1002/ece3.9448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
Some heritable endosymbionts can affect host mtDNA evolution in various ways. Amphipods host diverse endosymbionts, but whether their mtDNA has been influenced by these endosymbionts has yet to be considered. Here, we investigated the role of endosymbionts (microsporidians and Rickettsia) in explaining highly divergent COI sequences in Paracalliope fluviatilis species complex, the most common freshwater amphipods in New Zealand. We first contrasted phylogeographic patterns using COI, ITS, and 28S sequences. While molecular species delimitation methods based on 28S sequences supported 3-4 potential species (N, C, SA, and SB) among freshwater lineages, COI sequences supported 17-27 putative species reflecting high inter-population divergence. The deep divergence between NC and S lineages (~20%; 28S) and the substitution saturation on the 3rd codon position of COI detected even within one lineage (SA) indicate a very high level of morphological stasis. Interestingly, individuals infected and uninfected by Rickettsia comprised divergent COI lineages in one of four populations tested, suggesting a potential influence of endosymbionts in mtDNA patterns. We propose several plausible explanations for divergent COI lineages, although they would need further testing with multiple lines of evidence. Lastly, due to common morphological stasis and the presence of endosymbionts, phylogeographic patterns of amphipods based on mtDNA should be interpreted with caution.
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Affiliation(s)
- Eunji Park
- Department of ZoologyUniversity of OtagoDunedinNew Zealand,Department of BotanyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Robert Poulin
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
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de Gier W, Groenhof M, Fransen CH. Coming out of your shell or crawling back in: multiple interphylum host switching events within a clade of bivalve- and ascidian-associated shrimps (Caridea: Palaemonidae). CONTRIBUTIONS TO ZOOLOGY 2022. [DOI: 10.1163/18759866-bja10030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Marine symbiotic Palaemonidae, comprising over 600 species, live in association with marine invertebrates of different phyla, like Cnidaria, Echinodermata, Mollusca, Porifera, and Tunicata. A phylogenetic study is performed on a clade of bivalve- and ascidian-associated endosymbiotic shrimp species (Caridea: Palaemonidae), using morphological and molecular data. A Total Evidence approach is used in order to include all currently known ingroup species in an evolutionary framework. Ancestral state reconstruction analyses are performed to identify host-switching events and ancestral ranges. The clade, including Ascidonia, Conchodytes, Dactylonia, Odontonia, and Pontonia, and various smaller genera, is recovered as monophyletic, with an ascidian-associated ancestral host state. At least six interphylum host switches are tentatively identified, with members of Odontonia and Notopontonia switching back to an ascidian host affiliation after the ancestral host switch of the clade including Conchodytes, Odontonia and related genera, from an ascidian- to a bivalve host. The clade including Ascidonia and Pontonia was recovered to have an ancestor with an East Pacific/Atlantic distribution. The other studied genera remained in the original ancestral Indo-West Pacific range. We hypothesize that similar internal environments of shrimp hosts from different phyla will function as hot spots for interphylum host switching in various lineages of symbionts.
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Affiliation(s)
- Werner de Gier
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands,
| | - Mike Groenhof
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300, RA Leiden, The Netherlands
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Pereira RIDS, Maciel CR, Iketani G. Molecular features of Probopyrus sp. (Isopoda: Bopyridae) from Brazilian Amazonia and the parasitism of inland populations of Macrobrachium amazonicum (Decapoda: Palaemonidae). Parasitology 2022; 149:203-208. [PMID: 35234597 PMCID: PMC11010464 DOI: 10.1017/s0031182021001657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/09/2021] [Accepted: 09/17/2021] [Indexed: 11/06/2022]
Abstract
Bopyrid isopods of the genus Probopyrus are well-known parasites of freshwater prawns of the genus Macrobrachium. The parasitism of coastal populations of Macrobrachium amazonicum by Probopyrus bithynis, for example, has been documented since the late 1980s. Despite this, molecular data on different populations are not available for any Probopyrus species. The present study is the first to describe Probopyrus populations from distinct regions of the Amazon basin based on sequences of two genes, the mitochondrial cytochrome oxidase C subunit I (COI) and the nuclear 18S ribosomal DNA (18S rDNA) gene. The analyses indicated the presence of two Probopyrus species, each parasitizing either the coastal or the inland populations of M. amazonicum. The results indicated the potential use of the COI barcode for the identification of Probopyrus species. We discuss the potential implications of the findings for the taxonomy of Probopyrus bithynis and other species of the genus Probopyrus.
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Affiliation(s)
- Rosa Ilana dos Santos Pereira
- Laboratório de Educação e Evolução Prof. Horacio Schneider, Instituto de Ciências da Educação, Universidade Federal do Oeste do Pará – UFOPA, Av. Marechal Rondon, S/N, CEP 68040-070, Santarém, PA, Brasil
| | - Cristiana Ramalho Maciel
- Laboratório de Aqüicultura, Instituto de Estudos Costeiros – IECOS, Universidade Federal do Pará – UFPA, Campus de Bragança, Alameda Leandro Ribeiro, S/N, Aldeia, CEP 68600-000, Bragança, PA, Brasil
| | - Gabriel Iketani
- Laboratório de Educação e Evolução Prof. Horacio Schneider, Instituto de Ciências da Educação, Universidade Federal do Oeste do Pará – UFOPA, Av. Marechal Rondon, S/N, CEP 68040-070, Santarém, PA, Brasil
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DNA barcoding allows identification of undescribed crab megalopas from the open sea. Sci Rep 2021; 11:20573. [PMID: 34663862 PMCID: PMC8523566 DOI: 10.1038/s41598-021-99486-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/12/2021] [Indexed: 11/13/2022] Open
Abstract
Megalopas of 15 brachyuran crab species collected in the open sea plankton, and unknown until now, were identified using DNA barcodes (COI and 16S rRNA). Specimens belonging to the families Portunidae, Pseudorhombilidae and Xanthidae (Crustacea, Decapoda, Brachyura), and corresponding to the species Achelous floridanus, Arenaeus mexicanus, Callinectes amnicola, C. arcuatus, C. ornatus, C. toxones, Charybdis (Charybdis) hellerii, Portunus hastatus, Thalamita admete, Scopolius nuttingi, Etisus odhneri, Liomera cinctimanus, Neoliomera cerasinus, Pseudoliomera variolosa, and Williamstimpsonia stimpsoni, are described and illustrated, and compared with other congeneric species previously described. We also provide a new geographical record for N. cerasinus and the most remarkable features for each species.
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A multiplex real-time PCR screening assay for routine species identification of four commercially relevant crustaceans. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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8
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Ramirez JL, Rosas-Puchuri U, Cañedo RM, Alfaro-Shigueto J, Ayon P, Zelada-Mázmela E, Siccha-Ramirez R, Velez-Zuazo X. DNA barcoding in the Southeast Pacific marine realm: Low coverage and geographic representation despite high diversity. PLoS One 2020; 15:e0244323. [PMID: 33370342 PMCID: PMC7769448 DOI: 10.1371/journal.pone.0244323] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/07/2020] [Indexed: 11/25/2022] Open
Abstract
The Southeast Pacific comprises two Large Marine Ecosystems, the Pacific Central-American Coastal and the Humboldt Current System; and is one of the less well known in the tropical subregions in terms of biodiversity. To address this, we compared DNA barcoding repositories with the marine biodiversity species for the Southeast Pacific. We obtained a checklist of marine species in the Southeast Pacific (i.e. Colombia, Ecuador, Chile, and Peru) from the Ocean Biodiversity Information System (OBIS) database and compared it with species available at the Barcoding of Life Data System (BOLD) repository. Of the 5504 species records retrieved from OBIS, 42% of them had at least one registered specimen in BOLD (including specimens around the world); however, only 4.5% of records corresponded to publicly available DNA barcodes including specimens collected from a Southeast Pacific country. The low representation of barcoded species does not vary much across the different taxonomic groups or within countries, but we observed an asymmetric distribution of DNA barcoding records for taxonomic groups along the coast, being more abundant for the Humboldt Current System than the Pacific Central-American Coastal. We observed high-level of barcode records with Barcode Index Number (BIN) incongruences, particularly for fishes (Actinopterygii = 30.27% and Elasmobranchii = 24.71%), reflecting taxonomic uncertainties for fishes, whereas for Invertebrates and Mammalia more than 85% of records were classified as data deficient or inadequate procedure for DNA barcoding. DNA barcoding is a powerful tool to study biodiversity, with a great potential to increase the knowledge of the Southeast Pacific marine biodiversity. Our results highlight the critical need for increasing taxonomic sampling effort, the number of trained taxonomic specialists, laboratory facilities, scientific collections, and genetic reference libraries.
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Affiliation(s)
- Jorge L. Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
- * E-mail:
| | - Ulises Rosas-Puchuri
- National Zoological Park, Smithsonian Conservation Biology Institute, Center for Conservation and Sustainability, Washington, DC, United States of America
- Department of Biological Sciences, George Washington University, Washington, DC, United States of America
| | - Rosa Maria Cañedo
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Joanna Alfaro-Shigueto
- Facultad de Biología Marina, Universidad Científica del Sur, Lima, Perú
- ProDelphinus, Lima, Perú
| | | | - Eliana Zelada-Mázmela
- Facultad de Ciencias, Laboratorio de Genética, Fisiología y Reproducción, Universidad Nacional del Santa, Chimbote, Peru
| | | | - Ximena Velez-Zuazo
- National Zoological Park, Smithsonian Conservation Biology Institute, Center for Conservation and Sustainability, Washington, DC, United States of America
- Asociación Peruana para la Conservación de la Naturaleza, Lima, Peru
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Taylor CL, Barker NP, Barber-James HM, Villet MH, Pereira-da-Conceicoa LL. Habitat requirements affect genetic variation in three species of mayfly (Ephemeroptera, Baetidae) from South Africa. Zookeys 2020; 936:1-24. [PMID: 32547291 PMCID: PMC7272479 DOI: 10.3897/zookeys.936.38587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022] Open
Abstract
This study investigates genetic diversity in three species of Ephemeroptera, one eurytopic and therefore widespread (Afroptilumsudafricanum) and two stenotopic and thus endemic (Demoreptusnatalensis and Demoreptuscapensis) species, all of which co-occur in the southern Great Escarpment, South Africa. Mitochondrial DNA was analysed to compare the genetic diversity between the habitat generalist and the two habitat specialists. Afroptilumsudafricanum showed no indication of population genetic structure due to geographic location, while both Demoreptus species revealed clear genetic differentiation between geographic localities and catchments, evident from phylogenetic analyses and high FST values from AMOVA. In addition, the phylogenetic analyses indicate some deeper haplotype divergences within A.sudafricanum and Demoreptus that merit taxonomic attention. These results give important insight into evolutionary processes occurring through habitat specialisation and population isolation. Further research and sampling across a wider geographic setting that includes both major mountain blocks of the Escarpment and lowland non-Escarpment sites will allow for refined understanding of biodiversity and associated habitat preferences, and illuminate comparative inferences into gene flow and cryptic speciation.
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Affiliation(s)
- Chantal L Taylor
- Department of Zoology and Entomology, Rhodes University, Somerset Street, Makhanda (Grahamstown), 6140, South Africa
| | - Nigel P Barker
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, 0028, South Africa
| | - Helen M Barber-James
- Department of Zoology and Entomology, Rhodes University, Somerset Street, Makhanda (Grahamstown), 6140, South Africa.,Department of Freshwater Invertebrates, Albany Museum, Somerset Street, Makhanda (Grahamstown), 6140, South Africa
| | - Martin H Villet
- Department of Zoology and Entomology, Rhodes University, Somerset Street, Makhanda (Grahamstown), 6140, South Africa
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Venera-Pontón DE, Driskell AC, De Grave S, Felder DL, Scioli JA, Collin R. Documenting decapod biodiversity in the Caribbean from DNA barcodes generated during field training in taxonomy. Biodivers Data J 2020; 8:e47333. [PMID: 31966024 PMCID: PMC6960234 DOI: 10.3897/bdj.8.e47333] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/28/2019] [Indexed: 11/15/2022] Open
Abstract
DNA barcoding is a useful tool to identify the components of mixed or bulk samples, as well as to determine individuals that lack morphologically diagnostic features. However, the reference database of DNA barcode sequences is particularly sparsely populated for marine invertebrates and for tropical taxa. We used samples collected as part of two field courses, focused on graduate training in taxonomy and systematics, to generate DNA sequences of the barcode fragments of cytochrome c oxidase subunit I (COI) and mitochondrial ribosomal 16S genes for 447 individuals, representing at least 129 morphospecies of decapod crustaceans. COI sequences for 36% (51/140) of the species and 16S sequences for 26% (37/140) of the species were new to GenBank. Automatic Barcode Gap Discovery identified 140 operational taxonomic units (OTUs) which largely coincided with the morphospecies delimitations. Barcode identifications (i.e. matches to identified sequences) were especially useful for OTUs within Synalpheus, a group that is notoriously difficult to identify and rife with cryptic species, a number of which we could not identify to species, based on morphology. Non-concordance between morphospecies and barcode OTUs also occurred in a few cases of suspected cryptic species. As mitochondrial pseudogenes are particularly common in decapods, we investigate the potential for this dataset to include pseudogenes and discuss the utility of these sequences as species identifiers (i.e. barcodes). These results demonstrate that material collected and identified during training activities can provide useful incidental barcode reference samples for under-studied taxa.
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Affiliation(s)
- Dagoberto E. Venera-Pontón
- Smithsonian Tropical Research Institute, Balboa, PanamaSmithsonian Tropical Research InstituteBalboaPanama
- University of Louisiana at Lafayette, Lafayette, United States of AmericaUniversity of Louisiana at LafayetteLafayetteUnited States of America
| | - Amy C. Driskell
- Laboratories of Analytical Biology, Department of Invertebrate Zoology, Smithsonian Institution, Washington, D.C., United States of AmericaLaboratories of Analytical Biology, Department of Invertebrate Zoology, Smithsonian InstitutionWashington, D.C.United States of America
| | - Sammy De Grave
- Oxford University Museum of Natural History, Oxford, United KingdomOxford University Museum of Natural HistoryOxfordUnited Kingdom
| | - Darryl L. Felder
- University of Louisiana at Lafayette, Lafayette, United States of AmericaUniversity of Louisiana at LafayetteLafayetteUnited States of America
| | - Justin A. Scioli
- University of Louisiana at Lafayette, Lafayette, United States of AmericaUniversity of Louisiana at LafayetteLafayetteUnited States of America
| | - Rachel Collin
- Smithsonian Tropical Research Institute, Balboa, PanamaSmithsonian Tropical Research InstituteBalboaPanama
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11
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Shum P, Barney BT, O'Leary JK, Palumbi SR. Cobble community DNA as a tool to monitor patterns of biodiversity within kelp forest ecosystems. Mol Ecol Resour 2019; 19:1470-1485. [PMID: 31436907 DOI: 10.1111/1755-0998.13067] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 07/05/2019] [Accepted: 07/17/2019] [Indexed: 01/04/2023]
Abstract
Kelp forest ecosystems dominate 150,000 km of global temperate coastline, rivalling the coastal occurrence of coral reefs. Despite the astounding biological diversity and productive ecological communities associated with kelp forests, patterns of species richness and composition are difficult to monitor and compare. Crustose coralline algae are a critically important substrate for propagule settlement for a range of kelp forest species. Coralline-covered cobbles are home to hundreds of species of benthic animals and algae and form a replicable unit for ecological assays. Here, we use DNA metabarcoding of bulk DNA extracts sampled from cobbles to explore patterns of species diversity in kelp forests of the central California coast. The data from 97 cobbles within kelp forest ecosystems at three sites in Central California show the presence of 752 molecular operational taxonomic units (MOTUs) and 53 MOTUs assigned up to the species level with >95% similarity to current databases. We are able to detect spatial patterns of important management targets such as abalone recruits, and localized abundance of sea stars in 2012. Comparison of classic ecological surveys of these sites reveals large differences in species targets for these two approaches. In order to make such comparisons more quantitative, we use Presence/Absence Metabarcoding, using the fraction of replicate cobbles showing a species as a measure of its local abundance. This approach provides a fast and repeatable survey method that can be applied for biodiversity assessments across systems to shed light on the impact of different ecological disturbances and the role played by marine protected areas.
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Affiliation(s)
- Peter Shum
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
| | - Bryan T Barney
- Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Jennifer K O'Leary
- The Nature Conservancy, Tanzania Marine Parks Unit, Kenya Wildlife Service, & Seychelles National Parks Authority, Mombasa, Kenya
- California Sea Grant, 1 Grand Ave, San Luis Obispo, USA
- California Polytechnic State University, 1 Frand Ave, San Luis Obispo, USA
| | - Stephen R Palumbi
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
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Bezeng BS, van der Bank HF. DNA barcoding of southern African crustaceans reveals a mix of invasive species and potential cryptic diversity. PLoS One 2019; 14:e0222047. [PMID: 31525221 PMCID: PMC6746381 DOI: 10.1371/journal.pone.0222047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/20/2019] [Indexed: 11/27/2022] Open
Abstract
Globally, crustaceans represent one of the most taxonomically diverse and economically important invertebrate group. Notwithstanding, the diversity within this group is poorly known because most crustaceans are often associated with varied habits, forms, sizes and habitats; making species identification by conventional methods extremely challenging. In addition, progress towards understanding the diversity within this group especially in southern Africa has been severely hampered by the declining number of trained taxonomists, the presence of invasive alien species, over exploitation, etc. However, the advent of molecular techniques such as “DNA barcoding and Metabarcoding” can accelerate species identification and the discovery of new species. To contribute to the growing body of knowledge on crustacean diversity, we collected data from five southern African countries and used a DNA barcoding approach to build the first DNA barcode reference library for southern African crustaceans. We tested the reliability of this DNA barcode reference library to facilitate species identification using two approaches. We recovered high efficacy of specimen identification/discrimination; supported by both barcode gap and tree-base species identification methods. In addition, we identified alien invasive species and specimens with ‘no ID” in our DNA barcode reference library. The later; highlighting specimens requiring (i) further investigation and/or (ii) the potential presence of cryptic diversity or (iii) misidentifications. This unique data set although with some sampling gaps presents many opportunities for exploring the effect and extent of invasive alien species, the role of the pet trade as a pathway for crustacean species introduction into novel environments, sea food authentication, phylogenetic relationships within the larger crustacean groupings and the discovery of new species.
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Affiliation(s)
- Bezeng S. Bezeng
- African Centre for DNA Barcoding, University of Johannesburg, Auckland Park, Johannesburg, South Africa
- School of Mathematics & Natural Sciences, University of Venda, P. Thohoyandou, Venda, South Africa
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Auckland Park, Johannesburg, South Africa
- * E-mail:
| | - Herman F. van der Bank
- African Centre for DNA Barcoding, University of Johannesburg, Auckland Park, Johannesburg, South Africa
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Carreton M, Company JB, Planella L, Heras S, García-Marín JL, Agulló M, Clavel-Henry M, Rotllant G, dos Santos A, Roldán MI. Morphological identification and molecular confirmation of the deep-sea blue and red shrimp Aristeus antennatus larvae. PeerJ 2019; 7:e6063. [PMID: 30775163 PMCID: PMC6376935 DOI: 10.7717/peerj.6063] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/03/2018] [Indexed: 11/20/2022] Open
Abstract
The early life stages of the blue and red shrimp Aristeus antennatus (Decapoda: Dendrobranchiata: Penaeoidea: Aristeidae) were described by Heldt in 1955 based on plankton samples, larval rearing and assumptions of species habitat. Even with adequate keys, identification of its first larval stages remained a difficult task due to the lack of specific morphological characters which would differentiate them from other Penaeoidea species. Larvae of Aristeus antennatus were collected in the continental slope off the Spanish Mediterranean coast in August 2016 with a neuston net and preserved in ethanol 96%. DNA from the larvae was extracted and the molecular markers Cytochrome Oxidase I and 16S rDNA were sequenced and compared to that of adults with the objective of confirming the previous morphological description. Then, we present additional information to the morphological description of Aristeus antennatus larval stages through scanning electron microscopy and molecular analysis. This represents the first documented occurrence of Aristeus antennatus larvae off the Catalan coast and sets the grounds for further work on larval ecology and population connectivity of the species, which is an important contribution to a more sustainable fishery.
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Affiliation(s)
- Marta Carreton
- Institut de Ciències del Mar (ICM-CSIC), Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Joan B. Company
- Institut de Ciències del Mar (ICM-CSIC), Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Laia Planella
- Laboratori d’Ictiologia Genètica, Universitat de Girona, Girona, Spain
| | - Sandra Heras
- Laboratori d’Ictiologia Genètica, Universitat de Girona, Girona, Spain
| | | | - Melania Agulló
- Laboratori d’Ictiologia Genètica, Universitat de Girona, Girona, Spain
| | - Morane Clavel-Henry
- Institut de Ciències del Mar (ICM-CSIC), Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Guiomar Rotllant
- Institut de Ciències del Mar (ICM-CSIC), Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | | | - María Inés Roldán
- Laboratori d’Ictiologia Genètica, Universitat de Girona, Girona, Spain
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14
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Spielmann G, Diedrich J, Haszprunar G, Busch U, Huber I. Comparison of three DNA marker regions for identification of food relevant crustaceans of the order Decapoda. Eur Food Res Technol 2018. [DOI: 10.1007/s00217-018-3199-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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15
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Wang JD, Wang WZ, Lin ZL, Ali A, Fu HY, Huang MT, Gao SJ, Wang R. DNA Barcoding for Identification of Sugarcane Borers in China. NEOTROPICAL ENTOMOLOGY 2018; 47:362-368. [PMID: 28965311 DOI: 10.1007/s13744-017-0560-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/03/2017] [Indexed: 06/07/2023]
Abstract
Sugarcane borers are economically damaging insects with species that vary in distribution patterns both geographically and temporally, and vary based on ecological niche. Currently, identification of sugarcane borers is mostly based on morphological characters. However, morphological identification requires taxonomic expertise. An alternative method to identify sugarcane borers is the use of molecular data. DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has proven to be a useful tool for rapid and accurate species determination in many insect taxa. This study was conducted to test the effectiveness of DNA barcodes to discriminate among sugarcane borer species in China. Partial sequences of the COI gene (709 bp) were obtained from six species collected from different geographic areas. Results showed that the pairwise intraspecies genetic distance was < 0.02, whereas the interspecies genetic distance ranged from 0.117 to 0.182. Results from a neighbor-joining tree showed that the six sugarcane borer species were certainly separated. These results suggested that the partial COI sequences had high barcoding resolution in discriminating among sugarcane borer species. Our study emphasized the use of DNA barcodes for identification of the analyzed sugarcane borer species and represents an important step for building a comprehensive barcode library for sugarcane borers in China.
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Affiliation(s)
- J- D Wang
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China.
| | - W- Z Wang
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - Z- L Lin
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - A Ali
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - H- Y Fu
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - M- T Huang
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - S- J Gao
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - R Wang
- College of Forestry, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China.
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16
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Tempestini A, Rysgaard S, Dufresne F. Species identification and connectivity of marine amphipods in Canada's three oceans. PLoS One 2018; 13:e0197174. [PMID: 29791459 PMCID: PMC5965885 DOI: 10.1371/journal.pone.0197174] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/27/2018] [Indexed: 11/28/2022] Open
Abstract
Monitoring the distribution of marine biodiversity is a crucial step to better assess the impacts of global changes. Arctic marine fauna is dominated by amphipods in terms of abundance and biomass. These peracarids are an important marine order of crustaceans but the number of species found in the different Canadian oceans is currently unknown. Furthermore, most species are difficult to identify due to poor taxonomic descriptions and morphological convergence. The aim of this study was to assess the species diversity of marine amphipods in the three Canadian oceans using DNA barcoding. To do so, we produced a database of DNA barcodes of amphipods from the three Canadian Oceans publicly available from the BOLD website to which we added 310 new sequences from the Canadian Arctic Archipelago. We first delimited amphipod species based on barcode gap detection techniques and tree based method (bPTP) and then compared the composition of amphipods among the three oceans in order to assess the influence of past transarctic exchanges on Arctic diversity. Our analysis of 2309 sequences which represent more than 250 provisional species revealed a high connectivity between the Atlantic and Arctic Oceans. Our results also suggest that a single threshold to delimitate species is not suitable for amphipods. This study highlights the challenges involved in species delimitation and the need to obtain complete barcoding inventories in marine invertebrates.
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Affiliation(s)
- Astrid Tempestini
- Département de biologie et Québec Océan, Université du Québec à Rimouski, Rimouski, QC, Canada
- * E-mail:
| | - Søren Rysgaard
- University of Manitoba, Centre for Earth Observation Science, Winnipeg, MB, Canada
- Greenland Institute of Natural Resources, Nuuk, Greenland
- Aarhus University, Arctic Research Centre, Aarhus, Denmark
| | - France Dufresne
- Département de biologie et Centre d’étude Nordique, Université du Québec à Rimouski, Rimouski, QC, Canada
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17
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Raupach MJ, Hannig K, Moriniére J, Hendrich L. A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae). Zookeys 2018; 759:57-80. [PMID: 29853775 PMCID: PMC5968077 DOI: 10.3897/zookeys.759.24129] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/27/2018] [Indexed: 01/08/2023] Open
Abstract
The genus Amara Bonelli, 1810 is a very speciose and taxonomically difficult genus of the Carabidae. The identification of many of the species is accomplished with considerable difficulty, in particular for females and immature stages. In this study the effectiveness of DNA barcoding, the most popular method for molecular species identification, was examined to discriminate various species of this genus from Central Europe. DNA barcodes from 690 individuals and 47 species were analysed, including sequences from previous studies and more than 350 newly generated DNA barcodes. Our analysis revealed unique BINs for 38 species (81%). Interspecific K2P distances below 2.2% were found for three species pairs and one species trio, including haplotype sharing between Amara alpina/Amara torrida and Amara communis/Amara convexior/Amara makolskii. This study represents another step in generating an extensive reference library of DNA barcodes for carabids, highly valuable bioindicators for characterizing disturbances in various habitats.
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Affiliation(s)
- Michael J. Raupach
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Straße 9-11, 26111 Oldenburg, Germany
| | | | - Jérôme Moriniére
- Taxonomic coordinator – German Barcode of Life (GBOL), Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
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18
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Beermann J, Westbury MV, Hofreiter M, Hilgers L, Deister F, Neumann H, Raupach MJ. Cryptic species in a well-known habitat: applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida). Sci Rep 2018; 8:6893. [PMID: 29720606 PMCID: PMC5931980 DOI: 10.1038/s41598-018-25225-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 04/17/2018] [Indexed: 11/19/2022] Open
Abstract
Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.
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Affiliation(s)
- Jan Beermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Department of Functional Ecology, PO Box 120161, 27515, Bremerhaven, Germany.
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany.
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany.
| | - Michael V Westbury
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Michael Hofreiter
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Leon Hilgers
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Fabian Deister
- Carl von Ossietzky University Oldenburg, Institute for Biology and Environmental Sciences, PO Box 2503, 26111, Oldenburg, Germany
| | - Hermann Neumann
- Senckenberg am Meer, Department for Marine Research, Südstrand 40, 26382, Wilhelmshaven, Germany
| | - Michael J Raupach
- Carl von Ossietzky University Oldenburg, Institute for Biology and Environmental Sciences, PO Box 2503, 26111, Oldenburg, Germany
- Senckenberg am Meer, German Center of Marine Biodiversity (DZMB), Südstrand 44, 26382, Wilhelmshaven, Germany
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19
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Havemann N, Gossner MM, Hendrich L, Morinière J, Niedringhaus R, Schäfer P, Raupach MJ. From water striders to water bugs: the molecular diversity of aquatic Heteroptera (Gerromorpha, Nepomorpha) of Germany based on DNA barcodes. PeerJ 2018; 6:e4577. [PMID: 29736329 PMCID: PMC5936072 DOI: 10.7717/peerj.4577] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/14/2018] [Indexed: 11/20/2022] Open
Abstract
With about 5,000 species worldwide, the Heteroptera or true bugs are the most diverse taxon among the hemimetabolous insects in aquatic and semi-aquatic ecosystems. Species may be found in almost every freshwater environment and have very specific habitat requirements, making them excellent bioindicator organisms for water quality. However, a correct determination by morphology is challenging in many species groups due to high morphological variability and polymorphisms within, but low variability between species. Furthermore, it is very difficult or even impossible to identify the immature life stages or females of some species, e.g., of the corixid genus Sigara. In this study we tested the effectiveness of a DNA barcode library to discriminate species of the Gerromorpha and Nepomorpha of Germany. We analyzed about 700 specimens of 67 species, with 63 species sampled in Germany, covering more than 90% of all recorded species. Our library included various morphological similar taxa, e.g., species within the genera Sigara and Notonecta as well as water striders of the genus Gerris. Fifty-five species (82%) were unambiguously assigned to a single Barcode Index Number (BIN) by their barcode sequences, whereas BIN sharing was observed for 10 species. Furthermore, we found monophyletic lineages for 52 analyzed species. Our data revealed interspecific K2P distances with below 2.2% for 18 species. Intraspecific distances above 2.2% were shown for 11 species. We found evidence for hybridization between various corixid species (Sigara, Callicorixa), but our molecular data also revealed exceptionally high intraspecific distances as a consequence of distinct mitochondrial lineages for Cymatia coleoptrata and the pygmy backswimmer Plea minutissima. Our study clearly demonstrates the usefulness of DNA barcodes for the identification of the aquatic Heteroptera of Germany and adjacent regions. In this context, our data set represents an essential baseline for a reference library for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future. The existing data also opens new questions regarding the causes of observed low inter- and high intraspecific genetic variation and furthermore highlight the necessity of taxonomic revisions for various taxa, combining both molecular and morphological data.
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Affiliation(s)
- Nadine Havemann
- Fakultät V, Institut für Biologie und Umweltwissenschaften (IBU), Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany.,German Centre of Marine Biodiversity, Senckenberg Nature Research Society, Wilhelmshaven, Lower Saxony, Germany
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Lars Hendrich
- Sektion Insecta varia, SNSB-Bavarian State Collection of Zoology, Munich, Bavaria, Germany
| | - Jèrôme Morinière
- Taxonomic coordinator-German Barcode of Life (GBOL), SNSB-Bavarian State Collection of Zoology, Munich, Bavaria, Germany
| | - Rolf Niedringhaus
- Department of Biology, Earth and Environmental Sciences, Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany
| | - Peter Schäfer
- B.U.G.S. (Biologische Umwelt-Gutachten Schäfer), Telgte, North-Rhine Westphalia, Germany
| | - Michael J Raupach
- Fakultät V, Institut für Biologie und Umweltwissenschaften (IBU), Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany.,German Centre of Marine Biodiversity, Senckenberg Nature Research Society, Wilhelmshaven, Lower Saxony, Germany
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20
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Xu L, Wang L, Ning J, Li H, Ji Y, Du F. Diversity of marine planktonic ostracods in South China Sea: a DNA taxonomy approach. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:118-125. [PMID: 29671658 DOI: 10.1080/24701394.2018.1462349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Ostracods (Crustacea, Ostracoda) are small bivalved crustaceans, contributing over 200 described species to the marine zooplankton community. They are widely distributed and are relatively abundant components of the mesozooplankton, playing an important role in the transport of organic matter to deep layers. However, identification of ostracods based on micro-morphological characters is extremely difficult and time-consuming. Previous fragmentary taxonomic studies of ostracods in the South China Sea (SCA), were based solely on morphology. Here, by analysing the mitochondrial COI gene, we explore the taxa across the SCA using molecular tools for the first time. Our results show that sequence divergence among species varies within a large range, from 12.93% to 35.82%. Sixteen of the taxonomic units recovered by DNA taxonomy agree well with morphology, but Paraconchoecia oblonga, Conchoecia magna and Halocypris brevirostris split into two clades each, each of which contains cryptic species.
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Affiliation(s)
- Lei Xu
- a South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b Guangdong Provincial Key Laboratory of Fishery Ecology and Environment , Guangzhou , China.,c Key Laboratory of South China Sea Fishery Resources Development and Utilization, Ministry of Agriculture , Guangzhou , China
| | - Lianggen Wang
- a South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b Guangdong Provincial Key Laboratory of Fishery Ecology and Environment , Guangzhou , China.,c Key Laboratory of South China Sea Fishery Resources Development and Utilization, Ministry of Agriculture , Guangzhou , China
| | - Jiajia Ning
- a South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b Guangdong Provincial Key Laboratory of Fishery Ecology and Environment , Guangzhou , China.,c Key Laboratory of South China Sea Fishery Resources Development and Utilization, Ministry of Agriculture , Guangzhou , China
| | - Hong Li
- a South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b Guangdong Provincial Key Laboratory of Fishery Ecology and Environment , Guangzhou , China.,c Key Laboratory of South China Sea Fishery Resources Development and Utilization, Ministry of Agriculture , Guangzhou , China
| | - Yingying Ji
- a South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,d College of Marine Sciences , Shanghai Ocean University , Shanghai , China
| | - Feiyan Du
- a South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou , China.,b Guangdong Provincial Key Laboratory of Fishery Ecology and Environment , Guangzhou , China.,c Key Laboratory of South China Sea Fishery Resources Development and Utilization, Ministry of Agriculture , Guangzhou , China
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21
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Abstract
The discovery of fossilized brains and ventral nerve cords in lower and mid-Cambrian arthropods has led to crucial insights about the evolution of their central nervous system, the segmental identity of head appendages and the early evolution of eyes and their underlying visual systems. Fundamental ground patterns of lower Cambrian arthropod brains and nervous systems correspond to the ground patterns of brains and nervous systems belonging to three of four major extant panarthropod lineages. These findings demonstrate the evolutionary stability of early neural arrangements over an immense time span. Here, we put these fossil discoveries in the context of evidence from cladistics, as well as developmental and comparative neuroanatomy, which together suggest that despite many evolved modifications of neuropil centers within arthropod brains and ganglia, highly conserved arrangements have been retained. Recent phylogenies of the arthropods, based on fossil and molecular evidence, and estimates of divergence dates, suggest that neural ground patterns characterizing onychophorans, chelicerates and mandibulates are likely to have diverged between the terminal Ediacaran and earliest Cambrian, heralding the exuberant diversification of body forms that account for the Cambrian Explosion.
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Affiliation(s)
- Nicholas J Strausfeld
- Department of Neuroscience and Center for Insect Science, University of Arizona, Tucson, AZ 85721, USA.
| | - Xiaoya Ma
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Yunnan Key Laboratory for Palaeobiology, Yunnan University, Kunming 650091, People's Republic of China
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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22
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Mantelatto FL, Terossi M, Negri M, Buranelli RC, Robles R, Magalhães T, Tamburus AF, Rossi N, Miyazaki MJ. DNA sequence database as a tool to identify decapod crustaceans on the São Paulo coastline. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:805-815. [PMID: 28872375 DOI: 10.1080/24701394.2017.1365848] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
DNA barcoding has emerged as an efficient tool for taxonomy and other biodiversity fields. The vast and speciose group of decapod crustaceans is not an exception in the current scenario and comparing short DNA fragments has enabled researchers to overcome some taxonomic impediments to help broadening knowledge on the diversity of this group of crustaceans. Brazil is considered as an important area in terms of global marine biodiversity and some regions stand out in terms of decapod fauna, such as the São Paulo coastline. Thus, the aim of this study is to obtain sequences of the mitochondrial markers (COI and 16S) for decapod crustaceans distributed at the São Paulo coastline and to test the accuracy of these markers for species identification from this region by comparing our sequences to those already present in the GenBank database. We sampled along almost the 300 km of the São Paulo coastline from estuaries to offshore islands during the development of a multidisciplinary research project that took place for 5 years. All the species were processed to obtain the DNA sequences. The diversity of the decapod fauna on the São Paulo coastline comprises at least 404 species. We were able to collect 256 of those species and sequence of at least one of the target genes from 221. By testing the accuracy of these two DNA markers as a tool for identification, we were able to check our own identifications, including new records in GenBank, spot potential mistakes in GenBank, and detect potential new species.
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Affiliation(s)
- Fernando L Mantelatto
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Mariana Terossi
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Mariana Negri
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Raquel C Buranelli
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Rafael Robles
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Tatiana Magalhães
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Ana Francisca Tamburus
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Natália Rossi
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Mayara J Miyazaki
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
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23
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Bezeng B, Davies T, Daru B, Kabongo R, Maurin O, Yessoufou K, van der Bank H, van der Bank M. Ten years of barcoding at the African Centre for DNA Barcoding. Genome 2017; 60:629-638. [DOI: 10.1139/gen-2016-0198] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The African Centre for DNA Barcoding (ACDB) was established in 2005 as part of a global initiative to accurately and rapidly survey biodiversity using short DNA sequences. The mitochondrial cytochrome c oxidase 1 gene (CO1) was rapidly adopted as the de facto barcode for animals. Following the evaluation of several candidate loci for plants, the Plant Working Group of the Consortium for the Barcoding of Life in 2009 recommended that two plastid genes, rbcLa and matK, be adopted as core DNA barcodes for terrestrial plants. To date, numerous studies continue to test the discriminatory power of these markers across various plant lineages. Over the past decade, we at the ACDB have used these core DNA barcodes to generate a barcode library for southern Africa. To date, the ACDB has contributed more than 21 000 plant barcodes and over 3000 CO1 barcodes for animals to the Barcode of Life Database (BOLD). Building upon this effort, we at the ACDB have addressed questions related to community assembly, biogeography, phylogenetic diversification, and invasion biology. Collectively, our work demonstrates the diverse applications of DNA barcoding in ecology, systematics, evolutionary biology, and conservation.
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Affiliation(s)
- B.S. Bezeng
- African Centre for DNA Barcoding, University of Johannesburg, P.O. Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - T.J. Davies
- African Centre for DNA Barcoding, University of Johannesburg, P.O. Box 524, Auckland Park 2006, Johannesburg, South Africa
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield, Montreal, QC H3A 0G4, Quebec, Canada
| | - B.H. Daru
- Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA
| | - R.M. Kabongo
- African Centre for DNA Barcoding, University of Johannesburg, P.O. Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - O. Maurin
- African Centre for DNA Barcoding, University of Johannesburg, P.O. Box 524, Auckland Park 2006, Johannesburg, South Africa
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW93AB, United Kingdom
| | - K. Yessoufou
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, APK Campus 2006, Johannesburg, South Africa
| | - H. van der Bank
- African Centre for DNA Barcoding, University of Johannesburg, P.O. Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - M. van der Bank
- African Centre for DNA Barcoding, University of Johannesburg, P.O. Box 524, Auckland Park 2006, Johannesburg, South Africa
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24
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Sabia L, Di Capua I, Percopo I, Uttieri M, Amato A. ITS2 in calanoid copepods: reconstructing phylogenetic relationships and identifying a newly introduced species in the Mediterranean. EUROPEAN ZOOLOGICAL JOURNAL 2017. [DOI: 10.1080/11250003.2016.1276639] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- L. Sabia
- Department of Science and Technology, University of Naples “Parthenope”, Italy
| | - I. Di Capua
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Italy
| | - I. Percopo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Italy
| | - M. Uttieri
- Department of Science and Technology, University of Naples “Parthenope”, Italy
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Italy
- CoNISMa, Rome, Italy
| | - A. Amato
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Italy
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25
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Page TJ, Steinke D. No homology means there can be no analyses; a comment on Jose & Harikrishnan. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:220-221. [PMID: 28024422 DOI: 10.1080/24701394.2016.1267159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Timothy J Page
- a Australian Rivers Institute, Griffith University , Nathan , QLD , Australia.,b Water Planning Ecology, Queensland Dept. of Science , Information Technology and Innovation , Dutton Park , QLD , Australia
| | - Dirk Steinke
- c Biodiversity Institute of Ontario, University of Guelph , Guelph , ON , Canada
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26
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Raupach MJ, Hannig K, Morinière J, Hendrich L. A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa. Zookeys 2016; 592:121-41. [PMID: 27408547 PMCID: PMC4926639 DOI: 10.3897/zookeys.592.8316] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/23/2016] [Indexed: 12/23/2022] Open
Abstract
As molecular identification method, DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has been proven to be a useful tool for species determination in many insect taxa including ground beetles. In this study we tested the effectiveness of DNA barcodes to discriminate species of the ground beetle genus Bembidion and some closely related taxa of Germany. DNA barcodes were obtained from 819 individuals and 78 species, including sequences from previous studies as well as more than 300 new generated DNA barcodes. We found a 1:1 correspondence between BIN and traditionally recognized species for 69 species (89%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for three species pairs, including two species pairs with haplotype sharing (Bembidion atrocaeruleum/Bembidion varicolor and Bembidion guttula/Bembidion mannerheimii). In contrast to this, deep intraspecific sequence divergences with distinct lineages were revealed for two species (Bembidion geniculatum/Ocys harpaloides). Our study emphasizes the use of DNA barcodes for the identification of the analyzed ground beetles species and represents an important step in building-up a comprehensive barcode library for the Carabidae in Germany and Central Europe as well.
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Affiliation(s)
- Michael J. Raupach
- Molecular Taxonomy of Marine Organisms, German Centre of Marine Biodiversity Research (DZMB), Senckenberg am Meer, Südstrand 44, 26382 Wilhelmshaven, Germany
| | | | - Jérome Morinière
- Taxonomic coordinator – Barcoding Fauna Bavarica, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
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27
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Drastic underestimation of amphipod biodiversity in the endangered Irano-Anatolian and Caucasus biodiversity hotspots. Sci Rep 2016; 6:22507. [PMID: 26928527 PMCID: PMC4772388 DOI: 10.1038/srep22507] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/16/2016] [Indexed: 11/17/2022] Open
Abstract
Biodiversity hotspots are centers of biological diversity and particularly threatened by anthropogenic activities. Their true magnitude of species diversity and endemism, however, is still largely unknown as species diversity is traditionally assessed using morphological descriptions only, thereby ignoring cryptic species. This directly limits evidence-based monitoring and management strategies. Here we used molecular species delimitation methods to quantify cryptic diversity of the montane amphipods in the Irano-Anatolian and Caucasus biodiversity hotspots. Amphipods are ecosystem engineers in rivers and lakes. Species diversity was assessed by analysing two genetic markers (mitochondrial COI and nuclear 28S rDNA), compared with morphological assignments. Our results unambiguously demonstrate that species diversity and endemism is dramatically underestimated, with 42 genetically identified freshwater species in only five reported morphospecies. Over 90% of the newly recovered species cluster inside Gammarus komareki and G. lacustris; 69% of the recovered species comprise narrow range endemics. Amphipod biodiversity is drastically underestimated for the studied regions. Thus, the risk of biodiversity loss is significantly greater than currently inferred as most endangered species remain unrecognized and/or are only found locally. Integrative application of genetic assessments in monitoring programs will help to understand the true magnitude of biodiversity and accurately evaluate its threat status.
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Identification, Discrimination, and Discovery of Species of Marine Planktonic Ostracods Using DNA Barcodes. PLoS One 2016; 11:e0146327. [PMID: 26730595 PMCID: PMC4701487 DOI: 10.1371/journal.pone.0146327] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 12/16/2015] [Indexed: 01/24/2023] Open
Abstract
The Ostracoda (Crustacea; Class Ostracoda) is a diverse, frequently abundant, and ecologically important component of the marine zooplankton assemblage. There are more than 200 described species of marine planktonic ostracods, many of which (especially conspecific species) can be identified only by microscopic examination and dissection of fragile morphological characters. Given the complexity of species identification and increasing lack of expert taxonomists, DNA barcodes (short DNA sequences for species discrimination and identification) are particularly useful and necessary. Results are reported from analysis of 210 specimens of 78 species of marine planktonic ostracods, including two novel species, and 51 species for which barcodes have not been previously published. Specimens were collected during 2006 to 2008 from the Atlantic, Indian, and Southern Oceans, Greenland Sea and Gulf of Alaska. Samples were collected from surface to 5,000 m using various collection devices. DNA sequence variation was analyzed for a 598 base-pair region of the mitochondrial cytochrome oxidase subunit I (COI) gene. Kimura-2-Parameter (K2P) genetic distances within described species (mean = 0.010 ± 0.017 SD) were significantly smaller than between species (0.260 + 0.080), excluding eight taxa hypothesized to comprise cryptic species due to morphological variation (especially different size forms) and/or collection from different geographic regions. These taxa showed similar K2P distance values within (0.014 + 0.026) and between (0.221 ± 0.068) species. All K2P distances > 0.1 resulted from comparisons between identified or cryptic species, with no overlap between intra- and interspecific genetic distances. A Neighbor Joining tree resolved nearly all described species analyzed, with multiple sequences forming monophyletic clusters with high bootstrap values (typically 99%). Based on taxonomically and geographically extensive sampling and analysis (albeit with small sample sizes), the COI barcode region was shown to be a valuable character for discrimination, recognition, identification, and discovery of species of marine planktonic ostracods.
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